The 50 most-cited articles in F1000Research, 2019

The mammalian/mechanistic target of rapamycin (mTOR) is a key component of cellular metabolism that integrates nutrient sensing with cellular processes that fuel cell growth and proliferation. Although the involvement of the mTOR pathway in regulating life span and aging has been studied extensively in the last decade, the underpinning mechanisms remain elusive. In this review, we highlight the emerging insights that link mTOR to various processes related to aging, such as nutrient sensing, maintenance of proteostasis, autophagy, mitochondrial dysfunction, cellular senescence, and decline in stem cell function.

High-dimensional mass and flow cytometry (HDCyto) experiments have become a method of choice for high-throughput interrogation and characterization of cell populations. Here, we present an updated R-based pipeline for differential analyses of HDCyto data, largely based on Bioconductor packages. We computationally define cell populations using FlowSOM clustering, and facilitate an optional but reproducible strategy for manual merging of algorithm-generated clusters. Our workflow offers different analysis paths, including association of cell type abundance with a phenotype or changes in signalling markers within specific subpopulations, or differential analyses of aggregated signals. Importantly, the differential analyses we show are based on regression frameworks where the HDCyto data is the response; thus, we are able to model arbitrary experimental designs, such as those with batch effects, paired designs and so on. In particular, we apply generalized linear mixed models or linear mixed models to analyses of cell population abundance or cell-population-specific analyses of…

The master pro-inflammatory cytokine, tumour necrosis factor (TNF), has been shown to modulate multiple signalling pathways, with wide-ranging downstream effects. TNF plays a vital role in the typical immune response through the regulation of a number of pathways encompassing an immediate inflammatory reaction with significant innate immune involvement as well as cellular activation with subsequent proliferation and programmed cell death or necrosis. As might be expected with such a broad spectrum of cellular effects and complex signalling pathways, TNF has also been implicated in a number of disease states, such as rheumatoid arthritis, ankylosing spondylitis, and Crohn's disease. Since the time of its discovery over 40 years ago, TNF ligand and its receptors, TNF receptor (TNFR) 1 and 2, have been categorised into two complementary superfamilies, namely TNF (TNFSF) and TNFR (TNFRSF), and 19 ligands and 29 receptors have been identified to date. There have been significant advances in our understanding of TNF signalling pathways in the last decade, and this short review aims to…

Quality control is an essential first step in sequencing data analysis, and software tools for quality control are deeply entrenched in standard pipelines at most sequencing centers. Although the associated computations are straightforward, in many settings the total computing effort required for quality control is appreciable and warrants optimization. We present falco, an emulation of the popular FastQC tool that runs on average three times faster while generating equivalent results. Compared to FastQC, falco also provides greater scalability for datasets with longer reads and more flexible visualization of HTML reports.

Endometriosis is an enigmatic disease that could start at birth. Its pathogenesis is supported by different theories. Accumulating facts relate it to a multigenic disorder. In this review of recent publications, the principal symptoms of the disease, pain and infertility, as well as its pathogenesis, diagnosis, and classification will be addressed. Endometriosis presents three main variants: superficial peritoneal disease, deep infiltrating endometriosis, and ovarian endometriomas. The management of the disease, surgery, and medical and alternative therapies will be discussed. Special reference will be made to the quality of surgery and how to understand patients with endometriosis and endometriosis.

Adenomyosis is a benign uterine disorder in which endometrial glands and stroma are pathologically demonstrated in the uterine myometrium and it is considered a specific entity in the PALM-COEIN FIGO (polyp; adenomyosis; leiomyoma; malignancy and hyperplasia; coagulopathy; ovulatory dysfunction; endometrial; iatrogenic; and not yet classified - International Federation of Gynecology and Obstetrics) classification of causes of abnormal uterine bleeding (AUB). Although it has always been considered the classic condition of multiparous women over 40 years old who have pain and heavy menstrual bleeding, diagnosed at hysterectomy, the epidemiological scenario has completely changed. Adenomyosis is increasingly identified in young women with pain, AUB, infertility, or no symptoms by using imaging techniques such as transvaginal ultrasound and magnetic resonance. However, there is no agreement on the definition and classification of adenomyotic lesions from both the histopathology and the imaging point of view, and the diagnosis remains difficult and unclear. A uniform and shared reporting…

Infertility is a prevalent condition affecting an estimated 70 million people globally. The World Health Organization estimates that 9% of couples worldwide struggle with fertility issues and that male factor contributes to 50% of the issues. Male infertility has a variety of causes, ranging from genetic mutations to lifestyle choices to medical illnesses or medications. Recent studies examining DNA fragmentation, capacitation, and advanced paternal age have shed light on previously unknown topics. The role of conventional male reproductive surgeries aimed at improving or addressing male factor infertility, such as varicocelectomy and testicular sperm extraction, have recently been studied in an attempt to expand their narrow indications. Despite advances in the understanding of male infertility, idiopathic sperm abnormalities still account for about 30% of male infertility. With current and future efforts examining the molecular and genetic factors responsible for spermatogenesis and fertilization, we may be better able to understand etiologies of male factor infertility and thus…

Triple-negative breast cancer (TNBC) is a breast cancer subtype renowned for its capacity to affect younger women, metastasise early despite optimal adjuvant treatment and carry a poor prognosis. Neoadjuvant therapy has focused on combinations of systemic agents to optimise pathological complete response. Treatment algorithms now guide the management of patients with or without residual disease, but metastatic TNBC continues to harbour a poor prognosis. Innovative, multi-drug combination systemic therapies in the neoadjuvant and adjuvant settings have led to significant improvements in outcomes, particularly over the past decade. Recently published advances in the treatment of metastatic TNBC have shown impressive results with poly (ADP-ribose) polymerase (PARP) inhibitors and immunotherapy agents. Immunotherapy agents in combination with traditional systemic chemotherapy have been shown to alter the natural history of this devastating condition, particularly in patients whose tumours are positive for programmed cell death ligand 1 (PD-L1).

The sourmash software package uses MinHash-based sketching to create "signatures", compressed representations of DNA, RNA, and protein sequences, that can be stored, searched, explored, and taxonomically annotated. sourmash signatures can be used to estimate sequence similarity between very large data sets quickly and in low memory, and can be used to search large databases of genomes for matches to query genomes and metagenomes. sourmash is implemented in C++, Rust, and Python, and is freely available under the BSD license at http://github.com/dib-lab/sourmash.

Background: Data sets from long-read sequencing platforms (Oxford Nanopore Technologies and Pacific Biosciences) allow for most prokaryote genomes to be completely assembled – one contig per chromosome or plasmid. However, the high per-read error rate of long-read sequencing necessitates different approaches to assembly than those used for short-read sequencing. Multiple assembly tools (assemblers) exist, which use a variety of algorithms for long-read assembly. Methods: We used 500 simulated read sets and 120 real read sets to assess the performance of six long-read assemblers (Canu, Flye, Miniasm/Minipolish, Raven, Redbean and Shasta) across a wide variety of genomes and read parameters. Assemblies were assessed on their structural accuracy/completeness, sequence identity, contig circularisation and computational resources used. Results: Canu v1.9 produced moderately reliable assemblies but had the longest runtimes of all assemblers tested. Flye v2.6 was more reliable and did particularly well with plasmid assembly. Miniasm/Minipolish v0.3 was the only assembler which consistently…

Recent research in the field of osteoarthritis (OA) has focused on understanding the underlying molecular and clinical phenotypes of the disease. This narrative review article focuses on recent advances in our understanding of the phenotypes of OA and proposes that the disease represents a diversity of clinical phenotypes that are underpinned by a number of molecular mechanisms, which may be shared by several phenotypes and targeted more specifically for therapeutic purposes. The clinical phenotypes of OA supposedly have different underlying etiologies and pathogenic pathways and they progress at different rates. Large OA population cohorts consist of a majority of patients whose disease progresses slowly and a minority of individuals whose disease may progress faster. The ability to identify the people with relatively rapidly progressing OA can transform clinical trials and enhance their efficiency. The identification, characterization, and classification of molecular phenotypes of rapidly progressing OA, which represent patients who may benefit most from intervention, could…

The efficient healing of skin wounds is crucial for securing the vital barrier function of the skin, but pathological wound healing and scar formation are major medical problems causing both physiological and psychological challenges for patients. A number of tightly coordinated regenerative responses, including haemostasis, the migration of various cell types into the wound, inflammation, angiogenesis, and the formation of the extracellular matrix, are involved in the healing process. In this article, we summarise the central mechanisms and processes in excessive scarring and acute wound healing, which can lead to the formation of keloids or hypertrophic scars, the two types of fibrotic scars caused by burns or other traumas resulting in significant functional or aesthetic disadvantages. In addition, we discuss recent developments related to the functions of activated fibroblasts, the extracellular matrix and mechanical forces in the wound environment as well as the mechanisms of scarless wound healing. Understanding the different mechanisms of wound healing is pivotal for…

Airway neutrophilia is a common feature of many chronic inflammatory lung diseases and is associated with disease progression, often regardless of the initiating cause. Neutrophils and their products are thought to be key mediators of the inflammatory changes in the airways of patients with chronic obstructive pulmonary disease (COPD) and have been shown to cause many of the pathological features associated with disease, including emphysema and mucus hypersecretion. Patients with COPD also have high rates of bacterial colonisation and recurrent infective exacerbations, suggesting that neutrophil host defence mechanisms are impaired, a concept supported by studies showing alterations to neutrophil migration, degranulation and reactive oxygen species production in cells isolated from patients with COPD. Although the role of neutrophils is best described in COPD, many of the pathological features of this disease are not unique to COPD and also feature in other chronic inflammatory airway diseases, including asthma, cystic fibrosis, alpha-1 anti-trypsin deficiency, and bronchiectasis.…

Vasoactive intestinal peptide (VIP), a gut peptide hormone originally reported as a vasodilator in 1970, has multiple physiological and pathological effects on development, growth, and the control of neuronal, epithelial, and endocrine cell functions that in turn regulate ion secretion, nutrient absorption, gut motility, glycemic control, carcinogenesis, immune responses, and circadian rhythms. Genetic ablation of this peptide and its receptors in mice also provides new insights into the contribution of VIP towards physiological signaling and the pathogenesis of related diseases. Here, we discuss the impact of VIP on gastrointestinal function and diseases based on recent findings, also providing insight into its possible therapeutic application to diabetes, autoimmune diseases and cancer.

RCy3 is an R package in Bioconductor that communicates with Cytoscape via its REST API, providing access to the full feature set of Cytoscape from within the R programming environment. RCy3 has been redesigned to streamline its usage and future development as part of a broader Cytoscape Automation effort. Over 100 new functions have been added, including dozens of helper functions specifically for intuitive data overlay operations. Over 40 Cytoscape apps have implemented automation support so far, making hundreds of additional operations accessible via RCy3. Two-way conversion with networks from \textit{igraph} and \textit{graph} ensures interoperability with existing network biology workflows and dozens of other Bioconductor packages. These capabilities are demonstrated in a series of use cases involving public databases, enrichment analysis pipelines, shortest path algorithms and more. With RCy3, bioinformaticians will be able to quickly deliver reproducible network biology workflows as integrations of Cytoscape functions, complex custom analyses and other R packages.

Proximity-based labeling has emerged as a powerful complementary approach to classic affinity purification of multiprotein complexes in the mapping of protein-protein interactions. Ongoing optimization of enzyme tags and delivery methods has improved both temporal and spatial resolution, and the technique has been successfully employed in numerous small-scale (single complex mapping) and large-scale (network mapping) initiatives. When paired with quantitative proteomic approaches, the ability of these assays to provide snapshots of stable and transient interactions over time greatly facilitates the mapping of dynamic interactomes. Furthermore, recent innovations have extended biotin-based proximity labeling techniques such as BioID and APEX beyond classic protein-centric assays (tag a protein to label neighboring proteins) to include RNA-centric (tag an RNA species to label RNA-binding proteins) and DNA-centric (tag a gene locus to label associated protein complexes) assays.

Psoriasis is a multisystemic, inflammatory skin condition that can affect many areas of the body, but most commonly the extensor surfaces of the elbows and knees, and sometimes the intergluteal and umbilical area. It has a prevalence of 2-4% in western adults, and 20--30% of psoriasis patients will develop psoriatic arthritis (PsA). PsA is an inflammatory musculoskeletal disease associated with cutaneous psoriasis. It affects men and women almost equally with a peak age at onset of 40 and 50 years. It is a diverse disease that affects multiple organ systems includes peripheral and axial joints, entheses, skin, and nails. PsA is associated with comorbidities such as osteoporosis, uveitis, subclinical bowel inflammation, and cardiovascular disease. Given this heterogeneity, its diagnosis has been difficult. Here we present an updated review of its classification criteria CASPAR (classification criteria for PsA), use of screening tools to aid in early diagnosis, recent findings on pathogenesis, and new therapeutic approaches including new biologic medications.

RCy3 is an R package in Bioconductor that communicates with Cytoscape via its REST API, providing access to the full feature set of Cytoscape from within the R programming environment. RCy3 has been redesigned to streamline its usage and future development as part of a broader Cytoscape Automation effort. Over 100 new functions have been added, including dozens of helper functions specifically for intuitive data overlay operations. Over 40 Cytoscape apps have implemented automation support so far, making hundreds of additional operations accessible via RCy3. Two-way conversion with networks from \textit{igraph} and \textit{graph} ensures interoperability with existing network biology workflows and dozens of other Bioconductor packages. These capabilities are demonstrated in a series of use cases involving public databases, enrichment analysis pipelines, shortest path algorithms and more. With RCy3, bioinformaticians will be able to quickly deliver reproducible network biology workflows as integrations of Cytoscape functions, complex custom analyses and other R packages.

Necrotizing enterocolitis is a devastating intestinal disease affecting preterm infants. In spite of ongoing research and advancement in neonatal care, mortality remains high, especially in infants with advanced disease. The mechanism of disease development, the progression of intestinal injury, and management remain areas of ongoing research and controversy. In this review, we examine our current understanding of the disease, its epidemiology, the risk factors associated with the development of the disease, and its pathophysiology. We also describe current management and new emerging research highlighting potential future directions.

Tetralogy of Fallot (ToF) is the most common type of cyanotic congenital heart disease. Since the first surgical repair in 1954, treatment has continuously improved. The treatment strategies currently used in the treatment of ToF result in excellent long-term survival (30 year survival ranges from 68.5% to 90.5%). However, residual problems such as right ventricular outflow tract obstruction, pulmonary regurgitation, and (ventricular) arrhythmia are common and often require re-interventions. Right ventricular dysfunction can be seen following longstanding pulmonary regurgitation and/or stenosis. Performing pulmonary valve replacement or relief of pulmonary stenosis before irreversible right ventricular dysfunction occurs is important, but determining the optimal timing of pulmonary valve replacement is challenging for several reasons. The biological mechanisms underlying dysfunction of the right ventricle as seen in longstanding pulmonary regurgitation are poorly understood. Different methods of assessing the right ventricle are used to predict impending dysfunction. The…

Background : Dental caries is a chronic, multifactorial disease, with limited data available for the Egyptian population. The aim of this study is to assess the prevalence of dental caries among Egyptian children and adolescents in correlation with age, gender, body mass index, socioeconomic status, parental education, biological risk factors and dietary habits. Methods : A total number of 369 Egyptian children and adolescents (age ranges from 3-18 years) were examined over the period from 15 th November 2017 to 13 th January 2018. Socio-demographic data, oral hygiene measures and dietary habits for children were recorded. Dental status was analyzed using decayed, missing and filled tooth index (dmft) for deciduous dentition and (DMFT) index for permanent dentition. For mixed dentition (deft) index was used, d (decayed tooth indicated for filling), e (decayed tooth indicated for extraction) and f (filled tooth). Results : 74% of the children had dental caries with mean dmft: 3.23±4.07; deft: 4.21±3.21; DMFT: 1.04±1.56. In primary dentition, dmft of the children was positively…

The gut microbiota plays a fundamental role in host health and disease. Host diet is one of the most significant modulators of the gut microbial community and its metabolic activities. Evidence demonstrates that dietary patterns such as the 'Western diet' and perturbations in gut microbiome (dysbiosis) have strong associations with a wide range of human diseases, including obesity, metabolic syndrome, type-2 diabetes and cardiovascular diseases. However, consumption of Mediterranean-style diets is considered healthy and associated with the prevention of cardiovascular and metabolic diseases, colorectal cancers and many other diseases. Such beneficial effects of the Mediterranean diet might be attributed to high proportion of fibers, mono- and poly-unsaturated fatty acids, antioxidants and polyphenols. Concurrent literature has demonstrated beneficial modulation of the gut microbiome following a Mediterranean-style diet in humans as well as in experimental animal models such as rodents. We recently demonstrated similar positive changes in the gut microbiome of non-human primates…

Despite recent advancements in plant molecular biology and biotechnology, providing food security for an increasing world population remains a challenge. Drought (water scarcity), salinity, heat, and cold stress are considered major limiting factors that affect crop production both qualitatively and quantitatively. Therefore, the development of cost-effective and environmentally friendly strategies will be needed to resolve these agricultural problems. This will require a comprehensive understanding of transcriptomic alterations that occur in plants in response to varying levels of environmental stresses, singly and in combination. Here, we briefly discuss the current status and future challenges in plant research related to understanding transcriptional changes that occur in response to drought, salinity, heat, and cold stress.

Background: Single-cell RNA-seq is a powerful tool for measuring gene expression at the resolution of individual cells. A challenge in the analysis of this data is the large amount of zero values, representing either missing data or no expression. Several imputation approaches have been proposed to address this issue, but they generally rely on structure inherent to the dataset under consideration they may not provide any additional information, hence, are limited by the information contained therein and the validity of their assumptions. Methods: We evaluated the risk of generating false positive or irreproducible differential expression when imputing data with six different methods. We applied each method to a variety of simulated datasets as well as to permuted real single-cell RNA-seq datasets and consider the number of false positive gene-gene correlations and differentially expressed genes. Using matched 10X and Smart-seq2 data we examined whether cell-type specific markers were reproducible across datasets derived from the same tissue before and after imputation. Results: The…

Rapid advances in sequencing technology have led to an explosive increase in the number of genetic variants identified in patients with neurological disease and have also enabled the assembly of a robust database of variants in healthy individuals. A surprising number of variants in the GRIN genes that encode N -methyl-D-aspartate (NMDA) glutamatergic receptor subunits have been found in patients with various neuropsychiatric disorders, including autism spectrum disorders, epilepsy, intellectual disability, attention-deficit/hyperactivity disorder, and schizophrenia. This review compares and contrasts the available information describing the clinical and functional consequences of genetic variations in GRIN2A and GRIN2B. Comparison of clinical phenotypes shows that GRIN2A variants are commonly associated with an epileptic phenotype but that GRIN2B variants are commonly found in patients with neurodevelopmental disorders. These observations emphasize the distinct roles that the gene products serve in circuit function and suggest that functional analysis of GRIN2A and GRIN2B variation…

Intensive care unit-acquired weakness (ICU-AW) is the most common neuromuscular impairment in critically ill patients. We discuss critical aspects of ICU-AW that have not been completely defined or that are still under discussion. Critical illness polyneuropathy, myopathy, and muscle atrophy contribute in various proportions to ICU-AW. Diagnosis of ICU-AW is clinical and is based on Medical Research Council sum score and handgrip dynamometry for limb weakness and recognition of a patient's ventilator dependency or difficult weaning from artificial ventilation for diaphragmatic weakness (DW). ICU-AW can be caused by a critical illness polyneuropathy, a critical illness myopathy, or muscle disuse atrophy, alone or in combination. Its diagnosis requires both clinical assessment of muscle strength and complete electrophysiological evaluation of peripheral nerves and muscles. The peroneal nerve test (PENT) is a quick simplified electrophysiological test with high sensitivity and good specificity that can be used instead of complete electrophysiological evaluation as a screening test in…

The concept of interleukin-1 (IL-1) as a target in osteoarthritis (OA) has been an attractive one for many years. It is a highly potent inducer of cartilage degradation, causing the induction of mRNA and controlling the bioavailability of disease-relevant proteases such as ADAMTS5 and MMP13. It drives synovitis and can induce other disease-relevant genes such as nerve growth factor, a key pain sensitiser in OA. However, the quality of evidence for its involvement in disease is modest. Descriptive studies have demonstrated expression of IL-1α and β in OA cartilage and elevated levels in the synovial fluid of some patients. Agnostic transcriptomic and genomic analyses do not identify IL-1 as a key pathway.In vivomodels show a conflicting role for this molecule; early studies using therapeutic approaches in large animal models show a benefit, but most murine studies fail to demonstrate protection where the ligands (IL-1α/β), the cytokine activator (IL-1–converting enzyme), or the receptor (IL-1R) have been knocked out. Recently, a number of large double-blind randomised controlled…

Polycystic ovary syndrome (PCOS) is a multifaceted condition characterized by chronic anovulation and excess ovarian activity, in contrast to other causes of anovulation that involve ovarian dormancy or primary insufficiency. Recent studies indicated that PCOS is associated with low-grade chronic inflammation and that women with PCOS are at increased risk of non-alcoholic fatty liver disease. The inflammatory and metabolic derangements associated with PCOS are explained in part by the coexistence of insulin resistance and obesity but are further fueled by the androgen excess. New insights into the regulation of hormones and cytokines in muscle and fat tissue support the concept that PCOS is a systemic syndrome. The therapeutic plan should be tailored to the patient phenotype, complaints, and reproductive desire. Of note, the aromatase inhibitor letrozole seems to be more effective than the reference drug clomiphene citrate to treat infertility due to PCOS. Integral management by a multidisciplinary team may help the patients to adhere to lifestyle interventions and thereby reduce…

In February 2018, the 6th World Symposium on Pulmonary Hypertension (WSPH) brought together experts from various disciplines to review the most relevant clinical and scientific advances in the field of PH over the last 5 years. Based on careful review and discussions by members of the different task forces, major revisions were made on the hemodynamic definition for various forms of PH and new genes were added to the list of genetic markers associated with pulmonary arterial hypertension (PAH) and pulmonary veno-occlusive disease. In addition, the use of risk stratification tools was encouraged as a strategy to reduce one-year mortality risk in PAH patients through early implementation of PAH therapies. While members of the medical community are still debating some of the proposed changes, the new WSPH guidelines advocate early diagnosis and initiation of combination therapy to reduce mortality and improve quality of life in patients with PH.

Lumbar spinal stenosis is a degenerative process that is extremely frequent in today's aging population. It can result in impingement on the nerves of the cauda equina or on the thecal sac itself, and lead to debilitating symptoms such as severe leg pain, or restriction in the perimeter of ambulation, both resulting in dependency in daily activities. The impact of the disease is global and includes financial repercussions because of its involvement in the active work force group. Risk factors for the disease include some comorbidities such as obesity or smoking, daily habits such as an active lifestyle, but also genetic factors that are not completely elucidated yet. The diagnosis of lumbar stenosis can be difficult, and involves a combination of radiological and clinical findings. Treatment ranges from conservative measures with physical therapy and core strengthening, to steroid injections in the facet joints or epidural space, to a more radical solution with surgical decompression. The evidence available in the literature regarding the causes, diagnosis and treatment of lumbar…

This is a selective review of recent publications on dengue clinical features, epidemiology, pathogenesis, and vaccine development placed in a context of observations made over the past half century. Four dengue viruses (DENVs) are transmitted by urban cycle mosquitoes causing diseases whose nature and severity are influenced by interacting factors such as virus, age, immune status of the host, and human genetic variability. A phenomenon that controls the kinetics of DENV infection, antibody-dependent enhancement, best explains the correlation of the vascular permeability syndrome with second heterotypic DENV infections and infection in the presence of passively acquired antibodies. Based on growing evidencein vivoandin vitro, the tissue-damaging DENV non-structural protein 1 (NS1) is responsible for most of the pathophysiological features of severe dengue. This review considers the contribution of hemophagocytic histiocytosis syndrome to cases of severe dengue, the role of movement of humans in dengue epidemiology, and modeling and planning control programs and describes a…

Abstract RCy3 is an R package in Bioconductor that communicates with Cytoscape via its REST API, providing access to the full feature set of Cytoscape from within the R programming environment. RCy3 has been redesigned to streamline its usage and future development as part of a broader Cytoscape Automation effort. Over 100 new functions have been added, including dozens of helper functions specifically for intuitive data overlay operations. Over 40 Cytoscape apps have implemented automation support so far, making hundreds of additional operations accessible via RCy3. Two-way conversion with networks from igraph and graph ensures interoperability with existing network biology workflows and dozens of other Bioconductor packages. These capabilities are demonstrated in a series of use cases involving public databases, enrichment analysis pipelines, shortest path algorithms and more. With RCy3, bioinformaticians will be able to quickly deliver reproducible network biology workflows as integrations of Cytoscape functions, complex custom analyses and other R packages.

With a prevalence of 0.8 to 1.2%, epilepsy represents one of the most frequent chronic neurological disorders; 30 to 40% of patients suffer from drug-resistant epilepsy (that is, seizures cannot be controlled adequately with antiepileptic drugs). Epilepsy surgery represents a valuable treatment option for 10 to 50% of these patients. Epilepsy surgery aims to control seizures by resection of the epileptogenic tissue while avoiding neuropsychological and other neurological deficits by sparing essential brain areas. The most common histopathological findings in epilepsy surgery specimens are hippocampal sclerosis in adults and focal cortical dysplasia in children. Whereas presurgical evaluations and surgeries in patients with mesial temporal sclerosis and benign tumors recently decreased in most centers, non-lesional patients, patients requiring intracranial recordings, and neocortical resections increased. Recent developments in neurophysiological techniques (high-density electroencephalography [EEG], magnetoencephalography, electrical and magnetic source imaging, EEG-functional…

Intracerebral hemorrhage (ICH) is a stroke subtype associated with significant morbidity and mortality. The purpose of this review is to provide an update on important research on ICH over the past three years. Topics covered include risk factors, imaging predictors of hematoma expansion, scoring schema to predict hematoma expansion, hemostatic therapies, acute blood pressure lowering, intraventricular administration of alteplase for intraventricular hemorrhage, and the current status of surgical therapies.

Medically refractory epilepsy remains an area of intense clinical and scientific interest since a significant porportion of patients continue to suffer from debilitating seizures despite available therapies. In this setting, recent studies have focused on assessing the benefits of cannabidiol (CBD)-enriched cannabis, a plant based product without psychoactive properties which has been shown to decrease seizure frequency in animal models. More recently, several randomized controlled and open label trials have studied the effects of Epidiolex, a 99% pure oral CBD extract, on patients with refractory epilepsy. This in turn has led to the FDA approval of and more recently, to the Drug Enforcement Administration's placement of Epidiolex into schedule V of the Controlled Substances Act (CSA). In this review, we summarize the major findings of several recent large-scale studies using this product with a focus on its adverse effects.

Trichomonas vaginalisis the most common, curable non-viral sexually transmitted infection (STI) worldwide. Despite this burden of disease, it is not currently a reportable disease in the United States. Recent advances in the epidemiology, diagnosis, and management ofT. vaginalisinfection are described in this article. This includes updated global and U.S. prevalence data in women and men as well as recent epidemiological data in HIV-infected individuals and pregnant women. Advances in molecular diagnostics are also reviewed, as are data from recent clinical trials regarding the treatment of trichomonas in women.

The separation of sister chromatids at anaphase, which is regulated by an E3 ubiquitin ligase called the anaphase-promoting complex/cyclosome (APC/C), is arguably the most important irrevocable event during the cell cycle. The APC/C and cyclin-dependent kinase 1 (Cdk1) are just two of the many significant cell cycle regulators and exert control through ubiquitylation and phosphorylation, respectively. The temporal and spatial regulation of the APC/C is achieved by multiple mechanisms, including phosphorylation, interaction with the structurally related co-activators Cdc20 and Cdh1, loading of distinct E2 ubiquitin-conjugating enzymes, binding with inhibitors and differential affinities for various substrates. Since the discovery of APC/C 25 years ago, intensive studies have uncovered many aspects of APC/C regulation, but we are still far from a full understanding of this important cellular machinery. Recent high-resolution cryogenic electron microscopy analysis and reconstitution of the APC/C have greatly advanced our understanding of molecular mechanisms underpinning the enzymatic…

The GABAergic deficit hypothesis of depression states that a deficit of GABAergic transmission in defined neural circuits is causal for depression. Conversely, an enhancement of GABA transmission, including that triggered by selective serotonin reuptake inhibitors or ketamine, has antidepressant effects. Brexanolone, an intravenous formulation of the endogenous neurosteroid allopregnanolone, showed clinically significant antidepressant activity in postpartum depression. By allosterically enhancing GABAAreceptor function, the antidepressant activity of allopregnanolone is attributed to an increase in GABAergic inhibition. In addition, allopregnanolone may stabilize normal mood by decreasing the activity of stress-responsive dentate granule cells and thereby sustain resilience behavior. Therefore, allopregnanolone may augment and extend its antidepressant activity by fostering resilience. The recent structural resolution of the neurosteroid binding domain of GABAAreceptors will expedite the development of more selective ligands as a potential new class of central nervous system drugs.

Post-amputation phantom limb pain (PLP) is highly prevalent and very difficult to treat. The high-prevalence, high-pain intensity levels, and decreased quality of life associated with PLP compel us to explore novel avenues to prevent, manage, and reverse this chronic pain condition. This narrative review focuses on recent advances in the treatment of PLP and reviews evidence of mechanism-based treatments from randomized controlled trials published over the past 5 years. We review recent evidence for the efficacy of targeted muscle reinnervation, repetitive transcranial magnetic stimulation, imaginal phantom limb exercises, mirror therapy, virtual and augmented reality, and eye movement desensitization and reprocessing therapy. The results indicate that not one of the above treatments is consistently better than a control condition. The challenge remains that there is little level 1 evidence of efficacy for PLP treatments and most treatment trials are underpowered (small sample sizes). The lack of efficacy likely speaks to the multiple mechanisms that contribute to PLP both between…

Background: Profiling the microbiome of low-biomass samples is challenging for metagenomics since these samples are prone to contain DNA from other sources (e.g. host or environment). The usual approach is sequencing short regions of the 16S rRNA gene, which fails to assign taxonomy to genus and species level. To achieve an increased taxonomic resolution, we aim to develop long-amplicon PCR-based approaches using Nanopore sequencing. We assessed two different genetic markers: the full-length 16S rRNA (~1,500 bp) and the 16S-ITS-23S region from the rrn operon (4,300 bp). Methods: We sequenced a clinical isolate of Staphylococcus pseudintermedius , two mock communities and two pools of low-biomass samples (dog skin). Nanopore sequencing was performed on MinION™ using the 1D PCR barcoding kit. Sequences were pre-processed, and data were analyzed using EPI2ME or Minimap2 with rrn database. Consensus sequences of the 16S-ITS-23S genetic marker were obtained using canu. Results: The full-length 16S rRNA and the 16S-ITS-23S region of the rrn operon were used to retrieve the microbiota…

The rate of labor induction is steadily increasing and, in industrialized countries, approximately one out of four pregnant women has their labor induced. Induction of labor should be considered when the benefits of prompt vaginal delivery outweigh the maternal and/or fetal risks of waiting for the spontaneous onset of labor. However, this procedure is not free of risks, which include an increase in operative vaginal or caesarean delivery and excessive uterine activity with risk of fetal heart rate abnormalities. A search for "Induction of Labor" retrieves more than 18,000 citations from 1844 to the present day. The aim of this review is to summarize the controversies concerning the indications, the methods, and the tools for evaluating the success of the procedure, with an emphasis on the scientific evidence behind each.

Background: Dimethyl sulfoxide (DMSO) has been used for medical treatment and as a pharmacological agent in humans since the 1960s. Today, DMSO is used mostly for cryopreservation of stem cells, treatment of interstitial cystitis, and as a penetrating vehicle for various drugs. Many adverse reactions have been described in relation to the use of DMSO, but to our knowledge, no overview of the existing literature has been made. Our aim was to conduct a systematic review describing the adverse reactions observed in humans in relation to the use of DMSO. Methods: This systematic review was reported according to the PRISMA-harms (Preferred Reporting Items for Systematic reviews and Meta-Analysis) guidelines. The primary outcome was any adverse reactions occurring in humans in relation to the use of DMSO. We included all original studies that reported adverse events due to the administration of DMSO, and that had a population of five or more. Results: We included a total of 109 studies. Gastrointestinal and skin reactions were the commonest reported adverse reactions to DMSO. Most…

The process of entry into a host cell is a key step in the life cycle of most viruses. In recent years, there has been a significant increase in our understanding of the routes and mechanisms of entry for a number of these viruses. This has led to the development of novel broad-spectrum antiviral approaches that target host cell proteins and pathways, in addition to strategies focused on individual viruses or virus families. Here we consider a number of these approaches and their broad-spectrum potential.

Postoperative delirium is a common and harrowing complication in older surgical patients. Those with cognitive impairment or dementia are at especially high risk for developing postoperative delirium; ominously, it is hypothesized that delirium can accelerate cognitive decline and the onset of dementia, or worsen the severity of dementia. Awareness of delirium has grown in recent years as various medical societies have launched initiatives to prevent postoperative delirium and alleviate its impact. Unfortunately, delirium pathophysiology is not well understood and this likely contributes to the current state of low-quality evidence that informs perioperative guidelines. Along these lines, recent prevention trials involving ketamine and dexmedetomidine have demonstrated inconsistent findings. Non-pharmacologic multicomponent initiatives, such as the Hospital Elder Life Program, have consistently reduced delirium incidence and burden across various hospital settings. However, a substantial portion of delirium occurrences are still not prevented, and effective prevention and management…

In the last few years, single-cell profiling of taste cells and ganglion cells has advanced our understanding of transduction, encoding, and transmission of information from taste buds as relayed to the central nervous system. This review focuses on new knowledge from these molecular approaches and attempts to place this in the context of previous questions and findings in the field. The individual taste cells within a taste bud are molecularly specialized for detection of one of the primary taste qualities: salt, sour, sweet, umami, and bitter. Transduction and transmitter release mechanisms differ substantially for taste cells transducing sour (Type III cells) compared with those transducing the qualities of sweet, umami, or bitter (Type II cells), although ultimately all transmission of taste relies on activation of purinergic P2X receptors on the afferent nerves. The ganglion cells providing innervation to the taste buds also appear divisible into functional and molecular subtypes, and each ganglion cell is primarily but not exclusively responsive to one taste quality.

The development of adhesive connections between cells was critical for the evolution of multicellularity and for organizing cells into complex organs with discrete compartments. Four types of intercellular junction are present in vertebrates: desmosomes, adherens junctions, tight junctions, and gap junctions. All are essential for the development of the embryonic layers and organs as well as adult tissue homeostasis. While each junction type is defined as a distinct entity, it is now clear that they cooperate physically and functionally to create a robust and functionally diverse system. During evolution, desmosomes first appeared in vertebrates as highly specialized regions at the plasma membrane that couple the intermediate filament cytoskeleton at points of strong cell-cell adhesion. Here, we review how desmosomes conferred new mechanical and signaling properties to vertebrate cells and tissues through their interactions with the existing junctional and cytoskeletal network.

The symptoms of neurogenic bowel dysfunction (NBD) comprise constipation and fecal incontinence. These have a major impact on quality of life and dignity. Bowel symptoms occur in the majority of patients with chronic neurological diseases like multiple sclerosis, spinal cord injury, and Parkinson's disease. Management relies on obtaining a careful bowel history, including assessment of bowel function prior to the onset of neurological symptoms. Objective measures of NBD are available and important in terms of monitoring response for what are often intensely personal and difficult-to-elicit symptoms. Conservative management begins by establishing an effective and regular bowel regime by optimizing diet and laxative use. If this is insufficient, as seen in about half of patients, transanal irrigation has been shown to reduce NBD symptoms and improve quality of life. Failing that, there are more invasive surgical options available. This review aims to provide practical guidance for the clinician who encounters these patients, focusing on a stepwise approach to assessment,…

Erectile dysfunction (ED) is important to a man's well-being and health, since it not only affects the individual but also causes strain on a couple's lifestyle and relationship. There are multiple non-invasive treatments that exist for ED including lifestyle changes, oral medications (phosphodiesterase type 5 inhibitors), vacuum-assisted erectile devices, and intraurethral suppositories. While lifestyle changes and oral medications are typically first-line treatments for ED, more-invasive treatments including intracavernosal injections and surgically implanted prosthetic devices may be required for the management of complex cases. Additionally, novel therapies are currently being developed, and future treatment options may include shock-wave therapy, external prosthetic devices, and injection of stem cells or platelet-rich plasma. The current manuscript seeks to highlight advances in management and may eventually alter the treatment paradigm to allow more-inclusive care pathways.

Infections with Pseudomonas aeruginosa have been marked with the highest priority for surveillance and epidemiological research on the basis of parameters such as incidence, case fatality rates, chronicity of illness, available options for prevention and treatment, health-care utilization, and societal impact. P. aeruginosa is one of the six ESKAPE pathogens that are the major cause of nosocomial infections and are a global threat because of their capacity to become increasingly resistant to all available antibiotics. This review reports on current pre-clinical and clinical advances of anti-pseudomonal therapies in the fields of drug development, antimicrobial chemotherapy, vaccines, phage therapy, non-bactericidal pathoblockers, outer membrane sensitizers, and host defense reinforcement.

The metabolic syndrome (MetS) concept gathers in a single entity a set of metabolic abnormalities that have in common a close relationship with ectopic deposit of lipids, insulin resistance, and chronic low-grade inflammation. It is a valuable teaching tool to help health professionals to understand and integrate the consequences of lipotoxicity and the adverse metabolic consequences of insulin resistance. Also, it is useful to identify subjects with a high risk for having incident type 2 diabetes. Systems biology studies have gained a prominent role in understanding the interaction between adipose tissue dysfunction, insulin action, and the MetS traits and co-morbidities (that is, non-alcoholic steatohepatitis, or NASH). This approach may allow the identification of new therapeutic targets (that is, de novo lipogenesis inhibitors for NASH). Treatment targets on MetS are the adoption of a healthy lifestyle, weight loss, and the control of the co-morbidities (hyperglycemia, dyslipidemia, arterial hypertension, among others). The long-term goals are the prevention of type 2 diabetes,…