Search

The Michaelis constant KM describes the affinity of an enzyme for a specific substrate and is a central parameter in studies of enzyme kinetics and cellular physiology. As measurements of KM are often difficult and time-consuming, experimental estimates exist for only a minority of enzyme–substrate combinations even in model organisms. Here, we build and train an organism-independent model that successfully predicts KM values for natural enzyme–substrate combinations using machine and deep learning methods. Predictions are based on a task-specific molecular fingerprint of the substrate, generated using a graph neural network, and on a deep numerical representation of the enzyme’s amino acid sequence. We provide genome-scale KM predictions for 47 model organisms, which can be used to approximately relate metabolite concentrations to cellular physiology and to aid in the parameterization of kinetic models of cellular metabolism., To understand the action of an enzyme, we need to know its affinity for its substrates, quantified by Michaelis constants, but these are difficult to measure experimentally. This study shows that a deep learning model that can predict them from structural features of the enzyme and substrate, providing KM predictions for all enzymes across 47 model organisms.

Lorenz von Seidlein and Nicholas White introduce a Collection on Plasmodium vivax malaria.

Introduction This meta-analysis aimed to summarize the available evidence to compare angiotensin-converting enzyme (ACE) inhibitors with angiotensin II receptor blockers (ARBs) on improving insulin sensitivity in hypertensive patients. Methods Randomized controlled trials (RCTs) comparing ACE inhibitors versus ARBs published with outcomes on homeostasis model assessment of IR (HOMA-IR), glucose infusion rate (GIR), the quantitative insulin sensitivity check index (QUICKI), insulin sensitivity index (ISI) composite, fasting plasma glucose (FPG), fasting plasma insulin (FPI), systolic blood pressure (SBP), and diastolic blood pressure (DBP) were searched through 5 databases. Data were searched from their inception to July 5, 2020. Stata 14.0 was used to perform the meta-analysis. Results Eleven RCTs (n = 1015) were included in this meta-analysis. Pooled analysis of studies showed no significant difference in HOMA-IR between ARBs and ACE inhibitors (WMD = -0.09, 95% CI: -0.69 to 0.50, P = 0.755); however, subgroup analysis of therapeutic duration showed a significant difference in HOMA-IR between ARBs and ACE inhibitors among the long-term intervention subgroup (>12 weeks) (WMD = 0.41, 95% CI: 0.06 to 0.76, P = 0.022) and hypertensive patients with diabetes mellitus subgroup (WMD = 0.55, 95% CI: 0.49 to 0.61, P < 0.001); results showed no significant difference between ARBs and ACE inhibitors on QUICKI score (WMD = -0.00, 95% CI: -0.03 to 0.03, P = 0.953) in hypertensive patients; however, the efficacy of ACE inhibitors on improving GIR and ISI composite was significantly better than that of ARBs (WMD = -1.09, 95% CI: -1.34 to -0.85, P < 0.001; WMD = -0.80, 95% CI: -1.24 to -0.36, P < 0.001, respectively). Furthermore, no significant differences were noted on FPG (WMD = 0.72, 95% CI: -1.39 to 2.83, P = 0.505), FPI (WMD = -0.48, 95% CI: -1.60 to 0.64, P = 0.398), SBP (WMD = -0.65, 95% CI: -1.76 to 0.46, P = 0.254), and DBP (WMD = -0.30, 95% CI: -1.70 to 1.10, P = 0.675) between ARBs and ACE inhibitors. Conclusion Results from this meta-analysis showed that ACE inhibitors resulted in more effective improvement of HOMA-IR compared with ARBs among the long-term intervention and hypertensive patients with DM subgroup; furthermore, the efficacy of ACE inhibitors on improving GIR and ISI composite was significantly better than that of ARBs in hypertensive patients. However, ARBs had no significant difference in QUICKI score, FPG, FPI, SBP, and DBP compared with ACE inhibitors. Larger and better-designed studies are needed to further verify this conclusion.

Sensing and response to environmental cues, such as pH and chloride (Cl−), is critical in enabling Mycobacterium tuberculosis (Mtb) colonization of its host. Utilizing a fluorescent reporter Mtb strain in a chemical screen, we have identified compounds that dysregulate Mtb response to high Cl− levels, with a subset of the hits also inhibiting Mtb growth in host macrophages. Structure–activity relationship studies on the hit compound “C6,” or 2-(4-((2-(ethylthio)pyrimidin-5-yl)methyl)piperazin-1-yl)benzo[d]oxazole, demonstrated a correlation between compound perturbation of Mtb Cl− response and inhibition of bacterial growth in macrophages. C6 accumulated in both bacterial and host cells, and inhibited Mtb growth in cholesterol media, but not in rich media. Subsequent examination of the Cl− response of Mtb revealed an intriguing link with bacterial growth in cholesterol, with increased transcription of several Cl−-responsive genes in the simultaneous presence of cholesterol and high external Cl− concentration, versus transcript levels observed during exposure to high external Cl− concentration alone. Strikingly, oral administration of C6 was able to inhibit Mtb growth in vivo in a C3HeB/FeJ murine infection model. Our work illustrates how Mtb response to environmental cues can intersect with its metabolism and be exploited in antitubercular drug discovery., Responding to environmental cues such as pH and chloride is critical in enabling Mycobacterium tuberculosis to colonize its host. A chemical screen using an M. tuberculosis strain bearing a fluorescent reporter identifies a compound that perturbs the bacterial response to chloride and inhibits its growth in a murine infection model.

The efficacy of antibiotics to treat bacterial infections declines rapidly due to antibiotic resistance. This problem has stimulated the development of novel antibiotics, but most attempts have failed. Consequently, the idea of mining uncharacterized genes of pathogens to identify potential targets for entirely new classes of antibiotics was proposed. Without knowing the biochemical function of a protein, it is difficult to validate its potential for drug targeting; therefore, the functional characterization of bacterial proteins of unknown function must be accelerated. Here, we present a paradigm for comprehensively predicting the biochemical functions of a large set of proteins encoded by hypothetical genes in human pathogens to identify candidate drug targets. A high-throughput approach based on homology modelling with ten templates per target protein was applied to the set of 2103 P. aeruginosa proteins encoded by hypothetical genes. The >21000 homology modelling results obtained and available biological and biochemical information about several thousand templates were scrutinized to predict the function of reliably modelled proteins of unknown function. This approach resulted in assigning one or often multiple putative functions to hundreds of enzymes, ligand-binding proteins and transporters. New biochemical functions were predicted for 41 proteins whose essential or virulence-related roles in P. aeruginosa were already experimentally demonstrated. Eleven of them were shortlisted as promising drug targets that participate in essential pathways (maintaining genome and cell wall integrity), virulence-related processes (adhesion, cell motility, host recognition) or antibiotic resistance, which are general drug targets. These proteins are conserved in other WHO priority pathogens but not in humans; therefore, they represent high-potential targets for preclinical studies. These and many more biochemical functions assigned to uncharacterized proteins of P. aeruginosa, made available as PaPUF database, may guide the design of experimental screening of inhibitors, which is a crucial step towards the validation of the highest-potential targets for the development of novel drugs against P. aeruginosa and other high-priority pathogens.

The rapid decrease in sequencing cost has enabled genetic studies to discover rare variants associated with complex diseases and traits. Once this association is identified, the next step is to understand the genetic mechanism of rare variants on how the variants influence diseases. Similar to the hypothesis of common variants, rare variants may affect diseases by regulating gene expression, and recently, several studies have identified the effects of rare variants on gene expression using heritability and expression outlier analyses. However, identifying individual genes whose expression is regulated by rare variants has been challenging due to the relatively small sample size of expression quantitative trait loci studies and statistical approaches not optimized to detect the effects of rare variants. In this study, we analyze whole-genome sequencing and RNA-seq data of 681 European individuals collected for the Genotype-Tissue Expression (GTEx) project (v8) to identify individual genes in 49 human tissues whose expression is regulated by rare variants. To improve statistical power, we develop an approach based on a likelihood ratio test that combines effects of multiple rare variants in a nonlinear manner and has higher power than previous approaches. Using GTEx data, we identify many genes regulated by rare variants, and some of them are only regulated by rare variants and not by common variants. We also find that genes regulated by rare variants are enriched for expression outliers and disease-causing genes. These results suggest the regulatory effects of rare variants, which would be important in interpreting associations of rare variants with complex traits., Author summary It has been shown that rare variants may affect many diseases including both rare and common diseases with the advent of next-generation sequencing technology. An important question is how rare variants affect diseases or traits, especially whether or how they regulate gene expression as they may affect diseases through gene regulation. However, it is challenging to identify the regulatory effects of rare variants because it often requires large sample sizes and the existing statistical approaches are not optimized for it. Here, we develop a novel method, LRT-q, based on a likelihood ratio test that aggregates the effects of multiple rare variants nonlinearly to achieve higher statistical power than previous rare variant association methods. We apply LRT-q to the latest GTEx v8 dataset and identify regulatory effect of rare variants on individual genes. We also observe that genes regulated by rare variants are likely to be disease-causing genes. These results demonstrate the functional effects of rare variants, especially on gene expression, which provides important biological insights in understanding the genetic mechanism of rare variants in complex traits and diseases.

Background Cannabinoid-based medicines (CBMs) are being used widely in the elderly. However, their safety and tolerability in older adults remains unclear. We aimed to conduct a systematic review and meta-analysis of safety and tolerability of CBMs in adults of age ≥50 years. Methods and findings A systematic search was performed using MEDLINE, PubMed, EMBASE, CINAHL PsychInfo, Cochrane Library, and ClinicalTrials.gov (1 January 1990 to 3 October 2020). Randomised clinical trials (RCTs) of CBMs in those with mean age of ≥50 years for all indications, evaluating the safety/tolerability of CBMs where adverse events have been quantified, were included. Study quality was assessed using the GRADE (Grading of Recommendations Assessment, Development, and Evaluation) criteria and Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines were followed. Two reviewers conducted all review stages independently. Where possible, data were pooled using random-effects meta-analysis. Effect sizes were calculated as incident rate ratio (IRR) for outcome data such as adverse events (AEs), serious AEs (SAEs), and death and risk ratio (RR) for withdrawal from study and reported separately for studies using tetrahydrocannabinol (THC), THC:cannabidiol (CBD) combination, and CBD. A total of 46 RCTs were identified as suitable for inclusion of which 31 (67%) were conducted in the United Kingdom and Europe. There were 6,216 patients (mean age 58.6 ± 7.5 years; 51% male) included in the analysis, with 3,469 receiving CBMs. Compared with controls, delta-9-tetrahydrocannabinol (THC)-containing CBMs significantly increased the incidence of all-cause and treatment-related AEs: THC alone (IRR: 1.42 [95% CI, 1.12 to 1.78]) and (IRR: 1.60 [95% CI, 1.26 to 2.04]); THC:CBD combination (IRR: 1.58 [95% CI,1.26 to 1.98]) and (IRR: 1.70 [95% CI,1.24 to 2.33]), respectively. IRRs of SAEs and deaths were not significantly greater under CBMs containing THC with or without CBD. THC:CBD combination (RR: 1.40 [95% CI, 1.08 to 1.80]) but not THC alone (RR: 1.18 [95% CI, 0.89 to 1.57]) significantly increased risk of AE-related withdrawals. CBD alone did not increase the incidence of all-cause AEs (IRR: 1.02 [95% CI, 0.90 to 1.16]) or other outcomes as per qualitative synthesis. AE-related withdrawals were significantly associated with THC dose in THC only [QM (df = 1) = 4.696, p = 0.03] and THC:CBD combination treatment ([QM (df = 1) = 4.554, p = 0.033]. THC-containing CBMs significantly increased incidence of dry mouth, dizziness/light-headedness, and somnolence/drowsiness. Study limitations include inability to fully exclude data from those, Latha Velayudhan and co-workers report a meta-analysis on safety of cannabinoid-based medicines in people aged over 50 years., Author summary Why was this study done? Use of cannabinoid-based medicines (CBMs) has been growing steadily in recent years, including in the elderly. However, their safety and tolerability in older adults remains unclear. With increasing interest in the use of CBMs in older people and growing unlicensed use, there is a particular need to examine their safety and tolerability in older adults. We analysed data on safety and tolerability from previously published double-blind, randomised controlled trials (RCT) using delta-9-tetrahydorcannabinol (THC) and cannabidiol (CBD), the common constituents of most CBMs, alone or in combination, to examine their effect on older adults. What did the researchers do and find? We pooled data from 46 published RCTs (with information from 6,216 patients; with mean participant age ≥50 years) on adverse events, serious adverse events or death, and withdrawal from study. We also examined the relationship between the dose of THC used in THC-containing CBMs and the incidence of adverse consequences in older adults. Our results suggest that compared with the control condition, treatment with THC-containing CBMs was associated on average with significantly greater incidence of all-cause and treatment-related adverse events. There was no significant increase in the incidence of serious adverse events or death with any CBMs. The risk of withdrawal from study was increased only in those receiving THC:CBD combination treatment, and this was related to THC dose. What do these findings mean? These findings suggest that CBMs in general are safe and acceptable in older adults. Our findings that THC-containing CBMs are associated with side effects and that THC:CBD combinations may be less acceptable at the dose ranges typically used in RCTs is critical to prescribing in older people.

Missense variants are present amongst the healthy population, but some of them are causative of human diseases. A classification of variants associated with “healthy” or “diseased” states is therefore not always straightforward. A deeper understanding of the nature of missense variants in health and disease, the cellular processes they may affect, and the general molecular principles which underlie these differences is essential to offer mechanistic explanations of the true impact of pathogenic variants. Here, we have formalised a statistical framework which enables robust probabilistic quantification of variant enrichment across full-length proteins, their domains, and 3D structure-defined regions. Using this framework, we validate and extend previously reported trends of variant enrichment in different protein structural regions (surface/core/interface). By examining the association of variant enrichment with available functional pathways and transcriptomic and proteomic (protein half-life, thermal stability, abundance) data, we have mined a rich set of molecular features which distinguish between pathogenic and population variants: Pathogenic variants mainly affect proteins involved in cell proliferation and nucleotide processing and are enriched in more abundant proteins. Additionally, rare population variants display features closer to common than pathogenic variants. We validate the association between these molecular features and variant pathogenicity by comparing against existing in silico variant impact annotations. This study provides molecular details into how different proteins exhibit resilience and/or sensitivity towards missense variants and provides the rationale to prioritise variant-enriched proteins and protein domains for therapeutic targeting and development. The ZoomVar database, which we created for this study, is available at fraternalilab.kcl.ac.uk/ZoomVar. It allows users to programmatically annotate missense variants with protein structural information and to calculate variant enrichment in different protein structural regions., How do can one improve the classification of genetic variants as harmful or harmless? This study uses a robust statistical analysis to exploit the interplay between protein structure, proteomic measurements and functional pathways to enable better discrimination between missense variants in health and disease.

Many randomized controlled trials (RCTs) are biased and difficult to reproduce due to methodological flaws and poor reporting. There is increasing attention for responsible research practices and implementation of reporting guidelines, but whether these efforts have improved the methodological quality of RCTs (e.g., lower risk of bias) is unknown. We, therefore, mapped risk-of-bias trends over time in RCT publications in relation to journal and author characteristics. Meta-information of 176,620 RCTs published between 1966 and 2018 was extracted. The risk-of-bias probability (random sequence generation, allocation concealment, blinding of patients/personnel, and blinding of outcome assessment) was assessed using a risk-of-bias machine learning tool. This tool was simultaneously validated using 63,327 human risk-of-bias assessments obtained from 17,394 RCTs evaluated in the Cochrane Database of Systematic Reviews (CDSR). Moreover, RCT registration and CONSORT Statement reporting were assessed using automated searches. Publication characteristics included the number of authors, journal impact factor (JIF), and medical discipline. The annual number of published RCTs substantially increased over 4 decades, accompanied by increases in authors (5.2 to 7.8) and institutions (2.9 to 4.8). The risk of bias remained present in most RCTs but decreased over time for allocation concealment (63% to 51%), random sequence generation (57% to 36%), and blinding of outcome assessment (58% to 52%). Trial registration (37% to 47%) and the use of the CONSORT Statement (1% to 20%) also rapidly increased. In journals with a higher impact factor (>10), the risk of bias was consistently lower with higher levels of RCT registration and the use of the CONSORT Statement. Automated risk-of-bias predictions had accuracies above 70% for allocation concealment (70.7%), random sequence generation (72.1%), and blinding of patients/personnel (79.8%), but not for blinding of outcome assessment (62.7%). In conclusion, the likelihood of bias in RCTs has generally decreased over the last decades. This optimistic trend may be driven by increased knowledge augmented by mandatory trial registration and more stringent reporting guidelines and journal requirements. Nevertheless, relatively high probabilities of bias remain, particularly in journals with lower impact factors. This emphasizes that further improvement of RCT registration, conduct, and reporting is still urgently needed., Many randomized controlled trials (RCTs) are biased and difficult to reproduce due to methodological flaws and poor reporting. Analysis of 176,620 RCTs published between 1966 and 2018 reveals that the risk of bias in RCTs generally decreased. Nevertheless, relatively high probabilities of bias remain, showing that further improvement of RCT registration, conduct, and reporting is still urgently needed.

Novel strategies to re-engage and retain people living with HIV (PLWH) who are out of care are greatly needed. While mobile clinics have been used effectively for HIV testing and linkage, evidence guiding their use in providing HIV care domestically has been limited. To guide the development of a mobile HIV clinic (MHC) model as a strategy to re-engage and retain PLWH who are out of care, we aimed to explore stakeholder perceptions of barriers and facilitators to MHC implementation and use. From June 2019-July 2020, we conducted 41 in-depth interviews with HIV clinic providers, administrators, staff, legal authorities, and community advisory board members, PLWH, AIDS service organizations and city officials in Atlanta, Georgia, and domestic and international mobile health clinics to explore barriers and facilitators to use of MHCs. Interviews were transcribed, coded and thematically analysed. Barriers raised include potential for: breach of confidentiality with resulting heightened stigmatization, fractured continuity of care, safety concerns, staffing challenges, and low community acceptance of MHC presence in their locality. Participants provided suggestions regarding appropriate exterior design, location, timing, and co-delivery of non-HIV services that could facilitate MHC acceptance and address the concerns. In identifying key barriers and facilitators to MHC use, this study informs design and implementation of an MHC as a novel strategy for re-engaging and retaining PLWH who are out of care.

Cancer cell lines are widely used in basic research to study cancer development, growth, invasion, or metastasis. They are also used for the development and screening of anticancer drugs. However, there are no clear criteria for choosing the most suitable cell lines among the wide variety of cancer cell lines commercially available for research, and the choice is often based on previously published reports. Here, we investigated the characteristics of liver cancer cell lines by analyzing the gene expression data available in the Cancer Cell Line Encyclopedia. Unsupervised clustering analysis of 28 liver cancer cell lines yielded two main clusters. One cluster showed a gene expression pattern similar to that of hepatocytes, and the other showed a pattern similar to that of fibroblasts. Analysis of hepatocellular carcinoma gene expression profiles available in The Cancer Genome Atlas showed that the gene expression patterns in most hepatoma tissues were similar to those in the hepatocyte-like cluster. With respect to liver cancer research, our findings may be useful for selecting an appropriate cell line for a specific study objective. Furthermore, our approach of utilizing a public database for comparing the properties of cell lines could be an attractive cell line selection strategy that can be applied to other fields of research.

Background Soil-transmitted helminths (STH) are common in low and middle income countries where there is lack of access to clean water and sanitation. Effective diagnosis and treatment are essential for the control of STH infections. However, among STH parasites, Strongyloides stercoralis is the most neglected species, both in diagnostics and control strategies. Diagnostic methods cover different approaches, each with different sensitivities and specificities, such as serology, molecular techniques and microscopy based techniques. Of the later, the Baermann technique is the most commonly used procedure. In the literature, several ways have been described to perform the Baermann method, which illustrates the overall lack of a ‘(gold) reference standard’ method for the diagnosis of S. stercoralis infection. In this study we have evaluated the performance of three Baermann techniques in order to improve the reference standard for the microscopic diagnosis of S. stercoralis infection thereby facilitating individual case detection, mapping of the disease and proper evaluation of treatment responses. Methods/Principal findings A community based cross sectional study was conducted at Zenzelima, Bahir Dar Zuria Ethiopia. A total of 437 stool samples were collected and analyzed by the following procedures: conventional Baermann (CB), modified Baermann (MB), and modified Baermann with charcoal pre-incubation (MBCI). The diagnostic sensitivity and Negative Predictive Value (NPV) of each technique was calculated using the combination of all the three techniques as a composite reference standard. Our result indicated that larvae of S. stercoralis were detected in 151 (34.6%) stool samples. The prevalence of S. stercoralis infection based on the three diagnostic methods was 9.6%, 8.0%, and 31.3% by CB, MB, and MBCI respectively. The sensitivity and NPV for CB, MB, and MBCI were 26.7% and 70.8%, 22.1% and 69.6%, and 87.0% and 93.2%, respectively. The MBCI showed significant difference (P- value =, Author summary Strongyloidiasis is a poverty-related neglected tropical disease which can cause serious and potentially life-threatening symptoms, in particular in immunocompromised hosts. S. stercoralis is not yet included in the strategies coordinated by WHO for the control of STH, but there are plans for the establishment of a control strategy by 2030. Therefore, diagnostics and control tools to implement that strategy are needed. Different diagnostic approaches are used in different parts of the world and there is no standard diagnostic approach which can be used for routine diagnostic services and field studies. In this study, 437 stool samples from Northwest Ethiopia were analyzed using conventional Baermann, modified Baermann and modified Baermann with charcoal pre-incubation techniques. Using these procedures, we found high prevalence of S. stercoralis infection in the study area. The modified Baermann with charcoal pre-incubation technique worked significantly better than the others in recovering the S. stercoralis larvae, while the conventional Baermann, the most used in routine diagnostics, underestimates the true burden of the disease. The key findings in this study are important for future planning of intervention and control strategies against strongyloidiasis.

Many small parasitoid wasps have a black-orange-black (BOB) color pattern, which is usually present in both sexes. A likely function of this widespread pattern is aposematic (warning) coloration, but this has never been investigated. To test this hypothesis, we presented spider predators(Lyssomanes jemineus), both field-captured and lab-reared individuals, to a species with the BOB pattern and a congeneric all-black species in each of four scelionid genera (Baryconus, Chromoteleia, MacroteleiaandScelio). Each spider/wasp trial was filmed for 40 minutes under controlled conditions and three behavioral responses (detect, attack, avoid) were recorded in each of 136 trials, never using the same predator and prey more than once. In order to better understand the results obtained, two additional studies were performed. First, the reflection spectrum of the cuticle of the wasp and a theoretical visual sensibility model of the spider were used to calculate a parameter we called “absorption contrast” that allowed us to compare the perception contrast between black and orange in each wasp genus as viewed by the spider. Second, acute toxicity trials with the water flea,Daphnia magna, were performed to determine toxicity differences between BOB and non-BOB wasps. By combining the results from the three types of experiments, together with a statistical analysis, we confirmed that BOB color pattern plays an aposematic role.

Several issues have been identified with the current programs for the elimination of onchocerciasis that target only transmission by using mass drug administration (MDA) of the drug ivermectin. Alternative and/or complementary treatment regimens as part of a more comprehensive strategy to eliminate onchocerciasis are needed. We posit that the addition of “prophylactic” drugs or therapeutic drugs that can be utilized in a prophylactic strategy to the toolbox of present microfilaricidal drugs and/or future macrofilaricidal treatment regimens will not only improve the chances of meeting the elimination goals but may hasten the time to elimination and also will support achieving a sustained elimination of onchocerciasis. These “prophylactic” drugs will target the infective third- (L3) and fourth-stage (L4) larvae of Onchocerca volvulus and consequently prevent the establishment of new infections not only in uninfected individuals but also in already infected individuals and thus reduce the overall adult worm burden and transmission. Importantly, an effective prophylactic treatment regimen can utilize drugs that are already part of the onchocerciasis elimination program (ivermectin), those being considered for MDA (moxidectin), and/or the potential macrofilaricidal drugs (oxfendazole and emodepside) currently under clinical development. Prophylaxis of onchocerciasis is not a new concept. We present new data showing that these drugs can inhibit L3 molting and/or inhibit motility of L4 at IC50 and IC90 that are covered by the concentration of these drugs in plasma based on the corresponding pharmacological profiles obtained in human clinical trials when these drugs were tested using various doses for the therapeutic treatments of various helminth infections.

Background The community practice towards disposal of expired and unused medications in spite of its adverse impact have been widely neglected in many developing countries. The available guidelines in Tanzania focus on the disposal of expired medications and cosmetics in hospitals and community pharmacies only. Aim The aim of this study was to assess the disposal practice of expired and unused medications at household level in Mwanza city, north-western Tanzania. Methodology The household based cross-sectional study was conducted among 359 randomly selected household members. Semi-structured questionnaires were used for interview during data collection and while STATA® version 13 was used for analysis. Results Out 359 households visited, 252 (70.19%) had medications kept in their houses at the time of data collection. Among them, 10 (4.0%) households had kept medications at their houses because they were still continuing with treatment while 242 (96.0%) kept unused medications which were supposed to be discarded. The main reason for keeping unused or expired medications at home was uncompleted course of treatment (199 (82.20%) after feeling that they had recovered from illness. The main reason for discarding medications were recovering from illness (141(48.7%) and expiry (136 (46.9%). The major discarding practices for medications were disposing into domestic trashes (219 (75.5%) and pit latrines (45 (15.5%). Majority of respondents (273 (76%) were aware that improper disposal of expired medications are detrimental to human health and environment in general. Conclusion Improper disposal of unused and expired medications at household level was a common practice in the study area. Tailor-made interventions by the Food and Drugs Authority (FDA) and other national as well as local stake holders are urgently needed to address the situation.

Nicotinamide-nucleotide adenylyl transferase (Rv2421c) was selected as a potential drug target, because it has been shown, in vitro, to be essential for Mycobacterium tuberculosis growth. It is conserved between mycobacterium species, is up-regulated during dormancy, has a known 3D crystal structure and has no known human homologs. A model of Rv2421c in complex with nicotinic acid adenine dinucleotide and magnesium ion was constructed and subject tovirtual ligand screening against the Prestwick Chemical Library and the ZINC database, which yielded 155 potential hit molecules. Of the 155 compounds identified five were pursued further using an IC50 based 3D-QSAR study. The 3D-QSAR model validated the inhibition properties of the five compounds based on R2 value of 0.895 and Q2 value of 0.944 compared to known inhibitors of Rv2421c. Higher binding affinities was observed for the novel ZINC13544129 and two FDA approved compounds (Novobiocin sodium salt, Sulfasalazine). Similarly, the total interaction energy was found to be the highest for Cromolyn disodium system (-418.88 kJ/mol) followed by Novobiocin (-379.19 kJ/mol) and Sulfasalazine with (-330.13 kJ/mol) compared to substrate DND having (-185.52 kJ/mol). Subsequent in vitro testing of the five compounds identified Novobiocin sodium salt with activity against Mycobacterium tuberculosis at 50 μM, 25μM and weakly at 10μM concentrations. Novobiocin salt interacts with a MG ion and active site residues His20, Thr86, Gly107 and Leu164 similar to substrate DND of Mycobacterium tuberculosis Rv2421c. Additional in silico structural analysis of known Novobiocin sodium salt derivatives against Rv2421c suggest Coumermycin as a promising alternative for the treatment of Mycobacterium tuberculosis based on large number of hydrogen bond interactions with Rv2421c similar in comparison to Novobiocin salt and substrate DND.

Background Clinical trial participants are required to sign an informed consent form (ICF). However, information is lacking on the most effective methods to convey trial relevant information prior to inviting participants to sign the ICF, being particularly pertinent in low-income countries. A previous study on Pemba Island, Tanzania, found that a verbal information session (IS) was significantly better than providing an ICF alone. However, knowledge gaps remained. Building on these findings, we investigated the effect of adding a slideshow or a theater to the IS in the informed consent procedure of an anthelminthic clinical trial. Methodology/principal findings A total of 604 caregivers were randomized into the control group that only received an ICF (n = 150) or an ICF plus one of three intervention strategies: (i) verbal IS (n = 135), (ii) verbal IS with a slideshow (n = 174) or (iii) verbal IS followed by a theater (n = 145). All modes of information covered the same key messages. Participants’ understanding was assessed using a semi-structured questionnaire. The mean score of caregivers in the control group (ICF only) was 4.41 (standard deviation = 1.47). Caregivers attending the IS alone were more knowledgeable than those in the control group (estimated difference in mean scores: 2.40, 95% confidence interval (CI) 1.95 to 2.86, p < 0.01). However, there was no evidence of an improvement compared to the IS only when participants attended a slideshow (0.09, 95% CI -0.53 to 0.35, p = 0.68) or a theater (0.28, 95% CI -0.27 to 0.82, p = 0.32). Three out of 10 key messages remained largely misunderstood, regardless of the mode of information group. Conclusions/significance Our study confirmed that, in this setting, an ICF alone was not sufficient to convey clinical trial-related information. An IS was beneficial, however, additional theater and slideshows did not further improve understanding. Future research should explore methods to improve communication between study teams and participants for different key messages, study types and settings., Author summary Legally, participants of clinical trials must sign an informed consent form prior to the start of a trial. To be truly informed, participants (or their caregivers, if underaged) need to understand the trial objectives, procedures, benefits, potential risks and their rights throughout the study. However, in regions where literacy and health literacy are still quite low, delivering information exclusively in written format using an informed consent form is not the best way to convey information. A previous study on Pemba Island, Tanzania, found that a spoken information session in addition to the informed consent form alone, significantly improved the clinical trial-related knowledge of the caregivers of participants. However, not all questions could be answered correctly. In the current study, we explored the addition of two further modes of information to the information session: a slideshow or a theater show. Caregivers’ understanding was measured using a questionnaire. We confirmed that having an oral information session is significantly better than only receiving the informed consent form. However, adding a slideshow and theater did not further improve caregivers’ knowledge. We conclude that future studies should work on improving these modes of information or explore new ones.

Naegleria fowleri is a pathogenic, thermophilic, free-living amoeba which causes primary amebic meningoencephalitis (PAM). Penetrating the olfactory mucosa, the brain-eating amoeba travels along the olfactory nerves, burrowing through the cribriform plate to its destination: the brain’s frontal lobes. The amoeba thrives in warm, freshwater environments, with peak infection rates in the summer months and has a mortality rate of approximately 97%. A major contributor to the pathogen’s high mortality is the lack of sensitivity of N. fowleri to current drug therapies, even in the face of combination-drug therapy. To enable rational drug discovery and design efforts we have pursued protein production and crystallography-based structure determination efforts for likely drug targets from N. fowleri. The genes were selected if they had homology to drug targets listed in Drug Bank or were nominated by primary investigators engaged in N. fowleri research. In 2017, 178 N. fowleri protein targets were queued to the Seattle Structural Genomics Center of Infectious Disease (SSGCID) pipeline, and to date 89 soluble recombinant proteins and 19 unique target structures have been produced. Many of the new protein structures are potential drug targets and contain structural differences compared to their human homologs, which could allow for the development of pathogen-specific inhibitors. Five of the structures were analyzed in more detail, and four of five show promise that selective inhibitors of the active site could be found. The 19 solved crystal structures build a foundation for future work in combating this devastating disease by encouraging further investigation to stimulate drug discovery for this neglected pathogen.

A significant interaction between N-methyl-D-aspartate (NMDA) and muscarinic receptors has been suggested in the modulation of learning and memory processes. The present study further investigates this issue and explores whether d-cycloserine (DCS), a partial agonist at the glycine binding site of the NMDA receptors that has been regarded as a cognitive enhancer, would reverse scopolamine (SCOP)-induced amnesia in two olfactory learning tasks when administered into the prelimbic cortex (PLC). Thus, in experiment 1, DCS (10 µg/site) was infused prior to acquisition of odor discrimination (ODT) and social transmission of food preference (STFP), which have been previously characterized as paradigms sensitive to PLC muscarinic blockade. Immediately after learning such tasks, SCOP was injected (20 µg/site) and the effects of both drugs (alone and combined) were tested in 24-h retention tests. To assess whether DCS effects may depend on the difficulty of the task, in the STFP the rats expressed their food preference either in a standard two-choice test (experiment 1) or a more challenging three-choice test (experiment 2). The results showed that bilateral intra-PLC infusions of SCOP markedly disrupted the ODT and STFP memory tests. Additionally, infusions of DCS alone into the PLC enhanced ODT but not STFP retention. However, the DCS treatment reversed SCOP-induced memory deficits in both tasks, and this effect seemed more apparent in ODT and 3-choice STFP. Such results support the interaction between the glutamatergic and the cholinergic systems in the PLC in such a way that positive modulation of the NMDA receptor/channel, through activation of the glycine binding site, may compensate dysfunction of muscarinic neurotransmission involved in stimulus-reward and relational learning tasks.

Purpose Overall survival (OS) is the most significant endpoint for evaluation of treatment benefit with checkpoint inhibitors (CPI) in cancer. We evaluated serum C-reactive protein (CRP) in non-small cell lung cancer (NSCLC) trials with atezolizumab (anti-PD-L1) as an early OS surrogate. Methods Serum from patients enrolled in randomized Phase II (n = 240) and Phase III (n = 701) trials of NSCLC patients (POPLAR, OAK) who progressed on prior-platinum chemotherapy, were analyzed for CRP levels over time. Patients were grouped by changes in CRP levels post-treatment as either increased (≥ 1.5 fold), decreased (≤ 1.5 fold) or unchanged (within +1.5 fold) relative to pre-treatment levels to assess association with progression free survival (PFS) and OS. Results Decrease in serum CRP levels at 6 weeks relative to pre-treatment were observed in patients with RECIST1.1 based complete or partial responses (CR/PR) to atezolizumab whereas patients with disease progression (PD) demonstrated an increase in CRP levels in the Phase II POPLAR study, and confirmed in the Phase III OAK study. Decrease in serum CRP as early as six weeks post treatment predicted improved PFS and OS, even in patients who were determined as stable disease (SD) in their first scan. This effect was not observed in the chemotherapy arms. Conclusion Modulation of serum CRP correlates with clinical outcome post-atezolizumab treatment. This routine lab test may provide utility in informing OS signals as early as 6 weeks post-initiation of therapy with CPIs in NSCLC.

Current mass drug administration (MDA) programs for the treatment of human river blindness (onchocerciasis) caused by the filarial worm Onchocerca volvulus rely on ivermectin, an anthelmintic originally developed for animal health. These treatments are primarily directed against migrating microfilariae and also suppress fecundity for several months, but fail to eliminate adult O. volvulus. Therefore, elimination programs need time frames of decades, well exceeding the life span of adult worms. The situation is worsened by decreased ivermectin efficacy after long-term therapy. To improve treatment options against onchocerciasis, a drug development candidate should ideally kill or irreversibly sterilize adult worms. Emodepside is a broad-spectrum anthelmintic used for the treatment of parasitic nematodes in cats and dogs (Profender and Procox). Our current knowledge of the pharmacology of emodepside is the result of more than 2 decades of intensive collaborative research between academia and the pharmaceutical industry. Emodepside has a novel mode of action with a broad spectrum of activity, including against extraintestinal nematode stages such as migrating larvae or macrofilariae. Therefore, emodepside is considered to be among the most promising candidates for evaluation as an adulticide treatment against onchocerciasis. Consequently, in 2014, Bayer and the Drugs for Neglected Diseases initiative (DNDi) started a collaboration to develop emodepside for the treatment of patients suffering from the disease. Macrofilaricidal activity has been demonstrated in various models, including Onchocerca ochengi in cattle, the parasite most closely related to O. volvulus. Emodepside has now successfully passed Phase I clinical trials, and a Phase II study is planned. This Bayer–DNDi partnership is an outstanding example of “One World Health,” in which experience gained in veterinary science and drug development is translated to human health and leads to improved tools to combat neglected tropical diseases (NTDs) and shorten development pathways and timelines in an otherwise neglected area., Author summary Onchocerca volvulus is the causative agent of human river blindness, and current elimination programs rely on the use of ivermectin to kill microfilariae. Since no adulticidal drug is available and adult worms have a life span of up to 15 years, elimination programs need to be sustained over several decades. Emodepside is an anthelmintic that is licensed as a dewormer for cats and dogs. Due to its ability to eliminate nematodes located in various extraintestinal host tissues, including migrating larvae and adult filarial worms, it is considered to be an excellent candidate for the treatment of onchocerciasis. Intense collaboration between academia and the pharmaceutical industry has led to a deep understanding of the novel mode of action of the drug and of its parasite target spectrum. Phase I clinical trials with emodepside have demonstrated its safety and adulticide activity against the closely related cattle parasite Onchocerca ochengi. Currently, Phase II clinical trials are planned to confirm that emodepside, developed initially to improve animal health, has also the potential to improve human health by tackling a very important neglected tropical disease (NTD).

Background Drug-resistance in Mycobacterium tuberculosis complex remains a major health burden in human history and still is a major leading cause of death in developing countries including Ethiopia. Early detection of all forms of drug-resistant Tuberculosis(TB) is a key factor to reduce and contain the spread of these resistant strains. Methods A health facility-based cross-sectional study was employed, based on demographic, clinical, and laboratory data collected from 204 patients with bacteriological confirmed TB. Sputum samples were analyzed using conventional TB culture and identification test followed by molecular species identification, and then phenotypic drug susceptibility tests. Data were entered using an excel spreadsheet and exported to SPSS version 20 for analysis. Descriptive analysis; frequencies, and proportions were computed. Results Among the 204 sputum samples inoculated in culture media, Mycobacterium species were recovered from 165 specimens, with 160 Mycobacterium tuberculosis complex and five Non- Tuberculosis Mycobacterium(NTM) species. All Mycobacterium tuberculosis complex was found to be M. tuberculosis. Of the five NTM species, 2 M.fortuitum, 2 M.intracellulare, and 1 M.gordonae were identified. Among 160 species of M. tuberculosis isolates, 110(68.8%) were resistant to any of the anti-TB drugs. The resistance pattern was; INH (109, 68.1%), RIF (99, 61.9%), STM (73,45.6%), and EMB (32,20.0%). Mono-resistance was found for INH (7,4.3%) and STM (1,0.6%). Ninety-nine (61.9%) isolates become MDR, while resistance to any of the second-line anti-TB drugs was detected in 9 (5.6%) strains, with 8(5%) Pre-XDR and one (0.6%) XDR cases. Conclusion Our findings highlight high frequencies of drug resistance to first and second-line anti-TB drugs.Determining the drug-resistance pattern of MTB is important for programmatic management of drug-resistant TB in Ethiopia. The circulating Pre-XDR and XDR case identified in the current study is alarming to the tuberculosis control program in the country.

Objective The vaginal microbiota in bacterial vaginosis (BV) typically has low abundance of lactic acid producing lactobacilli. Lactic acid has properties that may make it effective for treating BV and/or restoring an optimal lactobacillus-dominated vaginal microbiota. We conducted a systematic review to describe the effect of intravaginal lactic acid-containing products on BV cure, and their impact on vaginal microbiota composition (PROSPERO registration: CRD42018115982). Methods PubMed, Embase and OVID were searched from inception to November 2019 to identify eligible studies. Included studies evaluated an intravaginal lactic acid-containing product and reported BV cure using established diagnostic methods, and/or vaginal microbiota composition using molecular methods. Studies were independently screened and assessed, and the proportion of women cured post-treatment was calculated. Study results were described in a qualitative manner. Results We identified 1,883 articles and assessed 57 full-texts for eligibility. Seven different lactic acid-containing products were evaluated and differed with respect to excipients, lactic acid concentration and pH. Most studies had medium or high risk of bias. Three trials compared the efficacy of a lactic acid-containing product to metronidazole for BV cure. One study found lactic acid to be equivalent to metronidazole and two studies found lactic acid to be significantly inferior to metronidazole. Two studies included a control group receiving a placebo or no treatment. One reported lactic acid to be superior than no treatment and the other reported lactic acid to be equivalent to placebo. Lactic acid-containing products did not significantly impact the vaginal microbiota composition. Conclusion There is a lack of high-quality evidence to support the use of lactic acid-containing products for BV cure or vaginal microbiota modulation. However, adequately powered and rigorous randomised trials with accompanying vaginal microbiota data are needed to evaluate the efficacy of lactic acid as a BV treatment strategy.

Mitochondrial alternative oxidase (AOX) is predicted to be present in mitochondria of several invertebrate taxa including tardigrades. Independently of the reason concerning the enzyme occurrence in animal mitochondria, expression of AOX in human mitochondria is regarded as a potential therapeutic strategy. Till now, relevant data were obtained due to heterologous AOX expression in cells and animals without natively expressed AOX. Application of animals natively expressing AOX could importantly contribute to the research. Thus, we decided to investigate AOX activity in intact specimens of the tardigrade Hypsibius exemplaris. We observed that H. exemplaris specimens’ tolerance to the blockage of the mitochondrial respiratory chain (MRC) cytochrome pathway was diminished in the presence of AOX inhibitor and the inhibitor-sensitive respiration enabled the tardigrade respiration under condition of the blockage. Importantly, these observations correlated with relevant changes of the mitochondrial inner membrane potential (Δψ) detected in intact animals. Moreover, detection of AOX at protein level required the MRC cytochrome pathway blockage. Overall, we demonstrated that AOX activity in tardigrades can be monitored by the animals’ behavior observation as well as by measurement of intact specimens’ whole-body respiration and Δψ. Furthermore, it is also possible to check the impact of the MRC cytochrome pathway blockage on AOX level as well as AOX inhibition in the absence of the blockage on animal functioning. Thus, H. exemplaris could be consider as a whole-animal model suitable to study AOX.

Inconsistent therapeutic efficacy of mesenchymal stem cells (MSCs) in regenerative medicine has been documented in many clinical trials. Precise prediction on the therapeutic outcome of a MSC therapy based on the patient’s conditions would provide valuable references for clinicians to decide the treatment strategies. In this article, we performed a meta-analysis on MSC therapies for cartilage repair using machine learning. A small database was generated from published in vivo and clinical studies. The unique features of our neural network model in handling missing data and calculating prediction uncertainty enabled precise prediction of post-treatment cartilage repair scores with coefficient of determination of 0.637 ± 0.005. From this model, we identified defect area percentage, defect depth percentage, implantation cell number, body weight, tissue source, and the type of cartilage damage as critical properties that significant impact cartilage repair. A dosage of 17 − 25 million MSCs was found to achieve optimal cartilage repair. Further, critical thresholds at 6% and 64% of cartilage damage in area, and 22% and 56% in depth were predicted to significantly compromise on the efficacy of MSC therapy. This study, for the first time, demonstrated machine learning of patient-specific cartilage repair post MSC therapy. This approach can be applied to identify and investigate more critical properties involved in MSC-induced cartilage repair, and adapted for other clinical indications., Author summary Cartilage damage affects the life quality of hundreds of millions of people, causing chronic joint pain and disability. Cartilage has poor regenerative capacity. Only minor damage could improve on its own or with passive treatments, while more severe damage often requires surgery. In recent decades, stem cell therapy has become a promising treatment option to reduce pain and repair cartilage. However, with complex mechanisms and various factors involved, efficient and consistent cartilage regeneration remains elusive. Our neural network learns information from clinical trials and animal studies to predict therapeutic outcomes along with the confidence level based on the patient’s condition. This machine learning approach provides an important reference and significant insights into the optimization of treatment strategies.

We reviewed the records of 337 confirmed cases of tuberculosis patients in Monrovia, the capital of Liberia, 2015. The risk factors affecting the survival and multidrug-resistance of tuberculosis patients were examined. Kaplan-Meier analysis and the log-rank test were used to assess the differences in survival among the patients, while Cox regression model was used for multivariate analysis. The qualitative data was tested with chi-square test in the single factor analysis of multidrug-resistant TB. Multivariate analysis was performed using binary logistic regression analysis. The significance level for all the tests were set at 0.05. The mean period of the follow-up of patients was 10 months. In the 337 patients, 33 (9.8%) died, the 21-month survival rate was 90.2%. The results of multivariate Cox regression analysis show that overcrowding (HR = 7.942, 95% CI 3.258–19.356), former smoking (HR = 3.773, 95% CI 1.601–8.889), current smoking (HR = 3.546, 95% CI 1.195–10.521), multidrug-resistance tuberculosis (HR = 4.632, 95% CI 1.913–11.217) were risk factors for death during anti-tuberculosis treatment in TB patients in Liberia. The results of binary logistic regression analysis show that extra-pulmonary (OR = 2.032, 95% CI 1.133–3.644), family history of TB (OR = 2.387, 95% CI 1.186–4.807) and current smoking (OR = 3.436, 95% CI 1.681–7.027) were risk factors for multidrug-resistant tuberculosis. These results can provide insights on local tuberculosis early intervention, increase public health awareness, and strengthen the control of factors that may affect the survival and multidrug-resistance of tuberculosis patients.

Immunomodulatory drugs could contribute to a functional cure for Human Immunodeficiency Virus (HIV). Interleukin-15 (IL-15) promotes expansion and activation of CD8+ T cell and natural killer (NK) cell populations. In one study, an IL-15 superagonist, N-803, suppressed Simian Immunodeficiency Virus (SIV) in non-human primates (NHPs) who had received prior SIV vaccination. However, viral suppression attenuated with continued N-803 treatment, partially returning after long treatment interruption. While there is evidence of concurrent drug tolerance, immune regulation, and viral escape, the relative contributions of these mechanisms to the observed viral dynamics have not been quantified. Here, we utilize mathematical models of N-803 treatment in SIV-infected macaques to estimate contributions of these three key mechanisms to treatment outcomes: 1) drug tolerance, 2) immune regulation, and 3) viral escape. We calibrated our model to viral and lymphocyte responses from the above-mentioned NHP study. Our models track CD8+ T cell and NK cell populations with N-803-dependent proliferation and activation, as well as viral dynamics in response to these immune cell populations. We compared mathematical models with different combinations of the three key mechanisms based on Akaike Information Criterion and important qualitative features of the NHP data. Two minimal models were capable of reproducing the observed SIV response to N-803. In both models, immune regulation strongly reduced cytotoxic cell activation to enable viral rebound. Either long-term drug tolerance or viral escape (or some combination thereof) could account for changes to viral dynamics across long breaks in N-803 treatment. Theoretical explorations with the models showed that less-frequent N-803 dosing and concurrent immune regulation blockade (e.g. PD-L1 inhibition) may improve N-803 efficacy. However, N-803 may need to be combined with other immune therapies to countermand viral escape from the CD8+ T cell response. Our mechanistic model will inform such therapy design and guide future studies., Author summary Immune therapy may be a critical component in the functional cure for Human Immunodeficiency Virus (HIV). N-803 is an immunotherapeutic drug that activates antigen-specific CD8+ T cells of the immune system. These CD8+ T cells eliminate HIV-infected cells in order to limit the spread of infection in the body. In one study, N-803 reduced plasma viremia in macaques that were infected with Simian Immunodeficiency Virus, an analog of HIV. Here, we used mathematical models to analyze the data from this study to better understand the effects of N-803 therapy on the immune system. Our models indicated that inhibitory signals may be reversing the stimulatory effect of N-803. Results also suggested the possibilities that tolerance to N-803 could build up within the CD8+ T cells themselves and that the treatment may be selecting for virus strains that are not targeted by CD8+ T cells. Our models predict that N-803 therapy may be made more effective if the time between doses is increased or if inhibitory signals are blocked by an additional drug. Also, N-803 may need to be combined with other immune therapies to target virus that would otherwise evade CD8+ T cells.

Classic micro-economic and psychology theories propose different implications of monetary incentives on performance. Empirical studies in sports settings show that athletes generally perform worse when the stakes are higher, while a range of lab studies involving cognitively demanding tasks have led to diverging results, supporting positive, negative and null-effects of higher (vs. lower) stakes. In order to further investigate this issue, we present a pre-registered, randomized, controlled trial of 149 participants solving both anagrams and math addition tasks. We do not find a statistically significant effect of the size of the reward on neither performance, self-reported effort nor intrinsic motivation. We propose that future studies should contrast the potential impact of rewards on different kinds of task, e.g. compare tasks that solely require cognitive effort vs. tasks that require motor skills, as in sports.