Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparing the profile of respiratory fungal pathogens amongst immunocompetent and immunocompromised hosts, their susceptibility pattern and correlation of various opportunistic respiratory fungal infections and their progression in relation to the CD4+T-cell counts

Introduction: Invasive fungal infections are increasingly common in the nosocomial setting. Materials and Methods: The patients were divided into two groups immunocompetent and immunocompromised that is, patients with significant neutropenia <500 neutrophils/μl for longer than 10 days. microscopy, culture, identification of isolates were done and some specilised tests on serum and BAL for antigen detection were performed. Results: Majority of the patients were young adult males in this study. A higher prevalence of 26.7% was seen in immunocompromised patients. Amongst yeasts, Candida albicans was the predominant species followed by the National AIDS Control that is, Candida glabrata, Candida dubliniensis, Candida parapsilosis and Candida tropicalis in the same order. Amongst moulds, Aspergillus fumigatus was the most common species followed by Aspergillus flavus and Aspergillus niger. Mucor and Penicillium marneffei were seen in a lower prevalence. By Broth microdilution method, isolates of Candida spp. were most sensitive to caspofungin, amphotericin B, ketoconazole and fluconazole in the same order. Isolates of Aspergillus spp. were most sensitive to caspofungin, amphotericin B and itraconazole in the same order. By disc diffusion method, resistance to fluconazole was observed in 6.9% isolates of C. albicans. 50% of C. dubliniensis and 20% of C. glabrata showed resistance to fluconazole. A total mortality of 27.7% was observed during this study. This was distributed as 24.1%, 26.7%, 50%, 50%, 100% and 0% among by patients of candidiasis, aspergillosis, cryptococcosis, pneumocystosis, mucormycosis and penicilliosis. Fifteen per cent were lost to follow-up. Conclusion: Patterns of invasive fungal infections are changing in many ways. In the midst of these evolving trends, IFI of the respiratory tractcontinue to remain important causes of morbidity and mortality. Diagnostic tools can be adequately used only if the treating physician is aware of the propensity of patients to acquire a fungal infection. Thus, continuous awareness and education is crucial for successful management of patients. Judicious use of antifungal medications as prophylactic measures must be employed, particularly in the critically ill and patients of HIV.
Molecular dynamics simulations of nucleotide release from the circadian clock protein KaiC reveal atomic-resolution functional insights

Significance Circadian rhythms enable organisms to adapt to the 24-h day/night cycle. The importance of these rhythms is evident from their prevalence across the kingdoms of life and their dysregulation in many diseases. The core clock of the cyanobacterium Synechococcus elongatus serves as a paradigm for molecular studies of circadian rhythms because its oscillations can be reconstituted in vitro. There is evidence that the action of KaiC, the central component of the oscillator, depends critically on whether its active sites bind ADP or ATP, metabolites that function as the energy currency in cells. Here, we use molecular dynamics simulations to develop an atomic-resolution picture of ADP release and, in turn, hypotheses for the regulation of ADP/ATP exchange. The cyanobacterial clock proteins KaiA, KaiB, and KaiC form a powerful system to study the biophysical basis of circadian rhythms, because an in vitro mixture of the three proteins is sufficient to generate a robust ∼24-h rhythm in the phosphorylation of KaiC. The nucleotide-bound states of KaiC critically affect both KaiB binding to the N-terminal domain (CI) and the phosphotransfer reactions that (de)phosphorylate the KaiC C-terminal domain (CII). However, the nucleotide exchange pathways associated with transitions among these states are poorly understood. In this study, we integrate recent advances in molecular dynamics methods to elucidate the structure and energetics of the pathway for Mg·ADP release from the CII domain. We find that nucleotide release is coupled to large-scale conformational changes in the KaiC hexamer. Solvating the nucleotide requires widening the subunit interface leading to the active site, which is linked to extension of the A-loop, a structure implicated in KaiA binding. These results provide a molecular hypothesis for how KaiA acts as a nucleotide exchange factor. In turn, structural parallels between the CI and CII domains suggest a mechanism for allosteric coupling between the domains. We relate our results to structures observed for other hexameric ATPases, which perform diverse functions.
Automatic Delineation of the Clinical Target Volume in Rectal Cancer for Radiation Therapy using Three-dimensional Fully Convolutional Neural Networks

Accurate, robust, and fast delineation of the clinical target volume (CTV) for the use in radiotherapy of rectal cancer (RC) is highly sought-after. Convolutional neural networks (CNNs) have proven themselves very effective in various segmentation tasks on medical images. Despite this, their application in CTV delineation is not yet fully explored. This study uses the three-dimensional fully convolutional neural network architecture called V-net for CTV delineation. The West China Hospital (Chengdu, China) provided this study with 120 annotated CT scans. For improved performance and to battle data scarcity, the available scans were augmented. Trained on 100 CT-scans for 20 hours and tested on 20 previously unseen CT-scans the network achieved a mean dice similarity coefficient (DSC) of 0.90 and a mean delineation time per CTV of 0.60 seconds. The proposed method is compared with two other state-of-the-art CNNs and is shown to be superior.
Risk Factors and Pathogenesis of HIV-Associated Neurocognitive Disorder: The Role of Host Genetics

Neurocognitive impairments associated with human immunodeficiency virus (HIV) infection remain a considerable health issue for almost half the people living with HIV, despite progress in HIV treatment through combination antiretroviral therapy (cART). The pathogenesis and risk factors of HIV-associated neurocognitive disorder (HAND) are still incompletely understood. This is partly due to the complexity of HAND diagnostics, as phenotypes present with high variability and change over time. Our current understanding is that HIV enters the central nervous system (CNS) during infection, persisting and replicating in resident immune and supporting cells, with the subsequent host immune response and inflammation likely adding to the development of HAND. Differences in host (human) genetics determine, in part, the effectiveness of the immune response and other factors that increase the vulnerability to HAND. This review describes findings from studies investigating the role of human host genetics in the pathogenesis of HAND, including potential risk factors for developing HAND. The similarities and differences between HAND and Alzheimer’s disease are also discussed. While some specific variations in host genes regulating immune responses and neurotransmission have been associated with protection or risk of HAND development, the effects are generally small and findings poorly replicated. Nevertheless, a few specific gene variants appear to affect the risk for developing HAND and aid our understanding of HAND pathogenesis.
Explaining Cross-Language Asymmetries in Prosodic Processing: The Cue-Driven Window Length Hypothesis

Cross-language studies have shown that English speakers use suprasegmental cues to lexical stress less consistently than speakers of Spanish and other Germanic languages ; accordingly, these studies have attributed this asymmetry to a possible trade-off between the use of vowel reduction and suprasegmental cues in lexical access. We put forward the hypothesis that this “cue trade-off” modulates intonation processing as well, so that English speakers make less use of suprasegmental cues in comparison to Spanish speakers when processing intonation in utterances causing processing asymmetries between these two languages. In three cross-language experiments comparing English and Spanish speakers’ prediction of hypo-articulated utterances in focal sentences and reporting speech, we have provided evidence for our hypothesis and proposed a mechanism, the Cue-Driven Window Length model, which accounts for the observed cross-language processing asymmetries between English and Spanish at both lexical and utterance levels. Altogether, results from these experiments illustrated in detail how different types of low-level acoustic information (e.g., vowel reduction versus duration) interacted with higher-level expectations based on the speakers’ knowledge of intonation providing support for our hypothesis. These interactions were coherent with an active model of speech perception that entailed real-time adjusting to feedback and to information from the context, challenging more traditional models that consider speech perception as a passive, bottom-up pattern-matching process.
Network Analysis of Autopsy Diagnoses: Insights into the “Cause of Death” from Unbiased Disease Clustering

Background: Autopsies usually serve to inform specific “causes of death” and associated mechanisms. However, multiple diseases can co-exist and interact leading to a final demise. We approached autopsy-produced data using network analysis in an unbiased fashion to inform about interaction among different diseases and identify possible targets of system-level health care. Methods: Reports of 261 full autopsies from one institution between 2011 and 2013 were reviewed. Comorbidities were recorded and their Spearman's association coefficients were calculated. Highly associated comorbidities (P < 0.01) were selected to construct a network in which each disease is represented by a node, and each link between the nodes represents significant co-occurrence. Results: The network comprised 140 diseases connected by 419 links. The mean number of connections per node was 6. The most highly connected nodes (“hubs”) represented infectious processes, whereas less connected nodes represented neoplasms and other chronic diseases. Eight clusters of biologically plausible associated diseases were identified. Conclusions: There is an unbiased relationship among autopsy-identified diseases. There were “hubs” (primarily infectious) with significantly more associations than others that could represent obligatory or important modulators of the final expression of other diseases. Clusters of co-occurring diseases, or “modules,” suggest the presence of clinically relevant presentations of pathobiologically related entities which are until now considered individual diseases. These modules may occur together prior to death and be amenable to interventions during life.
A machine-learning approach to volitional control of a closed-loop deep brain stimulation system

Objective. Deep brain stimulation (DBS) is a well-established treatment for essential tremor, but may not be an optimal therapy, as it is always on, regardless of symptoms. A closed-loop (CL) DBS, which uses a biosignal to determine when stimulation should be given, may be better. Cortical activity is a promising biosignal for use in a closed-loop system because it contains features that are correlated with pathological and normal movements. However, neural signals are different across individuals, making it difficult to create a ‘one size fits all’ closed-loop system. Approach. We used machine learning to create a patient-specific, CL DBS system. In this system, binary classifiers are used to extract patient-specific features from cortical signals and determine when volitional, tremor-evoking movement is occurring to alter stimulation voltage in real time. Main results. This system is able to deliver stimulation up to 87%–100% of the time that subjects are moving. Additionally, we show that the therapeutic effect of the system is at least as good as that of current, continuous-stimulation paradigms. Significance. These findings demonstrate the promise of CL DBS therapy and highlight the importance of using subject-specific models in these systems.
Self-reported treatment adherence among psychiatric in- and outpatients

Abstract Background: Poor adherence to psychiatric treatment is a common clinical problem, leading to unfavourable treatment outcome and increased healthcare costs. Aim: The aim of this study was to investigate the self-reported adherence and attitudes to outpatient visits and pharmacotherapy in specialized care psychiatric patients. Methods: Within the Helsinki University Psychiatric Consortium (HUPC) pilot study, in- and outpatients with schizophrenia or schizoaffective disorder (SSA, n = 113), bipolar disorder (BD, n = 99), or depressive disorder (DD, n = 188) were surveyed about their adherence and attitudes towards outpatient visits and pharmacotherapy. Correlates of self-reported adherence to outpatient and drug treatment were investigated using regression analysis. Results: The majority (78.5%) of patients reported having attended outpatient visits regularly or only partly irregularly. Most patients (79.2%) also reported regular use of pharmacotherapy. Self-reported non-adherence to preceding outpatient visits was consistently and significantly more common among inpatients than outpatients across all diagnostic groups (p < .001). Across all groups, hospital setting was the strongest independent correlate of poor adherence to outpatient visits (SSA β = –2.418, BD β = –3.417, DD β = –2.766; p < .001 in all). Another independent correlate of non-adherence was substance use disorder (SSA β = –1.555, p = .001; BD β = –1.535, p = .006; DD β = –2.258, p < .000). No other socio-demographic or clinical factor was significantly associated with poor adherence in multivariate regression models. Conclusions: Irrespective of diagnosis, self-reported adherence to outpatient care among patients with schizophrenia or schizoaffective disorder, bipolar disorder, and depression is associated strongly with two factors: hospital setting and substance use disorders. Thus, detection of adherence problems among former inpatients and recognition and treatment of substance misuse are important to ensure proper outpatient care.
Open niche regulation of mouse spermatogenic stem cells

In mammalian testes, robust stem cell functions ensure the continual production of sperm. In testicular seminiferous tubules, spermatogenic stem cells (SSCs) are highly motile and are interspersed between their differentiating progeny, while undergoing self‐renewal and differentiation. In such an “open niche” microenvironment, some SSCs proliferate, while others exit the stem cell compartment through differentiation; therefore, self‐renewal and differentiation are perfectly balanced at the population (or tissue) level, a dynamics termed “population asymmetry. ” This is in stark contrast to the classical perception of tissue stem cells being cells that are clustered in a specialized “closed niche” region and that invariantly undergo asymmetric divisions. However, despite its importance, how the self‐renewal and differentiation of SSCs are balanced in an open niche environment is poorly understood. Recent studies have thrown light on the key mechanism that enables SSCs to follow heterogeneous fates, although they are equally exposed to signaling molecules controlling self‐renewal and differentiation. In particular, SSCs show heterogeneous susceptibilities to differentiation‐promoting signals such as Wnt and retinoic acid. Heterogeneous susceptibility to the ubiquitously distributed fate‐controlling extracellular signal might be a key generic mechanism for the heterogeneous fate of tissue stem cells in open niche microenvironments.
The pathways between female garment workers’ experience of violence and development of depressive symptoms

Background The prevalence of intimate partner violence (IPV) is high (54%) in Bangladesh. Moreover, female garment workers report higher rates of IPV and are also vulnerable to workplace violence (WPV). Experience of violence puts women at increased risk of developing depressive symptoms, which are related with low self-esteem, lower life satisfaction and lower productivity. To our knowledge, there has been no previous research on depression among female garment workers and its connections to IPV and WPV in Bangladesh. This paper aims to address this gap by studying the relationship of IPV, WPV and depression among female garment workers. Methods The data for this paper comes from a cross-sectional survey of female garment workers (n = 800) conducted as baseline survey of a quasi-experimental study known as HERrespect. Survey data were collected during September-December, 2016 among randomly selected female garment workers from eight garment factories in and around Dhaka city. Structural equation modelling was conducted to explore the relationship among IPV, WPV and depression. Results The findings show high rates of any IPV (69%); WPV (73%, experienced or witnessed) and depressive symptomatology (40%) among female garment workers. The analysis of pathways shows that IPV impacts a woman’s experience of WPV and work related stress leading to the development of depression; while WPV had direct and mediated pathways to depression. Experience of controlling by their husband leads to WPV and increased work related stress, and thus leads to depression. It also reveals that a worker’s ability to mobilize resources in emergency, however, increased self-esteem and reduced work related stress. Conclusion This study shows the pathways through which experience of IPV and WPV lead to development of depressive symptoms among female garment workers. The link between women’s ability to mobilize resources with self-esteem and work related stress indicates the need for socio-economic empowerment of women and may suggest that combined intervention to address IPV and women’s empowerment could be successful in dealing with WPV and mental health.
Avoidance Behavior Prevents Modification of Fear Memory During Reconsolidation

Several studies have revealed that fear recovery is prevented when extinction training is conducted after retrieval of a fear memory. Postretrieval extinction training is related to modification of memory during reconsolidation. Providing new information during reconsolidation can modify the original memory. We propose that avoidance behavior is a relevant factor that prevents subjects from obtaining new safety information during reconsolidation. Postretrieval extinction training without avoidance behavior reduced the fear response to conditioned stimulus and prevented spontaneous recovery in the current study, which corresponded with previous studies. Under the condition of postretrieval extinction training with avoidance behavior, the fear response was not reduced as much as it was in the condition without avoidance. It is possible that avoidance behavior prevents receiving new safety information during postretrieval extinction training.
Cyanobacterial Blooms and Microcystins in Southern Vietnam

Studies on cyanobacteria in Vietnam are limited and mainly restricted to large reservoirs. Cyanobacterial blooms in small water bodies may pose a health risk to local people. We sampled 17 water bodies in the vicinity of urban settlements throughout the Mekong basin and in southeast Vietnam. From these, 40 water samples were taken, 24 cyanobacterial strains were isolated and 129 fish, 68 snail, 7 shrimp, 4 clam, and 4 duck samples were analyzed for microcystins (MCs). MCs were detected up to 11,039 µg/L or to 4033 µg/g DW in water samples. MCs were detected in the viscera of the animals. MC-LR and MC-RR were most frequently detected, while MC-dmLR, MC-LW, and MC-LF were first recorded in Vietnam. Microcystis was the main potential toxin producer and the most common bloom-forming species. A potential health hazard was found in a duck–fish pond located in the catchment of DauTieng reservoir and in the DongNai river where raw water was collected for DongNai waterwork. The whole viscera of fish and snails must be completely removed during food processing. Cyanobacterial monitoring programs should be established to assess and minimize potential public health risks.
Review of antimicrobial peptides with anti‐Helicobacter pylori activity

The emergence of antibiotic‐resistant Helicobacter pylori strains in recent years has increased the need for finding an alternative in the post‐antibiotic era. One of the fields being considered for this purpose is antimicrobial peptides. The aim of this review was to provide an obvious scheme from the studied anti‐H. pylori peptides and to investigate their common features.
Yield Visualization Based on Farm Work Information Measured by Smart Devices

This paper proposes a new approach to visualizing spatial variation of plant status in a tomato greenhouse based on farm work information operated by laborers. Farm work information consists of a farm laborer’s position and action. A farm laborer’s position is estimated based on radio wave strength measured by using a smartphone carried by the farm laborer and Bluetooth beacons placed in the greenhouse. A farm laborer’s action is recognized based on motion data measured by using smartwatches worn on both wrists of the farm laborer. As experiment, harvesting information operated by one farm laborer in a part of a tomato greenhouse is obtained, and the spatial distribution of yields in the experimental field, called a harvesting map, is visualized. The mean absolute error of the number of harvested tomatoes in each small section of the experimental field is 0.35. An interview with the farm manager shows that the harvesting map is useful for intuitively grasping the states of the greenhouse.