Miracle-dz/UniFAR-FTUs huggingface dataset:
High Levels of Dual-Class Drug Resistance in HIV-Infected Children Failing First-Line Antiretroviral Therapy in Southern Ethiopia

Clinical monitoring of pediatric HIV treatment remains a major challenge in settings where drug resistance genotyping is not routinely available. As a result, our understanding of drug resistance, and its impact on subsequent therapeutic regimens available in these settings, remains limited. We investigate the prevalence and correlates of HIV-1 drug resistance among 94 participants of the Ethiopia Pediatric HIV Cohort failing first-line combination antiretroviral therapy (cART) using dried blood spot-based genotyping. Overall, 81% (73/90) of successfully genotyped participants harbored resistance mutations, including 69% (62/90) who harbored resistance to both Nucleoside Reverse Transcriptase Inhibitors (NRTIs) and Non-nucleoside Reverse Transcriptase Inhibitors (NNRTIs). Strikingly, 42% of resistant participants harbored resistance to all four NRTIs recommended for second-line use in this setting, meaning that there are effectively no remaining cART options for these children. Longer cART duration and prior regimen changes were significantly associated with detection of drug resistance mutations. Replicate genotyping increased the breadth of drug resistance detected in 34% of cases, and thus is recommended for consideration when typing from blood spots. Implementation of timely drug resistance testing and access to newer antiretrovirals and drug classes are urgently needed to guide clinical decision-making and improve outcomes for HIV-infected children on first-line cART in Ethiopia.
Design and Analysis of Experiments, Volume 2: Advanced Experimental Design

The development and introduction of new experimental designs in the last fifty years has been quite staggering, brought about largely by an ever-widening field of applications. Design and Analysis of Experiments, Volume 2: Advanced Experimental Design is the second of a two-volume body of work that builds upon the philosophical foundations of experimental design set forth by Oscar Kempthorne half a century ago and updates it with the latest developments in the field. Designed for advanced-level graduate students and industry professionals, this text includes coverage of incomplete block and row-column designs; symmetrical, asymmetrical, and fractional factorial designs; main effect plans and their construction; supersaturated designs; robust design, or Taguchi experiments; lattice designs; and cross-over designs.
Control devices for electrically powered wheelchairs: prevalence, defining characteristics and user perspectives

Abstract Purpose: To determine the prevalence of control devices for electrically powered wheelchairs (EPWs), related characteristic features and users’ views on their utility. Method: Postal survey of users of a regional NHS wheelchair service using a purpose-designed questionnaire (n = 262, ≥18 years old). Results: Mean age 54.4 years, female 56.8%, mean duration EPW use 10.1 years, mean usage 6.7 days per week and 9.2 h per day. Largest diagnostic groups: Multiple Sclerosis 28.3%, Cerebral Palsy 13.8% and Spinal Cord Injury 11.7%. Control device types 94.6% hand joystick, 2.3% chin joystick, 2.7% switches and 0.4% foot control. 42.4% reported fatigue or tiredness and 38.8% pain or discomfort limited EPW use. 28.0% reported an accident or mishap. Conclusions: This is the first study of control devices on a large, general population of EPW users. The majority have control devices that meet their needs, with high levels of user satisfaction, though some might benefit from adjustments or modifications to their current provision and others might benefit by changing to a different type of control device. High proportions reported fatigue or tiredness and pain or discomfort limit their EPW use. The study provides indicators for prescribers and manufacturers of control devices for EPWs. Implications for Rehabilitation Most users have control devices that meet their needs, with high levels of satisfaction, but some would benefit from adjustments or modifications or a change of type. A high proportion reported fatigue or tiredness and pain or discomfort limit their use of their EPW and prescribers need to be mindful of these issues when determining the most suitable type of control device and where it should be positioned. The vast majority of users have a hand joystick as a control device with alternative control devices (such as chin joysticks and switches) being far less prevalent. Adverse incidents may arise due to difficulty with manoeuvring or accidental activation of the hand joystick that can lead to collisions and even entrapment.
Impact of anaemia on outcome in burn patients.

BACKGROUND Currently, most critical care physicians maintain a patient's haemoglobin levels at 7 to 8 g dL-1. However, little data have been available on haemoglobin-related outcomes in burn patients. The purpose of this study was to evaluate inpatients with greater than 20% total body surface area burns and the effects of haemoglobin below 8 g dL-1 on clinical outcomes. METHODS This study included 70 patients with burns amounting to greater than 20% of total body surface area. Data were retrospectively evaluated and included age, gender, adult respiratory distress syndrome presence, length of intensive care unit stay, length of mechanical ventilation, days requiring vasopressors, renal insufficiency, positive cultures/infections, cardiovascular complications, number of operations, inhalation injury, and mortality. Logistic regression analyses that were adjusted for age, sex, and percent total body surface area were used to assess the relationships between haemoglobin and multiple clinical outcomes. Odds ratios (OR) were estimated with 99% confidence intervals (99% CI). RESULTS Haemoglobin below 8 g dL-1 was associated with a need for vasopressors (OR = 2.17; 99% CI = 1.03-8.22). Furthermore, haemoglobin below 8 g dL-1 was associated with higher positive wound (OR = 2.86; 99% CI = 1.00-34.40), urine (OR = 4.63; 99% CI = 1.15-67.00), and lung cultures (OR = 2.24; 99% CI = 1.06-5.47). These associations largely remained after controlling for blood transfusions. CONCLUSIONS Contrary to most other patient groups, burn patients with burns amounting to greater than 20% of total body surface area and low haemoglobin levels were more likely to develop positive cultures in urine, wounds, and the lung and require vasopressor treatment.
Dental pain related to quality of life and mental health in South Korean adults

Abstract High levels of stress, anxiety and depression have been reported in patients with orofacial pain. Dental pain has the potential to reduce quality of life (QOL), and pain relief is important aspect of QOL. The purpose of this study was to assess the relationships of dental pain with QOL and mental health using a nationally representative, population-based study. This study analyzed data from the 2012 Korea National Health and Nutrition Examination Survey (N = 5469). Oral health status was assessed using the oral health questionnaire, and oral examination was performed by trained dentists. Health-related QOL (HRQOL) was evaluated using EQ-5D and EQ-VAS, and mental health was evaluated by questionnaires. Logistic regression was applied to estimate adjusted odds ratios (AOR) and 95% confidence intervals (CI). Among 5469 adults, 1992 (36.42%) presented self-reported dental pain. Participants with anxiety/depression or pain/discomfort, and participants with stress, melancholy, suicidal thought or depression showed significantly higher prevalence of dental pain. After adjusting for covariates, five aspects of QOL and five aspects of mental health were related with dental pain. The AORs (95% CI) for dental pain were 1.39 (1.06–1.81) for mobility, 1.77 (1.19–2.63) for self-care, 1.38 (1.02–1.85) for usual activities, 1.73 (1.43–2.09) for pain/discomfort and 1.50 (1.13–1.98) for anxiety/depression. For mental health status factors, the AORs (95% CI) for dental pain were 1.29 (1.11–1.51) for stress, 1.37 (1.09–1.74) for melancholy, 1.26 (1.01–1.58) for suicidal thoughts, 1.43 (.93–2.19) for consultation to psychiatrist and 1.53 (1.07–2.19) for depression. This study showed that dental pain has an association with lower HRQOL and worse mental health status in South Korean adults.
Genome Re-Sequencing of Diverse Sweet Cherry (Prunus avium) Individuals Reveals a Modifier Gene Mutation Conferring Pollen-Part Self-Compatibility

The S-RNase-based gametophytic self-incompatibility (GSI) reproduction barrier is important for maintaining genetic diversity in species of the families Solanaceae, Plantaginaceae and Rosaceae. Among the plant taxa with S-RNase-based GSI, Prunus species in the family Rosaceae exhibit Prunus-specific self-incompatibility (SI). Although pistil S and pollen S determinants have been identified, the mechanism underlying SI remains uncharacterized in Prunus species. A putative pollen-part modifier was identified in this study. Disruption of this modifier supposedly confers self-compatibility (SC) to sweet cherry (Prunus avium) 'Cristobalina'. To identify the modifier, genome re-sequencing experiments were completed involving sweet cherry individuals from 18 cultivars and 43 individuals in two segregating populations. Cataloging of subsequences (35 bp kmers) from the obtained genomic reads, while referring to the mRNA sequencing data, enabled the identification of a candidate gene [M locus-encoded GST (MGST)]. Additionally, the insertion of a transposon-like sequence in the putative MGST promoter region in 'Cristobalina' down-regulated MGST expression levels, probably leading to the SC of this cultivar. Phylogenetic, evolutionary and gene expression analyses revealed that MGST may have undergone lineage-specific evolution, and the encoded protein may function differently from the corresponding proteins encoded by GST orthologs in other species, including members of the subfamily Maloideae (Rosaceae). Thus, MGST may be important for Prunus-specific SI. The identification of this novel modifier will expand our understanding of the Prunus-specific GSI system. We herein discuss the possible functions of MGST in the Prunus-specific GSI system.
Closed-loop estimation of retinal network sensitivity reveals signature of efficient coding

According to the theory of efficient coding, sensory systems are adapted to represent natural scenes with high fidelity and at minimal metabolic cost. Testing this hypothesis for sensory structures performing non-linear computations on high dimensional stimuli is still an open challenge. Here we develop a method to characterize the sensitivity of the retinal network to perturbations of a stimulus. Using closed-loop experiments, we explore selectively the space of possible perturbations around a given stimulus. We then show that the response of the retinal population to these small perturbations can be described by a local linear model. Using this model, we computed the sensitivity of the neural response to arbitrary temporal perturbations of the stimulus, and found a peak in the sensitivity as a function of the frequency of the perturbations. Based on a minimal theory of sensory processing, we argue that this peak is set to maximize information transmission. Our approach is relevant to testing the efficient coding hypothesis locally in any context where no reliable encoding model is known.
Bacterial Spheroplasts as a Model for Visualizing Membrane Translocation of Antimicrobial Peptides

ABSTRACT Studies attempting to characterize the membrane translocation of antimicrobial and cell-penetrating peptides are frequently limited by the resolution of conventional light microscopy. This study shows that spheroplasts provide a valuable approach to overcome these limits. Spheroplasts produce less ambiguous images and allow for more systematic analyses of localization. Data collected with spheroplasts are consistent with studies using normal bacterial cells and imply that a particular peptide may not always follow the same mechanism of action.
Detecting Vague Words & Phrases in Requirements Documents in a Multilingual Environment

Vagueness in software requirements documents can lead to several maintenance problems, especially when the customer and development team do not share the same language. Currently, companies rely on human translators to maintain communication and limit vagueness by translating the requirement documents by hand. In this paper, we describe two approaches that automatically identify vagueness in requirements documents in a multilingual environment. We perform two studies for calibration purposes under strict industrial limitations, and describe the tool that we ultimately deploy. In the first study, six participants, two native Portuguese speakers and four native Spanish speakers, evaluated both approaches. Then, we conducted a field study to test the performance of the best approach in real-world environments at two companies. We describe several lessons learned for research and industrial deployment.
Gut hormone profiles in preterm and term infants during the first 2 months of life

Abstract Aim: To investigate changes of gut hormones in term and preterm infants in the first 2 months after birth, as the role and relationships of gut hormones in premature infants has not been well elucidated. Methods: In 29 preterm and five term infants, fasting serum concentrations of leptin, glucose-dependent insulinotropic polypeptide (GIP), glucagon-like peptide-1 (GLP-1), peptide YY (PYY), pancreatic polypeptide, insulin, amylin, and ghrelin were measured using a bead array system. Results: Serum leptin concentration soon after birth showed a positive correlation with gestational week in all infants (r=0.623, p<0.01). Serum leptin level rapidly decreased in all infants. In preterm infants, serum GLP-1 levels at birth showed negative correlations with gestational week (r=–0.447, p=0.02). Serum GIP, GLP-1, and PYY levels increased after birth and were persistently high until 10 weeks of life. Conclusion: Serum concentrations of different gut hormones changed postnatally in their specific ways in preterm infants.
Preclinical, phase I, and phase II investigational clinical trials for treatment of progressive supranuclear palsy

ABSTRACT Introduction: Our understanding of the pathological basis of progressive supranuclear palsy (PSP), as the most common atypical parkinsonian syndrome, has greatly increased in recent years and a number of disease-modifying therapies are under evaluation as a result of these advances. Areas covered: In this review, we discuss disease-modifying therapeutic options which are currently under evaluation or have been evaluated in preclinical or clinical trials based on their targeted pathophysiologic process. The pathophysiologic mechanisms are broadly divided into three main categories: genetic mechanisms, abnormal post-translational modifications of tau protein, and transcellular tau spread. Expert opinion: Once the best therapeutic approaches are identified, it is likely that some combination of interventions will need to be evaluated, but this will take time. It is critical to treat patients at early stages, and development of the Movement Disorder Society PSP diagnostic criteria is an important step in this direction. In addition, development of biological biomarkers such as tau PET and further refinement of tau ligands may help both diagnose early and measure disease progression. In the meantime, a comprehensive, personalized interdisciplinary approach to this disease is absolutely necessary.
Cyclic 3′,5′‐guanosine monophosphate‐dependent protein kinase inhibits colon cancer cell adaptation to hypoxia

Type 1 cyclic 3′,5′‐guanosine monophosphate‐dependent protein kinase (PKG) has recently been reported to inhibit tumor growth and angiogenesis. These effects suggest that PKG activation may have therapeutic value for colon cancer treatment, but the signaling downstream of this enzyme is poorly understood. The present study examined the mechanism underlying the inhibition of angiogenesis by PKG.
Entropy of Entanglement between Quantum Phases of a Three-Level Matter-Radiation Interaction Model

We show that the entropy of entanglement is sensitive to the coherent quantum phase transition between normal and super-radiant regions of a system of a finite number of three-level atoms interacting in a dipolar approximation with a one-mode electromagnetic field. The atoms are treated as semi-distinguishable using different cooperation numbers and representations of SU(3), variables which are relevant to the sensitivity of the entropy with the transition. The results are computed for all three possible configurations (Ξ, Λ and V) of the three-level atoms.
Specific Transcriptome Changes Associated with Blood Pressure Reduction in Hypertensive Patients After Relaxation Response Training

Abstract Objective: Mind–body practices that elicit the relaxation response (RR) have been demonstrated to reduce blood pressure (BP) in essential hypertension (HTN) and may be an adjunct to antihypertensive drug therapy. However, the molecular mechanisms by which the RR reduces BP remain undefined. Design: Genomic determinants associated with responsiveness to an 8-week RR-based mind–body intervention for lowering HTN in 13 stage 1 hypertensive patients classified as BP responders and 11 as nonresponders were identified. Results: Transcriptome analysis in peripheral blood mononuclear cells identified 1771 genes regulated by the RR in responders. Biological process- and pathway-based analysis of transcriptome data demonstrated enrichment in the following gene categories: immune regulatory pathways and metabolism (among downregulated genes); glucose metabolism, cardiovascular system development, and circadian rhythm (among upregulated genes). Further in silico estimation of cell abundance from the microarray data showed enrichment of the anti-inflammatory M2 subtype of macrophages in BP responders. Nuclear factor-κB, vascular endothelial growth factor, and insulin were critical molecules emerging from interactive network analysis. Conclusions: These findings provide the first insights into the molecular mechanisms that are associated with the beneficial effects of the RR on HTN.
Device-Free Wireless Sensing in Complex Scenarios Using Spatial Structural Information

Recent advances in device-free wireless sensing (DFS) have shown that it may eventually evolve traditional wireless networks into smart networks which could sense surrounding target location and activity information without equipping the target with any devices. Despite its promising application prospects, one challenging problem to be solved is that the performance of the DFS system degrades significantly in complex scenarios, such as through-wall and non-line-of-sight (NLOS) scenarios. To alleviate this problem, this paper seeks to explore and exploit more informative features from not only the time domain and frequency domain, but also the spatial structural domain. We partition the time domain and frequency domain measurement matrices into basic structure blocks, adopt self-organizing map networks to cluster the blocks into a number of categories, so as to make it feasible to characterize the block distributions. We further adopt coherence histograms to characterize the distribution of the blocks by considering the spatial relationship between adjacent blocks. Thanks to the additional information provided by the spatial structural domain, extensive experimental results achieved in through-wall and NLOS scenarios confirm the outstanding performance of the proposed multi-domain features based DFS system.
Physics and chemistry of partial discharge and corona - recent advances and future challenges

The focus of the present review is on relatively recent work published within the past fifteen years dealing primarily with the basic physical and chemical processes responsible for, or associated with, the discharge phenomenon. Particular emphasis is given to work carried out in the NIST laboratory using examples of results obtained for air, SF/sub 6/, and SF/sub 6//O/sub 2/ gas mixtures in point-plane or point-dielectric barrier gaps.
PAPep Inhibits Secretion of Poly(I:C)-Induced Inflammatory Cytokines and ICAM-1 Expression in Corneal Fibroblasts by Suppressing the NF-κB/p38 Pathway.

PURPOSE To assess the anti-inflammatory effect and mechanism of a novel peptide, PAPep, in poly(I:C)-stimulated corneal fibroblasts. METHODS Corneal fibroblasts were treated with poly(I:C) to elicit inflammation. Real-time polymerase chain reaction (PCR) and ELISA were used to measure the mRNA and protein levels of interleukin (IL)-6, monocyte chemotactic factor (MCP)-1, and interferon gamma (IFN-γ). Real-time PCR, immunofluorescence, and immunoblot were performed to determine ICAM-1 expression. Translocation of NF-κB p65 was observed by immunofluorescence. Phosphorylation of IκBα, NF-κB, and mitogen-activated protein kinase (MAPK) (p38, JNK and ERK) were detected by western blot. RESULTS The results showed that PAPep effectively decreased mRNA and protein expression of IL-6, MCP-1, and IFN-γ in corneal fibroblasts exposed to poly(I:C). In addition, PAPep reduced mRNA and protein levels of ICAM-1. The NF-κB and MAPK(p38) pathway were inhibited by PAPep treatment, as indicated by suppression of p65 nuclear translocation, and IκBα, NF-κB, and p38 activation. PAPep showed no effect on JNK or ERK activity. CONCLUSIONS PAPep attenuates the expression of inflammatory cytokines and ICAM-1 in corneal fibroblasts induced by poly(I:C) through blocking the NF-κB and MAPK(p38) pathway. PAPep may be considered a promising therapeutic agent for treating viral keratitis.
Machine learning of neuroimaging to diagnose cognitive impairment and dementia: a systematic review and comparative analysis

INTRODUCTION: Advanced machine learning methods might help to identify dementia risk from neuroimaging, but their accuracy to date is unclear. METHODS: We systematically reviewed the literature, 2006 to late 2016, for machine learning studies differentiating healthy ageing through to dementia of various types, assessing study quality, and comparing accuracy at different disease boundaries. RESULTS: Of 111 relevant studies, most assessed Alzheimer's disease (AD) vs healthy controls, used ADNI data, support vector machines and only T1-weighted sequences. Accuracy was highest for differentiating AD from healthy controls, and poor for differentiating healthy controls vs MCI vs AD, or MCI converters vs non-converters. Accuracy increased using combined data types, but not by data source, sample size or machine learning method. DISCUSSION: Machine learning does not differentiate clinically-relevant disease categories yet. More diverse datasets, combinations of different types of data, and close clinical integration of machine learning would help to advance the field.