Miracle-dz/UniFAR-FTUs huggingface dataset:
NanoPack: visualizing and processing long-read sequencing data

Summary: Here we describe NanoPack, a set of tools developed for visualization and processing of long read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences. Availability and Implementation: The NanoPack tools are written in Python3 and released under the GNU GPL3.0 Licence. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible with Linux, Mac OS and the MS Windows 10 subsystem for linux and are available as a graphical user interface, a web service at http://nanoplot.bioinf. be and command line tools. Contact: wouter.decoster@molgen.vib-ua.be Supplementary information: Supplementary tables and figures are available at Bioinformatics online.
IgG Responses to Anopheles gambiae Salivary Antigen gSG6 Detect Variation in Exposure to Malaria Vectors and Disease Risk

Assessment of exposure to malaria vectors is important to our understanding of spatial and temporal variations in disease transmission and facilitates the targeting and evaluation of control efforts. Recently, an immunogenic Anopheles gambiae salivary protein (gSG6) was identified and proposed as the basis of an immuno-assay determining exposure to Afrotropical malaria vectors. In the present study, IgG responses to gSG6 and 6 malaria antigens (CSP, AMA-1, MSP-1, MSP-3, GLURP R1, and GLURP R2) were compared to Anopheles exposure and malaria incidence in a cohort of children from Korogwe district, Tanzania, an area of moderate and heterogeneous malaria transmission. Anti-gSG6 responses above the threshold for seropositivity were detected in 15% (96/636) of the children, and were positively associated with geographical variations in Anopheles exposure (OR 1.25, CI 1.01–1.54, p = 0.04). Additionally, IgG responses to gSG6 in individual children showed a strong positive association with household level mosquito exposure. IgG levels for all antigens except AMA-1 were associated with the frequency of malaria episodes following sampling. gSG6 seropositivity was strongly positively associated with subsequent malaria incidence (test for trend p = 0.004), comparable to malaria antigens MSP-1 and GLURP R2. Our results show that the gSG6 assay is sensitive to micro-epidemiological variations in exposure to Anopheles mosquitoes, and provides a correlate of malaria risk that is unrelated to immune protection. While the technique requires further evaluation in a range of malaria endemic settings, our findings suggest that the gSG6 assay may have a role in the evaluation and planning of targeted and preventative anti-malaria interventions.
Effect of slosh mitigation on histologic markers of traumatic brain injury: laboratory investigation.

OBJECT Helmets successfully prevent most cranial fractures and skull traumas, but traumatic brain injury (TBI) and concussions continue to occur with frightening frequency despite the widespread use of helmets on the athletic field and battlefield. Protection against such injury is needed. The object of this study was to determine if slosh mitigation reduces neural degeneration, gliosis, and neuroinflammation. METHODS Two groups of 10 adult male Sprague-Dawley rats were subjected to impact-acceleration TBI. One group of animals was fitted with a collar inducing internal jugular vein (IJV) compression prior to injury, whereas the second group received no such collar prior to injury. All rats were killed 7 days postinjury, and the brains were fixed and embedded in paraffin. Tissue sections were processed and stained for markers of neural degeneration (Fluoro-Jade B), gliosis (glial fibrillary acidic protein), and neuroinflammation (ionized calcium binding adapter molecule 1). RESULTS Compared with the controls, animals that had undergone IJV compression had a 48.7%-59.1% reduction in degenerative neurons, a 36.8%-45.7% decrease in reactive astrocytes, and a 44.1%-65.3% reduction in microglial activation. CONCLUSIONS The authors concluded that IJV compression, a form of slosh mitigation, markedly reduces markers of neurological injury in a common model of TBI. Based on findings in this and other studies, slosh mitigation may have potential for preventing TBI in the clinical population.
Recent Advances in Modified Cellulose for Tissue Culture Applications

Tissue engineering is a rapidly advancing field in regenerative medicine, with much research directed towards the production of new biomaterial scaffolds with tailored properties to generate functional tissue for specific applications. Recently, principles of sustainability, eco-efficiency and green chemistry have begun to guide the development of a new generation of materials, such as cellulose, as an alternative to conventional polymers based on conversion of fossil carbon (e.g., oil) and finding technologies to reduce the use of animal and human derived biomolecules (e.g., foetal bovine serum). Much of this focus on cellulose is due to it possessing the necessary properties for tissue engineering scaffolds, including biocompatibility, and the relative ease with which its characteristics can be tuned through chemical modification to adjust mechanical properties and to introduce various surface modifications. In addition, the sustainability of producing and manufacturing materials from cellulose, as well as its modest cost, makes cellulose an economically viable feedstock. This review focusses specifically on the use of modified cellulose materials for tissue culturing applications. We will investigate recent techniques used to promote scaffold function through physical, biochemical and chemical scaffold modifications, and describe how these have been utilised to reduce reliance on the addition of matrix ligands such as foetal bovine serum.
All paediatric renal masses are not wilms’ tumor!

Background: Wilms’ tumor being the commonest primary malignant renal tumor in childhood, makes Surgeons rarely think of other aetiologies. Renal cell carcinoma (RCC) in paediatric age group is a rare entity and most children with renal tumor are diagnosed unexpectedly following nephrectomy for presumed Wilms’ tumor. Case presentation: We report an 8-year-old boy presenting with lump in the abdomen and haematuria for past 5 years. Abdominal ultrasound revealed a left renal mass measuring 10 × 10 cms, and a clinical diagnosis of Wilms’ tumor was made. Radical nephrectomy was performed, following which histological diagnosis of clear cell variant of renal cell carcinoma was made. Conclusion: The possibility of a paediatric renal cell carcinoma should be borne in mind when a patient presents with pain in the flank and a renal mass. RCC in a child is often a histological surprise and needs documentationinthe literature.
A 29-gene and cytogenetic score for the prediction of resistance to induction treatment in acute myeloid leukemia

Primary therapy resistance is a major problem in acute myeloid leukemia treatment. We set out to develop a powerful and robust predictor for therapy resistance for intensively treated adult patients. We used two large gene expression data sets (n=856) to develop a predictor of therapy resistance, which was validated in an independent cohort analyzed by RNA sequencing (n=250). In addition to gene expression markers, standard clinical and laboratory variables as well as the mutation status of 68 genes were considered during construction of the model. The final predictor (PS29MRC) consisted of 29 gene expression markers and a cytogenetic risk classification. A continuous predictor is calculated as a weighted linear sum of the individual variables. In addition, a cut off was defined to divide patients into a high-risk and a low-risk group for resistant disease. PS29MRC was highly significant in the validation set, both as a continuous score (OR=2.39, P=8.63·10−9, AUC=0.76) and as a dichotomous classifier (OR=8.03, P=4.29·10−9); accuracy was 77%. In multivariable models, only TP53 mutation, age and PS29MRC (continuous: OR=1.75, P=0.0011; dichotomous: OR=4.44, P=0.00021) were left as significant variables. PS29MRC dominated all models when compared with currently used predictors, and also predicted overall survival independently of established markers. When integrated into the European LeukemiaNet (ELN) 2017 genetic risk stratification, four groups (median survival of 8, 18, 41 months, and not reached) could be defined (P=4.01·10−10). PS29MRC will make it possible to design trials which stratify induction treatment according to the probability of response, and refines the ELN 2017 classification.
Structural correlates of mild cognitive impairment: A clinicovolumetric study

Context: Annually 10–12% of patients with mild cognitive impairment (MCI) are likely to progress to Alzheimer's Disease (AD). The morphometric profile in stable non-converters has not been adequately characterized. Aims: To determine the structural differences between amnestic MCI and early AD using volumetric magnetic resonance imaging (MRI) and its correlation with neuropsychological test performances. Settings and Design: This was a hospital-based case-control study. Materials and Methods: Twenty-four patients classified as having “non-progressor” MCI, 13 as having an early AD, and 25 controls, and assessed using neuropsychological evaluation, and three-dimensional T1-weighted 1.5T magnetic resonance maging (MRI) were included in the study. We used both voxel-based morphometry and automated regional volumetry to assess the topographical patterns of volume loss. Statistical Analysis Used: Post-hoc analysis of variance was done for comparison between means, and partial correlation analysis was done for correlating volumetric and cognitive measures. Results: Consistently, significant atrophy of the superior temporal gyrus, left hippocampus, and mesial frontoparietal regions were identified in patients with MCI in comparison to controls. Increased atrophy in the limbic regions, temporal neocortex, and precuneus was identified in patients with early AD in comparison to patients with MCI. While differences in retention and recall scores between the groups were independent of age and volumetric variables, significant correlations were observed between the learning and recall scores and the volume of hippocampus in patients with MCI as well as temporal neocortex in patients with AD. Atrophy of the superior temporal gyrus and mesial neocortical regions represents the structural correlate of amnestic MCI parallel to the development of hippocampal atrophy. Conclusions: Identification of the pattern of volumetric abnormalities in patients with amnestic MCI in addition to atrophy of the medial temporal lobes necessitates a close follow up to continuously assess these patients for their progression to early AD.
Speech recognition of aged voice in the AAL context: Detection of distress sentences

By 2050, about a third of the French population will be over 65. In the context of technologies development aiming at helping aged people to live independently at home, the CIRDO project aims at implementing an ASR system into a social inclusion product designed for elderly people in order to detect distress situations. Speech recognition systems present higher word error rate when speech is uttered by elderly speakers compared to when non-aged voice is considered. Two specialized corpora in French, AD80 and ERES38, were recorded in this framework by aged people, they were used first to study the possibility of adaptation of standard ASR to aged voice. Then we looked at whether the variability of the WER between speakers could be correlated with the level of dependence. Then, we assessed the performance of distress sentence detection by a filter and we demonstrated a significant drop in performance for those with the lowest degree of autonomy.
Health workers cohort study: methods and study design.

Objective: To examine different health outcomes that are associated with specific lifestyle and genetic factors. Materials and methods: From March 2004 to April 2006, a sample of employees from three different health and academic institutions, as well as their family members, were enrolled in the study after providing informed consent. At baseline and follow-up (2010-2013), participants completed a self-administered questionnaire, a physical examination, and provided blood samples. Results: A total of 10 729 participants aged 6 to 94 years were recruited at baseline. Of these, 70% were females, and 50% were from the Mexican Social Security Institute. Nearly 42% of the adults in the sample were overweight, while 20% were obese. Conclusion: Our study can offer new insights into disease mechanisms and prevention through the analysis of risk factor information in a large sample of Mexicans.
The relation between maximal voluntary force in m. palmaris longus and the temporal and spatial summation of muscle fiber recruitment in human subjects

This study aimed at looking at the frequency (T‐score) and the amplitude (S‐score) of fiber use during contraction of a forearm muscle, m. palmaris longus, as measured by acoustic myography (AMG). An additional aim was to relate the T‐ and S‐scores to the recorded force obtained from a hand dynamometer. The hypothesis being that temporal and spatial summation of muscle fiber contraction in a given muscle during a given movement, can together describe a given obtained force. Force measurements were carried out on 12 healthy human subjects aged 19–68 years (6 men & 6 women), while their m. palmaris longus contractile function was measured using an acoustic myography CURO device. Force production was varied from 90 to 10% of assessed maximal voluntary force (MVF), and also monitored over a 1 min period of 50% MVF. Linear regression analysis was applied to relate force to spatial and temporal summation. Muscle strength was sustained by changing the frequency and/or the number of active fibere at any given point in time. Force production, whilst stronger for men than women, was regulated in a similar fashion for both sexes and was closely correlated with the AMG T‐ and S‐scores. It is concluded that AMG is a noninvasive method which can be readily applied to accurately describe how a subject uses a given muscle during any given movement. These findings have relevance when considering training strategies in subjects with muscle trauma or disease, in the elderly, or for both amateur and top professional athletes.
Fast Automatic Differentiation for Large Scale Bundle Adjustment

A parallelized implementation of automatic differentiation that derives from the problem of bundle adjustment is proposed in this paper. Reverse mode of automatic differentiation is more efficient to compute the derivatives of functions with $n$ real-value parameters, which is the case of computing the Jacobian matrix in bundle adjustment problem. By reason of a large number of small derivative computing tasks being needed in bundle adjustment problem, we implement an automatic differentiation library based on operator overloading and OpenCL parallel framework. In order to parallelize the computation in the framework of OpenCL, we generate forward and reverse computational sequences from computational graph by topological sorting. This library enables us to write down the function formula elegantly and then evaluate the derivatives rapidly and automatically. Finally, large scale bundle adjustment data sets is used to evaluate our proposed implementation. The result shows that our implementation runs about 3.6 times faster than Ceres Solver, which utilizes OpenMP parallel programming model.
Social, reward, and attention brain networks are involved when online bids for joint attention are met with congruent versus incongruent responses

Joint attention (JA) is a cornerstone of adaptive human social functioning. Little functional magnetic resonance imaging (fMRI) research has examined, in interactive paradigms, neural activation underlying bids for JA, met with a congruent or an incongruent social response. We developed a highly naturalistic fMRI paradigm utilizing eye-tracking to create real-time, contingent social responses to participant-initiated JA. During congruent responses to JA bids, we observed increased activation in the right amygdala, the right fusiform gyrus, anterior and dorsal anterior cingulate cortices, striatum, ventral tegmental area, and posterior parietal cortices. Incongruent responses to JA bids elicited increased activity localized to the right temporoparietal junction (TPJ) and bilateral cerebellum. No differences in eye-gaze patterns were observed during congruent or incongruent trials. Our results highlight the importance of utilizing interactive fMRI paradigms in social neuroscience and the impact of congruency in recruiting integrated social, reward, and attention circuits for processing JA.
The significance of damage and defects and their detection in composite materials: A review

Abstract In this paper the various failure modes which occur in long fibre composites are described and discussed. The significance of each of these fracture mechanisms, in terms of their energy-dissipating capacity as well as their effect on the residual load-bearing properties, is considered. A brief review of both the destructive and non-destructive techniques used for detecting and characterizing defects and damage is presented. The ability of each technique to identify the various fracture mechanisms involved in the failure of long fibre reinforced composites is discussed and their overall suitability for damage detection evaluated.
The Burden of ADHD in Older Adults: A Qualitative Study

Objective: To explore how ADHD may have affected the lives of older adults who meet the diagnostic criteria of ADHD, but are unaware of their diagnosis. Our second aim was to examine whether the reported symptoms change over the life span. Method: A qualitative study was conducted. Seventeen Dutch older people (>65 years) diagnosed in this study with ADHD participated in in-depth interviews. Data were analyzed according to techniques of thematic approach. Results: Seven themes emerged from the analyses. Four themes correspond to ADHD symptoms: “being active,” “being impulsive,” “attention problems,” and “mental restlessness. ” In addition, the themes “low self-esteem,” “overstepping boundaries,” and “feeling misunderstood” emerged. The impact of ADHD symptoms seems to have declined with age. Conclusion: ADHD has a negative impact on late life, and older adults with the disorder may benefit from treatment. Moreover, this study’s findings call for early detection and treatment of ADHD in children and adults.
Efficacy of levomilnacipran extended release in treating major depressive disorder

ABSTRACT Introduction: Major depressive disorder (MDD) is the leading cause of disability worldwide with a heterogeneous symptom profile. Levomilnacipran extended release (ER) (Fetzima), a SNRI, has been approved by the Food and Drug Administration for treatment of MDD. While categorized as a SNRI, in contradistinction to other approved SNRIs, levomilnacipran exhibits differential affinity for the norepinephrine reuptake transporter when compared to the serotonin reuptake transporter. Areas covered: Completed clinical trials which focused on levomilnacipran ER administered in those with MDD were included in this drug evaluation. Expert opinion: Levomilnacipran ER, like all other first-line antidepressants exhibits significant efficacy in reducing total symptom severity. Levomilnacipran ER is particularly effective at improving measures of motivation, energy, and interest. Head to head comparative trials are not available with other antidepressants, and consequently, there are no claims of superior efficacy when compared to alternative antidepressants. Notwithstanding, it would be a viable and testable hypothesis that differential efficacy in favor of levomilnacipran may be obtained across select dimensions of depressive symptoms (e.g., fatigue and lack of motivation). Unfortunately, rigorous studies evaluating levomilnacipran for cognitive function in MDD have not been conducted. Levomilnacipran ER is generally well tolerated with minimal propensity for metabolic and weight disturbance.
Charging effect at grain boundaries of MoS2

Grain boundaries (GBs) are inherent extended defects in chemical vapor deposited (CVD) transition metal dichalcogenide (TMD) films. Characterization of the atomic structure and electronic properties of these GBs is crucial for understanding and controlling the properties of TMDs via defect engineering. Here, we report the atomic and electronic structure of GBs in CVD grown MoS2 on epitaxial graphene/SiC(0001). Using scanning tunneling microscopy/spectroscopy, we find that GBs mostly consist of arrays of dislocation cores, where the presence of mid-gap states shifts both conduction and valence band edges by up to 1 eV. Our findings demonstrate the first charging effect near GBs in CVD grown MoS2, providing insights into the significant impact GBs can have on materials properties.
Drosophila Regulate Yeast Density and Increase Yeast Community Similarity in a Natural Substrate

Drosophila melanogaster adults and larvae, but especially larvae, had profound effects on the densities and community structure of yeasts that developed in banana fruits. Pieces of fruit exposed to adult female flies previously fed fly-conditioned bananas developed higher yeast densities than pieces of the same fruits that were not exposed to flies, supporting previous suggestions that adult Drosophila vector yeasts to new substrates. However, larvae alone had dramatic effects on yeast density and species composition. When yeast densities were compared in pieces of the same fruits assigned to different treatments, fruits that developed low yeast densities in the absence of flies developed significantly higher yeast densities when exposed to larvae. Across all of the fruits, larvae regulated yeast densities within narrow limits, as compared to a much wider range of yeast densities that developed in pieces of the same fruits not exposed to flies. Larvae also affected yeast species composition, dramatically reducing species diversity across fruits, reducing variation in yeast communities from one fruit to the next (beta diversity), and encouraging the consistent development of a yeast community composed of three species of yeast (Candida californica, C. zemplinina, and Pichia kluvyeri), all of which were palatable to larvae. Larvae excreted viable cells of these three yeast species in their fecal pools, and discouraged the growth of filamentous fungi, processes which may have contributed to their effects on the yeast communities in banana fruits. These and other findings suggest that D. melanogaster adults and their larval offspring together engage in ‘niche construction’, facilitating a predictable microbial environment in the fruit substrates in which the larvae live and develop.
A performance and power co-optimization approach for modern processors

In embedded systems, performance and power are important inter-related issues that cannot be decoupled. Expensive and extensive simulations in a processor design space are usually required to verify whether a design meets both performance and power requirements. In this paper, an analytical co-optimization approach based on an integrated workload, performance and power model for modern processors is described and studied. A design space consisting of more than 15 architectural and workload parameters can be quickly explored for co-optimization. Validation with measured results obtained from simulators as well as physical processors showed that the model has a good degree of accuracy. We shall describe the details of approach and the model, and show how to apply the approach to the problem of co-optimizing the power and performance of processor design. With the completeness, flexibility and efficiency, our approach provides clear insights into the tradeoffs of designs for performance and power.