Miracle-dz/UniFAR-FTUs huggingface dataset:
In vivo Atoh1 targetome reveals how a proneural transcription factor regulates cerebellar development

The proneural, basic helix–loop–helix transcription factor Atoh1 governs the development of numerous key neuronal subtypes, such as cerebellar granule and brainstem neurons, inner ear hair cells, and several neurons of the proprioceptive system, as well as diverse nonneuronal cell types, such as Merkel cells and intestinal secretory lineages. However, the mere handful of targets that have been identified barely begin to account for Atoh1’s astonishing range of functions, which also encompasses seemingly paradoxical activities, such as promoting cell proliferation and medulloblastoma formation in the cerebellum and inducing cell cycle exit and suppressing tumorigenesis in the intestine. We used a multipronged approach to create a comprehensive, unbiased list of over 600 direct Atoh1 target genes in the postnatal cerebellum. We found that Atoh1 binds to a 10 nucleotide motif (AtEAM) to directly regulate genes involved in migration, cell adhesion, metabolism, and other previously unsuspected functions. This study expands current thinking about the transcriptional activities driving neuronal differentiation and provides a framework for further neurodevelopmental studies.
Role of calsequestrin evaluated from changes in free and total calcium concentrations in the sarcoplasmic reticulum of frog cut skeletal muscle fibres

Calsequestrin is a large‐capacity Ca‐binding protein located in the terminal cisternae of sarcoplasmic reticulum (SR) suggesting a role as a buffer of the concentration of free Ca in the SR ([Ca2+]SR) serving to maintain the driving force for SR Ca2+ release. Essentially all of the functional studies on calsequestrin to date have been carried out on purified calsequestrin or on disrupted muscle preparations such as terminal cisternae vesicles. To obtain information about calsequestrin's properties during physiological SR Ca2+ release, experiments were carried out on frog cut skeletal muscle fibres using two optical methods. One – the EGTA–phenol red method – monitored the content of total Ca in the SR ([CaT]SR) and the other used the low affinity Ca indicator tetramethylmurexide (TMX) to monitor the concentration of free Ca in the SR. Both methods relied on a large concentration of the Ca buffer EGTA (20 mm), in the latter case to greatly reduce the increase in myoplasmic [Ca2+] caused by SR Ca2+ release thereby almost eliminating the myoplasmic component of the TMX signal. By releasing almost all of the SR Ca, these optical signals provided information about [CaT]SR versus [Ca2+]SR as [Ca2+]SR varied from its resting level ([Ca2+]SR,R) to near zero. Since almost all of the Ca in the SR is bound to calsequestrin, this information closely resembles the binding curve of the Ca–calsequestrin reaction. Calcium binding to calsequestrin was found to be cooperative (estimated Hill coefficient = 2.95) and to have a very high capacity (at the start of Ca2+ release, 23 times more Ca was estimated to initiate from calsequestrin as opposed to the pool of free Ca in the SR). The latter result contrasts with an earlier report that only ∼25% of released Ca2+ comes from calsequestrin and ∼75% comes from the free pool. The value of [Ca2+]SR,R was close to the KD for calsequestrin, which has a value near 1 mm in in vitro studies. Other evidence indicates that [Ca2+]SR,R is near 1 mm in cut fibres. These results along with the known rapid kinetics of the Ca–calsequestrin binding reaction indicate that calsequestrin's properties are optimized to buffer [Ca2+]SR during rapid, physiological SR Ca2+ release. Although the results do not entirely rule out a more active role in the excitation–contraction coupling process, they do indicate that passive buffering of [Ca2+]SR is a very important function of calsequestrin.
The Influence of Single-level Versus Multilevel Decompression on the Outcome in Multisegmental Lumbar Spinal Stenosis: Analysis of the Lumbar Spinal Outcome Study (LSOS) Data

Study Design: This is prospective multicenter cohort study. Objective: To assess whether patients with confirmed multisegmental lumbar spinal stenosis benefit more from a single-level or a multilevel decompression. Summary of Background Data: In multisegmental lumbar spinal stenotic cases, the decision as to how many levels of stenosis need to be operated to achieve the best possible clinical outcome is still unknown and remains a controversy between spine surgeons. Materials and Methods: Patients of the Swiss Lumbar Stenosis Outcome Study (LSOS) with confirmed multisegmental LSS undergoing first-time decompression without fusion were enrolled in this study. The main outcomes of this study were Spinal Stenosis Measure (SSM) symptoms and function over time, measured at baseline, 6, 12, and 24 months follow-up. Further outcomes of interest were changes in SSM, numeric rating scale, feeling thermometer, the EQ-5D-EL, and the Roland and Morris disability questionnaire from baseline to 6, 12, and 24 months. Results: After 12 months, a total of 141 patients met the inclusion criteria; of these, 33 (23%) underwent a single-level and 108 (77%) a multilevel decompression. Multilevel decompression was associated with a significantly less favorable SSM symptoms and function score, respectively, as compared with single-level decompression. In all further outcomes of interest single-level as well as multilevel patients improved over time. Conclusions: Our study showed that in multisegmental stenotic cases a single-level decompression was associated with a significantly more favorable SSM symptoms and function score, respectively, as compared with multilevel decompression. This study provides evidence that in multisegmental stenotic cases a single-level decompression might be sufficient to improve patient’s symptoms and function.
The Co-Occurrence and Unique Mental Health Effects of Political Violence and Intimate Partner Violence

The global mental health ramifications of political violence and intimate partner violence (IPV) are well established. There also exists a growing body of evidence about the increased risks for IPV within situations of political violence. Yet, except for a few studies, there is little literature that simultaneously examines how political violence and IPV might result in unique risks for particular types of mental health sequela. Delineating possible divergent patterns between specific mental health conditions resulting from political violence and IPV takes on an increased urgency given that, although they are related, the two most commonly reported outcomes of these two types of violence—post-traumatic stress disorder (PTSD) and depression—not only require different types of treatment, but may in fact be generated or maintained by disparate paths. Using survey data from adult women in Palestine (n = 122), this study explores the relationships between IPV and political violence (both lifetime and past-month exposure) and tests their independent relationships to PTSD and depressive symptomology. After controlling for the other form of violence exposure, political violence was correlated with PTSD and not with depressive symptomology, while IPV was correlated with depressive symptomology and not with PTSD. Findings demonstrate that distinct forms of violence exposure might indeed be associated with specific mental health outcomes. Results illustrate the need to assess for both political violence and IPV when researching and designing interventions related to violence.
Concomitant leptospirosis-hantavirus co-infection in acute patients hospitalized in Sri Lanka: implications for a potentially worldwide underestimated problem

SUMMARY Two global (re-)emerging zoonoses, leptospirosis and hantavirus infections, are clinically indistinguishable. Thirty-one patients, hospitalized in Sri Lanka for acute severe leptospirosis, were after exclusion of other potentially involved pathogens, prospectively screened with IgM ELISA for both pathogens. Of these, nine (29·0%) were positive for leptospirosis only, one (3·2%) for hantavirus only, seven (22·5%) for both pathogens concomitantly, whereas 13 (41·9%) remained negative for both. Moreover, in a retrospective study of 23 former patients, serologically confirmed for past leptospirosis, six (26·0%) were also positive in two different IgG ELISA hantavirus formats. Surprisingly, European Puumala hantavirus (PUUV) results were constantly higher, although statistically not significantly different, than Asian Hantaan virus (HTNV), suggesting an unexplained cross-reaction, since PUUV is considered absent throughout Asia. Moreover, RT–PCR on all hantavirus IgM ELISA positives was negative. Concomitant leptospirosis-hantavirus infections are probably heavily underestimated worldwide, compromising epidemiological data, therapeutical decisions, and clinical outcome.
Supporting Biodiversity Studies by the EUBrazilOpenBio Hybrid Data Infrastructure

—EUBrazilOpenBio is a collaborative initiative addressing strategic barriers in biodiversity research by integrating open access data and user-friendly tools widely available in Brazil and Europe. The project deploys the EU-Brazil Hybrid Data Infrastructure that allows the sharing of hardware, software and data on-demand. This infrastructure provides access to several integrated services and resources to seamlessly aggregate taxonomic, biodiversity and climate data, used by processing services implementing checklist cross-mapping and ecological niche modelling. A Virtual Research Environment was created to provide users with a single entry point to processing and data resources. This article describes the architecture, demonstration use cases and experimental results.
The Tail of Integrins, Talin, and Kindlins

Tales of Talin, Kindlin, and Integrin The integrins are receptors on the surface of animal cells that mediate attachment to the extracellular matrix. Integrins also act as signaling molecules, activating signaling pathways when they bind to their ligands in the matrix. Furthermore, integrins can communicate signals from the inside to the outside of the cell when signals within the cell alter the affinity of integrins for their extracellular ligands. Moser et al. (p. 895) review recent advances in understanding the roles of the proteins talin and kindlin in such bidirectional signaling and how they influence the function of integrins in health and disease. Integrins are transmembrane cell–adhesion molecules that carry signals from the outside to the inside of the cell and vice versa. Like other cell surface receptors, integrins signal in response to ligand binding; however, events within the cell can also regulate the affinity of integrins for ligands. This feature is important in physiological situations such as those in blood, in which cells are always in close proximity to their ligands, yet cell-ligand interactions occur only after integrin activation in response to specific external cues. This review focuses on the mechanisms whereby two key proteins, talin and the kindlins, regulate integrin activation by binding the tails of integrin-β subunits.
Venous perfusion of the limb with antibiotics for osteomyelitis and other chronic infections.

A new approach to treatment of chronic infections of bone and soft tissue in limbs by perfusion is described. The method is based on a selective pressure technique; the antibiotic solution is introduced through an intravenous catheter distal to the focus of infection. Using a pressure dressing over the treated limb and a proximal tourniquet, the venous flow is shunted into the deep venous system and into the bone In some cases, surgical treatment was performed prior to the perfusion. The advantages of the method are: (1) simplicity and (2) delivery of effective antibiotics in high concentration to the infected region by diffusion through the infected or avascular scar tissue. The method was used in fifteen patients with chronic infections of bone or soft tissue. Sufficient time has not elapsed to warrant final evaluation of the results, but in all the cases there was immediate control of the infection and sterile cultures were obtained. In three cases, recurrence was noted. Temporary results are discussed.
A hybrid control approach to task priority based mobile manipulation

This paper proposes a hybrid control approach to task priority based mobile manipulation. More specifically, it uses a hybrid systems framework to address the problem of end-effector path following for a manipulator attached to a nonholonomic mobile platform where the joints are subject to constraints and the inputs signals are required to be bounded. A switched control strategy allows the robot to avoid infeasible and singular joint configurations while executing a bounded pseudo-inverse based feedback control law. The resulting closed loop system stabilizes the desired path, has a dwell time in each mode, and only switches a finite number of times.
MR of hypoxic encephalopathy in children after near drowning: correlation with quantitative proton MR spectroscopy and clinical outcome.

BACKGROUND AND PURPOSE Quantitative MR spectroscopy has a proved role in the investigation of hypoxia caused by near drowning. To date, no studies have addressed the MR imaging changes that may also accompany this condition. The purpose of this study was to describe the MR imaging findings in children with hypoxic encephalopathy caused by near drowning and to compare these findings with the results of qualitative and quantitative proton MR spectroscopy and clinical outcome. METHODS Twenty-two children (6 months to 11 years old) admitted to the pediatric intensive care unit after near drowning incidents underwent cerebral MR imaging and quantitative proton MR spectroscopy. Clinical and imaging studies were reviewed retrospectively, and subjects were grouped according to outcome: good result, persistent vegetative state, and death. Images were scored for edema, basal ganglia changes, and cortical changes, and were compared with MR spectra and outcome at days 1 to 2, 3 to 4, and 5 or more. RESULTS Six patients had a good outcome, four remained in a persistent vegetative state, and 12 died. Generalized/occipital edema correlated with poor outcome. Indistinct lentiform nuclei margins on T1-weighted images were a frequent finding (78%). Basal ganglia T2 hyperintensity correlated with poor outcome, progressing from a patchy/peripheral distribution to diffuse high intensity. Patchy high T2 signal in the cortex or subcortical lines were specific but insensitive for poor outcome, as were brain stem infarcts. CONCLUSION MR images in children with hypoxic encephalopathy after near drowning show a spectrum of changes. The most sensitive prognostic result may be achieved by combining MR imaging with qualitative and quantitative MR spectroscopic data.
[Genetic analysis of Yersinia pestis strains isolated in China].

OBJECTIVE The strains of Yersinia pestis isolated in different period and different natural foci in China were analyzed. METHODS Traditional and molecular biological methods were used. Rhamnose fermentation, rRNA gene copy number, nitrite reduction, and the glycerol fermentation were important characters for typing, and pulse field gel electrophoresis (PFGE) and random amplified polymorphic DNA (RAPD) profile could reflect the genetic distance between the strains. RESULTS The strains could be divided into 15 genetic types by those 6 characters with each of them covered an isolated geographical territories. CONCLUSION The characters of strains were described; the genetic relationship of different types, their evolution, and the forming and shift of plague natural foci were analyzed.
Diversity of rotavirus VP7 and VP4 genotypes in Northwestern Nigeria.

BACKGROUND Nigeria has recently been ranked third among the 10 countries with the greatest number of rotavirus disease-associated deaths per year. Estimates attribute up to 33,000 deaths annually to rotavirus disease in Nigerian children <5 years old. Although the introduction of the new oral, live attenuated rotavirus vaccines may not occur for another 4-6 years in developing countries, background data on burden of disease, cost of rotavirus disease, and characterization of circulating strains is required to hasten this introduction to children who would clearly benefit from the intervention. METHODS Between July 2002 and July 2004, fecal specimens were collected from 869 infants and young children <5 years of age presenting with diarrhea in Kaduna, Kebbi, Sokoto, and Zamfara states in northwestern Nigeria. In addition, 194 control specimens were also collected from children matched for age. Specimens were screened for the presence of rotavirus antigens. Rotavirus-positive specimens were further analyzed to determine electropherotype, subgroup specificity, and G and P genotypes. RESULTS Rotavirus was detected in 18% of children with diarrhea and 7.2% of the age-matched case control subjects. The highest rotavirus burden was detected in children aged <6 months. The majority of the rotavirus-positive specimens revealed viruses of long electropherotypes, subgroup II specificity, and G1P[8] genotypes. Furthermore, more than a quarter of specimens (37%) displayed mixed G and P genotypes, and almost a third could not be genotyped. CONCLUSIONS The high numbers of mixed rotavirus infections highlight the multitude of enteric pathogens to which children in African countries are exposed. Data on circulating rotavirus strains serve to inform African government officials to the serious health threat posed by rotavirus in their respective countries and to document the diversity of strains before vaccine introduction.
Pheochromocytoma and functional paraganglioma syndrome: No longer the 10% tumor

Pheochromocytomas and abdominal paragangliomas are catecholamine‐producing tumors of the sympathetic nervous system, while head and neck paragangliomas are non‐secreting tumors of parasympathetic origin. Recent developments in clinical and molecular research on these tumor forms have significantly clarified their genetic backgrounds and challenged the view of “pheochromocytoma as the 10% rule tumor. ” Firstly, a larger proportion of these tumors are today discovered in normotensive patients during imaging carried out for other reasons than suspicion of pheochromocytoma. Secondly, although the differential diagnosis between malignant and benign tumors remains a challenge, the risk of malignancy well exceeds the classical 10% in patients with extra‐adrenal disease, and/or carriers of germ‐line SDHB mutations. Finally, up to a third of patients carry a germ‐line mutation in a gene predisposing to pheochromocytoma and/or paraganglioma. Identification of a constitutional mutation in RET, VHL, SDHD, or SDHB has implications for clinical screening and follow‐up for both the patient and for relatives at risk who can be identified by screening for the same mutation. Genetic testing in apparently sporadic cases is therefore regarded as beneficial, especially in patients diagnosed before 50 years of age, and in patients with bilateral, multifocal, malignant and/or extra‐adrenal disease. J. Surg. Oncol. 2005;89:193–201. © 2005 Wiley‐Liss, Inc.
Performance measurement systems and environmental uncertainty effect on profitability

This study analyses how the changes in financial and non-financial measures, the scope of PMS and environmental uncertainty are associated with financial performance in accounting information system AIS. The empirical data was collected by a survey which was sent to 464 manufacturing companies with over 50 employees. We received 98 response rate 21.1% utilisable responses from the respondents with financial responsibility i.e., CEOs and CFO. According to statistical analysis, environmental uncertainty, PMS change and scope of PMS have an interactive association with performance. This association was found only after classifying aggregate PMS into three perspectives, i.e., customer, internal business process and employee. The highest performance occurred during changes in financial PMS, the emphasis on the customer or employee internal business process perspectives under low high environmental uncertainty.
Adoption of Innovative Technology for Business Transformation with Big Data in an Oil and Gas Company in South Africa

January 31, 2017 I Abstract Today, it is a known fact that Big Data (BD) lead to a competitive advantage for organisations. While several methodologies have been introduced to gain insights using BD, there is a lack in research regarding the adoption and usage of this knowledge within organizations for effective decision-making. By analysing a case of a South African oil and gas company, results of current research of innovation adoption have been adapted in order to find the reasons for the problem and fill this gap in current research. To collect data for this thesis, eight managers have been interviewed. The findings have then been analysed and assigned to a set of categories. The result of this research are three major criteria. Depending on the fulfilment or lack of the criteria, they act as enabler or barriers. The first criterion is the quality of the system, most important being data quality, next to performance and up-to-date data. Second is support and training, most important to find the right people for the right position and train them how to access the BD analytics and what is available. The right people have a passion for analysing data and bring with them creativity and innovativeness. The third influencer is (missing) features. It describes the possibilities to access information gained by BD. In the case of the oil and gas company, it was missing mobile reporting, predictive analytics and unstructured data. These three categories create a perceived value, which influences the adoption of BD analytics. The perceived value also effects the management, which themselves have been found as an influencer for the adoption.
Rapid Analysis of Network Connectivity

This research focuses on accelerating the computational time of two base network algorithms (k-simple shortest paths and minimum spanning tree for a subset of nodes)---cornerstones behind a variety of network connectivity mining tasks---with the goal of rapidly finding networkpathways andtrees using a set of user-specific query nodes. To facilitate this process we utilize: (1) multi-threaded algorithm variations, (2) network re-use for subsequent queries and (3) a novel algorithm, Key Neighboring Vertices (KNV), to reduce the network search space. The proposed KNV algorithm serves a dual purpose: (a) to reduce the computation time for algorithmic analysis and (b) to identify key vertices in the network (\textit ). Empirical results indicate this combination of techniques significantly improves the baseline performance of both algorithms. We have also developed a web platform utilizing the proposed network algorithms to enable researchers and practitioners to both visualize and interact with their datasets (PathFinder: http://www.path-finder.io.
Identification and characterization of E‐APC, a novel Drosophila homologue of the tumour suppressor APC

Mutations in the adenomatous polyposis coli (APC) tumour suppressor gene are implicated in the genesis of colorectal cancers. The product of the APC gene forms a complex with β‐catenin, glycogen synthase kinase 3β (GSK‐3β) and Axin/conductin, and induces the degradation of β‐catenin.