Miracle-dz/UniFAR-FTUs huggingface dataset:
Hospital Admissions Associated with Adverse Drug Reactions: A Systematic Review of Prospective Observational Studies

Objective: To determine the prevalence of hospital admissions associated with ADRs and examine differences in prevalence rates between population groups and methods of ADR detection. Data Sources: Studies were identified through electronic searches of Cumulative Index to Nursing and Allied Hearth Literature. EMBASE, and MEDLINE to August 2007. There were no language restrictions. Study Selection and Data Extraction: A systematic review was conducted of prospective observational studies that used the World Health Organization ADR definition. Subgroup analysis examined the influence of patient age groups and methods of ADR detection on reported ADR admission rates. All statistical analyses were performed using STATA v 9.0. Data Synthesis: Twenty-five studies were identified including 106, 586 patients who were hospitalized; 2143 of these patients had experienced ADRs. The prevalence rates of ADRs ranged from 0.16% to 15.7%, with an overall median of 5.3% (interquartile range [IQR] 2.7–9.0%). Median ADR prevalence rates varied between age groups: for children, the ADR admission rate was 4.1% (IQR 0.16–5.3%), while the corresponding rates for adults and elderly patients were 6.3% (IQR 3.9–9.0%) and 10.7% (IQR 9.6–13.3%), respectively. ADR rates also varied depending on the methods of ADR detection employed in the different studies. Studies that employed multiple ADR detection methods, such as medical record review and patient interview, reported higher ADR admission rates compared with studies that used medical record review alone. Antiinfective drugs were most often associated with ADR admissions in children; cardiovascular drugs were most often associated with ADR admissions in adults and elderly patients. Conclusions: Approximately 5.3% of hospital admissions were associated with ADRs. Higher rates were found in elderly patients who are likely to be receiving multiple medications for long-term illnesses. The methods used to detect ADRs are also likely to explain much of the variation in the reported ADR prevalence rates between different studies.
3D object instance recognition and pose estimation using triplet loss with dynamic margin

In this paper, we address the problem of 3D object instance recognition and pose estimation of localized objects in cluttered environments using convolutional neural networks. Inspired by the descriptor learning approach of Wohlhart et al. [1], we propose a method that introduces the dynamic margin in the manifold learning triplet loss function. Such a loss function is designed to map images of different objects under different poses to a lower-dimensional, similarity-preserving descriptor space on which efficient nearest neighbor search algorithms can be applied. Introducing the dynamic margin allows for faster training times and better accuracy of the resulting low-dimensional manifolds. Furthermore, we contribute the following: adding in-plane rotations (ignored by the baseline method) to the training, proposing new background noise types that help to better mimic realistic scenarios and improve accuracy with respect to clutter, adding surface normals as another powerful image modality representing an object surface leading to better performance than merely depth, and finally implementing an efficient online batch generation that allows for better variability during the training phase. We perform an exhaustive evaluation to demonstrate the effects of our contributions. Additionally, we assess the performance of the algorithm on the large BigBIRD dataset [2] to demonstrate good scalability properties of the pipeline with respect to the number of models.
Path loss modification and multi-user capacity analysis by dynamic rain models for 5G radio communications in millimetre waves

Based on outdoor microcellular measurements at 26 and 32 GHz, the path loss models are modified by a proposed dynamic rain model to see the difference of the path loss models between clear and rainy air with respect to rainfall intensities and transceiver distances. Moreover, a dynamic rain cell model for a multi-user system is developed to investigate the total rain attenuation. The results show that the parameters for floating-intercept (FI) model have a bigger change with different rainfall intensities than close-in (CI) model. When considering the dynamic rain model with a different radius and moving speeds, the larger rain cell radius, the larger path loss exponents in CI and FI models, the smaller path loss intercept in FI model and system capacity will be achieved. For a fixed rain cell radius, the larger moving speed of the rain cell, the shorter effective time on the path loss and system capacity will be achieved. In addition, the rain cell has a bigger effect on the path loss exponent, intercept and system capacity at higher frequency band with respect to its size, moving speed, and rainfall intensity.
Diagnostic utility of cardiac magnetic resonance for detection of cardiac involvement in female carriers of Duchenne muscular dystrophy

Background Cardiac involvement is a recognised complication in female carriers of Duchenne muscular dystrophy (DMD). Since segmental or global left ventricle (LV) wall motion abnormalities in DMD carriers can arise even without apparent muscle weakness, it is difficult to differentiate cardiac involvement of a DMD carrier from other heart diseases in a non-invasive manner. Cardiac magnetic resonance (CMR) with late gadolinium enhancement (LGE) enables assessment of regional wall motion abnormality and myocardial damage with high spatial resolution. Objective To assess the utility of CMR for detection of myocardial damage in female carriers of DMD. Methods and results Gadolinium-enhanced CMR was performed in seven female DMD carriers. Physical examination, electrocardiography, chest radiograph, measurements of total creatinine kinase and brain natriuretic peptide levels, and two-dimensional echocardiography were also performed. Four (57%) of the seven carriers had LGE, and LGE was frequently observed at the subepicardial layer in the inferolateral segment. Two carriers had a focal LGE at the LV inferolateral wall without LV dilation or wall motion abnormalities. Conclusion CMR findings of DMD carriers were characterised by subepicardial LGE, which was localised at inferolateral segments. CMR may be a useful modality for detecting cardiac involvement in DMD carriers.
In Silico Analysis of ORF1ab in Coronavirus HKU1 Genome Reveals a Unique Putative Cleavage Site of Coronavirus HKU1 3C‐Like Protease

Recently we have described the discovery and complete genome sequence of a novel coronavirus associated with pneumonia, coronavirus HKU1 (CoV‐HKU1). In this study, a detailed in silico analysis of the ORF1ab, encoding the 7,182‐amino acid replicase polyprotein in the CoV‐HKU1 genome showed that the replicase polyprotein of CoV‐HKU1 is cleaved by its papain‐like proteases and 3C‐like protease (3CLpro) into 16 polypeptides homologous to the corresponding polypeptides in other coronaviruses. Surprisingly, analysis of the putative cleavage sites of the 3CLpro revealed a unique putative cleavage site. In all known coronaviruses, the P1 positions at the cleavage sites of the 3CLpro are occupied by glutamine. This is also observed in CoV‐HKU1, except for one site at the junction between nsp10 (helicase) and nsp11 (member of exonuclease family), where the P1 position is occupied by histidine. This amino acid substitution is due to a single nucleotide mutation in the CoV‐HKU1 genome, CAG/A to CAT. This probably represents a novel cleavage site because the same mutation was consistently observed in CoV‐HKU1 sequences from multiple specimens of different patients; the P2 and P1′‐P12′ positions of this cleavage site are consistent between CoV‐HKU1 and other coronaviruses; and as the helicase is one of the most conserved proteins in coronaviruses, cleavage between nsp10 and nsp11 should be an essential step for the generation of the mature functional helicase. Experiments, including purification and C‐terminal amino acid sequencing of the CoV‐HKU1 helicase and trans‐cleavage assays of the CoV‐HKU1 3CLpro will confirm the presence of this novel cleavage site.
Asymmetric Atrophy of Paraspinal Muscles in Patients With Chronic Unilateral Lumbar Radiculopathy

Objective To assess the cross-sectional area (CSA) of the muscles for investigating the occurrence of asymmetry of the paraspinal (multifidus and erector spinae) and psoas muscles and its relation to the chronicity of unilateral lumbar radiculopathy using magnetic resonance imaging (MRI). Methods This retrospective study was conducted between January 2012 to December 2014. Sixty one patients with unilateral L5 radiculopathy were enrolled: 30 patients had a symptom duration less than 3 months (group A) and 31 patients had a symptom duration of 3 months or more (group B). Axial MRI measured the CSA of the paraspinal and psoas muscles at the middle between the lower margin of the upper vertebra and upper margin of the lower vertebra, and obtained the relative CSA (rCSA) which is the ratio of the CSA of muscles to that of the lower margin of L4 vertebra. Results There were no differences in the demographics between the two groups. In group B, rCSA of the erector spinae at the L4–5 level, and that of multifidus at the L4–5 and L5–S1 levels, were significantly smaller on the involved side as compared with the uninvolved side. In contrast, no significant muscle asymmetry was observed in group A. The rCSA of the psoas was not affected in either group. Conclusion The atrophy of the multifidus and erector spinae ipsilateral to the lumbar radiculopathy was observed only in patients suffering from unilateral radiculopathy for 3 months or more.
Self‐navigated spiral fMRI: Interleaved versus single‐shot

This study compares the measured activation volumes in motor cortex as well as the fluctuation noise and off‐resonance characteristics for 1‐, 2‐, and 4‐shot spiral gradient‐recalled echo blood oxygen level dependent contrast functional magnetic resonance imaging (fMRI) acquisitions, under conditions of constant resolution and scan time and with two readout durations. Reconstructions were made with and without self‐navigator correction. It was found that the navigator correction provided a 50% reduction in image fluctuation noise with 4‐shot acquisitions, and that multishot acquisitions perform as well as single‐shot techniques when self‐navigation is employed. An analysis of blurring showed that off‐resonance Af causes blurring when Δf > 1/(2*Tad), where Tad is the readout duration. Off‐resonance effects were readily corrected during reconstruction with retrospective linear shim, even with the longer readout duration needed for single‐shot methods. With navigator and shim correction, single‐shot and multishot spiral methods are highly effective for fMRI acquisitions.
Bedaquiline - A Novel Promising Discovery in Multidrug-Resistant Tuberculosis

After acquired immunodeficiency syndrome (AIDS), tuberculosis (TB) is the leading cause of death worldwide due to a single infectious agent. Recently, drug-resistant strains of mycobacterium tuberculosis reported more horrible version of tuberculosis. There is threatful increase in multidrug resistant tuberculosis (MDR-TB) and extensively drug-resistant TB (XDR-TB) all over the world, so better treatment options are needed to control the global MDR-TB and XDR-TB epidemic. Bedaquiline, a diarylquinoline has a unique mechanism of action i.e. causes inhibition of the proton pump activity of the ATP synthase in mycobacterium tuberculosis and targets the energy metabolism. It acts as a promising new agent in patients with MDR-TB came in market recently. Bedaquiline can be combined with antituberculosis and antiretroviral agents. The drug showed good oral absorption, long terminal half-life and is metabolized mainly by cytochrome 450P3A4. It is recently been approved by U.S. Food and Drug Administration on 28th December, 2012 for treating multi drug resistant TB (MDR-TB) in adults ≥18 years. It seems to be good option for multidrug-resistant tuberculosis patients as it has earlier and sustained antitubercular action, shorten duration of treatment, less chances of resistance and better safety as compared to existing second line drugs. Long term studies are needed to explore its safety.
Tumor necrosis factor receptor 1 gain‐of‐function mutation aggravates nonalcoholic fatty liver disease but does not cause insulin resistance in a murine model *

Ectodomain shedding of tumor necrosis factor receptor 1 (TNFR1) provides negative feedback to the inflammatory loop induced by TNFα. As the significance of this mechanism in obesity‐associated pathologies is unclear, we aimed to unravel how much TNFR1 ectodomain shedding controls the development of nonalcoholic fatty liver disease (NAFLD), as well as its role in the development of insulin resistance. We used knockin mice expressing a mutated TNFR1 ectodomain (p55Δns), incapable of shedding and dampen the inflammatory response. Our data show that persistent TNFα signaling through this inability of TNFR1 ectodomain shedding contributes to chronic low‐grade inflammation, which is confined to the liver. In spite of this, hepatic lipid levels were not affected by the nonshedding mutation in mice fed a chow diet, nor were they worse off following 12 weeks of high‐fat diet (HFD) than controls (p55+/+) fed an HFD. We detected inflammatory infiltrates, hepatocellular necrosis, and apoptosis in livers of p55Δns/Δns mice fed an HFD, suggesting advanced progression of NAFLD toward nonalcoholic steatohepatitis (NASH). Indeed, fibrosis was present in p55Δns/Δns mice, but absent in wildtype mice, confirming that the p55Δns/Δns mice had a more severe NASH phenotype. Despite low‐grade hepatic inflammation, insulin resistance was not observed in p55Δns/Δns mice fed a chow diet, and HFD‐induced insulin resistance was no worse in p55Δns/Δns mice than p55+/+ mice. Conclusion: TNFR1 ectodomain shedding is not an essential feedback mechanism in preventing the development of hepatic steatosis or insulin resistance. It is, however, pivotal in attenuating the progression from “simple steatosis” towards a more serious phenotype with many NASH features. Targeting TNFR1 could therefore be beneficial in attenuating NASH. (HEPATOLOGY 2013)
Long-distance correlations of rhinovirus capsid dynamics contribute to uncoating and antiviral activity

Human rhinovirus (HRV) and other members of the enterovirus genus bind small-molecule antiviral compounds in a cavity buried within the viral capsid protein VP1. These compounds block the release of the viral protein VP4 and RNA from inside the capsid during the uncoating process. In addition, the antiviral compounds prevent “breathing” motions, the transient externalization of the N-terminal regions of VP1 and VP4 from the inside of intact viral capsid. The site for externalization of VP1/VP4 or release of RNA is likely between protomers, distant to the binding cavity for antiviral compounds. Molecular dynamics simulations were conducted to explore how the antiviral compound, WIN 52084, alters properties of the HRV 14 capsid through long-distance effect. We developed an approach to analyze capsid dynamics in terms of correlated radial motion and the shortest paths of correlated motions. In the absence of WIN, correlated radial motion is observed between residues separated by as much as 85 Å, a remarkably long distance. The most frequently populated path segments of the network were localized near the fivefold symmetry axis and included those connecting the N termini of VP1 and VP4 with other regions, in particular near twofold symmetry axes, of the capsid. The results provide evidence that the virus capsid exhibits concerted long-range dynamics, which have not been previously recognized. Moreover, the presence of WIN destroys this radial correlation network, suggesting that the underlying motions contribute to a mechanistic basis for the initial steps of VP1 and VP4 externalization and uncoating.
Differences in the gastrointestinal micro biota of specific pathogen free mice: an often unknown variable in biomedical research

Large differences were found in the numbers of facultatively anaerobic Gram-negative bacteria in the gastrointestinal tract of mice from 3 major specific pathogen free (SPF) units in Australia. The species isolated also differed between mouse colonies. In one unit the presence of Enterobacter cloacae was found to dramatically influence the survival of mice following total body irradiation. This finding conforms with previous studies which have shown the influence of variation in gastrointestinal micro biota on the immune system and on susceptibility to infection. Given that the presence or absence of Enterobacteriaceae in the intestines of mice under investigation may influence experimental results, researchers using SPF rodents are encouraged to determine the baseline loading of these bacteria in their animals. Where results of immunological or irradiation studies from different colonies are likely to be compared, the enterobacterial status of the colony being used should be reported.
Disulfide core cross-linked PEGylated polypeptide nanogel prepared by a one-step ring opening copolymerization of N-carboxyanhydrides for drug delivery.

A novel disulfide core cross-linked PEGylated polypeptide nanogel has been synthesized by a one-step ring opening copolymerization of γ-benzyl L-glutamate N-carboxyanhydride and L-cystine N-carboxyanhydride using an amino group-terminated poly(ethylene glycol) methyl ether as initiator. Characterization of products confirms the formation of a core cross-linked PEGylated nanogel with disulfide linkages with a size of about 250 nm, and these studies also confirm that this nanogel can easily be broken by glutathione. Cell viability experiments show the good biocompatibility of the as-prepared polymer. Studies relating to loading and controlled release of indomethacin under reduction-sensitive conditions reveal that the nanogel is a good candidate for drug delivery systems.
Dynamic Stabilization of the Lumbar Spine and Its Effects on Adjacent Segments: An In Vitro Experiment

In recent years, nonfusion stabilization of the lumbar spine has gained more and more popularity. These nonfusion systems intend to maintain or restore the intersegmental motions to magnitudes of the intact spine and have no negative effects on the segments adjacent to the stabilized one. This study investigated the DYNESYS, a dynamic nonfusion system, which is designed to stabilize the bridged segments while maintaining the disc and the facet joints. To determine the magnitude of stabilization and the effect of the stabilization on the adjacent segment, six lumbar cadaver spines were fixed in a spine tester and loaded with pure moments in the three main motion planes. For each spine, four different stages were tested: intact, defect of the middle segment, fixation with the DYNESYS, and fixation with the internal fixator. Intersegmental motions were measured at all levels. For the bridged segment, the DYNESYS stabilized the spine and was more flexible than the internal fixator. This difference between the internal fixator and the DYNESYS was most pronounced in extension (P < 0.05), with the DYNESYS restoring the motion back to the level of the intact spine. The motion in the adjacent segments was not influenced by either stabilization method. Our results suggest that the DYNESYS provides substantial stability in case of degenerative spinal pathologies and can therefore be considered as an alternative method to fusion surgery in these indications while the motion segment is preserved.
Distributed processing of biological interactions using Hadoop

In this paper, we propose a software to support the functional genomics community in experiment design by allowing them the processing of large-scale gene or protein interactions. The software is written in Python and uses Apache Hadoop as a distributed environment. We show how the software was implemented as well as how it scales with exponentially growing amount of data. The software is open source and is freely available at https://github.com/benauer/Biogrid-Hadoop.
MUSIC‐ANN Analysis for Locating Structural Damages in a Truss‐Type Structure by Means of Vibrations

Abstract: This article presents a methodology for damage detection, location, and quantification based on vibration signature analysis and a comprehensive experimental study to assess the utility of the proposed structural health monitoring applied to a five‐bay truss‐type structure. The MUSIC algorithm introduced first by Jiang and Adeli for health monitoring of structures in 2007 is fused with artificial neural networks for an automated result. The developed methodology is based on feeding the amplitude of the natural frequencies as input of an artificial neural network, being the novelty of the proposed methodology its ability to identify, locate, and quantify the severity of damages with precision such as: external and internal corrosion and cracks in an automated monitoring process. Results show the proposed methodology is effective for detecting a healthy structure, a structure with external and internal corrosion, and a structure with crack. Therefore, the proposed fusion of MUSIC‐ANN algorithms can be regarded as a simple, effective, and automated tool without requiring sophisticated equipment, toward establishing a practical and reliable structural health monitoring methodology, which will help to evaluate the condition of the structure, in order to detect damages early and to make the corresponding maintenance decisions in the structures.
Massive Milky Way satellites in cold and warm dark matter: dependence on cosmology

We investigate the claim that the largest subhaloes in high resolution dissipationless cold dark matter (CDM) simulations of the Milky Way are dynamically inconsistent with observations of its most luminous satellites. We find that the inconsistency is largely attributable to the large values of \sigma_8 and n_s adopted in the discrepant simulations producing satellites that form too early and therefore are too dense. We find the tension between observations and simulations adopting parameters consistent with WMAP9 is greatly diminished making the satellites a sensitive test of CDM. We find the Via Lactea II halo to be atypical for haloes in a WMAP3 cosmology, a discrepancy that we attribute to its earlier formation epoch than the mean for its mass. We also explore warm dark matter (WDM) cosmologies for 1--4 keV thermal relics. In 1 keV cosmologies subhaloes have circular velocities at kpc scales ~ 60% lower than their CDM counterparts, but are reduced by only 10% in 4 keV cosmologies. Since relic masses < 2-3 keV are ruled out by constraints from the number of Milky Way satellites and Lyman-\alpha\ forest, WDM has a minor effect in reducing the densities of massive satellites. Given the uncertainties on the mass and formation epoch of the Milky Way, the need for reducing the satellite densities with baryonic effects or WDM is alleviated.
Streaming Text Analytics for Real-Time Event Recognition

A huge body of continuously growing written knowledge is available on the web in the form of social media posts, RSS feeds, and news articles. Real-time information extraction from such high velocity, high volume text streams requires scalable, distributed natural language processing pipelines. We introduce such a system for fine-grained event recognition within the big data framework Flink, and demonstrate its capabilities for extracting and geo-locating mobility- and industry-related events from heterogeneous text sources. Performance analyses conducted on several large datasets show that our system achieves high throughput and maintains low latency, which is crucial when events need to be detected and acted upon in real-time. We also present promising experimental results for the event extraction component of our system, which recognizes a novel set of event types. The demo system is available at http://dfki.de/sd4m-sta-demo/.