Miracle-dz/UniFAR-FTUs huggingface dataset:
International variation in disease burden of rotavirus gastroenteritis in children with community- and nosocomially acquired infection.

BACKGROUND The great impact of rotavirus disease on morbidity and medical health care costs in industrialized countries together with the withdrawal of the live oral rotavirus vaccine have made a reassessment of rotavirus gastroenteritis necessary. Such a reassessment should provide sufficient data for developing alternative disease prevention strategies and for allocating resources efficiently. OBJECTIVES To compare characteristics and management of community- and nosocomially acquired rotavirus disease in Austria, Germany and Switzerland. PATIENTS AND METHODS In a prospective, population-based, trinational (Austria, Germany, Switzerland), multicenter (9 cities, 10 hospitals and 30 pediatric practices) study, a total of 174 552 children months and 78 516 hospital days were evaluated. Participants were all children 4 years of age and younger, who either presented at one of the pediatric practices with community-acquired gastroenteritis, or who had acquired gastroenteritis nosocomially. From December, 1997, to May, 1998, prospective antigen testing was done by enzyme-linked immunosorbent assay, and serotyping was done by reverse transcription polymerase chain reaction. Disease severity was scored by the Vesikari severity scale. RESULTS Rotavirus was detected in 29.5, 27 and 37.5% of children with community-acquired gastroenteritis and in 57, 69 and 49% of children with nosocomial gastroenteritis in Austria, Germany and Switzerland, respectively. Severity of community-acquired rotavirus gastroenteritis was more pronounced in Austria (median severity score, 11) than in Germany (median score, 9) or Switzerland (median score, 10). However, only 2% of Austrian and Swiss children compared with 12% of German children presented to their pediatricians more than four times. Nosocomially acquired rotavirus gastroenteritis was mildest in Austria but occurred within the shortest median duration of hospitalization (4 days vs. 5 and 7 in Germany and Switzerland, respectively). In a multivariant analysis age, family size, day care, breast-feeding and nationality were not predictive factors for enhanced risk to contract rotavirus infection. Alimentation was changed frequently; diet was used between 23 and 83%; special formulas were used between 10 and 57%. CONCLUSION The cumulative experience from three European countries suggest that rotavirus is an important cause of diarrhea in Central Europe, but significant local differences clearly demonstrate the need for obtaining national data as a reliable basis for control and prevention of the disease.
All-silicon near-infrared phototransistor based on surface-state absorption

We demonstrate an all-silicon N-P-N phototransistor integrated on a silicon waveguide. The device has a high responsivity of 10 mA/W under 5 V bias at the 1550 nm telecommunication band, larger than the all-silicon P-I-N and P-N photodetectors.
Global Phylogeny of Mycobacterium tuberculosis Based on Single Nucleotide Polymorphism (SNP) Analysis: Insights into Tuberculosis Evolution, Phylogenetic Accuracy of Other DNA Fingerprinting Systems, and Recommendations for a Minimal Standard SNP Set

ABSTRACT We analyzed a global collection of Mycobacterium tuberculosis strains using 212 single nucleotide polymorphism (SNP) markers. SNP nucleotide diversity was high (average across all SNPs, 0.19), and 96% of the SNP locus pairs were in complete linkage disequilibrium. Cluster analyses identified six deeply branching, phylogenetically distinct SNP cluster groups (SCGs) and five subgroups. The SCGs were strongly associated with the geographical origin of the M. tuberculosis samples and the birthplace of the human hosts. The most ancestral cluster (SCG-1) predominated in patients from the Indian subcontinent, while SCG-1 and another ancestral cluster (SCG-2) predominated in patients from East Asia, suggesting that M. tuberculosis first arose in the Indian subcontinent and spread worldwide through East Asia. Restricted SCG diversity and the prevalence of less ancestral SCGs in indigenous populations in Uganda and Mexico suggested a more recent introduction of M. tuberculosis into these regions. The East African Indian and Beijing spoligotypes were concordant with SCG-1 and SCG-2, respectively; X and Central Asian spoligotypes were also associated with one SCG or subgroup combination. Other clades had less consistent associations with SCGs. Mycobacterial interspersed repetitive unit (MIRU) analysis provided less robust phylogenetic information, and only 6 of the 12 MIRU microsatellite loci were highly differentiated between SCGs as measured by GST. Finally, an algorithm was devised to identify two minimal sets of either 45 or 6 SNPs that could be used in future investigations to enable global collaborations for studies on evolution, strain differentiation, and biological differences of M. tuberculosis.
Genetic Divergence Analysis on some Bread Wheat Genotypes Grown in Ethiopia

An investigation was carried out with 49 bread wheat genotypes to assess the genetic diversity for yield and yield related traits. The Unweighted Pair Group Method using Arithmetic Averages (UPGMA) technique was used for the analysis. The genotypes were evaluated for 17 Characters and showed wide variability for the components studied. The cluster analysis grouped the 49 bread wheat genotypes into 22 different clusters. This indicates the presence of wide diversity among the tested genotypes. From cluster mean values, genotypes in cluster 9 and 13 deserve consideration for their direct use as parents in hybridization programs to develop high yielding wheat varieties. The genotypes in cluster 3 and 16 may be used for improvement of protein and gluten contents, early maturity-ness and other desirable characters other than grain yield. The result of the principal components analysis revealed that nine principal components (PC1 to PC9) accounted nearly 80 % of the total variation. It was also noted that differentiation of genotypes into different clusters was because of the small contribution of few character rather than the cumulative effect of a number of characters. The information obtained from this study can be used to plan crosses and maximize the use of genetic diversity and expression of heterosis.
Luminal long non-coding RNAs regulated by estrogen receptor alpha in a ligand-independent manner show functional roles in breast cancer

Estrogen Receptor alpha (ERα) activation by estrogenic hormones induces luminal breast cancer cell proliferation. However, ERα plays also important hormone-independent functions to maintain breast tumor cells epithelial phenotype. We reported previously by RNA-Seq that in MCF-7 cells in absence of hormones ERα down-regulation changes the expression of several genes linked to cellular development, representing a specific subset of estrogen-induced genes. Here, we report regulation of long non-coding RNAs from the same experimental settings. A list of 133 Apo-ERα-Regulated lncRNAs (AER-lncRNAs) was identified and extensively characterized using published data from cancer cell lines and tumor tissues, or experiments on MCF-7 cells. For several features, we ran validation using cell cultures or fresh tumor biopsies. AER-lncRNAs represent a specific subset, only marginally overlapping estrogen-induced transcripts, whose expression is largely restricted to luminal cells and which is able to perfectly classify breast tumor subtypes. The most abundant AER-lncRNA, DSCAM-AS1, is expressed in ERα+ breast carcinoma, but not in pre-neoplastic lesions, and correlates inversely with EMT markers. Down-regulation of DSCAM-AS1 recapitulated, in part, the effect of silencing ERα, i.e. growth arrest and induction of EMT markers. In conclusion, we report an ERα-dependent lncRNA set representing a novel luminal signature in breast cancer cells.
Serum Differentially Alters the Antifungal Properties of Echinocandin Drugs

ABSTRACT Antifungal efficacies of the echinocandin drugs caspofungin, micafungin, and anidulafungin were reduced significantly in the presence of 50% human serum, which yielded nearly equivalent MICs or minimum effective concentrations against diverse Candida spp. and Aspergillus spp. Consistent with a direct drug interaction, serum decreased the sensitivity of glucan synthase to echinocandin drugs.
Learning from global emissions scenarios

Scenarios of global greenhouse gas emissions have played a key role in climate change analysis for over twenty years. Currently, several research communities are organizing to undertake a new round of scenario development in the lead-up to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change (IPCC). To help inform this process, we assess a number of past efforts to develop and learn from sets of global greenhouse gas emissions scenarios. We conclude that while emissions scenario exercises have likely had substantial benefits for participating modeling teams and produced insights from individual models, learning from the exercises taken as a whole has been more limited. Model comparison exercises have typically focused on the production of large numbers of scenarios while investing little in assessing the results or the production process, perhaps on the assumption that later assessment efforts could play this role. However, much of this assessment potential remains untapped. Efforts such as scenario-related chapters of IPCC reports have been most informative when they have gone to extra lengths to carry out more specific comparison exercises, but in general these assessments do not have the remit or resources to carry out the kind of detailed analysis of scenario results necessary for drawing the most useful conclusions. We recommend that scenario comparison exercises build-in time and resources for assessing scenario results in more detail at the time when they are produced, that these exercises focus on more specific questions to improve the prospects for learning, and that additional scenario assessments are carried out separately from production exercises. We also discuss the obstacles to better assessment that might exist, and how they might be overcome. Finally, we recommend that future work include much greater emphasis on understanding how scenarios are actually used, as a guide to improving scenario production.
An algorithm for Boolean satisfiability based on generalized orthonormal expansion

This paper proposes an algorithm for deciding consistency of systems of Boolean equations in several variables with co-efficients in the two element Booleanalgebra B0 = {0,1} and find all satisfying assignments based on the generalized Boole-Shannon orthonormal (ON) expansion discussed in [11]. Paper [11] develops a condition for consistency of the equation f(X) = 0 for the special classes of Boolean functions 1) f in B(�(X)) for an ON ✷
Dynamic Hydraulic Conductivity Reconciles Mismatch Between Modeled and Observed Winter Subglacial Water Pressure

The link between subglacial hydrology and basal sliding has prompted work on basal hydrology models with water pressure and drainage capacity as prognostic variables. We find that the Glacier Drainage System model, which belongs to a commonly used family of subglacial hydrology models that include both channelized and distributed drainage components, underpredicts winter water pressure when compared to borehole observations from western Greenland given a wide range of plausible parameter values and inputs. This problem, though previously noted by other modelers, has not been addressed. Possible causes for the discrepancy including idealized model inputs or unconstrained parameters are investigated through a series of modeling experiments on both synthetic and realistic ice sheet geometries. Numerical experiments reveal that englacial storage and hydraulic conductivity in the distributed system are the primary controls on winter water pressure in Glacier Drainage System model. Observations of temperate layer thickness and englacial water content from western Greenland imply an upper bound on englacial storage, suggesting that a reduction in hydraulic conductivity is the most plausible cause of high winter water pressure. We conclude that hydraulic conductivity acts as a proxy for the subgrid‐scale connectivity of the linked cavity system and should therefore change seasonally in correspondence with melt water availability.
Spoken Language Outcomes after Hemispherectomy: Factoring in Etiology

We analyzed postsurgery linguistic outcomes of 43 hemispherectomy patients operated on at UCLA. We rated spoken language (Spoken Language Rank, SLR) on a scale from 0 (no language) to 6 (mature grammar) and examined the effects of side of resection/damage, age at surgery/seizure onset, seizure control postsurgery, and etiology on language development. Etiology was defined as developmental (cortical dysplasia and prenatal stroke) and acquired pathology (Rasmussen's encephalitis and postnatal stroke). We found that clinical variables were predictive of language outcomes only when they were considered within distinct etiology groups. Specifically, children with developmental etiologies had lower SLRs than those with acquired pathologies (p =.0006); age factors correlated positively with higher SLRs only for children with acquired etiologies (p =.0006); right-sided resections led to higher SLRs only for the acquired group (p =.0008); and postsurgery seizure control correlated positively with SLR only for those with developmental etiologies (p =.0047). We argue that the variables considered are not independent predictors of spoken language outcome posthemispherectomy but should be viewed instead as characteristics of etiology.
Do all fragments count?

We aim at finding the minimal set of fragments that achieves maximal parse accuracy in Data Oriented Parsing (DOP). Experiments with the Penn Wall Street Journal (WSJ) treebank show that counts of almost arbitrary fragments within parse trees are important, leading to improved parse accuracy over previous models tested on this treebank. We isolate a number of dependency relations which previous models neglect but which contribute to higher accuracy. We show that the history of statistical parsing models displays a tendency towards using more and larger fragments from training data.
Development of a Questionnaire to Assess Attitudes and Beliefs toward Organ Donation among Asians

In the United Kingdom, people from the Indian subcontinent have a higher incidence of kidney failure, are less likely to receive a kidney transplant, and have a higher mortality rate from renal disease. In addition, Asians are reluctant donors; white people make up 95% of the donor pool. We developed a questionnaire to determine the knowledge and attitudes toward organ donation in the Asian communities. The setting was a public forum; the aims were (1) to study the attitudes of Asians toward organ donation, (2) to validate our questionnaire, and (3) to initiate a campaign of increasing awareness of organ donation and transplantation in the Asian community in the greater Glasgow area. Our survey suggested that Asians have an awareness of organ donation and transplantation, and they would donate an organ to a family member; however, they did not carry a donor card. Respondents unanimously agreed that lobbying by religious leaders was the best means to promote awareness.
The C‐terminus of viral vascular endothelial growth factor‐E partially blocks binding to VEGF receptor‐1

Vascular endothelial growth factor (VEGF) family members play important roles in embryonic development and angiogenesis during wound healing and in pathological conditions such as tumor formation. Parapoxviruses express a new member of the VEGF family which is a functional mitogen that specifically activates VEGF receptor (VEGFR)‐2 but not VEGFR‐1. In this study, we show that deletion from the viral VEGF of a unique C‐terminal region increases both VEGFR‐1 binding and VEGFR‐1‐mediated monocyte migration. Enzymatic removal of O‐linked glycosylation from the C‐terminus also increased VEGFR‐1 binding and migration of THP‐1 monocytes indicating that both the C‐terminal residues and O‐linked sugars contribute to blocking viral VEGF binding to VEGFR‐1. The data suggest that conservation of the C‐terminal residues throughout the viral VEGF subfamily may represent a means of reducing the immunostimulatory activities associated with VEGFR‐1 activation while maintaining the ability to induce angiogenesis via VEGFR‐2.
Papaya Extract to Treat Dengue: A Novel Therapeutic Option?

Dengue is a viral disease that today affects a vast number of people in over 125 countries and is responsible for a sizable number of deaths. In the absence of an effective antiviral drug to treat the disease, various treatments are being investigated. Studies have indicated that the juice of the leaves of the Carica papaya plant from the family Caricaceae could help to increase the platelet levels in these patients. This review describes some of the published studies on this topic. The search was done independently by the two authors using PubMed, Google and the library database and included relevant articles of the last 10 years. A total of 7 studies were included in this review, which were one animal study, one case report, three case series and two randomized controlled trials. Although many of the studies and case reports published in literature lack adequate information, some of the studies do raise the possibility that this treatment could be an important option in the future. Further large-scale studies could establish the usefulness or ineffectiveness of this natural product in the treatment of dengue.
Direct Isosurface Extraction from Scattered Volume Data

Isosurface extraction is a standard visualization method for scalar volume data and has been subject to research for decades. Nevertheless, to our knowledge, no isosurface extraction method exists that directly extracts surfaces from scattered volume data without 3D mesh generation or reconstruction over a structured grid. We propose a method based on spatial domain partitioning using a kd-tree and an indexing scheme for efficient neighbor search. Our approach consists of a geometry extraction and a rendering step. The geometry extraction step computes points on the isosurface by linearly interpolating between neighboring pairs of samples. The neighbor information is retrieved by partitioning the 3D domain into cells using a kd-tree. The cells are merely described by their index and bitwise index operations allow for a fast determination of potential neighbors. We use an angle criterion to select appropriate neighbors from the small set of candidates. The output of the geometry step is a point cloud representation of the isosurface. The final rendering step uses point-based rendering techniques to visualize the point cloud. Our direct isosurface extraction algorithm for scattered volume data produces results of quality close to the results from standard isosurface extraction algorithms for gridded volume data (like marching cubes). In comparison to 3D mesh generation algorithms (like Delaunay tetrahedrization), our algorithm is about one order of magnitude faster for the examples used in this paper.
Regional Variation in the Mechanical and Microstructural Properties of the Human Anterior Cruciate Ligament

Background: The anteromedial (AM) bundle of the anterior cruciate ligament (ACL) has a higher modulus and failure stress than does the posterolateral (PL) bundle. However, it is unknown how these properties vary within each bundle. Purpose: To quantify mechanical and microstructural properties of samples within ACL bundles to elucidate any regional variation across the ligament. We hypothesized that there are no differences within each bundle in contrast to cross-bundle variation. Study Design: Descriptive laboratory study. Methods: Sixteen human ACLs were dissected into AM and PL bundles. Three samples were taken from each bundle in an ordered sequence from AM (region 1 AM bundle) to PL (region 6 PL bundle). Each sample was tested in uniaxial tension, using quantitative polarized light imaging (QPLI) to quantify collagen fiber alignment. After preconditioning, samples were subjected to a stress-relaxation (SR) test followed by quasistatic ramp-to-failure (RF). Peak and equilibrium stress values were computed from the SR test and modulus quantified in the toe- and linear-regions of the RF. QPLI values describing collagen orientation (angle of polarization [AoP]) and strength of alignment (degree of linear polarization [DoLP]) were computed for the SR test and at points corresponding to the zero, transition point, and linear region of the RF. Results: Toe- and linear-region modulus values decreased from region 1 to 6. Slopes of regression lines increased for the average DoLP during RF, with significance at higher strains. The standard deviation of AoP values decreased during RF, indicating tighter distribution of orientation angles, with significant correlations at all points of the RF. During SR, stress values uniformly decreased but did not show significant linear regression by region. DoLP and AoP values changed slightly during SR and demonstrated significant linear variation by region at both peak and equilibrium points. Conclusion: Most microstructural and material properties evaluated in this study appear to follow a linear gradient across the ACL, rather than varying by bundle. Clinical Relevance: This AM-to-PL variation provides a more accurate description of functional tissue anatomy and can be used to assess and guide techniques of ACL reconstruction.
Characterizing Afterslip and Ground Displacement Rate Increase Following the 2014 Iquique‐Pisagua Mw 8.1 Earthquake, Northern Chile

The 2014 Iquique‐Pisagua Mw 8.1 earthquake ruptured only parts of the 1877 Northern Chile‐Southern Peru seismic gap. Here we present a comprehensive analysis of 152 continuous and campaign Global Positioning System time series that captured more than a decade of interseismic loading prior to the event and 2 years of afterslip. In high spatiotemporal resolution, our data document upper plate response not only at the coseismically affected latitudes but also at the adjacent Loa plate segment to the south. Using a combination of elastic and viscoelastic half‐space models of different stages of the seismic cycle, we found that the highly coupled, former seismic gap contains a narrow low coupling zone at 21°S latitude. Just after the 2014 earthquake, this zone acts as a barrier impeding afterslip to continue southward. Possible reasons for this impediment could involve crustal heterogeneities or coupling discontinuities at the plate interface. After 2 years, afterslip cumulates to a maximum of ~89 cm and becomes negligible. Global Positioning System observations south of the inferred seismotectonic barrier reveal a deformation rate increase in the second year after the event. Our slip models suggest that this could be caused by a downdip coupling increase, perhaps bringing the highly coupled southern Loa segment closer to failure. Taken together, our results reveal (1) the interaction between different areas undergoing stress release and stress buildup in a major seismic gap, (2) constraints for the temporal variation of coupling degree in different stages of the seismic cycle, and (3) the influence of large earthquakes at adjacent segments.