Miracle-dz/UniFAR-FTUs huggingface dataset:
Inflammation-based prognostic scores predict disease severity in patients with acute cholecystitis

Background Although several investigators have reported that inflammation-based prognostic scores can predict disease severity in patients with various inflammatory diseases, whether or not these scores are associated with disease severity in patients with acute cholecystitis (AC) has not yet been fully clarified. Patients and methods Two hundred and sixty-two patients with AC were reviewed retrospectively. We evaluated the correlations between demographic or clinical variables, including the neutrophil-to-lymphocyte ratio (NLR), the Glasgow Prognostic Score (GPS), the modified Glasgow Prognostic Score (mGPS), and the C-reactive protein/albumin (CRP/Alb) ratio, as well as the disease severity grade on the basis of the revised Tokyo guidelines. Multivariate analyses were carried out to identify the clinical parameters associated with disease severity grade. Results The NLR (P<0.0001), GPS (P<0.0001), mGPS (P<0.0001), and CRP/Alb ratio (P<0.0001) were all elevated according to the severity grade. Multivariate analyses showed that the NLR [odds ratio (OR)=3.41–4.77; P<0.005], GPS (OR=2.49; P=0.012), mGPS (OR=2.79; P=0.005), and the CRP/Alb ratio (OR=12.53; P<0.0001) were associated independently with grade II/III AC. The value of the area under the curve of the CRP/Alb ratio (continuous 0.759) or NLR (continuous 0.753) was higher than that of other inflammation-based prognostic scores for diagnosing ≥grade II AC, grade III AC, respectively. Conclusion Inflammation-based prognostic scores could predict the severity grade independently in patients with AC. These scores may play a complementary role in predicting disease severity in patients with AC in conjunction with the Tokyo guidelines severity grade.
Yukawa unification predictions for the LHC

This paper is divided into two parts. In the first part we analyze the consequences, for the LHC, of gauge and third family Yukawa coupling unification with a particular set of boundary conditions defined at the GUT scale. We perform a global chi^2 analysis including the observables M_W, M_Z, G_F, 1/alpha_em, alpha_s(M_Z), M_t,m_b(m_b), M_tau, BR(B -> X_s gamma), BR(B_s -> mu^+ mu^-) and M_h. The fit is performed in the MSSM in terms of 9 GUT scale parameters, while tan beta and mu are fixed at the weak scale. Good fits suggest an upper bound on the gluino mass, M_gluino \lesssim 2 TeV. This constraint comes predominantly from fitting the bottom quark and Higgs masses (assuming a 125 GeV Higgs). Gluinos should be visible at the LHC in the 14 TeV run but they cannot be described by the typical simplified models. This is because the branching ratios for gluino -> t tbar neutralino, b bbar neutralino, t bbar chargino^-, b tbar chargino^+, g neutralino are comparable. Stops and sbottoms may also be visible. Charginos and neutralinos can be light with the LSP predominantly bino-like. In the second part of the paper we analyze a complete three family model and discuss the quality of the global chi^2 fits and the differences between the third family analysis and the full three family analysis for overlapping observables. We note that the light Higgs in our model couples to matter like the Standard Model Higgs. Any deviation from this would rule out this model.
Social capital and PTSD among PLWHA in China: the mediating role of resilience and internalized stigma

Abstract Post-traumatic Stress Disorder (PTSD) is frequent among people living with HIV/AIDS (PLWHA). Few studies have investigated social-psychological predictors of PTSD in China. This study aimed to examine relationships between social capital, stigma, resilience and PTSD among PLWHA in China, and to provide effective suggestions for PTSD intervention. A cross-sectional study of 520 PLWHA was conducted from November 2015 to January 2016. Survey data were collected using anonymous self-reported questionnaire. Multivariable analyses were used to examine related factors of PTSD, and causal mediation analyses were conducted to assess whether stigma and resilience were mediators. Results indicated that higher risk of PTSD was independent associated with stronger stigma, decreasing social capital and lower resilience. There was an indirect relationship of social capital on PTSD mediated through resilience and HIV-related stigma. Therefore, PTSD intervention programs should not only pay attention to the role of social capital on PTSD, but also attach importance to stigma and resilience on PTSD symptoms.
Quantitative proteomics in plant protease substrate identification.

Contents Summary 936 I. Introduction 936 II. The quest for plant protease substrates - proteomics to the rescue? 937 III. Quantitative proteome comparison reveals candidate substrates 938 IV. Dynamic metabolic stable isotope labeling to measure protein turnover in vivo 938 V. Terminomics - large-scale identification of protease cleavage sites 939 VI. Substrate or not substrate, that is the question 940 VII. Concluding remarks 941 Acknowledgements 941 References 941 SUMMARY: Proteolysis is a central regulatory mechanism of protein homeostasis and protein function that affects all aspects of plant life. Higher plants encode for hundreds of proteases, but their physiological substrates and hence their molecular functions remain mostly unknown. Current quantitative mass spectrometry-based proteomics enables unbiased large-scale interrogation of the proteome and its modifications. Here we provide an overview of proteomics techniques that allow profiling of changes in protein abundance, measurement of proteome turnover rates, identification of protease cleavage sites in vivo and in vitro and determination of protease sequence specificity. We discuss how these techniques can help to reveal protease substrates and determine plant protease function, illustrated by recent studies on selected plant proteases.
The Herschel Multi-tiered Extragalactic Survey: SPIRE-mm photometric redshifts

We investigate the potential of submmmm and submmmmradio photometric redshifts using a sample of mm-selected sources as seen at 250, 350 and 500 mu m by the SPIRE instrument on Herschel. From a sample of 63 previously identified mm sources with reliable radio identifications in the Great Observatories Origins Deep Survey North and Lockman Hole North fields, 46 (73 per cent) are found to have detections in at least one SPIRE band. We explore the observed submm/mm colour evolution with redshift, finding that the colours of mm sources are adequately described by a modified blackbody with constant optical depth tau=(/nu0)beta, where beta=+1.8 and nu 0=c/100 mu m. We find a tight correlation between dust temperature and IR luminosity. Using a single model of the dust temperature and IR luminosity relation, we derive photometric redshift estimates for the 46 SPIRE-detected mm sources. Testing against the 22 sources with known spectroscopic or good quality optical/near-IR photometric redshifts, we find submm/mm photometric redshifts offer a redshift accuracy of vertical bar Delta z vertical bar/(1+z)= 0.16 (\textlessvertical bar Delta z vertical bar \textgreater=0.51). Including constraints from the radiofar-IR correlation, the accuracy is improved to vertical bar Delta z vertical bar/(1+z)=0.15 (\textlessvertical bar Delta z vertical bar \textgreater=0.45). We estimate the redshift distribution of mm-selected sources finding a significant excess at z \textgreater 3 when compared to similar to 850 mu m selected samples.
Spirometric reference equations for Swedish adults

New spirometric reference equations for Swedish adults are required. Three different older sets of reference equations clinically used in Sweden have various drawbacks and the recently published ‘The Global Lung Function 2012 (GLI) equations’ have been shown not to be adequate for Swedish normal, healthy non‐smokers. We have recently concluded that a piecewise linear model presented by Lubinski and Gólczewski accurately describes the distribution of spirometric variables in a large Swedish random population sample. This piecewise linear model also offers the important advantage of implementing easily physiologically interpretable coefficients. The present study aimed at presenting piecewise linear reference equations for Swedish adults based on a random population sample of 6685 individuals aged 25–75 years. Predicted normal values by the piecewise linear reference equations and lower limit normal (LLN) were compared with the three reference equations frequently used clinically in Sweden and the GLI equations. We found predicted normal values according to the present piecewise linear reference equations close to 100% predicted normal as expected, whereas the other equations either overestimated or underestimated normal subjects. Concerning LLN, the present equations, i.e. 1·645 × RSD, showed the least deviation from the expected 5% and, e.g., the GLI equations systematically identified too few subjects below LLN. We conclude that the present piecewise linear reference equations, based on a relatively large general population sample, ought to be considered for clinical use in Sweden. Application of 1·645 × RSD below predicted value gave an acceptably accurate LLN.
Cytotoxic effect of spermine on retinal pigment epithelial cells.

PURPOSE A prior study showed inactivation of ornithine-delta-aminotransferase (OAT)-deficient human retinal pigment epithelial (RPE) cells by a specific irreversible inhibitor (5-fluoromethylornithine; 5-FMO) leading to cell death, in an in vitro model of gyrate atrophy (GA) of the choroid and retina. In the present study, the cytotoxicity of metabolites of ornithine, especially spermine, in RPE cells was investigated, to clarify the mechanism of ornithine cytotoxicity in RPE cells. METHODS RPE cells were incubated with ornithine or compounds involved in ornithine metabolic pathways. The effects on RPE cell viability and proliferative activity were evaluated using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) colorimetric and [(3)H]thymidine incorporation assays. Incorporation of spermine into RPE cells was examined by using [(14)C]spermine and dansyl-spermine. To assess spermine-induced RPE cell death, cells were double stained with annexin V and propidium iodide and subjected to flow cytometry. RESULTS Ornithine, arginine, glutamate, proline, creatine, glycine, and putrescine exhibited no effects on the viability and proliferative activities of RPE cells, whereas spermidine and spermine (10 mM) inhibited [(3)H]thymidine incorporation by 13% and 89%, respectively. The inhibition of [(3)H]thymidine incorporation by spermine was dose dependent and was observed as early as 4 hours after addition. Further, spermine was incorporated and accumulated in the perinuclear region of RPE cells. Apoptotic RPE cell death was induced by spermine in a dose-dependent manner. CONCLUSIONS The present results demonstrated that excessive spermine is cytotoxic to RPE cells and suggest that metabolites of ornithine, especially spermine, may be involved in the mechanism of RPE degeneration in GA.
Body composition and physical fitness in women with bulimia nervosa or binge‐eating disorder

Abstract Objective Knowledge about physical fitness in women with bulimia nervosa (BN) or binge‐eating disorder (BED) is sparse. Previous studies have measured physical activity largely through self‐report, and physical fitness variables are mainly restricted to body mass index (BMI) and bone mineral density. We expanded the current knowledge in these groups by including a wider range of physical fitness indicators and objective measures of physical activity, assessed the influence of a history of anorexia nervosa (AN), and evaluated predictive variables for physical fitness. Method Physical activity, blood pressure, cardiorespiratory fitness (CRF), muscle strength, body composition, and bone mineral density were measured in 156 women with BN or BED, with mean (SD) age 28.4 years (5.7) and BMI 25.3 (4.8) kg m−2. Results Level of physical activity was higher than normative levels, still <50% met the official physical activity recommendation. Fitness in women with BN were on an average comparable with recommendations or normative levels, while women with BED had lower CRF and higher BMI, VAT, and body fat percentage. We found 10–12% with masked obesity. A history of AN did not predict current physical fitness, still values for current body composition were lower when comparing those with history of AN to those with no such history. Discussion Overall, participants with BN or BED displayed adequate physical fitness; however, a high number had unfavorable CRF and body composition. This finding calls for inclusion of physical fitness in routine clinical examinations and guided physical activity and dietary recommendations in the treatment of BN and BED.
An Ingestion and Analytics Architecture for IoT Applied to Smart City Use Cases

As sensors are adopted in almost all fields of life, the Internet of Things (IoT) is triggering a massive influx of data. We need efficient and scalable methods to process this data to gain valuable insight and take timely action. Existing approaches which support both batch processing (suitable for analysis of large historical data sets) and event processing (suitable for real-time analysis) are complex. We propose the hut architecture, a simple but scalable architecture for ingesting and analyzing IoT data, which uses historical data analysis to provide context for real-time analysis. We implement our architecture using open source components optimized for Big Data applications and extend them, where needed. We demonstrate our solution on two real-world smart city use cases in transportation and energy management.
Variable Sensitivity of CCR5-Tropic Human Immunodeficiency Virus Type 1 Isolates to Inhibition by RANTES Analogs

Aminooxypentane (AOP)-RANTES efficiently and specifically blocks entry of non-syncytium-inducing (NSI), CCR5-tropic (R5) human immunodeficiency virus type 1 (HIV-1) into host cells. Inhibition appears to be mediated by increased intracellular retention of the CCR5 coreceptor- AOP-RANTES complex and/or competitive binding of AOP-RANTES with NSI R5 HIV-1 isolates for CCR5. Although AOP-RANTES and other β-chemokine analogs are potent inhibitors, the extreme heterogeneity of the HIV-1 envelope glycoproteins (gp120 and gp41) and variable coreceptor usage may affect the susceptibility of variant HIV-1 strains to these drugs. Using the same peripheral blood mononuclear cells (PBMC) with all isolates, we observed a significant variation in AOP-RANTES inhibition of 13 primary NSI R5 isolates; 50% inhibitory concentrations (IC50) ranged from 0.04 nM with HIV-1A-92RW009 to 1.3 nM with HIV-1B-BaL. Experiments performed on the same isolate (HIV-1B-BaL) with PBMC from different donors revealed no isolate-specific variation in AOP-RANTES IC50 values but did show a considerable difference in virus replication efficiency. Exclusive entry via the CCR5 coreceptor by these NSI R5 isolates suggests that variable inhibition by AOP-RANTES is not due to alternative coreceptor usage but rather differential CCR5 binding. Analysis of the envelope V3 loop sequence linked a threonine or arginine at position 319 (numbering based on the HXB2 genome) with AOP-RANTES resistance. With the exception of one isolate, A319 was associated with increased sensitivity to AOP-RANTES inhibition. Distribution of AOP-RANTES IC50 values with these isolates has promoted ongoing screens for new CCR5 agonists that show broad inhibition of HIV-1 variants.
5G Wireless Network Slicing for eMBB, URLLC, and mMTC: A Communication-Theoretic View

The grand objective of 5G wireless technology is to support three generic services with vastly heterogeneous requirements: enhanced mobile broadband (eMBB), massive machine-type communications (mMTCs), and ultra-reliable low-latency communications (URLLCs). Service heterogeneity can be accommodated by network slicing, through which each service is allocated resources to provide performance guarantees and isolation from the other services. Slicing of the radio access network (RAN) is typically done by means of orthogonal resource allocation among the services. This paper studies the potential advantages of allowing for non-orthogonal sharing of RAN resources in uplink communications from a set of eMBB, mMTC, and URLLC devices to a common base station. The approach is referred to as heterogeneous non-orthogonal multiple access (H-NOMA), in contrast to the conventional NOMA techniques that involve users with homogeneous requirements and hence can be investigated through a standard multiple access channel. The study devises a communication-theoretic model that accounts for the heterogeneous requirements and characteristics of the three services. The concept of reliability diversity is introduced as a design principle that leverages the different reliability requirements across the services in order to ensure performance guarantees with non-orthogonal RAN slicing. This paper reveals that H-NOMA can lead, in some regimes, to significant gains in terms of performance tradeoffs among the three generic services as compared to orthogonal slicing.
Structural Pathways Supporting Swift Acquisition of New Visuomotor Skills

Abstract Human skill learning requires fine‐scale coordination of distributed networks of brain regions linked by white matter tracts to allow for effective information transmission. Yet how individual differences in these anatomical pathways may impact individual differences in learning remains far from understood. Here, we test the hypothesis that individual differences in structural organization of networks supporting task performance predict individual differences in the rate at which humans learn a visuomotor skill. Over the course of 6 weeks, 20 healthy adult subjects practiced a discrete sequence production task, learning a sequence of finger movements based on discrete visual cues. We collected structural imaging data, and using deterministic tractography generated structural networks for each participant to identify streamlines connecting cortical and subcortical brain regions. We observed that increased white matter connectivity linking early visual regions was associated with a faster learning rate. Moreover, the strength of multiedge paths between motor and visual modules was also correlated with learning rate, supporting the potential role of extended sets of polysynaptic connections in successful skill acquisition. Our results demonstrate that estimates of anatomical connectivity from white matter microstructure can be used to predict future individual differences in the capacity to learn a new motor‐visual skill, and that these predictions are supported both by direct connectivity in visual cortex and indirect connectivity between visual cortex and motor cortex.
How to Integrate HIV and Sexual and Reproductive Health Services in Namibia, the Epako Clinic Case Study

Introduction: During the past two decades, HIV and Sexual and Reproductive Health services in Namibia have been provided in silos, with high fragmentation. As a consequence of this, quality and efficiency of services in Primary Health Care has been compromised. Methods: We conducted an operational research (observational pre-post study) in a public health facility in Namibia. A health facility assessment was conducted before and after the integration of health services. A person-centred integrated model was implemented to integrate all health services provided at the health facility in addition to HIV and Sexual and Reproductive Health services. Comprehensive services are provided by each health worker to the same patients over time (longitudinality), on a daily basis (accessibility) and with a good external referral system (coordination). Prevalence rates of time flows and productivity were done. Results: Integrated services improved accessibility, stigma and quality of antenatal care services by improving the provider-patient communication, reducing the time that patients stay in the clinic in 16% and reducing the waiting times in 14%. In addition, nurse productivity improved 85% and the expected time in the health facility was reduced 24% without compromising the uptake of TB, HIV, outpatient, antenatal care or first visit family planning services. Given the success on many indicators resulting from integration of services, the goal of this paper was to describe “how” health services have been integrated, the “process” followed and presenting some “results” from the integrated clinic. Conclusions: Our study shows that HIV and SRH services can be effectively integrated by following the person-centred integrated model. Based on the Namibian experience on “how” to integrate health services and the “process” to achieve it, other African countries can replicate the model to move away from the silo approach and contribute to the achievement of Universal Health Coverage.
Adherence to Methodological Standards in Research Using the National Inpatient Sample

Importance Publicly available data sets hold much potential, but their unique design may require specific analytic approaches. Objective To determine adherence to appropriate research practices for a frequently used large public database, the National Inpatient Sample (NIS) of the Agency for Healthcare Research and Quality (AHRQ). Design, Setting, and Participants In this observational study of the 1082 studies published using the NIS from January 2015 through December 2016, a representative sample of 120 studies was systematically evaluated for adherence to practices required by AHRQ for the design and conduct of research using the NIS. Exposures None. Main Outcomes and Measures All studies were evaluated on 7 required research practices based on AHRQ’s recommendations and compiled under 3 domains: (1) data interpretation (interpreting data as hospitalization records rather than unique patients); (2) research design (avoiding use in performing state-, hospital-, and physician-level assessments where inappropriate; not using nonspecific administrative secondary diagnosis codes to study in-hospital events); and (3) data analysis (accounting for complex survey design of the NIS and changes in data structure over time). Results Of 120 published studies, 85% (n = 102) did not adhere to 1 or more required practices and 62% (n = 74) did not adhere to 2 or more required practices. An estimated 925 (95% CI, 852-998) NIS publications did not adhere to 1 or more required practices and 696 (95% CI, 596-796) NIS publications did not adhere to 2 or more required practices. A total of 79 sampled studies (68.3% [95% CI, 59.3%-77.3%]) among the 1082 NIS studies screened for eligibility did not account for the effects of sampling error, clustering, and stratification; 62 (54.4% [95% CI, 44.7%-64.0%]) extrapolated nonspecific secondary diagnoses to infer in-hospital events; 45 (40.4% [95% CI, 30.9%-50.0%]) miscategorized hospitalizations as individual patients; 10 (7.1% [95% CI, 2.1%-12.1%]) performed state-level analyses; and 3 (2.9% [95% CI, 0.0%-6.2%]) reported physician-level volume estimates. Of 27 studies (weighted; 218 studies [95% CI, 134-303]) spanning periods of major changes in the data structure of the NIS, 21 (79.7% [95% CI, 62.5%-97.0%]) did not account for the changes. Among the 24 studies published in journals with an impact factor of 10 or greater, 16 (67%) did not adhere to 1 or more practices, and 9 (38%) did not adhere to 2 or more practices. Conclusions and Relevance In this study of 120 recent publications that used data from the NIS, the majority did not adhere to required practices. Further research is needed to identify strategies to improve the quality of research using the NIS and assess whether there are similar problems with use of other publicly available data sets.