julilili42/papers huggingface dataset:
Leptospirosis among Returned Travelers: A GeoSentinel Site Survey and Multicenter Analysis—1997–2016
2018-05-15

Leptospirosis is a potentially fatal emerging zoonosis with worldwide distribution and a broad range of clinical presentations and exposure risks. It typically affects vulnerable populations in (sub)tropical countries but is increasingly reported in travelers as well. Diagnostic methods are cumbersome and require further improvement. Here, we describe leptospirosis among travelers presenting to the GeoSentinel Global Surveillance Network. We performed a descriptive analysis of leptospirosis cases reported in GeoSentinel from January 1997 through December 2016. We included 180 travelers with leptospirosis (mostly male; 74%; mostly tourists; 81%). The most frequent region of infection was Southeast Asia (52%); the most common source countries were Thailand ( N = 52), Costa Rica ( N = 13), Indonesia, and Laos ( N = 11 each). Fifty-nine percent were hospitalized; one fatality was reported. We also distributed a supplemental survey to GeoSentinel sites to assess clinical and diagnostic practices. Of 56 GeoSentinel sites, three-quarters responded to the survey. Leptospirosis was reported to have been most frequently considered in febrile travelers with hepatic and renal abnormalities and a history of freshwater exposure. Serology was the most commonly used diagnostic method, although convalescent samples were reported to have been collected infrequently. Within GeoSentinel, leptospirosis was diagnosed mostly among international tourists and caused serious illness. Clinical suspicion and diagnostic workup among surveyed GeoSentinel clinicians were mainly triggered by a classical presentation and exposure history, possibly resulting in underdiagnosis. Suboptimal usage of available diagnostic methods may have resulted in additional missed, or misdiagnosed, cases.
Fast Abdominal Contrast-Enhanced Imaging With High Parallel-Imaging Factors Using a 60-Channel Receiver Coil Setup
2018-05-15

Purpose The aim of this study was to assess a novel 60-channel receiver body coil (B60) setup for accelerated contrast-enhanced abdominal magnetic resonance imaging (MR) imaging with respect to signal-to-noise ratio (SNR) and image quality using high parallel-imaging technique (PAT) factors in comparison to a standard 30-channel coil setup. Methods All imaging data were acquired on a 3 T MR scanner using a novel B60 receiver coil setup in comparison to a standard 30-channel setup serving as reference standard. Phantom measurements were performed to systematically evaluate SNR and geometry factor performance in an ex vivo setting. To assess the in vivo application, additional measurements in 5 healthy volunteers and 17 patients were performed using a 3-dimensional T1w gradient-echo sequences with different acceleration factors. At first, the volunteers were examined. In a second step, standard contrast-enhanced abdominal images were acquired in the 17 patients, who were randomly assigned into 2 groups (group A: 60-channel, n = 8; group B: 30-channel, n = 9). Image quality, noise, lesion conspicuity, and artifacts were assessed by 2 radiologists independently on a 5-point Likert scale (5 = excellent). Results The phantom study revealed substantial advantages (SNR and geometry factor) of the B60 coil for measurements in the head-to-feet phase encoding direction, whereas only minor differences were found in other directions. Comparison of image quality in volunteers revealed significantly higher ratings of the B60 setup for all acquisitions ( P ≤ 0.032), except for PAT = none. In patients, similar results were observed with comparable image quality at lower PAT factors and significantly superior image quality of the B60 setup for higher PAT factors (2 × 2 and 3 × 2; P = 0.008). Conclusions The 60-channel coil setup facilitates improved SNR and image quality at high PAT factors with diagnostic image quality, which allows for accelerated contrast-enhanced MR imaging of the abdomen.
Efficacy and safety of MK‐1293 insulin glargine compared with originator insulin glargine (Lantus) in type 2 diabetes: A randomized, open‐label clinical trial
2018-05-15

Aim To compare the efficacy and safety of MK‐1293 insulin glargine (Mk‐Gla) and Lantus (Sa‐Gla) in people with type 2 diabetes mellitus (T2DM). Materials and methods This Phase 3, randomized, active‐controlled, open‐label, 24‐week clinical trial ( ClinicalTrials.gov number NCT02059187) enrolled 531 participants with T2DM (HbA1c ≤11.0%) either eligible for or currently taking basal insulin (≥10 U/day). Participants were randomized 1:1 to once‐daily Mk‐Gla (n = 263) or Sa‐Gla (n = 263). Titration of insulin was guided by a fasting plasma glucose (FPG)‐based dosing algorithm. The primary efficacy objective was to demonstrate the non‐inferiority of change from baseline in HbA1c (margin of 0.40% [4.4 mmol/mol]) with Mk‐Gla versus Sa‐Gla after 24 weeks. The primary safety objective was anti‐insulin antibody development after 24 weeks. Results For Mk‐Gla and Sa‐Gla, the least squares (LS) mean HbA1c change from baseline (95% CI) was −1.28 (−1.41, −1.15)% (−14.0 [−15.4, −12.6] mmol/mol) and −1.30 (−1.43, −1.18)% (−14.2 [−15.6, −12.8] mmol/mol). The LS mean HbA1c difference (Mk‐Gla minus Sa‐Gla) was 0.03 (−0.12, 0.18)% (0.3 [−1.4, 1.9] mmol/mol), meeting non‐inferiority and equivalence (secondary objective) criteria. Insulin doses, FPG, and seven‐point plasma glucose profiles were similar between groups. Safety and tolerability, including anti‐insulin antibody responses, hypoglycaemia, adverse events and body weight, were similar between insulins. The efficacy and safety of Mk‐Gla and Sa‐Gla were similar both in participants who were insulin‐treated or insulin‐naïve at baseline. Conclusions Mk‐Gla and Sa‐Gla demonstrated similar efficacy and safety over 24 weeks of treatment in people with T2DM.
Short article: Influence of regulatory NLRC5 variants on colorectal cancer survival and 5-fluorouracil-based chemotherapy
2018-05-15

Background NLRC5 is an interferon γ-inducible protein, which plays a role in immune surveillance with a potential influence on cancer survival. Objective We aimed to evaluate the effect of potential regulatory variants in NLRC5 on overall survival and survival after 5-fluorouracil (5-FU)-based therapy of colorectal cancer (CRC) patients. Patients and methods We carried out a case-only study in a Czech population of 589 cases; 232 received 5-FU-based therapy. Eleven variants within NLRC5 were selected using in-silico tools. Associations between polymorphisms and survival were assessed by Cox regression analysis adjusting for age at diagnosis, sex, and TNM stage. Survival curves were derived using the Kaplan–Meier method. Results Two variants showed a significant association with survival. All patients and metastasis-free patients at the time of diagnosis (pM0) who were homozygous carriers of the minor allele of rs27194 had a decreased overall survival (OS all and OS pM0 ) and event-free survival (EFS pM0 ) under a recessive model (OS all P =0.003, OS pM0 P =0.005, EFS pM0 P =0.01, respectively). OS was also decreased for all patients and for pM0 patients who carried at least one minor allele of rs289747 (OS all P =0.03 and OS pM0 P =0.003, respectively). Among CRC patients, who underwent a 5-FU-based adjuvant regimen, rs12445252 was associated with OS all , OS pM0 and EFS pM0 , according to the dosage of the minor allele T (OS all P =0.0004, OS pM0 P =0.0001, EFS pM0 P =0.008, respectively). Conclusion Our results showed that polymorphisms in NLRC5 may be used as prognostic markers of survival of CRC patients, as well as for survival in response to 5-FU treatment.
Physical and cognitive doping in university students using the unrelated question model (UQM): Assessing the influence of the probability of receiving the sensitive question on prevalence estimation
2018-05-15

Study objectives: In order to increase the value of randomized response techniques (RRTs) as tools for studying sensitive issues, the present study investigated whether the prevalence estimate for a sensitive item π̂ assessed with the unrelated questionnaire method (UQM) is influenced by changing the probability of receiving the sensitive question p. Material and methods: A short paper-and-pencil questionnaire was distributed to 1.243 university students assessing the 12-month prevalence of physical and cognitive doping using two versions of the UQM with different probabilities for receiving the sensitive question (p ≈ 1/3 and p ≈ 2/3). Likelihood ratio tests were used to assess whether the prevalence estimates for physical and cognitive doping differed significantly between p ≈ 1/3 and p ≈ 2/3. The order of questions (physical doping and cognitive doping) as well as the probability of receiving the sensitive question (p ≈ 1/3 or p ≈ 2/3) were counterbalanced across participants. Statistical power analyses were performed to determine sample size. Results: The prevalence estimate for physical doping with p ≈ 1/3 was 22.5% (95% CI: 10.8-34.1), and 12.8% (95% CI: 7.6-18.0) with p ≈ 2/3. For cognitive doping with p ≈ 1/3, the estimated prevalence was 22.5% (95% CI: 11.0-34.1), whereas it was 18.0% (95% CI: 12.5-23.5) with p ≈ 2/3. Likelihood-ratio tests revealed that prevalence estimates for both physical and cognitive doping, respectively, did not differ significantly under p ≈ 1/3 and p ≈ 2/3 (physical doping: χ2 = 2.25, df = 1, p = 0.13; cognitive doping: χ2 = 0.49, df = 1, p = 0.48). Bayes factors computed with the Savage-Dickey method favored the null (‟the prevalence estimates are identical under p ≈ 1/3 and p ≈ 2/3“) over the alternative (‟the prevalence estimates differ under p ≈ 1/3 and p ≈ 2/3“) hypothesis for both physical doping (BF = 2.3) and cognitive doping (BF = 5.3). Conclusion: The present results suggest that prevalence estimates for physical and cognitive doping assessed by the UQM are largely unaffected by the probability for receiving the sensitive question p.
Osseous Frame Index calculations of the early medieval South-West Germany
2018-05-15

The proper description of former populations is one of the most difficult tasks in anthropology. Archaeological material is often limited due to fragmented and sometimes poorly preserved bone material resulting in incomplete data. Published skeletal raw data are available from the past, but much of this data is either unavailable or not used for scientific studies. The authors seek to elicit more information about prehistoric times by using this dataset to introduce a new method. The purpose is to provide an approach to reconstruct a former population in respect to robusticity and health status. For this in the pilot study the Body Mass Index (BMI) and Frame Index (FI) of early medieval South-West Germany have been analysed. The FI, in contrast to the BMI, has not yet been used for robusticity analysis utilizing only skeletal remains. As far as we know, this is the first time that the FI has been calculated using archaeological material. Due to unknown soft-tissue thickness we introduce the Osseous Frame Index (OFI). The measured OFI reveals new insights in (pre-)historic populations and allows comparisons with modern reference samples. Our OFI calculations are relatively similar to modern calculations. Males have a higher robusticity than females, slightly increasing during life-time compared to females. These calculations provide a better historical understanding of human body composition.
Formal Language Characterizations of P, NP, and PSPACE
2018-05-15

Based on the notions of locality and recognizability for -dimensional languages -dimensionally colourable 1-dimensional languages are introduced. It is shown: A language is in NP if and only if is -dimensionally colourable for some . An analogous characterization in terms of deterministic -dimensional colourability is obtained for P. The addition of one unbounded dimension for colouring leads to a characterization of PSPACE.
A low-cost hyperspectral scanner for natural imaging above and under water
2018-05-15

ABSTRACT Hyperspectral imaging is a widely used technology for industrial and scientific purposes, but the high cost and large size of commercial setups have made them impractical for most basic research. Here, we designed and implemented a fully open source and low-cost hyperspectral scanner based on a commercial spectrometer coupled to custom optical, mechanical and electronic components. We demonstrate our scanner’s utility for natural imaging in both terrestrial and underwater environments. Our design provides sub-nm spectral resolution between 350–1000 nm, including the UV part of the light spectrum which has been mostly absent from commercial solutions and previous natural imaging studies. By comparing the full light spectra from natural scenes to the spectral sensitivity of animals, we show how our system can be used to identify subtle variations in chromatic details detectable by different species. In addition, we have created an open access database for hyperspectral datasets collected from natural scenes in the UK and India. Together with comprehensive online build- and use-instructions, our setup provides an inexpensive and customisable solution to gather and share hyperspectral imaging data.
Mouse dLGN receives input from a diverse population of retinal ganglion cells with limited convergence
2018-05-15

SUMMARY In the mouse, the parallel output of more than 30 functional types of retinal ganglion cells (RGCs) serves as the basis for all further visual processing. Little is known about how the representation of visual information changes between the retina and the dorsolateral geniculate nucleus (dLGN) of the thalamus, the main relay station between the retina and cortex. Here, we functionally characterized responses of retrogradely labeled dLGN-projecting RGCs and dLGN neurons to the same set of visual stimuli. We found that many of the previously identified functional RGC types innervate the dLGN, which maintained a high degree of functional diversity. Using a linear model to assess functional connectivity between RGC types and dLGN neurons, we found that the responses of dLGN neurons could be predicted as a linear combination of inputs from on average five RGC types, but only two of those had the strongest functional impact. Thus, mouse dLGN receives input from a diverse population of RGCs with limited functional convergence.
Potential Adverse Effects of Violent Video Gaming: Interpersonal- Affective Traits Are Rather Impaired Than Disinhibition in Young Adults
2018-05-16

The increasing trend of mass shootings, which were associated with excessive use of violent video games, fueled the debate of possible effects violent video games may have on adolescents and young adults. The aim of this study was to investigate the possible link between violent video gaming effects and the disposition of adverse behavior traits such as interpersonal-affective deficits and disinhibition. Data of 167 young adults, collected by an online questionnaire battery, were analyzed for lifetime video game exposure differences (i.e., non-gamers, non-violent video gamers, stopped violent video game users, and ongoing violent video game users) as well as for recent exposure effects on adverse behavior traits (Levenson’s Psychopathy Scale), while controlling for other potentially confounding lifestyle factors. While interpersonal-affective deficits were significantly higher in participants with ongoing violent video game exposure compared to non-gamers and non-violent video gamers, disinhibition was significantly higher in both – stopped and ongoing – violent video game exposure groups compared to non-gamers. Recent violent video game exposure was a stronger predictor for interpersonal-affective deficits, but was also significant for disinhibition. Considering that we observed small to medium effects in a sample of young adults with little to moderate use of violent video games highlights the importance of further investigating the potential adverse effects of violent video games on quality of social relationships.
GvmR – A Novel LysR-Type Transcriptional Regulator Involved in Virulence and Primary and Secondary Metabolism of Burkholderia pseudomallei
2018-05-16

<i>Burkholderia pseudomallei</i> is a soil-dwelling bacterium able to survive not only under adverse environmental conditions, but also within various hosts which can lead to the disease melioidosis. The capability of <i>B. pseudomallei</i> to adapt to environmental changes is facilitated by the large number of regulatory proteins encoded by its genome. Among them are more than 60 uncharacterized LysR-type transcriptional regulators (LTTRs). Here we analyzed a <i>B. pseudomallei</i> mutant harboring a transposon in the gene BPSL0117 annotated as a LTTR, which we named <i>gvmR</i> (globally acting virulence and metabolism regulator). The <i>gvmR</i> mutant displayed a growth defect in minimal medium and macrophages in comparison with the wild type. Moreover, disruption of <i>gvmR</i> rendered <i>B. pseudomallei</i> avirulent in mice indicating a critical role of GvmR in infection. These defects of the mutant were rescued by ectopic expression of <i>gvmR</i>. To identify genes whose expression is modulated by GvmR, global transcriptome analysis of the <i>B. pseudomallei</i> wild type and <i>gvmR</i> mutant was performed using whole genome tiling microarrays. Transcript levels of 190 genes were upregulated and 141 genes were downregulated in the <i>gvmR</i> mutant relative to the wild type. Among the most downregulated genes in the <i>gvmR</i> mutant were important virulence factor genes (T3SS3, T6SS1, and T6SS2), which could explain the virulence defect of the <i>gvmR</i> mutant. In addition, expression of genes related to amino acid synthesis, glyoxylate shunt, iron-sulfur cluster assembly, and syrbactin metabolism (secondary metabolite) was decreased in the mutant. On the other hand, inactivation of GvmR increased expression of genes involved in pyruvate metabolism, ATP synthesis, malleobactin, and porin genes. Quantitative real-time PCR verified the differential expression of 27 selected genes. In summary, our data show that GvmR acts as an activating and repressing global regulator that is required to coordinate expression of a diverse set of metabolic and virulence genes essential for the survival in the animal host and under nutrient limitation.
Unmanned Aerial Vehicle (UAV) Survey with Commercial-Grade Instruments: A Case Study from the Eastern Ḫabur Archaeological Survey, Iraq
2018-05-16

Low-altitude photography in archaeology is now common practice at the scale of excavations; however, landscape-scale applications are a relatively new endeavor with promising analytical potential. From 2014–2016, an unmanned aerial vehicle (UAV) with a mounted camera was used to document sites recorded as part of the Eastern Ḫabur Archaeological Survey (EḪAS), an archaeological reconnaissance project in western Dohuk Province, Iraqi Kurdistan. The EḪAS team documented over 70 archaeological sites with the UAV, from single-phase artifact scatters, to archaeological remains with standing architecture, to tells that cover more than 30 hectares. Representative examples from this survey are presented here to outline the project workflow and primary output data layers, including digital orthomosaics and digital elevation models. The quality and utility of results are then assessed in relationship to available satellite-based data. Methods for analysis and interpretation are then considered to demonstrate applications in landscape archaeology. An A) orthomosaic and B) shaded relief model with surface collection area (in red) of site EHAS-C045 created from photographs taken from a UAV.
Stage 1 Registered Report: Effect of deficient phagocytosis on neuronal survival and neurological outcome after temporary middle cerebral artery occlusion (tMCAo)
2018-05-16

<ns4:p>Stroke is a major cause of death and disability worldwide. In addition to neuronal death resulting directly from energy depletion due to lack of blood supply, inflammation and microglial activation following ischemic brain injury has been increasingly recognized to be a key contributor to the pathophysiology of cerebrovascular disease. However, our understanding of the cross talk between the ischemic brain and the immune system is limited. Recently, we demonstrated that following focal ischemia, death of mature viable neurons can be executed through phagocytosis by microglial cells or recruited macrophages, i.e. through phagoptosis. It was shown that inhibition of phagocytic signaling pathways following endothelin-1 induced focal cerebral ischemia leads to increased neuronal survival and neurological recovery. This suggests that inhibition of specific phagocytic pathways may prevent neuronal death during cerebral ischemia. To further explore this potential therapeutic target, we propose to assess the role of phagocytosis in an established model of temporary (45min) middle cerebral artery occlusion (tMCAo), and to evaluate neuronal survival and neurological recovery in mice with deficient phagocytosis. The primary outcome of this study will be forelimb function assessed with the staircase test. Secondary outcomes constitute Rotarod performance, stroke volume (quantified on MR imaging or brain sections, respectively), diffusion tensor imaging (DTI) connectome mapping, and histological analyses to measure neuronal and microglial densities, and phagocytic activity. Male mice aged 10-12 weeks will be used for experiments.</ns4:p>
Efficacy and safety of MK‐1293 insulin glargine compared with originator insulin glargine (Lantus) in type 1 diabetes: A randomized, open‐label clinical trial
2018-05-16

Aim To compare the efficacy and safety of MK‐1293 insulin glargine (Mk‐Gla; 100 U/mL) with originator insulin glargine, Lantus (Sa‐Gla), in people with type 1 diabetes mellitus (T1DM). Materials and methods This phase 3, randomized, active‐controlled, open‐label, 52‐week study ( ClinicalTrials.gov NCT02059161) enrolled 508 people with T1DM (HbA1c ≤11.0%; 97 mmol/mol) taking basal and prandial insulin. Participants were randomized 1:1 to once‐daily Mk‐Gla (n = 245) or Sa‐Gla (n = 263). Dose titration of basal insulin was by a pre‐breakfast plasma glucose dosing algorithm. The primary efficacy objective was assessment of the non‐inferiority of HbA1c change from baseline (margin of 0.40% [4.4 mmol/mol]) for Mk‐Gla compared with Sa‐Gla over 24 weeks. The primary safety objective was assessment of anti‐insulin antibody development over 24 weeks. Results The least squares (LS) mean HbA1c change from baseline at week 24 was −0.62 (95% CI −0.79, −0.45)% (−6.8 [−8.7, −4.9] mmol/mol) and −0.66 (−0.82, −0.50)% (−7.2 [−9.0, −5.4] mmol/mol) for Mk‐Gla and Sa‐Gla. The LS mean HbA1c difference was 0.04 (−0.11, 0.19)% (0.4 [−1.2, 2.0] mmol/mol) for Mk‐Gla minus Sa‐Gla, meeting the primary and secondary objective criteria for non‐inferiority and equivalence. Week 24 mean insulin glargine dose for Mk‐Gla and Sa‐Gla was 0.46 and 0.48 U/kg, respectively. Similarity of HbA1c response and basal insulin dose trajectory persisted over the 52 weeks. Safety and tolerability, including anti‐insulin antibody responses, hypoglycaemia, adverse events and body weight, were similar between insulins over the 52‐week study duration. Conclusions Mk‐Gla and Sa‐Gla exhibited similar efficacy and safety over 52 weeks in people with T1DM. ClinicalTrials.gov : NCT02059161