julilili42/papers huggingface dataset:
Faculty Opinions recommendation of Disagreement among gastroenterologists using the mayo and rutgeerts endoscopic scores.
2018-08-02

Background: Endoscopy is routinely performed in patients with inflammatory bowel disease to evaluate disease severity and guide important clinical decisions. However, variability in the interpretation of endoscopic findings can significantly impact patient management.Methods: Fifty-eight gastroenterologists were invited to participate in an online survey including pictures and video recordings of colonoscopies performed in patients with ulcerative colitis (UC) and Crohn's disease (CD). Participants were asked to rate the colorectal mucosa in patients with UC using the Mayo endoscopic subscore (MES), and the neo-terminal ileum and anastomosis in operated patients with CD using the Rutgeerts score (RS). Overall interrater agreement (IRA) and for several key end points was assessed using Krippendorff's alpha test.Results: The IRAs for the MES and RS were 0.47 (95% confidence interval [CI], 0.41-0.54) and 0.33 (95% CI, 0.28-0.38). The IRAs for UC mucosal healing (MES ≤ 1) and complete mucosal healing (MES = 0) were 0.57 (95% CI, 0.40-0.72) and 0.89 (95% CI, 0.73-1) and for CD postoperative recurrence (RS ≥ i2), and IRAs for severe postoperative recurrence (RS ≥ 3) were 0.44 (95% CI, 0.24-0.62) and 0.54 (95% CI, 0.36-0.71), respectively. Unexpectedly, although clinical information significantly influenced the IRA, participant expertise and consultation of scores did not produce significant changes in the IRA.Conclusions: A high rate of disagreement in endoscopic scoring was found in this study, even among experienced physicians. The variability in the assessment of mucosal healing and postoperative recurrence may translate into relevant differences in patient management.© 2018 Crohn's & Colitis Foundation of America. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com PMID: 29361106
Faculty Opinions recommendation of Long-term Combination Therapy with Anti-TNF plus Vedolizumab Induces and Maintains Remission in Therapy-refractory Ulcerative Colitis.
2018-08-02

Read the full review for this Faculty Opinions recommended article: Long-term Combination Therapy with Anti-TNF plus Vedolizumab Induces and Maintains Remission in Therapy-refractory Ulcerative Colitis.
Faculty Opinions recommendation of Surgical rates in the era of biological therapy: up, down or unchanged?
2018-08-02

PURPOSE OF REVIEW: The aim of this review is to summarize data regarding surgical trends in inflammatory bowel disease in the prebiologic and biologic era, with a focus on population-based studies and randomized controlled trials (RCTs).RECENT FINDINGS: There is paucity of data in RCTs regarding surgical rates, with only a few clinical trials reporting them. From the available data, meta-analyses of RCTs have concluded that antitumor necrosis α agents (anti-TNF) reduce surgical rates in ulcerative colitis and Crohn's disease. A large body of evidence from population-based studies from different regions of the world is available to evaluate surgical trends before and after the introduction of anti-TNF agents. The risk of surgery decreased significantly over the past six decades; these decreasing trends continued in the biologic era, which might indicate a potential beneficial disease-modifying effect of biologics. There is lack of data with nonanti-TNF biologics (i.e. anti-integrins and ustekinumab) regarding the risk of surgery.SUMMARY: Although data from population-based studies and available RCTs suggest a protective effect from surgery of anti-TNF agents, definitive conclusions should be drawn only when more disease-modifying trials with different biologics and treatment strategies become available. PMID: 28463854
Faculty Opinions recommendation of Changes in medical management and colectomy rates: a population-based cohort study on the epidemiology and natural history of ulcerative colitis in Örebro, Sweden, 1963-2010.
2018-08-02

Read the full review for this Faculty Opinions recommended article: Changes in medical management and colectomy rates: a population-based cohort study on the epidemiology and natural history of ulcerative colitis in Örebro, Sweden, 1963-2010.
Competence in educational theory and practice: a critical discussion
2018-08-03

This paper first provides a brief overview of the history and current usage of the concept of competence in academic research, and then undertakes a critical discussion of how the term is currently used in educational policy. The running example used throughout the paper is competence in foreign language learning. The PISA study is discussed to demonstrate how the concept of competence has come to prominence in the international discourse on education in recent years. Following this, particular attention is given to the situation in Germany where there has been a shift towards competence as an aim of teaching in recent years, coupled with an increased focus on standards and accountability. The relationship between competence and standards is examined critically, since some authors appear to use the two interchangeably whether or not this is justified. Finally, the Common European Framework for Languages (CEFR) and a German curriculum document are examined critically with regard to their use of the concept of competence.
Preserving Kerr symmetries in deformed spacetimes
2018-08-03

We present a novel approach in constructing deviations of the Kerr spacetime whereas the symmetries can be preserved. The method was applied trivially in all known classical black-hole spacetimes tested, while provides the possibility of testing and inventing deformations of Kerr in a quick and innovative way. The methodology is based on earlier work by Benenti and Francaviglia (1979) on separability of geodesic equations while we exploited the elegant properties of Yano tensor in order to provide an additional way of getting the Carter constant.
Country and gender differences in the motivation of dental students—An international comparison
2018-08-03

Abstract Purpose The objective of this study, conducted in Germany, Finland and Turkey, was to identify whether motivations to study dentistry varied by country, gender or year of study. Methods The multicentre pilot study was conducted in English language in 2014. Participants (n = 469 dental students) were either in the first or last year of study. The response rate was 91%. Results The sample comprised 63% females and 37% males, reflecting the common gender distribution in dental education. A total of 236 first year students (50.3%) and 233 final year students (49.7%) took part in the study. The participants were aged 21‐25 years and of 15 different nationalities, mostly from Turkey, Germany and Finland. Considering who motivated them most to become a dentist, the most common answer was “self‐motivated” (49.5%). 23.4% of the students stated having been motivated by a “family member or friend, who is a dentist,” while 24.3% said they had been motivated by a “family member or friend, who is not a dentist.” —Very few students (2.8%) recorded having been motivated by a “high school or college counsellor.” Motivations for choosing dentistry as a career included “ability to help people,” “self‐employment,” “income potential,” “working with hands” and “status and prestige,” all of which were rated as highly important. “Time management” and “career variety” were rated as moderately important. Significant statistical differences were observed by country and gender. For the German students, a dental relative was significantly more often relevant than for the Finnish and Turkish students, who were more often influenced by family members or friends not working in the dental field. “Time management” seemed to be significantly more important to female than to male students. Conclusion In line with a feminisation of the workforce in dentistry, a well‐structured working environment and well‐thought‐out time management may play an increased role in future work force planning (Gender dentistry: International vergleichende Studie zu Karrierewahl und Spezialisierungswünschen von Zahnmedizinstudenten. Ulm: Universität Ulm).
Incubation, not sleep, aids problem-solving
2018-08-03

Solving a novel problem and finding innovative solutions requires a flexible and creative recombination of prior knowledge. It is thought that setting a problem aside before giving it another try aids problem-solving. The underlying mechanisms of such an incubation period could include unconscious processing that fosters spreading activation along associated networks and the restructuring of problem representations. Recently, it has been suggested that sleep may also support problem-solving by supporting the transformation and restructuring of memory elements. Since the effect of sleep on problem-solving has been mainly tested using the Remote Associates Test, we chose three different tasks-classical riddles, visual change detection, and anagrams-to examine various aspects of problem-solving and to pinpoint task-specific prerequisites for effects of sleep or incubation to emerge. Sixty-two participants were given two attempts to solve the problems. Both attempts either occurred consecutively or were spaced apart by a 3-hour incubation interval that was spent awake or asleep. We found that a period of incubation positively affected solutions rates in classical riddles, but not in visual change detection or anagram solving. Contrary to our hypothesis, spending the incubation period asleep, did not yield any additional benefit. Our study thus supports the notion that a period of letting a problem rest is beneficial for its solution and confines the role of sleep to memory transformations that do not directly impact on problem-solving ability.
Sensitivity of Simulated Hyporheic Exchange to River Bathymetry: The Steinlach River Test Site
2018-08-03

Abstract This study determines the aspects of river bathymetry that have the greatest influence on the predictive biases when simulating hyporheic exchange. To investigate this, we build a highly parameterized HydroGeoSphere model of the Steinlach River Test Site in southwest Germany as a reference. This model is then modified with simpler bathymetries, evaluating the changes to hyporheic exchange fluxes and transit time distributions. Results indicate that simulating hyporheic exchange with a high‐resolution detailed bathymetry using a three‐dimensional fully coupled model leads to nested multiscale hyporheic exchange systems. A poorly resolved bathymetry will underestimate the small‐scale hyporheic exchange, biasing the simulated hyporheic exchange towards larger scales, thus leading to overestimates of hyporheic exchange residence times. This can lead to gross biases in the estimation of a catchment's capacity to attenuate pollutants when extrapolated to account for all meanders along an entire river within a watershed. The detailed river slope alone is not enough to accurately simulate the locations and magnitudes of losing and gaining river reaches. Thus, local bedforms in terms of bathymetric highs and lows within the river are required. Bathymetry surveying campaigns can be more effective by prioritizing bathymetry measurements along the thalweg and gegenweg of a meandering channel. We define the gegenweg as the line that connects the shallowest points in successive cross‐sections along a river opposite to the thalweg under average flow conditions. Incorporating local bedforms will likely capture the nested nature of hyporheic exchange, leading to more physically meaningful simulations of hyporheic exchange fluxes and transit times.
Mean-field density functional theory of a nanoconfined classical, three-dimensional Heisenberg fluid. II. The interplay between molecular packing and orientational order
2018-08-03

As in Paper I of this series of papers [S. M. Cattes et al., J. Chem. Phys. 144, 194704 (2016)], we study a Heisenberg fluid confined to a nanoscopic slit pore with smooth walls. The pore walls can either energetically discriminate specific orientations of the molecules next to them or are indifferent to molecular orientations. Unlike in Paper I, we employ a version of classical density functional theory that allows us to explicitly account for the stratification of the fluid (i.e., the formation of molecular layers) as a consequence of the symmetry-breaking presence of the pore walls. We treat this stratification within the White Bear version (Mark I) of fundamental measure theory. Thus, in this work, we focus on the interplay between local packing of the molecules and orientational features. In particular, we demonstrate why a critical end point can only exist if the pore walls are not energetically discriminating specific molecular orientations. We analyze in detail the positional and orientational order of the confined fluid and show that reorienting molecules across the pore space can be a two-dimensional process. Last but not least, we propose an algorithm based upon a series expansion of Bessel functions of the first kind with which we can solve certain types of integrals in a very efficient manner.
Comparison of quantitative real‐time PCR and short‐term (18‐hour) microculture in diagnosis of fetal cytomegalovirus infection: Impact of hyperimmunoglobulin treatment
2018-08-03

Abstract Objective The prognostic value of human cytomegalovirus detection (HCMV) DNA levels from amniotic fluid (AF) for the outcome of the infected newborn is still a matter of debate, especially if the onset of maternal primary infection at amniocentesis is unknown. The objective of this study was to investigate the analytical performance in short‐term (18‐hour) microculture from preconcentrated samples and quantitative real‐time PCR (rtPCR) for diagnosis of fetal HCMV infection. Methods A retrospective diagnostic study was conducted on 51 AF samples taken from women that transmitted HCMV prenatally. Amniocentesis was performed around 22‐week gestation. The samples were tested for HCMV viral load via quantitative rtPCR and additionally with quantitative short‐term (18‐hour) microculture following preconcentration via a 50 000 g centrifugation step prior to inoculation to fibroblast monolayers. Results Both methods show correlating results ( ρ = 0.903). In 25 samples, the women received intravenous hyperimmunoglobulin prior to amniocentesis resulting in a lower correlation of both quantitative methods ( ρ = 0.445), in reduced median copy numbers of HCMV DNA ( P = .037) and reduced viral infectivity in short‐term microculture ( P = .025). Conclusion Both methods lead to correlating results using AF samples from HIG‐naïve women. Human cytomegalovirus viral load and infectivity in cell culture are reduced in samples following maternal hyperimmunoglobulin treatment.
GLOBAL WATER TRANSFER MEGAPROJECTS: A SOLUTION FOR THE WATER-FOOD-ENERGY NEXUS?
2018-08-03

Globally, freshwater is unevenly distributed, both in space and time. Climate change, land use alteration, and increasing human exploitation will further increase the pressure on water as a resource for human welfare and on inland water ecosystems. Water transfer megaprojects (WTMP), i.e. large-scale engineering interventions to divert water within and between catchments, represent an approach in coping with increasing water scarcity. These projects are most commonly associated with large-scale agricultural and energy development schemes, and many of them serve multiple purposes. Despite numerous case studies that focus on the social, economic and environmental impacts of individual projects, a global inventory of existing and planned WTMP is lacking. We carried out the first comprehensive global inventory of WTMP that are either planned or under construction. We collected key information (e.g. location, distance, volume, costs, purpose) on 33 existing and 76 future (planned or under construction) WTMP. If realized, the future projects will transfer a total volume of 1,923 km3 per year across a total distance exceeding more than twice the length of Earth’s equator. The largest WTMP planned or under construction are located in North America, Asia and Africa. The predicted total investments in these WTMP will exceed 2.6 trillion US$. Among future projects, 43 will serve purposes of agriculture development, 14 transfer water for hydropower development and 10 combine both purposes. Our results show that WTMP will create artificial connections between river basins, alter the global hydrological cycle, and change the natural functions and services freshwaters provide for humans and nature. The results also emphasize the need to include these projects in global hydrological models, in strategies related to the water-energy-food nexus, and in developing internationally agreed criteria to assess the ecological, social and economic consequences these projects may cause.
Corroborating evidence by exploring sources of bias in observational spinal cord injury studies
2018-08-04

Observational studies investigating large real-life datasets are a valuable resource in clinical research. Understanding the imperfect nature of clinical data, statistical approaches factoring in known confounders are instrumental for rigorously addressing bias.1 Our recent work identifying pneumonia and postoperative wound infections (Pn/Wi) as risk markers for impaired long-term functional recovery and survival after spinal cord injury (SCI)2 was considered as a strong statistical analysis.3 However, some unexplored putative confounders in terms of nonrandom loss to follow-up, temporal changes in clinical practice, and exclusion criteria were discussed.3 In order to evaluate and objectivize for the probability of attrition and temporal and selection bias, we apply and discuss an array of analytical tools extending beyond the format of the original publication.2
Autoimmunity in Chronic Chagas Disease: A Road of Multiple Pathways to Cardiomyopathy?
2018-08-06

Chagas disease (CD), a neglected tropical disease caused by the protozoan <i>Trypanosoma cruzi</i>, affects around six million individuals in Latin America. Currently, CD occurs worldwide, becoming a significant public health concern due to its silent aspect and high morbimortality rate. <i>T. cruzi</i> presents different escape strategies which allow its evasion from the host immune system, enabling its persistence and the establishment of chronic infection which leads to the development of chronic Chagas cardiomyopathy (CCC). The potent immune stimuli generated by <i>T. cruzi</i> persistence may result in tissue damage and inflammatory response. In addition, molecular mimicry between parasites molecules and host proteins may result in cross-reaction with self-molecules and consequently in autoimmune features including autoantibodies and autoreactive cells. Although controversial, there is evidence demonstrating a role for autoimmunity in the clinical progression of CCC. Nevertheless, the exact mechanism underlying the generation of an autoimmune response in human CD progression is unknown. In this review, we summarize the recent findings and hypotheses related to the autoimmune mechanisms involved in the development and progression of CCC.
Schistosoma haematobium effects on Plasmodium falciparum infection modified by soil-transmitted helminths in school-age children living in rural areas of Gabon
2018-08-06

Our results suggest that STH enhance the risk for P. falciparum infection in schistosomiasis-positive children, and when infected, that schistosomiasis enhances susceptibility to developing malaria in young children but not in older children.
Culture-Expanded Human Invariant Natural Killer T Cells Suppress T-Cell Alloreactivity and Eradicate Leukemia
2018-08-06

Graft-versus-host disease (GVHD) is a major cause of significant morbidity and mortality after allogeneic hematopoietic cell transplantation (HCT). Invariant natural killer T (iNKT) cells are potent regulators of immune responses, protect from lethal GVHD, and promote graft-versus-leukemia effects in murine studies. Since iNKT cells constitute less than 0.5% of human peripheral blood mononuclear cells (PBMCs), <i>in vitro</i> expansion with their glycolipid ligands is required before they can be used for cytotherapy and experimental purposes. Three weeks of cell culture and autologous restimulation with either KRN7000, PBS44, or PBS57 resulted in a robust proliferation of iNKT cells from human PBMCs. Next, iNKT cells were sorted to a purity higher than 90% being crucial for further experimental and clinical applications. These iNKT cells significantly decreased activation and proliferation of allogeneic CD3+ T lymphocytes. In addition, leukemia cell lines and primary leukemia cells were efficiently lysed by culture-expanded iNKT cells. Importantly, culture-expanded donor iNKT cells promoted robust antileukemia activity against HLA-matched allogeneic patient leukemia cells. Our data indicate that the adoptive transfer of culture-expanded iNKT cells could be a powerful cytotherapeutic approach to induce immune tolerance and prevent leukemia relapse after allogeneic HCT in humans.
Concordance of three alternative gestational age assessments for pregnant women from four African countries: A secondary analysis of the MIPPAD trial
2018-08-06

The alternative assessments do not result in comparable outcomes and discrepancies are far beyond the clinically acceptable range. Last menstrual period should not be used as the only estimator of gestational age. In the absence of reliable early ultrasound, symphysis-fundal height measurements may be most useful during pregnancy for fetal risk assessment and the New Ballard Score after delivery as a confirmation of these estimations and for further neonatal management. However, promotion of portable ultrasound devices is required for accurate assessment of gestational age in sub-Sahara Africa.
Informal Alliance: The Bilderberg Group and Transatlantic Relations during the Cold War, 1952-1968
2018-08-06

"Informal Alliance is the first archive-based history of the secretive Bilderberg Group, the high-level transatlantic elite network founded at the height of the Cold War. Making extensive use of the recently opened Bilderberg Group archives as well as a wide range of private and official collections, it shows the significance of informal diplomacy in a fast-changing world of Cold War, decolonization, and globalization. By analyzing the global mindset of the postwar transatlantic elite and by focusing on private, transnational modes of communication and coordination, this study provides important new insights into the history of transatlantic relations, anti-Americanism, Western anti-communism, and European integration during the 1950s and 1960s. Informal Alliance also debunks the persistent myth that the Bilderberg Group was created by the CIA and repudiates widespread conspiracy theories alleging that Bilderberg was some sort of secret world government"--
A tissue-based draft map of the murine MHC class I immunopeptidome
2018-08-07

Abstract The large array of peptides presented to CD8+ T cells by major histocompatibility complex (MHC) class I molecules is referred to as the MHC class I immunopeptidome. Although the MHC class I immunopeptidome is ubiquitous in mammals and represents a critical component of the immune system, very little is known, in any species, about its composition across most tissues and organs in vivo . We applied mass spectrometry (MS) technologies to draft the first tissue-based atlas of the murine MHC class I immunopeptidome in health. Peptides were extracted from 19 normal tissues from C57BL/6 mice and prepared for MS injections, resulting in a total number of 28,448 high-confidence H2D b /K b -associated peptides identified and annotated in the atlas. This atlas provides initial qualitative data to explore the tissue-specificity of the immunopeptidome and serves as a guide to identify potential tumor-associated antigens from various cancer models. Our data were shared via PRIDE (PXD008733), SysteMHC Atlas (SYSMHC00018) and SWATH Atlas. We anticipate that this unique dataset will be expanded in the future and will find wide applications in basic and translational immunology.