julilili42/papers huggingface dataset:
How causal is a reciprocal effect? Contrasting traditional and new methods to investigate the reciprocal effects model of self-concept and achievement
2022-01-14

The relationship between students’ subject-specific academic self-concept and their academic achievement is one of the most widely researched topics in educational psychology. A large body of this research has considered cross-lagged panel models (CLPMs), oftentimes synonymously referred to as reciprocal effects models (REMs), as a gold standard to investigate the causal relations between the two variables and has reported evidence for a reciprocal relationship between self-concept and achievement. However, more recent methodological research questioned the plausibility of assumptions that need to be satisfied in order to interpret results from traditional CLPMs causally. In this substantive-methodological synergy, we aimed at contrasting traditional and more recently developed methods to investigate reciprocal effects of students’ academic self-concept and achievement. Specifically, we compared results from CLPMs, from full forward CLPMs (FF-CLPMs), and from random intercept CLPMs (RI-CLPMs) with two weighting approaches developed to study causal effects of continuous treatment variables. To estimate these different models, we used rich longitudinal data of N = 3,757 students from lower secondary schools in Germany. Results from CLPMs, FF-CLPMs, and weighting methods support the reciprocal effects model, particularly when considering math self-concept and grades. In contrast, results from the RI-CLPMs were less consistent. Implications from our study for the interpretation of effects from the different models and methods as well as for school motivation theory are discussed.
Towards enantioselective ultrahigh performance liquid chromatography–mass spectrometry‐based metabolomics of branched‐chain fatty acids and anteiso‐fatty acids under reversed‐phase conditions using sub‐2‐μm amylose‐ and cellulose‐derived chiral stationary phases
2022-01-14

Abstract Branched‐chain fatty acids (BCFAs) are mostly saturated fatty acids with one or more methyl, seldom ethyl, branches in the alkyl chain. They are derived from branched‐chain amino acids, ruminant‐derived food, or biosynthetic side products of acetyl‐CoA carboxylase. They possess iso ‐ (branching at penultimate carbon) and anteiso ‐fatty acid structure (branching at antepenultimate carbon) or are branched at any other position of the carbon chain. Except for iso ‐fatty acids, BCFAs are chiral. They are commonly analyzed by GC‐MS, while there is a lack of enantioselective LC‐MS methods. In this work, we present a methodology for targeted enantioselective UHPLC‐ESI‐MS/MS metabolomics of BCFAs. It makes use of precolumn derivatization with 1‐naphthylamine and reversed‐phase elution conditions. A homologous series of short BCFA analytes with distinct chain lengths (having up to eight carbon atoms), branching type (methyl or ethyl), and position of branching (2, 3, and 4, anteiso and iso ) has been systematically studied on six commercially available polysaccharide UHPLC columns. Chiralpak IB‐U exhibited the highest and broadest enantioselectivity while IH‐U maintained enantioselectivity also for BCFAs with chirality distant from the carboxylic function (i.e., with other branching than in 2‐position). The method was used to assign the absolute configuration of a 4‐methylhexanoic acid side chain of a natural product from Streptomyces sp. SHP 22‐7. The potential of the corresponding UHPLC‐ESI‐QTOF‐MS/MS assay for analyzing stereoselectively BCFAs and other short organic acids by untargeted analysis in human urine was further elucidated in a preliminary proof‐of‐principle test.
Risk for Pelvic Metastasis and Role of Pelvic Lymphadenectomy in Node-Positive Vulvar Cancer-Results from the AGO-VOP.2 QS Vulva Study
2022-01-14

The need for pelvic treatment in patients with node-positive vulvar cancer (VSCC) and the value of pelvic lymphadenectomy (LAE) as a staging procedure to plan adjuvant radiotherapy (RT) is controversial. In this retrospective, multicenter analysis, 306 patients with primary node-positive VSCC treated at 33 gynecologic oncology centers in Germany between 2017 and 2019 were analyzed. All patients received surgical staging of the groins; nodal status was as follows: 23.9% (73/306) pN1a, 23.5% (72/306) pN1b, 20.4% (62/306) pN2a/b, and 31.9% (97/306) pN2c/pN3. A total of 35.6% (109/306) received pelvic LAE; pelvic nodal involvement was observed in 18.5%. None of the patients with nodal status pN1a or pN1b and pelvic LAE showed pelvic nodal involvement. Taking only patients with nodal status ≥pN2a into account, the rate of pelvic involvement was 25%. In total, adjuvant RT was applied in 64.4% (197/306). Only half of the pelvic node-positive (N+) patients received adjuvant RT to the pelvis (50%, 10/20 patients); 41.9% (122/291 patients) experienced recurrent disease or died. In patients with histologically-confirmed pelvic metastases after LAE, distant recurrences were most frequently observed (7/20 recurrences). Conclusions: A relevant risk regarding pelvic nodal involvement was observed from nodal status pN2a and higher. Our data support the omission of pelvic treatment in patients with nodal status pN1a and pN1b.
In vivo growth of Staphylococcus lugdunensis is facilitated by the concerted function of heme and non-heme iron acquisition mechanisms
2022-01-14

Abstract Acquisition of iron underpins the ability of pathogens to cause disease and Staphylococcus lugdunensis has increasingly been recognized as a pathogen that can cause serious infection. In this study, we sought to address the knowledge gap that exists regarding the iron acquisition mechanisms employed by S. lugdunensis , especially during infection of the mammalian host. Here we show that S. lugdunensis utilizes diverse genome encoded iron acquisition mechanisms to satisfy its need for this nutrient. Indeed, S. lugdunensis can usurp hydroxamate siderophores, and staphyloferrin A and B from S. aureus , using the fhuC ATPase-encoding gene. Acquisition of catechol siderophores and catecholamine stress hormones necessitates the presence of the sst-1 transporter-encoding locus, but not the sst-2 locus. Iron-dependent growth in acidic culture conditions necessitates the feoAB locus. Heme iron is acquired via expression of the iron-regulated surface determinant ( isd ) locus. During systemic infection of mice we demonstrate that while S. lugdunensis does not cause overt illness, it does colonize and proliferate to high numbers in the kidneys. By combining mutations in the various iron acquisition loci, we further demonstrate that only a strain mutated for all of isd , fhuC, sst-1, and feo , versus combination mutants carrying wild type copies of any one of those loci, was attenuated in its ability to proliferate to high numbers in kidneys. Taken together our data reveal that S. lugdunensis requires a repertoire of both heme and non-heme iron acquisition mechanisms to proliferate during systemic infection of mammals. Importance Acquisition of iron underpins the ability of pathogens to cause disease and Staphylococcus lugdunensis has increasingly been recognized as a pathogen that can cause serious infection. In this study, we sought to address the knowledge gap that exists regarding the iron acquisition mechanisms employed by S. lugdunensis , especially during infection of the mammalian host. Owing to an inability to synthesize siderophores, growth of S. lugdunensis is dramatically impaired in the presence of transferrin or serum, yet S . lugdunensis nonetheless uses several other genome-encoded iron acquisition mechanisms, in concert, to proliferate within the mammalian host. Therefore, the development of interventions that target bacterial iron acquisition systems should consider the overlapping function of distinct metal acquisition strategies deployed by bacterial pathogens.
FAIR and Quality Assured Data – The Use Case of Trueness
2022-01-14

The FAIR Guiding Principles do not address the quality of data and metadata. Therefore, data collections could be FAIR but useless. In a funding initiative of registries for health services research, trueness of data received special attention. Completeness in the definition of recall was selected to represent this dimension in a cross-registry benchmarking. The first analyses of completeness revealed a diversity of its implementation. No registry was able to present results exactly as requested in a guideline on data quality. Two registries switched to a source data verification as alternative, the three others downsized to the dimension integrity. The experiences underline that the achievement of appropriate data quality is a matter of costs and resources, whereas the current Guiding Principles quote for a transparent culture regarding data and metadata. We propose the extension to FAIR-Q, data collections should not only be findable, accessible, interoperable, and reusable, but also quality assured.
Reference pricing systems on the pharmaceutical market
2022-01-14

Abstract Constantly rising expenditures for pharmaceuticals require government intervention in firms’ pricing decisions. To this end, reference pricing systems are a frequently employed regulatory mechanism. This paper considers a duopoly market with vertically differentiated firms highlighting the effects of a reference pricing system on prices, consumer and producer surplus, expenditures and welfare. Reference pricing decreases equilibrium prices and induces a more competitive environment. It promotes generic usage leading to increased market coverage. Especially generic consumers benefit from a reference pricing regulation. The losses in producer surplus are mainly born by the brand-name firm. Introducing a reference pricing system unambiguously increases welfare.
Assessment of consumer VR-headsets’ objective and subjective field of view (FoV) and its feasibility for visual field testing
2022-01-15

Abstract Virtual reality as a research environment has seen a boost in its popularity during the last decades. Not only the usage fields for this technology have broadened, but also a research niche has appeared as the hardware improved and became more affordable. Experiments in vision research are constructed upon the basis of accurately displaying stimuli with a specific position and size. For classical screen setups, viewing distance and pixel position on the screen define the perceived position for subjects in a relatively precise fashion. However, projection fidelity in HMDs strongly depends on eye and face physiological parameters. This study introduces an inexpensive method to measure the perceived field of view and its dependence upon the eye position and the interpupillary distance, using a super wide angle camera. Measurements of multiple consumer VR headsets show that manufacturers’ claims regarding field of view of their HMDs are mostly unrealistic. Additionally, we performed a “Goldmann” perimetry test in VR to obtain subjective results as a validation of the objective camera measurements. Based on this novel data, the applicability of these devices to test humans’ field of view was evaluated.
Association of ultra‐rare coding variants with genetic generalized epilepsy: A case–control whole exome sequencing study
2022-01-15

Abstract Objective We aimed to identify genes associated with genetic generalized epilepsy (GGE) by combining large cohorts enriched with individuals with a positive family history. Secondarily, we set out to compare the association of genes independently with familial and sporadic GGE. Methods We performed a case–control whole exome sequencing study in unrelated individuals of European descent diagnosed with GGE (previously recruited and sequenced through multiple international collaborations) and ancestry‐matched controls. The association of ultra‐rare variants (URVs; in 18 834 protein‐coding genes) with epilepsy was examined in 1928 individuals with GGE (vs. 8578 controls), then separately in 945 individuals with familial GGE (vs. 8626 controls), and finally in 1005 individuals with sporadic GGE (vs. 8621 controls). We additionally examined the association of URVs with familial and sporadic GGE in two gene sets important for inhibitory signaling (19 genes encoding γ‐aminobutyric acid type A [GABA A ] receptors, 113 genes representing the GABAergic pathway). Results GABRG2 was associated with GGE ( p = 1.8 × 10 −5 ), approaching study‐wide significance in familial GGE ( p = 3.0 × 10 −6 ), whereas no gene approached a significant association with sporadic GGE. Deleterious URVs in the most intolerant subgenic regions in genes encoding GABA A receptors were associated with familial GGE (odds ratio [OR] = 3.9, 95% confidence interval [CI] = 1.9–7.8, false discovery rate [FDR]‐adjusted p = .0024), whereas their association with sporadic GGE had marginally lower odds (OR = 3.1, 95% CI = 1.3–6.7, FDR‐adjusted p = .022). URVs in GABAergic pathway genes were associated with familial GGE (OR = 1.8, 95% CI = 1.3–2.5, FDR‐adjusted p = .0024) but not with sporadic GGE (OR = 1.3, 95% CI = .9–1.9, FDR‐adjusted p = .19). Significance URVs in GABRG2 are likely an important risk factor for familial GGE. The association of gene sets of GABAergic signaling with familial GGE is more prominent than with sporadic GGE.
Seroprevalence of anti-SARS-CoV-2 antibodies in a population living in Bomassa village, Republic of Congo
2022-01-15

Seroprevalence against SARS-CoV-2 occurred in 25% of the indigenous population sample, with almost 50% of these seropositive participants possessing neutralizing antibodies. These findings suggest that the spread of SARS-CoV-2 has been underestimated in the Republic of Congo.
AI Denoising Significantly Improves Image Quality in Whole-Body Low-Dose Computed Tomography Staging
2022-01-17

(1) Background: To evaluate the effects of an AI-based denoising post-processing software solution in low-dose whole-body computer tomography (WBCT) stagings; (2) Methods: From 1 January 2019 to 1 January 2021, we retrospectively included biometrically matching melanoma patients with clinically indicated WBCT staging from two scanners. The scans were reconstructed using weighted filtered back-projection (wFBP) and Advanced Modeled Iterative Reconstruction strength 2 (ADMIRE 2) at 100% and simulated 50%, 40%, and 30% radiation doses. Each dataset was post-processed using a novel denoising software solution. Five blinded radiologists independently scored subjective image quality twice with 6 weeks between readings. Inter-rater agreement and intra-rater reliability were determined with an intraclass correlation coefficient (ICC). An adequately corrected mixed-effects analysis was used to compare objective and subjective image quality. Multiple linear regression measured the contribution of “Radiation Dose”, “Scanner”, “Mode”, “Rater”, and “Timepoint” to image quality. Consistent regions of interest (ROI) measured noise for objective image quality; (3) Results: With good–excellent inter-rater agreement and intra-rater reliability (Timepoint 1: ICC ≥ 0.82, 95% CI 0.74–0.88; Timepoint 2: ICC ≥ 0.86, 95% CI 0.80–0.91; Timepoint 1 vs. 2: ICC ≥ 0.84, 95% CI 0.78–0.90; all p ≤ 0.001), subjective image quality deteriorated significantly below 100% for wFBP and ADMIRE 2 but remained good–excellent for the post-processed images, regardless of input (p ≤ 0.002). In regression analysis, significant increases in subjective image quality were only observed for higher radiation doses (≥0.78, 95%CI 0.63–0.93; p &lt; 0.001), as well as for the post-processed images (≥2.88, 95%CI 2.72–3.03, p &lt; 0.001). All post-processed images had significantly lower image noise than their standard counterparts (p &lt; 0.001), with no differences between the post-processed images themselves. (4) Conclusions: The investigated AI post-processing software solution produces diagnostic images as low as 30% of the initial radiation dose (3.13 ± 0.75 mSv), regardless of scanner type or reconstruction method. Therefore, it might help limit patient radiation exposure, especially in the setting of repeated whole-body staging examinations.
HELLS Is Negatively Regulated by Wild-Type P53 in Liver Cancer by a Mechanism Involving P21 and FOXM1
2022-01-17

The major tumor suppressor P53 (TP53) acts primarily as a transcription factor by activating or repressing subsets of its numerous target genes, resulting in different cellular outcomes (e.g., cell cycle arrest, apoptosis and senescence). P53-dependent gene regulation is linked to several aspects of chromatin remodeling; however, regulation of chromatin-modifying enzymes by P53 is poorly understood in hepatocarcinogenesis. Herein, we identified Helicase, lymphoid specific (HELLS), a major epigenetic regulator in liver cancer, as a strong and selective P53 repression target within the SNF2-like helicase family. The underlying regulatory mechanism involved P53-dependent induction of P21 (CDKN1A), leading to repression of Forkhead Box Protein M1 (FOXM1) that in turn resulted in downregulation of HELLS expression. Supporting our in vitro data, we found higher expression of HELLS in murine HCCs arising in a Trp53−/− background compared to Trp53+/+ HCCs as well as a strong and highly significant correlation between HELLS and FOXM1 expression in different HCC patient cohorts. Our data suggest that functional or mutational inactivation of P53 substantially contributes to overexpression of HELLS in HCC patients and indicates a previously unstudied aspect of P53′s ability to suppress liver cancer formation.
Schistosomiasis in Gabon from 2000 to 2021 - A review
2022-01-17

Introduction: Schistosomiasis is a public health issue of concern in Gabon, with the disease being reported from all regions of the country. The topic has been of interest for the local researchers and physicians for over two decades. The objective of this narrative review was to provide an overview of the research activities in the area from 2000 to early 2021. Methods: We performed a narrative literature review. The search strategy was designed to get a broad overview of the different research topics on schistosomiasis and the national control programme, and included grey literature. Results: A total of 159 articles was screened, and 42 were included into the review in addition to the grey literature. During the past two decades, the work on schistosomiasis originated from five out of the nine provinces of the country, with diverse aspects of the disease investigated; including immunology, epidemiology, diagnosis and treatment. Several studies investigated various aspects of schistosomiasis-related morbidity in the respective study populations. The body of work demonstrates that much effort was made to understand the details of the host immune response to schistosomiasis, and the immune profile changes induced in patients treated with praziquantel. Although some MDA campaigns were conducted in the country; little, however, is known on the epidemiological situation of the disease, particularly of its distribution within the population, as well as co-infections with other parasitic diseases also endemic in the area. Conclusion: Progress has been made over the past two decades in the understanding of schistosomiasis in the country, including disease-related morbidity and its interaction with other parasitic infections, and the immunology and epidemiology of the disease. However, for optimising control of the disease, there is a need to fine-tune these findings with detailed local epidemiological and malacological data. We call for such studies to accomplish the knowledge of schistosomiasis in the country, particularly in areas of moderate or high endemicity, and recommend this approach to comparable schistosomiasis-endemic areas elsewhere.
Human Leucocyte Antigen G and Murine Qa-2 Are Critical for Myeloid Derived Suppressor Cell Expansion and Activation and for Successful Pregnancy Outcome
2022-01-17

During pregnancy, maternal immune system has to balance tightly between protection against pathogens and tolerance towards a semi-allogeneic organism. Dysfunction of this immune adaptation can lead to severe complications such as pregnancy loss, preeclampsia or fetal growth restriction. In the present study we analyzed the impact of the murine MHC class Ib molecule Qa-2 on pregnancy outcome in vivo . We demonstrate that lack of Qa-2 led to intrauterine growth restriction and increased abortion rates especially in late pregnancy accompanied by a disturbed trophoblast invasion and altered spiral artery remodeling as well as protein aggregation in trophoblast cells indicating a preeclampsia-like phenotype. Furthermore, lack of Qa-2 caused imbalanced immunological adaptation to pregnancy with altered immune cell and especially T-cell homeostasis, reduced T reg numbers and decreased accumulation and functional activation of myeloid-derived suppressor cells. Lastly, we show that application of sHLA-G reduced abortion rates in Qa-2 deficient mice by inducing MDSC. Our results highlight the importance of an interaction between HLA-G and MDSC for pregnancy success and the therapeutic potential of HLA-G for treatment of immunological pregnancy complications.
Self-protecting responses in randomized response designs: A survey on intimate partner violence during the coronavirus disease 2019 pandemic
2022-01-17

Randomized response techniques (RRTs) are applied to reduce response biases in self-report surveys on sensitive research questions (e.g., on socially undesirable characteristics). However, there is evidence that they cannot completely eliminate self-protecting response strategies. To address this problem, there are RRTs specifically designed to measure the extent of such strategies. Here we assessed the recently devised unrelated question model—cheating extension (UQMC) in a preregistered online survey on intimate partner violence (IPV) victimization and perpetration during the first contact restrictions as containment measures for the outbreak of the coronavirus disease 2019 pandemic in Germany in early 2020. The UQMC accounting for self-protecting responses described the data better than its predecessor model which assumes instruction adherence. The resulting three-month prevalence estimates were about 10% and we found a high proportion of self-protecting responses in the group of female participants queried about IPV victimization. However, unexpected results concerning the differences in prevalence estimates across the groups queried about victimization and perpetration highlight the difficulty of investigating sensitive research questions even using methods that guarantee anonymity and the importance of interpreting the respective estimates with caution.
Non-Destructive Extraction of DNA from Preserved Tissues in Medical Collections
2022-01-17

Museum specimens and histologically fixed material are valuable samples for the study of historical soft tissues and represent a possible pathogen-specific source for retrospective molecular investigations. However, current methods for molecular analysis are inherently destructive, posing a dilemma between performing a study with the available technology, thus damaging the sample, and conserving the material for future investigations. Here the authors present the first tests of a non-destructive alternative that facilitates genetic analysis of fixed wet tissues while avoiding tissue damage. The authors extracted DNA from the fixed tissues as well as their embedding fixative solution, to quantify the DNA that was transferred to the liquid component. The results show that human historical DNA can be retrieved from the fixative material of medical specimens and provide new options for sampling valuable collections.