julilili42/papers huggingface dataset:
Challenges in the Evaluation of Observational Data Trustworthiness From a Data Producers Viewpoint (FAIR+)
2022-01-20

Recent discussions in many scientific disciplines stress the necessity of “FAIR” data. FAIR data, however, does not necessarily include information on data trustworthiness, where trustworthiness comprises reliability, validity and provenience/provenance. This opens up the risk of misinterpreting scientific data, even though all criteria of “FAIR” are fulfilled. Especially applications such as secondary data processing, data blending, and joint interpretation or visualization efforts are affected. This paper intends to start a discussion in the scientific community about how to evaluate, describe, and implement trustworthiness in a standardized data evaluation approach and in its metadata description following the FAIR principles. It discusses exemplarily different assessment tools regarding soil moisture measurements, data processing and visualization and elaborates on which additional (metadata) information is required to increase the trustworthiness of data for secondary usage. Taking into account the perspectives of data collectors, providers and users, the authors identify three aspects of data trustworthiness that promote efficient data sharing: 1) trustworthiness of the measurement 2) trustworthiness of the data processing and 3) trustworthiness of the data integration and visualization. The paper should be seen as the basis for a community discussion on data trustworthiness for a scientifically correct secondary use of the data. We do not have the intention to replace existing procedures and do not claim completeness of reliable tools and approaches described. Our intention is to discuss several important aspects to assess data trustworthiness based on the data life cycle of soil moisture data as an example .
Continuum, cyclotron line, and absorption variability in the high-mass X-ray binary Vela X-1
2022-01-20

Because of its complex clumpy wind, prominent cyclotron resonant scattering features, intrinsic variability, and convenient physical parameters (close distance, high inclination, and small orbital separation), which facilitate the observation and analysis of the system, Vela X-1 is one of the key systems for understanding accretion processes in high-mass X-ray binaries on all scales. We revisit Vela X-1 with two new observations taken with NuSTAR at orbital phases ∼0.68–0.78 and ∼0.36–0.52, which show a plethora of variability and allow us to study the accretion geometry and stellar wind properties of the system. We follow the evolution of spectral parameters down to the pulse period timescale using a partially covered power law continuum with a Fermi-Dirac cutoff to model the continuum and local absorption. We are able to confirm anti-correlations between the photon index and the luminosity and, for low fluxes, between the folding energy and the luminosity, implying a change of properties in the Comptonising plasma. We were not able to confirm a previously seen correlation between the cyclotron line energy and the luminosity of the source in the overall observation, but we observed a drop in the cyclotron line energy following a strong flare. We see strong variability in absorption between the two observations and within one observation (for the ∼0.36–0.52 orbital phases) that can be explained by the presence of a large-scale structure, such as accretion and photoionisation wakes in the system, and our variable line of sight through this structure.
Roux-En-Y Gastric Bypass (RYGB) Surgery during High Liquid Sucrose Diet Leads to Gut Microbiota-Related Systematic Alterations
2022-01-20

Roux-en-Y gastric bypass (RYGB) surgery has been proven successful in weight loss and improvement of co-morbidities associated with obesity. Chronic complications such as malabsorption of micronutrients in up to 50% of patients underline the need for additional therapeutic approaches. We investigated systemic RYGB surgery effects in a liquid sucrose diet-induced rat obesity model. After consuming a diet supplemented with high liquid sucrose for eight weeks, rats underwent RYGB or control sham surgery. RYGB, sham pair-fed, and sham ad libitum-fed groups further continued on the diet after recovery. Notable alterations were revealed in microbiota composition, inflammatory markers, feces, liver, and plasma metabolites, as well as in brain neuronal activity post-surgery. Higher fecal 4-aminobutyrate (GABA) correlated with higher Bacteroidota and Enterococcus abundances in RYGB animals, pointing towards the altered enteric nervous system (ENS) and gut signaling. Favorable C-reactive protein (CRP), serine, glycine, and 3-hydroxybutyrate plasma profiles in RYGB rats were suggestive of reverted obesity risk. The impact of liquid sucrose diet and caloric restriction mainly manifested in fatty acid changes in the liver. Our multi-modal approach reveals complex systemic changes after RYGB surgery and points towards potential therapeutic targets in the gut-brain system to mimic the surgery mode of action.
Attractors of deterministic and random lattice difference equations
2022-01-20

Lattice difference equations are essentially difference equations on a Hilbert space of bi-infinite sequences. They are motivated by the discretization of the spatial variable in integrodifference equations arising in theoretical ecology. It is shown here that under similar assumptions to those used for such integrodifference equations they have a global attractor, to which the global attractors of finite-dimensional approximations converge upper-semi-continuously. Corresponding results are also shown for the lattice difference equations when only a finite number of interconnection weights are nonzero and when the interconnection weights themselves vary and converge in an appropriate manner.
Small‐ and medium‐sized mammals of the Kafa Biosphere Reserve, Ethiopia
2022-01-20

Abstract The Kafa Biosphere Reserve (KBR) is the largest montane forest reserve in Ethiopia and was declared officially a United Nations Educational, Scientific and Cultural Organization (UNESCO) biosphere reserve in 2010. Only recently, however, has the reserve been surveyed in terms of its small‐ and medium‐sized mammal inhabitant species. The KBR supports a diverse variety of habitat types, which are increasingly under pressure from anthropogenic degradation. During the 2014 dry season and 2019 wet season, we used traps, mist‐nets, acoustic signals, photography and roadkill surveys to assess the small‐ and medium‐sized mammals of the reserve. We recorded 17 small‐ and five medium‐sized mammal species, almost half (45.5%) being endemic to Ethiopia. The grayish‐brown shaggy rat ( Dasymys griseifrons ) and two fruit bats ( Epomophorus gambianus and Hypsignathus monstrosus ) were recorded in the reserve for the first time. As a next step, a large‐scale, detailed inventory of the mammals in a wider area of southwestern Ethiopian forests and wetlands, including prevailing anthropogenic threats, is required. Notwithstanding, immediate conservation action by regional and national authorities to prevent further habitat loss to reduce the risk of local extinction is needed, particularly for endemic species or those exhibiting limited range distributions in southwestern Ethiopia.
Metabolic Effects of Estradiol Versus Testosterone in Complete Androgen Insensitivity Syndrome
2022-01-20

Abstract Purpose To study differences in metabolic outcomes between testosterone and estradiol replacement in patients with complete androgen insensitivity syndrome (CAIS). Methods In this multicentre, double-blind, randomized crossover trial, 26 women with CAIS were included of whom 17 completed the study. After a two-months run in phase with estradiol, patients either received transdermal estradiol followed by crossover to transdermal testosterone or vice versa. After six months, differences in lipids, fasting glucose, insulin, hematocrit, liver parameters and blood pressure between the treatment phases were investigated. Results Linear mixed models adjusted for period and sequence did not reveal major group differences according to treatment for the investigated outcomes. In each treatment group, there were however significant uniform changes in BMI and cholesterol. BMI increased significantly, following six months of estradiol (+2.7%; p = 0.036) as well as testosterone treatment (+2.8%; p = 0.036). There was also a significant increase in total (+10.4%; p = 0.001) and LDL-cholesterol (+29.2%; p = 0.049) and a decrease in HDL-cholesterol (-15.8%; p &lt; 0.001) following six months of estradiol as well as six months of testosterone treatment (total cholesterol: +14.6%; p = 0.008; LDL-cholesterol: +39.1%; p = 0.005, HDL-cholesterol: -15.8%; p = 0.004). Other parameters remained unchanged. Conclusion Transdermal estradiol as well as testosterone treatment in women with CAIS results in worsening in lipid profiles. Given the relatively small sample size, subtle group differences in other metabolic parameters may have remained undetected.
Curcumin and NCLX Inhibitors Share Anti-Tumoral Mechanisms in Microsatellite-Instability-Driven Colorectal Cancer
2022-01-20

Abstract Colorectal cancer (CRC) is associated with high mortality worldwide and new targets are needed to overcome treatment resistance. Recent evidences highlight a role of the mitochondria calcium homeostasis in the development of CRC. In this context, we aimed to evaluate the role of the mitochondrial sodium-calcium-lithium exchanger (NCLX) and its targeting in CRC. We also identified curcumin as a new potential inhibitor of NCLX. In vitro, curcumin exerted strong anti-tumoral activity through its action on NCLX with mtCa2+ and reactive oxygen species overload associated with a mitochondrial membrane depolarization, leading to reduced ATP production and apoptosis through mitochondrial permeability transition pore opening concomitant with G2/M cell cycle arrest. NCLX inhibition with either CGP37157 (a benzodiazepine derivative), small interfering RNA-mediated knock-down or knockout approaches reproduced the effects of curcumin. Altered mitochondrial respiration, cellular aerobic glycolysis and endoplasmic reticulum–mitochondria membrane perturbations participated in these mechanisms. In a xenograft mouse model, NCLX inhibitors decreased CRC tumor growth. Both transcriptomic analysis of The Cancer Genome Atlas dataset and immunohistochemical analysis of tissue microarrays from 381 patients with microsatellite instability (MSI)-driven CRC demonstrated that higher NCLX expression was associated with MSI status and for the first time NCLX expression was significantly associated with recurrence-free survival in MSI CRC patients. Our findings provide strong evidence that blocking NCLX inhibits CRC in vitro and in vivo. We highlight a novel anti-tumoral mechanism of curcumin through its action on NCLX and mitochondria calcium overload that could benefit for therapeutic treatment of patients with MSI CRC.
Epistemic Beliefs in Science - An Integration of Evidence From Multiple Studies
2022-01-20

Recent research has integrated developmental and dimensional perspectives on epistemic beliefs by implementing an approach in which profiles of learners’ epistemic beliefs are modeled across multiple dimensions. Variability in study characteristics has impeded the comparison of profiles of epistemic beliefs and their relations with external variables across studies. We examined this comparability by integrating data on epistemic beliefs about the source, certainty, development, and justification of knowledge in science from six studies comprising N = 10,932 German students from elementary to upper secondary school. Applying latent profile analyses to these data, we found that profiles of epistemic beliefs that were previously conceptualized were robust across multiple samples. We found indications that profiles of epistemic beliefs homogenize over the course of students’ education, are related to school tracking, and demonstrate robust relations with students’ personal characteristics and socioeconomic background. We discuss implications for the theory, assessment, and education of epistemic beliefs.
Ion mobility studies of Pyrroloquinoline Quinone Aza-Crown Ether-Lanthanide Complexes
2022-01-20

Lanthanide-dependent enzymes and their biomimetic complexes have arisen as an interesting target of research in the last decade. These enzymes, specifically, pyrroloquinoline quinone (PQQ)-bearing methanol dehydrogenases, efficiently turn over alcohols to the respective aldehydes. To rationally design bioinspired alcohol dehydrogenation catalysts, it is imperative to understand the species involved in catalysis. However, given the extremely flexible coordination sphere of lanthanides, it is often difficult to assess the number and nature of the active species. Here we show how such questions can be addressed by using a combination of ion mobility spectrometry, mass spectrometry and quantum chemical calculations to study the test systems PQQ and lanthanide-PQQ-crown ether ligand complexes. Specifically, we determine the gas phase structures of [PQQH2]-, [PQQH2+H2O]-, [PQQH2+MeOH]-, [PQQ-15c5+H]+ and [PQQ-15c5+Ln+NO3]+ (Ln=La to Lu, except Pm). In the latter case a trend to smaller collision cross sections across the lanthanide series is clearly observable, in line with the well-known lanthanide contraction. We hope that in future such investigations will help to guide the design and understanding of lanthanide based biomimetic complexes optimized for catalytic function.
No Evidence for a Role of Oral Contraceptive-Use in Emotion Recognition But Higher Negativity Bias in Early Follicular Women
2022-01-21

Accuracy in facial emotion recognition has shown to vary with ovarian hormones, both in naturally cycling women, as well as in women taking oral contraceptives. It remains uncertain however, if specific – endogenous and exogenous – hormonal levels selectively impact recognition of certain basic emotions (or neutral faces) and if this relationship coincides with certain affective states. Therefore, we investigated 86 women under different hormonal conditions and compared their performance in an emotion recognition task as well as self-reported measures of affective states. Based on self-reported cycle days and ovulation testing, the participants have been split into groups of naturally cycling women during their early follicular phase (fNC, n = 30), naturally cycling women during their peri-ovulatory phase (oNC, n = 26), and women taking oral contraceptives (OC, n = 30). Participants were matched for age and did not differ in education or neuropsychological abilities. Self-reported anxiety and depressive affective state scores were similar across groups, but current affective state turned out to be significantly more negative in fNC women. Independent of negative affective state, fNC women showed a significantly higher negativity bias in recognizing neutral faces, resulting in a lower recognition accuracy of neutral faces compared to oNC and OC women. In the OC group only, negative affective state was associated with lower recognition accuracy and longer response times for neutral faces. Furthermore, there was a significant, positive association between disgust recognition accuracy and negative affective state in the fNC group. Low progesterone levels during the early follicular phase were linked to higher negative affective state, whereas in the peri-ovulatory phase they were linked to elevated positive affective state. Overall, previous findings regarding impaired emotion recognition during OC-use were not confirmed. Synthetic hormones did not show a correlation with emotion recognition performance and affective state. Considering the important role of emotion recognition in social communication, the elevated negativity bias in neutral face recognition found for fNC women may adversely impact social interactions in this hormonal phase.
The mediating effect of platform width on the size and shape of stone flakes
2022-01-21

To understand the ways in which past stone knappers controlled the morphology of the flakes they produced, archaeologists have focused on examining the effects of striking platform attributes on flake size and shape. Among the variables commonly considered, platform width has routinely been noted to correlate with flake size and hence used to explain past knapping behaviors. Yet, the influence of platform width on flake variation remains equivocal due to the fact that the attribute is not under the direct control of the knapper. Instead, platform width tends to be treated as a by-product of other independent knapping parameters, such as platform depth. In this study, we hypothesize that platform width acts as an intermediary that intervenes the effect of other independent variables on flake attributes. By analyzing experimental flakes produced under both controlled and replicative settings, the results support the hypothesis that platform width mediates the effect of platform depth on flake width, such that flakes with relatively larger platform widths are generally wider but no longer. This finding provides a way to incorporate platform width into discussions of the interrelationships among knapping variables, and highlights the importance of platform width for investigating how past knappers controlled flake production through platform manipulation.
Simultaneous detection of metabolite concentration changes, water BOLD signal and pH changes during visual stimulation in the human brain at 9.4T
2022-01-21

This study presents a method to directly link metabolite concentration changes and BOLD response in the human brain during visual stimulation by measuring the water and metabolite signals simultaneously. Therefore, the metabolite-cycling (MC) non-water suppressed semiLASER localization technique was optimized for functional 1 H MRS in the human brain at 9.4 T. Data of 13 volunteers were acquired during a 26:40 min visual stimulation block-design paradigm. Activation-induced BOLD signal was observed in the MC water signal as well as in the NAA-CH 3 and tCr-CH 3 singlets. During stimulation, glutamate concentration increased 2.3 ± 2.0% to a new steady-state, while a continuous increase over the whole stimulation period could be observed in lactate with a mean increase of 35.6 ± 23.1%. These increases of Lac and Glu during brain activation confirm previous findings reported in literature. A positive correlation of the MC water BOLD signal with glutamate and lactate concentration changes was found. In addition, a pH decrease calculated from a change in the ratio of PCr to Cr was observed during brain activation, particularly at the onset of the stimulation.
The Global case-fatality rate of COVID-19 has been declining disproportionately between top vaccinated countries and the rest of the world
2022-01-21

Abstract Globally 58.83% human population received at least one dose of the COVID-19 vaccines as of 5 January 2021. COVID-19 vaccination rollout is progressing at varied rates globally and data on the impact of mass vaccination on infection and case-fatality rates require definition. We compared the global reported cumulative case-fatality rate (rCFR) between top-20 countries with COVID-19 vaccination rates (&gt;125 doses/100 people) and the rest of the world, before and after commencement of vaccination programmes. We considered the 28th day of receiving the first vaccine in the world as a cut-off to compare the pre-vaccine period (Jan 1, 2020 – Jan 5, 2021) and the post-vaccine period (Jan 6, 2021-Jan 5, 2022). We used a Generalized linear mixed model (GLMM) with a beta distribution to investigate the association between the CFR and potential predictors of each country and reported the relative risk (RR) of each variable. The mean rCFR of COVID-19 in the top-20 countries with vaccination rates was 1.83 (95% CI: 1.24-2.43) on 5 Jan 2021 and 1.18 (95% CI: 0.73-1.62) on 5 Jan 2022. The CFR for the rest of the world on 5 Jan 2021 was 2.32 (95% CI: 1.86-2.79) and 2.20 (95% CI: 1.86-2.55) on 5 January 2022. In Sub-Saharan Africa, the CFR remained roughly unchanged at 1.97 (95% CI: 1.59-2.35) on 5 Jan 2021 and 1.98 (95% CI:1.58-2.37) on 5 Jan 2022. The GLMM showed vaccination (/100 population) (RR:0.37) and Stringency Index (RR:0.88) were strong protective factors for the country’s COVID-19 CFR indicating that both vaccination and lockdown measures help in the reduction of COVID-19 CFR. The rCFR of COVID-19 continues to decline, although at a disproportionate rate between top vaccinated countries and the rest of the world. Vaccine equity and faster roll-out across the world is critically important in reducing COVID-19 transmission and CFR. Key Questions What is already known Vaccination can reduce the case-fatality rate of COVID-19. Globally, the COVID-19 vaccination rollout is progressing at varied rates. What are the new findings In the top-20 countries with vaccination, &gt;200 doses of vaccines are given per 100 people on 5 th Jan 2022, In the rest of the word, the figure is 105, and in Sub-Saharan Africa (SSA) only 15.72 After the introduction of COVID-19 vaccination the reported case-fatality rate (rCFR) of COVID-19 has reduced by 35% in the top-20 countries with vaccination, 8% in the rest of the world roughly unchanged in SSA. The doses of COVID-19 vaccines (/100 people) and rCFR has a negative correlation on 5 Jan 2022 (r=-0.296, p&lt;0.001). The COVID-19 vaccination and Stringency Index are strong protective factors for the country’s COVID-19 rCFR indicating that both vaccination and lockdown measures help in reduction of COVID-19 rCFR. What do the new findings imply The disproportionate case-fatality rate of COVID-19 between top vaccinated countries and the rest of the world demand fast and equitable vaccine rollout globally to reduce COVID-19 transmission and CFR
Assessing fetal growth in Africa: Application of the international WHO and INTERGROWTH-21st standards in a Beninese pregnancy cohort
2022-01-21

Background Fetal growth restriction is a major complication of pregnancy and is associated with stillbirth, infant death and child morbidity. Ultrasound monitoring of pregnancy is becoming more common in Africa for fetal growth monitoring in clinical care and research, but many countries have no national growth charts. We evaluated the new international fetal growth standards from INTERGROWTH-21 st and WHO in a cohort from southern Benin. Methods Repeated ultrasound and clinical data were collected in women from the preconceptional RECIPAL cohort (241 women with singleton pregnancies, 964 ultrasounds). We modelled fetal biometric parameters including abdominal circumference (AC) and estimated fetal weight (EFW) and compared centiles to INTERGROWTH-21 st and WHO standards, using the Bland and Altman method to assess agreement. For EFW, we used INTERGROWTH-21 st standards based on their EFW formula (IG21st) as well as a recent update using Hadlock’s EFW formula (IG21hl). Proportions of fetuses with measurements under the 10 th percentile were compared. Results Maternal malaria and anaemia prevalence was 43% and 69% respectively and 11% of women were primigravid. Overall, the centiles in the RECIPAL cohort were higher than that of INTERGROWTH-21 st and closer to that of WHO. Consequently, the proportion of fetuses under 10 th percentile thresholds was systematically lower when applying IG21st compared to WHO standards. At 27–31 weeks and 33–38 weeks, respectively, 7.4% and 5.6% of fetuses had EFW &lt;10 th percentile using IG21hl standards versus 10.7% and 11.6% using WHO standards. Conclusion Despite high anemia and malaria prevalence in the cohort, IG21st and WHO standards did not identify higher than expected proportions of fetuses under the 10 th percentiles of ultrasound parameters or EFW. The proportions of fetuses under the 10 th percentile threshold for IG21st charts were particularly low, raising questions about its use to identify growth-restricted fetuses in Africa.