Miracle-dz/UniFAR-FTUs huggingface dataset:
Increasing recognition of historically marginalized scientists: Lessons learned from the Nomination Task Force

The Space Physics and Aeronomy (SPA) Section of the American Geophysical Union (AGU) created a Nomination Task Force (NTF) in 2017 upon concerns that the numbers of women nominated for AGU Fellow were significantly lower than would be expected based on SPA membership representation, including as low as zero in two of the four preceding years. Now that the NTF has been in existence through four cycles of AGU Honors and Awards, the outcomes indicate the success of the NTF in increasing the number of nominations for scientists from historically marginalized groups. These data indicate that the work of the NTF has enhanced the nomination pool rather than occurring at the expense of other nominees. Until recently, the ability to collect and distribute demographic information has been limited, and cisgender binary identities are often inferred. Moving forward it is a goal of AGU to be more inclusive and intentional with respect to gender, racial, and ethnic identities. We share our best practices and success stories with a broad audience to help others build upon the work of the NTF within their own institutions and professional groups. We also discuss challenges that we are still facing and provide suggestions for continuing to improve the process.
Meta-analysis of substitution value of maize with cassava (Manihot esculenta Cratnz) on growth performance of broiler chickens

There are variable results on the effect of cassava on the performance characteristics of broiler chickens. As a result, this meta-analysis was performed to determine the effect of cassava on feed intake, feed conversion ratio (FCR), and average daily gain (ADG) in broiler chickens. A methodical search performed on Google Scholar, Scopus, Web of Science, and PubMed databases as well as individual journals yielded 365 published articles. Out of 365 studies, 23 that met the inclusion criteria were used for the meta-analysis. Outcome measures were pooled using a random-effects model. Results were expressed as standardized mean differences (SMD) at 95% confidence intervals (CIs). Subgroup and meta-regression analyses were used to explore the effects of studied covariates (broiler strain, inclusion level of cassava, number of broilers per replicate, cassava processing methods, and cassava form) on measured outcomes. Results indicated that cassava had a small positive effect on feed intake (SMD = −0.07, 95% CI −0.26, 0.12) and FCR (SMD = 0.14; 95% CI 0.82, 1.746), but a large negative effect on ADG (SMD = −1.67; 95% CI −1.99, −1.35) compared to the controls. Subgroup analysis by cassava form showed that wet fermented cassava peel meal (WFCPM) had a moderate impact on feed intake (SMD = 0.62, 95% CI 0.47, 0.77) and ADG (SMD = 0.66, 95% CI 0.37, 0.95) in broiler chickens compared with the controls. Our results also found improved growth performance in broiler chickens fed cassava at 4–10%. There is evidence of between-study variance, and studied covariates explain most of the sources of heterogeneity. This study concluded that the replacement of maize with 4–10% WFCPM improved growth performance traits in broiler chickens.
Upstream-downstream asymmetries of drought impacts in major river basins of the European Alps

The European Alps, despite being Europe's water towers, are increasingly affected by droughts. In recent decades, when climate warming has intensified, drought impacts have illustrated the regions' vulnerability. Improved knowledge on the spatial distribution of drought impacts from high elevation headwater regions down to plateau and foothill areas is of tremendous importance to understand socio-economic drought dimensions. The region has an exceptional data availability including archived drought impact information. It is therefore a good test bed for the often-assumed general hypothesis that drought impacts occur more often downstream. The aim of this study was to investigate whether upstream-downstream differences in the distribution of drought impacts exist in the four major river basins of the European Alps - Rhine, Rhone, Po and Danube. Two different classifications were developed to divide these basins in up- and downstream areas. We based the first classification on the distances to the main sink, and the second classification on human influence. The EDIIALPS database provided qualitative data to analyze the distribution patterns of reported drought impacts from 2000 to 2020. The results suggest a strong regional variability regarding the temporal and spatial distribution of drought impacts within the individual basins. But they support the general hypothesis: for both classifications the number of drought impacts per area is higher in downstream regions. For the classification based on distances differences are statistically significant for the Rhine and Danube basin. Further, the analysis of the drought indices SPI-6 and SPEI-6 revealed that the drought event does not have a large impact on the upstream-downstream differences. The study provides support for the existence of upstream-downstream asymmetries, but most importantly, the spatial distributions of drought impacts found in the four major river basins of the European Alps highlight the need for a network based analysis with more consistent impact data within river basins. Climate change and enhanced cascading effects likely increase these asymmetries and consequently future drought management strategies should take them into account.
Evaluating the validity of a functional electrical stimulation clinical decision making tool: A qualitative study

Introduction Following central nervous system damage, the recovery of motor function is a priority. For some neurological populations, functional electrical stimulation (FES) is recommended in best practice guidelines for neurorehabilitation. However, limited resources exist to guide FES application, despite clinicians reporting that a lack of FES knowledge prevents use in clinical practice. The FES Clinical Decision Making Tool was developed to assist clinicians with FES application and translation into clinical practice. The purpose of this study was to evaluate the content validity of the Tool from the perspectives of Canadian physical and occupational therapists using FES in neurorehabilitation. Methods Thirteen participants (twelve women, one man), aged 40.5 ± 10.3 years, participated in individual semi-structured interviews to explore their clinical decision making experiences when applying FES and to evaluate the content validity (i.e., appropriateness, comprehensibility, and comprehensiveness) of the Tool. Interviews were analyzed using a qualitative conventional content analysis following the DEPICT model. Results Three themes were identified. 1) Clinician context influences FES usage. Participants' experiences with FES use varied and application was influenced by treatment goals. 2) Parameter selection in clinical practice. Participants identified decision-making strategies and the challenges of parameter selection. 3) With modifications, the Tool is a valid resource to inform FES applications. Participants discussed its strengths, limitations, and suggested changes. While the Tool is useful, a more extensive resource (e.g., appendix) for the Tool is warranted. Discussion A revised Tool was created to improve its comprehensiveness and comprehensibility. Thus, the Tool is a valid resource for applying FES in neurorehabilitation.
Nitrogen fertilizer application rates and ratios promote the biochemical and physiological attributes of winter wheat

Improper optimization of the rates and ratios of nitrogen application reduces grain yields and increases the nitrogen loss, thereby affecting environmental quality. In addition, scarcer evidence exists on the integrative approach of nitrogen, which could have effects on the biochemical and physiological characteristics of wheat. Treatments were arranged as nitrogen (N) rates of 00, 75, 150, 225, and 300 kg ha−1 in the main plots, and different nitrogen ratios were organized in subplots at 5:5:0:0 and 6:4:0:0, which were applied at the sowing, jointing, flowering, and grain filling stages. The results revealed that 225 kg N ha−1 significantly enhanced the stomatal conductance (G s), photosynthetic rate (P n), intercellular CO2 (C i), transpiration rate (T r), and total chlorophyll by 28.5%, 42.3%, 10.0%, 15.2%, and 50%, receptively, at the jointing stage in comparison to the control (0 kg N ha−1). Nitrogen application of 225 kg ha−1 increased the soil–plant analysis development (SPAD) value and the chlorophyll a, chlorophyll b, and carotenoid contents of winter wheat under the 6:4:0:0 ratio. The trend of the photosynthetic characteristics was observed to be greater at the 6:4:0:0 fertilization ratio compared to that at 5:5:0:0. The photosynthetic rate was significantly associated with the biochemical and physiological characteristics of winter wheat. In conclusion, the nitrogen dose of 225 kg ha−1 and the ratio of 6:4:0:0 (quantity applied at the sowing, jointing, flowering, and grain filling stages) effectively promoted the photosynthetic and other physiological characteristics of winter wheat.
Parametrized homology via zigzag persistence

This paper develops the idea of homology for 1-parameter families of topological spaces. We express parametrized homology as a collection of real intervals with each corresponding to a homological feature supported over that interval or, equivalently, as a persistence diagram. By defining persistence in terms of finite rectangle measures, we classify barcode intervals into four classes. Each of these conveys how the homological features perish at both ends of the interval over which they are defined.
Cytokine expression in rhinovirus- vs. respiratory syncytial virus-induced first wheezing episode and its relation to clinical course

Rhinovirus (RV) and respiratory syncytial virus (RSV) are common causes of bronchiolitis. Unlike an RSV etiology, an RV etiology is associated with a markedly increased risk of asthma. We investigated the cytokine profiles of RV- and RSV-induced first wheezing episode and their correlation with prognosis. We recruited 52 sole RV- and 11 sole RSV-affected children with a severe first wheezing episode. Peripheral blood mononuclear cells (PBMCs) were isolated during acute illness and 2 weeks later and stimulated in vitro with anti-CD3/anti-CD28. Culture medium samples were analyzed for 56 different cytokines by multiplex ELISA. Recurrences were prospectively followed for 4 years. In adjusted analyses, the cytokine response from PBMCs in the RV group was characterized by decreased expression of interleukin 1 receptor antagonist (IL-1RA), interleukin 1 beta (IL-1β), and monocyte chemoattractant protein-1 (MCP-1) and increased expression of eosinophil chemotactic protein 2 (eotaxin-2), thymus- and activation-regulated chemokine (TARC), and epithelial-derived neutrophil-activating peptide 78 (ENA-78) in the acute phase and increased expression of fractalkine in the convalescent phase compared to those in the RSV group. An analysis of the change in cytokine expression between study points revealed an increased expression of fractalkine and IL-1β and decreased expression of I-309 (CCL1) and TARC in the RV group compared to those in the RSV group. Considering hospitalization time, a significant non-adjusted group × cytokine interaction was observed in the levels of interferon gamma (IFN-γ), macrophage-derived chemokine (MDC), IL-1RA, and vascular endothelial growth factor (VEGF), indicating that a higher expression of cytokine was associated with shorter hospitalization time in the RSV group but not in the RV group. A significant interaction was also found in interleukin 6 (IL-6), but the cytokine response was not associated with hospitalization time in the RSV or RV group. In the RV group, increased expression of I-309 (CCL1) and TARC was associated with fewer relapses within 2 months, and decreased expression of interleukin 13 (IL-13) and increased expression of I-309 (CCL1) were associated with less relapses within 12 months. Differences in cytokine response from PBMCs were observed between RV- and RSV-induced first severe wheezing episode. Our findings also reveal new biomarkers for short- and medium-term prognosis in first-time wheezing children infected with RV or RSV.
Towards an accurate and robust analysis pipeline for somatic mutation calling

Accurate and robust somatic mutation detection is essential for cancer treatment, diagnostics and research. Various analysis pipelines give different results and thus should be systematically evaluated. In this study, we benchmarked 5 commonly-used somatic mutation calling pipelines (VarScan, VarDictJava, Mutect2, Strelka2 and FANSe) for their precision, recall and speed, using standard benchmarking datasets based on a series of real-world whole-exome sequencing datasets. All the 5 pipelines showed very high precision in all cases, and high recall rate in mutation rates higher than 10%. However, for the low frequency mutations, these pipelines showed large difference. FANSe showed the highest accuracy (especially the sensitivity) in all cases, and VarScan and VarDictJava outperformed Mutect2 and Strelka2 in low frequency mutations at all sequencing depths. The flaws in filter was the major cause of the low sensitivity of the four pipelines other than FANSe. Concerning the speed, FANSe pipeline was 8.8∼19x faster than the other pipelines. Our benchmarking results demonstrated performance of the somatic calling pipelines and provided a reference for a proper choice of such pipelines in cancer applications.
Probabilistic Permutation Synchronization Using the Riemannian Structure of the Birkhoff Polytope

We present an entirely new geometric and probabilistic approach to synchronization of correspondences across multiple sets of objects or images. In particular, we present two algorithms: (1) Birkhoff-Riemannian L-BFGS for optimizing the relaxed version of the combinatorially intractable cycle consistency loss in a principled manner, (2) Birkhoff-Riemannian Langevin Monte Carlo for generating samples on the Birkhoff Polytope and estimating the confidence of the found solutions. To this end, we first introduce the very recently developed Riemannian geometry of the Birkhoff Polytope. Next, we introduce a new probabilistic synchronization model in the form of a Markov Random Field (MRF). Finally, based on the first order retraction operators, we formulate our problem as simulating a stochastic differential equation and devise new integrators. We show on both synthetic and real datasets that we achieve high quality multi-graph matching results with faster convergence and reliable confidence/uncertainty estimates.
OGLE-2012-BLG-0950Lb: THE FIRST PLANET MASS MEASUREMENT FROM ONLY MICROLENS PARALLAX AND LENS FLUX

We report the discovery of a microlensing planet OGLE-2012-BLG-0950Lb with a planet/host mass ratio of . A long term distortion detected in both MOA and OGLE light curve can be explained by the microlens parallax due to the Earth’s orbital motion around the Sun. Although the finite source effect is not detected, we obtain the lens flux by the high resolution Keck AO observation. Combining the microlens parallax and the lens flux reveal the nature of the lens: a planet with mass of is orbiting around an M-dwarf with mass of with a planet-host projected separation of au located at kpc from us. This is the first mass measurement from only microlens parallax and the lens flux without the finite source effect. In the coming space observation-era with Spitzer, K2, Euclid, and WFIRST, we expect many such events for which we will not be able to measure any finite source effect. This work demonstrates an ability of mass measurements in such events.
The Role of Sfp1 in Candida albicans Cell Wall Maintenance

The cell wall is the first interface for Candida albicans interaction with the surrounding environment and the host cells. Therefore, maintenance of cell wall integrity (CWI) is crucial for C. albicans survival and host-pathogen interaction. In response to environmental stresses, C. albicans undergoes cell wall remodeling controlled by multiple signaling pathways and transcription regulators. Here, we explored the role of the transcription factor Sfp1 in CWI. A deletion of the SFP1 gene not only caused changes in cell wall properties, cell wall composition and structure but also modulated expression of cell wall biosynthesis and remodeling genes. In addition, Cas5 is a known transcription regulator for C. albicans CWI and cell wall stress response. Interestingly, our results indicated that Sfp1 negatively controls the CAS5 gene expression by binding to its promoter element. Together, this study provides new insights into the regulation of C. albicans CWI and stress response.
On Density-Critical Matroids

For a matroid $M$ having $m$ rank-one flats, the density $d(M)$ is $\tfrac{m}{r(M)}$ unless $m = 0$, in which case $d(M)= 0$. A matroid is density-critical if all of its proper minors of non-zero rank have lower density. By a 1965 theorem of Edmonds, a matroid that is minor-minimal among simple matroids that cannot be covered by $k$ independent sets is density-critical. It is straightforward to show that $U_{1,k+1}$ is the only minor-minimal loopless matroid with no covering by $k$ independent sets. We prove that there are exactly ten minor-minimal simple obstructions to a matroid being able to be covered by two independent sets. These ten matroids are precisely the density-critical matroids $M$ such that $d(M) > 2$ but $d(N) \le 2$ for all proper minors $N$ of $M$. All density-critical matroids of density less than $2$ are series-parallel networks. For $k \ge 2$, although finding all density-critical matroids of density at most $k$ does not seem straightforward, we do solve this problem for $k=\tfrac{9}{4}$.
Phaeosphaeridiols A–C: Three New Compounds from Undescribed Phaeosphaeriaceae sp. SGSF723

Fungi in forest litter are diverse as decomposers but natural products from these fungi are rarely investigated, especially for their antimicrobial activities against crop diseases. In this study, fungal isolate SGSF723 with antimicrobial activities was cultured. A multi-gene phylogenetic analysis showed SGSF723 was an undescribed species in the family Phaeosphaeriaceae. By bio-guided assay, three new compounds (Phaeosphaeridiols A–C) and two known compounds were purified from the ethyl acetate extract. The structures of Phaeosphaeridiols A–C were elucidated as 2-(2′-butenyl)-5 (3″-pentene)-1,3-benzenediol (1), 2-(2′-butenyl)-5-(3″S,4″S-pentane diol)-1,3-benzenediol (2), and 3-(4′-(2″-butenyl)-3′,5′-benzenediol phenol)-2-acrylic acid (3) by 2D NMR, HRESIMS, and Mosher’s method. Phaeosphaeridiols A–C exhibited moderate or weak antimicrobial activities against plant pathogens by 96-well plate and spore germination assays.
Role of Hyaluronic acid in various diseases with special emphasis on Periodontal inflammation - A review

Hyaluronic acid is a naturally occurring polysaccharide of extracellular matrix of connective tissues, synovial fluid, and other body tissues. It has an important role in regulating interactions intra and extracellularly between different growth factors, in addition to regulating osmotic pressure, maintaining tissue volume and lubrication. Periodontitis is an multifactorial inflammatory disease that affects teeth supporting structures which results in teeth loss. It is considered a wide world cause of teeth loss in adults. In addition to its local effect, teeth loss, it can have systemic impacts on many systemic organs. Although its main cause is bacteria, exaggerated host response and risk factors such as smoking, diabetes mellitus, HIV/AIDS, family history, and certain medications increase the disease progress. Hence teeth supporting structures are connective tissues and hyaluronic acid is a main component of connective tissues, a correlation of both in health and disease is explained in this article.
On various definitions of shadowing with average error in tracing

When computing a trajectory of a dynamical system, influence of noise can lead to large perturbations which can appear, however, with small probability. Then when calculating approximate trajectories, it makes sense to consider errors small on average, since controlling them in each iteration may be impossible. Demand to relate approximate trajectories with genuine orbits leads to various notions of shadowing (on average) which we consider in the paper. As the main tools in our studies we provide a few equivalent characterizations of the average shadowing property, which also partly apply to other notions of shadowing. We prove that almost specification on the whole space induces this property on the measure center which in turn implies the average shadowing property. Finally, we study connections among sensitivity, transitivity, equicontinuity and (average) shadowing.
Sylvester-Gallai type theorems for quadratic polynomials

We prove Sylvester-Gallai type theorems for quadratic polynomials. Specifically, we prove that if a finite collection Q, of irreducible polynomials of degree at most 2, satisfy that for every two polynomials Q1,Q2∈ Q there is a third polynomial Q3∈Q so that whenever Q1 and Q2 vanish then also Q3 vanishes, then the linear span of the polynomials in Q has dimension O(1). We also prove a colored version of the theorem: If three finite sets of quadratic polynomials satisfy that for every two polynomials from distinct sets there is a polynomial in the third set satisfying the same vanishing condition then all polynomials are contained in an O(1)-dimensional space. This answers affirmatively two conjectures of Gupta [Electronic Colloquium on Computational Complexity (ECCC), 21:130, 2014] that were raised in the context of solving certain depth-4 polynomial identities. To obtain our main theorems we prove a new result classifying the possible ways that a quadratic polynomial Q can vanish when two other quadratic polynomials vanish. Our proofs also require robust versions of a theorem of Edelstein and Kelly (that extends the Sylvester-Gallai theorem to colored sets).
The Effelsberg-Bonn H i Survey: Milky Way gas - First data release

Context. The Effelsberg–Bonn H i Survey (EBHIS) is a new 21-cm survey performed with the 100-m telescope at Effelsberg. It covers the whole northern sky out to a redshift of z ∼ 0.07 and comprises H i line emission from the Milky Way and the Local Volume. Aims. We aim to substitute the northern-hemisphere part of the Leiden/Argentine/Bonn Milky Way H i survey (LAB) with this first EBHIS data release∗, which presents the H i gas in the Milky Way regime. Methods. The use of a seven-beam L-band array made it feasible to perform this all-sky survey with a 100-m class telescope in a reasonable amount of observing time. State-of-the-art fast-Fourier-transform spectrometers provide the necessary data read-out speed, dynamic range, and spectral resolution to apply software radio-frequency interference mitigation. EBHIS is corrected for stray radiation and employs frequency-dependent flux-density calibration and sophisticated baseline-removal techniques to ensure the highest possible data quality. Results. Detailed analyses of the resulting data products show that EBHIS is not only outperforming LAB in terms of sensitivity and angular resolution, but also matches the intensity-scale of LAB extremely well, allowing EBHIS to be used as a drop-in replacement for LAB. Data products are made available to the public in a variety of forms. Most important, we provide a properly gridded Milky Way H i column density map in HEALPix representation. To maximize the usefulness of EBHIS data, we estimate uncertainties in the H i column density and brightness temperature distributions, accounting for systematic effects.