Miracle-dz/UniFAR-FTUs huggingface dataset:
Nuclear DNA Content Diversity in Chinese Soybean Introductions

Abstract Intraspecific nuclear DNA content has been documented in various angiosperm species. The purpose of this study was to determine the nuclear DNA content variation in soybean (Glycine max(L.) Merr. ). Several studies have suggested that DNA content variation exists in soybean. Ninety soybean lines representing diverse geographic locations in China were analysed by flow cytometry. Nuclei were isolated and stained with either the fluorochrome DAPI or PI. After analysis, it was determined that PI stained nuclei more accurately assessed the total DNA content in soybean. A 12% variation in nuclear DNA content was observed among the 90 lines. The amount of nuclear DNA in the lines was within the DNA range of United States cultivars previously examined. Nuclear DNA content variation in soybean is much less than the variation reported in maize. These results could be due to the lack of polymorphism in large chromosomal elements containing large blocks of repetitive DNA. In addition, unlike maize, the amounts of DNA variation did not decrease as a result of more intensive breeding in United States cultivars. Intraspecific nuclear DNA content variability is very different between these two major agronomic species.
Evaluation of yields of seven upland rice (Oryzae sativa) cultivars sown by three methods in Anyigba, Kogi State, Nigeria.

Yield is the characteristic by which a cultivar is commonly judge. A cultivar may be considered satisfactory only if it is able to produce a good yield in comparison to others at various times and in various situations. Trials were conducted in the rainy seasons of 2007 and 2008 at the Kogi State University Teaching and Research Farm (Longitude 07°06 1 N; 43°E), Anyigba, Kogi State, Nigeria to investigate the response of seven cultivars of upland (NERICA 1-7) rice sown by three sowing methods: broadcasting, dibbling and drilling. Treatments consisted of three sowing methods (drilling at 20 cm apart, dibbling at 20 × 20 cm and even broadcasting of seeds) of seven NERICA varieties. Results of statistical analysis revealed that crop establishment responded significantly to sowing method and cultivar. Significant influence of cultivar was also observed on final plant height and paddy yield. Significant interactions (sowing method × cultivar) were observed on establishment count and paddy yield/ha. The combined results of both seasons show that NERICA 5 gave the highest paddy yield. However, considering the individual years, the most consistent cultivar was NERICA 6. Thus, it is recommended for the experimental area.
The solar abundance problem and eMSTOs in clusters

In this study, we focus on the impact of accretion from protoplanetary discs on the stellar evolution of AFG-type stars. We used a simplified disc model that was computed using the Two-Pop-Py code, which contains the growth and drift of dust particles in the protoplanetary disc, to model the accretion scenarios for a range of physical conditions for protoplanetary discs. Two limiting cases were combined with the evolution of stellar convective envelopes that were computed using the Garstec stellar evolution code. We find that the accretion of metal-poor (gas) or metal-rich (dust) material has a significant impact on the chemical composition of the stellar convective envelope. As a consequence, the evolutionary track of the star diverts from the standard scenario predicted by canonical stellar evolution models, which assume a constant and homogeneous chemical composition after the assembly of the star is complete. In the case of the Sun, we find a modest impact on the solar chemical composition. Indeed, the accretion of metal-poor material reduces the overall metallicity of the solar atmosphere and it is consistent, within the uncertainty, with the solar Z reported by Caffau et al. (2011, Sol. Phys., 268, 255), but our model is not consistent with the measurement by Asplund et al. (2009, ARA&A, 47, 481). Another relevant effect is the change of the position of the star in the colour-magnitude diagram. By comparing our predictions with a set of open clusters from the Gaia DR2, we show that it is possible to produce a scatter close to the TO of young clusters that could contribute to explaining the observed scatter in CMDs. Detailed measurements of metallicities and abundances in the nearby open clusters will additionally provide a stringent observational test for our proposed scenario.
Red blood cell distribution width (RDW) in Hospitalized COVID-19 Patients

Introduction: Coronavirus disease-2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), is causing dramatic morbidity and mortality worldwide. The Red Blood Cell Distribution Width (RDW) has been strongly associated with increased morbidity and mortality in multiple diseases. Objective: To assess if elevated RDW is associated with unfavorable outcomes in hospitalized COVID-19. Methods: We retrospectively studied clinical outcomes of hospitalized COVID-19 patients for their RDW values. In-hospital mortality was defined as primary outcome, while septic shock, need for mechanical ventilation, and length of stay (LOS) were secondary outcomes. Results- A total of 294 COVID-19 patients were finally studied. Overall prevalence of increased RDW was 49.7% (146/294). RDW was associated with increased risk of in-hospital mortality (aOR, 4.5; 95%CI, 1.4-14.3) and septic shock (aOR, 4.6; 95%CI, 1.4-15.1) after adjusting for anemia, ferritin, and lactate. The association remained unchanged even after adjusting for other clinical confounders such as age, sex, body mass index, coronary artery disease, hypertension, diabetes mellitus, and chronic obstructive pulmonary disease. No association was found instead with mechanical ventilation and median LOS. Conclusion: Elevated RDW in hospitalized COVID-19 patients is associated with a significantly increased risk of mortality and septic shock.
H2O2 induces translocation of APE/Ref‐1 to mitochondria in the Raji B‐cell line

Reactive oxygen species (ROS) are generated as by‐products of respiration and are used as signal transducing intermediates in out–in signaling pathways. ROS are also generated during inflammatory responses and it has been shown that hydrogen peroxide may trigger activation of B‐lymphocytes, similar to cross‐linking of surface immunoglobulins. On the other hand, both exogenous and endogenous generated ROS are a major source of nuclear and mitochondrial DNA (mtDNA) damage. The base excision repair (BER) enzyme APE/Ref‐1 normally repairs small nuclear DNA lesion such as oxidized or alkylated bases. It is not clear though whether DNA repair mechanisms able to abolish oxidative damage from nuclear DNA are present into mitochondria too. Here we show by confocal microscopy and Western blot analysis that in the B‐lymphocyte Raji cell line a fraction of APE/Ref‐1 rapidly re‐localizes into mitochondria following H2O2 activation. Targeting of APE/Ref‐1 to mitochondria is not associated with cytochrome‐c loss or apoptosis induction. These findings indicate that the APE/Ref‐1 translocates to mitochondria in response to oxidative stress and thereby it might exert a protective function. © 2002 Wiley‐Liss, Inc.
Regorafenib Versus Nivolumab After Sorafenib Failure: Real‐World Data in Patients With Hepatocellular Carcinoma

Regorafenib and nivolumab are drugs approved for second‐line treatment of patients with hepatocellular carcinoma (HCC) after sorafenib failure. However, the effectiveness of regorafenib and nivolumab following sorafenib has not been directly compared. This study retrospectively evaluated 373 patients with HCC who were treated with regorafenib (n = 223) or nivolumab (n = 150) after sorafenib failure between July 2017 and February 2019. Progression‐free survival (PFS; hazard ratio [HR], 0.85; 95% confidence interval [CI], 0.69‐1.06; P = 0.150), time to progression (TTP; HR, 0.95; 95% CI, 0.77‐1.19; P = 0.680), and overall survival (OS; HR, 0.83; 95% CI, 0.64‐1.07; P = 0.154) did not differ significantly between groups of patients treated with regorafenib and nivolumab, findings consistently observed by multivariable‐adjusted, propensity score‐matched, and inverse probability treatment weighting (IPTW) analyses. However, the objective response rate was significantly higher in the nivolumab than in the regorafenib group (13.3% vs. 4.0%; P = 0.002). When the effectiveness of regorafenib and nivolumab was compared in nonprogressors to treatment, defined as patients who achieved complete response, partial response, or stable disease after first response evaluation, PFS (HR, 0.50; 95% CI, 0.33‐0.75; P = 0.001), TTP (HR, 0.48; 95% CI, 0.31‐0.73; P < 0.001), and OS (HR, 0.51; 95% CI, 0.31‐0.87; P = 0.013) were significantly longer in the 59 nonprogressors to nivolumab than in the 104 nonprogressors to regorafenib, findings also observed by multivariable‐adjusted and IPTW analyses. Conclusion: Survival outcomes in patients treated with regorafenib and nivolumab after sorafenib failure did not differ significantly. However, nivolumab may be more effective than regorafenib in nonprogressors.
Image analysis of maize root caps - Estimating cell numbers from 2-D longitudinal sections

The cap of the primary root of maize produces several thousand border cells that are shed from the outside of the cap each day. Border cell production is important in the penetration of soil by roots, and in influencing the activity of both beneficial and pathogenic organisms in the rhizosphere. To improve understanding of the dynamics of border cell production, it is desirable to know the number of cells in diAerent parts of the root cap. An image analysis procedure was used to quantify cell dimensions and locations in the median longitudinal section of maize (Zea mays L.) root caps. Calculations based on root symmetry were then used to estimate the number of cells in 3-dimensions. Our estimation procedure was tested initially using regular arrays of identical square and hexagonal shapes to represent cells. It was then tested using two diAerent tissues showing analogous arrays: a transverse section through the maize root cap junction, and a transverse section through a barley root. Good linear correlations were obtained between the number of cells estimated and the number of cells actually counted in the microscope. The numbers of cells in the whole maize root cap (8870+390) were then estimated from longitudinal sections. These numbers of cap cells agreed with values that had been estimated for maize by other methods. In the first tier of the cap meristem, tentimes more meristematic cells were located in the cap flanks (4500 cells) than were present in the columella portion. Similarly, only 7% of cells in the outermost layer of the root were associated with the columella region of the cap, a fraction which compared well with previous measurements of sloughed cells extracted from rhizosphere sand. This present technique can be applied to estimate the numbers of cells in any cylindrically symmetrical tissue from twodimensional sections. # 2001 Annals of Botany Company
Isolation and characterization of avian pathogenic Escherichia coli from broiler chickens in some Governorates of Egypt

A total of 80 samples (liver, heart, lung and gall bladder) were collected from diseased and freshly dead broiler chickens from different poultry farms reared in (Zagazig) Sharkia, Ismailaia, Sinai, (Dahshor) Giza and Kaluobaia Governorates for bacteriological examination for E-coli infection. The results revealed that 49 out of 80 samples (61%) were positive for Ecoli isolation. The result of in vitro Pathogenicity testing by Congo red (CR) binding assay indicates that 14 isolates (28.6 %) were CR positive. The most predominant serotypes were O125,O114 and O44 as each represent (2) isolates out of (14) followed by O78, O86, O158, O127, O91, O25, O119 and untypable as each represent (1) isolate out of (14) isolates. Now in this study we are straining and updating available circulating strains of avian pathogenic Escherichia coli (APEC) micro-organisms to control colibacillosis in broiler chickens either by treatment or vaccination.
Chopping the tail: how preventing superspreading can help to maintain COVID-19 control

Disease transmission is notoriously heterogeneous, and SARS-CoV-2 is no exception. A skewed distribution where few individuals or events are responsible for the majority of transmission can result in explosive, superspreading events, which produce rapid and volatile epidemic dynamics, especially early or late in epidemics. Anticipating and preventing superspreading events can produce large reductions in overall transmission rates. Here, we present a compartmental (SEIR) epidemiological model framework for estimating transmission parameters from multiple imperfectly observed data streams, including reported cases, deaths, and mobile phone-based mobility that incorporates individual-level heterogeneity in transmission using previous estimates for SARS-CoV-1 and SARS-CoV-2. We parameterize the model for COVID-19 epidemic dynamics by estimating a time-varying transmission rate that incorporates the impact of non-pharmaceutical intervention strategies that change over time, in five epidemiologically distinct settings---Los Angeles and Santa Clara Counties, California; Seattle (King County), Washington; Atlanta (Dekalb and Fulton Counties), Georgia; and Miami (Miami-Dade County), Florida. We find the effective reproduction number RE dropped below 1 rapidly following social distancing orders in mid-March, 2020 and remained there into June in Santa Clara County and Seattle, but climbed above 1 in late May in Los Angeles, Miami, and Atlanta, and has trended upward in all locations since April. With the fitted model, we ask: how does truncating the tail of the individual-level transmission rate distribution affect epidemic dynamics and control? We find interventions that truncate the transmission rate distribution while partially relaxing social distancing are broadly effective, with impacts on epidemic growth on par with the strongest population-wide social distancing observed in April, 2020. Given that social distancing interventions will be needed to maintain epidemic control until a vaccine becomes widely available, "chopping off the tail" to reduce the probability of superspreading events presents a promising option to alleviate the need for extreme general social distancing.
Implementation of PAR-CLIP to characterize RNA-protein interactions in prokaryotes at nucleotide resolution

The identification of RNAs that are recognized by RNA-binding proteins (RNA-BPs) using techniques such as “Crosslinking and Immunoprecipitation” (CLIP) has revolutionized the genome-wide discovery of RNA-BP RNA targets. Among the different versions of CLIP that have been developed, the use of photoactivable nucleoside analogs incorporated into cellular RNA has resulted in high efficiency photoactivable ribonucleoside-enhanced CLIP (PAR-CLIP). Nonetheless, PAR-CLIP has not yet been applied in prokaryotes. To determine if PAR-CLIP can be used in prokaryotes, we determined suitable conditions for the incorporation of 4-thiouridine (4SU), a photoactivable nucleoside, into E. coli RNA, and for the isolation of crosslinked RNA. Applying this technique to Hfq, a well-characterized regulator of small RNA (sRNA)-messenger RNA (mRNA) interactions, we showed that PAR-CLIP identified most of the known sRNA targets of Hfq, as well as functionally relevant sites of Hfq-mRNA interactions at nucleotide resolution. Based on our findings, PAR-CLIP represents an improved method to identify both the RNAs and the specific regulatory sites that are recognized by RNA-BPs in prokaryotes.
Development and transmission of Oswaldocruzia pipiens Walton, 1929 (Nematoda: Trichostrongylidae) in amphibians

Development of Oswaldocruzia pipiens was similar to that of other trichostrongyles which have been studied. First-stage larvae have a valved, rhabditiform oesophagus. Infective larvae are ensheathed and have a strongyliform oesophagus. Development to the infective stage occurred in faeces and transmission was by skin penetration. In frogs, early development occurred on the mucosa of the stomach: worms then migrated to the anterior portion of the intestine. The prepatent period was 14–18 days at 14–18 °C. Patent infections developed in experimentally infected tadpoles of Rana sylvatica. However, there was no evidence of natural infections in tadpoles. There were no significant fluctuations of prevalence and intensity between April and October, 1976 and 1977, in transformed R. sylvatica from a single marsh near Guelph, Ontario. Transmission apparently took place during spring and throughout the summer. Young frogs acquired infections rapidly.
Genetic Variants in the FGB and FGG Genes Mapping in the Beta and Gamma Nodules of the Fibrinogen Molecule in Congenital Quantitative Fibrinogen Disorders Associated with a Thrombotic Phenotype

Fibrinogen is a hexameric plasmatic glycoprotein composed of pairs of three chains (Aα, Bβ, and γ), which play an essential role in hemostasis. Conversion of fibrinogen to insoluble polymer fibrin gives structural stability, strength, and adhesive surfaces for growing blood clots. Equally important, the exposure of its non-substrate thrombin-binding sites after fibrin clot formation promotes antithrombotic properties. Fibrinogen and fibrin have a major role in multiple biological processes in addition to hemostasis and thrombosis, i.e., fibrinolysis (during which the fibrin clot is broken down), matrix physiology (by interacting with factor XIII, plasminogen, vitronectin, and fibronectin), wound healing, inflammation, infection, cell interaction, angiogenesis, tumour growth, and metastasis. Congenital fibrinogen deficiencies are rare bleeding disorders, characterized by extensive genetic heterogeneity in all the three genes: FGA, FGB, and FGG (enconding the Aα, Bβ, and γ chain, respectively). Depending on the type and site of mutations, congenital defects of fibrinogen can result in variable clinical manifestations, which range from asymptomatic conditions to the life-threatening bleeds or even thromboembolic events. In this manuscript, we will briefly review the main pathogenic mechanisms and risk factors leading to thrombosis, and we will specifically focus on molecular mechanisms associated with mutations in the C-terminal end of the beta and gamma chains, which are often responsible for cases of congenital afibrinogenemia and hypofibrinogenemia associated with thrombotic manifestations.
Foraging Behavior of a Desert Dwelling Arthropod-Gleaning Bat (Otonycteris hemprichii) During Pregnancy and Nursing

We studied the role of behavioral activities used by desert-dwelling, arthropod gleaning Hemprich's long-eared bat (Otonycteris hemprichii), hypothesizing that there is a trade off between their own and their offspring's food needs. Specifically, we tested the following predictions: 1) females will bring forward their emergence time from their roosts and increase foraging bout length progressively from the first through the second trimesters of pregnancy, and during nursing as their pups grow; but, that 2) during the last trimester of pregnancy, namely, in the final stages of foetus development, females will emerge later and there will be a reduction in foraging effort (time); and that 3) females will spend more time foraging during nursing than during pregnancy. We found that the bats emerged from their roosts to forage earlier during the first trimester, but not during the last two trimesters of pregnancy, and that they did not change their emergence time as nursing progressed. Bats that emerged later at night during pregnancy spent more time foraging, and, except for the third trimester, the length of the first daily foraging bout increased as both pregnancy and nursing progressed. Total daily foraging time increased as pregnancy and nursing progressed. Generally, these results support our hypothesis; through adjustment of their foraging behavior as embryos and pups develop, breeding female Hemprich's long-eared bats contend with the potentially conflicting food requirements of their offspring and their own needs.
A global analysis of song frequency in passerines provides no support for the acoustic adaptation hypothesis but suggests a role for sexual selection

Many animals use acoustic signals for communication, implying that the properties of these signals can be under strong selection. The acoustic adaptation hypothesis predicts that species living in dense habitats emit lower-frequency sounds than those in open areas, because low-frequency sounds generally propagate further in denser vegetation. Signal frequency may also be under sexual selection, because it correlates with body size and lower-frequency sounds are perceived as more intimidating. Here, we evaluate these hypotheses by analysing variation in peak song frequency across 5,085 passerine species (Passeriformes). A phylogenetically-informed analysis revealed that song frequency decreases with increasing body mass and with male-biased sexual size dimorphism. However, we found no support for the predicted relationship between frequency and habitat. Our results suggest that the global variation in passerine song frequency is mostly driven by natural and sexual selection causing evolutionary shifts in body size rather than by habitat-related selection on sound propagation. Statement of authorship TA and PM conceived and designed the study with input from all authors. TA and BK coordinated the study. PM collected the song data. MV performed the statistical analyses with input from WF. MB made the figures with help from MV and PM. TP and HB provided bioacoustic expertise. PM drafted the first version of the manuscript. TA, BK and PM revised and finalized the manuscript with input from all authors. Data availability statement The data used in this study were collected from publicly available databases. All data and computer code used to generate the results, as well as supplementary figures and tables will be freely available at https://osf.io/fa9ky/.
A Comprehensive Critical Assessment of Increased Fruit and Vegetable Intake on Weight Loss in Women

No previous reviews or meta-analyses have specifically assessed the effects of increased fruit and vegetable (FV) intake on weight loss with a primary focus on women. Several studies show differences between men and women in how increased FV intake affects their weight loss and maintenance, risk of becoming overweight or obese, and the influence of eating speed and frequency on weight control. This analysis provides a comprehensive and visual assessment of the effects of increasing FV intake and long-term weight change from observational studies and weight loss from randomized controlled trials (RCTs) in women. Consistent evidence from prospective studies and RCTs shows that increased intake of FV is a chief contributor to weight loss in women. This effect is enhanced with concurrent dietary restriction of high energy density (ED) or high-fat foods. Yet, the type of FV differentially impacts weight loss in women. Whole FV intake may influence weight through a variety of mechanisms including a reduction in eating rate, providing a satisfying, very-low to low energy density, low glycemic load or low-fat content. Also, FV are the primary source of dietary fiber, which can provide additional support for weight loss in women when consumed at adequate levels.