Miracle-dz/UniFAR-FTUs huggingface dataset:
Peristaltic transport of a couple stress fluid permeated with suspended particles

A B S T R A C T The peristaltic motion of a couple stress fluid permeated with suspended particles through a two dimensional flexible channel under long wave length approximation is studied. A perturbation method of solution is obtained in terms of wall slope parameter and closed form of expressions has been derived for axial velocity and transverse velocity in fluid phase and particle phase. The expression for pressure rise and friction force has been computed numerically using mathematics software mathematica. The graphical results have been presented to discuss the physical behavior of various physical parameters on pressure rise and friction force. It is observe that pressure rise decreases with increase in couple stress parameter and Dust concentration parameter. The friction force has an opposite behavior compared with pressure rise.
Electronic structures and optical properties of TM (Cr, Mn, Fe or Co) atom doped ZnSe nanosheets

The electronic structures and optical properties of pristine and transition-metal (TM) atom doped ZnSe nanosheets (ZnSeNSs) have been studied based on first-principles calculations. The results indicate that the pristine ZnSeNSs are nonmagnetic direct gap semiconductors, while Mn, Fe or Co doped ZnSeNSs are all spin-polarized, and the Cr doped one is half-metallic with 100% spin-polarized currents. Cr or Co doped ZnSeNSs can improve the absorption properties and broaden the absorption range, compared to pristine, Fe or Mn doped ZnSeNSs. Moreover, red-shift phenomena are observed. These results can provide an important reference for designing and fabricating infrared and visible photoelectric nanodevices.
Structural Transformation of 2:1 Dioctahedral Layer Silicates during Dehydroxylation-Rehydroxylation Reactions

The structural transformation of dioctahedral 2:1 layer silicates (illite, montmorillonite, glauconite, and celadonite) during a dehydoxylation-rehydroxylation process has been studied by X-ray diffraction. thermal analysis, and infrared spectroscopy. The layers of the samples differ in the distribution of the octahedral cations over the cis- and trans-sites as determined by the analysis of the positions and intensities of the 11l, 02l reflections, and that of the relative displacements of adjacent layers along the a axis (c cos ß/a), as well as by dehydroxylation-temperature values. One illite, glauconite, and celadonite consist of trans-vacant (tv) layers; Wyoming montmorillonite is composed of cis-vacant (cv) layers, whereas in the other illite sample tv and cv layers are interstratified. The results obtained show that the rehydroxylated Al-rich minerals (montmorillonite, illites) consist of tv layers whatever the distribution of octahedral cations over cis- and trans-sites in the original structure. The reason for this is that in the dehydroxylated state, both tv and cv layers are transformed into the same layer structure where the former trans-sites are vacant.The dehydroxylation of glauconite and celadonite is accompanied by a migration of the octahedral cations from former cis-octahedra to empty trans-sites. The structural transformation of these minerals during rehydroxylation depends probably on their cation composition. The rehydroxylation of celadonite preserves the octahedral-cation distribution formed after dehydroxylation. Therefore, most 2:1 layers of celadonite that rehydroxylate (~75%) have cis-vacant octahedra and, only in a minor part of the layers, a reverse cation migration from former trans-sites to empty octahedra occurred. In contrast, for a glauconite sample with a high content in IVA1 and VIAl the rehydroxylation is accompanied by the reverse cation migration and most of the 2:1 layers are transformed into tv layers.
Cohort Profile: Epigenetics in Pregnancy (EPIPREG)-population-based sample of European and South Asian pregnant women living in Norway with epigenome-wide DNA methylation (850k) in peripheral blood leukocytes

Purpose: Pregnancy is a valuable model to study the association between DNA methylation and several cardiometabolic traits, due to its direct potential to influence mother's and child's health. Epigenetics in Pregnancy (EPIPREG) is a population-based sample with the aim to study associations between DNA-methylation in pregnancy and cardiometabolic traits in South Asian and European pregnant women and their offspring. Participants: In EPIPREG we have quantified epigenome-wide DNA methylation in maternal peripheral blood leukocytes in gestational week 28 in Europeans (n=312) and South Asians (n=168) that participated in the population-based cohort STORK Groruddalen, in Norway. DNA methylation was measured with Infinium MethylationEPIC Kit (850k sites), with technical validation of four CpG sites using bisulphite pyrosequencing in a subset (n=30). The sample is well characterized with few missing data on e.g. genotype, universal screening for gestational diabetes, objectively measured physical activity, bioelectrical impedance, anthropometrics, biochemical measurements, and a biobank with maternal serum and plasma, urine, placenta tissue. In offspring, we have repeated ultrasounds during pregnancy, cord blood, and anthropometrics up to 4 years of age. Results to date: We have quantified DNA methylation in peripheral blood leukocytes in nearly all eligible women from the STORK Groruddalen study, to minimize the risk of selection bias. Genetic principal components distinctly separated Europeans and South Asian women, which fully corresponded with the self-reported ethnicity. Technical validation of 4 CpG sites from the methylation bead chip showed high concordance with bisulfite pyrosequencing (R=0.98, p<0.001). Future plans: We plan to study associations between DNA methylation and cardiometabolic traits and outcomes. We hope to identify cohorts with similar data to replicate our findings, collaborate on joint efforts such as meta-analysis, and serve as a replication cohort for other studies.
Development and validation of a simplified risk score for the prediction of critical COVID‐19 illness in newly diagnosed patients

Scores to identify patients at high risk of progression of coronavirus disease (COVID‐19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), may become instrumental for clinical decision‐making and patient management. We used patient data from the multicentre Lean European Open Survey on SARS‐CoV‐2‐Infected Patients (LEOSS) and applied variable selection to develop a simplified scoring system to identify patients at increased risk of critical illness or death. A total of 1946 patients who tested positive for SARS‐CoV‐2 were included in the initial analysis and assigned to derivation and validation cohorts (n = 1297 and n = 649, respectively). Stability selection from over 100 baseline predictors for the combined endpoint of progression to the critical phase or COVID‐19‐related death enabled the development of a simplified score consisting of five predictors: C‐reactive protein (CRP), age, clinical disease phase (uncomplicated vs. complicated), serum urea, and D‐dimer (abbreviated as CAPS‐D score). This score yielded an area under the curve (AUC) of 0.81 (95% confidence interval [CI]: 0.77–0.85) in the validation cohort for predicting the combined endpoint within 7 days of diagnosis and 0.81 (95% CI: 0.77–0.85) during full follow‐up. We used an additional prospective cohort of 682 patients, diagnosed largely after the “first wave” of the pandemic to validate the predictive accuracy of the score and observed similar results (AUC for the event within 7 days: 0.83 [95% CI: 0.78–0.87]; for full follow‐up: 0.82 [95% CI: 0.78–0.86]). An easily applicable score to calculate the risk of COVID‐19 progression to critical illness or death was thus established and validated.
Stopover ecology of fall migrating landbirds at an inland stopover site in northeastern Pennsylvania dominated by nonnative vegetation

ABSTRACT Landbirds are especially vulnerable during migration as they move through novel habitats and encounter enhanced predation risk, unpredictable food resources, enhanced competition, and inclement weather. Further, numerous studies suggest exotic vegetation species have the potential to alter habitat quality, in turn affecting the fitness of migratory birds. The purpose of this study was to evaluate fitness correlates associated with fall migrant use of shrubland habitat dominated by nonnative honeysuckle (Lonicera spp.) in northeastern Pennsylvania. Additionally, we looked for differences in stopover ecology between demographic cohorts (age, and in the case of Common Yellowthroat [Geothlypis trichas], both age and sex). We used estimates of mass change as our primary fitness indicator, assuming that evidence of positive mass change reflects fat deposition and hence indicates quality habitat. Our results suggest that of 7 species, 1 gained mass, 5 neither gained nor lost mass, and 1 lost mass. Further, while we found little evidence of age or sex differences in migratory timing, we did find evidence that older birds gained mass at a higher rate than younger in 2 species and that, while male Common Yellowthroats maintained mass while using our site, females lost mass. We conclude that our exotic-dominated shrubland habitat does not provide high-quality stopover habitat for most species.
Urban House Sparrow (Passer domesticus) populations decline in North America

ABSTRACT House Sparrow (Passer domesticus) populations declined across much of their global range in the late 20th century. Most research examining this decline is conducted in the species' native European range, but Europe encompasses a small portion of the species' current distribution. House Sparrow population trends in the United States and Canada, and the potential mechanisms driving these trends, remain relatively unexplored. We use 21 years of data from Project FeederWatch, a large-scale citizen science project, to investigate House Sparrow population trends in North America. We found winter flocks in urbanized areas were larger than flocks in rural areas, with widespread spatial heterogeneity in local population trends. Despite greater abundance in developed areas, House Sparrow populations declined in developed areas from 1995 to 2016 while remaining stable in rural areas. House Sparrow population declines coincide with an increase in populations and expansion of the winter distributions of Accipiter hawks, which are known predators of House Sparrows. However, we do not find a direct connection between the presence of Accipiter hawks at count sites and House Sparrow population declines in winter. These results expand our knowledge of widespread House Sparrow declines to North America and provide context for continuing research on House Sparrow declines in the introduced range.
Genome-wide mining of wheat B-BOX zinc finger (BBX) gene family provides new insights into light stress responses

Abstract. The B-BOX (BBX) proteins are an important class of zinc-finger transcription factors involved in the regulation of plant growth and development, and have been identified in many plant species. However, there is no systematic study of common wheat (Triticum aestivum L.) BBX genes. Through comprehensive bioinformatics analysis, we identified and characterised 96 BBX genes from wheat, and provided the genes with a unified nomenclature. We describe the chromosomal location, gene structure, conserved domains, phylogenetic relationships and promoter cis-elements of TaBBX family members. The expression patterns under different conditions, especially under different hormones and light–dark conditions, were studied in detail. According to the diversity of conserved domains, we divided TaBBX proteins into five subfamilies. Gene-duplication analysis showed that duplication of chromosome segments was the main reason for the expansion of the TaBBX gene family. Detecting the expression profiles of six TaBBX genes in different tissues by quantitative real-time PCR, we found that the six genes are regulated under light–dark treatment, and that some TaBBX genes (TaBBX2.11, TaBBX2.13, TaBBX2.15 and TaBBX3.10) are strongly induced by the plant hormones abscisic acid, indole-3-acetic acid and salicylic acid. Our analysis of wheat BBX genes at the genomic level will provide a solid foundation for further identifying the functions of specific genes in light stress responses.
Nest survival, predator assemblage, and patterns of predation at Veery (Catharus fuscescens) nests in a mature forest landscape

ABSTRACT Predation is typically the primary cause of nest failure for songbirds, even within unfragmented forested landscapes. In recent years, video cameras have been used to study causes and patterns of nest failure in a variety of habitats and regions. However, surprisingly few video camera studies have been performed in forests of northeastern North America. Over 5 years, we monitored Veery (Catharus fuscescens) nesting success in a mature forest landscape in northeastern Pennsylvania and used video cameras at a subset of nests to identify the predator assemblage and to describe relevant patterns of predation. Overall, we located 289 nests and recorded 67 of these nests with video cameras. Annual nest survival rates varied substantially across years (0.17–0.44) with this variation driven primarily by the dominant source of nest mortality: predation. Video cameras recorded 40 predation events by 12 predator species. Mammals (7 species), birds (4 species), and snakes (1 species) accounted for 75%, 20%, and 2.5% of predation events recorded, respectively. Predation events occurred during the day more often than expected by chance. Logistic exposure analyses indicated that both camera presence and nest age affected nest survival by influencing predation rates, but date did not. The diverse predator community observed depredating Veery nests led to low nesting success in some years, but also demonstrated that causes of nest failure vary by year and cannot be attributed to any single predator species or group. A greater apparent predation rate at nests with cameras likely resulted from a more frequent visitation rate to these nests by researchers compared to those without cameras and suggests a potential bias with artificially decreased nest survival estimates in years in which cameras were used.
ON THE THERMAL IGNITION OF WOOD WASTE

Self-heating tests on sawdust in ovens, using baskets of various shapes as sample containers, are reported and times to ignition measured according to a definition of such times different from that conventionally used. Findings are also discussed semiquantitatively in terms of the measured kinetic parameters. The possibility of reactivity loss by prior exposure to air is looked into directly.
Lodging tolerance of rice is improved without decreasing productivity by mixing lines with different maturity dates

Abstract. We hypothesised that mixing of rice lines with different maturity dates can improve the productivity per unit area while improving lodging resistance on account of the heterogeneous canopy. To test this hypothesis, we grew two lines, wild-type (WT) and early-maturing (EML), of each of two cultivars (Koshihikari and Hitomebore) in monoculture plantings and within-cultivar mixed plantings, with WT and EML plants alternating every one or two rows, over 2 years in northern Japan. The mixtures formed a canopy with different heading dates (5–7 days earlier than WT in Hitomebore and 14–19 days earlier in Koshihikari). For Koshihikari, the mixture increased grain yield per plant in the WT by 18–33%, but decreased it in the EML by 19–22%; however, for Hitomebore, there was no significant difference. Consequently, grain yield per unit area did not change relative to the mean of monocultures of WT and EML in either cultivar. Lodging tolerance improved significantly in the mixtures, especially for Koshihikari. Thus, mixing rice lines with different maturity dates improved lodging tolerance without decreasing productivity.
Prioritisation of candidate genes in QTL regions for seed germination and early seedling growth in bread wheat (Triticum aestivum) under salt-stress conditions

Abstract. Salinity and drought are major abiotic stresses affecting wheat (Triticum aestivum L.) production throughout the world, and discovery of loci for traits affecting yield under salinity may lead to the breeding for salt-tolerant plants. In the present study, 186 F10 recombinant inbred line (RIL) populations were evaluated under salt-stress conditions in order to identify main-effect and epistatic-effect quantitative trait loci (QTLs) for 15 traits in wheat during the germination and early-seedling stages. In total, 61 main-effect QTLs on 15 chromosomes and 21 epistatic interactions on 12 chromosomes were detected through composite interval mapping (CIM) and a mixed-model-based CIM method. Two major QTLs for primary-leaf fresh weight and coleoptile fresh weight were detected on chromosome (or linkage group) 5B2 and 2D, respectively, which contributed ∼44% and 43% of the phenotypic variance. Additionally, 12 QTL clusters including different traits were detected on 1A1, 3A, 4A, 2B1, 3B, 5B1 and 2D1. Candidate genes were identified within QTL regions and gene ontology (GO) enrichment analysis was performed. In total, 9134 candidate genes were grouped into 274 GO terms (including 79 GO terms involved in the ‘biological process’ category). These genes directly or indirectly play a vital role such as lipid localisation, biological regulation, fatty acid biosynthetic process, cellular process, DNA conformation change, translational elongation, carbohydrate metabolic process, Fe ion homeostasis, hydrogen peroxide metabolic process, and pigment biosynthetic process at the germination and early-seedling stages under salt-stress conditions.
Aggressive responses of Eastern Phoebes (Sayornis phoebe) and American Robins (Turdus migratorius) toward brood parasites and nest predators: A model presentation experiment

ABSTRACT Brood parasites reduce the reproductive success of many bird species by laying eggs in their nests. Hosts that reject parasitic eggs (“rejecters”) avoid most costs of brood parasitism altogether by physically ejecting eggs from nests or abandoning parasitized nesting attempts. Species that accept parasitic eggs once these are laid (“accepters”) may reduce or eliminate costs by aggressively responding to brood parasites at their nests to prevent parasitism from taking place. Accordingly, accepters should recognize brood parasites and nest predators as different nest threats with different levels of aggression, whereas rejecters may not. We exposed active Eastern Phoebe (Sayornis phoebe, an accepter host) and American Robin (Turdus migratorius, a rejecter host) nests to models of a female brood parasitic Brown-headed Cowbird (Molothrus ater), an eastern chipmunk (Tamias striatus, nest predator), and a European Starling (Sturnus vulgaris, nonthreatening control) during the incubation stage. Phoebes alarm-called equally toward the nest predator and brood parasite models, but attacked the nest predator model more than the brood parasite model. Robins, in contrast, alarm-called toward and attacked all 3 models equally. Interpreting these results is challenging due to experimental design elements, specifically small sample sizes and restricting the experiment to the incubation stage. Nonetheless, our experiment contributes to the paucity of comparative studies on accepter versus rejecter nest defense behavior in response to both nest parasites versus predators, and adds a new tested accepter species to the literature.
Behavioral impairment and cognition in Thai adolescents affected by HIV

Abstract Background Cognitive and behavioral impairment are common in children living with perinatally acquired HIV (pHIV) and children exposed to HIV in utero but uninfected (HEU). Methods We sought to determine the prevalence of adverse behavioral symptomatology using a Thai-translated and validated version of the SNAP-IV questionnaire and assess cognitive function utilizing the Children's Color Trails Test, Delis-Kaplan Executive Function System, and the Wechsler Intelligence Scales, in our cohort of Thai adolescents (10–20 years old) with well-controlled pHIV compared to HEU and HIV-unexposed, uninfected youth. We then evaluated the interaction between HIV status, behavioral impairment, and executive function outcomes independent of demographic variables. Results After controlling for demographic factors of age and household income, adolescents with pHIV had higher inattentive symptomatology and poorer neuropsychological test scores compared to uninfected controls. Significant interactions were found between inattention and executive function across multiple neurocognitive tests. Conclusions Behavioral impairment and poor executive functioning are present in adolescents with well-controlled pHIV compared to HIV-uninfected matched peers. The SNAP-IV questionnaire may be a useful tool to identify those with attentional impairment who may benefit from further cognitive testing in resource-limited settings.
Thermodynamic and physico-chemical descriptors of chloronaphthalenes: an attempt to select features explaining environmental behaviour and specific toxic effects of these compounds

physico-chemical descriptors were used to characterize all 75 congeners of chloronaphthalene in terms of their environmental stability and specific dioxin-like toxicity. A prepared basic thermodynamic and physico-chemical property data matrix of PCNs was interpreted using Principal Component Analysis (PCA). The PCA of the thermodynamic and physico-chemical data matrix created a four-dimensional model that explained 76% (58% + 9% + 5% + 4%) of the total variance. The loading plot shows that the first PC is influenced by variables describing degree of chlorination, molecular weight, polarizability and lipophilicity. The best positively correlated descriptors are: retention time, standard molar entropy, heat capacity, a first-order molecular connectivity index, logarithm of octanol-water partition coefficient, the Wiener Index, specific polarizability, a third order shape index for molecules, the sum of absolute of the charges on each atom of the molecule, molecular weight, polarizability, refractivity, solvent-accessible surface, van der Waals surface, solvent-accessible volume, van der Waals volume. Negatively correlated descriptors are: standard enthalpy of formation and energy of HOMO. The second PC is strongly influenced by energy of LUMO, while substitution pattern parameters, number of chlorine atoms at α-positions and vicinal (adjac- ent) carbon atoms substitution pattern are less important parameters. The third PC depends on dipole moment and the largest negative charge, and on substitution at position 2 of naphthalene nuclei, while the symmetry group parameter is determined by PC4. There are small groups consisting of compounds which have similar values of LUMO energy and substitution pattern. The congeners of CN substituted with chlorine at positions 1, 2, 3, 6 and 7 (Fv/Fv PCN congeners), and next those substituted at positions 1, 2, 3
Ecological Study of Spring-Early Summer Phytoplankton Blooms in A Semi-Enclosed Estuary

Abstract A sampling station in the Eastern Harbour of Alexandria was operated for 51 days between 2 March and 12 June, 1991. the harbour had different wide physical and chemical variations. Six distinct phytoplankton blooms occurred during this period. It is concluded that the physicochemical conditions affected the phytoplankton community structure and species composition. A dense diatom bloom could be maintained in a very weak and/or stabilized water column. A diatom bloom does not necessarily accompany an enhanced nutrient period. the depletion of nutrients and establishment of thermal stratification probably created favourable conditions for dinoflagellate and flagellate species to achieve blooms. the species composition could be shifted over the short term and a dense phytoplankton bloom could possibly dissipate in a few days.