syedzayyan/paper_mill_benchmark huggingface dataset:
Male fertility status is associated with DNA methylation signatures in sperm and transcriptomic profiles of bovine preimplantation embryos.

Infertility in dairy cattle is a concern where reduced fertilization rates and high embryonic loss are contributing factors.Studies of the paternal contribution to reproductive performance are limited.However, recent discoveries have shown that, in addition to dna, sperm delivers transcription factors and epigenetic components that are required for fertilization and proper embryonic development.Hence, characterization of the paternal contribution at the time of fertilization is warranted.We hypothesized that sire fertility is associated with differences in dna methylation patterns in sperm and that the embryonic transcriptomic profiles are influenced by the fertility status of the bull.Embryos were generated in vitro by fertilization with either a high or low fertility holstein bull.Blastocysts derived from each high and low fertility bulls were evaluated for morphology, development, and transcriptomic analysis using rna-sequencing.Additionally, dna methylation signatures of sperm from high and low fertility sires were characterized by performing whole-genome dna methylation binding domain sequencing.Results embryo morphology and developmental capacity did not differ between embryos generated from either a high or low fertility bull.However, rna-sequencing revealed 98 genes to be differentially expressed at a false discovery rate < 1%.A total of 65 genes were upregulated in high fertility bull derived embryos, and 33 genes were upregulated in low fertility derived embryos.Expression of the genes cycs, eea1, slc16a7, mepce, and tfb2m was validated in three new pairs of biological replicates of embryos.The role of the differentially expressed gene tfb2m in embryonic development was further assessed through expression knockdown at the zygotic stage, which resulted in decreased development to the blastocyst stage.Assessment of the epigenetic signature of spermatozoa between high and low fertility bulls revealed 76 differentially methylated regions.Conclusions despite similar morphology and development to the blastocyst stage, preimplantation embryos derived from high and low fertility bulls displayed significant transcriptomic differences.The relationship between the paternal contribution and the embryonic transcriptome is unclear, although differences in methylated regions were identified which could influence the reprogramming of the early embryo.Further characterization of paternal factors delivered to the oocyte could lead to the identification of biomarkers for better selection of sires to improve reproductive efficiency.

Journal: BMC genomics (2017)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Correlated quantum treatment of the photodissociation dynamics of formaldehyde oxide CH2OO.

An extended theoretical analysis of the photodissociation of the smallest criegee intermediate ch2oo following excitation to the b state is presented.It relies on explicitly correlated multireference electronic wavefunctions combined with a quantum dynamical treatment for two interacting (b-c) electronic states and three coupled nuclear degrees of freedom.The 3d model relies on pess along the o-o and c-o stretching as well as c-o-o bending modes for the two lowest excited states with a' symmetry, and is sufficiently accurate to reproduce the experimental b1a'-x1a' absorption spectrum, especially at the low-energy range to unprecedented accuracy.The existence of a deep well (∼0.4 e v) on the (diabatic) b state causes a considerable amount of the wavepacket to be reflected by the b state well, which can explain the vibronic structures appearing in the long wavelength range of 360-470 nm of the spectrum.The main progression appearing in the energy range from 360 to 470 nm is assigned to the o-o stretching mode while finer details are affected by couplings to the c-o stretching and c-o-o bending modes.The weakly avoided crossing between the b-state and c-state potential energy surfaces appearing near 3.1 e v excitation energy (for rs2-f12 method) causes considerable disturbance in the vibronic fine structure of the bands.The description of the latter is quite strongly affected by the type of electron correlation treatment adopted, either fully variational (mrci type) or perturbation theoretic (rs2 type).The results give novel insight into the complex interactions governing that intriguing process.

Journal: Physical chemistry chemical physics : PCCP (2022)
Publication types: Journal Article
Structural characterization of the water-soluble porphyrin complexes [FeII(TPPS) (NO•)]4─and [μ-O-([FeIII(TPPS)])2]8─.

Iron water-soluble porphyrins have been long used as biomimetic compounds for modelling the active sites found in heme-enzymes.In this regard, the anionic porphyrin [fe iii(tpps)]3─and its coordination complexes have been repeatedly chosen as suitable water-soluble platforms for bioinorganic chemistry studies.In this work we report for the first time the crystal structure of the water-soluble nitrosyl complex [fe ii(tpps) (no•)]4─along with that of oxodimeric ferric species [μ-o-([fe iii(tpps)])2]8─.

Journal: Heliyon (2022)
Publication types: Journal Article
Problematic alcohol use in young adults during the COVID-19 lockdown in Italy.

This study investigated the individual and contextual correlates of problematic alcohol use among young adults during covid-19 lockdown in italy.Participants were 1533 young adults aged 18 to 26 (mage= 23.12,sdage= 2.11; 73.2% women), who completed an online survey during national lockdown.Inclusion criteria for this study were the age-range (18-26 y.O.), and living in italy during covid-19 lockdown.Participants with low or very low socioeconomic levels (vs.Higher levels) were more at risk for problematic alcohol use, as well as participants who lived alone or with roommates/friends during lockdown.Conversely, participants who spent the lockdown with their family or partner were less at risk for problematic alcohol use.Finally, participants who had their job suspended due to pandemic (vs.Other job conditions) were more at risk for problematic alcohol use during lockdown.Implications for research and clinical practice are discussed.

Journal: Psychology, health & medicine (2022)
Publication types: Journal Article
Contribution of local climate zones to the thermal environment and energy demand.

Urban heat islands (uhis) and their energy consumption are topics of widespread concern.This study used remote sensing images and building and meteorological data as parameters, with reference to oke's local climate zone (lcz), to divide urban areas according to the height and density of buildings and land cover types.While analyzing the heat island intensity, the neural network training method was used to obtain temperature data with good temporal as well as spatial resolution.Combining degree-days with the division of lczs, a more accurate distribution of energy demand can be obtained by different regions.Here, the spatial distribution of buildings in shenyang, china, and the law of land surface temperature (lst) and energy consumption of different lcz types, which are related to building height and density, were obtained.The lst and energy consumption were found to be correlated.The highest heat island intensity, i.e., uhilcz 4, was 8.17°c.The correlation coefficients of lst with building height and density were -0.16 and 0.24, respectively.The correlation between urban cooling energy demand and building height was -0.17, and the correlation between urban cooling energy demand and building density was 0.17.The results indicate that low- and medium-rise buildings consume more cooling energy.

Journal: Frontiers in public health (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Kosovo women's knowledge and awareness of human papillomavirus (HPV) infection, HPV vaccination, and its relation to cervical cancer.

The objective of this study, the first of its kind in kosovo, is to determine the level of kosovo women's knowledge and awareness of hpv infection, hpv vaccination, and its relation to cervical cancer.Methods this cross-sectional study was conducted from july to october 2018 at the clinic of obstetrics and gynecology at the hospital and university clinical service of kosovo.Results out of 800 questionnaires distributed, 645 were completed and returned (80.6%).Only 0.5% of women were vaccinated against hpv.The majority of respondents (66.4%) had no previous knowledge of hpv (human papillomavirus).Only 27.6% of respondents were aware that hpv is responsible for cervical cancer.About two-thirds (70.1%) of respondents had never heard of the hpv vaccine, and only 24% knew that the hpv vaccine can prevent cervical cancer.Conclusion the level of vaccination against hpv and the level of knowledge and awareness of hpv infection is extremely low.Higher education, younger age, and living in an urban area were favorable factors and correlated with awareness of hpv infection, vaccination against it, and its relation to cervical cancer.Based on this study, there is an immediate need for developing an educational program on hpv infection and the importance of hpv vaccination as a preventative measure against developing cervical cancer.

Journal: BMC women's health (2021)
Publication types: Journal Article
Double-stranded RNA targeting vATPase B reveals a potential target for pest management of Henosepilachna vigintioctopunctata.

The development of genetic based techniques, specifically rna interference (rnai), has emerged as a powerful tool in novel pest management strategies for pestiferous coleoptera.The 28-spotted ladybird beetle, henosepilachna vigintioctopunctata, is a dynamic foliar pest of solenaceous plants, primarily potato plants, and has quickly become one of the most important pests attacking many crops in asian countries.In this study, we demonstrate the efficacy of dietary rnai targeting v atpase b, which led to significant gene silencing.Downstream effects of v atpase b silencing appeared to be both time- and partial dose-dependent.Our results indicate that silencing of v atpase b caused a significant decrease in survival rate, as well as reduced the food stuffs consumption and inhibited the overall development of h.Vigintioctopunctata.Furthermore, results demonstrate expression of insect melanism related genes, th and ddc, was significantly up regulated under the dsv atpase b (rnai molecule designed against v atpase b) treatment.The impact of oral dsv atpase b delivery on the survival of 1st, 3rd instars, and adults was investigated through bacterially expressed ds rna.The effectiveness of rnai-based gene silencing in h.Vigintioctopunctata provides a powerful reverse genetic tool for the functional annotation of its genes.This study demonstrates that v atpase b may represent a candidate gene for rnai-based control of h.Vigintioctopunctata.

Journal: Pesticide biochemistry and physiology (2020)
Publication types: Journal Article
Unique Neural Activity Patterns Among Lower Order Cortices and Shared Patterns Among Higher Order Cortices During Processing of Similar Shapes With Different Stimulus Types.

We investigated the neural mechanism of the processing of three-dimensional (3d) shapes defined by disparity and perspective.We measured blood oxygenation level-dependent signals as participants viewed and classified 3d images of convex-concave shapes.According to the cue (disparity or perspective) and element type (random dots or black and white dotted lines), three types of stimuli were used: random dot stereogram, black and white dotted lines with perspective, and black and white dotted lines with binocular disparity.The blood oxygenation level-dependent images were then classified by multivoxel pattern analysis.To identify areas selective to shape, we assessed convex-concave classification accuracy with classifiers trained and tested using signals evoked by the same stimulus type (same cue and element type).To identify cortical regions with similar neural activity patterns regardless of stimulus type, we assessed the convex-concave classification accuracy of transfer classification in which classifiers were trained and tested using different stimulus types (different cues or element types).Classification accuracy using the same stimulus type was high in the early visual areas and subregions of the intraparietal sulcus (ips), whereas transfer classification accuracy was high in the dorsal subregions of the ips.These results indicate that the early visual areas process the specific features of stimuli, whereas the ips regions perform more generalized processing of 3d shapes, independent of a specific stimulus type.

Journal: i-Perception (2021)
Publication types: Journal Article
Stress and Coping in Youth With Spina Bifida: A Brief Longitudinal Study in a Summer Camp Setting.

Introduction it is well established that youth with chronic conditions experience elevated levels of stress; the manner in which they respond to or cope with this stress is likely to impact both health and psychosocial outcomes.The current study examined stress and coping in youth and young adults with spina bifida (sb) using the response to stress questionnaire-sb version (rsq-sb; connor-smith et al., 2000).Methods data were collected as part of a camp-based psychosocial intervention for children (ages 7-13), adolescents (ages 14-19), and young adults (ages 20-38) with sb.Participants completed the rsq-sb as well as questionnaires assessing demographics and condition severity.Data were collected prior to camp (t1) and 1 month (t2) after camp ended.Self-report data were collected from adolescents and young adults; parents of children and adolescents reported on their child's stress and coping.Ratios of primary control coping, secondary control coping, disengagement coping, involuntary engagement, and involuntary disengagement coping were calculated.Descriptive statistics andt-tests were utilized to describe coping and stress responses and to determine potential change over time.t-tests were also used to compare youth and parent reported coping styles with those of youth with type 1 diabetes (t1d) and sickle cell disease (scd).Associations between demographic/disease factors and coping styles were also examined.Results parent and youth report indicated that youth with sb tend to use primary control coping.Youth with sb use more primary control coping and less disengagement coping compared to youth with scd and youth with t1d.Few significant changes in coping were found between t1 and t2.Iq and socioeconomic status were significantly associated with coping styles.Conclusion youth with sb use more primary control coping compared to other coping methods and as compared to other pediatric populations.Future studies should examine mechanisms by which primary control coping is advantageous for youth with sb.Future interventions should be more focused on promoting adaptive coping behaviors and be tailored to developmental age and access to resources.

Journal: Frontiers in psychology (2021)
Publication types: Journal Article
Prognostic Impact of Operator Experience and IVUS Guidance on Long-Term Clinical Outcomes After Complex PCI.

Although consistent clinical data support intravascular ultrasound (ivus) use during complex percutaneous coronary intervention (pci), long-term follow-up outcomes on differential effects of ivus according to operator experience are scarce.Objectives the current study aimed to evaluate the influence of operator experience on lesion complexity, long-term clinical outcomes, and the interactions of ivus guidance in patients undergoing complex pci.Methods a total of 6,005 patients who underwent pci with drug-eluting stents for complex lesions were recruited from the institutional registry of samsung medical center.The study population was stratified by the use of ivus and operator experience (less experienced operator [lifetime independent experience with pci ≤5 years] vs experienced operator).The primary endpoint was a composite of cardiac death or target vessel myocardial infarction (tvmi) up to 10 years.Results compared with less experienced operators, experienced operators used ivus more frequently (29.6% [1,128/3,805] vs 24.8% [546/2,200]; p < 0.001) and achieved a lower risk of cardiac death or tvmi (experienced vs less experienced, adjusted hr: 0.779; 95% ci: 0.663-0.915; p = 0.002).Ivus use was associated with a significantly lower risk of cardiac death or tvmi than angiography alone for less experienced operators (23.5% vs 11.4%; adjusted hr: 0.477; 95% ci: 0.337-0.673; p < 0.001) as well as experienced operators (18.0% vs 13.5%; adjusted hr: 0.747; 95% ci: 0.559-0.998; p = 0.048).There were significant interactions for the risk of cardiac death or tvmi between ivus use and operator experience (p = 0.037).Conclusions pci by experienced operators and the use of ivus during complex pci were independently associated with lower long-term risks of cardiac death or tvmi.The beneficial effects of ivus were more prominent for less experienced operators.(prospective percutaneous coronary intervention registry [smc-pci]; nct05624905).

Journal: JACC. Cardiovascular interventions (2023)
Publication types: Journal Article
Timing of Creatine Supplementation around Exercise: A Real Concern?

Creatine has been considered an effective ergogenic aid for several decades; it can help athletes engaged in a variety of sports and obtain performance gains.Creatine supplementation increases muscle creatine stores; several factors have been identified that may modify the intramuscular increase and subsequent performance benefits, including baseline muscle cr content, type ii muscle fibre content and size, habitual dietary intake of cr, aging, and exercise.Timing of creatine supplementation in relation to exercise has recently been proposed as an important consideration to optimise muscle loading and performance gains, although current consensus is lacking regarding the ideal ingestion time.Research has shifted towards comparing creatine supplementation strategies pre-, during-, or post-exercise.Emerging evidence suggests greater benefits when creatine is consumed after exercise compared to pre-exercise, although methodological limitations currently preclude solid conclusions.Furthermore, physiological and mechanistic data are lacking, in regard to claims that the timing of creatine supplementation around exercise moderates gains in muscle creatine and exercise performance.This review discusses novel scientific evidence on the timing of creatine intake, the possible mechanisms that may be involved, and whether the timing of creatine supplementation around exercise is truly a real concern.

Journal: Nutrients (2021)
Publication types: Journal Article;Review
Agathis robustaBark Essential Oil Effectiveness against COVID-19: Chemical Composition, In Silico and In Vitro Approaches.

Severe acute respiratory syndrome coronavirus 2 (sars-co v2), the causative agent of coronavirus disease 2019 (covid-19), has seriously threatened global health.Alongside the approved vaccines, the discovery of prospective anti-covid-19 drugs has been progressively targeted.Essential oils (eos) provide a rich source of compounds with valuable antiviral activities that may contribute as effective agents against covid-19.In this study, the eo of agathus robustabark was investigated for its chemical composition and its antiviral activity against sars-co v2.Overall, 26 constituents were identified by gas chromatography-mass spectrometry (gc-ms) analysis.α-pinene, tricyclene,α-terpineol, limonene,d-camphene,trans-pinocarveol,α-phellandren-8-ol, l-β-pinene and borneol were the major components.In silico docking of these constituents against viral key enzymes, spike receptor-binding domain (rbd), main protease (mpro) and rna-dependent rna polymerase (rd rp), using molecular operating environment (moe) software revealed good binding affinities of the components to the active site of the selected targets, especially, the rbd.In vitro antiviral mtt and cytopathic effect inhibition assays demonstrated a promising anti sars-co v2 for a.Robustabark eo, with a significant selectivity index of 17.5.The results suggested using this eo or its individual components for the protection against or treatment of covid-19.

Journal: Plants (Basel, Switzerland) (2022)
Publication types: Journal Article
Economic Analysis of the European Healthcare Burden of Sternal-Wound Infections Following Coronary Artery Bypass Graft.

Sternal wound infections (swis) can be some of the most complex surgical-site infections (ssis) and pose a considerable risk following coronary artery bypass graft surgery (cabg).objective:to capture the cost burden of swis following cabg across european countries.methods:we modeled a standardized care pathway for cabg, starting at the point of surgery and extending to 1-year post surgery.The markov model captures the incidence and cost of an swi (deep or superficial swis).The cost burden is calculated from a hospital perspective such that the main inputs relating to costs were intensive-care-unit (icu) and general-ward (gw) days.Outpatient care, not in the hospital setting, has no cost in this analysis.Model input parameters were taken from eurostat and a review of published, peer-reviewed literature.European countries were included in this analysis when values for 50% of the required input parameters per country were identified.Missing data points were interpolated from available data.The robustness of results was assessed via probabilistic sensitivity analysis.results:full required input data were available for 8 european countries; a further 18 countries had sufficient data for analysis.The median (interquartile range) for swi incidence across the 26 countries was 3.9% (2.9-5.6%).The total burden for all 26 countries of swis after cabg was €170.8 million.These costs were made up of 25,751 additional icu days, 137,588 additional gw days, and 7,704 readmissions.The mean cost of an swi ranged from €8,924 in poland to €21,321 in denmark.Relative to the costs of post-cabg care without an swi complication, the incremental cost of an swi was highest in greece (24.9% increase) and lowest in the uk (3.8% increase) with a median (interquartile range) of 12% (10-16%) across all 26 countries.conclusions:swis following cabg present a considerable burden to healthcare budgets.

Journal: Frontiers in public health (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Review