syedzayyan/paper_mill_benchmark huggingface dataset:
Eggshell decalcification and skeletal mineralization during chicken embryonic development: defining candidate genes in the chorioallantoic membrane.

During chicken embryonic development, skeleton calcification mainly relies on the eggshell, whose minerals are progressively solubilized and transported to the embryo via the chorioallantoic membrane (cam).However, the molecular components involved in this process remain undefined.We assessed eggshell demineralization and calcification of the embryo skeleton after 12 and 16 d of incubation, and analyzed the expression of several candidate genes in the cam: carbonic anhydrases that are likely involved in secretion of protons for eggshell dissolution (ca2, ca4, ca9), ions transporters and regulators (calb1, slc4a1, atp6v1b2, sgk1, scgn, pkd2) and vitamin-d binding protein (gc).Our results confirmed that eggshell weight, thickness, and strength decreased during incubation, with a concomitant increase in calcification of embryonic skeletal system.In the cam, the expression of ca2 increased during incubation while ca4 and ca9 were expressed at similar levels at both stages.Scl4a1 and scgn were expressed, but not differentially, between the two stages, while the expression of atp6v1b2 and pkd2 genes decreased.The expression of sgk1 and trpv6 increased over time, although the expression of the latter gene was barely detectable.In parallel, we analyzed the expression of these candidate genes in the yolk sac (ys), which mediates the transfer of yolk minerals to the embryo during the first half of incubation.In ys, ca2 expression increases during incubation, similar to the cam, while the expression of the other candidate genes decreases.Moreover, calb1 and gc genes were found to be expressed during incubation in the ys, in contrast to the cam where no expression of either was detected.This study demonstrates that the regulation of genes involved in the mobilization of egg minerals during embryonic development is different between the ys and cam extraembryonic structures.Identification of the full suite of molecular components involved in the transfer of eggshell calcium to the embryo via the cam should help to better understand the role of this structure in bone mineralization.

Journal: Poultry science (2022)
Publication types: Journal Article
Multilevel analysis of grand multiparity: Trend and its determinants in the Sidama National Regional State of Ethiopia: a cross-sectional study design from demographic and health survey 2000-2016.

The study was aimed at examining the magnitude, trends and determinants of grand multiparity in the sidama regional state of ethiopia.Design we retrieved cross-sectional data from the ethiopia demographic and health survey from 2000 to 2016.Setting community-based demographic and health survey (dhs) was conducted in ethiopia.Participants the study population was women (aged 15-49 years) who had delivered children with the available dhs data set.Outcomes multilevel multivariate logistic regression analyses assessed the relationship between grand multiparity and its determinants.Results the magnitude of grand multiparity was 70.8% (95% ci 68.5% to 72.9%).The multilevel multivariable logistic regression model showed illiteracy (adjusted or (aor)=2; 95% ci 1.25 to 3.75), non-use of any contraceptive (aor=3.8; 95% ci 1.2 to 12.2), early marriage (aor=4.5; 95% ci 2.6 to 7.9), polygamous marriage (aor=4.2; 95% ci 2.0 to 9.3), short birth intervals (aor=2.3; 95% ci 1.4 to 3.5) and husband's low education status (aor=5.8; 95% ci 2.1 to 16.1) were significantly associated with grand multiparity.Conclusions this study revealed that 7 of 10 women were grand multipara, and the magnitude did not show significant change over the last 16 years.Early marriage and early age at first birth, low literacy level, low family planning utilisation, polygamy, short interbirth interval and unmet need for family planning were determinants of grand multiparity.We recommended the stakeholders to design new strategies to address the root cause of high fertility factors in communities.

Journal: BMJ open (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
A Qualitative Study of Health Workers' Experiences During Early Surges in the COVID-19 Pandemic in the U.S.: Implications for Ongoing Occupational Health Challenges.

Health workers (hws) have faced significant threats to physical and psychological health during the covid-19 pandemic.The recent surges associated with the spread of the delta variant in the u.s., coupled with political resistance to effective public health mitigation strategies, indicate that the risks experienced early in the pandemic are not likely to abate soon.This study sought to better understand the experiences, thoughts, concerns, and recommendations of hws during one of the first major surges in the u.s.And to explore how these experiences might inform efforts to mitigate potential ongoing covid-related negative health and psychological impacts on hws.Methods hws were recruited using a multi-faceted approach tailored to public health mitigation guidelines.Semi-structured interviews were conducted via video conference with front line hws, support staff, and opioid use disorder service organization providers between april 1 and july 9, 2020 using the social-ecological model as a framework.Interviews were audio-recorded and professionally transcribed; transcripts were analyzed inductively and deductively using thematic analytic methods, generating major themes and subthemes.Results a total of 22 hws participated in the study; 14 were female; 3 identified as a member of a racial or ethnic minority population.Major themes identified included: (1) institutions, infrastructure, and the pandemic; (2) working under fire; (3) the political becomes personal and (4) hope.Themes and subthemes explicated the ways in which phenomena at personal, interpersonal, community, organizational, and societal levels affected hws experiences and suggested potential mechanisms through which negative effects on hw mental health and health may be mitigated.Conclusions previous global infectious disease epidemics have had profound negative effects on hws' health and mental health.This study suggests the potential for similar negative impacts that may be exacerbated by the u.s.'s current sociopolitical milieu.Efforts to systematically describe and quantify these effects and to intervene to mitigate them are warranted.

Journal: Frontiers in public health (2022)
Publication types: Journal Article
Comparison of Visual Outcomes of Ophthalmic Artery Aneurysms Treated with Microsurgical Clipping and Endovascular Coiling.

Post-treatment visual deficit is a major concern associated with both microsurgical clipping and endovascular coiling for the treatment of ophthalmic artery (oph a) aneurysms of the internal carotid artery.We aimed to compare the safety and effectiveness of the 2 modalities.Materials and methods we retrospectively reviewed and compared the baseline characteristics and postoperative visual and angiographic outcomes of oph a aneurysms treated by clipping or coiling between january 2010 and august 2018 at our hospital.In addition, the balloon occlusion test was performed to evaluate the safety of oph a occlusion.Results this study included 56 aneurysms treated by clipping and 82 aneurysms treated by coiling.Both the immediate and follow-up rates of incomplete aneurysm occlusion were comparable between the 2 groups (21.4% vs.22.0%; 24.4% vs.23.6%).The incidence of post-treatment visual deficits was higher in the clipping group than in the coiling group (16.1% vs.2.4%; p=0.010).We observed total ipsilateral oph a occlusion in 6 patients and near occlusion in 3 patients during endovascular coiling; however, only 1 patient with near oph a occlusion showed a post-treatment visual field defect.Conclusion oph a aneurysms treated by endovascular coiling exhibited an aneurysm occlusion rate similar to that of microsurgical clipping with fewer post-treatment visual deficits.The total occlusion of oph a with adequate collaterals did not cause post-treatment visual deficits.

Journal: Neurointervention (2022)
Publication types: Journal Article
GWYRE: A Resource for Mapping Variants onto Experimental and Modeled Structures of Human Protein Complexes.

Rapid progress in structural modeling of proteins and their interactions is powered by advances in knowledge-based methodologies along with better understanding of physical principles of protein structure and function.The pool of structural data for modeling of proteins and protein-protein complexes is constantly increasing due to the rapid growth of protein interaction databases and protein data bank.The gwyre (genome wide ph yre) project capitalizes on these developments by advancing and applying new powerful modeling methodologies to structural modeling of protein-protein interactions and genetic variation.The methods integrate knowledge-based tertiary structure prediction using phyre2 and quaternary structure prediction using template-based docking by a full-structure alignment protocol to generate models for binary complexes.The predictions are incorporated in a comprehensive public resource for structural characterization of the human interactome and the location of human genetic variants.The gwyre resource facilitates better understanding of principles of protein interaction and structure/function relationships.The resource is available at

Journal: Journal of molecular biology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Research Support, U.S. Gov't, Non-P.H.S.;Research Support, N.I.H., Extramural
Real-world management and long-term outcomes of diabetic macular oedema with good visual acuity.

To evaluate the management and long-term outcomes of patients with diabetic macular oedema (dmo) and good initial visual acuity in real-world settings.Methods we reviewed 122 eyes of 100 patients with treatment-naive dmo and initial best-corrected visual acuity (bcva) of 20/25 or better.We assessed clinical characteristics, log mar bcva, central subfield thickness (cst), cumulative intravitreal injections and laser treatments at yearly intervals, and characteristics at time of initial treatment.Linear mixed effects models were used to identify predictors of visual outcomes.Results at presentation, mean bcva was 0.057 ± 0.048 log mar (snellen 20/23) and mean cst was 288 ± 57 μm.After a median follow-up of 3 years, 51% of eyes underwent treatment.More eyes underwent intravitreal injection as initial treatment (54%), but lasers were initiated at an earlier time and at better bcva.Final bcva was associated with better bcva (p < 0.001) and earlier timing (p = 0.017) at initial treatment, but not cst at first treatment (p = 0.634) or cumulative number of injections or lasers (p = 0.441-0.606).Conclusion dmo with good initial visual acuity should be monitored closely, as delay in treatment initiation is associated with worse visual outcomes.Bcva at time of initial treatment is the strongest determinant of final visual acuity.

Journal: Eye (London, England) (2020)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Occurrence of infestation with the isopod,Alitropus typusM. Edwards (Crustacea: Flabellifera: Aegidae) on commercially important freshwater fishes of Kerala, India.

Rapidly rising temperatures and increasing organic load in the inland and coastal waters has led to a significant increase in parasite population.The isopod alitropus typusinfestation on fish in these waters have become more frequent, causing mortalities in both wild and cultured fishes.The present study was aimed to investigate the infestation on different fish hosts, mean intensity, prevalence, environmental influences on the parasite abundance and the histopathological changes it causes in the host.A total of 219 isopod specimens were collected from 149 infested fishes in two districts of kerala, india.Among the different fish hosts,channa striatawas found to be the most susceptible, followed by catla catla, cyprinus carpio, and wallago attu, with 81%, 10%, 7%, and 2% occurrence, respectively.The prevalence and mean intensity of infestation were found to be 69.8%, 44.4%, 68.2%, 62.5% and 1.33, 4.25, 1.26, 1.80 in c.Striata, w.Attu, c.Catla, and c.Carpio, respectively.The parasite abundance was directly influenced by temperature.The histopathology of affected gill tissues showed epithelial lifting, rupture of secondary gill filaments, vacuole formation and hemocytic infiltration.The findings indicated that the isopod parasite,a.Typushad a negative impact on fish health and appearance, causing economic losses to the small scale farmers/fishermen.This is the first reported record of the infestation of isopod parasite,a.Typuson the indian major carp c.Catlaand c.Carpiofrom india.

Journal: Journal of parasitic diseases : official organ of the Indian Society for Parasitology (2022)
Publication types: Journal Article
Esophageal cancer T-staging on MRI: A preliminary study using cine and static MR sequences.

S to evaluate the added value of cine mr in addition to static mri for t-staging assessment of esophageal cancer (ec).Materials and methods this prospective monocentric study included 54 patients (mean age 66.3 ± 9.4 years, 46 men) with histologically proven ec.They underwent mri on a 3 t-scanner in addition to the standard workup.Acquisitions included static and cine sequences (steady-state-free-precession and real-time true-fisp during water ingestion).Three radiologists independently assessed t-staging and diagnosis confidence by reviewing (1) static sequences (s-mri) and (2) adding cine sequences (sc-mri).Inter-reader agreement was performed.Mri t-staging was correlated to reference standard t-staging (histopathology or consensus on endoscopic ultrasonography and imaging findings) and to clinical outcome by log-rank test.Results both s-mri and sc-mri t-staging showed a significant correlation with reference t-staging (rs = 0.667, p < 0.001).Sc-mri showed a slightly better performance in distinguishing t1-t3 from t4 with a sensitivity, specificity and auc of 76.5% (95% ci: 50.1-93.2), 83.8% (68-93.8) and 0.801 (0.681-0.921) vs 70.6% (44-89.7), 83% (68-93.8) and 0.772 (0.645-0.899) for s-mri.Compared to s-mri, sc-mri increased inter-reader agreement for t4a and t4b (κ = 0.403 and 0.498) and t-staging confidence.Conclusion mri is accurate for t-staging of ec.The addition of cine sequences allows better differentiation between t1-t3 and t4 tumors with increased diagnostic confidence and inter-reader agreement.

Journal: European journal of radiology (2023)
Publication types: Journal Article
Extracellular K+reflects light-evoked changes in retinal energy metabolism.

Retinal neurons spend most of their energy to support the transmembrane movement of ions.Light-induced electrical activity is associated with a redistribution of ions, which affects the energy demand and results in a change in metabolism.Light-induced metabolic changes are expected to be different in distal and proximal retina due to differences in the light responses of different retinal cells.Extracellular k+concentration ([k+]o) is a reliable indicator of local electrophysiological activity, and the purpose of this work was to compare [k+]ochanges evoked by steady and flickering light in distal and proximal retina.Data were obtained from isolated mouse (c57bl/6j) retinae.Double-barreled k+-selective microelectrodes were used to simultaneously record [k+]oand local ergs.In the distal retina, photoreceptor hyperpolarization led to suppression of ion transfer, a decrease in [k+]oby 0.3-0.5 m m, reduced energy demand, and, as previously shown in vivo, decreased metabolism.Flickering light had the same effect on [k+]oin the distal retina as steady light of equivalent illumination.The conductance and voltage changes in postreceptor neurons are cell-specific, but the overall effect of steady light in the proximal retina is excitation, which is reflected in a [k+]oincrease there (by a maximum of 0.2 m m).In steady light the [k+]oincrease lasts only 1-2 s, but a sustained [k+]oincrease is evoked by flickering light.A squarewave low frequency (1 hz) flicker of photopic intensity produced the largest increases in [k+]o.Judging by measurements of [k+]o, steady illumination decreases energy metabolism in the distal retina, but not in the proximal retina (except for the first few seconds).Flickering light evokes the same decrease in the distal retina, but also evokes a sustained [k+]oincrease in the proximal retina, suggesting an increase of metabolic demand there, especially at 1 hz, when neurons of both on- and off-pathways appear to contribute maximally.This proximal retinal metabolic response to flicker correlates to the increase in blood flow during flicker that constitutes neurovascular coupling.

Journal: Experimental eye research (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural
Willingness to work during initial lockdown due to COVID-19 pandemic: Study based on an online survey among physicians of Bangladesh.

During the catastrophic situation of the covid-19 pandemic, the role of the health care workers (hcws) is the most crucial, and their absenteeism, whether due to inability or unwillingness, becomes a major concern for the national health system.Hence, the present study aimed to determine the willingness and its associated factors to work during the covid-19 pandemic among the physicians of bangladesh.Methods this was a cross-sectional study conducted from april 21 to may 10, 2020, using an online survey among the bangladeshi physicians living in the country.Both univariate and multivariable binary logistic regression models were used to determine the predictors of the willingness of the physicians to work during the covid-19 pandemic.Results more than 69% physicians reported that they were willing to work during the covid-19 pandemic, 8.9% reported that they were not willing, while 21.4% of participants were not sure about their willingness.Younger age, having experience of treating patients during previous pandemics, working in the emergency departments and high self-reported compliance to the recommended ppe were important predictors of being willing to work during covid-19 pandemic.Concern for family and risk of transmitting the infection to family members were most commonly reported as major barriers of working during the pandemic (30%) followed by having comorbidities (25%), lack of adequate safety measures (25%), fear of being infected (12.2%), not involved in clinical practice (12.5%) etc.Conclusions though the majority of the physicians were willing to work during the covid-19 pandemic, sufficient supply of ppe, support to maintain recommended quarantine and isolation policy after risky hospital duty along with adequate and effective training can increase their willingness to continue their sacred duty during this crucial pandemic.

Journal: PloS one (2021)
Publication types: Journal Article
What Is the Support for Conspiracy Beliefs About COVID-19 Vaccines in Latin America? A Prospective Exploratory Study in 13 Countries.

Conspiracy theories about covid-19 began to emerge immediately after the first news about the disease and threaten to prolong the negative impact of the covid-19 pandemic by limiting people's willingness of receiving a life-saving vaccine.In this context, this study aimed to explore the variation of conspiracy beliefs regarding covid-19 and the vaccine against it in 5779 people living in 13 latin american countries (argentina, bolivia, chile, colombia, cuba, ecuador, el salvador, guatemala, mexico, paraguay, peru, uruguay and venezuela) according to sociodemographic variables such as gender, age, educational level and source of information about covid-19.The study was conducted during the covid-19 pandemic between september 15 and october 25, 2021.The spanish-language covid-19 vaccine conspiracy beliefs scale (eccv-covid) and a sociodemographic survey were used.The results indicate that, in most countries, women, people with a lower educational level and those who receive information about the vaccine and covid-19 from family/friends are more supportive of conspiracy ideas regarding the covid-19 vaccine.In the case of age, the results vary by country.The analysis of the responses to each of the questions of the eccv-covid reveals that, in general, the countries evaluated are mostly in some degree of disagreement or indecision regarding conspiratorial beliefs about covid-19 vaccines.The findings could help open further study which could support prevention and treatment efforts during the covid-19 pandemic.

Journal: Frontiers in psychology (2022)
Publication types: Journal Article
Extrusion Simulation for the Design of Cereal and Legume Foods.

A 1d global twin-screw extrusion model, implemented in numerical software, ludovic®, was applied to predict extrusion variables and, therefore, to design various starchy products with targeted structure and properties.An experimental database was built with seven starchy food formulations for manufacturing dense and expanded foods made from starches, starch blends, breakfast cereals, pulse crop ingredients such as pea flour, fava bean flour, and fava bean starch concentrated, and wheat flour enriched with wheat bran.This database includes the thermal and physical properties of the formulations at solid and molten states, melt viscosity model, extruder configurations and operating parameters, and extruded foods properties.Using extrusion and viscosity models, melt temperature (t) and specific mechanical energy (sme) were satisfactorily predicted.A sensitivity analysis of variables at die exit was performed on formulation, extruder configuration, and operating parameters, generating the extruder operating charts.Results allowed the establishment of relationships between predicted variables (t, sme, melt viscosity) and product features such as starch and protein structural change, density and cellular structure, and functional properties.The extrusion operating conditions leading to targeted food properties can be assessed from these relationships and also the relationship between extrusion operating parameters and variables provided by simulation.

Journal: Foods (Basel, Switzerland) (2022)
Publication types: Journal Article
Identification and characterization of apoptosis-related gene serine/threonine kinase 17A (STK17A) from Japanese flounder Paralichthys olivaceus.

Apoptosis plays important roles in regulation of the immune response and has a direct impact on disease resistance in teleost.Death associated protein kinase (dapk)-related serine/threonine kinase 17a (stk17a) is a positive apoptosis regulator.However, the expression and function of stk17a in fish still remains uninvestigated.In this study, we identified and characterized a stk17a gene (termed po stk17a) from japanese flounder paralichthys olivaceus.We also investigated the pro-apoptotic role of po stk17a in fish.Real-time quantitative pcr analysis revealed that po stk17a is widely present in various japanese flounder tissues, and dominantly expressed in liver.Immune challenge experiments showed that po stk17a expression was upregulated by inflammatory challenge, edwardsiella tarda infection and dna-damaging agent cisplatin treatment as well.Immunofluorescence microscopy revealed that the recombinant po stk17a proteins are mainly located in the nucleus of japanese flounder fg-9307 cells, and human hela and mcf7 cells.However, po stk17a was translocated from the nucleus to cytoplasm following cisplatin treatment.Overexpression of po stk17a significantly increased the apoptosis in human mcf7 cells through both cisplatin-dependent and independent manners.Importantly, po stk17a also promotes the atp-gated p2x7 receptor-mediated apoptosis in japanese flounder fg-9307 cells.Collectively, we characterized an inducible stk17a gene (po stk17a) that may play a conserved pro-apoptotic role in fish.

Journal: Fish & shellfish immunology (2020)
Publication types: Journal Article