syedzayyan/paper_mill_benchmark huggingface dataset:
Time of Day and Muscle Strength: A Circadian Output?

For more than 20 years, physiologists have observed a morning-to-evening increase in human muscle strength.Recent data suggest that time-of-day differences are the result of intrinsic, nonneural, muscle factors.We evaluate circadian clock data sets from human and mouse circadian studies and highlight possible mechanisms through which the muscle circadian clock may contribute to time-of-day muscle strength outcomes.

Journal: Physiology (Bethesda, Md.) (2021)
Publication types: Journal Article;Research Support, N.I.H., Extramural
Pathogen reduction of double-dose platelet concentrates from pools of eight buffy coats: Product quality, safety, and economic aspects.

Pathogen reduction (pr) of platelet concentrates (pcs) contributes to the safety of platelet (plt) transfusion by reducing the risk of transfusion-transmitted infections and transfusion-associated graft-versus-host disease.In vitro quality of pathogen-reduced double-dose pc (pr-pc) made of eight whole blood (wb)-derived buffy coats (bcs) were evaluated.Methods eight small-volume wb bcs from donors with at least 200 × 109plt/l were pooled with an additive solution to produce double-dose pcs (dd-pcs), which were treated with amotosalen/ultraviolet a light in a dual storage processing set, yielding 2 units of pr-pc.Quality controls were undertaken as per european directive for the quality of medicines (edqm) guidelines.Plt recovery rates were measured.Production costs and savings were compared over the 3 years before and after pr implementation.Results in the pre-pr period, 19 666 pcs were produced, compared to 17 307 pcs in the pr period.Single bc in the pr period had 41 ± 2 m l, hematocrit 0.39 ± 0.04 and 1.06 ± 0.18 × 1011plts, and showed a recovery of 91% ± 8%.After pooling, separation, pr treatment of dd-pc, and splitting, each single pc had 189 ± 6 m l with 2.52 ± 0.34 × 1011plts, compared to 2.48 ± 0.40 in the pre-pr period.The plt recovery rate after pr was 87% ± 14%.Edqm requirements were met.An increase of about €12 (+7.5%) per pc from the pre-pr to the pr period was identified.Conclusion a new production method resulting in two pr-pcs made from pools of 8 bcs with use of one pr set was successfully introduced, and our experience of nearly 3 years demonstrated the high efficacy and in vitro quality of the pr-pcs obtained.

Journal: Transfusion (2020)
Publication types: Journal Article
Practising in a post-truth world: Pandemic ethics can inform patient autonomy and clinical communication.

The covid-19 pandemic posed an unprecedented challenge to modern bioethical frameworks in the clinical setting.Now, as the pandemic stabilises and we learn to 'live with covid', the medical community has a duty to evaluate its response to the challenge, and reassess our ethical reasoning, considering how we practise in the future.This article considers a number of clinical and bioethical challenges encountered by the author team and colleagues during the most severe waves of the pandemic.We argue that the changed clinical context may require reframing our ethical thought in such a manner as to adequately accommodate all parties in the clinical interaction.We argue that clinicians have become relatively disempowered by the 'infodemic', and do not necessarily have adequate skills or training to assess the scientific literature being published at an unprecedented rate.Conversely, we acknowledge that patients and families are more empowered by the infodemic, and bring this empowerment to bear on the clinical consultation.Sometimes these interactions can be unpleasant and threatening, and involve inviting clinicians to practise against best evidence or even illegally.Generally, these requests are framed within 'patient autonomy' (which some patients or families perceive to be unlimited), and several factors may prevent clinicians from adequately navigating these requests.In this article, we conclude that embracing a framework of shared decision-making (sdm), which openly acknowledges clinical expertise and in which patient and family autonomy is carefully balanced against other bioethics principles, could serve us well going forward.One such principle is the recognition of clinician expertise as holding weight in the clinical encounter, when framed in terms of non-maleficence and beneficence.Such a framework incorporates much of our learning and experience from advising and treating patients during the pandemic.

Journal: South African medical journal = Suid-Afrikaanse tydskrif vir geneeskunde (2022)
Publication types: Journal Article
The importance of the urinary output criterion for the detection and prognostic meaning of AKI.

Most reports on aki claim to use kdigo guidelines but fail to include the urinary output (uo) criterion in their definition of aki.We postulated that ignoring uo alters the incidence of aki, may delay diagnosis of aki, and leads to underestimation of the association between aki and icu mortality.Using routinely collected data of adult patients admitted to an intensive care unit (icu), we retrospectively classified patients according to whether and when they would be diagnosed with kdigo aki stage ≥ 2 based on baseline serum creatinine (screa) and/or urinary output (uo) criterion.As outcomes, we assessed incidence of aki and association with icu mortality.In 13,403 icu admissions (62.2% male, 60.8 ± 16.8 years, sofa 7.0 ± 4.1), incidence of kdigo aki stage ≥ 2 was 13.2% when based only the screa criterion, 34.3% when based only the uo criterion, and 38.7% when based on both criteria.By ignoring the uo criterion, 66% of aki cases were missed and 13% had a delayed diagnosis.The cause-specific hazard ratios of icu mortality associated with kdigo aki stage ≥ 2 diagnosis based on only the screa criterion, only the uo criterion and based on both criteria were 2.11 (95% ci 1.85-2.42), 3.21 (2.79-3.69) and 2.85 (95% ci 2.43-3.34), respectively.Ignoring uo in the diagnosis of kdigo aki stage ≥ 2 decreases sensitivity, may lead to delayed diagnosis and results in underestimation of kdigo aki stage ≥ 2 associated mortality.

Journal: Scientific reports (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Discovering human germ cell mutagens with whole genome sequencing: Insights from power calculations reveal the importance of controlling for between-family variability.

Mutations in germ cells pose potential genetic risks to offspring.However, de novo mutations are rare events that are spread across the genome and are difficult to detect.Thus, studies in this area have generally been under-powered, and no human germ cell mutagen has been identified.Whole genome sequencing (wgs) of human pedigrees has been proposed as an approach to overcome these technical and statistical challenges.Wgs enables analysis of a much wider breadth of the genome than traditional approaches.Here, we performed power analyses to determine the feasibility of using wgs in human families to identify germ cell mutagens.Different statistical models were compared in the power analyses (anova and multiple regression for one-child families, and mixed effect model sampling between two to four siblings per family).Assumptions were made based on parameters from the existing literature, such as the mutation-by-paternal age effect.We explored two scenarios: a constant effect due to an exposure that occurred in the past, and an accumulating effect where the exposure is continuing.Our analysis revealed the importance of modeling inter-family variability of the mutation-by-paternal age effect.Statistical power was improved by models accounting for the family-to-family variability.Our power analyses suggest that sufficient statistical power can be attained with 4-28 four-sibling families per treatment group, when the increase in mutations ranges from 40 to 10% respectively.Modeling family variability using mixed effect models provided a reduction in sample size compared to a multiple regression approach.Much larger sample sizes were required to detect an interaction effect between environmental exposures and paternal age.These findings inform study design and statistical modeling approaches to improve power and reduce sequencing costs for future studies in this area.

Journal: Mutation research. Genetic toxicology and environmental mutagenesis (2018)
Publication types: Journal Article
Forage quality and physiological performance of mowed alfalfa (Medicago sativaL.) subjected to combined light quality and drought.

Alfalfa (medicago sativa) can dwell in water-deficient habitats, where it is difficult to predict dry mass (dm) production and forage quality due to understory transmittance.Mowing is a recommended practice for alfalfa populations under drought, but its effect on forested land receives less attention.In a controlled indoor experiment, we found that drought better reduces shoot dm weight and crude fiber content (cfi) in blue light (33.7% red, 48.5% green, and 17.8% blue lights) than red light (71.7% red, 13.7% green, and 14.6% blue lights).Mowing decreases carbon (c) isotope signature (δ13c), cfi, and total c content in shoots but increases their accumulations in dm, nonstructural carbohydrates, and crude fat content (cfa).The results also demonstrated that mown alfalfa has higher starch content when exposed to green light (26.2% red, 56.4% green, and 17.4% blue lights) compared to the other two spectra.Multiple factorial regression indicated that higher soluble sugar content accounted for the increase of cfa and dm weight for cfi.Overall, mowing in blue-light-enriched understory stands is recommended and produces high-forage-quality alfalfa, which can be used as a lowered crude fiber component.

Journal: Frontiers in plant science (2022)
Publication types: Journal Article
High altitude arterialised capillary earlobe blood gas measurement using the Abbott i-STAT.

Introduction measurement of physiological parameters in extreme environments is essential to advancing knowledge, prophylaxis and treatment of altitude sickness.Point-of-care testing facilitates investigation in non-specialist and remote settings, as well as becoming increasingly popular at the bedside for real-time results in the clinical environment.Arterialised capillary earlobe blood gases are recommended as a valid alternative to arterial sampling in research.This study aimed to test the feasibility of obtaining and analysing daily earlobe samples at high altitude.Methods from 17 to 24 january 2016, 24 participants on a research expedition to ecuador underwent daily earlobe blood gas measurements including p h, partial pressure of oxygen and partial pressure of carbon dioxide to 5043 m.Samples were analysed using an abbott i-stat blood gas analyser and g3+ cartridges.Results daily measurements were successfully obtained and analysed at the point of care in 23/24 participants and were well tolerated with no adverse events.12% (27/220) cartridges failed and required repeat sampling.Conclusions daily earlobe blood gas analysis using the abbott i-stat is feasible in a protected environment at high altitude.Participants and equipment should be kept warm before and during testing.Spare cartridges should be available.This methodology may be useful for both research and therapeutic measurements in remote, rural and wilderness medicine.

Journal: Journal of the Royal Army Medical Corps (2018)
Publication types: Journal Article
Variation of psychological and anthropometrics measures before and after dieting and factors associated with body dissatisfaction and quality of life in a Lebanese clinical sample.

The primary objective of this study was to assess a change in the psychological states (stress, self-esteem, anxiety and depression), anthropometric measurements and physical/mental quality of life before and after diet in a sample of lebanese subjects visiting a diet clinic.The secondary objectives included the evaluation of factors associated with body dissatisfaction, mental and physical quality of life (qol) before the intervention of the diet program and the change in quality of life after this intervention among those participants.Methods this cross-sectional study, conducted between may and august 2018, enrolled 62 participants recruited from three diet clinics.The qol was measured using the 12-item short form health survey (sf-12) and the psychological states was measured using the following scales: the rosenberg self-esteem scale, perceived stress scale, hamilton anxiety rating scale and hamilton depression rating scale.Results a significant reduction in body dissatisfaction, anxiety, waist, weight and body fat and a significant increase in the physical and mental quality of life was seen after diet compared to before it (p < 0.001 for all).No significant variation in perceived stress (p = 0.072), self-esteem (p = 0.885), and depression (p = 0.353) after diet were found.Higher bmi (β = 0.440) and higher anxiety (β = 0.132) were associated with higher body dissatisfaction scores, whereas higher self-esteem (β = - 0.818) was significantly associated with lower body dissatisfaction.Higher perceived stress (β = - 0.711), higher body dissatisfaction (β = - 0.480) and being a female (β = - 4.094) were associated with lower mental qol.Higher physical activity index was significantly associated with higher mental and physical qol (β = 0.086 and β = 0.123 respectively).Conclusion the results indicate the effectiveness of diet programs in enhancing the quality of life, psychological and anthropometric measures.

Journal: BMC psychology (2021)
Publication types: Journal Article
Fruits ofHippophaë rhamnoidesin human leukocytes and Caco-2 cell monolayer models-A question about their preventive role in lipopolysaccharide leakage and cytokine secretion in endotoxemia.

Preparations from hippophaë rhamnoides l.(sea buckthorn) have been traditionally used in the treatment of skin and digestive disorders, such as gastritis, gastric and duodenal ulcers, uterine erosions, as well as oral, rectal, and vaginal mucositis, in particular in the himalayan and eurasian regions.An influence of an aqueous extract from the fruits of h.Rhamnoides(hr) on leakage of lipopolysaccharide (lps) from escherichia colithrough gut epithelium developed from the human colorectal adenocarcinoma (caco-2) monolayerin vitroand glucose transporter 2 (glut2) translocation were the principal objectives of the study.Additionally, the effect of hr on the production of pro- and anti-inflammatory cytokines (interleukins: il-8, il-1β, il-10, il-6; tumor necrosis factor: tnf-α) by the caco-2 cell line, human neutrophils (pmn), and peripheral blood mononuclear cells (pbmc) was evaluated.The concentration of lps on the apical and basolateral sides of the caco-2 monolayer was evaluated with a limulus amebocyte lysate (lal) assay.Glut2 translocation was evaluated using an immunostaining assay, whereas secretion of cytokines by cell cultures was established with an enzyme-linked immunosorbent (elisa) assay.Hr (500 μg/ml) significantly inhibited lps leakage through epithelial monolayerin vitroin comparison with non-treated control.The treatment of caco-2 cells with hr (50-100 μg/ml) showed glut2 expression similar to the non-treated control.Hr decreased the secretion of most pro-inflammatory cytokines in all tested models.Hr might prevent low-grade chronic inflammation caused by metabolic endotoxemia through the prevention of the absorption of lps and decrease of chemotactic factors released by immune and epithelial cells, which support its use in metabolic disorders in traditional medicine.

Journal: Frontiers in pharmacology (2022)
Publication types: Journal Article
The effect of resting and compression time post-centrifugation on the characteristics of platelet rich fibrin (PRF) membranes.

To evaluate the effect of resting and compression time after centrifugation on the physical properties of platelet rich fibrin (prf) membranes, and to provide optimal guidance regarding the clinical preparation of prf.Materials and methods a total of 12 volunteers enrolled in this study divided into 2 groups equally.For each volunteer, 6 tubes of 10 m l venous whole blood was drawn.To evaluate the influence of resting time after centrifugation, prf clots were taken out 0, 1, 3, 5, 7, and 10 min from tubes following centrifugation, and then the weight, size, maximum stress, and maximum strain of each group were measured.To evaluate the influence of compression time on the preparation of prf membranes, the weight ratio of prf membranes to prf clots was calculated by compression for 10 s, 30 s, 60 s, 90 s, 120 s, and 180 s, respectively.Scanning electron microscopy was performed to observe the cross-linking of the fibers within membranes, and the maximum stress and strain of prf membranes were tested followed by stress-strain curve analysis.Results the weight and volume of prf clots and prf membranes increased in size and weight reached the top at 3 min, followed by a decrease after 7-min resting.The maximum strain of the prf membranes after 10 min decreased significantly compared to the 3-min and 5-min groups.The maximum stress was found at 3 min followed by a statistical decrease when resting time went on.Scanning electron microscopy demonstrated that the internal fibrous structure of the prf membranes was looser when the compression time was less than 60 s when comparing the 90-s group.The maximum stress of prf membranes was shown using a wait period of 3 min post-centrifugation followed by compression for 120 s.Conclusion the findings from the present study demonstrate that the time post-centrifugation of prf membranes showed a maximum weight, volume, and mechanical properties after resting for 3-5 min in the tube post-centrifugation followed by a compression time of 120 s.Clinical relevance although research to date has focused primarily on centrifugation protocols, this study revealed for the first time that the resting time post-centrifugation greatly affected the mechanical properties of prf.This study demonstrated that the resting and compression time after centrifugation influences the mechanical strength of prf membranes, which might explain differences in prf characteristics prepared by different clinicians that may provide a standard guide for preparation of prf membranes.

Journal: Clinical oral investigations (2022)
Publication types: Journal Article
Bulky Polyfluorinated Terphenyldiphenylboranes: Water Tolerant Lewis Acids.

Protocols for the synthesis of the bulky polyfluorinated triarylboranes 2,6-(c6f5)2c6f3b(c6f5)2(1), 2,6-(c6f5)2c6f3b[3,5-(cf3)2c6h3] (2), 2,4,6-(c6f5)3c6h2b(c6f5)2(3), 2,4,6-(c6f5)3c6h2b[3,5-(cf3)2c6h3] (4) were developed.All boranes are water tolerant and according to the gutmann-beckett method, 1-3 display lewis acidities larger than that of the prominent b(c6f5)3.

Journal: Chemistry (Weinheim an der Bergstrasse, Germany) (2021)
Publication types: Journal Article
Polyethylene glycol functionalized reduced graphene oxide coupled with zinc oxide composite adsorbent for removal of phenolic wastewater.

The development of agricultural activities and industrialization recently has various adverse impacts on living organisms.The ever-increasing problem of organic pollution has been an environmental concern to the community.Among these, phenolic pollutants like 2,4-dichlorophenol (2,4-dcp), phenol, 2-chlorophenol (2-cp), and bisphenol-a (bpa) are priority toxic pollutants that are continuously released into environment from many industries.In this work, a biocompatible zinc oxide incorporated polyethylene glycol functionalized reduced graphene oxide composite (rgo-peg-zn o) was synthesized and explored for the adsorptive removal of toxic phenolic pollutants from water.The optimized adsorption parameters were solution p h 7, adsorption time 60 min, temperature 25 °c, and dosage 0.25 g/l.The isotherms were well fitted by the langmuir model for bpa and phenol, whereas for 2-cp, and 2,4-dcp, freundlich was the best-fitted model, and the maximum uptake of bpa, phenol, 2-cp, and 2,4-dcp were 485.756, 511.248, 531.804, 570.641 mg/g, respectively.The kinetic data for all the phenolic pollutants follow the pseudo-second-order model.The thermodynamic analysis shows that gibb's free energy (δgo) values for all the pollutants were negative, confirming that the process was spontaneous.The positive values of change in enthalpy (δho) 28.261, 37.205, 46.182, and 61.682 k j/mol for bpa, phenol, 2-cp, and 2,4-dcp, respectively, confirm that the above adsorption process was endothermic.The composite can be used for up to five cycles with a small reduction in the removal percentage.Adsorption performance of the synthesized composite for synthetic industrial effluents shows that up to 86.54% removal occurred in 45 min adsorption time.Based on the remarkably rapid adsorption and high adsorption capacity, rgo-peg-zn o composite can be considered an efficient adsorbent for treating phenolic pollutants from wastewater.

Journal: Environmental research (2022)
Publication types: Journal Article
Delving Deeper Into Mask Utilization in Video Object Segmentation.

This paper focuses on the mask utilization of video object segmentation (vos).The mask here mains the reference masks in the memory bank, i.e., several chosen high-quality predicted masks, which are usually used with the reference frames together.The reference masks depict the edge and contour features of the target object and indicate the boundary of the target against the background, while the reference frames contain the raw rgb information of the whole image.It is obvious that the reference masks could play a significant role in the vos, but this is not well explored yet.To tackle this, we propose to investigate the mask advantages of both the encoder and the matcher.For the encoder, we provide a unified codebase to integrate and compare eight different mask-fused encoders.Half of them are inherited or summarized from existing methods, and the other half are devised by ourselves.We find the best configuration from our design and give valuable observations from the comparison.Then, we propose a new mask-enhanced matcher to reduce the background distraction and enhance the locality of the matching process.Combining the mask-fused encoder, mask-enhanced matcher and a standard decoder, we formulate a new architecture named mask vos, which sufficiently exploits the mask benefits for vos.Qualitative and quantitative results demonstrate the effectiveness of our method.We hope our exploration could raise the attention of mask utilization in vos.

Journal: IEEE transactions on image processing : a publication of the IEEE Signal Processing Society (2022)
Publication types: Journal Article
Personalized communication with parents of children born at less than 25 weeks: Moving from doctor-driven to parent-personalized discussions.

Communication with parents is an essential component of neonatal care.For extremely preterm infants born at less than 25 weeks, this process is complicated by the substantial risk of mortality or major morbidity.For some babies with specific prognostic factors, the majority die.Although many of these deaths occur after admission to the intensive care unit, position statements have focused on communication during the prenatal consultation.This review takes a more comprehensive approach and covers personalized and parent-centered communication in the clinical setting during three distinct yet inter-related phases: the antenatal consultation, the neonatal intensive care hospitalization, and the dying process (when this happens).We advocate that a 'one-size-fits-all' communication model focused on standardizing information does not lead to partnerships.It is possible to standardize personalized approaches that recognize and adapt to parental heterogeneity.This can help clinicians and parents build effective partnerships of trust and affective support to engage in personalized decision-making.These practices begin with self-reflection on the part of the clinician and continue with practical frameworks and stepwise approaches supporting personalization and parent-centered communication.

Journal: Seminars in perinatology (2022)
Publication types: Journal Article;Review