syedzayyan/paper_mill_benchmark huggingface dataset:
Differences in incubation behaviour and niche separation of two competing flycatcher species.

Food availability sets the stage for incubation behaviour of a female bird and thereby indirectly determines the nest temperature, which in turn affects development and metabolism of avian embryos.Changes in development and metabolism in turn are known to influence offspring's ability to adjust to environmental changes later in life.However, few studies have investigated the role of interspecific differences in incubation behaviour in relation to niche separation between competing sibling species.We studied the effects of habitat quality (in terms of caterpillar availability) on incubation behaviour of two ecologically similar and closely related species, collared and pied flycatchers (ficedula albicollisand f.Hypoleuca), in their hybrid zone on the island of öland, sweden.Even though both species prefer caterpillar-rich deciduous forests as nesting sites, collared flycatchers, whose nestlings have higher energetic demands, are able to nest only in deciduous forests, whereas pied flycatchers have more flexible habitat requirements.Overall, higher food availability was associated with increased nest attendance, higher incubation temperature and a lower number of foraging trips across species.In addition, collared flycatchers had more frequent and shorter foraging trips across habitat types, allocated more heat to eggs and therefore maintained higher nest temperatures compared to pied flycatchers.We argue that the higher heat allocation or the need to maintain a higher nest temperature for embryo development may constrain collared flycatchers to focus on relatively more profitable prey.Our results highlight the importance of considering incubation behaviour in the context of understanding species differences in niche use.Significance statement niche separation plays an important role in mitigating effects of competition between closely related species.Whether species differences in incubation behaviour relate to differences in niche use remains unknown.We compared incubation behaviour of two sympatric flycatcher species that differ in sensitivity to food availability.The competitively more dominant and larger species, the collared flycatcher, whose nestlings are more sensitive to food shortages, made more frequent foraging trips but allocated more heat to eggs, leading to higher nest temperature despite lower nest attendance, compared to pied flycatchers.These interspecific differences may be a result of differences in embryo sensitivity or female physiology and contribute to the niche separation between the species, which in turn can facilitate coexistence.

Journal: Behavioral ecology and sociobiology (2020)
Publication types: Journal Article
Molecular Diagnostics of Ciliopathies and Insights Into Novel Developments in Diagnosing Rare Diseases.

The definition of a rare disease in the european union describes genetic disorders that affect less than 1 in 2,000 people per individual disease; collectively these numbers amount to millions of individuals globally, who usually manifest a rare disease early on in life.At present, there are at least 8,000 known rare conditions, of which only some are clearly molecularly defined.Over the recent years, the use of genetic diagnosis is gaining ground into informing clinical practice, particularly in the field of rare diseases, where diagnosis is difficult.To demonstrate the complexity of genetic diagnosis for rare diseases, we focus on ciliopathies as an example of a group of rare diseases where an accurate diagnosis has proven a challenge and novel practices driven by scientists are needed to help bridge the gap between clinical and molecular diagnosis.Current diagnostic difficulties lie with the vast multitude of genes associated with ciliopathies and trouble in distinguishing between ciliopathies presenting with similar phenotypes.Moreover, ciliopathies such as autosomal recessive polycystic kidney disease (arpkd) and meckel-gruber syndrome (mks) present with early phenotypes and may require the analysis of samples from foetuses with a suspected ciliopathy.Advancements in next generation sequencing (ngs) have now enabled assessing a larger number of target genes, to ensure an accurate diagnosis.The aim of this review is to provide an overview of current diagnostic techniques relevant to ciliopathies and discuss the applications and limitations associated with these techniques.

Journal: British journal of biomedical science (2022)
Publication types: Journal Article;Review
Immune dysregulation associated with co-occurring germline CBL and SH2B3 variants.

Cbl syndrome is a rasopathy caused by heterozygous germline mutations of the casitas b-lineage lymphoma (cbl) gene.It is characterized by heterogeneous clinical phenotype, including developmental delay, facial dysmorphisms, cardiovascular malformations and an increased risk of cancer development, particularly juvenile myelomonocytic leukemia (jmml).Although the clinical phenotype has been progressively defined in recent years, immunological manifestations have not been well elucidated to date.Methods we studied the genetic, immunological, coagulative, and clinical profile of a family with cbl syndrome that came to our observation after the diagnosis of jmml, with homozygous cbl mutation, in one of the members.Results variant analysis revealed the co-occurrence of cbl heterozygous mutation (c.1141 t &gt; c) and sh2b3 mutation (c.1697g &gt; a) in two other members.Patients carrying both mutations showed an alps-like phenotype characterized by lymphoproliferation, cytopenia, increased double-negative t-cells, impaired fas-mediated lymphocyte apoptosis, altered cell death in pbmc and low trecs expression.A coagulative work-up was also performed and showed the presence of subclinical coagulative alterations in patients carrying both mutations.Conclusion in the reported family, we described immune dysregulation, as part of the clinical spectrum of cbl mutation with the co-occurrence of sh2b3.

Journal: Human genomics (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Clinical Trials in Hepatopancreatobiliary Surgery: Assessing Trial Characteristics, Early Discontinuation, Result Reporting, and Publication.

Hepatopancreaticobiliary (hpb) diseases carry high morbidity despite efforts aimed at their reduction.An assessment of their trial characteristics is paramount to determine trial design adequacy and highlight areas for improvement.As such, the aim of this study is to assess hpb surgery trial characteristics, summarize logistic, financial, and practical reasons behind early discontinuation, and propose potential interventions to prevent this in the future.Methods all clinical trials investigating hpb surgery registered on clinical trials.gov from october 1st, 2007 (inclusive), to april 20th, 2021 (inclusive), were examined.Trial characteristics were collected including, but not limited to, study phase, duration, patient enrollment size, location, and study design.Peer-reviewed publications associated with the selected trials were also assessed to determine outcome reporting.Results a total of 1776 clinical trials conducted in 43 countries were identified, the majority of which were conducted in the usa.Of these trials, 32% were reported as "completed" whereas 12% were "discontinued." the most common cause of trial discontinuation was low accrual, which was reported in 37% of terminated studies.These resulted in 413 published studies.Most trials had multiple assignment, randomized, or open-label designs.Treatment was the most common study objective (73%) with pharmacological therapy being the most commonly studied intervention.Conclusions the main reasons for early discontinuation of clinical trials in hpb surgery are poor patient recruitment and inadequate funding.Improved trial design, recruitment strategies and increased funding are needed to prevent trial discontinuation and increase publication rates of hpb surgery clinical trials.

Journal: Journal of gastrointestinal surgery : official journal of the Society for Surgery of the Alimentary Tract (2022)
Publication types: Journal Article
Gut virome profiling identifies a widespread bacteriophage family associated with metabolic syndrome.

There is significant interest in altering the course of cardiometabolic disease development via gut microbiomes.Nevertheless, the highly abundant phage members of the complex gut ecosystem -which impact gut bacteria- remain understudied.Here, we show gut virome changes associated with metabolic syndrome (met s), a highly prevalent clinical condition preceding cardiometabolic disease, in 196 participants by combined sequencing of bulk whole genome and virus like particle communities.Met s gut viromes exhibit decreased richness and diversity.They are enriched in phages infecting streptococcaceae and bacteroidaceae and depleted in those infecting bifidobacteriaceae.Differential abundance analysis identifies eighteen viral clusters (vcs) as significantly associated with either met s or healthy viromes.Among these are a met s-associated roseburia vc that is related to healthy control-associated faecalibacterium and oscillibacter vcs.Further analysis of these vcs revealed the candidatus heliusviridae, a highly widespread gut phage lineage found in 90+% of participants.The identification of the temperate ca.Heliusviridae provides a starting point to studies of phage effects on gut bacteria and the role that this plays in met s.

Journal: Nature communications (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Rapid genome sequencing for pediatrics.

The advancements made in next-generation sequencing (ngs) technology over the past two decades have transformed our understanding of genetic variation in humans and had a profound impact on our ability to diagnose patients with rare genetic diseases.In this review, we discuss the recently developed application of rapid ngs techniques, used to diagnose pediatric patients with suspected rare diseases who are critically ill.We highlight the challenges associated with performing such clinical diagnostics tests in terms of the laboratory infrastructure, bioinformatic analysis pipelines, and the ethical considerations that need to be addressed.We end by looking at what future developments in this field may look like and how they can be used to augment the genetic data to further improve the diagnostic rates for these high-priority patients.

Journal: Human mutation (2022)
Publication types: Journal Article;Review;Research Support, Non-U.S. Gov't
Novel MRI deformation-heterogeneity radiomic features are associated with molecular subgroups and overall survival in pediatric medulloblastoma: Preliminary findings from a multi-institutional study.

Introduction medulloblastoma (mb) is a malignant, heterogenous brain tumor.Advances in molecular profiling have led to identifying four molecular subgroups of mb (wnt, shh, group 3, group 4), each with distinct clinical behaviors.We hypothesize that (1) aggressive mb tumors, growing heterogeneously, induce pronounced local structural deformations in the surrounding parenchyma, and (b) these local deformations as captured on gadolinium (gd)-enhanced-t1w mri are independently associated with molecular subgroups, as well as overall survival in mb patients.Methods in this work, a total of 88 mb studies from 2 institutions were analyzed.Following tumor delineation, gd-t1wscan for every patient was registered to a normal age-specific t1w-mri template via deformable registration.Following patient-atlas registration, local structural deformations in the brain parenchyma were obtained for every patient by computing statistics from deformation magnitudes obtained from every 5mm annular region, 0 < d < 60 mm, where d is the distance from the tumor infiltrating edge.Results multi-class comparison via anova yielded significant differences between deformation magnitudes obtained for group 3, group 4, and shh molecular subgroups, observed up to 60-mm outside the tumor edge.Additionally, kaplan-meier survival analysis showed that the local deformation statistics, combined with the current clinical risk-stratification approaches (molecular subgroup information and chang's classification), could identify significant differences between high-risk and low-risk survival groups, achieving better performance results than using any of these approaches individually.Discussion these preliminary findings suggest there exists significant association of our tumor-induced deformation descriptor with overall survival in mb, and that there could be an added value in using the proposed radiomic descriptor along with the current risk classification approaches, towards more reliable risk assessment in pediatric mb.

Journal: Frontiers in oncology (2022)
Publication types: Journal Article
The complete plastid genome of an Antarctic mossChorisodontium aciphyllum(Hook. f. & Wilson) Broth (Dicranaceae, Dicranales).

Plastid genomes are useful markers in resolving plant phylogenetic relationships for various taxonomic groups.Here, we sequenced andde novoassembled the complete plastid genome sequence of an antarctic moss chorisodontium aciphyllum(hook.F.& wilson) broth using genome skimming data.The newly generated plastid genome is conserved in structure and gene content compared with that of other bryopsida.Plastid phylogenetic analysis of mosses recovered a robust phylogeny in which chorisodontium aciphyllumclustered with fissidens nobilisfrom the dicranales.The plastid genome sequence of c.Aciphyllumwill aid future evolution and diversification studies of land plants.

Journal: Mitochondrial DNA. Part B, Resources (2022)
Publication types: Journal Article
Usefulness of Video Review of Possible Concussions in National Youth Rugby League.

A new concussion interchange rule (cir) was introduced in 2014 for the national rugby league and national youth competition (nyc).The cir allows a player suspected of having sustained a concussion to be removed from play and assessed without an interchange being tallied against the player's team.Participants included all nyc players who used the cir during the 2014 season.2 raters completed video analysis of 131 (of a total of 156 reported) uses of the cir, describing injury characteristics, situational factors, and concussion signs.The incidence rate was 44.9 (95% ci: 38.5-52.3) uses of the cir per 1 000 nyc player match hours, or approximately one cir use every 1.3 games.Apparent loss of consciousness/unresponsiveness was observed in 13% of cases, clutching the head in 65%, unsteadiness of gait in 60%, and a vacant stare in 23%.Most incidences occurred from a hit-up (82%).There appeared to be some instances of video evidence of injury but the athlete was cleared to return to play in the same game.Video review appears to be a useful adjunct for identifying players suffering possible concussion.Further research is required on the usefulness of video review for identifying signs of concussive injury.

Journal: International journal of sports medicine (2017)
Publication types: Journal Article
Atomic-Scale Engineering of CuOx-Au Interfaces over AuCu Single-Nanoparticles.

A face-centered tetragonal (fct) au cu particle with a size of 7.1 nm and an au/cu molar ratio of 1/1 was coated by a silica shell of 6 nm thickness.Segregation of cu atoms from the metal particle under an oxidative atmosphere precisely mediated the cu ox-au interfacial structure by simply varying the temperature.As raising the temperature from 473 to 773 k, more cu atoms emigrated from the au cu particle and were oxidized into cu oxlayers that grew up to 0.8 nm in thickness.Simultaneously, the size of the au-rich particle lowered moderately while the crystalline structure transformed from the fct phase into the face-centered cubic (fcc) phase.The cu ox-au interface shifted from the cu oxmonolayer bound to au single-atoms to au@cu oxcore-shell geometry, while the catalytic activity for co oxidation at 433 k decreased dramatically.Moreover, a sharp loss in activity was observed as the crystal-phase transition occurred.This change in catalytic performance was ascribed to the geometrical configuration at the interfacial sites: the synergetic effect between the fct-au cu particle and cu oxmonolayer contributed to the much higher activity, whereas the fcc-au cu/au particle weakened its interaction with the thicker cu oxlayer and thus decreased the activity.

Journal: ACS applied materials & interfaces (2022)
Publication types: Journal Article
Primary Cranial Vault Lymphoma Extending between Subcutaneous Tissue and Brain Parenchyma without Skull Destruction after Mild Head Trauma: A Case Report and Literature Review.

Malignant lymphoma of the head rarely arises outside of the brain parenchyma as primary cranial vault lymphoma (pcvl).A case of pcvl that invaded from subcutaneous tissue into the brain, passing through the skull, and occurred after mild head trauma is reported along with a review of the literature.The patient was a 75-year-old man with decreased activity.One month before his visit to our hospital, he bruised the left frontal area of his head.Magnetic resonance imaging showed homogeneously enhanced tumors with contrast media in the subcutaneous tissue corresponding to the head impact area and the cerebral parenchyma, but no obvious abnormal findings in the skull.A biopsy with craniotomy was performed under general anesthesia.The pathological diagnosis was diffuse large b-cell lymphoma.On histological examination, tumor cells grew aggressively under the skin.Tumor cells invaded along the emissary vein into the external table without remarkable bone destruction and extended across the skull through the haversian canals in the diploe.Tumor cells were found only at the perivascular areas in the dura mater and extended into the brain parenchyma.Considering the history of head trauma and the neuroimaging and histological findings, the pcvl in the present case arose primarily under the skin, passed though the skull and dura mater, and invaded along vessels and reached the brain.

Journal: Case reports in oncology (2021)
Publication types: Case Reports;Journal Article
What Does Honors Mean? National Analysis of Medical School Clinical Clerkship Grading.

Medical student performance evaluation (mspe) letters provide critical comparative information about clerkship performance, and are a crucial part of the surgical residency application.The elimination of usmle step 1 numeric reporting increases the importance of transparency, standardization, and accessibility of comparative information reported on the mspe.The objective of our study was to measure the variability in clerkship grade reporting on the mspe from us medical schools, particularly focusing on the highest (honors) grades.Design, setting, and participants we identified representative mspe letters from us medical schools and recorded the percentage of honors for 5 core clerkships.We grouped medical schools according to medical school rankings, geographic region, and number of grading categories results: of 122 medical schools, 106 schools (87%) reported their grading scheme and percent honors.The most commonly used grading scheme was a 4-tier system (51/122; 42%).The percentage of honors was highly variable (from 1-91%) and did not vary by region.However, schools in the top 20 research ranking were less likely to report grade comparisons (30% vs.10%), and more likely to award more students honors in 4 of the 5 clerkships.Schools in the top 20 primary care ranking were more likely to award more honors in the medicine clerkship.Conclusions there is significant variability in the number of grading tiers used and the percentage of students awarded honors across us medical schools.Factors that correlated to higher grades included schools with higher rankings, and higher ranked schools were less likely to report comparative information at all.

Journal: Journal of surgical education (2022)
Publication types: Journal Article
A neurocognitive investigation of the impact of socializing with a robot on empathy for pain.

To what extent can humans form social relationships with robots?In the present study, we combined functional neuroimaging with a robot socializing intervention to probe the flexibility of empathy, a core component of social relationships, towards robots.Twenty-six individuals underwent identical f mri sessions before and after being issued a social robot to take home and interact with over the course of a week.While undergoing f mri, participants observed videos of a human actor or a robot experiencing pain or pleasure in response to electrical stimulation.Repetition suppression of activity in the pain network, a collection of brain regions associated with empathy and emotional responding, was measured to test whether socializing with a social robot leads to greater overlap in neural mechanisms when observing human and robotic agents experiencing pain or pleasure.In contrast to our hypothesis, functional region-of-interest analyses revealed no change in neural overlap for agents after the socializing intervention.Similarly, no increase in activation when observing a robot experiencing pain emerged post-socializing.Whole-brain analysis showed that, before the socializing intervention, superior parietal and early visual regions are sensitive to novel agents, while after socializing, medial temporal regions show agent sensitivity.A region of the inferior parietal lobule was sensitive to novel emotions, but only during the pre-socializing scan session.Together, these findings suggest that a short socialization intervention with a social robot does not lead to discernible differences in empathy towards the robot, as measured by behavioural or brain responses.We discuss the extent to which long-term socialization with robots might shape social cognitive processes and ultimately our relationships with these machines.This article is part of the theme issue 'from social brains to social robots: applying neurocognitive insights to human-robot interaction'.

Journal: Philosophical transactions of the Royal Society of London. Series B, Biological sciences (2019)
Publication types: Journal Article;Research Support, Non-U.S. Gov't