syedzayyan/paper_mill_benchmark huggingface dataset:
A hereditary spastic paraplegia predominant phenotype caused by variants in the NEFL gene.

Introduction this study reports a large series of patients with a clinical picture dominated by spastic paraplegia in whom variants in the nefl gene, a known cause for charcot-marie-tooth disease, were identified.Methods index patients referred for a suspicion of hereditary spastic paraplegia (hsp) were clinically assessed and genetic analysis by next-generation sequencing was undertaken.Additional family members were clinically examined and subjected to targeted testing.Results we identified two different heterozygous dominant variants in the nefl gene in 25 patients from 14 families.Most of them (21/25) had a clinical diagnosis of hsp, often with a concomitant clinical diagnosis of polyneuropathy (16/21).Two patients were identified with a polyneuropathy with a pyramidal reflex pattern, but without spasticity.Two patients had isolated polyneuropathy.Out of the 21 patients with a diagnosis of hsp, two had co-occurring cerebellar signs.The c.262a > c p.(thr88pro) variant was detected in 13 families.Genealogical analysis showed shared ancestors or a similar geographical origin in 12, suggesting a founder effect.The other variant, c.296a > c p.(asp99ala), was found in only one family, in which limited segregation analysis could be performed.Discussion variants in the nefl gene can cause hsp, with or without co-existing polyneuropathy, and should be included in diagnostic testing strategies for hsp patients.

Journal: Parkinsonism & related disorders (2020)
Publication types: Journal Article
Skeletal dysplasia-like syndromes in wild giraffe.

Skeletal dysplasias, cartilaginous or skeletal disorders that sometimes result in abnormal bone development, are seldom reported in free-ranging wild animals.Here, we use photogrammetry and comparative morphometric analyses to describe cases of abnormal appendicular skeletal proportions of free-ranging giraffe in two geographically distinct taxa: a nubian giraffe (giraffa camelopardalis camelopardalis) in murchison falls national park, uganda and an angolan giraffe (giraffa giraffa angolensis) on a private farm in central namibia.Results these giraffe exhibited extremely shortened radius and metacarpal bones relative to other similarly aged giraffe.Both giraffe survived to at least subadult life stage.This report documents rare occurrences of these apparent skeletal dysplasias in free-ranging wild animals and the first records in giraffe.

Journal: BMC research notes (2020)
Publication types: Journal Article
Preliminary evaluation of BioFire FilmArray®Gastrointestinal Panel for the detection of noroviruses and other enteric viruses from wastewater and shellfish.

The bio fire film array®gastrointestinal panel was evaluated for the rapid detection of adenovirus, astrovirus, norovirus, rotavirus and sapovirus from influent and effluent wastewater and shellfish.The multiplex bio fire film array®gastrointestinal panel compared well to singleplex q pcr/rt-q pcr methods for the detection of adenovirus, astrovirus, rotavirus and sapovirus from influent and effluent wastewater samples.However, the bio fire film array®gastrointestinal panel showed poor performance for the detection of norovirus, significantly underestimating its presence in wastewater and shellfish samples when compared with the singleplex norovirus gi and gii rt-q pcr assays.Therefore, improvement on detection efficiency for norovirus from environmental and food samples is necessary before using results from the film array®gastrointestinal panel to assess associated public health risks.

Journal: Environmental science and pollution research international (2018)
Publication types: Journal Article
Learning With Patients, Students, and Peers: Continuing Professional Development in the Solo Practitioner Workplace.

Conceptualizations of workplace learning have moved from knowledge acquisition to learning as participation in the practices and cultures of the workplace environment.Along with this has come an appreciation of applicability of sociocultural learning theories, which frame learning as occurring within "communities of practice" or learning being "situated" within a workplace environment where collaboration and social interaction are fundamental to the learning process.These conceptualizations of workplace learning are ideally suited to health professions where learners are supervised in clinical work environments and then continue to work in team-based environments as graduates.However, what happens to workplace learning for novice practitioners who have limited periods of clinical supervision and then graduate into solo or small group practices (which may also be in rural or remote locations) and embark on long working careers without supervision?This paper argues workplace learning needs to be scaffolded and supported to reach its full potential in these environments.Drawing on workplace-based learning theory, we highlight the ubiquitous nature of learning in the workplace, the importance of active engagement, reflection, and individual meaning making.Through this reframing of traditional notions of continuing professional development, we emphasize the importance of patients, students, and other practitioners as partners in workplace learning for solo practitioners.We also focus on the role of educators, professional associations, and regulators in helping solo practitioners recognize, access, and maximize the learning opportunities inherent in relatively isolated practice environments.

Journal: The Journal of continuing education in the health professions (2020)
Publication types: Journal Article
Heterogeneous distribution of shell matrix proteins in the pearl oyster prismatic layer.

Shell formation in molluscan bivalves is regulated by organic matrices composed of biological macromolecules, but how these macromolecules assemble in vitro remains elusive.Prismatic layer in the pearl oyster pinctada fucata consists of polygonal prisms enveloped by thick organic matrices.In this study, we found that the organic matrices were heterogeneously distributed, with highly acidic fractions (edta-soluble and edta-insoluble) embedded inside the prism columns, while basic edta-insoluble faction as inter-column framework enveloping the prisms.The intra-column matrix was enriched in aspartic acid whereas the inter-column matrix was enriched in glycine, tyrosine and phenylalanine.Moreover, the intra-column matrix contained sulfo group further contributing to its acidic property.Proteomics data showed that the intra-column proteins mainly consisted of acidic proteins, while some typical matrix proteins were absent.The absent matrix proteins such as shematrin family and krmp family were highly basic and contained aromatic amino acids, suggesting that electric charge and hydrophobic effect might play a role in the matrix heterogeneity.Interestingly, chitin metabolism related proteins were abundant in the inter-column matrix, which may be involved in reconstructing the prism organic matrix.Overall, our study suggests that each single prism grew in an enclosed organic envelope and the organic matrix undergoes rearrangement, thus leading to the peculiar growth of the prismatic layer.

Journal: International journal of biological macromolecules (2021)
Publication types: Journal Article
Case Fatality and Adverse Outcomes Are Reduced in Pregnant Women With Severe Sepsis or Septic Shock Compared With Age-Matched Comorbid-Matched Nonpregnant Women.

S case fatality in pregnancy-associated severe sepsis or septic shock appears reduced compared with nonpregnant women with severe sepsis or septic shock.It remains unclear if this difference is due to pregnancy or better baseline health status, among others.Our study compared adverse outcomes of pregnancy-associated severe sepsis or septic shock with nonpregnant women with severe sepsis or septic shock while controlling for age and chronic comorbidities.Design retrospective cohort study.Setting nationwide inpatient sample, a stratified sample of 20% acute care hospital admissions in the united states.Each entry includes patient and hospital characteristics as well as international classification of diseases, 9th revision, clinical modification, diagnoses and procedures.Subjects women of childbearing age (15-44 yr) with severe sepsis or septic shock-related hospitalizations during 1998-2012 identified using international classification of diseases, 9th revision, clinical modification, codes.Outcomes case fatality, hospital length of stay, length of stay until death, number of organ failures, rates of mechanical ventilation, and hemodialysis were compared in women according to pregnancy status, controlling for age, and chronic comorbidities.Measurements and main results we identified 5,968 pregnancy-associated severe sepsis or septic shock and 85,240 nonpregnant women with severe sepsis or septic shock hospitalizations.Crude case fatality of pregnancy-associated severe sepsis or septic shock (9.6%) was lower than nonpregnant women with severe sepsis or septic shock (16.8%).The rate ratio for case fatality adjusted for socioeconomic status and race was 0.57 (95% ci, 0.52-0.62) while sequential adjustments for age and chronic comorbidities did not eliminate the association (rate ratio, 0.62 [95% ci, 0.57-0.68]) and 0.63 [95% ci, 0.57-0.68], respectively).Pregnancy-associated severe sepsis or septic shock was associated with shorter hospital length of stay (-0.83 d [95% ci, -1.32 to -0.34 d]), longer length of stay until death (2.61 d; [95% ci, 1.28-3.94 d]), and fewer organ failures (rate ratio, 0.95 [95% ci, 0.94-0.97]).Conclusions case fatality and adverse outcomes are reduced in women with pregnancy-associated severe sepsis or septic shock compared with nonpregnant women with severe sepsis or septic shock, and this is not explained by differences in age or chronic comorbidities alone.A less severe presentation of sepsis or protective effect of pregnancy may account for the difference observed with pregnancy-associated severe sepsis or septic shock.

Journal: Critical care medicine (2018)
Publication types: Journal Article
Status report, The Public Health and Planning 101 project: strengthening collaborations between the public health and planning professions.

Introduction land use planning is a complex field comprised of legislation, policies, processes and tools.A growing body of evidence supports the relationship between land use planning decisions, community design and health.The built environment has been shown to be associated with physical inactivity, obesity, cardiovascular disease, respiratory disease and mental illness.Consequently, there is a growing interest within public health to work with planners on land use planning initiatives such as official plans and transportation master plans.Methods two surveys were developed: one for public health professionals and the other for planning professionals (survey questions available upon request to the corresponding author).The surveys were pilot tested in two separate focus group sessions with public health and planning professionals.Focus group volunteers helped to validate the surveys by verifying survey questions, design and overall flow.Results in early 2012, 304 public health professionals and 301 planning professionals completed the two separate surveys, comprising the total survey respondents for each respective profession used to calculate proportions.The survey results represent a convenience sample and are not generalizable to the entire population of public health and planning professionals in ontario.Results compare survey responses from both groups where appropriate.Most respondents worked either as public health staff (78%) or planners/senior planners (58%).A smaller percentage of public health and planning professionals worked either as managers (15% and 11%, respectively) or directors (5% and 9%, respectively).Conclusion health is associated with how communities are planned and built, and the services and resources provided within them.Inspired by the results of our survey and based on user feedback from the pilot tests, a free online training program entitled "public health and planning 101: an online course for public health and planning professionals to create healthier built environments" was launched in 2016 by opha as a collaborative project with oppi and phac.This course is designed to bridge the gaps between the two professions, as well as provide greater opportunities for developing collaborative partnerships to help create and foster healthy built environments.

Journal: Health promotion and chronic disease prevention in Canada : research, policy and practice (2017)
Publication types: Journal Article
On the energy of nonlinear water waves.

This article presents results concerning the excess kinetic and potential energies for exact nonlinear water waves.In particular, it is proven, for periodic travelling irrotational water waves, that the excess kinetic energy density is always negative, whereas the excess potential energy density is always positive, in the steady reference frame.A characterization of the total excess energy density as a weighted mean of the kinetic energy along the wave surface profile is also presented.

Journal: Proceedings. Mathematical, physical, and engineering sciences (2021)
Publication types: Journal Article
Comparison of the Performance of the Leap Motion ControllerTMwith a Standard Marker-Based Motion Capture System.

Over the last few years, the leap motion controllertm (lmc) has been increasingly used in clinical environments to track hand, wrist and forearm positions as an alternative to the gold-standard motion capture systems.Since the lmc is marker-less, portable, easy-to-use and low-cost, it is rapidly being adopted in healthcare services.This paper demonstrates the comparison of finger kinematic data between the lmc and a gold-standard marker-based motion capture system, qualisys track manager (qtm).Both systems were time synchronised, and the participants performed abduction/adduction of the thumb and flexion/extension movements of all fingers.The lmc and qtm were compared in both static measuring finger segment lengths and dynamic flexion movements of all fingers.A bland-altman plot was used to demonstrate the performance of the lmc versus qtm with pearson's correlation (r) to demonstrate trends in the data.Only the proximal interphalangeal joint (pip) joint of the middle and ring finger during flexion/extension demonstrated acceptable agreement (r= 0.9062;r= 0.8978), but with a high mean bias.In conclusion, the study shows that currently, the lmc is not suitable to replace gold-standard motion capture systems in clinical settings.Further studies should be conducted to validate the performance of the lmc as it is updated and upgraded.

Journal: Sensors (Basel, Switzerland) (2021)
Publication types: Journal Article
Predicting Hemodynamic Shock from Thermal Images using Machine Learning.

Proactive detection of hemodynamic shock can prevent organ failure and save lives.Thermal imaging is a non-invasive, non-contact modality to capture body surface temperature with the potential to reveal underlying perfusion disturbance in shock.In this study, we automate early detection and prediction of shock using machine learning upon thermal images obtained in a pediatric intensive care unit of a tertiary care hospital.539 images were recorded out of which 253 had concomitant measurement of continuous intra-arterial blood pressure, the gold standard for shock monitoring.Histogram of oriented gradient features were used for machine learning based region-of-interest segmentation that achieved 96% agreement with a human expert.The segmented center-to-periphery difference along with pulse rate was used in longitudinal prediction of shock at 0, 3, 6 and 12 hours using a generalized linear mixed-effects model.The model achieved a mean area under the receiver operating characteristic curve of 75% at 0 hours (classification), 77% at 3 hours (prediction) and 69% at 12 hours (prediction) respectively.Since hemodynamic shock associated with critical illness and infectious epidemics such as dengue is often fatal, our model demonstrates an affordable, non-invasive, non-contact and tele-diagnostic decision support system for its reliable detection and prediction.

Journal: Scientific reports (2019)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
p110α activity at the M-to-G1 transition is critical for cellular proliferation and reentry into the cell cycle.

Phosphoinositide 3-kinase (pi3k) signaling pathway is essential for normal physiology and is impaired in diseases such as premalignant hyperproliferative disorders, primary immunodeficiency, metabolic disorders, and cancer.Although the core pi3k pathway components are known today, a long-standing gap in our knowledge of pi3k signaling concerns how distinct pi3k isoforms and their activity patterns contribute to the functional consequences of pathway upregulation.In order to address this issue, we devised a molecular genetic cell model, which allowed temporal regulation of the indispensable pi3k isoform, p110α in distinct stages of the cell cycle.We found that late m and early g1 presence of p110α is key for proper cell cycle progression, whereas its s-phase abundance was redundant.Our results also emphasize a critical dependence of cell cycle reentry on early g1 activity of p110α.Collectively, our findings provide a temporal perspective to p110α activation and offer insight into which wave of pi3k activity could be essential for cell cycle progression.

Journal: Turkish journal of biology = Turk biyoloji dergisi (2022)
Publication types: Journal Article
Initiation of bone-targeted agents in patients with bone metastases and breast or castrate-resistant prostate cancer actively treated in routine clinical practice in Europe.

Guidelines recommend starting bone-targeted agents (bta), such as zoledronic acid and denosumab, as soon as bone metastases (bms) are definitively diagnosed in all patients with breast cancer (bc) or castration-resistant prostate cancer (crpc) whether they are symptomatic or not.Methods data were analyzed from 1364 patients with bc and 1161 patients with crpc who had bms and were receiving anti-cancer therapy in hospitals across six european countries (belgium, france, germany, italy, spain and the uk).The 731 physicians (medical oncologists or urologists) provided insights in the decision-making factors driving their management of bone health for these patients, and the patient medical records indicated how these decisions were reflected in routine clinical practice.Results within three months of a bm diagnosis, 74% of bc and 51% of crpc patients had initiated treatment with a bta.Around 12% of bc and 23% of crpc patients did not receive a bta following bm diagnosis.Irrespective of the tumour type (bc or crpc), most physicians prescribed either denosumab or zoledronic acid as first bta therapy.Physicians reported bone pain as a major decision-making factor to initiate a bta.The presence of bone complications at bm diagnosis and bone pain at bm diagnosis were found to be significant predictive factors for a bta initiation, irrespective of tumour type.Conclusions despite european society for medical oncology (esmo) guidance on bone protection irrespective of symptomatic disease, not all patients with bms received a bta following a bm diagnosis.This suggests that clinical judgements and patients' communication of their pain to their physicians contributed to the decision to prescribe bone protection therapy in cancer patients.

Journal: Bone (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Ketamine decreases neuronally released glutamate via retrograde stimulation of presynaptic adenosine A1 receptors.

Ketamine produces a rapid antidepressant response in patients with major depressive disorder (mdd), but the underlying mechanisms appear multifaceted.One hypothesis, proposes that by antagonizing nmda receptors on gabaergic interneurons, ketamine disinhibits afferens to glutamatergic principal neurons and increases extracellular glutamate levels.However, ketamine seems also to reduce rapid glutamate release at some synapses.Therefore, clinical studies in mdd patients have stressed the need to identify mechanisms whereby ketamine decreases presynaptic activity and glutamate release.In the present study, the effect of ketamine and its antidepressant metabolite, (2r,6r)-hnk, on neuronally derived glutamate release was examined in rodents.We used fast methodology to measure depolarization-evoked extracellular glutamate levels in vivo in freely moving or anesthetized animals, synaptosomes to detect synaptic recycling ex vivo and primary cortical neurons to perform functional imaging and to examine intracellular signaling in vitro.In all these versatile approaches, ketamine and (2r,6r)-hnk reduced glutamate release in a manner which could be blocked by ampa receptor antagonism.Antagonism of adenosine a1 receptors, which are almost exclusively expressed at nerve terminals, also counteracted ketamine's effect on glutamate release and presynaptic activity.Signal transduction studies in primary neuronal cultures demonstrated that ketamine reduced p-t286-cam kii and p-s9-synapsin, which correlated with decreased synaptic vesicle recycling.Moreover, systemic administration of a1r antagonist counteracted the antidepressant-like actions of ketamine and (2r,6r)-hnk in the forced swim test.To conclude, by studying neuronally released glutamate, we identified a novel retrograde adenosinergic feedback mechanism that mediate inhibitory actions of ketamine on glutamate release that may contribute to its rapid antidepressant action.

Journal: Molecular psychiatry (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Development of a Clinical Prediction Model for In-hospital Mortality from the South African Cohort of the African Surgical Outcomes Study.

Data on the factors that influence mortality after surgery in south africa are scarce, and neither these data nor data on risk-adjusted in-hospital mortality after surgery are routinely collected.Predictors related to the context or setting of surgical care delivery may also provide insight into variation in practice.Variation must be addressed when planning for improvement of risk-adjusted outcomes.Our objective was to identify the factors predicting in-hospital mortality after surgery in south africa from available data.Methods a multivariable logistic regression model was developed to identify predictors of 30-day in-hospital mortality in surgical patients in south africa.Data from the south african contribution to the african surgical outcomes study were used and included 3800 cases from 51 hospitals.A forward stepwise regression technique was then employed to select for possible predictors prior to model specification.Model performance was evaluated by assessing calibration and discrimination.The south african surgical outcomes study cohort was used to validate the model.Results variables found to predict 30-day in-hospital mortality were age, american society of anesthesiologists physical status category, urgent or emergent surgery, major surgery, and gastrointestinal-, head and neck-, thoracic- and neurosurgery.The area under the receiver operating curve or c-statistic was 0.859 (95% confidence interval: 0.827-0.892) for the full model.Calibration, as assessed using a calibration plot, was acceptable.Performance was similar in the validation cohort as compared to the derivation cohort.Conclusion the prediction model did not include factors that can explain how the context of care influences post-operative mortality in south africa.It does, however, provide a basis for reporting risk-adjusted perioperative mortality rate in the future, and identifies the types of surgery to be prioritised in quality improvement projects at a local or national level.

Journal: World journal of surgery (2021)
Publication types: Journal Article;Multicenter Study