syedzayyan/paper_mill_benchmark huggingface dataset:
Views of medical residents on a research training program: A qualitative study.

Introduction the american university of beirut medical center (aubmc) developed the fellowship and residency research program (frrp) to provide residents and clinical fellows with a supervised and structured research experience.The objective of this study was to explore the views of frrp participants about the training program and how to enhance it.Methods in 2018, we conducted a qualitative study targeting residents where we invited potential participants through email and via snowball sampling.We continued the data collection until we reached data saturation with 21 participants (n = 21) and used thematic analysis to identify emerging themes.Results thematic analysis generated four emerging themes: one related to the expectations of residents, while the remaining three themes related to how the program is working to meet those expectations, specifically: coordination, mentorship, and capacity building.For these three latter themes, we discussed the strengths and challenges related to each.In terms of coordination, few residents complained that the deadlines to submit deliverables are not evenly distributed across the years.In terms of mentorship, participants appreciated the flexibility in choosing the mentor.In terms of capacity building activities, participants found the lecture series, both real time and virtual, to be helpful.Finally, participants pointed out that the frrp program should be mandatory.Discussion to provide residents and clinical fellows with a supervised and structured research experience, we have built on our findings to introduce several changes to our program such as ensuring the availability and commitment of faculty mentors, and providing capacity building activities to the program participants.

Journal: PloS one (2022)
Publication types: Journal Article
Detection of changes in synaptic density in amyotrophic lateral sclerosis patients using18F-SynVesT-1 positron emission tomography.

And purpose synaptic loss is well established as the major correlate of characteristic and consistent pathology in amyotrophic lateral sclerosis (als).We aimed to assess the possible discriminant diagnostic value of18f-syn ves t-1 positron emission tomography (pet) as a marker of als pathology and investigate whether specific synaptic density signatures are present in als with different subtypes.Methods twenty-one patients with als and 25 healthy controls (hcs) were recruited.All participants underwent18f-syn ves t-1-pet.Synaptic density between als and hcs and between different als subgroups were compared.Correlation between synaptic density and clinical features in als was also analyzed.Results low uptake distribution was found in the group comprising 21 als patients as compared with hcs in the right temporal lobe and the bilateral inferior frontal gyrus, anterior cingulate, and hippocampus-insula region.We also found low uptake in the bilateral superior temporal gyrus, hippocampus-insula, anterior cingulate, and left inferior frontal gyrus in als patients with cognitive impairment compared to hcs.Furthermore, compared to spinal onset als, bulbar onset als showed low uptake in the bilateral cingulate gyrus and high uptake in the bilateral superior temporal gyrus and left occipital lobe.No significant result was found in correlation analysis.Conclusions this approach may provide a direct measure of synaptic density, and it therefore might represent a potentially useful biomarker for als diagnosis, as well as for estimating the cognitive decline and site of onset in als.18f-syn ves t-1-pet is presently not justified as a routine investigation to detect evidence of brain dysfunction leading to progression in als.

Journal: European journal of neurology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Genetic mapping of sexually dimorphic volatile and non-volatile floral secondary chemistry of a dioecious willow.

Secondary chemistry often differs between sexes in dioecious plant species, a pattern attributed to its possible role in the evolution and/or maintenance of dioecy.We used gc-ms to measure floral volatiles emitted from, and lc-ms to quantitate non-volatile secondary compounds contained in, female and male salix purpurea willow catkins from an f2 family.Using the abundance of these chemicals, we then performed quantitative trait locus (qtl) mapping to locate them on the genome, identified biosynthetic candidate genes in the qtl intervals, and examined expression patterns of candidate genes using rna-seq.Male flowers emitted more total terpenoids than females, but females produced more benzenoids.Male tissue contained greater amounts of phenolic glycosides, but females had more chalcones and flavonoids.A flavonoid pigment and a spermidine derivative were found only in males.Male catkins were almost twice the mass of females.Forty-two qtl were mapped for 25 chemical traits and catkin mass across 16 of the 19 s.Purpurea chromosomes.Several candidate genes were identified, including a chalcone isomerase associated with seven compounds.A better understanding of the genetic basis of the sexually dimorphic chemistry of a dioecious species may shed light on how chemically mediated ecological interactions may have helped in the evolution and maintenance of dioecy.

Journal: Journal of experimental botany (2022)
Publication types: Journal Article;Research Support, U.S. Gov't, Non-P.H.S.
Clinical audit of retinoblastoma management: a retrospective single-institution study.

The primary aim of this study was to identify the frequency of death, metastasis, enucleation, and use of external beam radiation therapy (ebrt) among retinoblastoma patients.The secondary aim was to determine whether any events were associated with suboptimal clinical management to identify areas for clinical care improvement.Methods patients diagnosed with retinoblastoma between january 1, 2000, and december 31, 2015, at the hospital for sick children were included.Medical records of eligible patients underwent a comprehensive 2-part review.First, a chart review collected diagnostic details, treatment course, and occurrence of 4 events: death, metastasis, use of ebrt, and enucleation.Next, events were reviewed in detail, and a multidisciplinary committee reached consensus on cases managed suboptimally.Results the study included 209 patients (292 eyes).There were 8 deaths, 11 metastases, 177 enucleations (143 primary, 34 secondary), and 8 uses of ebrt.Thirteen patients were reviewed by the multidisciplinary committee, which confirmed that 5 of these patients had events associated with suboptimal clinical management.Three patients developed metastases leading to death (misdiagnosis and mismanagement of trilateral retinoblastoma [1], parental refusal of enucleation [1], and inaccurate histopathology after primary enucleation [1]).One patient developed extraocular extension related to scleral invasion following aggressive focal therapy.One patient underwent secondary enucleation for a group b eye related to mismanagement of a treatment complication.Discussion deaths, metastases, and enucleations with documented instances of suboptimal care highlighted a need to enhance medical team and patient communication, histopathology interpretation, laser treatment guidelines, and trilateral retinoblastoma management.Routine clinical audit of retinoblastoma management can identify areas for clinical practice change.

Journal: Canadian journal of ophthalmology. Journal canadien d'ophtalmologie (2022)
Publication types: Journal Article
Multiple-step chromosomal integration of divided segments from a large DNA fragment via CRISPR/Cas9 in Escherichia coli.

Although crispr/cas9-mediated gene editing technology has developed vastly in escherichia coli, the chromosomal integration of large dna fragment is still challenging compared with gene deletion and small fragment integration.Moreover, to guarantee sufficient cas9-induced double-strand breaks, it is usually necessary to design several g rnas to select the appropriate one.Accordingly, we established a practical daily routine in the laboratory work, involving multiple-step chromosomal integration of the divided segments from a large dna fragment.First, we introduced and optimized the protospacers from streptococcus pyogenes in e.Coli w3110.Next, the appropriate fragment size for each round of integration was optimized to be within 3-4 kb.Taking advantage of the optimized protospacer/g rna pairs, a dna fragment with a total size of 15.4 kb, containing several key genes for uridine biosynthesis, was integrated into w3110 chromosome, which produced 5.6 g/l uridine in shake flask fermentation.Using this strategy, dna fragments of virtually any length can be integrated into a suitable genomic site, and two g rnas can be alternatively used, avoiding the tedious construction of g rna-expressing plasmids.This study thus presents a useful strategy for large dna fragment integration into the e.Coli chromosome, which can be easily adapted for use in other bacteria.

Journal: Journal of industrial microbiology & biotechnology (2019)
Publication types: Journal Article
Differentiating Malignant from Benign Pigmented or Non-Pigmented Skin Tumours-A Pilot Study on 3D Hyperspectral Imaging of Complex Skin Surfaces and Convolutional Neural Networks.

Several optical imaging techniques have been developed to ease the burden of skin cancer disease on our health care system.Hyperspectral images can be used to identify biological tissues by their diffuse reflected spectra.In this second part of a three-phase pilot study, we used a novel hand-held sicsurfis spectral imager with an adaptable field of view and target-wise selectable wavelength channels to provide detailed spectral and spatial data for lesions on complex surfaces.The hyperspectral images (33 wavelengths, 477-891 nm) provided photometric data through individually controlled illumination modules, enabling convolutional networks to utilise spectral, spatial, and skin-surface models for the analyses.In total, 42 lesions were studied: 7 melanomas, 13 pigmented and 7 intradermal nevi, 10 basal cell carcinomas, and 5 squamous cell carcinomas.All lesions were excised for histological analyses.A pixel-wise analysis provided map-like images and classified pigmented lesions with a sensitivity of 87% and a specificity of 93%, and 79% and 91%, respectively, for non-pigmented lesions.A majority voting analysis, which provided the most probable lesion diagnosis, diagnosed 41 of 42 lesions correctly.This pilot study indicates that our non-invasive hyperspectral imaging system, which involves shape and depth data analysed by convolutional neural networks, is feasible for differentiating between malignant and benign pigmented and non-pigmented skin tumours, even on complex skin surfaces.

Journal: Journal of clinical medicine (2022)
Publication types: Journal Article
Hypnobiome: A New, Potential Frontier of Hypnotherapy in the Treatment of Irritable Bowel Syndrome-A Narrative Review of the Literature.

Increasing evidence suggests that the gut-brain axis may play a key role in health and disease via a bidirectional communication network involving neural and immunoendocrine pathways.This complex interplay deeply influences both gut microbiota and brain behavior.Pathobiome or gut dysbiosis is relevant for the pathogenesis of functional gastrointestinal disorders, such as ibs, chronic pain syndromes, and neurological and mental disorders.As a consequence, targeting the gut microbiota is emerging as a novel, effective therapeutic perspective.Among many treatment options, psychological interventions, including hypnosis, have been used to target the so-called psychobiome and its hypnotic analogue, i.e., hypnobiome, referring to their potential efficacy to modulate the mind-gut axis in ibs patients.A narrative review of the recent literature is provided and circumstantial evidence suggests that hypnobiome may represent a new promising frontier of hypnotherapy.

Journal: The International journal of clinical and experimental hypnosis (2022)
Publication types: Journal Article;Review
Tissue Tolerance Coupled With Ionic Discrimination Can Potentially Minimize the Energy Cost of Salinity Tolerance in Rice.

Salinity is one of the major constraints in rice production.To date, development of salt-tolerant rice cultivar is primarily focused on salt-exclusion strategies, which incur greater energy cost.The present study aimed to evaluate a balancing strategy of ionic discriminationvis-à-vistissue tolerance, which could potentially minimize the energy cost of salt tolerance in rice.Four rice genotypes,viz., fl478, ir29, kamini, and ac847, were grown hydroponically and subjected to salt stress equivalent to 12 d s m-1at early vegetative stage.Different physiological observations (leaf chlorophyll content, chlorophyll fluorescence traits, and tissue na+and k+content) and visual scoring suggested a superior na+-partitioning strategy operating in fl478.A very low tissue na+/k+ratio in the leaves of fl478 after 7 days of stress hinted the existence of selective ion transport mechanism in this genotype.On the contrary, kamini, an equally salt-tolerant genotype, was found to possess a higher leaf na+/k+ratio than does fl478 under similar stress condition.Salt-induced expression of different na+and k+transporters indicated significant upregulation of sos,hkt,nhx, and hakgroups of transporters in both leaves and roots of fl478, followed by kamini.The expression of plasma membrane and vacuolar h+pumps (os aha1,os aha7, and os v-atpase) were also upregulated in these two genotypes.On the other hand, ir29 and ac847 showed greater salt susceptibility owing to excess upward transport of na+and eventually died within a few days of stress imposition.But in the "leaf clip" assay, it was found that both ir29 and kamini had high tissue-tolerance and chlorophyll-retention abilities.On the contrary, fl478, although having higher ionic-discrimination ability, showed the least degree of tissue tolerance as evident from the lc50score (amount of na+required to reduce the initial chlorophyll content to half) of 336 mmol g-1as against 459 and 424 mmol g-1for ir29 and kamini, respectively.Overall, the present study indicated that two components (ionic selectivity and tissue tolerance) of salt tolerance mechanism are distinct in rice.Unique genotypes like kamini could effectively balance both of these strategies to achieve considerable salt tolerance, perhaps with lesser energy cost.

Journal: Frontiers in plant science (2020)
Publication types: Journal Article
In silico prediction of peptide variants from chia (S. hispanica L.) with antimicrobial, antibiofilm, and antioxidant potential.

Plants are known as a rich source of bioactive peptides, and a variety of plant peptides have been studied as potential alternatives to conventional antimicrobial, antibiofilm, and antioxidant agents in food products to prolong their shelf-life, which could pose potential health risks for consumers.Regardless of their high functional potential, no plant peptides are currently used in the food industry for these purposes.In this study, it is performed the selection and optimization of peptides that are not currently reported in any database, derived from a chia peptide fraction.Computer-aided tools were used to identify multifunctional peptides with antimicrobial, antibiofilm, and antioxidant potential.Two peptide sequences (yaclkvk and klkknl) showing the highest probability scores for antimicrobial activity were identified from a total of 1067 de novo sequences in a chia peptide fraction (f<1 k da).Subsequently, the peptides yaclkvk and klkknl were used to create scrambled libraries containing permutations of these sequences to explore the antibiofilm potential of different amino acid arrangements.The peptide variants with the highest probability scores for antibiofilm activity were subjected to optimization for the improvement of their activity.Finally, the optimized sequences were analyzed to determine the presence of antioxidant fragments.This computational approach could be a solution for the screening of a large number of peptides with more than one function, allowing the development of multifunctional peptides as alternatives to traditional food preservatives.

Journal: Computational biology and chemistry (2022)
Publication types: Journal Article
Internet use and pro-environmental behavior: Evidence from China.

Solving environmental problems relies upon cultivating pro-environmental behavior in the society.While the internet has been widely used to facilitate information transmission and communication, it's important to understand its function in promoting pro-environmental behavior.Using the data from the china general social survey 2013, the relationship between the use of internet and the individual's pro-environmental behavior is investigated, and overall positive effects are found.The results show that, the influence of internet use is more pronounced on the private pro-environmental behavior when further dividing pro-environmental behavior into private and public types.Moreover, the positive effect of internet use on pro-environmental behavior is more pronounced among low-income and female groups, compared to middle to high income and male counterparts, respectively, when considering the heterogeneity across different groups of individuals.We further explore the plausible channels of providing information, encouraging participation in pro-environmental campaigns and improving social relationships through which internet use facilitates pro-environmental behavior.

Journal: PloS one (2022)
Publication types: Journal Article
Fabrication of a light screen-aperture integrated flexible thin film micro-lens array for a biomimetic superposition compound eye.

Micro-lens array, an artificial compound eye vision system, provides a wide field of view and multi-perspective view.However, it has not been adopted as a computer vision application due to its limited visible range and high optical interference.In this research, a novel fabrication method for the flexible polydimethylsiloxane micro-lens array with a polytetrafluoroethylene light screen-aperture integrated layer was established by the simple protrusion method.The integrated layer provided longer visible range by one meter while maintaining the wide field-of-view of 100 °.The resulting images were used for obtaining depth information of a target as an example and for analyzing the rectangular and hexagonal arrangements of the micro-lenses for the future applications.With the improved visual range, wide field-of-view and flexibility, the fabricated micro-lens array can be applied to the small and curved cmos image sensors in the future.

Journal: Optics express (2021)
Publication types: Journal Article
Interaction of Vitamin D with Peptide Hormones with Emphasis on Parathyroid Hormone, FGF23, and the Renin-Angiotensin-Aldosterone System.

The seminal discoveries that parathyroid hormone (pth) and fibroblast growth factor 23 (fgf23) are major endocrine regulators of vitamin d metabolism led to a significant improvement in our understanding of the pivotal roles of peptide hormones and small proteohormones in the crosstalk between different organs, regulating vitamin d metabolism.The interaction of vitamin d, fgf23 and pth in the kidney is essential for maintaining mineral homeostasis.The proteohormone fgf23 is mainly secreted from osteoblasts and osteoclasts in the bone.Fgf23 acts on proximal renal tubules to decrease production of the active form of vitamin d (1,25(oh)2d) by downregulating transcription of 1α-hydroxylase (cyp27b1), and by activating transcription of the key enzyme responsible for vitamin d degradation, 24-hydroxylase (cyp24a1).Conversely, the peptide hormone pth stimulates 1,25(oh)2d renal production by upregulating the expression of 1α-hydroxylase and downregulating that of 24-hydroxylase.The circulating concentration of 1,25(oh)2d is a positive regulator of fgf23 secretion in the bone, and a negative regulator of pth secretion from the parathyroid gland, forming feedback loops between kidney and bone, and between kidney and parathyroid gland, respectively.In recent years, it has become clear that vitamin d signaling has important functions beyond mineral metabolism.Observation of seasonal variations in blood pressure and the subsequent identification of vitamin d receptor (vdr) and 1α-hydroxylase in non-renal tissues such as cardiomyocytes, endothelial and smooth muscle cells, suggested that vitamin d may play a role in maintaining cardiovascular health.Indeed, observational studies in humans have found an association between vitamin d deficiency and hypertension, left ventricular hypertrophy and heart failure, and experimental studies provided strong evidence for a role of vitamin d signaling in the regulation of cardiovascular function.One of the proposed mechanisms of action of vitamin d is that it functions as a negative regulator of the renin-angiotensin-aldosterone system (raas).This finding established a novel link between vitamin d and raas that was unexplored until then.During recent years, major progress has been made towards a more complete understanding of the mechanisms by which fgf23, pth, and raas regulate vitamin d metabolism, especially at the genomic level.However, there are still major gaps in our knowledge that need to be filled by future research.The purpose of this review is to highlight our current understanding of the molecular mechanisms underlying the interaction between vitamin d, fgf23, pth, and raas, and to discuss the role of these mechanisms in physiology and pathophysiology.

Journal: Nutrients (2022)
Publication types: Journal Article;Review
Skin necrosis in spinal muscular atrophy: Case report and review of the literature.

Spinal muscular atrophy (sma) type 0 is the most severe phenotype of sma and is characterized by hypotonia, muscle weakness, and respiratory distress.Cutaneous necrosis, first described in an sma mouse model, can occur in patients with severe disease; the use of targeted treatment versus supportive measures in the setting of skin necrosis is debated.We present a male infant with sma type 0 with cutaneous necrosis of proximal and distal limbs who improved with supportive care.The seven previously reported cases of sma skin necrosis are reviewed.

Journal: Pediatric dermatology (2021)
Publication types: Case Reports;Review;Journal Article
Programming by maternal obesity: a pathway to poor cardiometabolic health in the offspring.

There is an ever increasing prevalence of maternal obesity worldwide such that in many populations over half of women enter pregnancy either overweight or obese.This review aims to summarise the impact of maternal obesity on offspring cardiometabolic outcomes.Maternal obesity is associated with increased risk of adverse maternal and pregnancy outcomes.However, beyond this exposure to maternal obesity during development also increases the risk of her offspring developing long-term adverse cardiometabolic outcomes throughout their adult life.Both human studies and those in experimental animal models have shown that maternal obesity can programme increased risk of offspring developing obesity and adipose tissue dysfunction; type 2 diabetes with peripheral insulin resistance and β-cell dysfunction; cvd with impaired cardiac structure and function and hypertension via impaired vascular and kidney function.As female offspring themselves are therefore likely to enter pregnancy with poor cardiometabolic health this can lead to an inter-generational cycle perpetuating the transmission of poor cardiometabolic health across generations.Maternal exercise interventions have the potential to mitigate some of the adverse effects of maternal obesity on offspring health, although further studies into long-term outcomes and how these translate to a clinical context are still required.

Journal: The Proceedings of the Nutrition Society (2022)
Publication types: Journal Article;Review;Research Support, Non-U.S. Gov't