syedzayyan/paper_mill_benchmark huggingface dataset:
Whole-Kidney Three-Dimensional Staining with CUBIC.

Although conventional pathology provided numerous information about kidney microstructure, it was difficult to know the precise structure of blood vessels, proximal tubules, collecting ducts, glomeruli, and sympathetic nerves in the kidney due to the lack of three-dimensional (3d) information.Optical clearing is a good strategy to overcome this big hurdle.Multiple cells in a whole organ can be analyzed at single-cell resolution by combining tissue clearing and 3d imaging technique.However, cell labeling methods for whole-organ imaging remain underdeveloped.In particular, whole-mount organ staining is challenging because of the difficulty in antibody penetration.The present protocol developed a whole-mount mouse kidney staining for 3d imaging with the cubic (clear, unobstructed brain/body imaging cocktails and computational analysis) tissue clearing method.The protocol has enabled visualizing renal sympathetic denervation after ischemia-reperfusion injury and glomerulomegaly in the early stage of diabetic kidney disease from a comprehensive viewpoint.Thus, this technique can lead to new discoveries in kidney research by providing a macroscopic perspective.

Journal: Journal of visualized experiments : JoVE (2022)
Publication types: Journal Article;Video-Audio Media
Specific type of childhood trauma and borderline personality disorder in Chinese patients.

Childhood maltreatment (cm) is a known risk factor for the development of mental disorders.An extensive body of literature about cm and mental health has been developed in wealthy countries, but information about this connection is lacking in developing countries including china.Aims to explore the possible relationship between specific types of cm and borderline personality disorder (bpd) in patients with mental disorders in china.Methods a survey was conducted in 2006, involving over 3,402 chinese individuals aged 18-60 years who were randomly selected from the outpatients in the shanghai mental health center.The patients were screened with the personality diagnostic questionnaire and cm was assessed using the childhood trauma questionnaire.The final sample comprised 178 patients with bpd, 178 patients with other personality disorders (pds), and 178 patients without pds.Results in chinese patients, compared to other pds, patients with bpds are more likely to have experienced cm.Emotional maltreatment (emotional abuse and neglect) was the strongest predictor of bpd.Female gender and sexual abuse are significant predictors of the self-harm/suicidal risk of bpd patients.Conclusion this is a pioneering study conducted on a large set of chinese clinical samples with paired controls to establish and compare the associations between specific cm and bpd.Further studies in this field are necessary to elucidate the mechanism of how various types of childhood trauma have influenced pds.

Journal: Frontiers in psychiatry (2022)
Publication types: Journal Article
Impact of the CYP2C19*17 Allele on Outcomes in Patients Receiving Genotype-Guided Antiplatelet Therapy After Percutaneous Coronary Intervention.

Genotyping for cyp2c19 no function alleles to guide antiplatelet therapy after percutaneous coronary intervention (pci) improves clinical outcomes.Although results for the increased function cyp2c19*17 allele are also reported, its clinical relevance in this setting remains unclear.A collaboration across nine sites examined antiplatelet therapy prescribing and clinical outcomes in 3,342 patients after implementation of cyp2c19-guided antiplatelet therapy.Risk of major atherothrombotic and bleeding events over 12 months after pci were compared across cytochrome p450 2c19 isozyme (cyp2c19) metabolizer phenotype and antiplatelet therapy groups by proportional hazards regression.Clopidogrel was prescribed to a similar proportion of cyp2c19 normal (84.5%), rapid (82.9%), and ultrarapid metabolizers (80.6%) (p = 0.360).Clopidogrel-treated normal metabolizers (20.4 events/100 patient-years; adjusted hazard ratio (hr) 1.00, 95% confidence interval (ci), 0.75-1.33, p = 0.993) and clopidogrel-treated rapid or ultrarapid metabolizers (19.1 events/100 patient-years; adjusted hr 0.95, 95% ci, 0.69-1.30, p = 0.734) exhibited no difference in major atherothrombotic events compared with patients treated with prasugrel or ticagrelor (17.6 events/100 patient-years).In contrast, clopidogrel-treated intermediate and poor metabolizers exhibited significantly higher atherothrombotic event risk compared with prasugrel/ticagrelor-treated patients (adjusted hr 1.56, 95% ci, 1.12-2.16, p = 0.008).When comparing clopidogrel-treated rapid or ultrarapid metabolizers to normal metabolizers, no difference in atherothrombotic (adjusted hr 0.97, 95% ci, 0.73-1.29, p = 0.808) or bleeding events (adjusted hr 1.34, 95% ci, 0.83-2.17, p = 0.224) were observed.In a real-world setting of genotype-guided antiplatelet therapy, the cyp2c19*17 allele did not significantly impact post-pci prescribing decisions or clinical outcomes.These results suggest the cyp2c19 *1/*17 and *17/*17 genotypes have limited clinical utility to guide antiplatelet therapy after pci.

Journal: Clinical pharmacology and therapeutics (2021)
Publication types: Journal Article;Multicenter Study;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Effect of Mono- and Multichlorinated Organic Compounds-Chlorocyclohexane and Hexachloro-p-xylene-On the Catalytic Properties of Titanium-Magnesium Catalysts in the Homo- and Copolymerization of Ethylene with 1-Hexene.

Ethylene polymerization and ethylene/1-hexene copolymerization over the titanium-magnesium catalytic system in the presence of chlorocyclohexane (chc) and hexachloro-p-xylene (hcpx) has been studied.Modification of tmc with chlorocyclohexane and hexachloro-p-xylene increased catalyst activity severalfold for both ethylene polymerization and ethylene/1-hexene copolymerization.The key kinetic regularities of ethylene homopolymerization and ethylene/1-hexene copolymerization in the presence of chc and hcpx were determined, and the copolymerization constants were measured.Molecular characteristics and the copolymer composition were determined for the synthesized samples of ethylene homopolymers and ethylene/hexene copolymers.Modification of the titanium-magnesium catalyst with chlorinated organic compounds reduced 1-hexene content in the copolymer; polymerization was sensitive to 1-hexene as a regulator of polymer molecular weight.The potential mode of action of chlorinated organic modifiers on catalytic properties of titanium-magnesium catalyst is discussed.

Journal: International journal of molecular sciences (2022)
Publication types: Journal Article
Perceptibility and Acceptability of Surface Gloss Variations in Dentistry.

To assess the visual perception of observers regarding perceptibility and acceptability of surface gloss variations of resin composites and to determine the limit of perceptibility and acceptability of gloss variations.Methods eight resin composite specimens and one human tooth specimen were fabricated.The resin specimens were polished to reach a surface gloss, in gloss units (gus), of 10 gu, 20 gu, 30 gu, 40 gu, 50 gu, 60 gu, 70 gu, and 80 gu, and the human tooth specimen had a surface gloss of 80 gu.Sixty observers were selected to compare the surface gloss of the specimens in a light booth.For the perceptibility assessment, specimens were randomly displayed two at a time.Each observer performed a total of 144 observations.Observers answered two specific questions for determining the level and limit of perceptibility of gloss variations.The acceptability limit of gloss was determined by comparing the resin specimens with the tooth specimen.The observations were performed with dental practice scenarios (illuminant conditions, visualization field, and observers' education).Data were submitted to a nonlinear probit model and nonlinear regression estimation probit (5%).Results differences in perceptibility and acceptability were observed for surface gloss variations (δgu) (p 20>30>40>50>60=70).Acceptability and perceptibility limits were 6.4 gu and 35.7 gu, respectively.Conclusions perceptibility and acceptability of surface gloss are influenced by gloss variations.A variation of 6.4 gu was required for 50% of observers to notice gloss variations.Concerning acceptability, observers required a variation of 35.7 gu to consider differences in gloss not acceptable.

Journal: Operative dentistry (2020)
Publication types: Journal Article
Non-Coding RNAs in Pancreatic Cancer Diagnostics and Therapy: Focus on lncRNAs, circRNAs, and piRNAs.

Pancreatic cancer is an aggressive malignance with high mortality.The lack of early diagnosis and effective therapy contributes to the high mortality of this deadly disease.For a long time being, the alterations in coding rnas have been considered as major targets for diagnosis and treatment of pancreatic cancer.However, with the advances in high-throughput next generation of sequencing more alterations in non-coding rnas (nc rnas) have been discovered in different cancers.Further mechanistic studies have demonstrated that nc rnas such as long noncoding rnas (lnc rna), circular rnas (circ rna) and piwi-interacting rna (pi rna) play vital roles in the regulation of tumorigenesis, tumor progression and prognosis.In recent years, increasing studies have focused on the roles of nc rnas in the development and progression of pancreatic cancer.Novel findings have demonstrated that lnc rna, circ rna, and pi rna are critically involved in the regulation of gene expression and cellular signal transduction in pancreatic cancer.In this review, we summarize the current knowledge of roles of lnc rna, circ rna, and pi rna in the diagnosis and prognosis of pancreatic cancer, and molecular mechanisms underlying the regulation of these nc rnas and related signaling in pancreatic cancer therapy.The information provided here will help to find new strategies for better treatment of pancreatic cancer.

Journal: Cancers (2021)
Publication types: Journal Article;Review
Nutritional quality and consumer health perception of online delivery food in the context of China.

Today, the popularization of mobile internet technology has enabled the public's need for food convenience and diversity arising from modern fast-paced lifestyles to be met at a relatively low cost.The digital age of the restaurant industry has arrived.Online food delivery (ofd) is rapidly developing globally.However, the public's awareness of the nutritional quality of food through ofd and their knowledge of dietary nutrition remain to be investigated.Methods in the context of china, this study attempts to evaluate the nutritional quality of best-selling ofd set meals (i.e., meal combos) based on the current official chinese dietary guidelines 2022.It accomplishes this by collecting data on popular ofd restaurants among consumers in 115 chinese universities from the restaurants' delivery addresses.Moreover, 20,430 valid questionnaires were collected online from undergraduates, graduate students, and other young groups aged 18-30 throughout china for descriptive analysis to investigate consumers' perceptions of the nutritional quality of food through ofd and its health impact.Results the results of the nutritional quality evaluation of the ofd set meals ranged widely from 15 to 85, with a mean of 36.57 out of a possible maximum score of 100; and 89.56% scored less than 50.The nutritional quality of ofd foods was thus generally low.The nutritional quality of foods was negatively correlated with their popularity among consumers.Conclusions young ofd consumers generally paid low attention to dietary nutrition knowledge and seldom paid attention to nutritional quality when choosing ofd foods while the nutritional quality of ofd foods was generally low.Respondents subjectively reported that long-term consumption of ofd food caused weight gain, increased blood lipids, and gastrointestinal discomfort.They thought that the reason might be excessive oil, salt, and sugar in the food, while ignoring the balance between different types of food.

Journal: BMC public health (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Workplace Bullying and Patient Aggression Related to COVID-19 and its Association with Psychological Distress among Health Care Professionals during the COVID-19 Pandemic in Japan.

The novel coronavirus disease (covid-19) pandemic has spread throughout the world.Poor mental health has been reported among healthcare professionals responding to covid-19.However, no study has examined the impact of covid-19-related workplace bullying or patient aggression on the mental health of healthcare professionals during the covid-19 outbreak.This study examined the prevalence of covid-19-related workplace bullying and patient aggression and its association with psychological distress among healthcare professionals during the covid-19 outbreak in japan.This was a cross-sectional study conducted from may 22 to 26, 2020, inviting participants (n = 1,421) from an online survey of full-time employees.We limited the sample to healthcare professionals for further analyses.Using an online self-report questionnaire, workplace bullying and patient aggression related to covid-19 was measured using nine items with dichotomous response options.Psychological distress was measured using the japanese version of brief job stress questionnaire.Among 1,032 participants (72.6%) who completed the survey, 111 healthcare professionals were identified.Among them, 19 participants (17.1%) had experienced any covid-19-related workplace bullying or patient aggression: 11 participants (9.9%) had experienced any workplace bullying and 12 participants (10.8%) had experienced any patient aggression.Multiple linear regression analysis showed that any bullying or patient aggression related to covid-19 significantly correlated with psychological distress.It was suggested that a non-negligible proportion of participants experienced workplace bullying or patient aggression related to covid-19.Preventing and reducing workplace bullying and patient aggression may be effective in improving mental health of healthcare professionals during the covid-19 outbreak.

Journal: The Tohoku journal of experimental medicine (2021)
Publication types: Journal Article
Pediatric oncology infrastructure and workforce training needs: A report from the Pediatric Oncology East and Mediterranean (POEM) Group.

Inadequate numbers of trained health care providers (hcps) contribute to poor pediatric oncology (po) outcomes, particularly in low- and lower middle-income countries (l/lmics).An understanding of the characteristics of the workforce challenges is vital for addressing these problems.Methods the pediatric oncology east and mediterranean (poem) group surveyed po centers in countries of north africa, middle east, central asia, and indian subcontinent on infrastructure and workforce capacity, service availability, and training opportunities for hcps.Participating centers were categorized by the world bank income levels for their countries and correlated with services, workload and staffing characteristics, and training needs.Results fifty of 82 member centers (61%) from 21 countries responded to the survey.Two hundred ninety-nine pediatric oncologists and 1176 nurses treated 12 496 new po patients/year, with a 1451-bed utilization.The majority (71%) of new cases occurred in l/lmics.The availability of hcps correlated with country income level, as did pediatric subspecialty access, while availability of support services was unrelated.Twenty-five centers in 11 countries offered po fellowship training for physicians, whereas 13 po nurse training centers in nine countries had the capacity to train 273 nurses annually.The survey respondents indicated that, among their existing workforce, an average of 3.5 physicians and 14 nurses per institution would benefit from additional po training opportunities.Conclusions the participating centers exhibited intraregional heterogeneity in financial resources, infrastructure, workload, workforce, and medical services.Our findings provide insight into the disparities and regional resources available to poem, which can be mobilized to rectify specific deficiencies.

Journal: Pediatric blood & cancer (2021)
Publication types: Journal Article
Definition and classification of chyle leak after pancreatic operation: A consensus statement by the International Study Group on Pancreatic Surgery.

Recent literature suggests that chyle leak may complicate up to 10% of pancreatic resections.Treatment depends on its severity, which may include chylous ascites.No international consensus definition or grading system of chyle leak currently is available.Methods the international study group on pancreatic surgery, an international panel of pancreatic surgeons working in well-known, high-volume centers, reviewed the literature and worked together to establish a consensus on the definition and classification of chyle leak after pancreatic operation.Results chyle leak was defined as output of milky-colored fluid from a drain, drain site, or wound on or after postoperative day 3, with a triglyceride content ≥110 mg/d l (≥1.2 mmol/l).Three different grades of severity were defined according to the management needed: grade a, no specific intervention other than oral dietary restrictions; grade b, prolongation of hospital stay, nasoenteral nutrition with dietary restriction, total parenteral nutrition, octreotide, maintenance of surgical drains, or placement of new percutaneous drains; and grade c, need for other more invasive in-hospital treatment, intensive care unit admission, or mortality.Conclusion this classification and grading system for chyle leak after pancreatic resection allows for comparison of outcomes between series.As with the other the international study group on pancreatic surgery consensus statements, this classification should facilitate communication and evaluation of different approaches to the prevention and treatment of this complication.

Journal: Surgery (2017)
Publication types: Journal Article;Review
Wheat TaPUB1 protein mediates ABA response and seed development through ubiquitination.

Abscisic acid (aba) is an important regulator of plant growth, development, and biotic and abiotic stress responses.Ubiquitination plays important roles in regulating aba signaling.E3 ligase, a key member in ubiquitination, actively participates in the regulation of biosynthesis, de-repression, and activation of aba response and degradation of signaling components.In this study, we found that that overexpression of wheat e3 ligase ta pub1 decreased the sensitivity of wheat seedlings to aba, whereas ta pub1-rna interference (ta pub1-rnai) lines increased wheat sensitivity to aba during germination, root growth, and stomatal opening.Ta pub1 influenced the expression of several aba-responsive genes, and also interacted with ta pyl4 and ta abi5, which are involved in aba signal transduction, and promoted their degradation.Additionally, we observed that ta pub1-oe lines resulted in lower single-split grain numbers, larger seed size, and higher thousand kernel weight, when compared with the wt lines.Contrasting results were obtained for ta pub1-rnai lines.It suggests that ta pub1 acts as a negative regulator in the aba signaling pathway by interacting with ta pyl4 and ta abi5, subsequently affecting seed development in wheat.In addition, the enhanced abiotic tolerance of overexpression lines due to enhanced photosynthesis and root development may be related to the degradation of ta abi5 by ta pub1.

Journal: Plant science : an international journal of experimental plant biology (2021)
Publication types: Journal Article
Effects of Replacing Alfalfa Hay With Native Grass Hay in Pelleted Total Mixed Ration on Physicochemical Parameters, Fatty Acid Profile, and Rumen Microbiota in Lamb.

This study aimed to investigate the effects of replacing alfalfa with native grass on growth performance, meat quality, and rumen microbiota of lambs.Forty-five 6-month-old ujimqin lambs with live body weight (bw) of 29.50 ± 0.26 kg were used for the experiment, and the lambs were assigned to three diet treatments (three pens per treatment and five lambs per pen) with 30 square meters per pen in semi-open housing based on similar bw.The lambs have received 30% alfalfa (ha, high alfalfa percentage group), 20% alfalfa (ma, moderate alfalfa percentage group), and 10% alfalfa (la, low alfalfa percentage group) diets, respectively (dry matter basis).The diet treatments had a significant (p 0.05) difference was found in protein.As native grass hay percentages increased in the diet, the contents of palmitic (c16:0) and palmitoleic (c16:1cis-9) in the ha and ma groups were significantly (p 0.05) difference was observed in the dominant rumen bacteria at the phyla and genus levels.In conclusion, the meat quality and fatty acid profile analysis revealed that replacing alfalfa hay with native grass hay is more beneficial for mongolian lambs, and the meat from la diet treatment is better than the others.In addition, correlation analysis of the association of rumen microbiome with growth performance, meat quality, and fatty acid profile provides us with a comprehensive understanding of the composition and function of rumen microbiota.These findings could provide knowledge of how the diet affects the animal performance, meat quality of lambs, and microbiota of the rumen, laying a theoretical basis for replacing alfalfa with native grass.

Journal: Frontiers in microbiology (2022)
Publication types: Journal Article
Evaluation of microglia in a rodent model of Parkinson's disease primed with L-DOPA after sub-anesthetic ketamine treatment.

Parkinson's disease (pd) is a neurodegenerative disease caused by the death of dopaminergic neurons in the substantia nigra pars compacta (snpc), characterized by motor dysfunction.While pd symptoms are well treated with l-dopa, continuous use can cause l-dopa-induced dyskinesia (lid).We have previously demonstrated that sub-anesthetic ketamine attenuated lid development in rodents, measured by abnormal involuntary movements (aims), and reduced the density of maladaptive striatal dendritic mushroom spines.Microglia may play a role by phagocytosing maladaptive neuronal spines.In this exploratory study, we hypothesized that ketamine would prevent aims and change microglia ramified morphology - an indicator of a microglia response.Unilaterally 6-hydroxydopamine (6-ohda)-lesioned rats were primed with daily injections of l-dopa for 14 days, treated on days 0 and 7 for 10-hours with sub-anesthetic ketamine (i.p.), and we replicated that this attenuated lid development.We further extended our prior work by showing that while ketamine treatment did lead to an increase of striatal interleukin-6 in dyskinetic rats, indicating a modulation of an inflammatory response, it did not change microglia number or morphology in the dyskinetic striatum.Yet an increase of cd68 in the snpc of 6-ohda-lesioned hemispheres post-ketamine indicates increased microglia phagocytosis suggestive of a lingering microglial response to 6-ohda injury in the snpc pointing to possible anti-inflammatory action in the pd model in addition to anti-dyskinetic action.In conclusion, we provide further support for sub-anesthetic ketamine treatment of lid.The mechanisms of action for ketamine, specifically related to inflammation and microglia phagocytic functions, are emerging, and require further examination.

Journal: Neuroscience letters (2021)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't