syedzayyan/paper_mill_benchmark huggingface dataset:
Black coffee mitigates diethyl phthalate disrupted folliculogenesis, reduced gonadotropins, and ovarian lesions in female albino mice.

Phthalates are multifunctional compounds with extensive applications and emerging environmental pollutants.Due to their ubiquity in the environment and unavoidable exposure to humans, concerns have been voiced about public health dangers.This study was aimed to explore the diethyl phthalate (dep) toxicity and the potential protective effect of black coffee in female swiss albino mice.Four-week-old mice, weighing 12 ± 1 g were segregated into five groups (n = 10), designated as g-i (without any treatment), g-ii (treated with corn oil), g-iii (exposed to 1.5 mg/g body wt.(b.w.) dep), g-iv (received 2 μg/g b.w coffee), and g-v (co-administrated with 1.5 mg/g dep and 2 μg/g b.w coffee).Before dose administration, the coffee extract was assessed for its antioxidant potential through frap, tpc, and gc-ms analyses.Respective phthalates/coffee doses were administrated orally, once a day for 8 weeks consecutively starting from the prepubescent stage.After 56 days, mice were acclimated for 4 days then dissected.Morphological assessments showed an irregular shape of the ovaries in dep-treated mice as compared to the control.The average bodyweight of dep-intoxicated mice (p ≤ 0.05) increased notably against control, while dep plus coffee group showed a regular gain in the average weight of mice.The gonado-somatic index showed non-significant variations among all groups.Micrometric studies showed that the diameter of secondary follicles (115 μm) in the ovaries of dep-exposed mice (p ≤ 0.001) decreased significantly as compared to control (204 μm); conversely, follicular diameter in the coffee control group (248) increased significantly.Serum fsh and lh levels were significantly increased in dep-exposed mice with a noteworthy decrease in estrogen level while hormonal levels of all other groups were comparable to control.Histological sections of dep-exposed mice ovaries showed anatomical disruptions contrary to other groups, which were comparable with control.Antioxidant potential was checked in ovaries homogenates; frap values showed a notable decrease in dep group in comparison with the control group, in contrast to g-v, when dep was co-administrated with coffee.This study concluded that black coffee has protective effect, against dep-instigated reproductive toxicity in swiss albino female mice.

Journal: Environmental science and pollution research international (2022)
Publication types: Journal Article
SH-It happens: S-H bonds as intrinsic 2D-IR labels in proteins.

Cysteine s-h bonds have a spectroscopically convenient stretching frequency of ∼2550 cm-1.However, their cross section is low, and the band can be strongly broadened in heterogeneous environments, making detection very challenging.With two-dimensional infrared (2d-ir) setups achieving ever higher sensitivities in recent years, systematic use of the weak cysteine sulfhydryls (cys-shs) absorption band is now within reach, even at low millimolar protein concentrations.Here, we demonstrate the capabilities of cys-sh as an intrinsic 2d-ir label in pyruvate oxidase from e.Coli, an enzyme with ten cysteines in its native sequence.1d-ir measurements on the wild-type and individual cysteine knock-out variants show that two such residues have especially narrow sh signatures, caused by their intrahelical hydrogen bonding.2d-ir analysis of these bands reveals an extraordinarily high anharmonicity (∼110 cm-1) and a long vibrational lifetime (∼4 ps).This allows monitoring spectral diffusion via center line slope analysis for up to 10 ps-separately for both the ground and excited states.The unique spectroscopic features and its ease of introduction make cys-sh a useful ir spectroscopic label.

Journal: The Journal of chemical physics (2022)
Publication types: Journal Article
Study of renal parenchymal changes by diffusion tensor imaging in diabetic nephropathy.

To evaluate differences in diffusion imaging parameters, including fractional anisotropy (fa) and the apparent diffusion coefficient (adc), in control and diabetic subjects, and to assess changes in these parameters to patient's urine albumin/protein levels, estimated glomerular filtration rate (e gfr), and glycated haemoglobin (hb a1c).Material and methods this is a cross-sectional analytical study involving 100 patients who underwent diffusion imaging including diffusion tensor imaging (dti) of the kidneys in our hospital from 2019 to 2020.Diffusion imaging parameters (adc and fa) were obtained from the medulla and cortex of both kidneys using dedicated software.Statistical analysis was done.Results out of 100 subjects, 27 were controls and 73 were diabetics (19 normoalbuminuric, 23 microalbuminuric, and 31 proteinuric).The medullary fa (0.419 ± 0.024 vs.0.346 ± 0.042), cortical fa (0.194 ± 0.035 vs.0.303 ± 0.067), and cortical adc (3.307 ± 0.341 vs.2.309 ± 0.515) values showed significant differences between controls and diabetics.Medullary fa and cortical adc values showed a decreasing trend with an increasing amount of albumin/protein in the urine, decreasing renal function (reducing e gfr), and increasing hb a1c, whereas the trend was opposite for cortical fa.In addition, on roc curve analysis a cut-off value for medullary fa of 0.4 had a sensitivity of 64% and specificity of 80.95% to differentiate healthy volunteers and diabetics with normo-albuminuria.Conclusions dti has the potential to be a promising non-invasive test for the detection of early renal parenchymal changes in diabetic nephropathy.

Journal: Polish journal of radiology (2022)
Publication types: Journal Article
Chimeric antigen receptor T-cell therapy targeting a MAGE A4 peptide and HLA-A*02:01 complex for unresectable advanced or recurrent solid cancer: protocol for a multi-institutional phase 1 clinical trial.

Introduction adoptive cell transfer of genetically engineered t cells is a promising treatment for malignancies; however, there are few ideal cancer antigens expressed on the cell surface, and the development of chimeric antigen receptor t cells (car-t cells) for solid tumour treatment has been slow.Car-t cells, which recognise major histocompatibility complex and peptide complexes presented on the cell surface, can be used to target not only cell surface antigens but also intracellular antigens.We have developed a car-t-cell product that recognises the complex of hla-a*02:01 and an epitope of the mage-a4 antigen equipped with a novel signalling domain of human gitr (investigational product code: mu-ma402c) based on preclinical studies.Methods and analysis this is a dose-escalation, multi-institutional, phase 1 study to evaluate the tolerability and safety of mu-ma402c for patients with mage a4-positive and hla-a*02:01-positive unresectable advanced or recurrent solid cancer.Two dose cohorts are planned: cohort 1, mu-ma402c 2×108/person; cohort 2, mu-ma402c 2×109/person.Prior to car-t-cell infusion, cyclophosphamide (cpa) and fludarabine (flu) will be administered as preconditioning chemotherapy.Three evaluable subjects per cohort, for a total of 6 subjects (maximum of 12 subjects), will be recruited for this clinical trial.The primary endpoints are safety and tolerability.The severity of each adverse event will be evaluated in accordance with common terminology criteria for adverse events v.5.0.The secondary endpoint is efficacy.Antitumour response will be evaluated according to response evaluation criteria in solid tumours v.1.1.Ethics and dissemination this clinical trial will be conducted in accordance with the current version of good clinical practice.The protocol was approved by the clinical research ethics review committee of mie university hospital (approval number f-2021-017).The trial results will be published in peer-reviewed journals and/or disseminated through international conferences.Trial registration number j rct2043210077.

Journal: BMJ open (2022)
Publication types: Clinical Trial Protocol;Journal Article;Research Support, Non-U.S. Gov't
Effects of Hot-Water Extract from Vine Tea (Ampelopsisgrossedentata) on Acrylamide Formation, Quality and Consumer Acceptability of Bread.

Acrylamide is a harmful substance that could be inhibited by natural products.Vine tea is an edible herb belonging to the vitaceae family and has been approved by chinese authorities as a new food ingredient in 2013.However, the effects of vine tea extract on acrylamide formation and bread quality are rarely investigated.In this study, the polyphenol composition of hot-water extract from vine tea was characterized by ultrahigh-performance liquid chromatography coupled with high-resolution mass spectrometry (uhplc-esi-hrms/ms), and its effects on acrylamide formation, quality, and consumer acceptability of bread were investigated.Vine tea extract and its main polyphenol, dihydromyricetin, significantly inhibited the acrylamide formation in bread, especially the low dose of vine tea extract (1.25 g/kg), which decreased the acrylamide formation by 58.23%.The color and texture of bread were significantly affected by vine tea extract or dihydromyricetin, whereas the moisture content was not changed remarkably.Triangle and paired preference tests indicated that, although the aroma, appearance, and taste of the bread with vine tea extract significantly differ from those of the control bread, vine tea extract did not significantly affect the consumer acceptability.In conclusion, the addition of vine tea extract could be used to develop a new and healthy bread product with low acrylamide content.

Journal: Foods (Basel, Switzerland) (2020)
Publication types: Journal Article
Effects of Neohesperidin Dihydrochalcone (NHDC) on Oxidative Phosphorylation, Cytokine Production, and Lipid Deposition.

The sweetener neohesperidin dihydrochalcone (nhdc) is a precursor for anthocyanins and has been reported to have various bioactivities, including antioxidant and hepatitis inhibitory effects.However, its inflammatory functions and mechanisms of action are poorly understood.In this study, raw 264.7 murine macrophages were treated with nhdc and its metabolite dihydrocaffeic acid (dhca), after which cytokine production and mitochondrial respiration were assessed.Dhca significantly down-regulated the secretion of pro-inflammatory cytokines.In contrast, nhdc had a marginal effect, suggesting that the biological metabolism of nhdc to dhca is required for its anti-inflammatory function.However, both nhdc and dhca rescued lps-induced suppression of oxidative phosphorylation, which is a hallmark of anti-inflammatory m2 macrophages.3t3-l1 adipocytes showed lower fat deposition in the presence of dhca, while sugar-containing nhdc showed a slight increase in fat deposition.In high-fat diet-induced obese mice, treatment with nhdc successfully down-regulated body weight gain in a dose-dependent manner.Furthermore, m2 polarized bone-marrow-derived macrophages (bmdm) from nhdc-fed mice secreted an increased amount of the anti-inflammatory cytokine il-10.Overall, these results indicate that nhdc and its physiological metabolite dhca have the potential to suppress the inflammatory response and obese status.

Journal: Foods (Basel, Switzerland) (2021)
Publication types: Journal Article
Correction: Selective light driven reduction of CO2to HCOOH in water using a {MoV9}n(n= 1332-3600) based soft-oxometalate (SOM).

Correction for 'selective light driven reduction of co2to hcooh in water using a {mo v9}n(n= 1332-3600) based soft-oxometalate (som)' by soumitra barmanet al.,chem.Commun., 2018,54, 2369-2372,

Journal: Chemical communications (Cambridge, England) (2022)
Publication types: Published Erratum
A nitric oxide and hydrogen sulfide dual-donating nanosystem for highly synergistic gas-radiotherapy against hepatocellular carcinoma.

A drug delivery system (dds) based on gold-capped mesoporous silica nanoparticles (msn) is fabricated for loading nosh-aspirin, a nitric oxide (no) and hydrogen sulfide (h2s) dual-donating cytotoxic molecule.The liver targeting and tumor microenvironment responsive properties of the nanosystem enable, for the first time, the concurrent delivery of no and h2s from a dds into hepatocellular carcinoma (hcc) cells.Combined gas-radiotherapy (gt-rt) from drug-loaded dds (nosh@msn-au-gal) and x-ray irradiation shows highly synergistic anti-cancer activity against both normoxic and hypoxic hcc cells.Further studies revealed that the combined gt-rt not only retains the well-known anticancer mechanism of no, h2s, and x-ray individually, but also alleviates hcc hypoxia via no- and h2s- involved unique pathways.In mice, the gt-rt greatly slows the growth of both subcutaneous and orthotopic hcc tumors and shows high biocompatibility.The current work is expected to promote the clinical application of combined gt-rt as an effective cancer treatment.

Journal: Biomaterials advances (2023)
Publication types: Journal Article
Facial Anatomical Landmark Detection Using Regularized Transfer Learning With Application to Fetal Alcohol Syndrome Recognition.

Fetal alcohol syndrome (fas) caused by prenatal alcohol exposure can result in a series of cranio-facial anomalies, and behavioral and neurocognitive problems.Current diagnosis of fas is typically done by identifying a set of facial characteristics, which are often obtained by manual examination.Anatomical landmark detection, which provides rich geometric information, is important to detect the presence of fas associated facial anomalies.This imaging application is characterized by large variations in data appearance and limited availability of labeled data.Current deep learning-based heatmap regression methods designed for facial landmark detection in natural images assume availability of large datasets and are therefore not well-suited for this application.To address this restriction, we develop a new regularized transfer learning approach that exploits the knowledge of a network learned on large facial recognition datasets.In contrast to standard transfer learning which focuses on adjusting the pre-trained weights, the proposed learning approach regularizes the model behavior.It explicitly reuses the rich visual semantics of a domain-similar source model on the target task data as an additional supervisory signal for regularizing landmark detection optimization.Specifically, we develop four regularization constraints for the proposed transfer learning, including constraining the feature outputs from classification and intermediate layers, as well as matching activation attention maps in both spatial and channel levels.Experimental evaluation on a collected clinical imaging dataset demonstrate that the proposed approach can effectively improve model generalizability under limited training samples, and is advantageous to other approaches in the literature.

Journal: IEEE journal of biomedical and health informatics (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Clinical and Legal Considerations Regarding Breastfeeding on Psychiatric Units.

Women in the postpartum period are at especially high risk of developing psychiatric disorders, and in severe cases, they may require inpatient psychiatric hospitalization.Because of the lack of specialized units for peripartum mothers in the united states, this treatment is usually relegated to general inpatient psychiatric units.Despite the clear benefit of breastfeeding for both mother and child, lactation can be a barrier to placement on a general inpatient psychiatric unit and often is not supported during the hospital stay.Limiting access to inpatient psychiatric care for postpartum mothers with mental illness could be considered sex discrimination under the affordable care act (aca) because of failure to accommodate lactation.With improvements in education and accommodations around breastfeeding, general inpatient psychiatric units could provide appropriate care for this population.

Journal: The journal of the American Academy of Psychiatry and the Law (2022)
Publication types: Journal Article
Genome-Wide Association Study of Resistance toPhytophthora capsiciin the Pepper (Capsicumspp.) Collection.

One of the most serious pepper diseases is phytophthora blight, which is caused by phytophthora capsici.it is crucial to assess the resistance of pepper genetic resources to phytophthora blight, understand the genetic resistances, and develop markers for selecting resistant pepper materials in breeding programs.In this study, the resistance of 342 pepper accessions to p.Capsiciwas evaluated.The disease severity score method was used to evaluate the phenotypic responses of pepper accessions inoculated with the kcp7 isolate.A genome-wide association study (gwas) was performed to identify single nucleotide polymorphisms (snps) linked to p.Capsici(isolate kcp7) resistance.The pepper population was genotyped using the genotype-by-sequencing (gbs) method, and 45,481 snps were obtained.A gwas analysis was performed using resistance evaluation data and snp markers.Significantly associated snps for p.Capsiciresistance at 4 weeks after inoculation of the gwas pepper population were selected.These snps for phytophthora blight resistance were found on all chromosomes except chr.05, chr.09, and chr.11.One of the snps found on chr.02 was converted into a high-resolution melting (hrm) marker, and another marker (qtl5-1) from the previous study was applied to pepper accessions and breeding lines for validation and comparison.This snp marker was selected because the resistance phenotype and the hrm marker genotype matched well.The selected snp was named chr02-1126 and was located at 112 mb on chr.02.The chr02-1126 marker predicted p.Capsiciresistance with 78.5% accuracy, while the qtl5-1 marker predicted resistance with 80.2% accuracy.Along with the marker for major quantitative traits loci (qtls) on chr.05, this chr02-1126 marker could be used to accurately predict phytophthora blight resistance in pepper genetic resources.Therefore, this study will assist in the selection of resistant pepper plants in order to breed new phytophthora blight-resistant varieties.

Journal: Frontiers in plant science (2022)
Publication types: Journal Article
Fuzzy Approximate Entropy of Extrema Based on Multiple Moving Averages as a Novel Approach in Obstructive Sleep Apnea Screening.

Obstructive sleep apnea (osa) is a respiratory disease associated with autonomic nervous system dysfunction.As a novel method for analyzing osa depending on heart rate variability, fuzzy approximate entropy of extrema based on multiple moving averages (emma-f ap en) can effectively assess the sympathetic tension limits, thereby realizing a good performance in the disease severity screening.Method sixty 6-h electrocardiogram recordings (20 healthy, 16 mild/moderate osa and 34 severe osa) from the physio net database were used in this study.The performances of minima of emma-f ap en (f ap en-minima), maxima of emma-f ap en (f ap en-maxima) and classic time-frequency domain indices for each recording were assessed by significance analysis, correlation analysis, parameter optimization and osa screening.Results f ap en-minima and f ap en-maxima had significant differences between the severe osa group and the other two groups, while the mean value (mean) and the ratio of low-frequency power and high-frequency power (lh) could significantly differentiate osa recordings from healthy recordings.The correlation coefficient between f ap en-minima and apnea-hypopnea index was the highest (|r| = 0.705).Machine learning methods were used to evaluate the performances of the above four indices.Random forest (rf) achieved the highest accuracy of 96.67% in osa screening and 91.67% in severe osa screening, with a good balance in both.Conclusion emma-f ap en may be used as a simple preliminary detection tool to assess the severity of osa prior to polysomnography analysis.

Journal: IEEE journal of translational engineering in health and medicine (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Returning to home cage serves as an effective reward for maze learning in rats.

This study examined the effectiveness in rats of 'returning to home cage' as a reward for learning a lashley iii maze.Rats could return to their home cage directly (direct hc group) or they could be removed manually by an experimenter from the maze's goal box (indirect hc group).In the third group, hungry rats received a food reward in the goal box (food group).The direct hc group reliably learned the maze and its performance was very similar to that of the food group.In contrast, performance by the indirect hc group was significantly poorer than the direct hc group, as well as the food group, possibly due to the negative impact of handling during removal from the goal box.These results suggest that a 'home cage reward' is as effective a procedure for rats in maze learning as previously reported in mice (blizard et al., 2003, 2006).

Journal: Behavioural processes (2019)
Publication types: Journal Article
The Role of Immunotherapy in the Management of Soft Tissue Sarcomas: Current Landscape and Future Outlook.

Soft tissue sarcomas (sts) are a subset of sarcoma, a rare group of heterogeneous malignancies of mesenchymal origin.Current standard of care involves surgical resection with systemic chemotherapy used to treat high-risk localized and metastatic disease.Though classically thought to be immunologically quiet tumors, sts interact with the immune system, undergoing immunoediting that alters tumor immunogenicity and the tumor microenvironment.Recent advances with immune checkpoint inhibition have led to clinical trials exploring the efficacy of immunotherapy in treating sts.Results from these trials point to histologic subtype-specific clinical activity of immune checkpoint blockade.In addition, combinatorial strategies adding immune checkpoint inhibition to local or systemic therapies for sts have further increased their efficacy.Targeted immunotherapies using engineered t-cell receptor-based approaches also show increasing promise as treatment options for some patients with sts.Adoptive transfer of autologous t cells targeting ny-eso-1 and mage-a4 have high response rates in sarcomas expressing these antigens, although recurrence is often seen in responding patients.Future work must focus on identifying primary and acquired mechanisms of resistance to these therapies, and extend t-cell receptor discovery to other tumor-associated antigens.

Journal: Journal of the National Comprehensive Cancer Network : JNCCN (2022)
Publication types: Journal Article;Review