syedzayyan/paper_mill_benchmark huggingface dataset:
XMCD andab initiostudy of interface-engineered ultrathin Ru/Co/W/Ru films with perpendicular magnetic anisotropy and strong Dzyaloshinskii-Moriya interaction.

Understanding the nature of recently discovered spin-orbital induced phenomena and a definition of a general approach for "ferromagnet/heavy-metal" layered systems to enhance and manipulate spin-orbit coupling, spin-orbit torque, and the dzyaloshinskii-moriya interaction (dmi) assisted by atomic-scale interface engineering are essential for developing spintronics and spin-orbitronics.Here, we exploit x-ray magnetic circular dichroism (xmcd) spectroscopy at the l2,3-edges of 5d and 4d non-magnetic heavy metals (w and ru, respectively) in ultrathin ru/co/w/ru films to determine their induced magnetic moments due to the proximity to the ferromagnetic layer of co.The deduced orbital and spin magnetic moments agree well with the theoretically predicted values, highlighting the drastic effect of constituting layers on the system's magnetic properties and the strong interfacial dmi in ru/co/w/ru films.As a result, we demonstrate the ability to simultaneously control the strength of magnetic anisotropy and intermixing-enhanced dmi through the interface engineered inversion asymmetry in thin-film chiral ferromagnets, which are a potential host for stable magnetic skyrmions.

Journal: Physical chemistry chemical physics : PCCP (2022)
Publication types: Journal Article
Stereotactic body radiotherapy for recurrent and oligometastatic soft tissue sarcoma.

Soft tissue sarcoma (sts) is a malignant tumor of highly heterogeneous mesenchymal origin.Sts has a biological pattern and clinical transformation with localized invasive growth and is susceptible to hematogenous metastasis.Local therapeutic strategies may treat recurrent and oligometastatic sts, including surgery and radiation therapy.This study aimed to evaluate the safety and efficacy of stereotactic body radiotherapy (sbrt) for recurrent and oligometastatic sts.Methods we retrospectively analyzed 37 recurrent and oligometastatic sts patients with 58 lesions treated with sbrt from 2009 to 2019 at our institution.Oligometastatic is defined as metastatic lesions less than or equal to 3.The primary endpoint was local control (lc); secondary endpoints were survival and toxicity.Results the median follow-up was 21.0 months (3.0 to 125.0 months).Among 37 patients, 18 were recurrent patients, and 19 were oligometastatic patients.Median lc was 25.0 months (95% ci 20.0-45.0).The 1-, 2-, and 3-year lc rates were 80.2%, 58.3%, and 46.6%, respectively.Median overall survival (os) was 24.0 months (95% ci 13.0-28.0), and the survival rates after sbrt were 71.5%, 40.0%, and 29.1% at 1, 2, and 3-year, respectively.Median progression-free survival (pfs) was 10.0 months (95% ci 8.0-15.0 months), pfs rate after sbrt was 43.6%, 26.8%, and 18.4% at 1, 2, and 3 years, respectively.Late grade 3 radiation dermatitis was observed in one patient (2.7%).Using univariate and multivariate cox analysis, better os, pfs, and lc were obtained in the histologic grade 1(g1) group, and tumor size and a number of lesions influenced lc.Conclusions sbrt is a safe and effective treatment for patients with recurrent and oligometastatic sts.Histological grade influences local control and survival.Sbrt may be a promising treatment option for recurrent and oligometastatic sts.

Journal: World journal of surgical oncology (2022)
Publication types: Journal Article;Review
Circulating saturated fatty acids and risk of gestational diabetes mellitus: A cross-sectional study and meta-analysis.

Previous studies have analyzed the associations between the circulating saturated fatty acids (sfas) and gestational diabetes mellitus (gdm), but no consistent conclusions have been reached.The aim of this study was to evaluate whether plasma sfas were in correlation with gdm risks in our in-house women cross-sectional study and to better define their associations on the clinical evidence available to date by a dose-response meta-analysis.Methods we carried out a cross-sectional study of 807 pregnant women in 2018-2019 (shanghai, china).Gdm was defined according to the criteria of the international association of diabetes and pregnancy study groups (iadpsg).Gas chromatography was used to determine the plasma fatty acids (fas) in the 24-28 gestational weeks.The sfas levels of non-gdm and gdm participants were compared by mann-whitney test, and the association between sfas and gdm was explored by multivariate logistic models.Further, the potential diagnostic value of plasma sfas was evaluated using the method of receiver operating characteristic (roc) analysis.For meta-analysis, five databases were systematically searched from inception to march 2022, and we included 25 relevant studies for calculating pooled standard mean differences (smds) and 95% ci to describe the differences in sfas profiles between non-gdm and gdm women.Study-specific, multivariable-adjusted ors and 95% ci were also pooled using a fixed-effect model or random-effects model according to the heterogeneity to evaluate the associations between circulating sfas and gdm prevalence.Results in our cross-sectional study, we found plasma proportion of palmitic acid (c16:0) was positively associated (a or: 1.10 per 1% increase; 95% ci: 1.04, 1.17), while plasma stearic acid (c18:0) (a or: 0.76 per 1% increase; 95% ci: 0.66, 0.89), arachidic acid (c20:0) (a or: 0.92 per 0.1% increase; 95% ci: 0.87, 0.97), behenic acid (c22:0) (a or: 0.94 per 0.1% increase; 95% ci: 0.92, 0.97), and lignoceric acid (c24:0) (a or: 0.94 per 0.1% increase; 95% ci: 0.92, 0.97) were inversely associated with gdm.The area under the receiver operative characteristic curve increased from 0.7503 (the basic diagnostic model) to 0.8178 (p= 0.002) after adding total very-long-chain sfas (vlc sfas).A meta-analysis from 25 studies showed the circulating levels of three individual sfas of gdm women were different from those of normal pregnant women.The summarized ors for gdm was 1.593 (95% ci: 1.125, 2.255,p= 0.009), 0.652 (95% ci: 0.472, 0.901,p= 0.010) and 0.613 (95% ci: 0.449, 0.838,p= 0.002), respectively, comparing the highest vs.Lowest quantile of the concentrations of c16:0, c22:0, and c24:0.Conclusion our results, combined with the findings from meta-analysis, showed that women with gdm had a particular circulating sfa profile, characterized by higher levels of palmitic acid, and lower levels of vlc sfas.Alterations in the chain lengths of blood sfa profile were shown to be associated with the occurrence of gdm.

Journal: Frontiers in nutrition (2022)
Publication types: Journal Article
Specificity of Human Sulfiredoxin for Reductant and Peroxiredoxin Oligomeric State.

Human peroxiredoxins (prx) are a family of antioxidant enzymes involved in a myriad of cellular functions and diseases.During the reaction with peroxides (e.g., h2o2), the typical 2-cys prxs change oligomeric structure between higher order (do)decamers and disulfide-linked dimers, with the hyperoxidized inactive state (-so2h) favoring the multimeric structure of the reduced enzyme.Here, we present a study on the structural requirements for the repair of hyperoxidized 2-cys prxs by human sulfiredoxin (srx) and the relative efficacy of physiological reductants hydrogen sulfide (h2s) and glutathione (gsh) in this reaction.The crystal structure of the toroidal prx1-srx complex shows an extended active site interface.The loss of this interface within engineered prx2 and prx3 dimers yielded variants more resistant to hyperoxidation and repair by srx.Finally, we reveal for the first time prx isoform-dependent use of and potential cooperation between gsh and h2s in supporting srx activity.

Journal: Antioxidants (Basel, Switzerland) (2021)
Publication types: Journal Article
Designing anisotropic inorganic nanocapsulesviaself-assembly of polymer-like ultrathin Au nanowires.

Anisotropic assembly of nanomaterials into hollow structures is an attractive technique in biomedicine and biosensing.Commonly used polymer materials are easy to assemble yet it is hard to form anisotropic morphologies.Here in this work, we successfully prepared a novel gold nanocapsule with an anisotropic ellipsoidal shape and cavity structure by the self-assembly of ultrathin au nanowires.The assembly mechanism is further studied by tuning the assembly conditions such as nanowire concentration, solvent composition, and temperature.It is found that the controlling forces of the nanowire assembly process are mainly the symmetric interfacial tension and the asymmetric nanowire deformation potential, which contribute together to result in anisotropic nanocapsules.Finally, the obtained au nanocapsules were used as nanocarriers to load pyrene as a model drug, showing great drug loading ability and p h-responsive drug release behavior.We believe that this unique anisotropic assembly product will bring new insights into nanostructure design and soft matter research.

Journal: Nanoscale (2022)
Publication types: Journal Article
Regulation of the Proliferation of Diabetic Vascular Endothelial Cells by Degrading Endothelial Cell Functional Genes with QKI-7.

Diabetes has emerged as one of the most serious and common chronic diseases of our times, causing life-threatening, disabling and costly complications, and reducing life expectancy.Studies have shown that cardiovascular morbidity is 1-3 times higher in diabetic patients than in normal people.There are many clinical and experimental data that prove that most of the complications of diabetes are related to atherosclerosis, which suggests that chronic hyperglycemia may induce an imbalance in the proliferation of vascular endothelial cells.Purpose this study aims to explore the relationship between qki-7 and vascular endothelial cell dysfunction and lay a foundation for further clarifying the molecular mechanism of endothelial cell damage in the process of diabetes with atherosclerosis.Methods we chose blood samples and pluripotent stem cells and vascular endothelial cells of hospitalized patients with diabetes and diabetes atherosclerosis as research subjects.The expression levels of endothelial cell proliferation and genes related to endothelial cell proliferation were analyzed by rt-q pcr and western blot, to study the influence of qki-7 on the physiological state of endothelial cells.Through gene knockdown experiment, the effects of qki-7 knockdown on functional genes and physiological functions of endothelial cells were analyzed.Finally, rna immunoprecipitation was used to test the mutual effect among qki-7 and the transcription level of functional genes, and the m rna attenuation experiment proved that qki-7 participated in the degradation process of functional genes.Results the findings of the rt-q pcr and western blot tests revealed that qki-7 was highly expressed in blood samples of diabetic patients and atherosclerosis as well as in endothelial cells induced by human pluripotent stem cells and human vascular endothelial cells after high-glucose treatment.Overexpression and high glucose of qki-7 resulted in inhibiting expressed function genes cd144, nlgn1, and tsg6 and upregulation of inflammatory factors tnf-α, il-1β, and ifn-γ, leading to excessive proliferation of endothelial cells.After qki-7 gene knockdown, the expression levels of cd144, nlgn1, and tsg6, inflammatory factors tnf-α, il-1β, and ifn-γ, and the cell proliferation rate all returned to normal levels.Rna immunoprecipitation showed that qki-7 interacted with cd144, nlgn1, and tsg6 m rnas and was involved in the transcriptional degradation of functional genes through their interactions.Conclusion this research initially revealed the relevant molecular mechanism of qki-7 leading to the excessive proliferation of endothelial cells in diabetic and atherosclerotic patients.In view of the role of qki-7 in diabetic vascular complications, we provided a potential target for clinical diabetes treatment strategies in the future.

Journal: Contrast media & molecular imaging (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Zebrafish Optomotor Response and Morphology Are Altered by Transient, Developmental Exposure to Bisphenol-A.

Estrogen-specific endocrine disrupting compounds (edcs) are potent modulators of neural and visual development and common environmental contaminants.Using zebrafish, we examined the long-term impact of abnormal estrogenic signaling by testing the effects of acute, early exposure to bisphenol-a (bpa), a weak estrogen agonist, on later visually guided behaviors.Zebrafish aged 24 h postfertilization (hpf), 72 hpf, and 7 days postfertilization (dpf) were exposed to 0.001 μm or 0.1 μm bpa for 24 h, and then allowed to recover for 1 or 2 weeks.Morphology and optomotor responses (omrs) were assessed after 1 and 2 weeks of recovery for 24 hpf and 72 hpf exposure groups; 7 dpf exposure groups were additionally assessed immediately after exposure.Increased notochord length was seen in 0.001 μm exposed larvae and decreased in 0.1 μm exposed larvae across all age groups.Positive omr was significantly increased at 1 and 2 weeks post-exposure in larvae exposed to 0.1 μm bpa when they were 72 hpf or 7 dpf, while positive omr was increased after 2 weeks of recovery in larvae exposed to 0.001 μm bpa at 72 hpf.A time-delayed increase in eye diameter occurred in both bpa treatment groups at 72 hpf exposure; while a transient increase occurred in 7 dpf larvae exposed to 0.1 μm bpa.Overall, short-term developmental exposure to environmentally relevant bpa levels caused concentration- and age-dependent effects on zebrafish visual anatomy and function.

Journal: Journal of developmental biology (2021)
Publication types: Journal Article
An Automatic Stage Identification MATLAB Tool to Reveal Notch Expression Pattern in Drosophila Egg Chambers.

Many highly conserved pathways control the development and determine cell fate in organisms.One of these pathways is the notch signaling pathway that allows for local cell-cell communication.Researchers have found that the timing for when notch signaling activates the target gene is important for maintaining normal gene expression.Any alterations in the downstream gene expression could cause issues with development or certain diseases.The drosophila oogenesis is a widely used model in developmental biology for analyzing the notch pathway.However, determining the stage of oogenesis is difficult and varies depending on individual analyzing it.Here, we provide a matlab tool to automatically identify the stage of a drosophila egg chamber and reveal the notch expression pattern.

Journal: Methods in molecular biology (Clifton, N.J.) (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
The effect of arthroscopic rotator cuff repair on sleep in degenerative full-thickness tears.

S and background shoulder pathologies are frequently linked to sleep disturbances.The aim of this study is to investigate the effect on sleep disorders in patients with arthroscopic rotator cuff repair.Materials and methods thirty-three patients who underwent arthroscopic rotator cuff repair due to a full-thickness rotator cuff tear were prospectively analyzed.The pittsburgh sleep quality index (psqi), the american shoulder and elbow surgeons shoulder score (ases), visual analog scale (vas), and constant and murley shoulder scores before surgery and at 6 months postoperatively.Preoperative clinical and radiological parameters of the patients were also evaluated.Results the study analyzed 33 patients with a median age of 59.79 ± 9.0 years.There was a significant difference preoperatively versus postoperatively in terms of all psqi global scores and subdivisions (p < 0.001).A statistically significant improvement was determined by the simple shoulder test, the constant and murley shoulder scores, and vas (p < 0.001).Conclusion sleep disturbance is common in patients with symptomatic rotator cuff tear, and sleep disturbance can resolve after arthroscopic rotator cuff repair.

Journal: Nigerian journal of clinical practice (2022)
Publication types: Journal Article
OX40 Agonist Tumor Immunotherapy Does Not Impact Regulatory T Cell Suppressive Function.

Ox40 is a costimulatory molecule from the tnfr family.In mice, it is expressed on foxp3+regulatory t cells (tregs) constitutively and on conventional cd4 (tconv) and cd8 t cells after ag encounter.Ox40 agonists are in clinical development to enhance antitumor immune responses, and one proposed mechanism of action is loss of treg suppressive function.Studies have postulated that agonist ox40 therapy can impair treg suppressive function.Using tools developed since the initial studies were published, we evaluated a direct effect of ox40 agonism on treg function.We conclude that ox40 agonist abs do not intrinsically impair treg function but rather enhance tconv cell il-2 production, increasing treg and tconv cell proliferation.Ox40-stimulated tregs retain suppressive function, but also gain ifn-γ, tnf-α, and granzyme b expression.These data help resolve mechanistic questions regarding ox40 agonist immunotherapy and thus are relevant to developing combination therapies that target distinct t cell functions.

Journal: Journal of immunology (Baltimore, Md. : 1950) (2019)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
High sensitivity and high-confidence compound identification with a flexible BoxCar acquisition method.

Liquid chromatography-mass spectrometry (lc-ms) is in wide use for compound identification and quantification in complex matrices.While advances in mass spectrometry and the incorporation of new acquisition methods have resulted in greatly improved detection, there is an ongoing need to expand the limits of highly sensitive and confident identification of low abundance species in complex samples.The data acquisition method known as "box car" was originally designed to achieve in-depth proteome profiling on an orbitrap mass analyzer by decomposing ions into segments with narrow m/z windows.Using this method, selected segments are packaged in c-trap and all ions are then sent to orbitrap for detection.In this study, we developed a flexible box car acquisition method by placing more segments in the low m/z range for small molecule profiling.This new ms1 acquisition method was successfully integrated with iterative data dependent ms/ms acquisition by generating an inclusion list of ions detected in the flexible box car to trigger the fragmentation of parent ions.The developed acquisition method was applied to the analysis of cell culture media, which plays a key role in antibody production.This challenging goal is of critical importance, as none of the currently available methods provide a comprehensive understanding of how individual components, metabolites, and impurities associated with the cell culture process might influence recombinant antibody production.Even when present at relatively low abundance, some components or impurities in the cell culture medium could have a profound impact on the quality and titer of the antibodies produced.The complex soy hydrolysate cell culture medium used in antibody generation has not been fully characterized.Using the developed flexible box car acquisition method, we achieved 90 % higher sensitivity in experiments designed to detect spiked chemical substances at low abundance at the ms1 level compared to the full scan method.Iterative data-dependent acquisition (dda) based on the targeted inclusion list generated much higher quality ms2 spectra and facilitated confident identification of low-abundance compounds.Our method achieved a 50 % increase in ms2 coverage of compounds present at low concentrations compared to conventional dda methods.The results of our study demonstrate that this data acquisition workflow can be easily operated on orbitrap mass spectrometers and used as a highly effective approach to improve sensitivity and high-confidence small molecule profiling in soy hydrolysate-based cell culture medium and thus provides significant support for therapeutic monoclonal antibody production.

Journal: Journal of pharmaceutical and biomedical analysis (2022)
Publication types: Journal Article
Role of Circulating Tumor DNA Profiling in Patients with Non-Small Cell Lung Cancer Treated with EGFR Inhibitor.

S during targeted therapy, tumor heterogeneity can drive the evolution of multiple tumor subclones harboring unique resistance mechanisms.Sequential profiling of plasma cell-free dna (cf dna) provides a noninvasive method for early detection of patient progression.We investigated whether the genetic dynamics detected in cf dna during treatment can act as a predictive or prognostic marker of outcome.Methods patients with advanced egfr-mutated non-small cell lung cancer (nsclc) were included for consecutive blood sampling during egfr-tyrosine kinase inhibitor (tki) treatment.Blood samples were serially collected from patients at baseline, first follow-up, and progression.Extracted cf dna was analyzed with next-generation sequencing.Results serial plasma samples (n = 187) from 63 patients were analyzed, and 44 patients showed circulating tumor dna (ct dna).Egfr mutations were detected in 36 of the 44 patients at baseline (81.8%).Egfr mutations were no longer detected in 19 of 36 shedders (52.8%) at 2 months after egfr-tki treatment and rebounded with resistant egfr mutations (t790m or c797s) at progression.Other driver mutations such as kras g12d and braf v600e were found at baseline regardless of tissue egfr status, suggesting tumor heterogeneity.Detection of ct dna (shedder) at baseline associated with poor overall survival (p = 0.04) compared to nonshedder.Furthermore, in patients showing egfr mutations in plasma at baseline, the clearing rate of those during the first 8 weeks of treatment served as a positive predictor for clinical outcome.Conclusion longitudinal liquid biopsies capture spatial and temporal heterogeneity underlining resistance to egfr-tkis in nsclc.Thus, ct dna monitoring during egfr-tki treatment is useful for detecting resistance mutations or predicting response.Dense serial monitoring using blood enables early prediction of treatment failure and provides a window of opportunity for well-timed intervention.

Journal: Oncology (2022)
Publication types: Journal Article