syedzayyan/paper_mill_benchmark huggingface dataset:
Graph-Theoretic Molecular Fragmentation for Potential Surfaces Leads Naturally to a Tensor Network Form and Allows Accurate and Efficient Quantum Nuclear Dynamics.

Molecular fragmentation methods have revolutionized quantum chemistry.Here, we use a graph-theoretically generated molecular fragmentation method, to obtain accurate and efficient representations for multidimensional potential energy surfaces and the quantum time-evolution operator, which plays a critical role in quantum chemical dynamics.In doing so, we find that the graph-theoretic fragmentation approach naturally reduces the potential portion of the time-evolution operator into a tensor network that contains a stream of coupled lower-dimensional propagation steps to potentially achieve quantum dynamics with reduced complexity.Furthermore, the fragmentation approach used here has previously been shown to allow accurate and efficient computation of post-hartree-fock electronic potential energy surfaces, which in many cases has been shown to be at density functional theory cost.Thus, by combining the advantages of molecular fragmentation with the tensor network formalism, the approach yields an on-the-fly quantum dynamics scheme where both the electronic potential calculation and nuclear propagation portion are enormously simplified through a single stroke.The method is demonstrated by computing approximations to the propagator and to potential surfaces for a set of coupled nuclear dimensions within a protonated water wire problem exhibiting the grotthuss mechanism of proton transport.In all cases, our approach has been shown to reduce the complexity of representing the quantum propagator, and by extension action of the propagator on an initial wavepacket, by several orders, with minimal loss in accuracy.

Journal: Journal of chemical theory and computation (2022)
Publication types: Journal Article
Enhanced Electrochemical Capacity of Spherical Co-Free Li1.2Mn0.6Ni0.2O2Particles after a Water and Acid Treatment and its Influence on the Initial Gas Evolution Behavior.

Li-rich layered oxides (lrlo) with specific energies beyond 900 wh kg-1are one promising class of high-energy cathode materials.Their high mn-content allows reducing both costs and the environmental footprint.In this work, co-free li1.2mn0.6ni0.2o2was investigated.A simple water and acid treatment step followed by a thermal treatment was applied to the lrlo to reduce surface impurities and to establish an artificial cathode electrolyte interface.Samples treated at 300 °c show an improved cycling behavior with specific first cycle capacities of up to 272 m ah g-1, whereas powders treated at 900 °c were electrochemically deactivated due to major structural changes of the active compounds.Surface sensitive analytical methods were used to characterize the structural and chemical changes compared to the bulk material.Online dems measurements were conducted to get a deeper understanding of the effect of the treatment strategy on o2and co2evolution during electrochemical cycling.

Journal: ChemSusChem (2022)
Publication types: Journal Article
Aptamer-functionalized 2D photonic crystal hydrogels for detection of adenosine.

Aptamer-functionalized two-dimensional photonic crystal (2dpc) hydrogels are reported for the detection of adenosine (ad).As a molecular recognition group, an ad-binding aptamer was covalently attached to 2dpc hydrogels.This aptamer selectively and sensitively binds ad, changing the conformation of the aptamer from a long single-stranded structure (ad-free conformation) to a short hairpin loop structure (ad-bound conformation).The ad-binding-induced changes of aptamer conformation reduced the volume of the 2dpc hydrogels and decreased the interparticle spacing of the 2dpc embedded in the hydrogel network.The particle spacing changes being dependent on ad concentration were determined by measuring 2dpc light diffraction using a simple laser pointer.The 2dpc hydrogel sensor showed a large particle spacing decrease of ~ 110 nm in response to 1 m m ad in phosphate-buffered saline (pbs).The linear range of determination of ad was 0.1 n m to 1 m m and the limit of detection was 0.09 n m.The hydrogel sensor response for real samples was then validated in diluted fetal bovine serum (fbs) and human urine.The average % difference in particle spacing changes measured between diluted fbs and pure pbs was only 3.99%.In diluted human urine, the recoveries for the detection of ad were 95-101% and the relative standard deviations were 4.9-7.8%.The results demonstrate the potential applicability of the hydrogel sensor for real samples.This sensing concept, using the aptamer-functionalized 2dpc hydrogels, allows for a simple, sensitive, selective, and reversible detection of ad.It may enable sensor development for a wide variety of analytes by simply changing the aptamer recognition group.

Journal: Mikrochimica acta (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Oxidative stress state inhibits exosome secretion of hPDLCs through a specific mechanism mediated by PRMT1.

And objectives periodontitis, the most common chronic inflammation characterized by persistent alveolar bone resorption in the periodontitis, affects almost half of the adult population worldwide.Oxidative stress is one of the pathophysiological mechanisms underlying periodontitis, which affects the occurrence and development of periodontitis.Exosomes are increasingly recognized as vehicles of intercellular communication and are closely related to periodontitis.However, the effects of oxidative stress on exosome secretion and the specific mechanisms remain elusive in human periodontal ligament cells (h pdlcs).The relationship between exosome secretion and the osteogenic differentiation of h pdlcs also needs to be investigated.Methods isolated pdlscs were identified using flow cytometry.Osteogenesis was measured using alizarin red staining and alp staining.Expression of exosomal markers and prmt1 was analyzed using western blot.Immunofluorescence was used to measure exosome uptake and the expression of eea1.Results the secretion capacity of exosomes was markedly suppressed under oxidative stress.Protein arginine methyltransferase 1 (prmt1) has been strongly associated with both oxidative stress and inflammation, and prmt1 was significantly upregulated under oxidative stress conditions.Lentivirus-mediated overexpression of prmt1 caused a significant reduction in the secretion of exosomes, but multivesicular bodies (mvbs) containing a large number of intraluminal vesicles (ilvs) were increased.Rab11a and rab27a expression, which mediate mvbs fusion with cell membranes, decreased, although this phenomenon was restored after knocking down prmt1 expression under oxidative stress.Conclusions these results indicated that prmt1 mediated a decrease in exosome secretion of h pdlcs.The decrease in rab11a and rab27a leads to a large accumulation of mvbs in cells and is one of the main reasons for impaired exosome secretion.The decrease in osteogenic differentiation of h pdlcs caused by h2o2may originate in part from the inhibition of exosome secretion.

Journal: Journal of periodontal research (2022)
Publication types: Journal Article
Interpenetrating interfaces for efficient perovskite solar cells with high operational stability and mechanical robustness.

The perovskite solar cell has emerged rapidly in the field of photovoltaics as it combines the merits of low cost, high efficiency, and excellent mechanical flexibility for versatile applications.However, there are significant concerns regarding its operational stability and mechanical robustness.Most of the previously reported approaches to address these concerns entail separate engineering of perovskite and charge-transporting layers.Herein we present a holistic design of perovskite and charge-transporting layers by synthesizing an interpenetrating perovskite/electron-transporting-layer interface.This interface is reaction-formed between a tin dioxide layer containing excess organic halide and a perovskite layer containing excess lead halide.Perovskite solar cells with such interfaces deliver efficiencies up to 22.2% and 20.1% for rigid and flexible versions, respectively.Long-term (1000 h) operational stability is demonstrated and the flexible devices show high endurance against mechanical-bending (2500 cycles) fatigue.Mechanistic insights into the relationship between the interpenetrating interface structure and performance enhancement are provided based on comprehensive, advanced, microscopic characterizations.This study highlights interface integrity as an important factor for designing efficient, operationally-stable, and mechanically-robust solar cells.

Journal: Nature communications (2021)
Publication types: Journal Article
Morphological and functional characteristics of mitral annular calcification and their relationship to stroke.

Mitral annular calcification (mac) is associated with risk of stroke.This study aimed to define the morphological and functional characteristics of mac that are related to stroke.Methods a total of 460 subjects with mac from transthoracic echocardiography in a single center from 2012 to 2016 was retrospectively reviewed.Subjects were classified into two groups according to history of stroke [group 1 (n = 366): without stroke; group 2 (n = 94): with stroke].Morphological and functional features of mac on echocardiogram were scored from 0 to 3 according to mac mobility, presence of echodense mass with central echolucencies in the periannular region suggesting caseous necrosis, and functional stenosis.Results significantly more patients in group 2 were men and had history of diabetes mellitus, dyslipidemia, atrial fibrillation, or infective endocarditis.Although mac thickness and extent did not differ between the two groups, group 2 showed a considerably higher mac score than group 1 (0.50 ± 0.77 vs.0.23 ±0.52 p<0.001) as a result of the higher prevalence of each component in group 2 [mobility (22 vs.11%, p = 0.003), echodense mass with central areas of echolucencies suggesting caseous necrosis (23 vs.7%, p<0.001), and functional mitral stenosis (12 vs.7%, p = 0.042)].On logistic regression analysis, mac score was independently associated with stroke and showed significant incremental value to demographic factors and comorbidities in association with stroke in a consecutive manner.Conclusions in conclusion, morphological and functional characteristics of mac had incremental value in association with stroke over traditional risk factors.Mac score consisting of mac mobility, typical echodense mass with central echolucencies suggesting caseous necrosis, and functional mitral stenosis was independently associated with stroke.Mac with high-risk features may act as a source of stroke or more potent composite surrogate markers for stroke-related risk factors.

Journal: PloS one (2020)
Publication types: Journal Article
Intraoperative Sentinel Lymph Node Imprint Cytology Diagnosis in Breast Cancer Patients by General Surgical Pathologists: A Single-Institution Experience of 4327 Cases.

Context sentinel lymph node (sln) biopsy is the standard of care for breast cancer (bc) patient staging.The axillary node status can be evaluated by frozen section (fs) or imprint cytology (ic).Despite the major disadvantages of tissue loss and freezing artifact in fs, many pathologists consider sln ic a more difficult task requiring special expertise and prefer fs to ic.Aims to conduct a large cohort study to evaluate the results of intraoperative sln ic, compare them with those of fs and permanent section (ps), and determine the best method for general pathologists.Settings and design a very large cohort study with many pathologists engaged was designed and the diagnostic results were compared.Materials and methods with 12 pathologists engaged, we conducted the largest patient cohort study of sln ic to date, including 4,327 consecutive bc patients undergoing sln biopsy during the past 15 years.The touch imprints were stained using three different methods and evaluated.The ps was used as the gold standard for evaluation.Statistical analysis the false positivity, false negativity, accuracy, sensitivity, and specificity of the ic and fs for each pathologist were evaluated and compared.Results our results showed an overall sensitivity of 82.7%, specificity of 99.3%, and an accuracy rate of 95.9% for sln ic, which were comparable to those of fs.The accuracy rate did not correlate with the length of working experience and the staining method.Conclusions intraoperative hematoxylin and eosin (h&e)-stained ic preparation was found to be the best sln examination method for general pathologists.

Journal: Journal of cytology (2022)
Publication types: Journal Article
Aspergillus fumigatus induction of IL-33 expression in chronic rhinosinusitis is PAR2-dependent.

In the pathophysiology of chronic rhinosinusitis with nasal polyps (crsw np), aspergillus fumigatus (a.Fumigatus) can upregulate il-33 from human sinonasal epithelial cells (snecs), which then activates innate lymphoid cells causing release of il-13, an important driver of allergic inflammation.However, the mechanism by which a.Fumigatus mediates the induction of il-33 expression remains to be elucidated.The objectives of this study were to determine the specific fungal component(s) and the receptor responsible for mediating the a.Fumigatus induced increase in il-33 expression in snecs from patients with crsw np.Methods snecs from crsw np patients were cultured and stimulated with various fungal components in the absence or presence of 4-(2-aminoethyl)benzenesulfonyl fluoride hydrochloride, an irreversible serine protease inhibitor, or gb83, a reversible protease activated receptor 2 (par2) inhibitor.Il-33 expression was evaluated using quantitative real-time polymerase chain reaction (q rt-pcr).Par2 expression was examined in inflamed mucosa from nonatopic control and crsw np patients.Results elevation of il-33 expression in primary snecs was found in response to fungal protease but not fungal cell wall components.Par2 expression was elevated in inflamed mucosa from crsw np patients in comparison to controls.The a.Fumigatus fungal protease-mediated elevation in il-33 expression by human snecs was serine protease- and par2-dependent.Conclusion these data suggest that serine protease activity of a.Fumigatus is capable of inducing il-33 expression in crsw np snecs via par2, a potential therapeutic target in the treatment of crsw np.Level of evidence na laryngoscope, 129:2230-2235, 2019.

Journal: The Laryngoscope (2019)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Prioritising national dementia guidelines for general practice: A Delphi approach.

S australian guidelines for dementia cover 109 recommendations for dementia care.Knowing which recommendations to implement poses a challenge for general practitioners (gps).This study aimed to gather general practice perspectives of priority recommendations for gps in their practice.Methods to explore which recommendations are most important and those requiring the greatest support in gp implementation, a delphi study was conducted.Thirty-six gps, 4 practice nurses and 1 medical services director completed two rounds of email questionnaires.Results recommendations requiring support for gp implementation relate to early assessment of behavioural and psychological symptoms; mental health interventions tailored to the person's preferences and abilities; language and cultural barriers in access to information and services; and cognitive and learning needs in treatment delivery.Conclusions it is critical to understand where support may be needed for gps to successfully implement recommendations to improve care provided to people with dementia and their carers.

Journal: Australasian journal on ageing (2022)
Publication types: Journal Article
Elucidating Carbohydrate-Protein Interactions Using Nanoparticle-Based Approaches.

Carbohydrates are present on every living cell and coordinate important processes such as self/non-self discrimination.They are amongst the first molecular determinants to be encountered when cellular interactions are initiated.In particular, they resemble essential molecular fingerprints such as pathogen-, danger-, and self-associated molecular patterns guiding key decision-making in cellular immunology.Therefore, a deeper understanding of how cellular receptors of the immune system recognize incoming particles, based on their carbohydrate signature and how this information is translated into a biological response, will enable us to surgically manipulate them and holds promise for novel therapies.One approach to elucidate these early recognition events of carbohydrate interactions at cellular surfaces is the use of nanoparticles coated with defined carbohydrate structures.These particles are captured by carbohydrate receptors and initiate a cellular cytokine response.In the case of endocytic receptors, the capturing enables the engulfment of exogenous particles.Thereafter, the particles are sorted and degraded during their passage in the endolysosomal pathway.Overall, these processes are dependent on the nature of the endocytic carbohydrate receptors and consequently reflect upon the carbohydrate patterns on the exogenous particle surface.This interplay is still an under-studied subject.In this review, we summarize the application of nanoparticles as a promising tool to monitor complex carbohydrate-protein interactions in a cellular context and their application in areas of biomedicine.

Journal: Frontiers in chemistry (2021)
Publication types: Journal Article;Review
The effect of Vitamin-K1and Colchicine on Vascular Calcification Activity in subjects with Diabetes Mellitus (ViKCoVaC): A double-blind 2x2 factorial randomized controlled trial.

There is currently no treatment for attenuating progression of arterial calcification.18f-sodium fluoride positron emission tomography (18f-na f pet) locates regions of calcification activity.We tested whether vitamin-k1or colchicine affected arterial calcification activity.Methods 154 patients with diabetes mellitus and coronary calcification, as detected using computed tomography (ct), were randomized to one of four treatment groups (placebo/placebo, vitamin-k1[10 mg/day]/placebo, colchicine [0.5 mg/day]/placebo, vitamin-k1[10 mg/day]/ colchicine [0.5 mg/day]) in a double-blind, placebo-controlled 2x2 factorial trial of three months duration.Change in coronary calcification activity was estimated as a change in coronary maximum tissue-to-background ratio (tbrmax) on18f-na f pet.Results 149 subjects completed follow-up (vitamin-k1: placebo = 73:76 and colchicine: placebo = 73:76).Neither vitamin-k1nor colchicine had a statistically significant effect on the coronary tbrmax compared with placebo (mean difference for treatment groups 0·00 ± 0·16 and 0·01 ± 0·17, respectively, p > 0.05).There were no serious adverse effects reported with colchicine or vitamin-k1.Conclusions in patients with type 2 diabetes, neither vitamin-k1nor colchicine significantly decreases coronary calcification activity, as estimated by18f-na f pet, over a period of 3 months.Clinical trial registration actrn12616000024448.

Journal: Journal of nuclear cardiology : official publication of the American Society of Nuclear Cardiology (2022)
Publication types: Journal Article;Randomized Controlled Trial;Research Support, Non-U.S. Gov't
Prevalence of sleep-disordered breathing in opioid users with chronic pain: a systematic review and meta-analysis.

Study objectives opioids have been reported to increase the risk for sleep-disordered breathing (sdb) in patients with noncancer chronic pain on opioid therapy.This study aims to determine the pooled prevalence of sdb in opioid users with chronic pain and compare it with patients with pain:no opioids and no pain:no opioids.Methods a literature search of pub med, medline, embase, and cochrane central register of controlled trials was conducted.We included all observational studies that reported the prevalence of sdb in patients with chronic pain on long-term opioid therapy (≥3 months).The primary outcome was the pooled prevalence of sdb in opioid users with chronic pain (pain:opioids group) and a comparison with pain:no opioids and no pain:no opioids groups.The meta-analysis was performed using a random-effects model.Results after screening 1,404 studies, 9 studies with 3,791 patients were included in the meta-analysis (pain:opioids group, n = 3181 [84%]; pain:no opioids group, n = 359 [9.4%]; no pain:no opioids group, n = 251 [6.6%]).The pooled prevalence of sdb in the pain:opioids, pain:no opioids, and no pain:no opioids groups were 91%, 83%, and 72% in sleep clinics and 63%, 10%, and 75% in pain clinics, respectively.Furthermore, in the pain: opioids group, central sleep apnea prevalence in sleep and pain clinics was 33% and 20%, respectively.Conclusions the pooled prevalence of sdb in patients with chronic pain on opioid therapy is not significantly different compared with pain:no opioids and no pain:no opioids groups and varies considerably depending on the site of patient recruitment (ie, sleep vs pain clinics).The prevalence of central sleep apnea is high in sleep and pain clinics in the pain:opioids group.Clinical trial registration: registry: prospero: international prospective register of systematic reviews; name: prevalence of sleep disordered breathing, hypoxemia and hypercapnia in patients on oral opioid therapy for chronic pain management; url: identifier: crd42018103298.

Journal: Journal of clinical sleep medicine : JCSM : official publication of the American Academy of Sleep Medicine (2020)
Publication types: Journal Article;Meta-Analysis;Research Support, Non-U.S. Gov't;Systematic Review
Normal weight obesity is associated with hypercholesterolemia and low muscle mass in persons living with HIV on antiretroviral treatment.

S normal weight obesity (nwo) is defined as a condition of normal body weight, but with high body fat percentage.Clinical and immunologic implications of nwo in persons living with hiv (plhiv) remain unknown.The aim of this study was to examine nwo prevalence and its associations with metabolic and immunologic measurements in a cohort of plhiv on antiretroviral treatment (art).Methods we enrolled 73 adult plhiv on art.Body composition was assessed by dual-energy x-ray absorptiometry.Nwo was defined as body mass index 18.5 to 24.9 kg/m2and body fat ≥25%.We determined triacylglycerols, total cholesterol, high-density lipoprotein, low-density lipoprotein, blood glucose, blood pressure, bone mineral density, inflammatory cytokines (interleukin [il]-1β, tumor necrosis factor-α and il-6) and cd4+ and cd8+ t-cell activation.Results the prevalence of nwo was 49% (36 of 73).Participants with nwo showed lower cd4+ t-cell percentage (25 versus 27%, p = 0.03), lower cd4/cd8 ratio (0.62 versus 0.82, p = 0.02), lower muscle mass (6.84 versus 7.11 kg/m2, p = 0.01) and higher prevalence of hypercholesterolemia (26% versus 6%, p = 0.03) than individuals with normal body composition.No differences in inflammation/activation markers were observed between groups (p > 0.05 in all cases).Conclusion nwo was frequent in a cohort of mexican plhiv on art and was associated with lower muscle mass, hypercholesterolemia, lower cd4+ t-cell percentage, and lower cd4/cd8 ratio.The incorporation of body fat measurements in the regular physical examination of plhiv could contribute to early identification of the nwo condition and lead to better management of possible long-term morbidity.

Journal: Nutrition (Burbank, Los Angeles County, Calif.) (2022)
Publication types: Journal Article