syedzayyan/paper_mill_benchmark huggingface dataset:
A Multifunctional Light-Driven Swimming Soft Robot for Various Application Scenarios.

The locomotor behavior of creatures in nature can bring a lot of inspiration for the fabrication of soft actuators.In this paper, we fabricated a bionic light-driven swimming soft robot that can perform grasping of tiny objects and achieve the task of object transfer.By adding carbon nanotubes (cnts), the temperature-sensitive hydrogels can be endowed with light-responsive properties.The fabricated composite hydrogel structure can control the contraction and expansion of volume by light, which is similar to the contraction and diastole behavior of muscles.The oscillation of the fish tail and the grasping action of the normally closed micromanipulator can be achieved by the control of the irradiation of the xenon light source.The bending of the bionic arm can be controlled by the irradiation of a near-infrared (nir) laser, which transforms the spatial position and posture of the micromanipulator.The proposed scheme is feasible for miniaturized fabrication and application of flexible actuators.This work provides some important insights for the study of light-driven microrobots and light-driven flexible actuators.

Journal: International journal of molecular sciences (2022)
Publication types: Journal Article
Investigating Protective Factors Associated With Mental Health Outcomes in Sexual Minority Youth.

The aim of this study is to identify and evaluate the efficacy of adolescent protective factors against mental health (mh) outcomes in young adulthood of sexual minority identifying youth (smy).Methods using data from the national longitudinal study of adolescent to adult health, we identified potential protective factors (e.g., individual factors like self-esteem, family factors like family communication, and community factors like caring teachers) at baseline (1994) when the sample was school-aged for smy.Smy included those who identified their sexual identity as mostly heterosexual, bisexual, mostly homosexual, or 100% homosexual.Mh outcomes (depression, anxiety, or suicidality) were assessed at 14-year follow-up.Results approximately 14,800 youth completed baseline and follow-up surveys, where 13.5% identified as smy.Of smy, 57% had a mh outcome compared to 37% of non-smy (p < .05).Not all factors were protective for smy.At the individual level, emotional well-being (adjusted odds ratio [aor] .56, 95% confidence interval [ci] .41-.78) and self-esteem (aor .79, 95% ci .66-.95) were found to be protective for mh outcomes in regression models.At the family level, family connectedness (aor .82, 95% ci .71-.95) was found to be protective.At the community level, school connectedness (aor .78, 95% ci .66-.92) and caring teachers (aor .76, 95% ci .58-.99) were found to be protective for smy.Conclusion factors at the individual, family, and community (e.g., caring teachers) levels appear to be protective against mh outcomes unique to smy.Developing interventions focused on protective factors have potential to prevent health disparities.

Journal: The Journal of adolescent health : official publication of the Society for Adolescent Medicine (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Influence of Asp Isomerization on Trypsin and Trypsin-like Proteolysis.

Long-lived proteins (llps), although less common than their short-lived counterparts, are increasingly recognized to play important roles in age-related diseases such as alzheimer's.In particular, spontaneous chemical modifications can accrue over time that serve as both indicators of and contributors to disrupted autophagy.For example, isomerization in llps is common and occurs in the absence of protein turnover while simultaneously interfering with the protein turnover by impeding proteolysis.In addition to the biological implications this creates, isomerization may also interfere with its own analysis.To clarify, bottom-up proteomics experiments rely on protein digestion by proteases, most commonly trypsin, but the extent to which isomerization might interfere with trypsin digestion is unknown.Here, we use a combination of liquid chromatography and mass spectrometry to examine the effect of isomerization on proteolysis by trypsin and chymotrypsin.Isomerized aspartic acid and serine residues (which represent the most common sites of isomerization in llps) were placed at various locations relative to the preferred protease cleavage point to evaluate the influence on digestion efficiency.Trypsin was found to be relatively tolerant of isomerization, except when present at the residue immediately c-terminal to arg/lys.For chymotrypsin, the influence of isomerization on digestion was less predictable, resulting in long-range interference for some isomer/peptide combinations.Given the trypsin- and chymotrypsin-like behaviors of the 20s proteasome, and to further establish the biological relevance of isomerization in llps, substrates with isomerized sites were also tested against proteasomal degradation.Significant disruption of 20s proteolysis was observed, suggesting that if llps persist long enough to isomerize, it will be difficult for the cells to digest them.

Journal: Analytical chemistry (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Research Support, N.I.H., Extramural
Low-carbohydrate diets and type 2 diabetes treatment: a meta-analysis of randomized controlled trials.

To assess whether lc diets are associated with long-term improvement in glycemic control and weight loss in people with t2dm, and their cardiovascular and renal safety.Methods meta-analysis of randomized controlled trials lasting more than 3 months, retrieved through extensive search on pub med, embase, clinical trial.gov, cochrane databases up to march 1st, comparing lc diets and balanced carbohydrate diets in people with t2dm.Results we retrieved 37 trials, including 3301 patients.Average carbohydrate intake in lc diets was 36% of total energy.Lc diets were associated with significant reduction of hb a1c at 3 months (md - 0.17%, 95% ci - 0.27, - 0.07), no difference at 6 and 12 months, and significant increase at 24 months (md 0.23%, 95% ci md 0.02, 0.44).Vlc diets were associated with significant hb a1c reduction at 3 and 6 months (md - 0.43% - 0.60, - 0.26%, and md - 0.40% 95% ci - 0.59, - 0.22, respectively), but not at 12 and 24 months.Lc diets were associated with significant bmi reduction at 6 months (- 1.35 kg/m295% ci, - 2.18, - 0.52), but not at other time points.Only a minority of trials reported data on renal function, so renal safety could not be assessed.No significant differences in body weight, lipid profile, or blood pressure were found in the long term.Conclusion lc diets may produce small short-term improvements in hb a1c and weight, which are not maintained in the long term.Data on their renal safety are insufficient.

Journal: Acta diabetologica (2020)
Publication types: Journal Article;Meta-Analysis
Comparative transcriptome analysis reveals significant differences in gene expression between pathogens of apple Glomerella leaf spot and apple bitter rot.

Apple glomerella leaf spot (gls) and apple bitter rot (abr) are two devastating foliar and fruit diseases on apples.The different symptoms of gls and abr could be related to different transcriptome patterns.Thus, the objectives of this study were to compare the transcriptome profiles of colletotrichum gloeosporioides species complex isolates gc20190701, fl180903, and fl180906, the pathogen of gls and abr, and to evaluate the involvement of the genes on pathogenicity.Results a relatively large difference was discovered between the gls-isolate gc20190701 and abr-isolates fl180903, fl180906, and quite many differential expression genes associated with pathogenicity were revealed.The degs between the gls- and abr-isolate were significantly enriched in go terms of secondary metabolites, however, the categories of degradation of various cell wall components did not.Many genes associated with secondary metabolism were revealed.A total of 17 cytochrome p450s (cyp), 11 of which were up-regulated while six were down-regulated, and five up-regulated methyltransferase genes were discovered.The genes associated with the secretion of extracellular enzymes and melanin accumulation were up-regulated.Four genes associated with the degradation of the host cell wall, three genes involved in the degradation of cellulose, and one gene involved in the degradation of xylan were revealed and all up-regulated.In addition, genes involved in melanin syntheses, such as tyrosinase and glucosyltransferase, were highly up-regulated.Conclusions the penetration ability, pathogenicity of gls-isolate was greater than that of abr-isolate, which might indicate that gls-isolate originated from abr-isolates by mutation.These results contributed to highlighting the importance to investigate such degs between gls- and abr-isolate in depth.

Journal: BMC genomics (2022)
Publication types: Journal Article
Detecting the Deformation Behavior of Bimodal Ti-6Al-4V Using a Digital Image Correlation Technique.

The evolution of a local strain of the ti-6al-4v alloy subjected to tensile loading was investigated in situ by using the digital image correlation technique.The results show that some local strain concentration areas have already appeared in the elastic deformation stage, which then connected and became concentrated in the gauge region when the specimen yielded.The strain compatibility of grains in the macroscopic region is kept constant.The deformation process is further divided into six parts based on the development of the maximum strain gradient, and the strain compatibility of each stage of the alloy is summarized and analyzed.The quasi-in situ experiment reveals that the primaryα(αp) grains undertake the main deformation at the micro-scale.

Journal: Materials (Basel, Switzerland) (2022)
Publication types: Journal Article
Geoarchaeological evidence of the AD 1642 Yellow River flood that destroyed Kaifeng, a former capital of dynastic China.

Rising global temperatures will increase the number of extreme weather events, creating new challenges for cities around the world.Archaeological research on the destruction and subsequent reoccupation of ancient cities has the potential to reveal geological and social dynamics that have historically contributed to making urban settings resilient to these extreme weather events.Using a combination of archaeological and geological methods, we examine how extreme flood events at kaifeng, a former capital of dynastic china, have shaped the city's urban resilience.Specifically, we focus on an extreme yellow river flood event in ad 1642 that historical records suggest killed around 300,000 people living in kaifeng.Our recent archaeological excavations have discovered compelling geological and archaeological evidence that corroborates these documents, revealing that the ad 1642 yellow river flood destroyed kaifeng's inner city, entombing the city and its inhabitants within meters of silt and clay.We argue that the ad 1642 flood was extraordinarily catastrophic because kaifeng's city walls only partly collapsed, entrapping most of the flood waters within the city.Both the geology of the yellow river floods as well as the socio-political context of kaifeng shaped the city's resilience to extreme flood events.

Journal: Scientific reports (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Alterations of the Gut Microbiota in Patients With Severe Chronic Heart Failure.

Chronic heart failure (chf) is the final outcome of almost all forms of cardiovascular diseases, remaining the main cause of mortality worldwide.Accumulating evidence is focused on the roles of gut microbial community in cardiovascular disease, but few studies have unveiled the alterations and further directions of gut microbiota in severe chf patients.Aimed to investigate this deficiency, fecal samples from 29 chf patients diagnosed with nyha class iii-iv and 30 healthy controls were collected and then analyzed using bacterial 16s r rna gene sequencing.As a result, there were many significant differences between the two groups.Firstly, the phylum firmicuteswas found to be remarkably decreased in severe chf patients, and the phylum proteobacteriawas the second most abundant phyla in severe chf patients instead of phylum bacteroidesstrangely.Secondly, the α diversity indices such as chao1, pd-whole-tree and shannon indices were significantly decreased in the severe chf versus the control group, as well as the notable difference in β-diversity between the two groups.Thirdly, our result revealed a remarkable decrease in the abundance of the short-chain fatty acids (scfa)-producing bacteria including genera ruminococcaceae ucg-004,ruminococcaceae ucg-002,lachnospiraceae fcs020 group,dialisterand the increased abundance of the genera in enterococcusand enterococcaceaewith an increased production of lactic acid.Finally, the alternation of the gut microbiota was presumably associated with the function including cell cycle control, cell division, chromosome partitioning, amino acid transport and metabolism and carbohydrate transport and metabolism through scfa pathway.Our findings provide the direction and theoretical knowledge for the regulation of gut flora in the treatment of severe chf.

Journal: Frontiers in microbiology (2021)
Publication types: Journal Article
An innovative extraction strategy for herbal medicine by adopting p-sulphonatocalix[6]/[8]arenes.

Introduction alkaloids exist in various herbal medicine widely and exhibit diverse biological and pharmacological activities.P-sulphonatocalix[6]arenes (sc6a) and p-sulphonatocalix[8]arenes (sc8a) are water-soluble supramolecular macrocycles and are applied to the extraction of alkaloids from herbal products.Objective in this study, an innovative method of sc6a/sc8a assisted extraction of the alkaloids from herbs was established.Methods sc6a and sc8a were designed to extract 27 alkaloids from seven herbal medicines.Based on the significant solubilisation and extraction effect, stephaniae tetrandrae radix (fangji, fj) was selected to obtain the optimal extraction process by adopting single factor test and orthogonal experiment.Then, the alkaloids and sc6a/sc8a were separated by one-step alkalisation and scn a were reused.The host-guest complexes between alkaloids and scn a were determined by competitive fluorescence titration, differential scanning calorimetry (dsc), fourier-transform infrared (ftir) and proton nuclear magnetic resonance (1h-nmr) analysis.Results the optimum condition for sc6a assisted extraction was 5:1:80 (g/g/m l) for herbs/sc6a/solution ratio, 355-250 μm particle size and ultrasonicate 0.5 h, whilst 10:1:40 (g/g/m l) for herbs/sc8a/solution ratio, 355-250 μm particle size and ultrasonicate 0.5 h for sc8a assisted extraction.The total yield of alkaloids (fangchinoline and tetrandrine) from fj was increased by 4.87 times and 5.97 times with sc6a and sc8a.Moreover, a good reusability of sc6a/sc8a was achieved by alkalisation dissociation.Host-guest complexes were determined by competitive fluorescence titration at a molar ratio of 1:1 between most alkaloids (25/27, except evodiamine and rutaecarpine) and sc6a/sc8a.The complex structure was proved by dsc, ftir and1h-nmr analysis.Conclusion the study provided an effective eco-friendly and energy-saving extraction method of alkaloids from herbal medicine.

Journal: Phytochemical analysis : PCA (2022)
Publication types: Journal Article
Seasonal variation of 25-Hydroxyvitamin D and indices of carbohydrate and lipid metabolism in postmenopausal women.

Some studies indicate vitamin d's significant contribution to metabolic processess.Therefore, the purpose of this study was to evaluate the level of carbohydrate and lipid metabolism indices in relation to seasonal changes in 25-hydroxyvitamin d (25(oh)d) concentration in postmenopausal women.Methods sixteen postmenopausal women meeting health criteria and not using vitamin d supplementation were included in the study.Seasonal variation of somatic features and the serum concentration of 25(oh)d, glucose, insulin, parathormon, sclerostin and lipid profile were determined on two terms (autumn-winter).Results comparative analysis of the variables between the study terms revealed a marked decrease in the concentration of 25(oh)d (p≤ 0.0001), insulin (p< 0.05), insulin resistance index (homa-ir), (p< 0.05).The significant positive correlations of changes (δ) between autumn and winter in 25(oh)d with body mass (p< 0.05), and fat mass (p≤ 0.01), measured in the first study term, in the group of women with normal body mass index (bmi), and negative correlation with fat mass (p< 0.05) in women with a bmi value above the reference values, were found.The relationship analysis showed that in women with normal bmi, the decrease in 25(oh)d concentrations was greater when the body fat percentage was higher, whereas in women with a bmi value above the reference values, the higher the fat percentage, the smaller was the decrease in 25(oh)d concentration.Conclusions seasonal changes in 25(oh)d concentration did not significantly affect the concentration of carbohydrate and lipid metabolism indices.The magnitude of decline in 25(oh)d levels depends on the fat mass.We suppose that environmental or lifestyle-related factors, e.g., nutritional behaviours, may have had more influence on metabolic indices than changes in 25(oh)d.

Journal: PeerJ (2021)
Publication types: Journal Article
Impact of COVID-19 on hip fracture care in Ireland: findings from the Irish Hip Fracture Database.

To describe the impact of covid-19 on hip fracture care during the first 6 months of the pandemic.Methods a secondary analysis of 4385 cases in the irish hip fracture database from 1st june 2019 to 31st august 2020 was conducted.Results hip fracture admissions decreased by 15% during the study period (p < 0.001).Patient characteristics were largely unchanged as the majority of cases occurred in females over 80 years admitted from home.Adherence to many of the irish hip fracture standards (ihfs) changed following the covid-19 pandemic.There was an increase in patients admitted to an orthopaedic ward from emergency department (ed) within 4 h from 27 to 36% (p < 0.001).However, the proportion of patients reviewed by a geriatrician reduced from 85% pre-covid to 80% (p < 0.001).Fewer patients received a bone health assessment [90% from 95% (p < 0.001)] and specialist falls assessment [(82% from 88% (p < 0.001)].No change was seen in time to surgery or incidence of pressure injuries.There was a significant decrease in length of stay from 18 to 14 days (p < 0.001).There was an increase in patients discharged home during the covid-19 period and a decrease in patients discharged to rehabilitation, convalescence or nursing home care.There was no statistically significant change in mortality.Conclusion healthcare services were widely restructured during the pandemic, which had implications for hip fracture patients.There was a notable change in compliance with the ihfs.Multidisciplinary teams involved in hip fracture care should be preserved throughout any subsequent waves of the pandemic.

Journal: European geriatric medicine (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Objective Supervised Machine Learning-Based Classification and Inference of Biological Neuronal Networks.

The classification of biological neuron types and networks poses challenges to the full understanding of the human brain's organisation and functioning.In this paper, we develop a novel objective classification model of biological neuronal morphology and electrical types and their networks, based on the attributes of neuronal communication using supervised machine learning solutions.This presents advantages compared to the existing approaches in neuroinformatics since the data related to mutual information or delay between neurons obtained from spike trains are more abundant than conventional morphological data.We constructed two open-access computational platforms of various neuronal circuits from the blue brain project realistic models, named neurpy and neurgen.Then, we investigated how we could perform network tomography with cortical neuronal circuits for the morphological, topological and electrical classification of neurons.We extracted the simulated data of 10,000 network topology combinations with five layers, 25 morphological type (m-type) cells, and 14 electrical type (e-type) cells.We applied the data to several different classifiers (including support vector machine (svm), decision trees, random forest, and artificial neural networks).We achieved accuracies of up to 70%, and the inference of biological network structures using network tomography reached up to 65% of accuracy.Objective classification of biological networks can be achieved with cascaded machine learning methods using neuron communication data.Svm methods seem to perform better amongst used techniques.Our research not only contributes to existing classification efforts but sets the road-map for future usage of brain-machine interfaces towards an in vivo objective classification of neurons as a sensing mechanism of the brain's structure.

Journal: Molecules (Basel, Switzerland) (2022)
Publication types: Journal Article
Treatment preferences for medication or surgery in patients with deep endometriosis and bowel involvement - a discrete choice experiment.

To study the preferences of women with deep endometriosis (de) with bowel involvement when they have to choose between conservative (medication) or surgical treatment.Design labelled discrete choice experiment (dce).Setting dutch academic and non-academic hospitals and online recruitment.Population or sample a total of 169 women diagnosed with de of the bowel.Methods baseline characteristics and the fear of surgery were collected.Women were asked to rank attributes and choose between hypothetical conservative or surgical treatment in different choice sets (scenarios).Each choice set offered different levels of all treatment attributes.Data were analysed by using multinomial logistic regression.Main outcome measures the following attributes - effect on/risk of pain, fatigue, pregnancy, endometriosis lesions, mood swings, osteoporosis, temporary stoma and permanent intestinal symptoms - were used in this dce.Results in the ranking, osteoporosis was ranked with low importance, whereas in the dce, a lower chance of osteoporosis was one of the most important drivers when choosing a conservative treatment.Women with previous surgery showed less fear of surgery compared with women without surgery.Low anterior resection syndrome was almost equally important for patients as the chance of pain reduction.Pain reduction had higher importance than improving fertility chances, even in women with desire for a future child.Conclusions the risk of developing low anterior resection syndrome as a result of treatment is almost equally important as the reduction of pain symptoms.Women with previous surgery experience less fear of surgery compared with women without a surgical history.Tweetable abstract first discrete choice experiment in patients with deep endometriosis.

Journal: BJOG : an international journal of obstetrics and gynaecology (2022)
Publication types: Journal Article