syedzayyan/paper_mill_benchmark huggingface dataset:
Improving the enzyme property of D-allulose 3-epimerase from a thermophilic organism of Halanaerobium congolense through rational design.

The rare sugar d-allulose is an attractive sucrose substitute due to its sweetness and ultra-low caloric value.It can be produced from d-fructose using d-allulose 3-epimerase (dae) as the biocatalyst.However, most of the reported daes show low catalytic efficiency and poor thermostability, which limited their further use in food industrial.Here, a putative d-allulose 3-epimerase from a thermophilic organism of halanaerobium congolense (hc dae) was characterized, showing optimal activity at p h 8.0 and 70 °c in the presence of mg2+.Saturation mutagenesis of y7, c66, and i108, the putative residues responsible for substrate recognition at the o-4, -5, and -6 atoms of d-fructose was performed, and it yielded the triple mutant y7h/c66l/i108a with improved activity toward d-fructose (345 % of wild-type enzyme).The combined mutant y7h/c66l/i108a/r156c/k260c exhibited a half-half (t1/2) of 5.2 h at 70 °c and an increase of the tmvalue by 6.5 °c due to the introduction of disulfide bridges between intersubunit with increased interface interactions.The results indicate that mutants could be used as industrial biocatalysts for d-allulose production.

Journal: Enzyme and microbial technology (2021)
Publication types: Journal Article
Defining minimum volume thresholds to increase quality of care: a new patient-oriented approach using mixed integer programming.

A positive relationship between treatment volume and outcome quality has been demonstrated in the literature and is thus evident for a variety of procedures.Consequently, policy makers have tried to translate this so-called volume-outcome relationship into minimum volume regulation (mvr) to increase the quality of care-yet with limited success.Until today, the effect of strict mvr application remains unclear as outcome quality gains cannot be estimated adequately and restrictions to application such as patient travel time and utilization of remaining hospital capacity are not considered sufficiently.Accordingly, when defining mvr, its effectiveness cannot be assessed.Thus, we developed a mixed integer programming model to define minimum volume thresholds balancing utility in terms of outcome quality gain and feasibility in terms of restricted patient travel time and utilization of hospital capacity.We applied our model to the german hospital sector and to four surgical procedures.Results showed that effective mvr needs a minimum volume threshold of 125 treatments for cholecystectomy, of 45 and 25 treatments for colon and rectum resection, respectively, of 32 treatments for radical prostatectomy and of 60 treatments for total knee arthroplasty.Depending on procedure type and incidence as well as the procedure's complication rate, outcome quality gain ranged between 287 (radical prostatectomy) and 977 (colon resection) avoidable complications (11.7% and 11.9% of all complications).Ultimately, policy makers can use our model to leverage mvr's intended benefit: concentrating treatment delivery to improve the quality of care.

Journal: The European journal of health economics : HEPAC : health economics in prevention and care (2022)
Publication types: Journal Article
Gestational Diabetes, Subsequent Type 2 Diabetes, and Food Security Status: National Health and Nutrition Examination Survey, 2007-2018.

Introduction despite many studies linking various risk factors to the association between gestational diabetes and subsequent type 2 diabetes, little is known about how food insecurity affects their association.We aimed to assess how the association between gestational diabetes and subsequent type 2 diabetes varies by food security status among women in the us.Methods this study is a secondary data analysis of 9,505 us women aged 20 years or older who had at least 1 live birth; we used cross-sectional data from the national health and nutrition examination survey (nhanes) from 2007 through 2018.The main outcome was a diagnosis of type 2 diabetes in the subsequent years after the first live birth.We used multivariable survey-weighted negative binomial regressions to examine whether the association between gestational diabetes and subsequent type 2 diabetes differed by food security status, with and without adjusting for health behavior factors.Results gestational diabetes was significantly associated with subsequent type 2 diabetes (incidence rate ratio [irr], 2.57; 95% ci, 2.45-2.69).The association between gestational diabetes and subsequent type 2 diabetes was significantly different by food security status (irr, 2.34; 95% ci, 2.23-2.45 among food-secure women; irr, 2.99; 95% ci, 2.70-3.28 among food-insecure women).Conclusion the association between gestational diabetes and subsequent type 2 diabetes differs significantly by food security status.Public health and health care practitioners should consider food security status when designing and implementing diabetes prevention interventions for women with a history of gestational diabetes.

Journal: Preventing chronic disease (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural
Nano-Bio Selenium Synthesized by Bacillus subtilis Modulates Broiler Performance, Intestinal Morphology and Microbiota, and Expression of Tight Junction's Proteins.

A green and ecofriendly bio-based synthesis of nano selenium particles was performed using the bacillus subtilis and the products were characterized by field emission scanning electron microscope (fesem), dynamic light scattering (dls) and transmission electron microscopy (tem) methods.Dietary treatments included a control diet nonsupplemented with selenium and control diet supplemented with different sources of selenium (sodium selenite, organic se, and nano-bio se), resulting in a total of 4 treatments with 6 replicates of 10 chicks.Broilers were assessed for performance measures, ileum morphometry, and microbial population and jejunum tight junction proteins' relative expression.The particle size of the synthesized selenium nanoparticles ranges 40 to 150 nm, with crystalline spherical shape.Inclusion of selenium increased body weight (bw) and improved fcr compared to the control diet (p < 0.05).Among the selenium sources, the highest bw were achieved in chicks fed sodium selenite or nano-bio se.Selenium supplementation meaningfully (p < - 0.01) changed ileum morphology and reduced ileum microbiota.Inclusion of selenium increased the relative weight of the carcass, breast, and thigh and reduced the relative weight of the liver and bursa of fabricius on day 42 (p < 0.01).The relative length of duodenum, jejunum, and ileum were increased on day 14 but reduced on day 42 by inclusion of selenium (p < 0.05).Supplementation of selenium increased (p < 0.01) the expression of claudin-1, occludin, and zonula occluden-1 and reduced (p < 0.01) the expression of claudin-5 and zonula occluden-2 on day 28.Inclusion of nano-bio selenium increased (p < 0.05) the expression of occludin, zonula occluden-1, and zonula occluden-2 and reduced (p < 0.05) the expression of claudin-5 compared to the organic selenium and sodium selenite on day 42.In conclusion, this data suggest feasibility of the biosynthesis of selenium nanoparticles by bacillus subtilis.Additionally, the data reported herein demonstrate that nano-bio selenium can effectively improve performance and intestinal integrity compared to the common organic and inorganic sources of selenium.

Journal: Biological trace element research (2022)
Publication types: Journal Article
NAC blocks Cystatin C amyloid complex aggregation in a cell system and in skin of HCCAA patients.

Hereditary cystatin c amyloid angiopathy is a dominantly inherited disease caused by a leucine to glutamine variant of human cystatin c (h cc).L68q-h cc forms amyloid deposits in brain arteries associated with micro-infarcts, leading ultimately to paralysis, dementia and death in young adults.To evaluate the ability of molecules to interfere with aggregation of h cc while informing about cellular toxicity, we generated cells that produce and secrete wt and l68q-h cc and have detected high-molecular weight complexes formed from the mutant protein.Incubations of either lysate or supernatant containing l68q-h cc with reducing agents glutathione or n-acetyl-cysteine (nac) breaks oligomers into monomers.Six l68q-h cc carriers taking nac had skin biopsies obtained to determine if h cc deposits were reduced following nac treatment.Remarkably, ~50-90% reduction of l68q-h cc staining was observed in five of the treated carriers suggesting that l68q-h cc is a clinical target for reducing agents.

Journal: Nature communications (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Robotic-assisted Surgery: Expanding Indication to Colon Cancer in Japan.

In recent years, robotic-assisted surgery has demonstrated remarkable progress as a minimally invasive procedure for colorectal cancer.While there have been fewer studies investigating robotic-assisted surgery for the treatment of colon cancer than rectal cancer, evidence regarding robotic-assisted colectomy has been accumulating due to increasing use of the procedure.Robotic-assisted colectomy generally requires a long operative time and involves high costs.However, as evidence is increasingly supportive of its higher accuracy and less invasive nature compared to laparoscopic colectomy, the procedure is anticipated to improve the ratio of conversion to laparotomy and accelerate postoperative recovery.Robotic-assisted surgery has also been suggested for a specific level of effectiveness in manipulative procedures, such as intracorporeal anastomosis, and is increasingly indicated as a less problematic procedure compared to conventional laparoscopy and open surgery in terms of long-term oncological outcomes.Although robotic-assisted colectomy has been widely adopted abroad, only a limited number of institutions have been using this procedure in japan.Further accumulation of experience and studies investigating surgical outcomes using this approach are required in japan.

Journal: Journal of the anus, rectum and colon (2022)
Publication types: Journal Article;Review
Vaccine Hesitancy as a Challenge or Vaccine Confidence as an Opportunity for Childhood Immunisation in India.

Vaccines have contributed substantially to decreasing the morbidity and mortality rates of many infectious diseases worldwide.Despite this achievement, an increasing number of parents have adopted hesitant behaviours towards vaccines, delaying or even refusing their administration to children.This has implications not only on individuals but also society in the form of outbreaks for e.g.Measles, chicken pox, hepatitis a, etc.A review of the literature was conducted to identify the determinants of vaccine hesitancy (vh) as well as vaccine confidence and link them to challenges and opportunities associated with vaccination in india, safety concerns, doubts about the need for vaccines against uncommon diseases and suspicions towards new vaccines were identified as major vaccine-specific factors of vh.Lack of awareness and limited access to vaccination sites were often reported by hesitant parents.Lastly, socio-economic level, educational level and cultural specificities were contextual factors of vh in india.Controversies and rumours around some vaccines (e.g., human papillomavirus) have profoundly impacted the perception of the risks and benefits of vaccination.Challenges posed by traditions and cultural behaviours, geographical specificities, socio-demographic disparities, the healthcare system and vaccine-specific features are highlighted, and opportunities to improve confidence are identified.To overcome vh and promote vaccination, emphasis should be on improving communication, educating the new generation and creating awareness among the society.Tailoring immunisation programmes as per the needs of specific geographical areas or communities is also important to improve vaccine confidence.Fig.1 plain language summary.

Journal: Infectious diseases and therapy (2020)
Publication types: Journal Article;Review
Tryptophan Oxidation of a Monoclonal Antibody Under Diverse Oxidative Stress Conditions: Distinct Oxidative Pathways Favor Specific Tryptophan Residues.

Tryptophan oxidation can play an important role in selecting therapeutic monoclonal antibodies for commercialization.Monoclonal antibodies that harbor particularly sensitive tryptophan residues are typically discarded in favor of oxidation resistant antibodies.The susceptibility of any individual tryptophan residue to oxidation is typically evaluated through forced degradation studies during the molecule development process.We compared the results of several common forced degradation "stress tests" for each tryptophan residue in a monoclonal antibody and found that high-stress oxidation conditions consistently provide a different ranking of oxidative sensitivity across the individual tryptophan residues compared to long-term thermal stability or low-stress conditions.We subsequently determined that this difference in ranking is largely due to an overabundance of double oxidation (i.e.Detected as +32 da) of specific tryptophan residues under high stress conditions compared to single oxidation (i.e.+16 da).We posit that this double oxidation is in fact mechanistically distinct from the observed single oxidation and that high stress conditions favor the double oxidation mechanism (and double oxidation sensitive tryptophan residues) while single oxidation appears to be the primary mode of oxidation under h2o2stress and long-term thermal stability and favors different tryptophan residues which are more susceptible to the single oxidation mechanism.

Journal: Journal of pharmaceutical sciences (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
A series of COVID-19 autopsies with clinical and pathologic comparisons to both seasonal and pandemic influenza.

Autopsies of patients who have died from covid-19 have been crucial in delineating patterns of injury associated with sars-co v-2 infection.Despite their utility, comprehensive autopsy studies are somewhat lacking relative to the global burden of disease, and very few comprehensive studies contextualize the findings to other fatal viral infections.We developed a novel autopsy protocol in order to perform postmortem examinations on victims of covid-19 and herein describe detailed clinical information, gross findings, and histologic features observed in the first 16 complete covid-19 autopsies.We also critically evaluated the role of ancillary studies used to establish a diagnosis of covid-19 at autopsy, including immunohistochemistry (ihc), in situ hybridization (ish), and electron microscopy (em).Ihc and ish targeting sars-co v-2 were comparable in terms of the location and number of infected cells in lung tissue; however, nonspecific staining of bacteria was seen occasionally with ihc.Em was unrevealing in blindly sampled tissues.We then compared the clinical and histologic features present in this series to six archival cases of fatal seasonal influenza and six archival cases of pandemic influenza from the fourth wave of the 'spanish flu' in the winter of 1920.In addition to routine histology, the inflammatory infiltrates in the lungs of covid-19 and seasonal influenza victims were compared using quantitative ihc.Our results demonstrate that the clinical and histologic features of covid-19 are similar to those seen in fatal cases of influenza, and the two diseases tend to overlap histologically.There was no significant difference in the composition of the inflammatory infiltrate in covid-19 and influenza at sites of acute lung injury at the time of autopsy.Our study underscores the relatively nonspecific clinical features and pathologic changes shared between severe cases of covid-19 and influenza, while also providing important caveats to ancillary methods of viral detection.

Journal: The journal of pathology. Clinical research (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Understanding Parahydrogen Hyperpolarized Urine Spectra: The Case of Adenosine Derivatives.

Parahydrogen hyperpolarization has emerged as a promising tool for sensitivity-enhanced nmr metabolomics.It allows resolution and quantification of nmr signals of certain classes of low-abundance metabolites that would otherwise be undetectable.Applications have been implemented in pharmacokinetics and doping drug detection, demonstrating the versatility of the technique.Yet, in order for the method to be adopted by the analytical community, certain limitations have to be understood and overcome.One such question is nmr signal assignment.At present, the only reliable way to establish the identity of an analyte that gives rise to certain parahydrogen hyperpolarized nmr signals is internal standard addition, which can be laborious.Herein we show that analogously to regular nmr metabolomics, generating libraries of hyperpolarized analyte signals is a viable way to address this limitation.We present hyperpolarized spectral data of adenosines and give an early example of identifying them from a urine sample with the small library.Doing so, we verify the detectability of a class of diagnostically valuable metabolites: adenosine and its derivatives, some of which are cancer biomarkers, and some are central to cellular energy management (e.g., atp).

Journal: Molecules (Basel, Switzerland) (2022)
Publication types: Journal Article
A qualitative exploration on the needs of health care providers working with adolescents who are undergoing bariatric surgery.

With increasing prevalence of severe obesity in youth, more adolescents are becoming candidates for bariatric surgery.In canada, bariatric surgery in adolescents is in its infancy, and long-term health outcomes are not well known.It is unknown what health care providers (hcps) are using to prepare and guide their adolescent patients for bariatric surgery.The needs of hcps should be explored with the aim to improve patient outcomes.Therefore, the purpose of this study was to investigate the resource needs of hcps working with adolescents living with severe obesity who are undergoing bariatric surgery.Methods this qualitative study consisted of a focus group with seven hcps from an adolescent bariatric program using a semi-structured interview guide.The focus group discussion was audio-recorded, and the recording was transcribed verbatim.A thematic analysis was conducted.Results four data-generated themes emerged highlighting the perceived needs and challenges faced by hcps.These included (1) gaps in patient education materials on the subject of the bariatric surgery process, obesity as a chronic disease and mental health, (2) the need for designing resources that are teen-friendly, adaptable, and accessible, (3) the need for resources to facilitate decision-making and patient evaluation delivering more streamlined care and; (4) challenges to addressing resource needs due to limited clinical time and budgets.Conclusion this needs assessment study highlights the need for appropriate resources for patient education, as well as pre and post-operative preparation.The hope is that hcps can improve quality of care delivered and positively impact surgical outcomes in their patients.

Journal: Obesity pillars (2023)
Publication types: Journal Article
Habitat Partitioning and its Possible Genetic Background Between Two Sympatrically Distributed Eel Species in Taiwan.

The geographical distributions of the japanese eel (anguilla japonica) and giant-mottled eel (a.Marmorata) overlap in many regions in east asia and therefore suffer from interspecific competition in the same rivers.After a long period of adaptation, the japanese eel and giant-mottled eel may exhibit habitat partitioning in the rivers to diminish the interspecific competition between them.In this study, we conducted a field investigation in the fengshan river in taiwan to survey the habitat distributions of the japanese eel and giant-mottled eel throughout a river.Moreover, we investigated whether their habitat distributions are related to their swimming and upstream migration.Thus, the m rna expression levels of several candidate genes that may be associated with the swimming and upstream migration of eel were examined in the glass eels of the japanese eel and giant-mottled eel.Field investigation indicated that the japanese eel mainly inhabited the lower and middle reaches of the fengshan river, but the giant- mottled eel was distributed over the middle to upper reaches.The m rna expression levels off myh,dio2,gria3, andneurod1were higher in the giant-mottled eel than in the japanese eel, implying that giant- mottled eels might have better swimming bursts and more active upstream migration than japanese eels.These results suggest that there is a habitat partition at which these two eel species coexist in a river, and their habitat distributions may be linked to their swimming bursts and upstream migration.Determining the habitat distributions of freshwater eels is important for developing applicable plans for eel conservation and resource management.

Journal: Zoological studies (2019)
Publication types: Journal Article
Thammasat-NECTEC-Chula's Thai Language and Cognition Assessment (TLCA): The Thai Alzheimer's and Mild Cognitive Impairment Screening Test.

Thammasat-nectec-chula's thai language and cognition assessment (tlca) is a cognitive paper-based test consisting of 21 tasks that cover 3 domains: memory, language, and other cognitive abilities.The tlca follows some aspects of the existing tests (thai addenbrooke's cognitive examination-revised (thai-ace-r) and the thai montreal cognitive assessment test (thai-mo ca)) and many parts were reconstructed to be more adapted to the thai culture.Data obtained from the test will be able to precisely distinguish between patients with mild cognitive impairment (mci), alzheimer's disease (ad), and normal healthy controls (nc).The tlca was tested on 90 participants (32 on the paper-based version and 58 on the computerized version) using a scoring procedure and speech features from verbal responses with machine learning classification.The scoring results showed significant difference between non-ad (nc + mci) vs ad participants in 3 domains and could differentiate between nc and mci, while machine classification could classify in three settings: nc vs non-nc (mci + ad), ad vs non-ad and nc vs mci vs ad.These promising results suggest that tlca could be further verified and used as an efficient assessment in mci and ad screening for thais.clinical relevance- the speech feature analysis of tlca showed promising result for screening mci and ad for thais.

Journal: Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference (2021)
Publication types: Journal Article