syedzayyan/paper_mill_benchmark huggingface dataset:
Sulfane Sulfur Posttranslationally Modifies the Global Regulator AdpA to Influence Actinorhodin Production and Morphological Differentiation of Streptomyces coelicolor.

The transcription factor adp a is a key regulator controlling both secondary metabolism and morphological differentiation in streptomyces.Due to its critical functions, its expression undergoes multilevel regulations at transcriptional, posttranscriptional, and translational levels, yet no posttranslational regulation has been reported.Sulfane sulfur, such as hydro polysulfide (hsn h,n≥ 2) and organic polysulfide (rsn h,n≥ 2), is common inside microorganisms, but its physiological functions are largely unclear.Here, we discovered that sulfane sulfur posttranslationally modifies adp a in streptomyces coelicolor via specifically reacting with cys62of adp a to form a persulfide (cys62-ssh).This modification decreases the affinity of adp a to its self-promoter padp a, allowing increased expression ofadp a, further promoting the expression of its target genesact ii-4andwbl a.Act ii-4 activates actinorhodin biosynthesis, and wbl a regulates morphological development.Bioinformatics analyses indicated that adp a-cys62is highly conserved in streptomyces, suggesting the prevalence of such modification in this genus.Thus, our study unveils a new type of regulation on the adp a activity and sheds a light on how sulfane sulfur stimulates the production of antibiotics in streptomyces.importancestreptomycesspecies produce a myriad of natural products with (potential) clinical applications.While the database of biosynthetic gene clusters is quickly expanding, their regulation mechanisms are rarely known.Sulfane sulfur species are commonly present in microorganisms with unclear functions.Here, we discovered that sulfane sulfur increases actinorhodin (act) production in s.Coelicolor.The underlying mechanism is that sulfane sulfur specifically reacts with adp a, a global transcription factor controlling both act gene cluster and morphological differentiation-related genes, to form sulfhydrated adp a.This modification changes the dynamics of adp a-controlled gene networks and leads to high expression of act biosynthetic genes.Given the wide prevalence of adp a and sulfane sulfur in streptomyces, this mechanism may represent a common regulating pattern of all adp a-controlled biosynthetic pathways.Thus, this finding provides a new strategy for mining and activating valuable biosynthetic gene clusters.

Journal: mBio (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Addressing virtual care disparities for patients with limited English proficiency.

During a surge of covid-19 cases, the majority of care delivery at a large academic medical center moved to virtual care.Due to covid-19-associated regulatory changes, virtual care is now delivered through telephone and videoconferencing platforms.Although virtual platforms allow patients to access care while socially distancing, patients with limited english proficiency (lep) face structural barriers to these platforms, including lack of access to technology, need for medical interpreters, unfriendly patient portals, and increased privacy concerns.Strategies for increasing access to virtual platforms and technology for patients with lep included offering patient education in multiple languages, reducing barriers to patient portal enrollment, and addressing the technology literacy gap through the use of tablets and bilingual interns.Strategies for addressing privacy concerns for patients with lep included developing a low-literacy script and other actions that address patient concerns about immigration and customs enforcement and mitigate perceived risk, as well as identifying a virtual platform that meets privacy regulations and does not require a patient to download an application to their phone or computer to join.Strategies for integrating medical interpreters into virtual visits included assessing existing virtual platforms for the ability to host a third party, changing the electronic health record software (epic) interface, and convening directors of interpreter departments at each site to ensure comprehensive system rollout.Health care organizations that rely heavily on virtual visits to provide patient care will need to take all these challenges into consideration for patients with lep.

Journal: The American journal of managed care (2022)
Publication types: Journal Article
A Mobile Health Breast Cancer Educational and Screening Intervention Tailored for Low-Income, Uninsured Latina Immigrants.

To investigate the efficacy of mobile health (m health) intervention strategies that delivered either personalized, culturally, and linguistically tailored cell phone voice messages or text messages related to breast cancer and prevention, compared to the control group, to determine which strategy is more likely to increase breast cancer knowledge and screening mammography among low-income latina immigrants.methods:this randomized controlled trial assigned 256 latina immigrants 40 years of age or older to one of three groups: an automated cell phone voice message group, an automated text message group, or the control group (mail).The m health intervention employed a comprehensive approach that included breast cancer and prevention education and free mammography screening.Outcome measures included knowledge of breast cancer and breast cancer prevention, and adherence to screening mammography.results:there was a general increase in breast cancer knowledge after the educational intervention for all the groups [p= 0.01,t(199) = 3.996].Knowledge increase and mammography adherence did not differ based on group.conclusion:more important than the actual method of communication ishowbreast cancer and prevention messages are constructed,whothe messenger is, and the enabling factors that facilitate screening adherence.A breast cancer preventive intervention program that is personalized, culturally and linguistically tailored, and offers a free or low-cost mammogram holds promise to be an effective method in reaching an underserved latina population with a high breast cancer burden.

Journal: Women's health reports (New Rochelle, N.Y.) (2021)
Publication types: Journal Article
Standardized incidence ratios of malignant neoplasms among patients with pneumoconiosis.

Patients with pneumoconiosis, such as silicosis and asbestosis, have a high risk of lung cancer.However, whether these patients are at high risk for neoplasms other than lung cancer and mesothelioma remains inconclusive.Aims to examine whether patients with pneumoconiosis have a higher incidence of malignant neoplasms other than lung cancer.Methods we conducted a cohort study using the medical records of patients with pneumoconiosis who visited our two hospitals from 1 january 1991 through 31 december 2017.We identified the occurrence of malignant neoplasms and calculated the incidences and standardized incidence ratios (sirs) compared with those of the general population.Results one hundred and seventy patients with pneumoconiosis (163 men, 7 women) including 142 patients with silicosis, 24 with asbestosis and 4 with pneumoconiosis were identified.The mean age was 66.8 years.The proportion of smokers was 79%.Forty-seven malignant neoplasms occurred.Most malignant neoplasms were lung cancer (n = 22), while some were digestive cancers such as gastric cancer (n = 9), oesophageal cancer (n = 3) and colorectal cancer (n = 3).Participants presented increased risks for lung cancer (sir: 10.86, 95% confidence interval [ci]: 7.15-16.49), gastric cancer (sir: 2.55, 95% ci: 1.22-5.35) and oesophageal cancer (sir: 5.78, 95% ci: 1.86-17.92).Conclusions compared with the general population, patients with pneumoconiosis had an increased risk of malignant neoplasms of the digestive system in addition to lung cancer.Clinicians should consider testing for digestive system cancers as well as for lung cancers in these patients.

Journal: Occupational medicine (Oxford, England) (2022)
Publication types: Journal Article
DLPacker: Deep learning for prediction of amino acid side chain conformations in proteins.

Prediction of side chain conformations of amino acids in proteins (also termed "packing") is an important and challenging part of protein structure prediction with many interesting applications in protein design.A variety of methods for packing have been developed but more accurate ones are still needed.Machine learning (ml) methods have recently become a powerful tool for solving various problems in diverse areas of science, including structural biology.In this study, we evaluate the potential of deep neural networks (dnns) for prediction of amino acid side chain conformations.We formulate the problem as image-to-image transformation and train a u-net style dnn to solve the problem.We show that our method outperforms other physics-based methods by a significant margin: reconstruction rmsds for most amino acids are about 20% smaller compared to scwrl4 and rosetta packer with rmsds for bulky hydrophobic amino acids phe, tyr, and trp being up to 50% smaller.

Journal: Proteins (2022)
Publication types: Journal Article;Research Support, U.S. Gov't, Non-P.H.S.
Plasma neurofilament light chain levels suggest neuroaxonal stability following therapeutic remyelination in people with multiple sclerosis.

Chronic demyelination is a major contributor to axonal vulnerability in multiple sclerosis (ms).Therefore, remyelination could provide a potent neuroprotective strategy.The re build trial was the first study showing evidence for successful remyelination following treatment with clemastine in people with ms (pw ms) with no evidence of disease activity or progression (nedap).Whether remyelination was associated with neuroprotection remains unexplored.Methods plasma neurofilament light chain (nf l) levels were measured from re build trial's participants.Mixed linear effect models were fit for individual patients, epoch and longitudinal measurements to compare nf l concentrations between samples collected during the active and placebo treatment period.Results nf l concentrations were 9.6% lower in samples collected during the active treatment with clemastine (n=53, geometric mean=6.33 pg/m l) compared to samples collected during treatment with placebo (n=73, 7.00 pg/m l) (b=-0.035 [-0.068 to -0.001], p=0.041).Applying age- and body mass index-standardised nf l z-scores and percentiles revealed similar results (0.04 vs 0.35, and 27.5 vs 33.3, p=0.023 and 0.042, respectively).Higher nf l concentrations were associated with more delayed p100 latencies (b=1.33 [0.26 to 2.41], p=0.015).In addition, improvement of p100 latencies between visits was associated with a trend for lower nf l values (b=0.003 [-0.0004 to 0.007], p=0.081).Based on a cohen's d of 0.248, a future 1:1 parallel-arm placebo-controlled study using a remyelinating agent with comparable effect as clemastine would need 202 subjects per group to achieve 80% power.Conclusions in pw ms, treatment with the remyelinating agent clemastine was associated with a reduction of blood nf l, suggesting that neuroprotection is achievable and measurable with therapeutic remyelination.Trial registration number nct02040298.

Journal: Journal of neurology, neurosurgery, and psychiatry (2022)
Publication types: Journal Article
Bacterial Diversity and Community Structure of a Municipal Solid Waste Landfill: A Source of Lignocellulolytic Potential.

Omics have given rise to research on sparsely studied microbial communities such as the landfill, lignocellulolytic microorganisms and enzymes.The bacterial diversity of municipal solid waste sediments was determined using the illumina mi seq system after dna extraction and polymerase chain reactions.Data analysis was used to determine the community's richness, diversity, and correlation with environmental factors.Physicochemical studies revealed sites with mesophilic and thermophilic temperature ranges and a mixture of acidic and alkaline p h values.Temperature and moisture content showed the highest correlation with the bacteria community.The bacterial analysis of the community dna revealed 357,030 effective sequences and 1891 operational taxonomic units (otus) assigned.Forty phyla were found, with the dominant phyla proteobacteria,firmicutes,actinobacteria, and bacteroidota, while aerococcus,stenotrophomonas, and sporosarcinawere the dominant species.Picrust provided insight on community's metabolic function, which was narrowed down to search for lignocellulolytic enzymes' function.Cellulase, xylanase, esterase, and peroxidase were gene functions inferred from the data.This article reports on the first phylogenetic analysis of the pulau burung landfill bacterial community.These results will help to improve the understanding of organisms dominant in the landfill and the corresponding enzymes that contribute to lignocellulose breakdown.

Journal: Life (Basel, Switzerland) (2021)
Publication types: Journal Article
RelevantFusariumMycotoxins in Malt and Beer.

Mycotoxins are secondary fungal metabolites of high concern in the food and feed industry.Their presence in many cereal-based products has been numerously reported.Beer is the most consumed alcoholic beverage worldwide, and fusariummycotoxins originating from the malted and unmalted cereals might reach the final product.This review aims to describe the possible fusariumfungi that could infect the cereals used in beer production, the transfer of mycotoxins throughout malting and brewing as well as an insight into the incidence of mycotoxins in the craft beer segment of the industry.Studies show that germination is the malting step that can lead to a significant increase in the level of all fusariummycotoxins.The first step of mashing (45 °c) has been proved to possess the most significant impact in the transfer of hydrophilic toxins from the grist into the wort.However, during fermentation, a slight reduction of deoxynivalenol, and especially of zearalenone, is achieved.This review also highlights the limited research available on craft beer and the occurrence of mycotoxins in these products.

Journal: Foods (Basel, Switzerland) (2022)
Publication types: Journal Article;Review
Assessment of reliability and validity of the adapted Persian version of the Spinal Appearance Questionnaire in adolescents with idiopathic scoliosis.

This study investigates the reliability and validity of the adapted persian version of the spinal appearance questionnaire (p-saq).Methods the stages of cross-cultural adaptation were conducted according to an internationally accepted guidelines.Reliability of the p-saq was measured by evaluating internal consistency and test-retest reproducibility using cronbach's α and intraclass correlation coefficient (icc).Validity of the p-saq was assessed by factor analysis, and convergent and known-groups validities.Convergent validity was assessed through participant response on the p-saq and the revised 22-item persian version of the scoliosis research society (srs-22r) questionnaire.Known-groups validity was assessed by comparing the p-saq scores according to the patients curve magnitude and treatment type.Results a total of 106 patients with a diagnosis of adolescent idiopathic scoliosis (ais) were included.The p-saq demonstrated an acceptable internal consistency with a cronbach's α of 0.77 (range 0.65-0.72).The test-retest reliability was excellent (range icc 0.85-0.98).There was a correlation between the total score, average scores of the general, curve, rib prominence, kyphosis, and trunk shift subscales of the p-saq and subtotal and total scores of the srs-22r, r = - 0.2 to - 0.4, p < 0.05.The p-saq discriminated between patients with differing cobb angle magnitudes and treatment types (p < 0.01).Factor analysis supported the use of the appearance and expectations items as separate scales for the p-saq.Conclusion the p-saq is a valid and reliable tool that could be utilized to evaluate the perception of appearance for persian-speaking ais patients with different curve magnitude and treatment strategies.Level of evidence level i- diagnostic studies.

Journal: Spine deformity (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Global longitudinal strain predicts responders after cardiac resynchronization therapy-a systematic review and meta-analysis.

To evaluate the association between baseline global longitudinal strain (gls) and δgls (difference of baseline gls and follow-up) and cardiac resynchronization therapy (crt) response defined either with clinical or with echocardiographic characteristics.This meta-analysis was performed in accordance to both the meta-analysis of observational studies in epidemiology and strengthening the reporting of observational studies in epidemiology guidelines.Two independent investigators performed a comprehensive systematic search in med line, embase and cochrane databases through september 2019 without limitations.Data analysis was performed by using the review manager software (rev man), version 5.3, and stata 13 software.A p value of less than 0.05 (two-tailed) was considered statistically significant.Twelve studies (1004 patients, mean age 63.8 years old, males 69.4%) provided data on the association of baseline gls with the response to crt therapy.We found that crt responders had significantly better resting gls values compared with non-responders [gls mean difference -2.13 (-3.03, -1.23), p < 0.001, i278%].Furthermore, crt responders had significantly greater improvement of gls at follow-up compared with non-responders [δgls mean difference -3.20 (-4.95, -1.45), p < 0.001, i266%].These associations remained significant in a subgroup analysis including only studies with similar crt response definition.In this meta-analysis, we found that crt responders had a baseline and δgls significantly higher than the non-responders strengthening the central role of gls as a tool for selecting candidates for crt.Furthermore, improved gls values after crt may be used to better define crt responders.

Journal: Heart failure reviews (2022)
Publication types: Journal Article;Meta-Analysis;Review;Systematic Review
Efficacy of clinically used anthelmintics against toxocariasis of buffalo calves in Bangladesh.

Toxocariasis is a paramount parasitic disease having > 50% prevalence among newborn buffalo calves in bangladesh.The objective of this study was to compare the efficacy of clinically used anthelmintics and their subsequent effect on the haematological parameters and body weight in buffalo calves in commercial buffalo farms in coastal region.Thirty-two buffalo calves below 3 months of age with clinical toxocarainfection had been selected and treated with albendazole (abz), levamisole (lvm) and ivermectin (ivm).The epg counts, hematological parameters and initial body weight of buffalo calves were recorded on the day of anthelmintic treatment (day 0).Fecal samples were collected on day 14 and 28 including hematological parameters and body weight were recorded on day 28 post-treatment.The efficacy (%) of anthelmintics were estimated by fecal egg count reduction test (fecrt).The parameters like hb, pcv, esr, tec, tlc were analyzed from the blood samples.The fecrt revealed 96.83% efficacy for ivm followed by 94.23% and 85.84% for lvm and abz, respectively.Anthelmintic treated calves showed significant (p< 0.01) increase in hb, pcv, tec and body weight, and decrease in esr and tlc as a result of worm expulsion from buffalo calves after 28 days of post-treatment.Among the tested anthelmintics, ivm was found to be more effective against toxocariasis in buffalo calves.This is a novel information on anthelmintics efficacy in buffalo calves in bangladesh.Details study is recommended on the efficacy of anthelmintics in different buffalo management systems by in vitro egg hatch assay (eha) test.

Journal: Journal of parasitic diseases : official organ of the Indian Society for Parasitology (2022)
Publication types: Journal Article
Enhancement of the intestinal absorption of bortezomib by self-nanoemulsifying drug delivery system.

Intestinal drug absorption is one of the main factors that govern the fraction of oral dose absorbed (fa) of drugs.It is reported that oral absorption of bortezomib (btz) can be restricted by its low intestinal permeability.In this study, we aimed to evaluate the impact of self-nanoemulsifying drug delivery systems (snedds) on the intestinal absorption and faof btz.methods:intestinal permeability studies were conducted usingin situsingle-pass intestinal perfusion (spip) technique in rats.Human intestinal absorption (peff (human)) and favalues of btz and btz-snedds were predicted based on spip data.results:based on the obtained data,peff (rat)values of (3.36 ± 0.5) × 10-5and (8.9 ± 3) × 10-5cm/s (mean ± sem) were calculated for btz and btz-snedds, respectively.Meanwhile,peff (human)values of (7 × 10-5) and (68 × 10-5) cm/sec were predicted for btz and btz-snedds, respectively.Besides,fa (human)values of 72.5 and 97% were estimated for btz and btz-snedds, respectively.conclusions:according to the obtained data, it is concluded that snedds can be considered as a promising drug delivery system to improve the intestinal absorption and favalues of btz.

Journal: Pharmaceutical development and technology (2020)
Publication types: Journal Article
Stereotactic breast biopsy: A review & applicability in the Indian context.

Stereotactic biopsy is used for sampling of suspicious non-palpable lesions identified on mammography or digital breast tomosynthesis which are not visible on ultrasound.Stereotactic biopsy is preferable to surgical excision biopsy and helps avoid surgery for benign lesions.Providing tissue diagnosis in patients with early breast cancer may help in formulating a management strategy.Stereotactic biopsy can be carried out using either a dedicated prone table with the patient lying prone or an upright mammographic add-on system with the patient in a sitting or lateral decubitus position.This review focuses on the advantages and disadvantages of both these systems, the indications, contraindications and the complications inherent with this technique.The important pitfalls and their management as well as ways to ensure quality assurance have also been elaborated upon.Data regarding uptake of stereotactic biopsy in other parts of the world have been discussed using evidence from existing registries and databases and attempts made to quantify the need of the technique in the indian set-up.In the absence of a national breast screening programme and limited resources in india, a hub and spoke model has been proposed as a viable model for healthcare providers for providing stereotactic biopsy.

Journal: The Indian journal of medical research (2021)
Publication types: Journal Article;Review
Genetic variations and in vitro root-colonizing ability for an ericaceous host in Sarcoleotia globosa (Geoglossomycetes).

We discovered that sarcoleotia globosa (geoglossomycetes) fruited on the soil of ornamental erica pot cultures, and its ascospores can germinate on plain agar.These findings prompted us to collect isolates from horticultural and natural environments in japan and analyze their phylogeny and root colonizing ability.Pure cultures were successfully obtained from ascospores and surface-sterilized ericaceous roots.Phylogenetic analysis based on r rna internal transcribed spacer sequences revealed that japanese samples were separated into three strongly supported clades.Individual clade consisted of samples derived from (1) erica pot cultures, (2) rhododendron planted in a garden or vaccinium pot culture, and (3) natural habitats in hokkaido.Colony characteristics and in vitro root-colonizing morphology observed may correspond to these phylogenetic variations.Irrespective of the clades, all tested strains formed hyphal coils in vital rhizodermal cells of v.Virgatum seedlings, which resembled those of ericoid mycorrhizae.Our results represent novel findings that can be the first step in unraveling the currently unknown ecology of geoglossoid fungi.

Journal: Fungal biology (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't