syedzayyan/paper_mill_benchmark huggingface dataset:
Native Cultivable Bacteria from the Blueberry Microbiome as Novel Potential Biocontrol Agents.

Blueberry production is affected by fungal postharvest pathogens, including botrytis cinereaand alternaria alternata, the causative agents of gray mold disease and alternaria rot, respectively.Biocontrol agents adapted to blueberries and local environments are not known to date.Here, we report on the search for and the identification of cultivable blueberry epiphytic bacteria with the potential to combat the aforementioned fungi.Native, blueberry-borne bacterial strains were isolated from a plantation in tucumán, argentina and classified based on 16s r rna gene sequences.Antagonistic activities directed at b.Cinereaand a.Alternatawere studied in vitro and in vivo.The 22 bacterial strains obtained could be attributed to eleven different genera:rosenbergiella,fictibacillus,bacillus,pseudomonas,microbacterium,asaia,acinetobacter,curtobacterium,serratia,sphingomonasand xylophilus.Three strains displaying antagonistic impacts on the fungal pathogens were identified as bacillus velezensis(ba3 and ba4) and asaia spathodeae(bmef1).These strains are candidates for biological control agents of local blueberry production and might provide a basis for the development of eco-friendly, sustainable alternatives to synthetic pesticides.

Journal: Microorganisms (2022)
Publication types: Journal Article
Thioredoxin reductase: An emerging pharmacologic target for radiosensitization of cancer.

Novel agents are required to increase the radiosensitivity of cancer and improve the outcome of radiotherapy.Thioredoxin (trx) and thioredoxin reductase (trx r) reduce the oxidized cysteine thiols in several proteins, which regulate cellular redox, survival, proliferation, dna synthesis, transcription factor activity and apoptosis.Trx r is essential for maintaining a conducive redox state for tumor growth, survival and resistance to therapy.Therefore, it is an appealing pharmacological target for the radiosensitization of tumors.Ionizing radiation (ir) is known to cause cytotoxicity through ros, oxidative stress and dna damage.Inhibition of thioredoxin system augments ir induced oxidative stress and potentiates cytotoxic effects.However, trx r also regulates several critical cellular processes in normal cells.Here, we highlight the pre-clinical research and pharmacological studies to surmise possible utility of different trx r inhibitors for radiosensitization.This review provides a succinct perspective on the role of trx r inhibitors during the radiotherapy of cancer.

Journal: Translational oncology (2022)
Publication types: Journal Article;Review
Virtual simulation of the biomechanics of the abdominal wall with different stoma locations.

An ostomy is a surgical procedure by which an artificial opening in the abdominal wall, known as a stoma, is created.We assess the effects of stoma location on the abdominal wall mechanics.We perform three-dimensional finite element simulations on an anatomy model which was generated on the basis of medical images.Our simulation methodology is entirely based on open source software.We consider seventeen different locations for the stoma incision (trephine) and we simulate the mechanical response of the abdominal wall when an intraabdominal pressure as high as 20 k pa is applied.We focus on factors related to the risk of parastomal hernia development such as the deformation experienced by the abdominal wall, the stress levels supported by its tissues and the corresponding level of trephine enlargement.No significant dependence was found between stoma location and the levels of abdominal wall deformations or stress supported by tissues, except for the case with a stoma located on the linea alba.Trephine perimeter and area respectively increased by as much as [formula: see text] and [formula: see text].The level of trephine deformation depends on stoma location with considerably higher trephine enlargements found in stomas laterally located with respect to the rectus abdominis muscle.

Journal: Scientific reports (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
A Mentorship Program to Develop Biorisk Manuals for Laboratories in Pakistan.

Introduction institutions implementing a biorisk management system need to establish comprehensive guidance to support the implementation of biosafety and biosecurity practices.A biorisk manual describes how a biorisk management system will be implemented in an organization and includes topics such as facility-specific policies and procedures to safely and securely handle, store, and dispose of biological agents and toxins in adherence with international guidance.Methods to promote the adoption of biosafety and biosecurity in pakistan, the pakistan biological safety association and health security partners developed a biorisk manual writing project in 2019 in partnership with experts from the bio risk association of the philippines 2015, inc.This project helped 13 researchers and laboratory professionals in pakistan develop biorisk manuals for their institutions.The project comprised two phases: an in-person group training on how to develop a laboratory biorisk manual, and 10 months of additional remote mentoring assistance for the development and finalization of the biorisk manual tailored to each institution's specific needs.By the end of the project, 12 of the 13 participants had customized biorisk manuals for their institutions in place.In january 2022, a survey was conducted among the workshop participants to learn how successful they were in implementing the developed manual in their institutions.Results participants reported varying degrees of successful implementation.They also suggested that the biosafety and biosecurity associations should engage top management at institutions to strengthen administrative support and provide a sufficient workforce to promote implementation.

Journal: Applied biosafety : journal of the American Biological Safety Association (2022)
Publication types: Journal Article
Revealing the Architecture of the Cell Wall in Living Plant Cells by Bioimaging and Enzymatic Degradation.

Plant cell walls consist mostly of crystalline cellulose fibrils embedded in a matrix of complex polysaccharides, but information on their morphological features has generally been limited to that obtained from nonliving plant specimens.Here, we characterized the primary cell wall of a living plant cell (from the tobacco by-2 suspension culture) at nanometer resolution using high-speed atomic force microscopy and at micrometer resolution using confocal laser scanning microscopy.Our results showed aligned and disordered cellulose fibrils coexisting in the outermost layer of the cell wall.We investigated the orientation of the aligned cellulose fibrils in the outer lamellae of the cell wall of living plant cells after removing cellulose, hemicellulose, and pectin by enzymatic degradation to make the cellulose fibrils more visible and, accordingly, to reveal the structure of the nanoachitecture formed by these fibrils within the cell wall.We observed that the cellulose fibrils in the outermost layer were usually oriented close to the direction of cell growth, whereas the orientation of the cellulose fibrils in the successive lamellae further inward changed randomly.Such organization should be crucial to render the plant cell wall both rigid and flexible.This finding provides insight not only into the structure of the functional plant cell wall but also into its growth mechanism.

Journal: Biomacromolecules (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
The Evolving Role of Omega 3 Fatty Acids in Cardiovascular Disease: Is Icosapent Ethyl the Answer?

Atherosclerotic cardiovascular disease (ascvd) remains the leading cause of morbidity and mortality globally.Despite significant advances in pharmacotherapies and the beneficial effects of statin therapy on ascvd outcomes and progression of atherosclerosis, residual cardiovascular (cv) risk remains.Extensive evidence has identified the contribution of atherogenic dyslipidaemia, which is particularly characterised by elevated triglycerides (tgl) as a key driver of cv risk, even if low-density lipoprotein cholesterol levels are well controlled.Epidemiologic and genetic/mendelian randomisation studies have demonstrated that elevated tgl levels serve as an independent marker for an increased risk of ischaemic events, highlighting tgls as a suitable therapeutic target.Clinical studies have shown that omega 3 fatty acids (om3fa) are effective in lowering tgls; however, to date, trials and meta-analyses of combined om3fa products have not demonstrated any clinical cv outcome benefit in patients receiving statins.However, icosapent ethyl (ipe) - a highly purified, stable ethyl ester of eicosapentaenoic acid (epa) - has been rigorously demonstrated in multiple studies to be a useful adjunctive therapy to address residual cv risk.Epa is an omega-3 polyunsaturated fatty acid that is incorporated into membrane phospholipid bilayers and is reported to exert multiple beneficial effects along the pathway of coronary atherosclerosis.In this brief review, we will provide an overview of the mode of action of ipe in coronary atherosclerosis, the robust clinical evidence and trial data supporting its use, and expert consensus/recommendations on its use in specific populations, as an adjunct to existing anti-atherosclerotic therapies.

Journal: Heart international (2021)
Publication types: Journal Article;Review
Microneurosurgical management of aneurysms of the A1 segment of the anterior cerebral artery: Anatomy and surgical technique.

Aneurysms of the a1 segment of the anterior cerebral artery (aca) are rare and have characteristics differentiating them from other intracranial aneurysms.Their microsurgical management is challenging and requires different strategies.In this article, we review the surgical anatomy of the a1 segment of the aca with cadaveric dissections and describe the microsurgical management of complex a1 aneurysms with illustrative cases.Methods a right pterional craniotomy and sylvian dissection were performed on a formalin-fixed and silicone-injected cadaver head to depict the key anatomic structures and surgical corridors for microsurgical clipping of a1 segment aneurysms.The microneurosurgical management of ruptured and unruptured aneurysms of the a1 segment of the aca is described with case illustrations.Results the a1 segment of the aca can be subdivided into proximal, middle, and distal subsegments, the former having abundant perforating branches.Both patients treated with microsurgical clipping had excellent and durable outcomes and postoperative cerebral angiograms showed complete aneurysm occlusion.Conclusion small a1 aneurysms may require early treatment as their rupture risk appears to be higher.A1 aneurysms are usually embedded in perforators, especially those arising from the proximal a1 subsegment, and require careful distal to proximal microdissection and strategic placement of the aneurysm clip blades.The approach, arachnoid dissection, and angles of attack are carefully planned after accounting for the aneurysm dome projection, precise location of the aneurysm neck and perforators, and the presence or absence of subarachnoid hemorrhage.

Journal: Surgical neurology international (2022)
Publication types: Journal Article
Religious leaders' role in pregnant and breastfeeding women's decision making and willingness to use biomedical HIV prevention strategies: a multi-country analysis.

Oral pre-exposure prophylaxis (pr ep) is an established option, and the dapivirine vaginal ring is emerging as a promising strategy for hiv prevention option for women.Because of this, understanding the contextual and cultural factors that will support the increased uptake of these products is crucial.In sub-saharan africa, religious leaders may be important stakeholders to involve in product information, education and roll-out.We conducted a sub-analysis of data from 232 participants taking part in the mtn-041/mamma study to explore religious leaders' involvement in pregnant and breastfeeding women's health.Study participants viewed biomedicine and spirituality as interlinked and believed that women could seek health-related care from medical experts and turn to faith-based organisations for religious or spiritual needs.Religious leaders were invested in the health of their congregations, endorsed a variety of sexual health strategies, and were eager to learn more about emerging hiv prevention technologies.These data signal the role of religious leaders in supporting their communities, and the importance of involving religious leaders in efforts to roll out new hiv prevention products to facilitate uptake.

Journal: Culture, health & sexuality (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural
Shedding of infectious SARS-CoV-2 despite vaccination.

The sars-co v-2 delta variant of concern is highly transmissible and contains mutations that confer partial immune escape.The emergence of delta in north america caused the first surge in covid-19 cases after sars-co v-2 vaccines became widely available.To determine whether individuals infected despite vaccination might be capable of transmitting sars-co v-2, we compared rt-pcr cycle threshold (ct) data from 20,431 test-positive anterior nasal swab specimens from fully vaccinated (n = 9,347) or unvaccinated (n = 11,084) individuals tested at a single commercial laboratory during the interval 28 june- 1 december 2021 when delta variants were predominant.We observed no significant effect of vaccine status alone on ct value, nor when controlling for vaccine product or sex.Testing a subset of low-ct (<25) samples, we detected infectious virus at similar rates, and at similar titers, in specimens from vaccinated and unvaccinated individuals.These data indicate that vaccinated individuals infected with delta variants are capable of shedding infectious sars-co v-2 and could play a role in spreading covid-19.

Journal: PLoS pathogens (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Research Support, U.S. Gov't, P.H.S.
Subgroup Analysis in Pulmonary Hypertension-Specific Therapy Clinical Trials: A Systematic Review.

Pulmonary hypertension (ph) treatment decisions are driven by the results of randomized controlled trials (rcts).Subgroup analyses are often performed to assess whether the intervention effect will change due to the patient's characteristics, thus allowing for individualized decisions.This review aimed to evaluate the appropriateness and interpretation of subgroup analyses performed in ph-specific therapy rcts published between 2000 and 2020.Claims of subgroup effects were evaluated with prespecified criteria.Overall, 30 rcts were included.Subgroup analyses presented: a high number of subgroup analyses reported, lack of prespecification, and lack of interaction tests.The trial protocol was not available for most rcts; significant differences were found in those articles that published the protocol.Authors reported 13 claims of subgroup effect, with 12 claims meeting four or fewer of sun's criteria.Even when most rcts were generally at low risk of bias and were published in high-impact journals, the credibility and general quality of subgroup analyses and subgroup claims were low due to methodological flaws.Clinicians should be skeptical of claims of subgroup effects and interpret subgroup analyses with caution, as due to their poor quality, these analyses may not serve as guidance for personalized care.

Journal: Journal of personalized medicine (2022)
Publication types: Journal Article;Review
Epidemiological links and antimicrobial resistance of clinicalSalmonella entericaST198 isolates: a nationwide microbial population genomic study in Switzerland.

Salmonellais a leading cause of foodborne outbreaks and systemic infections worldwide.Emerging multi-drug resistant salmonellalineages such as a ciprofloxacin-resistant subclade (cipr) within salmonella entericaserovar kentucky st198 threaten the effective prevention and treatment of infections.To understand the genomic diversity and antimicrobial resistance gene content associated with s.Kentucky in switzerland, we whole-genome sequenced 70 human clinical isolates obtained between 2010 and 2020.Most isolates belonged to st198-cipr.High- and low-level ciprofloxacin resistance among ciprisolates was associated with variable mutations inram randacr bin combination with stable mutations in quinolone-resistance determining regions (qrdrs).Analysis of isolates from patients with prolonged st198 colonization indicated subclonal adaptions with theram rlocus as a mutational hotspot.Snp analyses identified multiple clusters of near-identical isolates, which were often associated with travel but included spatiotemporally linked isolates from switzerland.The largest snp cluster was associated with travellers returning from indonesia, and investigation of global data linked >60 additional st198 salmonellosis isolates to this cluster.Our results emphasize the urgent need for implementing whole-genome sequencing as a routine tool for salmonellasurveillance and outbreak detection.

Journal: Microbial genomics (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Uses of equipoise in discussions of the ethics of randomized controlled trials of COVID-19 therapies.

Early in the covid-19 pandemic, the urgent need to discover effective therapies for covid-19 prompted questions about the ethical problem of randomization along with its widely accepted solution: equipoise.In this scoping review, uses of equipoise in discussions of randomized controlled trials (rct) of covid-19 therapies are evaluated to answer three questions.First, how has equipoise been applied to covid-19 research?Second, has equipoise been employed accurately?And third, do concerns about equipoise pose a barrier to the ethical conduct of covid-19 rcts?Methods google scholar and pubmed were searched for articles containing substantial discussion about equipoise and covid-19 rcts.347 article titles were screened, 91 full text articles were assessed, and 48 articles were included.Uses of equipoise were analyzed and abstracted into seven categories.Results and discussion approximately two-thirds of articles (33/48 articles) used equipoise in a way that is consistent with the concept.They invoked equipoise to support (1) rcts of specific therapies, (2) rcts in general, and (3) the early termination of rcts after achieving the primary outcome.Approximately one-third of articles (15/48 articles) used equipoise in a manner that is inconsistent with the concept.These articles argued that physician preference, widespread use of unproven therapies, patient preference, or expectation of therapeutic benefit may undermine equipoise and render rcts unethical.In each case, the purported ethical problem can be resolved by correcting the use of equipoise.Conclusions our findings highlight the continued relevance of equipoise as it supports the conduct of well-conceived rcts and provides moral guidance to physicians and researchers as they search for effective therapies for covid-19.

Journal: BMC medical ethics (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Tuning the local electronic structure of SrTiO3catalysts to boost plasma-catalytic interfacial synergy.

Boosting plasma-catalyst synergy to enhance volatile organic compounds (vocs) decomposition remains a challenge.Herein, rich oxygen vacancies (vo) were engineered into the sr ti o3catalysts through a facile nitrogen incorporation strategy for the plasma-catalytic decomposition of toluene and ethyl acetate.100% toluene conversion with 81% co2selectivity at a competitive energy efficiency was achieved under ambient conditions.The characterization results and theoretical calculations evidenced that the partial substitution of oxygen by nitrogen triggered the electronic reconstruction and local disorder, thus modulating the electronic properties and coordination structures contributed to the formation of vo-ti3+pairs.Quasi in-situ epr, operando oes, and operando drifts originally demonstrated that the vo-ti3+pairs as active sites promoted the plasma-catalytic synergy instead of isolated vo.Importantly, the vo-ti3+pairs with favorable electron transfer characteristics energetically preferred to capture and utilize vibrationally excited oxygen species.And the lattice oxygen supplied by the vo-ti3+pairs were more vigorously activated by the plasma to participate in the surface/interface reaction.This work advances our understanding of the real active sites in plasma-catalytic interfacial synergy and thus paving the way for the rational design of efficiently heterogeneous catalysts.

Journal: Journal of hazardous materials (2022)
Publication types: Journal Article
Quantification of the ossification of the lateral cuneiform in the feet of young children with unilateral congenital talipes equinovarus.

S after the initial correction of congenital talipes equinovarus (ctev) using the ponseti method, a subsequent dynamic deformity is often managed by transfer of the tendon of tibialis anterior (tatt) to the lateral cuneiform.Many surgeons believe the lateral cuneiform should be ossified before surgery is undertaken.This study quantifies the ossification process of the lateral cuneiform in children with ctev between one and three years of age.Patients and methods the length, width and height of the lateral cuneiform were measured in 43 consecutive patients with unilateral ctev who had been treated using the ponseti method.Measurements were taken by two independent observers on standardised anteroposterior and lateral radiographs of both feet taken at one, two and three years of age.Results all dimensions of the lateral cuneiform on the affected side increased annually but remained smaller than the corresponding dimensions of the unaffected foot (p < 0.01).The lateral cuneiform resembled a 9 mm cube at two years and an 11 mm cube at three years.Conclusion at one and two years, the ossification centre of the lateral cuneiform may not be large enough to accommodate a drill hole for tendon transfer.However, by three years, it has undergone sufficient ossification to do so.Cite this article:bone joint j2017;99-b:1109-14.

Journal: The bone & joint journal (2017)
Publication types: Journal Article
Mapping breast cancer survivors' psychosocial coping along disease trajectory: A language approach.

This article reports a language analysis of breast cancer patients' posts in an online support group.Adopting web-scraping techniques, the study analyzed 27,078 online posts contributed by 1443 users along multiple linguistic dimensions to investigate the trajectory of the patients' psychosocial adaptation of the disease.The findings suggested that breast cancer patients' emotional experiences and adjustment in the course of illness vary from one stage to another.They reached the peak of emotional expression, struggle and despair, and self-focus at stage iii, whereas wiped out negative emotions and signaled a desire for connections with others at stage iv.

Journal: Journal of health psychology (2021)
Publication types: Journal Article