syedzayyan/paper_mill_benchmark huggingface dataset:
Microbiology laboratories involved in disease and antimicrobial resistance surveillance: Strengths and challenges of the central African states.

Laboratory systems have been largely neglected on the margins of health systems in africa.However, since the 2000s, many african countries have benefited from massive investments to strengthen laboratory capacities through projects fighting priority diseases (hiv/aids, tuberculosis, malaria).This review examined the laboratory capacities of the economic community of central african states (eccas).Online research using specific terms was carried out.Studies published between 2000 and 2021 on the role of the laboratory in disease and antimicrobial resistance surveillance in the 11 eccas countries were considered.The number of human and animal health laboratories meeting international standards was very low in the sub-region.There were only seven international organization for standardization (iso) 15189-accredited human health laboratories, with five in cameroon and two in rwanda.There were five high biosafety level (bsl) laboratories (one bsl3 laboratory each in cameroon, the central african republic, democratic republic of congo and the republic of congo, and one bsl4 laboratory in gabon) and three iso 17025-accredited laboratories in the eccas sub-region.Only six countries currently have whole-genome sequencing devices, which is insufficient for a sub-region as large and populous as eccas.Yet, a plethora of pathogens, particularly haemorrhagic viruses, are endemic in these countries.The need for laboratory capacity strengthening following a one health approach is imperative.Since emerging and re-emerging zoonotic infectious diseases are projected to triple in frequency over the next 50 years and given the inextricable link between human and animal health, actors in the two health sectors must collaborate to preserve world health.

Journal: African journal of laboratory medicine (2022)
Publication types: Journal Article;Review
Low-dose AAV-CRISPR-mediated liver-specific knock-in restored hemostasis in neonatal hemophilia B mice with subtle antibody response.

Aav-delivered crispr/cas9 (aav-crispr) has shown promising potentials in preclinical models to efficiently insert therapeutic gene sequences in somatic tissues.However, the aav input doses required were prohibitively high and posed serious risk of toxicity.Here, we performed aav-crispr mediated homology-independent knock-in at a new target site in m alb 3'utr and demonstrated that single dose of aavs enabled long-term integration and expression of h f9 transgene in both adult and neonatal hemophilia b mice (m f9 -/-), yielding high levels of circulating human factor ix (h fix) and stable hemostasis restoration during entire 48-week observation period.Furthermore, we achieved hemostasis correction with a significantly lower aav dose (2 × 109vg/neonate and 1 × 1010vg/adult mouse) through liver-specific gene knock-in using hyperactive h f9r338lvariant.The plasma antibodies against cas9 and aav in the neonatal mice receiving low-dose aav-crispr were negligible, which lent support to the development of aav-crispr mediated somatic knock-in for treating inherited diseases.

Journal: Nature communications (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Evaluating the longitudinal effectiveness of preventive measures against COVID-19 and seroprevalence of IgG antibodies to SARS-CoV-2 in cancer outpatients and healthcare workers.

It has been assumed that cancer patients, especially those undergoing chemotherapy, are at increased risk for infection and severe illness from severe acute respiratory syndrome coronavirus 2 (sars-co v-2) compared to the general population.After the first alert message from the local healthcare service, a series of drastic measures were taken at our outpatient clinic to contain the spread of coronavirus disease 2019 (covid-19).Methods in this retrospective study, all consecutive cancer outpatients completed a baseline sars-co v‐2 test via real-time polymerase chain reaction (rt-pcr) from 15 march to 26 may 2020.In the later phase, after the peak of the pandemic, patients as well as healthcare workers were tested for anti-sars-co v‐2 ig g antibodies.Results between 15 march and 26 may 2020, 0.78% (n = 5/640) cancer patients tested positive for sars-co v‐2 by rt-pcr.Between 22 june and 17 july 2020, anti-sars-co v‐2 ig g antibodies were detected in 2 out of 250 (0.8%) cancer patients and 2 out of 36 (5.5%) healthcare workers.In only 1 out of 4 cancer patients with confirmed covid-19 infection, could sars-co v‐2 antibodies be detected.Conclusion our findings suggest that the majority of our patients and healthcare workers had not been infected with sars-co v‐2 and rapidly implemented measures were effective.Maintenance of preventive measures should be continued until vaccines or specific treatments are available.

Journal: Wiener klinische Wochenschrift (2021)
Publication types: Journal Article
Healthcare costs and hospitalizations in US patients with type 2 diabetes and cardiovascular disease: A retrospective database study (OFFSET).

To investigate the budget implications of treatment with glucagon-like peptide-1 receptor agonists (glp-1 ras) versus other glucose-lowering treatment (here termed 'standard of care' [so c]) during 2012-2019.Materials and methods glp-1 ra-naïve adults with type 2 diabetes (t2d) in the ibm market scan database with at least one glucose-lowering medication claim within 6 months after their first cardiovascular disease (cvd) hospitalization were included (index date was the date of first claim for a glp-1 ra for the glp-1 ra group, and the date of the first claim, independent of medication type, for the so c group).Monthly healthcare costs and hospitalization risk over 12 months postindex date were compared for those who initiated a glp-1 ra posthospitalization versus those with a claim for any other glucose-lowering medication.Results postindex date, mean observed total costs were lower for patients receiving a glp-1 ra compared with so c ($3853 vs.$4288).In adjusted analysis, both groups had similar total healthcare costs (p = .56).This was driven by significantly lower inpatient and outpatient costs and higher drug costs in the glp-1 ra group compared with so c (p < .001).Risks of all-cause (adjusted hazard ratio: 0.85) and cvd-related hospitalization (0.76) were significantly lower in the glp-1 ra group compared with so c (p < .001).Similar results were observed in a subgroup with atherosclerotic cvd.Conclusions these findings suggest that, in us patients with t2d and a cvd-related hospitalization, the added medical cost of treatment with glp-1 ras is offset by lower inpatient and outpatient care costs, resulting in budget neutrality against so c.

Journal: Diabetes, obesity & metabolism (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Systematic control of collective variables learned from variational autoencoders.

Variational autoencoders (vaes) are rapidly gaining popularity within molecular simulation for discovering low-dimensional, or latent, representations, which are critical for both analyzing and accelerating simulations.However, it remains unclear how the information a vae learns is connected to its probabilistic structure and, in turn, its loss function.Previous studies have focused on feature engineering, ad hoc modifications to loss functions, or adjustment of the prior to enforce desirable latent space properties.By applying effectively arbitrarily flexible priors via normalizing flows, we focus instead on how adjusting the structure of the decoding model impacts the learned latent coordinate.We systematically adjust the power and flexibility of the decoding distribution, observing that this has a significant impact on the structure of the latent space as measured by a suite of metrics developed in this work.By also varying weights on separate terms within each vae loss function, we show that the level of detail encoded can be further tuned.This provides practical guidance for utilizing vaes to extract varying resolutions of low-dimensional information from molecular dynamics and monte carlo simulations.

Journal: The Journal of chemical physics (2022)
Publication types: Journal Article
The role of Protein Disulfide Isomerase and thiol bonds modifications in activation of integrin subunit alpha11.

Integrins belong to a family of transmembrane receptors that mediate cell migration and adhesion to ecm.Extracellular domains of integrin heterodimers contain cysteine-rich regions, which are potential sites of thiol-disulfide exchanges.Rearrangements of extracellular disulfide bonds regulate activation of integrin receptors by promoting transition from an inactive state into a ligand-binding competent state.Modifications of integrin disulfide bonds dependent on oxidation-reduction can be mediated by protein disulfide isomerse (pdi).This paper provides evidences that binding to integrin ligands initiate changes in free thiol pattern on cell surface and that thiol-disulfide exchange mediated by pdi leads to activation of integrin subunit α11.By employing co-immunoprecipitation and confocal microscopy analysis we showed that α11β1 and pdi create complexes bounded by disulfide bonds.Using surface plasmon resonance we provide biochemical evidence that pdi can interact directly with integrin subunit α11.

Journal: Biochemical and biophysical research communications (2018)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Athena Speciality Certificate Examination case for formulation and systemic therapy.

This athena case describes possible differential diagnoses in a patient with multiple blisters.Histopathology showed subepidermal clefting and superficial dermal inflammation, while immunohistochemistry showed linear deposition of ig g and c3 along the basement membrane zone.

Journal: Clinical and experimental dermatology (2022)
Publication types: Journal Article
Leaching of Atoms, Clusters, and Nanoparticles.

Since the elucidation of the leaching process by mizoroki in the 1970s, the research focused on this problem has increased.As a result, it has been discovered that the leached metals can not only hinder product yield, but they can also remain as contaminants of the final products.Thus, it can be concluded that metal leaching needs to be diminished or avoided more efficiently.This problem is important for the industry and the environment because of the increases in costs and pollution.In 2014, we reported a brief review related to this important feature; now we would like to report on the latest findings on this important phenomenon, including an update on the mechanisms used to explain leaching and the reactions that support those mechanisms and including patents related to leaching in catalysis that have appeared in recent years.

Journal: Recent patents on nanotechnology (2021)
Publication types: Journal Article
Using Iterative RE-AIM to enhance hospitalist adoption of lung ultrasound in the management of patients with COVID-19: an implementation pilot study.

Lung ultrasound (lus) is a clinician-performed evidence-based imaging modality that has multiple advantages in the evaluation of dyspnea caused by multiple disease processes, including covid-19.Despite these advantages, few hospitalists have been trained to perform lus.The aim of this study was to increase adoption and implementation of lus during the 2020 covid-19 pandemic by using recurrent assessments of re-aim outcomes to iteratively revise our implementation strategies.Methods in an academic hospital, we implemented guidelines for the use of lus in patients with covid-19 in july 2020.Using a novel "re-aim dashboard," we used an iterative process of evaluating the high-priority outcomes of reach, adoption, and implementation at twice monthly intervals to inform revisions of our implementation strategies for lus delivery (i.e., iterative re-aim process).Using a convergent mixed methods design, we integrated quantitative re-aim outcomes with qualitative hospitalist interview data to understand the dynamic determinants of lus reach, adoption, and implementation.Results over the 1-year study period, 453 luss were performed in 298 of 12,567 eligible inpatients with covid-19 (reach = 2%).These 453 lus were ordered by 43 out of 86 eligible hospitalists (lus order adoption = 50%).However, the luss were performed/supervised by only 8 of these 86 hospitalists, 4 of whom were required to complete lus credentialing as members of the hospitalist procedure service (proceduralist adoption 75% vs 1.2% non-procedural hospitalists adoption).Qualitative and quantitative data obtained to evaluate this iterative re-aim process led to the deployment of six sequential implementation strategies and 3 key findings including (1) there were covid-19-specific barriers to lus adoption, (2) hospitalists were more willing to learn to make clinical decisions using lus images than obtain the images themselves, and (3) mandating the credentialing of a strategically selected sub-group may be a successful strategy for improving reach.Conclusions mandating use of a strategically selected subset of clinicians may be an effective strategy for improving reach of lus.Additionally, use of iterative re-aim allowed for timely adjustments to implementation strategies, facilitating higher levels of lus adoption and reach.Future studies should explore the replicability of these preliminary findings.

Journal: Implementation science communications (2022)
Publication types: Journal Article
Pattern Analysis of Organellar Maps for Interpretation of Proteomic Data.

Localization of organelle proteins by isotope tagging (lopit) maps are a coordinate-directed representation of proteome data that can aid in biological interpretation.Analysis of organellar association for proteins as displayed using lopit is evaluated and interpreted for two types of proteomic data sets.First, test and control group protein abundances and fold change data obtained in a proximity labeling experiment are plotted on a lopit map to evaluate the likelihood of true protein interactions.Selection of true positives based on co-localization of proteins in the organellar space is shown to be consistent with carboxylase enrichment which serves as a positive control for biotinylation in streptavidin affinity selected proteome data sets.The mapping in organellar space facilitates discrimination between the test and control groups and aids in identification of proteins of interest.The same representation of proteins in organellar space is used in the analysis of extracellular vesicle proteomes for which protein abundance and fold change data are evaluated.Vesicular protein organellar localization patterns provide information about the subcellular origin of the proteins in the samples which are isolates from the extracellular milieu.The organellar localization patterns are indicative of the provenance of the vesicular proteome origin and allow discrimination between proteomes prepared using different enrichment methods.The patterns in lopit displays are easy to understand and compare which aids in the biological interpretation of proteome data.

Journal: Proteomes (2022)
Publication types: Journal Article
Single-fraction stereotactic radiosurgery for spindle cell oncocytoma: preliminary experience and systematic review of the literature.

Spindle cell oncocytoma (sco) is a rare benign pituitary tumor.No patient series regarding stereotactic radiosurgery (srs) for sco has been published.We report the clinical outcomes of sco treated with single-fraction srs, as well as a systematic review of the literature.Methods retrospective cohort series and systematic literature review.Results five patients (four male, one female) having single-fraction srs for persistent or recurrent sco between 2002 and 2018.Median age was 56 (range 54-79) years.Pre-srs treatments included transsphenoidal resection (tsr) (n = 3), multiple tsr (n = 1), and tsr, radiotherapy, and craniotomy (n = 1).Median target volume was 4.7 (range 1.8-8.4) cm3, with a median tumor margin dose of 17 (range 14-20) gy.Median follow-up was 24 (range 10-69) months.All radiation-naïve patients achieved tumor control after srs; tumor progression was noted 24 months after srs in one patient who failed prior radiotherapy.No radiation-induced complications were observed after srs.Systematic literature review of 43 cases in addition to the five cases presented here showed that tumor progression/recurrence was more frequent after str compared to gtr (p < 0.001).Ten previous cases of radiotherapy for sco have been reported, but most did not detail radiation volumes, doses, or outcomes.Conclusions sco are uncommon sellar lesions with a propensity for progression or recurrence.Based on the clinically aggressive course of these tumors, adjuvant srs after str or at the time of tumor recurrence should be considered.Further case accumulation and follow-up is required to better understand the long-term treatment outcomes after single-fraction srs for these rare tumors.

Journal: Journal of neuro-oncology (2019)
Publication types: Journal Article;Systematic Review
External validation of an artificial intelligence tool for radiographic knee osteoarthritis severity classification.

To externally validate an artificial intelligence (ai) tool for radiographic knee osteoarthritis severity classification on a clinical dataset.Method this retrospective, consecutive patient sample, external validation study used weight-bearing, non-fixed-flexion posterior-anterior knee radiographs from a clinical production pacs.The index test was ordinal kellgren-lawrence grading by an ai tool, two musculoskeletal radiology consultants, two reporting technologists, and two resident radiologists.Grading was repeated by all readers after at least four weeks.Reference test was the consensus of the two consultants.The primary outcome was quadratic weighted kappa.Secondary outcomes were ordinal weighted accuracy, multiclass accuracy and f1-score.Results 50 consecutive patients between september 24, 2019 and october 22, 2019 were retrospectively included (3 excluded) totaling 99 knees (1 excluded).Quadratic weighted kappa for the ai tool and the consultant consensus was 0.88 ci95% (0.82-0.92).Agreement between the consultants was 0.89 ci95% (0.85-0.93).Intra-rater agreements for the consultants were 0.96 ci95% (0.94-0.98) and 0.94 ci95% (0.91-0.96) respectively.For the ai tool it was 1 ci95% (1-1).For the ai tool, ordinal weighted accuracy was 97.8% ci95% (96.9-98.6 %).Average multiclass accuracy and f1-score were 84% (83/99) ci95% (77-91%) and 0.67 ci95% (0.51-0.81).Conclusions the ai tool achieved the same good-to-excellent agreement with the radiology consultant consensus for radiographic knee osteoarthritis severity classification as the consultants did with each other.

Journal: European journal of radiology (2022)
Publication types: Journal Article
Serum soluble B7-H3 is a prognostic marker for patients with non-muscle-invasive bladder cancer.

B7-h3 is a member of the b7 family of immune-regulatory ligands and is a costimulatory molecule promoting the t cell response in vitro.We herein investigated the clinical utility of serum soluble b7-h3 (s b7-h3) in patients with non-muscle invasive bladder cancer (nmibc).Methods we analyzed 555 patients in whom nmibc was diagnosed at tokyo metropolitan tama medical center between 2008 and 2013.We measured the serum s b7-h3 (s b7-h3) level using the enzyme-linked immunosorbent assay (elisa) and evaluated the utility of s b7-h3 as a prognostic biomarker for nmibc.We used the cox proportional hazards regression model to assess recurrence-free survival (rfs) and progression-free survival (pfs) with the s b7-h3 level.Results we detected high levels of s b7-h3 in the sera of 47% of patients with nmibc versus only 8% in healthy donors.The increase of s b7-h3 was significantly associated with poor rfs and pfs.Multivariate analysis showed that elevated s b7-h3 was an independent prognostic factor of rfs and pfs.According to the european organization for research and treatment of cancer (eortc), in intermediate-low and intermediate-high risk groups, the presence of s b7-h3 significantly determined the rate of recurrence and progression.Conclusions our data suggested that evaluating serum s b7-h3 expression is a useful tool for predicting the prognosis of patients with nmibc.

Journal: PloS one (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Technical note: A fast and robust integrator of delay differential equations in DCM for electrophysiological data.

Dynamic causal models (dcms) of electrophysiological data allow, in principle, for inference on hidden, bulk synaptic function in neural circuits.The directed influences between the neuronal elements of modeled circuits are subject to delays due to the finite transmission speed of axonal connections.Ordinary differential equations are therefore not adequate to capture the ensuing circuit dynamics, and delay differential equations (ddes) are required instead.Previous work has illustrated that the integration of ddes in dcms benefits from sophisticated integration schemes in order to ensure rigorous parameter estimation and correct model identification.However, integration schemes that have been proposed for dcms either emphasize speed (at the possible expense of accuracy) or robustness (but with computational costs that are problematic in practice).In this technical note, we propose an alternative integration scheme that overcomes these shortcomings and offers high computational efficiency while correctly preserving the nature of delayed effects.This integration scheme is available as open-source code in the translational algorithms for psychiatry-advancing science (tapas) toolbox and can be easily integrated into existing software (spm) for the analysis of dcms for electrophysiological data.While this paper focuses on its application to the convolution-based formalism of dcms, the new integration scheme can be equally applied to more advanced formulations of dcms (e.g.Conductance based models).Our method provides a new option for electrophysiological dcms that offers the speed required for scientific projects, but also the accuracy required for rigorous translational applications, e.g.In computational psychiatry.

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