syedzayyan/paper_mill_benchmark huggingface dataset:
Determining the time frame of maximum clinical improvement in surgical decompression for cervical spondylotic myelopathy when stratified by preoperative myelopathy severity: a cervical Quality Outcomes Database study.

While surgical decompression is an important treatment modality for cervical spondylotic myelopathy (csm), it remains unclear if the severity of preoperative myelopathy status affects potential benefit from surgical intervention and when maximum postoperative improvement is expected.This investigation sought to determine if retrospective analysis of prospectively collected patient-reported outcomes (pros) following surgery for csm differed when stratified by preoperative myelopathy status.Secondary objectives included assessment of the minimal clinically important difference (mcid).Methods a total of 1151 patients with csm were prospectively enrolled from the quality outcomes database at 14 us hospitals.Baseline demographics and pros at baseline and 3 and 12 months were measured.These included the modified japanese orthopaedic association (m joa) score, neck disability index (ndi), quality-adjusted life-years (qalys) from the eq-5d, and visual analog scale from the eq-5d (eq-vas).Patients were stratified by preoperative myelopathy severity using criteria established by the ao spine study group: mild (m joa score 15-17), moderate (m joa score 12-14), or severe (m joa score < 12).Univariate analysis was used to identify demographic variables that significantly varied between myelopathy groups.Then, multivariate linear regression and linear mixed regression were used to model the effect of severity and time on pros, respectively.Results for ndi, eq-vas, and qaly, patients in all myelopathy cohorts achieved significant, maximal improvement at 3 months without further improvement at 12 months.For m joa, moderate and severe myelopathy groups demonstrated significant, maximal improvement at 3 months, without further improvement at 12 months.The mild myelopathy group did not demonstrate significant change in m joa score but did maintain and achieve higher pro scores overall when compared with more advanced myelopathy cohorts.The mcid threshold was reached in all myelopathy cohorts at 3 months for m joa, ndi, eq-vas, and qaly, with the only exception being mild myelopathy qaly at 3 months.Conclusions as assessed by statistical regression and mcid analysis, patients with cervical myelopathy experience maximal improvement in their quality of life, neck disability, myelopathy score, and overall health by 3 months after surgical decompression, regardless of their baseline myelopathy severity.An exception was seen for the m joa score in the mild myelopathy cohort, improvement of which may have been limited by ceiling effect.The data presented here will aid surgeons in patient selection, preoperative counseling, and expected postoperative time courses.

Journal: Journal of neurosurgery. Spine (2022)
Publication types: Journal Article
A novel 10-gene ferroptosis-related prognostic signature in acute myeloid leukemia.

Acute myeloid leukemia (aml) is one of the most common hematopoietic malignancies and exhibits a high rate of relapse and unfavorable outcomes.Ferroptosis, a relatively recently described type of cell death, has been reported to be involved in cancer development.However, the prognostic value of ferroptosis-related genes (frgs) in aml remains unclear.In this study, we found 54 differentially expressed ferroptosis-related genes (defrgs) between aml and normal marrow tissues.18 of 54 defrgs were correlated with overall survival (os) (p<0.05).Using the least absolute shrinkage and selection operator (lasso) cox regression analysis, we selected 10 defrgs that were associated with os to build a prognostic signature.Data from aml patients from the international cancer genome consortium (icgc) cohort as well as the first affiliated hospital of wenzhou medical university (fahwmu) cohort were used for validation.Notably, the prognostic survival analyses of this signature passed with a significant margin, and the riskscore was identified as an independent prognostic marker using cox regression analyses.Then we used a machine learning method (shap) to judge the importance of each feature in this 10-gene signature.Riskscore was shown to have the highest correlation with this 10-gene signature compared with each gene in this signature.Further studies showed that aml was significantly associated with immune cell infiltration.In addition, drug-sensitive analysis showed that 8 drugs may be beneficial for treatment of aml.Finally, the expressions of 10 genes in this signature were verified by real-time quantitative polymerase chain reaction.In conclusion, our study establishes a novel 10-gene prognostic risk signature based on ferroptosis-related genes for aml patients and frgs may be novel therapeutic targets for aml.

Journal: Frontiers in oncology (2022)
Publication types: Journal Article
SSIF: Subsumption-based Sub-term Inference Framework to audit Gene Ontology.

Motivation the gene ontology (go) is the unifying biological vocabulary for codifying, managing and sharing biological knowledge.Quality issues in go, if not addressed, can cause misleading results or missed biological discoveries.Manual identification of potential quality issues in go is a challenging and arduous task, given its growing size.We introduce an automated auditing approach for suggesting potentially missing is-a relations, which may further reveal erroneous is-a relations.Results we developed a subsumption-based sub-term inference framework (ssif) by leveraging a novel term-algebra on top of a sequence-based representation of go concepts along with three conditional rules (monotonicity, intersection and sub-concept rules).Applying ssif to the october 3, 2018 release of go suggested 1938 unique potentially missing is-a relations.Domain experts evaluated a random sample of 210 potentially missing is-a relations.The results showed ssif achieved a precision of 60.61, 60.49 and 46.03% for the monotonicity, intersection and sub-concept rules, respectively.Availability and implementation ssif is implemented in java.The source code is available at supplementary information supplementary data are available at bioinformatics online.

Journal: Bioinformatics (Oxford, England) (2020)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, U.S. Gov't, Non-P.H.S.
Domino-like transient dynamics at seizure onset in epilepsy.

The international league against epilepsy (ilae) groups seizures into "focal", "generalized" and "unknown" based on whether the seizure onset is confined to a brain region in one hemisphere, arises in several brain region simultaneously, or is not known, respectively.This separation fails to account for the rich diversity of clinically and experimentally observed spatiotemporal patterns of seizure onset and even less so for the properties of the brain networks generating them.We consider three different patterns of domino-like seizure onset in idiopathic generalized epilepsy (ige) and present a novel approach to classification of seizures.To understand how these patterns are generated on networks requires understanding of the relationship between intrinsic node dynamics and coupling between nodes in the presence of noise, which currently is unknown.We investigate this interplay here in the framework of domino-like recruitment across a network.In particular, we use a phenomenological model of seizure onset with heterogeneous coupling and node properties, and show that in combination they generate a range of domino-like onset patterns observed in the ige seizures.We further explore the individual contribution of heterogeneous node dynamics and coupling by interpreting in-vitro experimental data in which the speed of onset can be chemically modulated.This work contributes to a better understanding of possible drivers for the spatiotemporal patterns observed at seizure onset and may ultimately contribute to a more personalized approach to classification of seizure types in clinical practice.

Journal: PLoS computational biology (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Bimetallic Metal-Organic Framework Fe/Co-MIL-88(NH2) Exhibiting High Peroxidase-like Activity and Its Application in Detection of Extracellular Vesicles.

Metal-organic frameworks (mofs) have many attractive features, including tunable composition, rigid structure, controllable pore size, and large specific surface area, and thus are highly applicable in molecular analysis.Depending on the mof structure, a high number of unsaturated metal sites can be exposed to catalyze chemical reactions.In the present work, we report that using both co(ii) and fe(iii) to prepare the mil-88(nh2) mof, we can produce the bimetallic mof that can catalyze the conversion of 3,3',5,5′′-tetramethylbenzidine (tmb) to a color product through a reaction with h2o2at a higher reaction rate than the monometallic fe-mil-88(nh2).The michaelis constants (km) of the catalytic reaction for tmb and h2o2are 3-5 times smaller, and the catalytic constants (kcat) are 5-10 times higher than those of the horseradish peroxidase (hrp), supporting ultrahigh peroxidase-like activity.These values are also much more superior to those of the hrp-mimicking mofs reported previously.Interestingly, the bimetallic mof can be coupled with glucose oxidase (gox) to trigger the cascade enzymatic reaction for highly sensitive detection of extracellular vesicles (evs), a family of important biomarkers.Through conjugation to the aptamer that recognizes the marker protein on ev surface, the mof can help isolate the evs from biological matrices, which are subsequently labeled by gox via antibody recognition.The cascade enzymatic reaction between mof and gox enables the detection of evs at a concentration as low as 7.8 × 104particles/m l.The assay can be applied to monitor ev secretion by cultured cells and also can successfully detect the different ev quantities in the sera samples collected from cancer patients and healthy controls.Overall, we prove that the bimetallic fe/co-mil-88(nh2) mof, with its high peroxidase activity and high biocompatibility, is a valuable tool deployable in clinical assays to facilitate disease diagnosis and prognosis.

Journal: ACS applied materials & interfaces (2022)
Publication types: Journal Article
Temperature Dependence for Survival, Development, and Reproduction of the Cactus CochinealDactylopius opuntiae(Cockerell).

The effect of temperature on dactylopius opuntiae(cockerell) life cycle parameters was evaluated at 20, 23, 26, 32, and 40 ± 1 °c, 65 ± 5% rh, and a photoperiod of 12 l:8 d.Temperatures ranging from 26 °c to 32 °c were suitable for survival, development, and reproduction of d.Opuntiae.The total developmental time of females ranged from 94.23 d (20 °c) to 43.55 d (40 °c).The average development time of males from egg to death ranged from 26.97 days at 32 °c to 50.75 days at 20 °c.The probability that a newly laid egg would survive to the adult stage was highest at 26 °c and 32 °c (44-60%).The parthenogenesis in females was not observed during our study.The longest oviposition period was observed when the cochineal was reared at 32 °c (17.97 days), and the highest fecundity was observed at 32 °c (355.29 egg/female).The highest proportion of females (0.80) was observed at 40 °c.According to the age-stage-two-sex life table, the highest value of the intrinsic rate of natural increase (rm) was recorded at 32 °c.The lower developmental thresholds for the total pre-adult female and male and adult female and male stages, were 10.15, 12.21, 10.54, and 21.04 °c, respectively.dactylopius opuntiaefemales needed a higher thermal constant (769.23 d°) than males (357.14 d°) to achieve their development and reach the mature adult stage.These findings will be useful for the development of an integrated pest management strategy for d.Opuntiae.

Journal: Insects (2022)
Publication types: Journal Article
Lung Transplantation in a Patient With COVID-19-Associated Acute Respiratory Failure.

Coronavirus disease 2019 (covid-19) is currently a significant cause of acute respiratory failure worldwide, leading to irreversible fibrotic lung disease.In patients with persistent respiratory failure after acute covid-19 infection, lung transplant is an emerging option.Here, we have presented a case where the patient required venovenous extracorporeal membrane oxygenation (vv-ecmo) support for 33 days until a bilateral lung transplant was performed on day 71 after the initial covid-19 infection.The early outcomes have been favorable.Currently, no guidelines exist for an acceptable time period after initial covid-19 infection, duration of negative covid polymerase chain reaction (pcr) testing, or negative vero cell culture in the setting of persistent positive covid pcr testing before listing for a lung transplant.Due to a lack of standardized guidelines, this patient was not listed for a lung transplant until the covid-19 pcrs came negative on days 47 and 49 after the infection.

Journal: Cureus (2021)
Publication types: Case Reports;Journal Article
The emerging molecular biology toolbox for the study of long noncoding RNA biology.

Long noncoding rnas (lnc rnas) have been implicated in many biological processes.However, due to the unique nature of lnc rnas and the consequential difficulties associated with their characterization, there is a growing disparity between the rate at which lnc rnas are being discovered and the assignment of biological function to these transcripts.Here we present a molecular biology toolbox equipped to help dissect aspects of lnc rna biology and reveal functionality.We outline an approach that begins with a broad survey of genome-wide, high-throughput datasets to identify potential lnc rna candidates and then narrow the focus on specific methods that are well suited to interrogate the transcripts of interest more closely.This involves the use of imaging-based strategies to validate these candidates and observe the behaviors of these transcripts at single molecule resolution in individual cells.We also describe the use of gene editing tools and interactome capture techniques to interrogate functionality and infer mechanism, respectively.With the emergence of lnc rnas as important molecules in healthy and diseased cellular function, it remains crucial to deepen our understanding of their biology.

Journal: Epigenomics (2017)
Publication types: Journal Article;Review;Research Support, Non-U.S. Gov't
Correlation between Characteristics of Coronary Plaque and Chinese Medicine Syndromes of Coronary Heart Disease: A Cross-Sectional Study Analysed by Intravascular Ultrasound.

To analyse the correlation between the characteristics of coronary plaque in coronary heart disease (chd) patients with phlegm-blood stasis syndrome (pbs) and blood stasis syndrome (bss).Methods patients were divided into different groups based on chinese medicine (cm) syndrome differentiation.The baseline demographics and clinical variables were collected from the medical records.Additionally, the characteristics of plaque and pathological manifestations in coronary artery were evaluated using intravascular ultrasound (ivus).Results a total of 213 chd patients were enrolled in two groups: 184 were diagnosed with pbs and the remaining 29 were diagnosed with bss.There were no significant differences in age, body mass index, proportions of patients with high blood pressure, diabetes mellitus, smoking, hyperlipidemia, history of coronary artery bypass graft and percutaneous coronary intervention, medications, index from cardiac ultrasound image, blood lipids and c-reactive protein between the two groups (p>0.05), except gender, weight and proportions of ivus observed target vessels (p<0.05 or p<0.01).More adverse events such as acute myocardial infarction (p=0.003) and unstable angina (p=0.048) were observed in bss.Additionally, dissection, thrombus and coronary artery ectasia were significantly increased in bss (p<0.05 or p<0.01).In contrast, pbs had more patients with stable angina and chronic total occlusion with significantly higher syntax (synergy between percutaneous coronary intervention with taxus and coronary artery bypass surgery) scores (p<0.05 or p<0.01).Moreover, dense-calcium was significantly elevated in pbs (p<0.01).Conclusions coronary plaque characteristics were correlated with different cm syndromes.Patients with pbs were associated with a higher degree of calcified plaque and severe coronary artery stenosis, indicating poor clinical prognosis but with a low probability of acute coronary events.In contrast, the degree of calcified plaque in patients with bss remained relatively low, and plaque was more vulnerable, resulting in the possibility of the occurrence of acute coronary events remaining high.

Journal: Chinese journal of integrative medicine (2022)
Publication types: Journal Article
Evidence for poplar PtaPLATZ18 in the regulation of plant growth and vascular tissues development.

Introduction plant a/t-rich protein and zinc-binding protein (platz) are plant-specific transcription factors playing a role in plant development and stress response.To assess the role of platzs in vascular system development and wood formation in poplar, a functional study for pta platz18, whose expression was associated with the xylem, was carried out.Methods poplar dominant repressor lines for pta platz18were produced by overexpressing a pta platz18-srdxfusion.The phenotype of three independent transgenic lines was evaluated at morphological, biochemical, and molecular levels and compared to the wild type.Results the pta platz18-srdx lines showed increased plant height resulting from higher internode length.Besides, a higher secondary xylem thickness was also evidenced in these dominant repression lines as compared to the wild type suggesting an activation of cambial activity.A higher amount of lignin was evidenced within wood tissue as compared to the wild type, indicating an alteration in cell wall composition within xylem cell types.This latter phenotype was linked to an increased expression of genes involved in lignin biosynthesis and polymerization.Discussion the phenotype observed in the pta platz18-srdx lines argues that this transcription factor targets key regulators of plant growth and vascular tissues development.

Journal: Frontiers in plant science (2023)
Publication types: Journal Article
mRNA vaccines in the prevention and treatment of diseases.

Messenger ribonucleic acid (m rna) vaccines made their successful public debut in the effort against the covid-19 outbreak starting in late 2019, although the history of m rna vaccines can be traced back decades.This review provides an overview to discuss the historical course and present situation of m rna vaccine development in addition to some basic concepts that underly m rna vaccines.We discuss the general preparation and manufacturing of m rna vaccines and also discuss the scientific advances in the in vivo delivery system and evaluate popular approaches (i.e., lipid nanoparticle and protamine) in detail.Next, we highlight the clinical value of m rna vaccines as potent candidates for therapeutic treatment and discuss clinical progress in the treatment of cancer and coronavirus disease 2019.Data suggest that m rna vaccines, with several prominent advantages, have achieved encouraging results and increasing attention due to tremendous potential in disease management.Finally, we suggest some potential directions worthy of further investigation and optimization.In addition to basic research, studies that help to facilitate storage and transportation will be indispensable for practical applications.

Journal: MedComm (2022)
Publication types: Journal Article;Review
SARS-CoV-2-Specific T Cell Immunity in HIV-Associated Kaposi Sarcoma Patients in Zambia.

Severe acute respiratory syndrome coronavirus type 2 (sars-co v-2) virus is the cause of coronavirus disease 2019 (covid-19).It has caused millions of infections and deaths globally over a 2-year period.Some populations including those living with hiv and/or cancer are reported to be at a higher risk of infection and severe disease.Hiv infection leads to a depletion of cd4+t cells which impairs cell-mediated immunity and increases the risk of malignancies such as kaposi sarcoma (ks) and viral infections such as sars-co v-2.However, several other factors including level of immunosuppression and chemotherapy may also affect the immune response against sars-co v-2.In this study, we investigated factors affecting sars-co v-2-specific t cell immunity towards the spike, nucleoprotein, membrane protein, and other open reading frame proteins in individuals with hiv-associated ks.The ks patients were sars-co v-2 seropositive with detectable t cell responses, but had no history of symptomatic sars-co v-2 infection.We observed that the t cell responses increase from baseline levels during follow-up, with responses towards the nmo peptide pool being statistically significant.Low cd4 counts below 200 cells/μl were associated with lower sars-co v-2-specific t cell responses.Cancer chemotherapy and ks t staging did not have a significant effect on the t cell responses.

Journal: Journal of immunology research (2022)
Publication types: Journal Article
Correlation of metabolic syndrome with serum omentin-1 and visfatin levels and disease severity in psoriasis and psoriatic arthritis.

Psoriasis and psoriatic arthritis (ps a) have been linked to metabolic syndrome (ms).The impact of adipokines on psoriasis, ps a, and ms pathogenesis has recently received investigative attention.A total of 80 subjects with psoriasis, 40 subjects with ps a, and 60 healthy controls were enrolled.Serum omentin and visfatin levels were measured, and ms presence was determined.Pasi and das28 were used to measure disease severity for psoriasis and ps a, respectively.The prevalence of ms was determined to be 49% in psoriasis, 48% in ps a, and 28% in control groups.Rates were similar in psoriasis and ps a groups and was significantly greater when compared to control (p = .028).Diastolic blood pressure and waist circumference were significantly greater in the psoriasis group.Although the presence of ms positively correlated with age and disease duration in the psoriasis group, no significant relationships with pasi and das28 were found.Among all groups combined, there was no significant relationship with omentin and visfatin levels.In the psoriasis group, omentin and visfatin levels were greater in those with ms compared to those without ms.The relationships between omentin and visfatin levels with ms in patients with psoriasis and ps a has not yet been fully elucidated.These results suggest that elevated omentin and visfatin levels seen in psoriasis may be linked to ms rather than psoriasis itself.Additional research is needed to investigate the utility of these measurements as indicators of ms in patients with psoriasis.

Journal: Dermatologic therapy (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't