syedzayyan/paper_mill_benchmark huggingface dataset:
Individual recombinant repeats of MUC16 display variable binding to CA125 antibodies.

Despite its importance in the clinical management of ovarian cancer, the ca125 biomarker-located on the mucin protein muc16-is still not completely understood.Questions remain about muc16's function and structure, specifically the identity and location of the ca125 epitopes.Objective the goal of this study was to characterize the interaction of individual recombinant repeats from the tandem repeat domain of muc16 with antibodies used in the clinical ca125 ii test.Methods using e.Coliexpression, we isolated nine repeats from the putative antigenic domain of ca125.Amino acid composition of recombinant repeats was confirmed by high-resolution mass spectrometry.We characterized the binding of four antibodies-oc125, m11, "oc125-like," and "m11-like"-to nine recombinant repeats using western blotting, indirect enzyme-linked immunosorbent assay (elisa), and localized surface plasmon resonance (spr) spectroscopy.Results each recombinant repeat was recognized by a different combination of ca125 antibodies.Oc125 and "oc125-like" antibodies did not bind the same set of recombinant repeats, nor did m11 and "m11-like" antibodies.Conclusions characterization of the interactions between muc16 recombinant repeats and ca125 antibodies will contribute to ongoing efforts to identify the ca125 epitopes and improve our understanding of this important biomarker.

Journal: bioRxiv : the preprint server for biology (2023)
Publication types: Preprint;Journal Article
The full cohort of 512 patients and the nested controlled trial in 93 patients in the Pulmonary Metastasectomy in Colorectal Cancer (PulMiCC) study raise doubts about the effective size at present claimed.

A comparison of the relative merits of video-assisted pulmonary metastasectomy versus thoracotomy is predicated on the assumption that removal of asymptomatic lung metastases favourably influences survival and that it does so by a large degree.Recently published but long-awaited evidence from a prospective cohort study and a randomised trial of pulmonary metastasectomy in colorectal cancer (pul mi cc) challenges that assumption.

Journal: Journal of cardiothoracic surgery (2022)
Publication types: Letter;Randomized Controlled Trial
Abdominal multiorgan procurement from slaughterhouse pigs: a bespoke model in organ donation after circulatory death forex vivoorgan perfusion compliant with the 3 Rs (Reduction, Replacement & Refinement).

Advances in organ preservation, reconditioning and assessment have been driven by the increasing necessity to utilise organs from extended criteria donors, particularly donors after circulatory death.Research efforts in this area have aided translation of machine perfusion technology into clinical practice.Pigs are anatomically and physiologically similar to humans and are an excellent model.However, conducting large animal experimental research is challenging and typically limited by ethical and economic constraints.Here we describe a reproducible, cost-effective multi-organ abdominal procurement model of porcine organs from the slaughterhouse.Methods domestic pigs are electrically stunned and exsanguinated following the standard abattoir process.Via a longitudinal midline incision, the thoracoabdominal viscera are removeden blocby incising along the anterior vertebral plane.The abdominal organs are isolated, perfused and separated preserving their respective vasculature, allowing individual organ use for specific experiments.Results the warm ischaemic time is kept between 15-30 minutes.Using this highly protocolized procurement technique we have procured 12 livers, 162 kidneys and 12 pancreata for research, the majority of which have been utilized forex situperfusion experiments.Conclusions we have described a reliable and reproducible procedure for abdominal multi-organ procurement from slaughterhouse pigs.

Journal: Annals of translational medicine (2022)
Publication types: Journal Article
Enabling Attribute-Based Access Control in Linux Kernel.

Linux has built-in security features based on discretionary access control that can be enhanced using the linux security module (lsm) framework.However, so far there has been no reported work on strengthening linux with attribute-based access control (abac), which is gaining in popularity in recent years due to its flexibility and dynamic nature.In this paper, a method for enabling abac for linux file system objects using lsm is proposed.We report initial experimental results and also share our public repository links for integrating abac in any linux installation.

Journal: Asia CCS '22 : proceedings of the 2022 ACM Asia Conference on Computer and Communications Security : May 30-June 3, 2022, Nagasaki, Japan. ACM Asia Conference on Computer and Communications Security (17th : 2022 : Nagasaki-shi, Japan ; ... (2022)
Publication types: Journal Article
Soluble forms of PD-1/PD-L immune checkpoint receptor and ligand in blood serum of breast cancer patients: association with clinical pathologic factors and molecular type of the tumor.

Results of enzyme-linked immunosorbent assay of the soluble forms of pd-1/pd-l immune checkpoint receptor and ligand (s pd-1 and s pd-l1) in pretreatment blood serum of 88 breast cancer patients at various disease stages aged 30-83 years are presented.The control group included 55 practically healthy women aged 19-82 years.Serum s pd-1 and s pd-l1 levels in breast cancer patients highly significantly (p<0.0001) differ from control and these changes are opposite: soluble receptor level is more than 6-fold decreased, while soluble ligand concentration - 5.5 fold increased.Both markers separately, as well as their ratio demonstrate very high sensitivity (94-100%) and specificity (95-100%) in relation to healthy control.No statistically significant associations of s pd-1 and s pd-l1 levels with clinical stage, individual tnm system criteria, tumor histological structure, grade, receptor status, and molecular type were established.In particular, no significant peculiarities of the markers' levels in triple negative breast cancer successfully treated with anti-pd-1/pd-l1 preparations were revealed.Long-term follow-up and dynamic studies of s pd-1 and s pd-l1serum levels in the course of treatment are required for evaluation of their independent from clinical and morphological factors prognostic significance and the possibility of application as low invasive tests for prediction and monitoring of corresponding targeted therapy efficiency.

Journal: Klinicheskaia laboratornaia diagnostika (2022)
Publication types: Journal Article
Survey data showing the influences of school attachment among secondary school students in Albania.

This data article provides datasheet summary of the investigation conducted to determine the levels of school attachment among secondary school students in albania based on a five scaled assessment: 1) students feelings for school, 2) students interest in learning, 3) students attitudes towards peers, 4) students attitudes towards teachers, and 5) students perception of the school.The study primarily indicates validation of a self-report through a five-scaled assessment of school attachment based on the data collected from high school students (n= 1506) with equal distribution of regions (n= 6; prefectures) by reaching more than 1% of the total target population.The reliability of the entire scale was α = 0.737 with no mean difference between participant schools but with a mean difference of 1.55 in gender as secondary schools in albania had more female students according to instat.Data was gathered based on conclusive research design.Stratified and purposive sampling techniques were adopted.The research instrument was confirmed to have all the necessary psychometric values considered appropriate for the research.Some descriptive statistical analyses were carried out to further clarify the data and provide the necessary platform for further analyses.

Journal: Data in brief (2021)
Publication types: Journal Article
Outcomes from a Spanish Expanded Access Program on cannabidiol treatment in pediatric and adult patients with epilepsy.

To evaluate the effectiveness and tolerability of cannabidiol (cbd) in patients with developmental and epileptic encephalopathies, including dravet syndrome (ds), and lennox-gastaut syndrome (lgs), in a spanish expanded access program (eap).Methods this was a multicenter, retrospective, observational study of patients treated with purified cbd in 14 hospitals across spain.Patients with (1) written informed consent and (2) at least 6 months follow-up before the closure of the database were included.Primary effectiveness endpoints included reductions (100 %, ≥75 %, ≥50 %, ≥25 %, or 0 %) or worsening in seizure frequency (all seizure types and most disabling seizures) at 1-, 3-, 6-, and 12-month visits and at the last visit, and median relative seizure reduction between baseline and last visit.Secondary effectiveness endpoints included retention rate, reduction in seizure severity, status epilepticus, healthcare utilization, and quality of life.Primary safety endpoints included rates of adverse events (aes) and aes leading to discontinuation.Results one hundred and two patients (ds 12 %; lgs 59 %; other epilepsy syndromes 29 %) with a mean age of 15.9 years were enrolled.Patients were highly refractory to antiseizure medications (asms); mean number of prior failed asms was 7.5 (sd 3.7).The mean cbd dose was 13.0 mg/kg/day at the last visit.The proportion of patients with ≥50 % reduction in the total number of seizures from baseline was 44.9 % at 6 months and 38.9 % at 12 months.The median number of total seizures per month reduced by 47.6 % from baseline to the last visit.At 12 months, seizure severity was lower in 33/54 patients (61.1 %) and unchanged in 17/54 patients (31.5 %).Quality of life, based on the cave scale, increased from a mean score of 17.9 ± 4.7 (n = 54) at baseline to 21.7 ± 5.5 (n = 51) at the last patient visit (21.2 % improvement).The mean treatment retention time was 10.3 months.There were no statistically significant changes in the number of status epilepticus episodes, but lower healthcare utilization was observed.Adverse events occurred in sixty-eight patients (66.7 %), and the most common were somnolence (34.3 %) and diarrhea (12.7 %).Cannabidiol was discontinued exclusively due to aes in 7.8 % of patients, increasing to 25.5 % when both lack of efficacy and aes were considered together.Conclusions cannabidiol demonstrated promising effectiveness and tolerability in patients with developmental and epileptic encephalopathies taking part in a spanish eap.

Journal: Epilepsy & behavior : E&B (2022)
Publication types: Observational Study;Multicenter Study;Journal Article;Research Support, Non-U.S. Gov't
Evaluation of theIn VitroAntimicrobial Activities ofDelphinium roylei: An Insight from Molecular Docking and MD-Simulation Studies.

Ethnopharmacological relevance the burden of antimicrobial resistance demands a continued search for new antimicrobial drugs.The synthetic drugs used clinically have serious side effects.Natural products or compounds derived from natural sources show diversity in structure and play an essential role in drug discovery and development.Objective delphinium roylei is an important medicinal herb of kashmir himalaya, india.Traditionally this medicinal plant treats liver infections, skin problems, and chronic lower back pain.The current study evaluates the antimicrobial potential of various extracts by in -vitro and in -silico studies.Methods three extracts and 168 bioactive compounds analysed through lc-ms data, with the vast majority of them having therapeutic applications.D.Roylei have been screened for the antimicrobial activity against bacteria (escherichai coli, streptococcus pneumonia, haemophilus influenzae, neisseria mucosa) and fungi (candida albicans, candida glabrata, candida paropsilosis) species through molecular docking using autodock vina, md simulation and a broth microdilution method for minimum inhibitory concentration (mic) evaluation.Results the extracts and the compounds analyzed through the lc-ms technique of delphinium roylie showed significant antimicrobial activity.Conclusion our study established that the leaf extracts of delphinium roylei exhibit antimicrobial activity and thus confirm its importance in traditional medicine.

Journal: Medicinal chemistry (Shariqah (United Arab Emirates)) (2022)
Publication types: Journal Article
Inhibitory Effect ofLactobacillus delbrueckiisubsp.bulgaricusKSFY07 on Kappa-Carrageenan-Induced Thrombosis in Mice and the Regulation of Oxidative Damage.

A mouse thrombosis model was established by kappa-carrageenan to observe the inhibitory effect of lactobacillus delbrueckiisubsp.bulgaricus ksfy07 (ldsb-ksfy07) on thrombosis and the oxidative stress response.Mouse serum, liver tissue-related indicators, and intestinal microbial composition were measured by examining the expression of microbes in mouse faeces using a biochemical kit, slice observations, and quantitative polymerase chain reaction (q pcr) experiments.The results showed that ldsb-ksfy07 effectively reduced the degree of black tail in thrombotic mice, increased activated partial thromboplastin time (aptt), and decreased thrombin time (tt), fibrinogen (fib), and prothrombin time (pt) in thrombotic mice.Ldsb-ksfy07 was also able to reduce malondialdehyde (mda) levels and increase superoxide dismutase (sod), catalase (cat), and glutathione peroxidase (gsh-px) levels in the serum and liver tissues of thrombotic mice.Pathological observations showed that ldsb-ksfy07 reduced liver tissue lesions and tail vein thrombosis.Further, experimental results showed that ldsb-ksfy07 was able to upregulate the m rna expression of copper/zinc-sod (cu/zn-sod), manganese-sod, and gsh-px in the liver tissue of thrombotic mice.Moreover, ldsb-ksfy07 was also able to downregulate the m rna expression of nf-κb p65, intercellular cell adhesion molecule-1 (icam-1), vascular cell adhesion molecule-1 (vcam-1), and e-selectin in tail vein vascular tissue.Meanwhile, ldsb-ksfy07 could raise plasminogen activator inhibitor-1 (pai-1) m rna expression and reduce tissue plasminogen activator (t-pa) expression in heart and tail vein vascular tissues of thrombotic mice.A mouse faeces examination revealed that ldsb-ksfy07 could also upregulate bacteroides,lactobacterium, and bifidobacteriummicrobial expression and downregulate firmicutesexpression in the gut.These results indicate that ldsb-ksfy07 was able to inhibit mouse thrombosis and reduce liver oxidative stress damage in thrombus mice and show that high concentrations of ldsb-ksfy07 provided a better response similar to that of the drug heparin.

Journal: Cardiovascular therapeutics (2022)
Publication types: Journal Article
Insight into genomic organization of pathogenic coronaviruses, SARS-CoV-2: Implication for emergence of new variants, laboratory diagnosis and treatment options.

Sars-co v-2 is a novel zoonotic positive-sense rna virus (ss rna+) belonging to the genus beta coronaviruses (co vs) in the coronaviridae family.It is the causative agent for the outbreak of the disease, covid-19.It is the third co v causing pneumonia around the world in the past 2 decades.To date, it has caused significant deaths worldwide.Notably, the emergence of new genetic variants conferring efficient transmission and immune evasion remained a challenge, despite the reduction in the number of death cases, owing to effective vaccination regimen (boosting) and safety protocols.Thus, information harnessed from sars-co v-2 genomic organization is indispensable for seeking laboratory diagnosis and treatment options.Here in, we review previously circulating variants of sars-co v-2 designated variant of concern (voc) including the alpha (united kingdom), beta (south africa), gamma (brazil), delta (india), and recently circulating voc, omicron (south africa) and its divergent subvariants (ba.1, ba.2, ba.3, ba.2.12.1, ba.4 and ba.5) with ba.5 currently becoming dominant and prolonging the covid pandemic.In addition, we address the role of computational models for mutagenesis analysis which can predict important residues that contribute to transmissibility, virulence, immune evasion, and molecular detections of sars-co v-2.Concomitantly, the importance of harnessing the immunobiology of sars-co v-2 and host interaction for therapeutic purpose; and use of an in slilico based biocomputational approaches to achieve this purposeviapredicting novel therapeutic agents targeting prr such as toll like receptor, design of universal vaccine and chimeric antibodies tailored to the emergent variant have been highlighted.

Journal: Frontiers in molecular medicine (2022)
Publication types: Journal Article;Review
Immune benefit of combined heart and liver transplantation.

Of review understanding the mechanisms involved in immune protection provided by a hepatic allograft is imperative as further therapies for highly sensitized patients could be developed and thus expanding the donor pool and improving outcomes.Recent findings the clinical data from immune protection comes mainly from combined liver and kidney transplants with excellent results in overall survival and also that of the allograft.This phenomenon has also been observed in dual liver transplants with heart, lung, skin and intestines, albeit with less data.In heart transplant recipients, the liver allograft has proven to be protective even in cases of highly sensitized patients with at least equal survival and rejection outcomes to recipients of heart alone.Although not fully understood, the mechanisms for immune benefit proposed are extensive at different levels of the hepatic immune system.Some of these mechanisms include chimerism, t-cell deletion, the presence of peripheral regulatory t cells and donor-specific antibody neutralization.Summary combined heart and liver transplantation is an infrequent but growing procedure due to increasing need in the adult congenital heart disease and cardiac amyloid populations.Given the ever expanding need for heart transplantation, understanding immunological phenomena that could expand the donor pool could, subsequently, increase the number of transplants.

Journal: Current opinion in organ transplantation (2020)
Publication types: Journal Article;Review
More microbial manipulation and plant defense than soil fertility for biochar in food production: A field experiment of replanted ginseng with different biochars.

The role of biochar-microbe interaction in plant rhizosphere mediating soil-borne disease suppression has been poorly understood for plant health in field conditions.Chinese ginseng (panax ginseng c.A.Meyer) is widely cultivated in alfisols across northeast china, being often stressed severely by pathogenic diseases.In this study, the topsoil of a continuously cropped ginseng farm was amended at 20 t ha-1, respectively, with manure biochar (pb), wood biochar (wb), and maize residue biochar (mb) in comparison to conventional manure compost (mc).Post-amendment changes in edaphic properties of bulk topsoil and the rhizosphere, in root growth and quality, and disease incidence were examined with field observations and physicochemical, molecular, and biochemical assays.In the 3 years following the amendment, the increases over mc in root biomass were parallel to the overall fertility improvement, being greater with mb and wb than with pb.Differently, the survival rate of ginseng plants increased insignificantly with pb but significantly with wb (14%) and mb (21%), while ginseng root quality was unchanged with wb but improved with pb (32%) and mb (56%).For the rhizosphere at harvest following 3 years of growing, the total content of phenolic acids from root exudate decreased by 56, 35, and 45% with pb, wb, and mb, respectively, over mc.For the rhizosphere microbiome, total fungal and bacterial abundance both was unchanged under wb but significantly increased under mb (by 200 and 38%), respectively, over mc.At the phyla level, abundances ofarbuscular mycorrhizaland bryobacteras potentially beneficial microbes were elevated while those of fusariumand ilyonectriaas potentially pathogenic microbes were reduced, with wb and mb over mc.Moreover, rhizosphere fungal network complexity was enhanced insignificantly under pb but significantly under wb moderately and mb greatly, over mc.Overall, maize biochar exerted a great impact rather on rhizosphere microbial community composition and networking of functional groups, particularly fungi, and thus plant defense than on soil fertility and root growth.

Journal: Frontiers in microbiology (2022)
Publication types: Journal Article
Inhibition of TXNDC5 attenuates lipopolysaccharide-induced septic shock by altering inflammatory responses.

Sepsis and its severe form, septic shock, represent the leading cause of death among hospitalized patients.Thioredoxin is a ubiquitous protein essential for cellular redox balance and its aberrant expression is associated with a wide spectrum of inflammation-related pathological conditions.The current study aimed to compare the expression of thioredoxin domain containing 5 (txndc5) in septic patients with or without septic shock and to explore the potential regulatory effects of txndc5 in sepsis.We analyzed the rna expression data downloaded from the gene expression omnibus database and measured the plasma level of txndc5 in septic patients.The results showed that txndc5 was upregulated in patients with septic shock compared to septic patients without shock or healthy controls.We further treated wild-type mice and cultured macrophages with lipopolysaccharide (lps) and found that txndc5 was highly expressed in mice with lps-induced sepsis and macrophages subjected to lps stimulation compared to corresponding controls.Then a mouse strain with targeted depletion of txndc5 was generated.Txndc5 depletion reduced inflammatory cytokine production and affected the recruitment of macrophages and neutrophils into the blood and peritoneum of mice challenged with lps.Further analysis revealed that txndc5 inhibition alleviated lps-induced sepsis by inhibiting the nf-κb signaling pathway.In summary, these findings suggested that the inhibition of txndc5 may be a potential approach to treat sepsis and related syndromes.

Journal: Laboratory investigation; a journal of technical methods and pathology (2022)
Publication types: Journal Article