syedzayyan/paper_mill_benchmark huggingface dataset:
MicroRNA-21 contributes to the discrimination of chemoresistance in metastatic gastric cancer.

Multidrug resistance in gastric cancer greatly impedes the efficacy of chemotherapy.Objective to explore the efficacy of micro rna-21 (mir-21) in distinguishing metastatic gastric cancer (mgc) with chemoresistance.Methods from april 2012 to may 2015, 92 mgc patients were enrolled.Cisplatin and fluorouracil-based systemic chemotherapy was given, and patients' characteristics and follow-up data were collected.In addition, mi r-21 expression was determined in tumor tissue and plasma.Results sixty-seven patients responded to chemotherapy, and chemotherapy resistance was observed in 25 patients.Mi r-21 expression in tumor tissue and plasma was significantly elevated in the chemotherapy-resistant group (crg) compared to the chemotherapy-sensitive group (csg) (p< 0.001).Mi r-21 expression in tissue was associated with tumor differentiation (p= 0.042), and plasma mi r-21 was correlated with gender (p= 0.016), tumor differentiation (p= 0.003), and number of metastatic sites (p< 0.001).Receiver operating characteristic (roc) analysis indicated that mi r-21 in tissue yielded an area under the roc curve (auc) of 0.830 (95%ci: 0.737-0.900, sensitivity: 88.0%, specificity: 68.7%) in distinguishing crg from csg; and plasma mi r-21 yielded an auc of 0.759 (95%ci: 0.658-0.842, sensitivity: 52.0%, specificity: 88.1%) in distinguishing crg form csg.Log-rank test and cox proportional hazard regression analysis indicated that patients with higher mi r-21 expression in tissue and plasma experienced shorter overall survival (p< 0.001).Conclusion mi r-21 could serve as a potential biomarker to identify mgc with chemoresistance.

Journal: Cancer biomarkers : section A of Disease markers (2017)
Publication types: Journal Article
Trends in BMI Percentile and Body Fat Percentage in Children 12 to 17 Years of Age.

This study evaluates the cross-sectional trends in body fat percentage (bf%) and body mass index (bmi) percentile rank, and the relationship between the two in 332 (177 boys, 155 girls) 12- to 17-year-old children.Body mass index (bmi) was calculated using measured height and body mass, and sex-specific bmi for age percentile rank was determined using cdc growth charts.Body fat percentage (bf%) was measured with dexa.Fat mass index (fmi) and fat-free mass index (ffmi) were calculated by normalizing the fat mass and fat-free mass for height.Compared to boys of the same age, girls had significantly higher bf% and fmi values and lower ffmi values.Compared to boys, at a given bmi percentile rank, females had a higher bf% and fmi, and a lower ffmi.In both boys and girls, there was an exponential increase in adiposity above the 70th percentile rank.Bmi percentile rank is not an equivalent indicator of body fatness in boys and girls.Other measures of body composition can further inform the practitioner of a child's adiposity.

Journal: Children (Basel, Switzerland) (2022)
Publication types: Journal Article
Virulence potential of faecal Escherichia coli strains isolated from healthy cows and calves on farms in Perm Krai.

Cattle are a reservoir of pathogenic and potentially pathogenic escherichia coli (e.Coli) strains, which can pose a threat to human and animal health.The aim of the study was to evaluate the occurrence of 22 virulence-associated genes (vags), as well as the prevalence of antimicrobial drug resistance and three different bla-genes among 49 e.Coli strains isolated from healthy cattle.The presence of vags that are common among diarrheagenic e.Coli (dec) strains and/or extraintestinal pathogenic e.Coli (ex pec) strains was determined by amplifying specific gene sequences by pcr.The following vags associated with dec were found: east1 in 24.5 % of the studied e.Coli strains, est i in 10.2 %, ehx a in 8.2 %, stx2 in 6.1 %, elt a in 4.1 %, est ii and stx1 in 2.0 % of the studied strains.The prevalence of ex pec vags was: fim h - 91.8 %, afa/dra bc - 61.2 %, iut a - 44.9 %, flu - 32.7 %, sfa de and hly f - 30.6 %, iro n - 22.4 %, omp t and pap c - 20.4 %, kps mtii and hly a - 18.4 %, iss - 14.3 %, usp - 2.0 %, cnf1 and iha were not detected among the studied strains.Based on the found co-occurrence of vags "classical", hetero-pathogenic and hybrid-pathogenic e.Coli strains were found.E.Coli strains isolated from cows had a higher diarrheagenic potential, whereas e.Coli strains isolated from calves more frequently contained genes associated with the ex pec pathotype.Among the studied e.Coli strains, 77.6 % were resistant to ampicillin, 49.0 % to tetracycline, 20.4 % to chloramphenicol, 16.3 % to cefoperazone, 16.3 % to ceftriaxone, 16.3 % to aztreonam, 14.3 % to cefepime, 10.2 % to norfloxacin, 10.2 % to ciprofloxacin, 6.1 % to levofloxacin and 2.0 % to gentamicin.All strains were sensitive to meropenem and amikacin.32.7 % of the studied e.Coli strains were found to be multidrug resistant, as they were resistant to at least three groups of antibiotics.With pcr, the bla tem, bla shv, and bla ctx-m genes were detected in 100, 31.6, and 26.3 %, respectively, of strains resistant to at least one of the beta-lactam antibiotics.Thus, it was shown that the studied faecal e.Coli of healthy cows and calves had a high hetero-pathogenic potential, therefore in the future molecular genetic characterization of these bacteria shall be an important part of the epizootic monitoring.

Journal: Vavilovskii zhurnal genetiki i selektsii (2022)
Publication types: Journal Article
Characterization of DNA-PK-Bound End Fragments Using GLASS-ChIP.

Endonucleolytic cleavage of dna ends by the human mre11-rad50-nbs1 (mrn) complex occurs in a manner that is promoted by dna-dependent protein kinase (dna-pk).A method is described to isolate dna-pk-bound fragments released from chromatin in human cells using a modified gentle lysis and size selection chromatin immunoprecipitation (glass-ch ip) protocol.This method, combined with real-time pcr or next-generation sequencing, can identify sites of mrn endonucleolytic cutting adjacent to dna-pk binding sites in human cells.

Journal: Methods in molecular biology (Clifton, N.J.) (2022)
Publication types: Journal Article
Cervical Sympathetic Chain Schwannoma-Our Experience.

Tumours arising from the parapharyngeal space are uncommon.The most common tumour arising primarily from this region is a neurogenic tumour, especially schwannoma.The most common site of origin of a schwannoma in parapharyngeal space is vagus nerve.Cervical sympathetic chain (csc) schwannomas are extremely rare.Here, we discuss a case of a 30-year old female with cervical sympathetic chain schwannoma, the clinical presentation, diagnosis and management.

Journal: Indian journal of otolaryngology and head and neck surgery : official publication of the Association of Otolaryngologists of India (2022)
Publication types: Journal Article
Reduced cutaneous CD200:CD200R1 signaling in psoriasis enhances neutrophil recruitment to skin.

Introduction the skin immune system is tightly regulated to prevent inappropriate inflammation in response to harmless environmental substances.This regulation is actively maintained by mechanisms including cytokines and cell surface receptors and its loss results in inflammatory disease.In the case of psoriasis, inappropriate immune activation leads to il-17-driven chronic inflammation, but molecular mechanisms underlying this loss of regulation are not well understood.Immunoglobulin family member cd200 and its receptor, cd200r1, are important regulators of inflammation.Therefore, we determined if this pathway is dysregulated in psoriasis, and how this affects immune cell activity.Methods human skin biopsies were examined by quantitative polymerase chain reaction, flow cytometry, and immunohistochemistry.The role of cd200r1 in regulating psoriasis-like skin inflammation was examined using cd200r1 blocking antibodies in mouse psoriasis models.Cd200r1 blocking antibodies were also used in an in vivo neutrophil recruitment assay and in vitro assays to examine macrophage, innate lymphoid cell, γδ t cell, and neutrophil activity.Results we reveal that cd200 and signaling via cd200r1 are reduced in non-lesional psoriasis skin.In mouse models of psoriasis cd200r1 was shown to limit psoriasis-like inflammation by enhancing acanthosis, ccl20 production and neutrophil recruitment, but surprisingly, macrophage function and il-17 production were not affected, and neutrophil reactive oxygen species production was reduced.Conclusion collectively, these data show that cd200r1 affects neutrophil function and limits inflammatory responses in healthy skin by restricting neutrophil recruitment.However, the cd200 pathway is reduced in psoriasis, resulting in a loss of immune control, and increased neutrophil recruitment in mouse models.In conclusion, we highlight cd200r1:cd200 as a pathway that might be targeted to dampen inflammation in patients with psoriasis.

Journal: Immunity, inflammation and disease (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Potential biomarkers for diagnosis and assessment of disease activity in systemic lupus erythematosus.

Systemic lupus erythematosus (sle) is a chronic autoimmune disease involving multiple system functions.Our study aimed to screen out more effective new indicators that can assist clinical diagnosis and judge disease activity.Methods we first screened serum levels of 45 cytokines of sle patients (n = 3) and healthy controls (n = 3).Subsequently, we selected five elevated cytokines for verification with an expanded sample size.Then, the relationship between cytokines and laboratory parameters was also investigated.Finally, we used receiver operating characteristic (roc) curves to assess the clinical value of these cytokines.Results through screening of 45 cytokines, 15 were found to be elevated in sle patients.We chose five cytokines (il-6, il-10, il-1ra, ip-10 and lif) for further research and found elevated expression of all five cytokines in sle patients.Serum levels of il-10, il-1ra and lif were positively correlated with sledai-2k score.Besides, the level of il-10 was significantly positively correlated with serum ig g and erythrocyte sedimentation rate (esr); il-1ra was significantly negatively correlated with c3 and c4; and lif was significantly positively correlated with serum ig g, c-reactive protein (crp), and esr.Furthermore, il-1ra and lif were strongly positively correlated with 24-hour urine protein levels.The roc analysis showed that il-1ra has good diagnostic value, and il-10 and lif levels can be utilized to discriminate between active and inactive sle.Conclusion il-1ra can be used as a biomarker for diagnosing sle, while il-10 and lif can be indicators to discriminate between active and inactive sle.

Journal: International immunopharmacology (2022)
Publication types: Journal Article
Population structure of chum salmon and selection on the markers collected for stock identification.

Genetic stock identification (gsi) is a major management tool of pacific salmon (oncorhynchus spp.) that has provided rich genetic baseline data of allozymes, microsatellites, and single-nucleotide polymorphisms (snps) across the pacific rim.Here, we analyzed published data sets for adult chum salmon (oncorhynchus keta), namely 10 microsatellites, 53 snps, and a mitochondrial dna locus (mt dna3, control region, and nadh-3 combined) in samples from 495 locations in the same distribution range (n= 61,813).Tree mix analysis of the microsatellite loci identified the greatest convergence toward japanese/korean populations and suggested two admixture events from japan/korea to russia and the alaskan peninsula.The snps had been purposively collected from rapidly evolving genes to increase the power of gsi.The largest expected heterozygosity was observed in japanese/korean populations for microsatellites, whereas it was largest in western alaskan populations for snps, reflecting the snp discovery process.A regression of snp population structures on those of microsatellites indicated the selection of the snp loci according to deviations from the predicted structures.Specifically, we matched the sampling locations of the snps with those of the microsatellites and performed regression analyses of snp allele frequencies on a 2-dimensional scaling (mds) of matched locations obtained from microsatellite pairwise fstvalues.The mds first axis indicated a latitudinal cline in american and russian populations, whereas the second axis showed differentiation of japanese/korean populations.The top five outlier snps included mt dna3, u502241 (unknown), gn rh373, ras1362, and tcp178, which were identified by principal component analysis.We summarized the functions of 53 nuclear genes surrounding snps and the mt dna3 locus by referring to a gene database system and propose how they may influence the fitness of chum salmon.

Journal: Ecology and evolution (2021)
Publication types: Journal Article
From shaping to functionalization of micro-droplets and particles.

The structure of microdroplet and microparticle is a critical factor in their functionality, which determines the distribution and sequence of physicochemical reactions.Therefore, the technology of precisely tailoring their shape is requisite for implementing the user demand functions in various applications.This review highlights various methodologies for droplet shaping, classified into passive and active approaches based on whether additional body forces are applied to droplets to manipulate their functions and fabricate them into microparticles.The passive approaches cover batch emulsification, solvent evaporation and diffusion, micromolding, and microfluidic methods.In active approaches, the external forces, such as electrical and magnetic fields or optical lithography, are applied to microdroplets.Special attention is also given to latest technologies using microdroplets and microparticles, especially in the fields of biological, optical, robotic, and environmental applications.Finally, this review aims to address the advantages and disadvantages of the introduced approaches and suggests the direction for further development in this field.

Journal: Nanoscale advances (2021)
Publication types: Journal Article;Review
Sweet light o' mine: Photothermal and photodynamic inactivation of tenacious pathogens using conjugated polymers.

Each year a rising number of infections can not be successfully treated owing to the increasing pandemic of antibiotic resistant pathogens.The global shortage of innovative antibiotics fuels the emergence and spread of drug resistant microbes.Basic research, development, and applications of alternative therapies are urgently needed.Since the 90 ́s, light-mediated therapies have promised to be the next frontier combating multidrug-resistance microbes.These platforms have demonstrated to be a reliable, rapid, and efficient alternative to eliminate tenacious pathogens while avoiding the emergence of resistance mechanisms.Among the materials showing antimicrobial activity triggered by light, conjugated polymers (cps) have risen as the most promising option to tackle this complex situation.These materials present outstanding characteristics such as high absorption coefficients, great photostability, easy processability, low cytotoxicity, among others, turning them into a powerful class of photosensitizer (ps)/photothermal agent (pta) materials.Herein, we summarize and discuss the advances in the field of cps with applications in photodynamic inactivation and photothermal therapy towards bacteria elimination.Additionally, a section of current challenges and needs in terms of well-defined benchmark experiments and conditions to evaluate the efficiency of phototherapies is presented.

Journal: Journal of photochemistry and photobiology. B, Biology (2022)
Publication types: Journal Article
Long-term efficacy and safety of migalastat treatment in Fabry disease: 30-month results from the open-label extension of the randomized, phase 3 ATTRACT study.

Results from the 18-month randomized treatment period of the phase 3 attract study demonstrated the efficacy and safety of oral migalastat compared with enzyme replacement therapy (ert) in patients with fabry disease who previously received ert.Here, we report data from the subsequent 12-month, migalastat-only, open-label extension (ole) period.Attract (study at1001-012; nct01218659) was a randomized, open-label, active-controlled study in patients aged 16-74 years with fabry disease, an amenable gla variant, and an estimated glomerular filtration rate (e gfr) ≥30 m l/min/1.73 m2.During the ole, patients who received migalastat 150 mg every other day (qod) during the randomized period continued receiving migalastat (group 1 [mm]); patients who received ert every other week discontinued ert and started migalastat treatment (group 2 [em]).Outcome measures included e gfr, left ventricular mass index (lvmi), composite clinical outcome (renal, cardiac or cerebrovascular events), and safety.Forty-six patients who completed the randomized treatment period continued into the ole (group 1 [mm], n = 31; group 2 [em], n = 15).E gfr remained stable in both treatment groups.Lvmi decreased from baseline at month 30 in group 1 (mm) in patients with left ventricular hypertrophy at baseline.Only 10% of patients experienced a new composite clinical event with migalastat treatment during the ole.No new safety concerns were reported.In conclusion, in patients with fabry disease and amenable gla variants, migalastat 150 mg qod was well tolerated and demonstrated durable, long-term stability of renal function and reduction in lvmi.

Journal: Molecular genetics and metabolism (2020)
Publication types: Clinical Trial, Phase III;Journal Article;Randomized Controlled Trial;Research Support, Non-U.S. Gov't
Unique diagnostic challenge in surgery: hepatic abscess versus malignancy.

A man in his 30s had presented with a history of abdominal pain, vomiting and high-grade fever.He had tender hepatomegaly with peritonism in the upper abdomen.Investigations revealed a neutrophilic leucocytosis, and contrast-enhanced ct had shown several well-defined peripherally enhancing thick-walled cystic lesions with non-enhancing centres throughout the liver suggestive of pyogenic liver abscess, treated initially with antibiotics.However, ultrasonography-guided fine needle aspiration revealed atypical neoplastic cells, and a trucut biopsy showed squamous cell carcinoma (scc).He developed acute shortness of breath.Ct pulmonary angiogram confirmed pulmonary thromboembolism (pte).Incidentally, here we saw a solitary nodule in the right middle lobe, probably a neoplastic lesion.His condition deteriorated rapidly secondary to pte and died.A pathological review was positive for ck7, p40, p63 and ck19 confirming scc.We concluded the primary was a pulmonary scc with multiple hepatic metastases.Hepatic metastases can mimic an abscess; trucut biopsy with immunohistochemistry was critical for a definitive diagnosis.

Journal: BMJ case reports (2022)
Publication types: Case Reports;Journal Article
Calcium Looping: On the Positive Influence of SO2and the Negative Influence of H2O on CO2Capture by Metamorphosed Limestone-Derived Sorbents.

The co2capture performance of sorbents derived from three distinct limestones, including a metamorphosed limestone, is studied under conditions relevant for calcium looping co2capture from power plant flue gas.The combined and individual influence of flue gas h2o and so2content, the influence of textural changes caused by sequential calcination/carbonation cycles, and the impact of ca so4accumulation on the sorbents' capture performance were examined using bubbling fluidized bed reactor systems.The metamorphosed limestone-derived sorbents exhibit atypical capture behavior: flue gas h2o negatively influences co2capture performance, while limited sulfation can positively influence co2capture, with space time significantly impacting co2and so2co-capture performance.The morphological characteristics influencing sorbents' capture behavior were examined using imaging and material characterization tools, and a detailed discussion is presented.This insight into the morphology responsible for metamorphosed limestone-derived sorbent's anomalous capture behavior can guide future sorbent selection and design efforts.

Journal: ACS omega (2020)
Publication types: Journal Article
Quantum binding energies of checkpoint CTLA-4 in complex with the immuno-oncological drug ipilimumab.

Inhibition of the checkpoint protein ctla-4 by the us-fda's approved monoclonal antibody ipilimumab has delivered breakthrough therapies against a wide range of cancers, being an important issue for clinical research.To date, many structural properties of this drug have been unveiled.However, the binding energy features of the receptor ctla-4 in complex with its drug inhibitor, based on crystallographic data, need a deeper understanding.Within this context, by employing quantum chemistry we investigate in silico the binding energy features of the checkpoint protein ctla-4 in complex with its drug inhibitor, highlighting the most relevant residue-residue interactions, looking for new insights into the mechanisms of pathway blockade to further engineer its affinity and selectivity.Our computational results not only give a better understanding of the binding mechanisms, but also point to an efficient alternative towards the development of antibody-based drugs, leading to new treatments for cancer therapy based upon immunotherapy.

Journal: Physical chemistry chemical physics : PCCP (2021)
Publication types: Journal Article
Backbone-driven host-dopant miscibility modulates molecular doping in NDI conjugated polymers.

Molecular doping is the key to enabling organic electronic devices, however, the design strategies to maximize doping efficiency demands further clarity and comprehension.Previous reports focus on the effect of the side chains, but the role of the backbone is still not well understood.In this study, we synthesize a series of ndi-based copolymers with bithiophene, vinylene, and acetylenic moieties (p1g, p2g, and p3g, respectively), all containing branched triethylene glycol side chains.Using computational and experimental methods, we explore the impact of the conjugated backbone using three key parameters for doping in organic semiconductors: energy levels, microstructure, and miscibility.Our experimental results show that p1g undergoes the most efficient n-type doping owed primarily to its higher dipole moment, and better host-dopant miscibility with n-dmbi.In contrast, p2g and p3g possess more planar backbones than p1g, but the lack of long-range order, and poor host-dopant miscibility limit their doping efficiency.Our data suggest that backbone planarity alone is not enough to maximize the electrical conductivity (σ) of n-type doped organic semiconductors, and that backbone polarity also plays an important role in enhancingσ viahost-dopant miscibility.Finally, the thermoelectric properties of doped p1g exhibit a power factor of 0.077 μw m-1k-2, and ultra-low in-plane thermal conductivity of 0.13 w m-1k-1at 5 mol% of n-dmbi, which is among the lowest thermal conductivity values reported for n-type doped conjugated polymers.

Journal: Materials horizons (2022)
Publication types: Journal Article