syedzayyan/paper_mill_benchmark huggingface dataset:
Immune activation in irritable bowel syndrome: what is the evidence?

Irritable bowel syndrome (ibs) is a chronic functional gastrointestinal disorder that is characterized by abdominal pain and an altered defecation pattern.It affects between 5 and 20% of the general population and can seriously impact quality of life.The pathophysiology of ibs is rather complex and multifactorial including, for example, altered signalling by the gut-brain axis, dysbiosis, abnormal visceral pain signalling and intestinal immune activation.The latter has gained particular interest in recent years, with growing insight into the bidirectional communication between the nervous system and the immune system.In this review, we detail the current evidence suggesting that immune activation contributes to the pathology seen in patients with ibs and discuss the potential mechanisms involved.Moreover, we describe how immune mediators, particularly those released by mast cells, can directly activate or sensitize pain-transmitting nerves, leading to increased pain signalling and abdominal pain.Finally, we discuss the potential of interventions targeting immune activation as a new therapeutic strategy for patients suffering from ibs.

Journal: Nature reviews. Immunology (2022)
Publication types: Journal Article;Review;Research Support, Non-U.S. Gov't
The effect of online cognitive behavioral therapy on depressive symptoms in recovered patients with COVID-19.

Covid-19 virus is on the rise globally, and people with the disease experience a variety of physical and mental problems.According to studies, depression can be a complication of the virus.So far, limited measures have been taken to prevent and treat emotional-psychological complications of covid-19.The aim of this study was to evaluate the effect of online cognitive behavioral therapy (cbt) on depressive symptoms in recovered patients with covid-19.Materials and methods this study was conducted in a quasi-experimental design.A sample of 150 recovered patients with covid-19 who referred to imam reza hospital in tabriz city, were selected by random sampling method.The patients' emotional-psychological status was assessed by the beck depression inventory, and they entered the treatment process according to the inclusion criteria.As a therapeutic intervention, a scientific and valid approach called cbt was implemented, which two occupational therapists performed in eight treatment sessions in the context of a social communication application.Paired samplet-test was used to analyze the time sequence of quantitative data due to its normality.Results after the last session of the intervention, the effect of this therapeutic approach on reducing the depressive symptoms of patients was evaluated.According to the findings, the beck score of the participants decreased significantly after the intervention (md = -45/9,p< 0/001).Conclusion therefore, in order to promote the recovery of patients with covid-19 and help health authorities to develop preventive measures and effective treatment of emotional-psychological problems caused by this virus, it is recommended to use the online cbt approach.

Journal: Journal of education and health promotion (2022)
Publication types: Journal Article
Human papillomavirus genotyping by Linear Array and Next-Generation Sequencing in cervical samples from Western Mexico.

The linear array® (la) genotyping test is one of the most used methodologies for human papillomavirus (hpv) genotyping, in that it is able to detect 37 hpv genotypes and co-infections in the same sample.However, the assay is limited to a restricted number of hpv, and sequence variations in the detection region of the hpv probes could give false negatives results.Recently, 454 next-generation sequencing (ngs) technology has been efficiently used also for hpv genotyping; this methodology is based on massive sequencing of hpv fragments and is expected to be highly specific and sensitive.In this work, we studied hpv prevalence in cervixes of women in western mexico by la and confirmed the genotypes found by ngs.Methods two hundred thirty three cervical samples from women without cervical lesions (wcl, n = 48), with cervical intraepithelial neoplasia grade 1 (cin i, n = 98), or with cervical cancer (cc, n = 87) were recruited, dna was extracted, and hpv positivity was determined by pcr amplification using pgmy09/11 primers.All hpv- positive samples were genotyped individually by la.Additionally, pools of amplicons from the pgmy-pcr products were sequenced using 454 ngs technology.Results obtained by ngs were compared with those of la for each group of samples.Results we identified 35 hpv genotypes, among which 30 were identified by both technologies; in addition, the hpv genotypes 32, 44, 74, 102 and 114 were detected by ngs.These latter genotypes, to our knowledge, have not been previously reported in mexican population.Furthermore, we found that la did not detect, in some diagnosis groups, certain hpv genotypes included in the test, such as 6, 11, 16, 26, 35, 51, 58, 68, 73, and 89, which indicates possible variations at the species level.Conclusions there are hpv genotypes in mexican population that cannot be detected by la, which is, at present, the most complete commercial genotyping test.More studies are necessary to determine the impact of hpv-44, 74, 102 and 114 on the risk of developing cc.A greater number of samples must be analyzed by ngs for the most accurate determination of mexican hpv variants.

Journal: Virology journal (2015)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Application of the International System for Reporting Serous Fluid Cytopathology (TIS): A retrospective institutional study.

Cytology of serous effusions is an important diagnostic tool for the diagnosis of cancer, staging, and prognosis of the patient.Herein, we retrospectively applied the international system for reporting serous fluid cytopathology (tis) and provided the corresponding risks of malignancy (roms).Methods pleural, pericardial, and peritoneal effusion samples were retrieved from the archives of our department and reclassified according to the tis.The rom for each category was calculated based on available surgical follow-up.Results a total of 3790 effusions were studied.Pleural samples (1292) were reclassified as follows: 27 (2.1%) as non-diagnostic (nd), 1014 (78.5%) as negative for malignancy (nfm), 86 (6.6%) as atypia of undetermined significance (aus), 29 (2.3%) as suspicious of malignancy (sfm), and 136 (10.5%) as malignant (m).Pericardial samples (241) were reclassified as follows: 4 (1.6%) as nd, 173 (71.8%) as nfm, 10 (4.1%) as aus, 7 (3%) as sfm, and 47 (19.5%), as m.Peritoneal cases (2257) were re-categorised as follows: 31 (1.4%) as nd, 1897 (84%) as nfm, 39 (1.7%) as aus, 53 (2.4%) as sfm, and 237 (10.5%) as m.The respective rom values for each category were 18.5%, 15%, 45.3%, 93%, and 100% in pleural effusions; 25%, 13.2%, 35%, 100%, and 100% in pericardial effusions; and 19.3%, 10.4%, 43.5%, 100%, and 100% in peritoneal effusions.Conclusions pleural, pericardial, and peritoneal cytology show high specificity and moderate sensitivity in the evaluation of serous effusions.The roms reported in our study were mostly concordant with those published according to the tis.

Journal: Cytopathology : official journal of the British Society for Clinical Cytology (2022)
Publication types: Journal Article
Dyadobacter diqingensis sp. nov., isolated from Baima snow mountain of Diqing Tibetan Autonomous Prefecture in Yunnan province, south-west China.

A gram-negative, aerobic, nonmotile, rod-shaped and yellow-pigment-producing bacteria was isolated from baima snow mountain of diqing tibetan autonomous prefecture in yunnan province, south-west china and characterized using a polyphasic approach.The results of 16s r rna gene sequence similarity analysis showed that strain yim b04101twas closely related to the type strain of dyadobacter koreensis dsm 19938t(97.81%) and dyadobacter frigoris ar-3-8t(97.95%).The predominant respiratory quinone was menaquinone-7 (mk-7).The major polar lipid was phosphatidylethanolamine.The major fatty acids were summed feature 3 (c16:1ω7c/c16:1ω6c), c18:1ω9c and c16:0.The dna g + c content was 43.5 mol%.Phylogenetic analysis based on 16s r rna gene sequences indicated that the strain yim b04101tbelonged to a cluster comprising species of the genus dyadobacter.However, it differed from its closest relative, dyadobacter koreensis kctc 12537tand dyadobacter frigoris ar-3-8t, in many physiological properties.Based on these phenotypic characteristics and phylogenetic distinctiveness, strain yim b04101tis considered to be a novel species of the genus dyadobacter, for which the name dyadobacter diqingensis sp.Nov.Is proposed.The type strain is yim b04101t(= cgmcc 1.19249t= cctcc ab 2021270).

Journal: Archives of microbiology (2022)
Publication types: Journal Article
Regional impact of COVID-19 on the production and food security of common bean smallholder farmers in Sub-Saharan Africa: Implication for SDG's.

Concerns about the implications of covid-19 on agriculture and food security in sub-saharan africa abound.Containment measures in response to the pandemic have markedly different outcomes depending on the degree of enforcement of the measures and the existing vulnerabilities pre-covid.In this descriptive study, we document the possible impacts of the pandemic on bean production and food security using data collected from march to april 2020 in eleven countries in four sub-regions in sub-saharan africa.The results reveal that covid-19 created significant bean production challenges across the sub-regions, including low access to seed, farm inputs, hired labor, and agricultural finance.We also show that covid-19 threatens to reverse gains made in the achievement of sustainable development goals number 1 and 2.Countries in southern and eastern africa are likely to suffer temporal food shortages than those in western and central africa.Although governments have responded by offering economic stimulus packages, much needs to be done to enable the sub-sector to recover from ruins caused by the pandemic.We recommend building sustainable and resilient food systems through strengthening and enabling public-private partnerships.Governments should invest directly in input supply systems and short food supply chains through digital access and food delivery.

Journal: Global food security (2021)
Publication types: Journal Article
Predictive Patterns of Glutamine Synthetase Immunohistochemical Staining in CTNNB1-mutated Hepatocellular Adenomas.

Some hepatocellular adenoma (hca) subtypes are characterized by different ctnnb1 mutations, leading to different beta-catenin activation levels, hence variable immunostaining patterns of glutamine synthetase (gs) expression, and different risks of malignant transformation.In a retrospective multicentric study of 63 resected inflammatory (n=33) and noninflammatory (n=30) molecularly confirmed ctnnb1-mutated b-(i)hca, we investigated the predictive potential of 3 known gs patterns as markers for ctnnb1 exon 3, 7/8 mutations.Pattern 1 (diffuse homogenous) allowed recognition of 17/21 exon 3 non-s45 mutated b-(i)hca.Pattern 2 (diffuse heterogenous) identified all b-(i)hca harboring exon 3 s45 mutation (20/20).Pattern 3 (focal patchy) distinguished 12/22 b-(i)hca with exon 7/8 mutations.In exon 3 s45 and 7/8 mutations, both b-hca and b-ihca showed a gs+/cd34- rim with diffuse cd34 positivity in the center of the lesion.Interobserver reproducibility was excellent for exon 3 mutations.Comparative analysis of gs patterns with molecular data showed 83% and 80% sensitivity (b-hca/b-ihca) and 100% specificity for exon 3 non-s45.For exon 3 s45, sensitivity was 100% for b-(i)hca, and specificity 93% and 92% (b-hca/b-ihca).For exon 7/8, sensitivity was 55% for both subtypes and specificity 100% and 96% (b-hca/b-ihca).Preliminary data from 16 preoperative needle biopsies from the same patients suggest that this panel may also be applicable to small samples.In surgically resected hca, 2 distinct gs patterns can reliably predict ctnnb1 exon 3 mutations, which are relevant because of the higher risk for malignant transformation.The third pattern, although specific, was less sensitive for the identification of exon 7/8 mutation, but the gs+/cd34- rim is a valuable aid to indicate either an exon 3 s45 or exon 7/8 mutation.

Journal: The American journal of surgical pathology (2021)
Publication types: Journal Article;Multicenter Study
Enhanced Sinterability, Thermal Conductivity and Dielectric Constant of Glass-Ceramics with PVA and BN Additions.

With the rapid development of the microelectronics industry, many efforts have been made to improve glass-ceramics' sinterability, thermal conductivity, and dielectric properties, which are essential components of electronic materials.In this study, low-alkali borosilicate glass-ceramics with pva addition and glass-bn composites were prepared and successfully sintered at 770 °c.The phase composition, density, microstructure, thermal conductivity, and dielectric constant were investigated.It was shown that pva addition contributes to the densification process of glass-ceramics (~88% relative density, with closed/open pores in the microstructure) and improves the thermal conductivity of glass material from 1.489 to 2.453 w/k.m.On the other hand, increasing bn addition improves microstructures by decreasing porosities and thus increasing relative densities.A glass-12 wt.% bn composite sample exhibited almost full densification after sintering and presented apparent and open pores of 2.6 and 0.08%, respectively.A high thermal conductivity value of 3.955 w/k.m and a low dielectric constant of 3.00 (at 5 mhz) were observed in this material.Overall, the resulting glass-ceramic samples showed dielectric constants in the range of 2.40-4.43, providing a potential candidate for various electronic applications.

Journal: Materials (Basel, Switzerland) (2022)
Publication types: Journal Article
Introducing the Node Reporting and Data System 1.0 (Node-RADS): a concept for standardized assessment of lymph nodes in cancer.

"node-rads" addresses the lack of consensus in the radiologic assessment of lymph node involvement by cancer and meets the increasing demand for structured reporting on the likelihood of disease involvement.Node reporting and data system 1.0 (node-rads) systematically classifies the degree of suspicion of lymph node involvement based on the synthesis of established imaging findings.Straightforward definitions of imaging findings for two proposed scoring categories "size" and "configuration" are combined into assessment categories between 1 ("very low likelihood") and 5 ("very high likelihood").This scoring system is suitable for assessing likely involvement of lymph nodes on ct and mri scans.It can be applied at any anatomical site, and to regional and non-regional lymph nodes in relation to a primary tumor location.Node-rads will improve communication with referring physicians and promote the consistency of reporting for primary staging and in response assessment settings.Key points: • node-rads standardizes reporting of possible cancer involvement of regional and distant lymph nodes on ct and mri.• node-rads proposes the scoring categories "size" and "configuration" for assigning the 5-point node-rads score from 1 ("very low likelihood") to 5 ("very high likelihood").• node-rads aims to increase consensus among radiologists for primary staging and in response assessment settings.

Journal: European radiology (2021)
Publication types: Journal Article
Mystery of love, goiter and death in flu pandemic.

Ivan mestrovic (1883-1962), a croatian sculptor and architect, portrayed his close friend marija banac (born racic) with a goiter.She died from flu in 1918 in rome, just few days apart from her brother edi racic and his fiancée.In the tragic memory of the racic family that disappeared in the burst of a terrible pandemic, mestrovic built a church and mausoleum in cavtat near dubrovnik.

Journal: Journal of endocrinological investigation (2022)
Publication types: Journal Article
Review of Sensor Technologies in Animal Breeding: Phenotyping Behaviors of Laying Hens to Select Against Feather Pecking.

Damaging behaviors, like feather pecking (fp), have large economic and welfare consequences in the commercial laying hen industry.Selective breeding can be used to obtain animals that are less likely to perform damaging behavior on their pen-mates.However, with the growing tendency to keep birds in large groups, identifying specific birds that are performing or receiving fp is difficult.With current developments in sensor technologies, it may now be possible to identify laying hens in large groups that show less fp behavior and select them for breeding.We propose using a combination of sensor technology and genomic methods to identify feather peckers and victims in groups.In this review, we will describe the use of "-omics" approaches to understand fp and give an overview of sensor technologies that can be used for animal monitoring, such as ultra-wideband, radio frequency identification, and computer vision.We will then discuss the identification of indicator traits from both sensor technologies and genomics approaches that can be used to select animals for breeding against damaging behavior.

Journal: Animals : an open access journal from MDPI (2019)
Publication types: Journal Article;Review
Epistemic injustices in clinical communication: the example of narrative elicitation in person-centred care.

The increasing popularity of the term 'person-centred' in the healthcare literature and a wide range of ideals and practices it implies point to the need for a more inclusive and holistic healthcare provision.A framework developed in a swedish context suggested narrative elicitation as a key practice in transition to person-centred care.Initiating clinical communication by inviting people to tell their stories makes persistent yet often subtle problems in clinical communication visible.By drawing upon an observational study on narrative elicitation and vignette-based focus group interviews with nurses, our aim is to trace 'credibility deficits' (fricker 2007.Epistemic injustice.Power and the ethics of knowing.Oxford: oxford university press) and 'credibility excesses' (medina 2011, social epistemology, 25, 1, 15-35, 2013, the epistemology of resistance: gender and racial oppression, epistemic injustice, and the social imagination.Oxford: oxford university press) in narrative elicitation.We argue that narrative elicitation may be one way to tackle epistemic injustices by giving voice to previously silenced groups, yet it is not enough to erase the effects of 'credibility deficits' in clinical communication.Rather than judging individual professionals' success or failure in eliciting narratives, we underline some extrinsic problems of narrative elicitation, namely structural and positional inequalities reflecting on narrative elicitation and the credibility of patients.'credibility excesses' can be useful and indicative to better understand where they are missing.

Journal: Sociology of health & illness (2021)
Publication types: Journal Article;Observational Study;Research Support, Non-U.S. Gov't
Brain Tumor Cell Membrane-Coated Lanthanide-Doped Nanoparticles for NIR-IIb Luminescence Imaging and Surgical Navigation of Glioma.

Intraoperative visualization of the full extent of brain tumor by luminescence imaging helps to improve the degree and accuracy of brain tumor resection, thereby prolonging the survival of patients.However, the limited imaging depth and spatial resolution and the poor blood-brain barrier (bbb) permeability of most currently available luminescent probes restrict the imaging performance and surgical resection efficiency of brain tumor.Here, a brain tumor cell membrane-coated lanthanide-doped nanoparticles (cc-ln nps) in the near-infrared-iib window (nir-iib, 1500-1700 nm) is designed for brain tumor imaging and surgical navigation.The coating of brain tumor cell membrane endows cc-ln nps with immune escape, bbb crossing, and homotypic targeting abilities, which are inherited from the source brain tumor cells.In addition, compared with clinically approved imaging agent indocyanine green, cc-ln nps present higher temporal and spatial resolution, higher stability, and lower background signals, enabling clear visualization of the brain tumor boundary.With the guidance of nir-iib fluorescence, the glioma tissue (size 3 mm) could be clearly visualized and completely removed as a proof of concept.This study offers new insight for the future design of nanoprobe to image brain tumor and to achieve precise diagnosis and surgical navigation of brain tumor.

Journal: Advanced healthcare materials (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
A prospective multicenter assessor-blinded randomized controlled study to compare the efficacy of short versus long protocols of electroconvulsive therapy as an augmentation strategy to clozapine in patients with ultra-resistant schizophrenia (SURECT study).

Although clozapine is the most effective antipsychotic drug for treatment-resistant schizophrenia, it leads to a poor or partial response in 40 to 70% of patients.Augmentation of clozapine with electroconvulsive therapy (ect) is a highly effective and relatively safe treatment for these clozapine-resistant patients.However, parameters are not yet well specified, such as the optimal number of sessions, their frequency, and the relevance of maintenance ect.Our objective is to compare the efficacy and tolerance between two protocols of combined ect and clozapine treatment in patients with ultra-resistant schizophrenia (urs): a 6-month protocol (short protocol with 20 ect sessions) and a 12-month protocol (long protocol with 40 ect sessions).Methods sixty-four patients with schizophrenia with persistent psychotic symptoms despite clozapine treatment will be enrolled in a prospective multicentric assessor-blinded randomized controlled trial.Patients will be randomly assigned to the short or the long protocol.The main outcome is the response rate assessed by the positive and negative symptoms scale (panss) 3 months after the end of the treatment in patients following the long protocol compared to those following the short protocol.The response was defined as a 30% reduction on the panss baseline.Clinical assessments (panss, bprs, hamd-21, ymrs, cgi, gaf, modified overt aggression scale (moas), and subjective scale to investigate cognition in schizophrenia (sstics)) and plasma clozapine concentration will be performed at baseline and at 2, 4, 6, 9, 12, and 15 months.Neuropsychological measures (mmse, rl/ri-16, doors test, d2 test of attention, copy of the rey-osterrieth complex figure) will be performed at baseline and at 6 and 15 months.Discussion the aims of this research are to optimize protocols of combined ect with clozapine in patients with urs and to offer specific recommendations for these patients' care.Trial registration clinical trials.gov nct03542903 .Registered on may 31, 2018.Id rcb: 2017-a02657-46.

Journal: Trials (2021)
Publication types: Clinical Trial Protocol;Journal Article