syedzayyan/paper_mill_benchmark huggingface dataset:
Left ventricle- and skeletal muscle-derived fibroblasts exhibit a differential inflammatory and metabolic responsiveness to interleukin-6.

Interleukin-6 (il-6) is an important player in chronic inflammation associated with heart failure and tumor-induced cachexia.Fibroblasts are salient mediators of both inflammation and fibrosis.Whereas the general outcome of il-6 on the heart's function and muscle wasting has been intensively studied, the influence of il-6 on fibroblasts of the heart and skeletal muscle (sm) has not been analyzed so far.We illustrate that sm-derived fibroblasts exhibit higher basal m rna expression of α-sma, extracellular matrix molecules (collagen1a1/3a1/5a1), and chemokines (ccl2, ccl7, and cx3cl1) as compared to the left ventricle (lv)-derived fibroblasts.Il-6 drives the transdifferentiation of fibroblasts into myofibroblasts as indicated by an increase in α-sma expression and upregulates nlrp3 inflammasome activity in both lv- and sm-derived fibroblasts.Il-6 increases the release of ccl7 to cx3cl1 in the supernatant of sm-derived fibroblasts associated with the attraction of more pro(ly6chi) versus anti(ly6clo) inflammatory monocytes as compared to unstimulated fibroblasts.Il-6-stimulated lv-derived fibroblasts attract less ly6chito ly6clomonocytes compared to il-6-stimulated sm-derived fibroblasts.In addition, sm-derived fibroblasts have a higher mitochondrial energy turnover and lower glycolytic activity versus lv-derived fibroblasts under basal and il-6 conditions.In conclusion, il-6 modulates the inflammatory and metabolic phenotype of lv- and sm-originated fibroblasts.

Journal: Frontiers in immunology (2022)
Publication types: Journal Article
Identification of Fusion Genes and Targets for Genetically Matched Therapies in a Large Cohort of Salivary Gland Cancer Patients.

Introduction:salivary gland cancer (sgc) is a rare cancer for which systemic treatment options are limited.Therefore, it is important to characterize its genetic landscape in search for actionable aberrations, such as ntrkgene fusions.This research aimed to identify these actionable aberrations by combining ngs-based analysis of rna (gene fusions) and dna (single and multiple nucleotide variants, copy number variants, microsatellite instability and tumor mutational burden) in a large cohort of sgc patients.methods:rna and dna were extracted from archival tissue of 121 patients with various sgc subtypes.Gene fusion analysis was performed using a customized rna-based targeted ngs panel.Dna was sequenced using a targeted ngs panel encompassing 523 cancer-related genes.Cross-validation of ngs-based ntrkfusion detection and pan-trk immunohistochemistry (ihc) was performed.results:fusion transcripts were detected in 50% of the cases and included both known (myb-nfib, mybl1-nfib, crtc1-maml2) and previously unknown fusions (including transcripts involving ret, brafor rad51b).Only one ntrkfusion transcript was detected, in a secretory carcinoma case.Pan-trk ihc (clone epr17341) was false positive in 74% of cases.The proportion of patients with targets for genetically matched therapies differed among subtypes (salivary duct carcinoma: 82%, adenoid cystic carcinoma 28%, mucoepidermoid carcinoma 50%, acinic cell carcinoma 33%).Actionable aberrations were most often located in pik3ca(n= 18, 15%),erbb2(n= 15, 12%),hrasand notch1(bothn= 9, 7%).conclusions:actionable genetic aberrations were seen in 53.7% of all sgc cases on the rna and dna level, with varying percentages between subtypes.

Journal: Cancers (2022)
Publication types: Journal Article
Is Human Aging a Form of Phenoptosis?

A much debated question is whether aging is the cumulative consequence of degenerative factors insufficiently opposed by natural selection, or, on the contrary, an ordered process, genetically determined and regulated, modeled by natural selection, and for which the definition of phenoptotic phenomenon would be entirely appropriate.In this review, theoretical arguments and empirical data about the two hypotheses are exposed, with more evidence in support of the thesis of aging as a form of phenoptosis.However, as the thesis of aging as an adaptive and programmed phenomenon necessarily requires the existence of specific mechanisms that determine to age, such as the subtelomere-telomere theory proposed for this purpose, the evidence supporting the mechanisms described by this theory is reported.In particular, it is highlighted that the recent interpretation of the role of terra sequences in the context of subtelomere-telomere theory is a fundamental point in supporting the hypothesized mechanisms.Furthermore, some characteristics of the mechanisms proposed by the theory, such as epigenetic modifications in aging, gradual cell senescence, cell senescence, limits in cell duplications, and fixed size of the telomeric heterochromatin hood, are exposed in their compatibility with both the thesis of aging as phenoptotic phenomenon and the opposite thesis.In short, aging as a form of phenoptosis appears a scientifically sound hypothesis while the opposite thesis should clarify the meaning of various phenomena that appear to invalidate it.

Journal: Biochemistry. Biokhimiia (2022)
Publication types: Journal Article;Review
Umbilical cord mesenchymal stem cells and breast cancer: a good therapeutic candidate or not? A minireview.

Breast cancer (bc), as the most common cancer among women, affects a great number of subjects around the world.This heterogenic disease is divided into several types and subtypes, and each subtype has various phenotypes and genotypes.Against bc, several options have been proposed, such as surgery, radiotherapy, and chemotherapeutic agents.However, these approaches may have detrimental effects on health and life quality of patients.Hence, harnessing a therapeutic tool with high effectiveness and low side effects is required.Recently, mesenchymal stem cells (mscs) have created a new window to treat various disorders, like cancer, and among these, umbilical cord (uc)-derived mscs have acquired much interest due to their advantages.Therefore, in this narrative review, the influences of uc-derived mscs on bc were reviewed and summarized with a focus on the molecular mechanisms involved in its pathogenesis and treatment.

Journal: Molecular biology reports (2022)
Publication types: Journal Article;Review
Efficacy of retrograde innervation through the distal stump of the thoracodorsal nerve in single-stage neurovascular latissimus dorsi transfer for facial reanimation: A retrospective analysis of 30 cases.

The aim of the study was to analyze the efficacy of retrograde innervation of single-stage free latissimus dorsi (ld) flap for facial reanimation by the distal stump of thoracodorsal nerve (tdn).After the main trunk of tdn was split in half to preserve the function of transverse branch, the proximal stump was coapted with the contralateral facial nerve, and the distal stump was coapted with the ipsilateral masseteric nerve, or vice versa.The length of each nerve stump and the time required for voluntary and spontaneous muscle contraction after surgical treatment were reviewed.Among a total of 30 patients, there was no statistically significant difference in the successful recovery ratio of voluntary smile (antegrade, 86.7%; retrograde, 92.3%; p = 0.323) and of spontaneous smile (antegrade, 61.5%; retrograde, 100.0%; p = 0.079).There was no significant difference in the speed of nerve regeneration of voluntary smile (antegrade, 1.32 cm/month; retrograde, 1.14 cm/month; p = 0.213) and of spontaneous smile (antegrade, 0.91 cm/month; retrograde, 1.09 cm/month, p = 0.120).Within the limitations of the study, it seems that retrograde innervation of neurovascular muscle grafts has the potential to serve as a relevant alternative to other established options of neurovascular muscle transfer, because it provides comparable results in terms of rehabilitation success.

Journal: Journal of cranio-maxillo-facial surgery : official publication of the European Association for Cranio-Maxillo-Facial Surgery (2022)
Publication types: Journal Article
Assessing the understandability, actionability, and quality of online resources for the self-management of bipolar disorder.

Introduction this study aims to assess the understandability, actionability, and quality of online resources for the self-management (sm) of bipolar spectrum disorders in adults.Methods an online search using google, bing, and yahoo!Search engines was conducted to identify resources for bipolar disorder.Those that were published in english, discussed at least 1 method directed at improving an sm task, and were within the first 25 nonadvertisement results for each search were included.Resources directed specifically at adolescents were excluded.Understandability and actionability of the online resources were evaluated using the patient education materials assessment tool (pemat).Quality of the online resources was evaluated using the discern instrument.The number of sm tasks each resource discussed was also evaluated.Overall mean appropriateness was calculated by averaging the percentage scores of understandability, actionability, and quality.Results fifty-two resources were included.The mean sample scores were 8.4 (sd, 2.1; range, 2-13; maximum, 15) for understandability, 2.2 (sd, 1.2; range, 0-4; maximum, 5) for actionability, and 46.1 (sd, 8.9; range, 30-57; maximum, 75) for quality.The overall mean appropriateness percentage was 53.5% (sd, 11.7%; range, 18%-77%), with a goal of at least 70%.Included resources addressed a mean of 7.1 tasks (sd, 2.5; range, 1-14; maximum, 20).Discussion most online resources for the sm of bipolar disorder scored poorly for understandability and actionability based on pemat scores and had low to moderate scores for quality using the discern instrument.Future online resources should be designed with the goal of increasing appropriateness for patients.

Journal: The mental health clinician (2022)
Publication types: Journal Article
Postpolypectomy fever in patients with serious infection: a report of two cases.

Postpolypectomy fever (ppf) is a rare complication in patients after colonoscopy.Because of the absence of evidence of microperforation and abdominal tenderness, patients with ppf usually present mild clinical symptoms with a good prognosis.Case presentation in this study, all patients who underwent colonoscopic examination in our hospital between january 2019 and december 2019 were enrolled.Of these, two patients developed ppf after polypectomy, exhibiting serious infection without definitive fever foci.One patient experienced rapidly aggravated type 1 respiratory failure and abnormal hepatic function, which were attributed to colonoscopy-associated infection.After active antibiotic therapy, both patients were discharged without any complications.Conclusions in summary, our study provides novel insights into patients with ppf who develop serious infections with life-threatening complications.

Journal: BMC gastroenterology (2022)
Publication types: Case Reports;Journal Article
The Application of Chitosan Nanostructures in Stomatology.

Chitosan (cs) is a natural polymer with a positive charge, a deacetylated derivative of chitin.Chitosan nanostructures (nano-cs) have received increasing interest due to their potential applications and remarkable properties.They offer advantages in stomatology due to their excellent biocompatibility, their antibacterial properties, and their biodegradability.Nano-css can be applied as drug carriers for soft tissue diseases, bone tissue engineering and dental hard tissue remineralization; furthermore, they have been used in endodontics due to their antibacterial properties; and, finally, nano-cs can improve the adhesion and mechanical properties of dental-restorative materials due to their physical blend and chemical combinations.In this review, recent developments in the application of nano-cs for stomatology are summarized, with an emphasis on nano-cs's performance characteristics in different application fields.Moreover, the challenges posed by and the future trends in its application are assessed.

Journal: Molecules (Basel, Switzerland) (2021)
Publication types: Journal Article;Review
A Clinical Update on Antiplatelet Therapy in Secondary Prevention of Ischemic Stroke.

Of review antiplatelet therapy remains the standard of care in secondary stroke prevention for non-cardioembolic ischemic stroke and transient ischemic attack.We aim to examine the use of antiplatelet agents in secondary prevention through highlighting relevant clinical trials and meta-analyses as well as providing commentary regarding our practice.Recent findings in the point and chance trials, dual antiplatelet therapy reduced recurrent stroke compared to aspirin monotherapy.Sub-analyses of these trials suggest that genetic polymorphisms could play a role in diminishing the effectiveness of clopidogrel.Similarly, thales demonstrated better outcomes with ticagrelor-aspirin combination therapy over aspirin monotherapy.Combination antiplatelet therapy with aspirin and the p2y12 inhibitors, clopidogrel and ticagrelor, reduced stroke recurrence in those presenting with mild ischemic stroke or high risk tia.Genetic polymorphisms may play a role in determining the appropriate regimen.Questions remain regarding the optimal duration of combination antiplatelet therapy for various stroke etiologies.

Journal: Current cardiology reports (2021)
Publication types: Journal Article;Review
Post-Covid-19 Rhino-Cerebral Mucormycosis: an Observational Study During the Second Wave.

Mucormycosis is one of the most lethal and rapidly spreading fungal infection which is caused by fungus of the order mucorales.The swiftness of spreading and high mortality rate that characterize mucormycosis cases added more burden to the enormous challenge brought by the covid-19 pandemic globally.The aim of this article is to identify and discuss mucormycosis and review the literature related to its diagnosis and management.A total of 15 mucormycosis cases with a history of covid-19 infection were identified in the department of dentistry of shri b m patil medical college hospital and research centre blde (deemed to be university), vijayapura, india.The duration of the study was between april 1st and mid-september 2021.Nasal swab and tissue samples from oral and maxillofacial region were collected.Blood investigations, rt-pcr and hb a1c tests and radiography revealed changes in the trabecular pattern and bone loss associated with periodontal inflammation.Mucormycosis is a life-threatening infection.Hence, dental and other clinical professionals must be aware of this possible fatal complication, so as to avoid an unfavorable outcome in clinical practice.

Journal: Maedica (2022)
Publication types: Editorial
Citrus Canker Pathogen, Its Mechanism of Infection, Eradication, and Impacts.

Citrus canker is a ravaging bacterial disease threatening citrus crops.Its major types are asiatic canker, cancrosis b, and cancrosis c, caused by xanthomonas citripv.citri(xcc),xanthomonas citripv.aurantifoliipathotype-b (xau b), and pathotype-c (xau c), respectively.The bacterium enters its host through stomata and wounds, from which it invades the intercellular spaces in the apoplast.It produces erumpent corky necrotic lesions often surrounded by a chlorotic halo on the leaves, young stems, and fruits, which causes dark spots, defoliation, reduced photosynthetic rate, rupture of leaf epidermis, dieback, and premature fruit drop in severe cases.Its main pathogenicity determinant gene ispth a, whose variants are present in all citrus canker-causing pathogens.Countries where citrus canker is not endemic adopt different methods to prevent the introduction of the pathogen into the region, eradicate the pathogen, and minimize its dissemination, whereas endemic regions require an integrated management program to control the disease.The main aim of the present manuscript is to shed light on the pathogen profile, its mechanism of infection, and fruitful strategies for disease management.Although an adequate method to completely eradicate citrus canker has not been introduced so far, many new methods are under research to abate the disease.

Journal: Plants (Basel, Switzerland) (2022)
Publication types: Journal Article;Review
Post-Dieselgate: Evidence of NOxEmission Reductions Using On-Road Remote Sensing.

The dieselgate scandal which broke in september 2015 demonstrated that vehicle manufacturers, such as the volkswagen group (vwg), engaged in software-based manipulation which led to vehicles passing laboratory-based emission testing limits but were far more polluting while being driven on roads.Using 23 000 on-road remote sensing measurements of light-duty euro 5 diesel vehicles in the united kingdom between 2012 and 2018, vwg vehicles with the "dieselgate-affected" ea189 engine demonstrated anomalous noxemission behavior between the pre- and post-dieselgate periods which was not observed in other vehicle makes or models.These anomalous changes can be explained by voluntary vwg hardware and software fixes which have led to improved noxemission control.The vgw 1.6 l vehicles, with a simple hardware fix and a software upgrade, resulted in a 36% reduction in nox, whereas the 2.0 l vehicles that required a software-only fix showed a 30% reduction in noxonce controlled for ambient temperature effects.These results show that even minor changes or upgrades can considerably reduce noxemissions, which has implications for future emission control activities and local air quality.

Journal: Environmental science & technology letters (2020)
Publication types: Journal Article
Dual supervised sampling networks for real-time segmentation of cervical cell nucleus.

The morphology of the cervical cell nucleus is the most important consideration for pathological cell identification.And a precise segmentation of the cervical cell nucleus determines the performance of the final classification for most traditional algorithms and even some deep learning-based algorithms.Many deep learning-based methods can accurately segment cervical cell nuclei but will cost lots of time, especially when dealing with the whole-slide image (wsi) of tens of thousands of cells.To address this challenge, we propose a dual-supervised sampling network structure, in which a supervised-down sampling module uses compressed images instead of original images for cell nucleus segmentation, and a boundary detection network is introduced to supervise the up-sampling process of the decoding layer for accurate segmentation.This strategy dramatically reduces the convolution calculation in image feature extraction and ensures segmentation accuracy.Experimental results on various cervical cell datasets demonstrate that compared with unet, the inference speed of the proposed network is increased by 5 times without losing segmentation accuracy.The codes and datasets are available at

Journal: Computational and structural biotechnology journal (2022)
Publication types: Journal Article
Large plasmonic color metasurfaces fabricated by super resolution deep UV lithography.

In this paper, we demonstrate plasmonic color metasurfaces as large as ∼60 cm2fabricated by deep uv projection lithography employing an innovative combination of resolution enhancement techniques.Briefly, in addition to the established off-axis dipole illumination, double- and cross-exposure resolution enhancement of lithography, we introduce a novel element, the inclusion of transparent assist features to the mask layout.With this approach, we demonstrate the fabrication of relief arrays having critical dimensions such as 159 nm nanopillars or 210 nm nanoholes with 300 nm pitches, which is near the theoretical resolution limit expressed by the rayleigh criterion for the 248 nm lithography tool used in this work.The type of surface structure,i.e.nanopillar or nanohole, and their diameters can be tailored simply by changing the width of the assist features included in the mask layout.By coating the obtained nanopatterns with thin layers of either au or al, we observe color spectra originating from the phenomenon known as localized surface plasmon resonance (lspr).We demonstrate the generation of color palettes representing a broad spectral range of colors, and we employ finite element modelling to corroborate the measured lspr fingerprint spectra.Most importantly, the ∼60 cm2nanostructure arrays can be written in only a few minutes, which is a tremendous improvement compared to the more established techniques employed for fabricating similar structures.

Journal: Nanoscale advances (2021)
Publication types: Journal Article
SPOP and CUL3 Modulate the Sonic Hedgehog Signal Response Through Controlled Degradation of GLI Family Transcription Factors.

The speckle-type poz protein (spop) functions as a guardian of genome integrity and controls transcriptional regulation by functioning as a substrate adaptor for cul3/ring-type e3 ubiquitin ligase complexes.Spop-containing cul3 complexes target a myriad of dna-binding proteins involved in dna repair and gene expression, and as such, are essential modulators of cellular homeostasis.Gli transcription factors are effectors of the hedgehog (hh) pathway, a key driver of tissue morphogenesis and post-developmental homeostasis that is commonly corrupted in cancer.Cul3-spop activity regulates amplitude and duration of hh transcriptional responses by controlling stability of gli family members.Spop and gli co-enrich in phase separated nuclear droplets that are thought to serve as hot spots for cul3-mediated gli ubiquitination and degradation.A similar framework exists in drosophila, in which the hedgehog-induced math (meprin and traf homology) and btb (bric à brac, tramtrack, broad complex) domain containing protein (hib) targets the gli ortholog cubitus interruptus (ci) for cul3-directed proteolysis.Despite this functional conservation, the molecular mechanisms by which hib and spop contribute to drosophilaand vertebrate hh signaling differ.In this mini-review we highlight similarities between the two systems and discuss evolutionary divergence in gli/ci targeting that informs our understanding of how the gli transcriptional code is controlled by spop and cul3 in health and disease.

Journal: Frontiers in cell and developmental biology (2021)
Publication types: Journal Article;Review
Metformin and risk of gingival/periodontal diseases in diabetes patients: A retrospective cohort study.

To compare the risk of gingival and periodontal diseases (gpd) between ever users and never users of metformin in patients with type 2 diabetes mellitus.Methods the taiwan's national health insurance database was used to enroll 423,949 patients with new onset diabetes mellitus from 1999 to 2005.After excluding ineligible patients, 60,309 ever users and 5578 never users were followed up for the incidence of gpd from january 1, 2006 until december 31, 2011.Propensity score-weighted hazard ratios were estimated by cox regression.Results gpd was newly diagnosed in 18,528 ever users (incidence: 7746.51 per 100,000 person-years) and 2283 never users (incidence: 12158.59 per 100,000 person-years).The hazard ratio that compared ever users to never users was 0.627 (95% confidence interval: 0.600-0.655).When metformin use was categorized by tertiles of cumulative duration and cumulative dose, the risk significantly reduced in a dose-response pattern when the cumulative duration reached approximately 2 years or the cumulative dose reached 670 grams.Analyses on the tertiles of defined daily dose of metformin showed that the reduction of gpd risk could be seen in all three subgroups but the benefit would be greater when the daily dose increased.Conclusion long-term use of metformin is associated with a significantly reduced risk of gpd.

Journal: Frontiers in endocrinology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't