syedzayyan/paper_mill_benchmark huggingface dataset:
Plasma Metabolomics Identifies the Dysregulated Metabolic Profile of Primary Immune Thrombocytopenia (ITP) Based on GC-MS.

Itp is a common autoimmune bleeding disorder with elusive pathogenesis.Our study was implemented to profile the plasma metabolic alterations of patients diagnosed with itp, aiming at exploring the potential novel biomarkers and partial mechanism of itp.The metabolomic analysis of plasma samples was conducted using gc-ms on 98 itp patients and 30 healthy controls (hcs).Age and gender matched samples were selected to enter the training set or test set respectively.Opls-da, t-test with fdr correction and roc analyses were employed to screen out and evaluate the differential metabolites.Possible pathways were enriched based on metabolomics pathway analysis (met pa).A total of 85 metabolites were investigated in our study and 17 differential metabolites with diagnostic potential were identified between itp patients and hcs.Met pa showed that the metabolic disorders of itp patients were mainly related to phenylalanine, tyrosine and tryptophan biosynthesis, phenylalanine metabolism and glyoxylate and dicarboxylate metabolism.Additionally, we discriminated 6 differential metabolites and 5 enriched pathways in predicting the resistance to glucocorticoids in chronic itp patients.The distinct metabolites discovered in our study could become novel biomarkers for the auxiliary diagnosis and prognosis prediction of itp.Besides, the dysregulated pathways might contribute to the development of itp.

Journal: Frontiers in pharmacology (2022)
Publication types: Journal Article
Epitaxy Induced Highly Ordered Sm2Co17-SmCo5Nanoscale Thin-Film Magnets.

Utilizing the molecular beam epitaxy technique, a nanoscale thin-film magnet ofc-axis-oriented sm2co17and sm co5phases is stabilized.While typically in the prototype sm(co, fe, cu, zr)7.5-8pinning-type magnets, an ordered nanocomposite is formed by complex thermal treatments, here, a one-step approach to induce controlled phase separation in a binary sm-co system is shown.A detailed analysis of the extended x-ray absorption fine structure confirmed the coexistence of sm2co17and sm co5phases with 65% sm2co17and 35% sm co5.The sm co5phase is stabilized directly on an al2o3substrate up to a thickness of 4 nm followed by a matrix of sm2co17intermixed with sm co5.This structural transition takes place through coherent atomic layers, as revealed by scanning transmission electron microscopy.Highly crystalline growth of well-aligned sm2co17and sm co5phases with coherent interfaces result in strong exchange interaction, leading to enhanced magnetization and magnetic coupling.The arrangement of sm2co17and sm co5phases at the nanoscale is reflected in the observed magnetocrystalline anisotropy and coercivity.As next-generation permanent magnets require designing of materials at an atomic level, this work enhances our understanding of self-assembling and functioning of nanophased magnets and contributes to establishing new concepts to engineer the microstructure for beyond state-of-the-art magnets.

Journal: ACS applied materials & interfaces (2021)
Publication types: Journal Article
Assessment of BCOR Internal Tandem Duplications in Pediatric Cancers by Targeted RNA Sequencing.

Alterations in the bcor gene, including internal tandem duplications (itds) of exon 15 have emerged as important oncogenic changes that define several diagnostic entities.In pediatric cancers, bcor itds have recurrently been described in clear cell sarcoma of kidney (ccsk), primitive myxoid mesenchymal tumor of infancy (pmmti), and central nervous system high-grade neuroepithelial tumor with bcor itd in exon 15 (hgnet-bcor itdex15).In adults, bcor itds are also reported in endometrial and other sarcomas.The utility of multiplex targeted rna sequencing for the identification of bcor itd in pediatric cancers was investigated.All available archival cases of ccsk, pmmti, and hgnet-bcor itdex15 were collected.Each case underwent anchored multiplex pcr library preparation with a custom-designed panel, with bcor targeted for both fusions and itds.Bcor itd was detected in all cases across three histologic subtypes using the rna panel, with no other fusions identified in any of the cases.All bcor itds occurred in the final exon, within 16 codons from the stop sequence.Multiplex targeted rna sequencing from formalin-fixed, paraffin-embedded tissue is successful at identifying bcor internal tandem duplications.This analysis supports the use of anchored multiplex pcr targeted rna next-generation sequencing panels for identification of bcor itds in pediatric tumors.The use of post-analytic algorithms to improve the detection of bcor itd using dna panels was also explored.

Journal: The Journal of molecular diagnostics : JMD (2021)
Publication types: Journal Article;Validation Study
Constructing Accurate and Efficient Deep Spiking Neural Networks With Double-Threshold and Augmented Schemes.

Spiking neural networks (snns) are considered as a potential candidate to overcome current challenges, such as the high-power consumption encountered by artificial neural networks (anns); however, there is still a gap between them with respect to the recognition accuracy on various tasks.A conversion strategy was, thus, introduced recently to bridge this gap by mapping a trained ann to an snn.However, it is still unclear that to what extent this obtained snn can benefit both the accuracy advantage from ann and high efficiency from the spike-based paradigm of computation.In this article, we propose two new conversion methods, namely ter mapping and aug mapping.The ter mapping is a straightforward extension of a typical threshold-balancing method with a double-threshold scheme, while the aug mapping additionally incorporates a new scheme of augmented spike that employs a spike coefficient to carry the number of typical all-or-nothing spikes occurring at a time step.We examine the performance of our methods based on the mnist, fashion-mnist, and cifar10 data sets.The results show that the proposed double-threshold scheme can effectively improve the accuracies of the converted snns.More importantly, the proposed aug mapping is more advantageous for constructing accurate, fast, and efficient deep snns compared with other state-of-the-art approaches.Our study, therefore, provides new approaches for further integration of advanced techniques in anns to improve the performance of snns, which could be of great merit to applied developments with spike-based neuromorphic computing.

Journal: IEEE transactions on neural networks and learning systems (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
The Role of Transoral Robotic Surgery for Parapharyngeal Space: Experience of a Tertiary Center.

The parapharyngeal space (pps) is an anatomically and functionally complex region of the craniofacial district.Tumors that originate from this region are rare, and surgery is currently the best practice in the vast majority of cases with different surgical approaches being reported in the literature.Recently, mini-invasive robotic/endoscopic techniques have begun to emerge as effective alternatives in selected cases.In this work, we retrospectively analyzed 17 patients affected by pps tumors, and managed by transoral robotic surgery (tors) as a therapeutic or diagnostic procedure.Tors was used alone or combined with a transcervical approach for huge lesions of the pps, at risk of fragmentation (curative intent).Tors also permitted biopsies of unknown lesions of the pps to be conducted (diagnostic intent) otherwise unreachable without performing a mandibulotomy.All patients treated with curative intent benefited from radical surgery.No major complications were observed, and tumor fragmentation occurred only in 2 of 17 patients (11.8%).All patients receiving tors with diagnostic intent were successfully referred to nonsurgical treatments based on the final histhopathological findings.This work also demonstrated tors to be effective and safe on a larger group of patients compared to our preliminary study in 2016.Tors provides good oncological and functional outcomes when used with curative intent and is an effective diagnostic tool in cases of suspicious lesions of the pps.

Journal: The Journal of craniofacial surgery (2020)
Publication types: Journal Article
"Late-onset" ADHD symptoms in young adulthood: Is this ADHD?

We investigated whether "late-onset" adhd that emerges in adolescence/adulthood is similar in risk factor profile to: (1) child-onset adhd, but emerges later because of scaffolding/compensation from childhood resources; and (2) depression, because it typically onsets in adolescence/adulthood and shows symptom and genetic overlaps with adhd.methods:we examined associations between late-onset adhd and adhd risk factors, cognitive tasks, childhood resources and depression risk factors in a population-based cohort followed-up to age 25 years (n=4224-9764).results:parent-rated late-onset adhd was like child-onset persistent adhd in associations with adhd polygenic risk scores and cognitive task performance, although self-rated late-onset adhd was not.Late-onset adhd was associated with higher levels of childhood resources than child-onset adhd and did not show strong evidence of association with depression risk factors.conclusions:late-onset adhd shares characteristics with child-onset adhd when parent-rated, but differences for self-reports require investigation.Childhood resources may delay the onset of adhd.

Journal: Journal of attention disorders (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Comparison of case-based learning combined with Rain Classroom teaching and traditional method in complete denture course for undergraduate interns.

Complete denture, as an important restoration method for edentulism, is difficult to study for beginners, especially in linking the theory with clinical practice.Objective this study was aimed to compare the teaching effects between case-based learning combined with rain classroom teaching and traditional lecture method in the clinical course of complete denture prosthesis for undergraduate interns.Methods in a course called "problems and treatment strategies of complete denture after wearing", interns were divided into two groups: one for traditional lecture-based teaching with power point slideshow (the control group, n = 28); and the other for case-based learning combined with rain classroom teaching, which published information before class, discussed specific clinic cases in class and got real-time interns' feedback via we chat (the test group, n = 22).Both groups received the same exam and questionnaire survey after class.The q&a participation of interns in class, theoretical test scores and questionnaire survey responses were used to evaluate the teaching effects.An independent sample t-test and the chi-square test or fisher's exact test were used for statistical analysis in this study.Results the q&a participation of interns in the test group was much better than that of the control group.The average score on the theoretical test after class in the test group (72.14 ± 12.24) was significantly higher than that in the control group (61.29 ± 20.12) (p < 0.05).In the test group, 94.54% (21/22) of the interns preferred the new teaching mode.Conclusion case-based learning combined with rain classroom teaching is helpful to enliven the classroom atmosphere, inspire studying enthusiasm, and achieve a good learning effect in both theory and clinical practice related to complete denture prosthesis.

Journal: BMC medical education (2022)
Publication types: Journal Article
HtrA2 is required for inflammatory responses in BMDMs via controlling TRAF2 stability in collagen-induced arthritis.

Rheumatoid arthritis (ra) is an autoimmune inflammatory disease characterized by the destruction of cartilage and bone.The present study aims to investigate the role of htr a serine peptidase 2 (htr a2) in the collagen-induced arthritis.The expressions of htr a2 were determined in the database bio gps and bone marrow-derived macrophages (bmdms).The populations of myeloid and lymphoid cells were determined in wild type and htr a2 knockout (htr a2mko) mice using flow cytometry.In addition, the expressions of pro-inflammatory cytokines (il6, tnf, and il1β) were determined in the activated bmdms from wild type (wt) and htr a2mkomice.String database was used to predict the interactive proteins of htr a2 and co-immunoprecipitation was used to confirm these interactions.A collagen-induced arthritis model was established to investigate the effects of htr a2 on the arthritis symptoms.It was found that htr a2 reduction was associated with the activation of myeloid cells.Interestingly, htr a2 deficiency did not affect the development of myeloid and lymphoid cells.Further studies demonstrated that htr a2 deficiency suppressed the production of pro-inflammatory cytokines in bmdms induced by lipopolysaccharide or cp g.Co-immunoprecipitation results demonstrated that htr a2 enhanced the stability of tnf receptor-associated factor 2 (traf2).Htr a2 participated in the activation of the inflammatory response in a collagen-induced arthritis model.In summary, htr a2 modulates inflammatory responses in bmdms by controlling traf2 stability in a collagen-induced arthritis mouse model.

Journal: Molecular immunology (2021)
Publication types: Journal Article
The usage of Cyanobacteria in wastewater treatment: prospects and limitations.

The applicability of cyanobacteria executes various roles in the treatment of wastewater, assembling of superfluous food and, thus, produces valued biomass which has various applications.Besides this, they enrich and improve the quality of water as they are photosynthetic autotrophs.Currently, cyanobacteria gained momentum for remediation of wastewaters because firstly, they enhances the o2content of waters through photosynthesis and perform bioremediation of some heavy metals.Secondly, cyanobacteria play significant roles in distressing the biological oxygen demand, chemical oxygen demand, turbidity, minerals and microbes; thirdly, they can be used either as axenic cultures or as mixed cultures both offering distinct advantages.Lastly, some species are tolerant towards extreme temperatures both low and high, acidic p h, high salt concentrations and heavy metals, which makes them outstanding candidates for the wastewater treatment plants.The suitable immobilization methods must evolve, better understanding of their morphological and biochemical parameters is required for the optimum growth, easy methods of harvesting the biomass after the treatment are required and more trials on large-scale basis are required before they can be launched on full-fledged basis for wastewater treatments.

Journal: Letters in applied microbiology (2022)
Publication types: Journal Article;Review
Interaction between hyperphosphorylated tau and pyroptosis in forskolin and streptozotocin induced AD models.

Amyloid-β (aβ) activating the pyroptotic cell pathway has been reported to act as a component in the progression of alzheimer's disease (ad).As another major pathophysiological protein process in ad, the abnormal hyperphosphorylation of tau proteins exerts neurotoxic effects through a variety of mechanisms.However, data describing the relationship between hyperphosphorylated tau proteins and pyroptosis are very scarce.In this study, we used two hyperphosphorylated tau models, intracerebroventricular (icv) forskolin (fsk, a pka activator) rat model and icv-streptozotocin (stz) rat model; also, fsk and stz treated pc12 cells as in vitro models to test the relationship between hyperphosphorylated tau proteins and pyroptosis.We found that fsk and stz significantly increased the hyperphosphorylated tau level, pyroptosis-related protein in pc12 cell and rats' brain, and inhibited the activity of caspase-1 by caspase-1 inhibitor, caspase-1 si rna, or incubated with interleukin(il)-1β/il-18 neutralizing antibody could notably alleviate the fsk and stz induced pc12 cells damage and improve the cognitive disorder in icv-fsk and icv-stz rats.Suppressed the level of hyperphosphorylated tau by li cl also significantly decreased caspase-1 activity and the content of inflammatory cytokines in fsk or stz treated pc12 cells.In summary, our results demonstrated that inflammasomes mediated pyroptosis at least one underlying pathogenic mechanism for the neurotoxicity induced by hyperphosphorylated tau in pc12 cells and dementia rats.Il-1β and il-18, the downstream of caspase-1, in turn increased hyperphosphorylated tau while spreading neuroinflammation.

Journal: Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie (2020)
Publication types: Journal Article
NMR Study of the Secondary Structure and Biopharmaceutical Formulation of an Active Branched Antimicrobial Peptide.

The synthetic antimicrobial peptide set-m33 is being developed as a possible new antibacterial candidate for the treatment of multi-drug resistant bacteria.Set-m33 is a branched peptide featuring higher resistance and bioavailability than its linear analogues.Set-m33 shows antimicrobial activity against different species of multi-resistant gram-negative bacteria, including clinically isolated strains of pseudomonas aeruginosa,klebsiella pneumoniae,acinetobacter baumaniiand escherichia coli.The secondary structure of this 40 amino acid peptide was investigated by nmr to fully characterize the product in the framework of preclinical studies.The possible presence of helixes or β-sheets in the structure had to be explored to predict the behavior of the branched peptide in solution, with a view to designing a formulation for parenteral administration.Since the final formulation of set-m33 will be strictly defined in terms of counter-ions and additives, we also report the studies on a new salt form, set-m33 chloride, that retains its activity against gram-negative bacteria and gains in solubility, with a possible improvement in the pharmacokinetic profile.The opportunity of using a chloride counter-ion is very convenient from a process development point of view and did not increase the toxicity of the antimicrobial drug.

Journal: Molecules (Basel, Switzerland) (2019)
Publication types: Journal Article
Mandibular Movement Analysis to Assess Efficacy of Oral Appliance Therapy in OSA.

Rationale the respiratory effort index derived from vertical mandibular movements (mm-rei) is a potential marker of increased respiratory effort during sleep.We evaluated the effectiveness of mandibular advancement splint therapy using mm-rei, in comparison with the apnea-hypopnea index (ahi) and oxygen desaturation index (odi).Methods fifty-six subjects (median age, 47 years) with osa treated with a custom mandibular advancement splint (herbst appliance) were evaluated at the end of the titration procedure when snoring was reported absent by the sleep partner.We employed a magnetometer to capture mandibular movements (brizzy; nomics).Mandibular advancement splint efficacy was assessed as the percent change from baseline, using bayesian multilevel models.Results at the end of titration, all indices of osa severity decreased compared with baseline: ahi (-48.9% to -71.1%), odi (-49.5% to -77.2%), with obstructive hypopnea index and mm-rei showing the largest responses (-70.6% to -88.5% and -69.5% to -96.3%, respectively).Mm-rei normalization via reductions in both mandibular movement event rate and duration accurately reflected efficacy of the appliance.Conclusions the reduction of vertical respiratory mandibular movements estimated by mm-rei and sleep respiratory effort duration accompanied the decrease in obstructive hypopneas, ahi, and odi when snoring resolved in subjects with osa treated with an optimally titrated mandibular advancement splint.

Journal: Chest (2018)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Praxis der Teledermatologie.

Hintergrund teledermatologische anwendungen werden im deutschen versorgungssystem in den nächsten jahren erheblich an bedeutung gewinnen.Das vorliegende empfehlungspapier wurde als expertenkonsens auf der basis einer qualifizierten literaturrecherche und eines strukturierten entscheidungsprozesses der autorengruppe entwickelt.Zielsetzung: a) die ist-analyse zum einsatz der telemedizin in der dermatologie, b) die bewertung der evidenz ihres nutzens und ihrer sicherheit und, c) die entwicklung von verfahrensstandards für die ärztliche praxis in den deutschsprachigen ländern.Auf der basis dieser erkenntnisse soll durch einen expertenkonsens eine handlungsorientierung für den einsatz der teledermatologie gegeben werden.Methoden dreistufiges vorgehen: 1) systematische literaturrecherche in den internationalen medizinischen onlinedatenbanken pubmed und embase, 2) weitere, teils manuelle recherchen, 3) expertenkonsens mit einem systematischen entscheidungsverfahren mit 21 teilnehmern.Ergebnisse in der strukturierten literaturrecherche fanden sich 204 wissenschaftliche originalarbeiten, in denen anwendungen der telemedizin bei hautkrankheiten thematisiert wurden.Diese wurden systematisch aufgearbeitet, analysiert und bewertet.In der zweiten stufe wurden in einer handsuche zusätzliche relevante schriften identifiziert und ebenfalls ausgewertet.Das expertengremium entwickelte dann auf der basis der externen evidenz sowie der internen diskussion handlungsempfehlungen für die praxis.Schlussfolgerung der wissenschaftlichen studienlage ist, dass die telemedizinische unterstützung der dermatologischen behandlung und prävention bei einsatz leistungsfähiger systeme, kenntnis ihrer anwendung sowie beachtung der indikationen und kontrainidikationen einen erheblichen mehrnutzen darstellt.Schlussfolgerungen die teledermatologie hat in den deutschsprachigen ländern wie auch weltweit einen zunehmenden stellenwert und bietet aufgrund des hohen innovationsgrades eine vorreiter- und vorbildfunktion für weitere telemedizinische anwendungen anderer fachrichtungen.Eine qualitätsgesicherte teledermatologische behandlung ist in den deutschsprachigen ländern praktikabel und kann zu einem relevanten mehrnutzen in der versorgung führen.Ihr einsatz ist immer dann in erwägung zu ziehen, wenn relevante zusatznutzen für die patienten ohne relevante nachteile für sie und für die versorgenden zu erwarten sind.Für die teledermatologische behandlung wurden mit dem vorliegenden konsensuspapier praxisrelevante maßgaben festgelegt.Etwaige situationsabhängige limitationen in der versorgung sind stets zu beachten.

Journal: Journal der Deutschen Dermatologischen Gesellschaft = Journal of the German Society of Dermatology : JDDG (2018)
Publication types: Journal Article