syedzayyan/paper_mill_benchmark huggingface dataset:
Symptomatic Gastric Sarcoidosis in a Patient with Pulmonary and Neurosarcoidosis: A Case Report.

Sarcoidosis is an inflammatory condition with multisystem involvement of unknown etiology that is characterized by noncaseating granulomas.Gastrointestinal (gi) involvement of sarcoidosis is not commonly seen in patients with extrapulmonary disease but can result in luminal narrowing, ulceration, and, less commonly, bleeding and obstruction.Patients that present with symptomatic gastric sarcoidosis are extremely rare.Definitive diagnosis can be challenging due to the need for endoscopic biopsy, which may not be performed if the diagnosis is not considered.Biopsy may be falsely negative due to the patchy mucosal involvement of this disease.Case report this case describes a 38-year-old mixed-race man who presented to the emergency department with gi symptoms including nausea, vomiting, and abdominal pain, which persisted after being recently discharged from an outside hospital.The patient had a known history of multisystem sarcoid including pulmonary and neurosarcoidosis, and was maintained on immunosuppressive therapy.The patient underwent upper endoscopy with biopsy confirming a new diagnosis of gastric sarcoidosis.Conclusions there is an important role for early endoscopy in the diagnosis of patients with symptomatic gastric sarcoidosis to facilitate early treatment initiation and escalation or titration of immunosuppressive therapy, especially in patients with a known history of sarcoidosis with extrapulmonary involvement.The described endoscopic appearance of gastric sarcoidosis is variable in the published literature; endoscopic biopsy is therefore essential to diagnosing this disease.This type of disease progression should be considered in all sarcoid patients with persistent gi symptoms that do not resolve with conservative management, including those who are already on established immunosuppressive therapy.

Journal: The American journal of case reports (2022)
Publication types: Case Reports;Journal Article
Self and Others: Empirical and Neuropsychoanalytic Considerations of Superego and Conscience.

Freud's mature theorizing about human morality entrenched the functioning of the superego in anxiety stemming from the fear of punishment, a view with which many later psychoanalysts took issue, producing a debate as to the distinction between superego and conscience.This debate would later be mirrored more broadly in academic psychology concerning distinctions between shame and guilt.This is an area where the clinical observations and theoretical discussions of psychoanalysis have subtly guided research in cognitive psychology and the cognitive and affective neurosciences.These areas, in turn, have both clarified and supported psychoanalytic theory and practice without negating the rich phenomenological and theoretical basis on which psychoanalysis rests.

Journal: Psychoanalytic review (2023)
Publication types: Journal Article
Provocative ideas on human placental biology: A prerequisite for prevention and treatment of neonatal health challenges.

A 2-day invite-only meeting on generating "provocative ideas on human placental research" was organized on 1-2 december 2015 at the translational health science and technology institute, faridabad.This meeting was sponsored by department of biotechnology, ministry of science and technology, govt.Of india.The objectives of this meeting were the critical evaluation of placental physiology and its development.Special emphasis was placed on understanding the consequences and implications of placental development in sustenance of pregnancy and in pregnancy-associated complications such as preeclampsia, intrauterine growth restriction, and preterm birth.This meeting brought together experienced as well as novice clinicians and biologists who have a keen interest in the field of placental biology, including development of new technologies and methods for evaluating the role of placenta in predicting pregnancy outcomes.The meeting primarily focused on (i) high-throughput "-omics" approaches, (ii) maternal nutrition and placental function, (iii) placental infection and inflammation, (iv) real-time evaluation of placental development: tools for placental research, and (v) epidemiologic relevance of placental-based research.Unanimous consensus emerged among the participants to carry out additional work focused on these areas.In this article, we summarize the talks and review the published literature on the above-mentioned niches.As a direct outcome of this meeting, a request for applications has been announced by the department of biotechnology, government of india, for pursuing research in this vital but understudied domain.

Journal: American journal of reproductive immunology (New York, N.Y. : 1989) (2017)
Publication types: Congress
Cascaded systems analysis of anatomic noise in digital mammography and dual-energy digital mammography.

In x-ray based imaging of the breast, contrast between fibroglandular (fg) tissue and adipose (ad) tissue is a source of anatomic noise.The goal of this work was to validate by simulation and experiment a mathematical framework for modelling the fg component of anatomic noise in digital mammograpy (dm) and dual-energy (de) dm.Our mathematical framework unifies and generalizes existing approaches.We compared mathematical predictions directly with empirical measurements of the anatomic noise power spectrum of the cirs br3d structured breast phantom using two clinical mammography systems and four beam qualities.Our simulation and experimental results showed agreement with mathematical predictions.As a demonstration of utility, we used our mathematical framework in a theoretical spectral optimization of dm for the task of detecting breast masses.Our theoretical optimization showed that the optimal tube voltage for dm may be higher than that based on predictions that do not account for anatomic noise, in agreement with recent theoretical findings.Additionally, our theoretical optimization predicts that filtering tungsten-anode x-ray spectra with rhodium has little influence on lesion detectability, in contrast with previous findings.The mathematical methods validated in this work can be incorporated easily into cascaded systems analysis of breast imaging systems and will be useful when optimizating novel techniques for x-ray-based imaging of the breast.

Journal: Physics in medicine and biology (2019)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Sink or source? Insights into the behavior of copper and zinc in the sediment porewater of a constructed wetland by peepers.

The h-02 free water surface constructed wetland has been applied to remove heavy metals, mainly copper (cu) and zinc (zn), from wastewater on the savannah river site (aiken, sc, usa).More and more studies focus on the metal behavior between the sediment and the overlying water, which directly reflects the stability of metals after sedimentation in constructed wetlands.This study focused on the biogeochemical pathways in metal bioavailability and remobilization in the sediment after metals were removed from the overlying water.The dialysis sampling device (peeper) was used to collect porewater samples from eight depths in the sediment for the measurement of cu, zn, dissolved organic carbon (doc), and major anions (sulfate and chloride).Surface water samples were also collected for the measurement of cu, zn, doc, and anions.Different temporal trends were observed for dissolved cu between the surface and bottom waters, but not for dissolved zn.There were no obvious changes in porewater metal concentrations with increasing depths in the sediment.Sediment served as a sink for cu as only 3% of porewater samples showed higher labile cu concentrations than the surface water during the entire year, and these samples were collected below the sediment-water interface.However, sediment served as a source for zn in summer and winter as 32% of porewater samples showed higher labile zn concentrations than the surface water, and these samples were collected at all sediment depths.We think the seasonal changes in the behaviors of cu and zn are primarily controlled by the sulfur dynamics and the metal removal processes in the constructed wetland, as well as the different complexing chemistry between cu and zn.Also, our study supports that peeper is a powerful tool for studying the biogeochemistry of metals in the sediment.

Journal: The Science of the total environment (2022)
Publication types: Journal Article
Whole Genome Characterization of the High-Risk Clone ST383Klebsiella pneumoniaewith a Simultaneous Carriage ofblaCTX-M-14on IncL/M Plasmid andblaCTX-M-15on Convergent IncHI1B/IncFIB Plasmid from Egypt.

Recently, egypt has witnessed the emergence of multidrug-resistant (mdr)klebsiella pneumoniae,which has posed a serious healthcare challenge.The accelerated dissemination ofbla ctx-mgenes among these mdrk.Pneumoniae, particularlybla ctx-m-14andbla ctx-m-15, have been noted.In this study, we investigated the occurrence ofbla ctx-m-ivamong k.Pneumoniaerecovered from the laboratory of a major hospital in alexandria.The 23 tested isolates showed an mdr phenotype and thebla ctx-m-ivgene was detected in ≈22% of the isolates.The transformation of plasmids harboringbla ctx-m-ivto chemically competent cells of escherichia coli dh5α was successful in three out of five of the testedbla ctx-m-iv-positive isolates.Whole genome sequencing of k22 indicated that the isolate belonged to the high-risk clone st383, showing a simultaneous carriage ofbla ctx-m-14on inc l/m plasmid, i.e., p egy22_ctx-m-14, andbla ctx-m-15on a hybrid inc hi1b/inc fib plasmid, p egy22_ctx-m-15.Alignment of both plasmids revealed high similarity with those originating in the uk, germany, australia, russia, china, saudi arabia, and morocco.P egy22_ctx-m-15 was a mosaic plasmid that demonstrated convergence of mdr and virulence genes.The emergence of such a plasmid with enhanced genetic plasticity constitutes the perfect path for the evolution of k.Pneumoniaeisolates causing invasive untreatable infections especially in a country with a high burden of infectious diseases such as egypt.Therefore there is an imperative need for countrywide surveillances to monitor the prevalence of these superbugs with limited therapeutic options.

Journal: Microorganisms (2022)
Publication types: Journal Article
SOLO-SLAM: A Parallel Semantic SLAM Algorithm for Dynamic Scenes.

Simultaneous localization and mapping (slam) is a core technology for mobile robots working in unknown environments.Most existing slam techniques can achieve good localization accuracy in static scenes, as they are designed based on the assumption that unknown scenes are rigid.However, real-world environments are dynamic, resulting in poor performance of slam algorithms.Thus, to optimize the performance of slam techniques, we propose a new parallel processing system, named solo-slam, based on the existing orb-slam3 algorithm.By improving the semantic threads and designing a new dynamic point filtering strategy, solo-slam completes the tasks of semantic and slam threads in parallel, thereby effectively improving the real-time performance of slam systems.Additionally, we further enhance the filtering effect for dynamic points using a combination of regional dynamic degree and geometric constraints.The designed system adds a new semantic constraint based on semantic attributes of map points, which solves, to some extent, the problem of fewer optimization constraints caused by dynamic information filtering.Using the publicly available tum dataset, solo-slam is compared with other state-of-the-art schemes.Our algorithm outperforms orb-slam3 in accuracy (maximum improvement is 97.16%) and achieves better results than dyna-slam with respect to time efficiency (maximum improvement is 90.07%).

Journal: Sensors (Basel, Switzerland) (2022)
Publication types: Journal Article
Innate immunity stimulation via CpG oligodeoxynucleotides ameliorates Alzheimer's disease pathology in aged squirrel monkeys.

Alzheimer's disease is the most common cause of dementia and the only illness among the top 10 causes of death for which there is no disease-modifying therapy.The failure rate of clinical trials is very high, in part due to the premature translation of successful results in transgenic mouse models to patients.Extensive evidence suggests that dysregulation of innate immunity and microglia/macrophages plays a key role in alzheimer's disease pathogenesis.Activated resident microglia and peripheral macrophages can display protective or detrimental phenotypes depending on the stimulus and environment.Toll-like receptors (tlrs) are a family of innate immune regulators known to play an important role in governing the phenotypic status of microglia.We have shown in multiple transgenic alzheimer's disease mouse models that harnessing innate immunity via tlr9 agonist cp g oligodeoxynucleotides (odns) modulates age-related defects associated with immune cells and safely reduces amyloid plaques, oligomeric amyloid-β, tau pathology, and cerebral amyloid angiopathy (caa) while promoting cognitive benefits.In the current study we have used a non-human primate model of sporadic alzheimer's disease pathology that develops extensive caa-elderly squirrel monkeys.The major complications in current immunotherapeutic trials for alzheimer's disease are amyloid-related imaging abnormalities, which are linked to the presence and extent of caa; hence, the prominence of caa in elderly squirrel monkeys makes them a valuable model for studying the safety of the cp g odn-based concept of immunomodulation.We demonstrate that long-term use of class b cp g odn 2006 induces a favourable degree of innate immunity stimulation without producing excessive or sustained inflammation, resulting in efficient amelioration of both caa and tau alzheimer's disease-related pathologies in association with behavioural improvements and in the absence of microhaemorrhages in aged elderly squirrel monkeys.Cp g odn 2006 has been well established in numerous human trials for a variety of diseases.The present evidence together with our earlier, extensive preclinical research, validates the beneficial therapeutic outcomes and safety of this innovative immunomodulatory approach, increasing the likelihood of cp g odn therapeutic efficacy in future clinical trials.

Journal: Brain : a journal of neurology (2021)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Evidence-Based Decision Support for a Structured Care Program on Polypharmacy in Multimorbidity: A Guideline Upgrade Based on a Realist Synthesis.

Evidence-based clinical guidelines generally consider single conditions, and rarely multimorbidity.We developed an evidence-based guideline for a structured care program to manage polypharmacy in multimorbidity by using a realist synthesis to update the german polypharmacy guideline including the following five methods: formal prioritization in focus groups; systematic guideline review of evidence-based multimorbidity/polypharmacy guidelines; evidence search/synthesis and recommendation development; multidisciplinary consent of recommendations; feasibility test of updated guideline.We identified the need for a better description of the target group, decision support, prioritization of medication, consideration of patient preferences and anticholinergic properties, and of healthcare interfaces.We conducted a systematic guideline review of eight guidelines and extracted and synthesized recommendations using the ariadne principles.We also included 48 systematic reviews.We formulated and agreed upon 34 recommendations for the revised guideline.During the feasibility test, guideline use enabled 57% of gps to identify problems, leading to medication changes in 49% and self-assessed improvement in 56% of patients.Although 58% of gps felt that it was too long, 92% recommended it.Polypharmacy should be systematically reviewed at least annually.Patients, family members, and healthcare professionals should monitor and adjust it using prospective process validation, taking into account patient preferences and agreed treatment goals.

Journal: Journal of personalized medicine (2022)
Publication types: Journal Article
Protectin D1 protects against lipopolysaccharide-induced acute lung injury through inhibition of neutrophil infiltration and the formation of neutrophil extracellular traps in lung tissue.

Protectin d1 (pd1), a dha-derived lipid mediator, has recently been shown to possess anti-inflammatory and pro-resolving properties.To date, little is known about the effect of pd1 on lipopolysaccharide (lps)-induced acute lung injury (ali) in mice.The aim of the present study was to investigate the therapeutic effects of pd1 on lps-induced ali and its potential mechanisms of action.Ali was induced via an intraperitoneal injection of lps, where pd1 (2 ng/mouse) was administered intravenously 30 min after lps challenge.Mice were sacrificed 24 h after modeling.Lung histopathological changes were assessed using hematoxylin and eosin staining and myeloperoxidase (mpo) activity was tested using immunohistochemistry.Tumor necrosis-α and interleukin-6 levels in the bronchoalveolar lavage fluid (balf) and serum were measured using elisa.To detect neutrophil extracellular traps produced by infiltrated neutrophils in the lung tissue, immunofluorescence staining was performed using anti-mpo and anti-histone h3 antibodies.The results indicated that pd1 significantly attenuated histological damage and neutrophil infiltration in lung tissue, reduced the lung wet/dry weight ratio, protein concentration and proinflammatory cytokine levels in balf and decreased proinflammatory cytokine levels in serum.Moreover, neutrophil citrullinated histone h3 (cit h3) expression was also reduced after pd1 administration.In conclusion, pd1 attenuated lps-induced ali in mice via inhibition of neutrophil extracellular trap formation in lung tissue.Therefore, pd1 administration may serve to be a new strategy for treating ali.

Journal: Experimental and therapeutic medicine (2021)
Publication types: Journal Article
Second primary malignancy in myelofibrosis patients treated with ruxolitinib.

Ruxolitinib (rux), the first jak1/jak2 inhibitor approved for myelofibrosis (mf) therapy, has recently been associated with the occurrence of second primary malignancies (spms), mainly lymphomas and non-melanoma skin cancers (nmscs).We analyzed the incidence, risk factors and outcome of spms in 700 mf patients treated with rux in a real-world context.Median follow-up from starting rux was 2·9 years.Overall, 80 (11·4%) patients developed 87 spms after rux start.Nmscs were the most common spms (50·6% of the cases).Multivariate analysis demonstrated that male sex [hazard ratio (hr): 2·37, 95% confidence interval (95%ci): 1·22-4·60, p = 0·01] and thrombocytosis> 400 × 109/l at rux start (hr:1·98, 95%ci: 1·10-4·60, p = 0·02) were associated with increased risk for spms.Risk factors for nmsc alone were male sex (hr: 3·14, 95%ci: 1·24-7·92, p = 0·02) and duration of hydroxycarbamide and rux therapy > 5 years (hr: 3·20, 95%ci: 1·17-8·75, p = 0·02 and hr: 2·93, 95%ci: 1·39-6·17, p = 0·005 respectively).In spms excluding nmscs, male sex (hr: 2·41, 95%ci: 1·11-5·25, p = 0·03), platelet > 400 × 109/l (hr: 3·30, 95%ci: 1·67-6·50, p = 0·001) and previous arterial thromboses (hr: 3·47, 95%ci: 1·48-8·14, p = 0·004) were shown to be associated with higher risk of spms.While it is reassuring that no aggressive lymphoma was documented, active skin surveillance is recommended in all patients and particularly after prolonged hydroxycaramide therapy; oncological screening should be triggered by thrombocytosis and arterial thrombosis, particularly in males.

Journal: British journal of haematology (2021)
Publication types: Journal Article
The complete chloroplast genome sequence ofAconitum tschangbaischanense(Ranunculaceae).

The perennial herbal medicine species aconitum tschangbaischanense, is endemic to changhai mountain, jilin province.In this study, we attempted to uncover the complete chloroplast (cp) genome of a.Tschangbaischanensebased on sequencing data using the illumina sequencing technology.As per the results: (1) the length of its complete cp genome is 155,881 bp with a typical tetrad structure; (2) the structure of its cp genome contains large single-copy and small single-copy (lsc and ssc) regions of 86,351 and 16,9444 bp, respectively, isolated by two inverted repeat regions (irs) of 26,293 bp; (3) we annotated a total 131 genes, consisting of 86 protein-coding genes, eight r rna genes, and 37 t rna genes.According to the maximum-likelihood phylogenetic tree based on complete cp genomes,a.Tschangbaischanense, showed close association with a.Carmichaelii, which belongs to clade i.Finally, this study provides the characteristics of the cp genome of a.Tschangbaischanense, and its phylogenetic position.

Journal: Mitochondrial DNA. Part B, Resources (2023)
Publication types: Journal Article
Effectiveness of interventions for reducing TB incidence in countries with low TB incidence: a systematic review of reviews.

S what is the evidence base for the effectiveness of interventions to reduce tuberculosis (tb) incidence in countries which have low tb incidence?Methods we conducted a systematic review of interventions for tb control and prevention relevant to low tb incidence settings (<10 cases per 100 000 population).Our analysis was stratified according to "direct" or "indirect" effects on tb incidence.Review quality was assessed using amstar2 criteria.We summarised the strength of review level evidence for interventions as "sufficient", "tentative", "insufficient" or "no" using a framework based on the consistency of evidence within and between reviews.Results we found sufficient review level evidence for direct effects on tb incidence/case prevention of vaccination and treatment of latent tb infection.We also found sufficient evidence of beneficial indirect effects attributable to drug susceptibility testing and adverse indirect effects (measured as sub-optimal treatment outcomes) in relation to use of standardised first-line drug regimens for isoniazid-resistant tb and intermittent dosing regimens.We found insufficient review level evidence for direct or indirect effects of interventions in other areas, including screening, adherence, multidrug-resistant tb, and healthcare-associated infection.Discussion our review has shown a need for stronger evidence to support expert opinion and country experience when formulating tb control policy.

Journal: European respiratory review : an official journal of the European Respiratory Society (2019)
Publication types: Journal Article;Systematic Review
Molecular evidences on anti-inflammatory, anticancer, and memory-boosting effects of frankincense.

Chemical diversity of natural products with drug-like features has attracted much attention from medicine to develop more safe and effective drugs.Their anti-inflammatory, antitumor, analgesic, and other therapeutic properties are sometimes more successful than chemical drugs in controlling disease due to fewer drug resistance and side effects and being more tolerable in a long time.Frankincense, the oleo gum resin extracted from the boswellia species, contains some of these chemicals.The anti-inflammatory effect of its main ingredient, boswellic acid, has been traditionally used to treat many diseases, mainly those target memory functions.In this review, we have accumulated research evidence from the beneficial effect of frankincense consumption in memory improvement and the prevention of inflammation and cancer.Besides, we have discussed the molecular pathways mediating the therapeutic effects of this natural supplement.

Journal: Phytotherapy research : PTR (2022)
Publication types: Journal Article;Review