syedzayyan/paper_mill_benchmark huggingface dataset:
ProtPlat: an efficient pre-training platform for protein classification based on FastText.

For the past decades, benefitting from the rapid growth of protein sequence data in public databases, a lot of machine learning methods have been developed to predict physicochemical properties or functions of proteins using amino acid sequence features.However, the prediction performance often suffers from the lack of labeled data.In recent years, pre-training methods have been widely studied to address the small-sample issue in computer vision and natural language processing fields, while specific pre-training techniques for protein sequences are few.Results in this paper, we propose a pre-training platform for representing protein sequences, called prot plat, which uses the pfam database to train a three-layer neural network, and then uses specific training data from downstream tasks to fine-tune the model.Prot plat can learn good representations for amino acids, and at the same time achieve efficient classification.We conduct experiments on three protein classification tasks, including the identification of type iii secreted effectors, the prediction of subcellular localization, and the recognition of signal peptides.The experimental results show that the pre-training can enhance model performance effectively and prot plat is competitive to the state-of-the-art predictors, especially for small datasets.We implement the prot plat platform as a web service ( ) that is accessible to the public.Conclusions to enhance the feature representation of protein amino acid sequences and improve the performance of sequence-based classification tasks, we develop prot plat, a general platform for the pre-training of protein sequences, which is featured by a large-scale supervised training based on pfam database and an efficient learning model, fast text.The experimental results of three downstream classification tasks demonstrate the efficacy of prot plat.

Journal: BMC bioinformatics (2022)
Publication types: Journal Article
Royal Flying Doctor Service Coronavirus Disease 2019 Activity and Surge Modeling in Australia.

There is a coronavirus disease 2019 (covid-19) pandemic.We aimed to describe the characteristics of patients transported by the royal flying doctor service (rfds) for confirmed or suspected covid-19 and to investigate the surge capacity of and operational implications for the rfds in dealing with covid-19.Methods this was a prospective cohort study.To determine the characteristics of patients transported for confirmed or suspected covid-19, we included patient data from february 2, 2020, to may 6, 2020.To investigate the surge capacity and operational implications for the rfds in dealing with covid-19, we built and validated an interactive operations area-level discrete event simulation decision support model underpinned by rfds air medical activity data from 2015 to 2019 (4 years).This model was subsequently used in a factorial in silico experiment to systematically investigate both the supply of rfds air medical services and the increased rates of demand for these services for diseases of the respiratory system.Results the rfds conducted 291 patient episodes of care for confirmed or suspected covid-19.This included 288 separate patients, including 136 men and 119 women (sex missing = 33), with a median age of 62.0 years (interquartile range, 43.5-74.9 years).The simulation decision support model we developed is capable of providing dynamic and real-time support for rfds decision makers in understanding the system's performance under uncertain covid-19 demand.With increased covid-19-related demand, the ability of the rfds to cope will be driven by the number of aircraft available.The simulation model provided each aviation section with estimated numbers of aircraft required to meet a range of anticipated demands.Conclusion despite the lack of certainty in the actual level of covid-19-related demand for rfds services, modeling demonstrates that the robustness of meeting such demand increases with the number of operational and medically staffed aircraft.

Journal: Air medical journal (2020)
Publication types: Journal Article
Isotype Heterojunction-Boosted CO2Photoreduction to CO.

Photocatalytic conversion of co2to high-value products plays a crucial role in the global pursuit of carbon-neutral economy.Junction photocatalysts, such as the isotype heterojunctions, offer an ideal paradigm to navigate the photocatalytic co2reduction reaction (crr).Herein, we elucidate the behaviors of isotype heterojunctions toward photocatalytic crr over a representative photocatalyst, g-c3n4.Impressively, the isotype heterojunctions possess a significantly higher efficiency for the spatial separation and transfer of photogenerated carriers than the single components.Along with the intrinsically outstanding stability, the isotype heterojunctions exhibit an exceptional and stable activity toward the co2photoreduction to co.More importantly, by combining quantitative in situ technique with the first-principles modeling, we elucidate that the enhanced photoinduced charge dynamics promotes the production of key intermediates and thus the whole reaction kinetics.

Journal: Nano-micro letters (2022)
Publication types: Journal Article
Venlafaxine and O-desmethylvenlafaxine serum levels are positively associated with antidepressant response in elder depressed out-patients.

Therapeutic drug monitoring (tdm) represents one of the most promising tools in clinical practice to optimise antidepressant treatment.Nevertheless, little is still known regarding the relationship between clinical efficacy and serum concentration of venlafaxine (ven).The aim of our study was to investigate the association between serum concentration of venlafaxine + o-desmethylvenlafaxine (scvo) and antidepressant response (ar).Methods 52 depressed outpatients treated with ven were recruited and followed in a naturalistic setting for three months.Hamilton depression rating scale-21 was administered at baseline, at month 1 and at month 3 to assess ar.Scvo was measured at steady state.Linear regression analysis and nonlinear least-squares regression were used to estimate association between scvo and ar.Results our results showed an association between ar and scvo that follows a bell-shaped quadratic function with a progressive increase of ar within the therapeutic reference range of scvo (i.e.100-400 ng/m l) and a subsequent decrease of ar at higher serum levels.Discussion this study strongly suggests that tdm could represent a more appropriate tool than the oral dosage to optimise the treatment with ven.Specifically, highest efficacy might be achieved by titrating patients at scvo levels around 400 ng/m l.

Journal: The world journal of biological psychiatry : the official journal of the World Federation of Societies of Biological Psychiatry (2022)
Publication types: Journal Article
Case report: Multimodal neoadjuvant and adjuvant chemotherapy for hepatic undifferentiated embryonal sarcoma in a young adult.

Hepatic undifferentiated embryonal sarcoma of the liver (uesl) is a rare hepatic malignancy found more commonly in pediatric patients.It has been associated with poor outcomes in adults and the role and timing of systemic therapy is unclear.There have been very few case reports detailing combination neoadjuvant and adjuvant chemotherapy use for hepatic undifferentiated embryonal sarcoma in adults.In this report, a 22-year-old male admitted with right upper quadrant pain was diagnosed with a 20 x 10 x 10 cm well-circumscribed, highly vascularized hepatic mass in the entirety of the left lobe.Biopsy confirmed the diagnosis of uesl.Pet/ct showed no evidence of metastatic disease, and he received four cycles of doxorubicin and ifosfamide with demonstrated reduction in size and decrease in pet avidity.He underwent left hepatectomy with periportal lymphadenectomy, cholecystectomy, and partial gastrectomy with negative margins and received adjuvant doxorubicin, ifosfamide and mesna.At 48 months, the patient was alive without evidence of disease.We hereby emphasize the potential advantages of combination chemotherapy and surgical resection in the management of uesl in adults.

Journal: Frontiers in oncology (2022)
Publication types: Case Reports;Journal Article
Age-related somatic mutation burden in human tissues.

The genome of multicellular organisms carries the hereditary information necessary for the development of all organs and tissues and to maintain function in adulthood.To ensure the genetic stability of the species, genomes are protected against changes in sequence information.However, genomes are not static.de novomutations in germline cells are passed on to offspring and generate the variation needed in evolution.Moreover, postzygotic mutations occur in all somatic cells during development and aging.These somatic mutations remain limited to the individual, generating tissues that are genome mosaics.Insight into such mutations and their consequences has been limited due to their extremely low abundance, with most mutations unique for each cell.Recent advances in sequencing, including whole genome sequencing at the single-cell level, have now led to the first insights into somatic mutation burdens in human tissues.Here, we will first briefly describe the latest methodology for somatic mutation analysis, then review our current knowledge of somatic mutation burden in human tissues and, finally, briefly discuss the possible functional impact of somatic mutations on the aging process and age-related diseases, including cancer and diseases other than cancer.

Journal: Frontiers in aging (2022)
Publication types: Journal Article;Review
Ultrasound-Propelled Janus Rod-Shaped Micromotors for Site-Specific Sonodynamic Thrombolysis.

Antithrombosis therapy is confronted with short half-lives of thrombolytic agents, limited therapeutic effects, and bleeding complications.Drug delivery systems of thrombolytic agents face challenges in effective penetration into thrombi, which are characterized by well-organized fibrin filled with abundant activated platelets.Herein, janus rod (jr)-shaped micromotors are constructed by side-by-side electrospinning and cryosection, possessing advantages in controlling the janus structure and aspect ratio of microrods.Silicon phthalocyanine (pc) and ca o2nanoparticles (nps) are loaded into the separate sides of jrs, and arg-gly-asp (rgd) peptides are grafted on the surface to obtain pc/ca@r-jrs for the sonodynamic therapy (sdt) of thrombosis without using any thrombolytic agents.Decomposition of ca o2nps ejects o2bubbles from one side of jrs, and ultrasonication of o2bubbles produces the cavitation effect, both generating mechanical force to drive the thrombus penetration.The integration of ultrasonication-propelled motion and rgd mediation effectively increases the targeting capabilities of r-jrs to activated platelets.In addition to mechanical thrombolysis, ultrasonication of the released pc produces1o2to destruct fibrin networks of clots.In vitro thrombolysis of whole blood clots shows that ultrasonication of pc/ca@r-jrs has a significantly higher thrombolysis rate (73.6%) than those without propelled motion or rgd-mediated clot targeting.In a lower limb thrombosis model, intravenous administration of pc/ca@r-jrs indicates 3.4-fold higher accumulations at the clot site than those of jrs, and ultrasonication-propelled motion further increases thrombus retention 2.1 times.Treatment with pc/ca@r-jrs and ultrasonication fully removes thrombi and significantly prolongs tail bleeding time.Thus, this study has achieved precise and prompt thrombolysis through selective targeting to clots, efficient penetration into dense networks of thrombi, and sdt-executed thrombolysis.

Journal: ACS applied materials & interfaces (2021)
Publication types: Journal Article
High-flow nasal oxygen therapy decrease the risk of mortality and the use of invasive mechanical ventilation in patients with severe SARS-CoV-2 pneumonia? A retrospective and comparative study of 265 cases.

Introduction corona virus disease (covid-19) affects the airways and induces pulmonary lesions, patients with this disease require oxygen therapy as the disease progresses.Several oxygenation options have been used, l'hfno had showed beneficial effects.The objective of this study to evaluate the efficacy of high-flow nasal oxygen hfno versus non-invasive ventilation in covid-19.Methods this is a retrospective and comparative study conducted over a period of 10 months from march 2020 to december 2020 and involving 600 patients hospitalized in the intensive care unit of the chu mohammed vi of oujda for the management of acute respiratory failure caused by covid-19.Results out of 600 patients with acute respiratory failure, 265 patients were included in the analyses.162 (61.10%) patients were treated with hfno, the intubation rate was 49.7% (80 patients out of 162) of which 63 died intubated (78.8%).Concerning the 82 non-intubated patients, only 16 died (19.8%).the total number of patients who received niv was 71 (26.8%), 33 (46.5%) required mechanical ventilation.In-hospital mortality in patients treated with niv was 100%.the difference in mortality outcome between the two groups was significantly (p < 0.0001) reduced in hfno.Conclusions treatment with high-flow oxygen improved survival in patients with acute hypoxemic respiratory failure compared with noninvasive ventilation, although no difference was observed in intubation rate.

Journal: Annals of medicine and surgery (2012) (2022)
Publication types: Journal Article
Ethnicity, disease severity, and survival in Canadian patients with primary biliary cholangitis.

And aims we investigated associations between ethnicity, survival, and disease severity in a diverse canadian cohort of patients with primary biliary cholangitis (pbc).Approach and results patients with pbc were included from the canadian network for autoimmune liver disease.Ethnicity was defined using a modified list adopted from statistics canada, and ethnicities with small samples were grouped.Clinical events were defined as liver decompensation, hcc, liver transplantation, or death.Clinical event-free and liver transplantation-free survival were analyzed using cox regression.Trajectories of serum liver function tests were assessed over time using mixed-effects regression.Health-related quality of life was assessed using the short form 36, the pbc-40 questionnaire, and the 5-d itch scale and analyzed using mixed-effects regression.The cohort included 1538 patients with pbc from six sites and was comprised of 82% white, 4.7% indigenous, 5.5% east asian, 2.6% south asian, and 5.1% miscellaneous ethnicities.Indigenous patients were the only ethnic group with impaired liver transplant-free and event-free survival compared to white patients (hr, 3.66; 95% ci, 2.23-6.01; hr, 3.09; 95% ci, 1.94-4.92).Indigenous patients were more likely to have a clinical event before diagnosis (10%) than all other ethnic groups despite similar age at diagnosis.Indigenous patients presented with higher alkaline phosphatase, total bilirubin, and globe scores than white patients; and these relative elevations persisted during follow-up.Conclusions indigenous canadians with pbc present with advanced disease and have worse long-term outcomes compared to white patients.

Journal: Hepatology (Baltimore, Md.) (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Work-family trajectories and health: A systematic review.

Work and family lives interact in complex ways across individuals' life courses.In the past decade, many studies constructed work-family trajectories, some also examined the relation with health.The aims of this systematic review were to summarise the evidence from studies constructing work-family trajectories, and to synthesise the evidence on the association between work-family trajectories and health.Methods we searched medline, embase, psyc info, soc index and web of science databases.Key search terms related to work, family and trajectories.Studies that built combined work-family trajectories or examined the relationship between work and family trajectories were included.Risk of bias was assessed independently by two authors.The identified work-family trajectories were summarised and presented for men and women, age cohorts and contexts.The evidence on the association with health as antecedent or consequence was synthesised.Results forty-eight studies, based on 29 unique data sources, were included.Thirty-two studies (67%) were published in 2015 or later, and sequence analysis was the primary analytic technique used to construct the trajectories (n = 43, 90%).Trajectories of women were found to be more diverse and complex in comparison with men.Work-family trajectories differed by age cohorts and contexts.Twenty-three studies (48%) examined the association between work-family trajectories and health and most of these studies found significant associations.The results indicate that work-family trajectories characterised by an early transition to parenthood, single parenthood, and weak ties to employment are associated with worse health outcomes.Conclusions work-family trajectories differed greatly between men and women, but differences seemed to decrease in the youngest cohorts.Given the current changes in labour markets and family formation processes, it is important to investigate the work and family lives of younger cohorts.Work-family trajectories were associated with health at different life stages.Future research should examine longitudinal associations of work-family trajectories with health and focus on elucidating why and under which circumstances some trajectories are associated with better or worse health compared with other trajectories.

Journal: Advances in life course research (2022)
Publication types: Systematic Review;Journal Article;Review;Research Support, Non-U.S. Gov't
Fitz-Hugh-Curtis Syndrome Presenting as Perihepatic and Subcapsular Enhancement on MRI.

Fitz-hugh-curtis syndrome (fhcs) is a rare complication of pelvic inflammatory disease and its mri findings remain poorly described.A 34-year-old woman was raced to our hospital with slight fever and severe right upper quadrant pain.Gadoxetic acid-enhanced magnetic resonance imaging revealed high-intensity regions in the surface and subcapsule of the right liver on t2-weighted imaging and on diffusion-weighted imaging.A definitive diagnosis of fhcs was confirmed based on high titers of serum ig a and ig g antibodies to chlamydia trachomatis.She was treated with oral azithromycin and discharged 6 days after admission with improvement of her symptoms.To our knowledge, this report represents a valuable addition to the fhcs literature describing mri findings in the early stage of fhcs onset.

Journal: Case reports in gastroenterology (2022)
Publication types: Case Reports;Journal Article
H2O2-Responsive prodrug-nanosystem based on auto-fluorescent perylenetetracarboxylic diimide hinders the foaming progress in RAW264.7 cells.

Oxidative stress can lead to a variety of diseases, and oxalate bonds can consume excess reactive oxygen species (ros) in cells.In this study, a h2o2-responsive prodrug-nanosystem was synthesized using oxalate-bond-connecting water-soluble drugs (tre) with a fluorescent indicator (pbi).The maximum fluorescence emission wavelength of pbi-tre was at 548 nm, and the changes of nanoparticles could be directly observed in the cells.Pbi-tre was coated with hyaluronic acid (ha) to improve their intracellular uptake and ability to target macrophages.The particle size of ha-pbi-tre was 200-300 nm, and the zeta potential was -36.9 m v.The results showed that the nano-drug loading system could easily decrease the ros level, inhibit the production of inflammatory factors, remove the accumulation of lipids in foam cells.These nanoparticles could hinder foaming progress in the raw264.7 cell line.

Journal: Journal of materials chemistry. B (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Development of a Reverse Transcription Loop - Mediated Isothermal Amplification [RT-LAMP] as a early rapid detection assay for Crimean Congo Hemorrhagic Fever virus.

Presently diagnosis of crimean congo hemorrhagic fever virus (cchfv) infection relies on real-time and end-point rt-pcr, and serodiagnostic assay.These assays are time consuming and cannot be used as a routine screening test.The objective of this study was to develop a rapid diagnostic test that could be completed in < 60 minutes.Rapid detection of cchfv infection is important for faster delivery of appropriate therapeutics, clinical management of patient and also important to contain the outbreak.In the present study, we have developed a rapid and sensitive single tube reverse transcription loop-mediated isothermal amplification (rt-lamp) assay for detection of cchfv.The limit of detection of rt-lamp vis-a-vis real-time rt-pcr assay is 10 rna copies.Further, cchfv specific rt-lamp assay was successfully evaluated with human and tick samples.The assay correctly picked up diverse cchfv isolates indicating its applicability for different strains.A comparative evaluation of the rt-lamp assay vis-à-vis with the real-time rt-pcr revealed 100% concordance with 100 % sensitivity and specificity respectively.No cross reactivity with related flaviviruses and hemorrhagic fever viruses was observed.The assay is a rapid, isothermal, simple to perform molecular diagnostic, which can be performed in a portable heating block device.Cchf rt-lamp assay can be used in low resource laboratories for monitoring of cchfv outbreaks in remote rural regions in affected countries.

Journal: Acta tropica (2022)
Publication types: Journal Article
Q-Learning for Feedback Nash Strategy of Finite-Horizon Nonzero-Sum Difference Games.

In this article, we study the feedback nash strategy of the model-free nonzero-sum difference game.The main contribution is to present the q -learning algorithm for the linear quadratic game without prior knowledge of the system model.It is noted that the studied game is in finite horizon which is novel to the learning algorithms in the literature which are mostly for the infinite-horizon nash strategy.The key is to characterize the q -factors in terms of the arbitrary control input and state information.A numerical example is given to verify the effectiveness of the proposed algorithm.

Journal: IEEE transactions on cybernetics (2022)
Publication types: Journal Article
Keep flexible-Keep switching? Boundary conditions of the influence of forced task switching on voluntary task switching.

Frequent forced switching between tasks has been shown to reduce switch costs and increase voluntary switch rates.So far, however, the boundary conditions of the influence of forced task switching on voluntary task switching are unknown.Thus, the present study was aimed to test different aspects of generalizability (across items, tasks, and time) of switching-induced flexibility established in forced-choice trials on voluntary switching in free-choice trials.To this end, stimuli and tasks were systematically varied between forced- and free-choice trials in a hybrid task-switching paradigm.In a series of three experiments, we manipulated forced-choice switch probability (25% vs.75%) and found that switching-induced flexibility generalizes to new items, but arguably not to new tasks.This task-specific effect is rather short-lived, limited to the first free-choice trial following a forced-choice trial.Underlying mechanisms of switching-induced flexibility, the versatility of flexibility and implications for the trainability of cognitive flexibility are discussed.(psyc info database record (c) 2022 apa, all rights reserved).

Journal: Journal of experimental psychology. Learning, memory, and cognition (2022)
Publication types: Journal Article