syedzayyan/paper_mill_benchmark huggingface dataset:
A conservative screening algorithm to determine candidacy for robotic mitral valve surgery.

Patient selection for robotically assisted mitral valve repair remains controversial.We assessed outcomes of a conservative screening algorithm developed to select patients with degenerative mitral valve disease for robotic surgery.Methods from january 2014 to january 2019, a screening algorithm that included transthoracic echocardiography and computed tomography scanning was rigorously applied by 3 surgeons to assess candidacy of 1000 consecutive patients with isolated degenerative mitral valve disease (age 58 ± 11 years, 67% male) for robotic surgery.Screening results and hospital outcomes of those selected for robotic versus sternotomy approaches were compared.Results with application of the screening algorithm, 605 patients were selected for robotic surgery.Common reasons for sternotomy (n = 395) were aortoiliac atherosclerosis (n = 74/292, 25%), femoral artery diameter <7 mm (n = 60/292, 20%), mitral annular calcification (n = 83/390, 21%), aortic regurgitation (n = 100/391, 26%), and reduced left ventricular function (n = 126/391, 32%).Mitral valve repair was accomplished in 996.Compared with sternotomy, patients undergoing robotic surgery had less new-onset atrial fibrillation (n = 144/582, 25% vs n = 125/373, 34%; p = .002), fewer red blood cell transfusions (n = 61/601, 10% vs 69/395, 17%; p < .001), and shorter hospital stay (5.2 ± 2.9 days vs 5.9 ± 2.1 days; p < .001).No hospital deaths occurred, and occurrence of postoperative stroke in the robotic (n = 3/605, 0.50%) and sternotomy (n = 4/395, 1.0%; p = .3) groups was similar.Conclusions this conservative screening algorithm qualified 60% of patients with isolated degenerative mitral valve disease for robotic surgery.Outcomes were comparable with those obtained with sternotomy, validating this as an approach to select patients for robotic mitral valve surgery.

Journal: The Journal of thoracic and cardiovascular surgery (2022)
Publication types: Journal Article
Sporangiospore Viability and Oospore Production in the Spinach Downy Mildew Pathogen,Peronospora effusa.

Downy mildew of spinach, caused by the obligate pathogen peronospora effusa, remains the most important constraint in the major spinach production areas in the united states.This disease can potentially be initiated by asexual sporangiospores via "green bridges", sexually derived oospores from seed or soil, or dormant mycelium.However, the relative importance of the various types of primary inoculum is not well known.The ability of p.Effusasporangiospores to withstand abiotic stress, such as desiccation, and remain viable during short- and long-distance dispersal and the ability of oospores to germinate and infect seedlings remain unclear.Thus, the primary objectives of this research were to evaluate the impact of desiccation on sporangiospore survival and infection efficiency and examine occurrence, production, and germination of oospores.Results indicate that desiccation significantly reduces sporangiospore viability as well as infection potential.Leaf wetness duration of 4 h was needed for disease establishment by spinach downy mildew sporangiospores.Oospores were observed in leaves of numerous commercial spinach cultivars grown in california in 2018 and arizona in 2019.Frequency of occurrence varied between the two states-years.The presence of opposite mating types in spinach production areas in the united states was demonstrated by pairing isolates in controlled crosses and producing oospores on detached leaves as well as intact plants.Information from the study of variables that affect sporangiospore viability and oospore production will help in improving our understanding of the epidemiology of this important pathogen, which has implications for management of spinach downy mildew.

Journal: Plant disease (2020)
Publication types: Journal Article
Development of mobile health-based self-management support for patients with lung cancer: A stepwise approach.

To develop self-management support platform on mobile for chinese patients with lung cancer.Design a stepwise approach with combination of methods.Methods literature review was carried out to construct preliminary framework and develop detailed content for self-management modules.A semistructured interview was conducted to elicit preference in the content and platform of self-management modules with 15 patients with lung cancer.Delphi study was performed to evaluate and improve the content of modules with 13 experts.A pilot study was conducted to test the mobile health-based self-management support modules with 13 patients with lung cancer.Results a social network software-based we chat public account "symptom self-management" for patients with lung cancer was developed and preliminarily tested with positive feedback.Three modules were designed and presented, including symptom management (cancer-related fatigue, cough, dyspnoea, pain, nausea and vomiting), emotion management and role management.Conclusion this study showed that patients with lung cancer have diversified supportive care needs after discharge.A bottom-up and stepwise approach to develop mobile health-based self-management support tool has shown to be feasible and valuable.Theory guidance, user requirement exploration, evidence-based information and expert evaluation are key elements of the process.Implications for practice the we chat public account "symptom self-management" could be used as sustainable platform to support patients with lung cancer in dealing with common challenges.It provides professional information, self-assessment tools, self-management skills and peer-support platform.Information presented in both text and audio forms enables patients' easy access to the platform.

Journal: Nursing open (2022)
Publication types: Journal Article;Review;Research Support, Non-U.S. Gov't
Hashimoto's Encephalopathy Masquerading as Rapidly Progressive Dementia and Extrapyramidal Failure.

Hashimoto's encephalopathy is a rare immune-mediated disorder characterized by subacute encephalopathy with elevated thyroid antibodies.Hashimoto's encephalopathy is also known as steroid-responsive encephalopathy associated with autoimmune thyroiditis.We report a rare presentation of hashimoto's encephalopathy presenting with acute neuropsychiatric disturbances, rapidly progressive dementia, seizures, and extrapyramidal failure.Neuroimaging revealed multifocal vasculitides of major cerebral vessels that support the autoimmune vasculitic theory as the underlying pathogenesis for hashimoto's encephalopathy.Unfortunately, permanent irreversible cerebral damage has already ensued before her presentation to our center, which rendered steroid therapy ineffective.Serological testing for hashimoto's thyroiditis must be in the investigation of all rapidly progressive dementias as early diagnosis and timely management of autoimmune thyroiditis may salvage sizable and eloquent cerebral tissues.The rarity of the condition should not preclude the investigation of hashimoto's disease even in the presence of normal levels of thyroid hormones.Delayed diagnosis may result in irreversibly catastrophic encephalopathy in patients who once presented with potentially curable dementia.

Journal: Journal of neurosciences in rural practice (2022)
Publication types: Journal Article
Dynamics of Spin Crossover Molecular Complexes.

We review the current understanding of the time scale and mechanisms associated with the change in spin state in transition metal-based spin crossover (sco) molecular complexes.Most time resolved experiments, performed by optical techniques, rely on the intrinsic light-induced switching properties of this class of materials.The optically driven spin state transition can be mediated by a rich interplay of complexities including intermediate states in the spin state transition process, as well as intermolecular interactions, temperature, and strain.We emphasize here that the size reduction down to the nanoscale is essential for designing sco systems that switch quickly as well as possibly retaining the memory of the light-driven state.We argue that sco nano-sized systems are the key to device applications where the "write" speed is an important criterion.

Journal: Nanomaterials (Basel, Switzerland) (2022)
Publication types: Journal Article;Review
Clinical profile and disease progression of HIV in adolescents and young adults in Vadodara, India.

Introduction adolescents are vulnerable to hiv for many reasons.Unfortunately, there are little data available on adolescents and young adults who have contracted hiv.Only few studies have been conducted in india with an aim to assess the clinical presentation, disease progression, and clinical profile of hiv in adolescents.Materials and methods there was a cohort study conducted at the antiretroviral therapy (art) center at a teaching hospital in western india.The study participants were kept under observation for 1 year.The end point of the cohort analysis was hiv disease progression.Patient details such as sociodemographic profile, cd4 counts at presentation, date of initiation of art, who clinical stage of hiv at presentation, episodes of opportunistic infections, and laboratory investigations were recorded.Descriptive statistics and survival analysis were used for analyzing disease progression, improvement in health conditions, and factors affecting the same.Results of 155 participants, 100 were followed up till the end of the study.Seventy-two percent participants were adolescents and 53% were female.The mean age at presentation was 16.7 years, and the common modes of transmission were mother-to-child transmission (mtct) (48%), heterosexual relationships (23%), and blood transfusion (12%).Cd4 counts at presentation were <350 cells/mm3among 70 participants.Among those infected through mtct, the median survival duration was 15 years (95% confidence interval: 12.98-17.07).The risk of progression of the disease among young adults was thrice than that of adolescents (p< 0.05).Conclusion hiv/aids screening and health services shall be tailored to address the special needs of adolescents and young adults.Teaching hospitals shall explore opportunities for student-involved longitudinal research studies to better understand the source of hiv infection, treatment seeking behavior, disease progression and outcome in a comprehensive manner.

Journal: Indian journal of sexually transmitted diseases and AIDS (2021)
Publication types: Journal Article
Impacts of Treatment Modalities on Physical Activity After First Acute Myocardial Infarction in Jordan.

Promoting physical activity is a priority after coronary revascularisation for effective long-term cardiovascular care and to avoid further disease progression and complications.But little is known about the effect of different types of acute myocardial infarction (ami) treatment modalities in changes in physical activity level post-ami.Objective this study aimed to examine changes in physical activity among patients treated with different treatment modalities post-first ami during early recovery phase at week 2 (time 1) and week 6 (time 2) after hospitalization.Methods a descriptive study was done using a repeated-measures design.Physical activity was measured by a body-worn activity monitor (activ pal3 monitor) for 24 hours a day for full 7 consecutive days at time 1 and time 2 after hospitalization.Demographic and clinical data were collected from patients' records.The study was conducted in 1 setting in jordan.Participants were met at time 1 and time 2.The study recruited a convenience sample of 94 patients with ami.Participants did not have access to cardiac rehabilitation.The participants were categorized according to type of ami treatment modalities into 3 groups: st-elevation myocardial infarction treated by primary percutaneous coronary intervention, st-elevation myocardial infarction treated by thrombolytic therapy, and non-st-elevation myocardial infarction treated by medication.Results patients treated by primary percutaneous coronary intervention had a statistically significant effect on changes in mean steps count and mean stepping time per day better than patients treated by other treatment modalities between weeks 2 and 6 after hospitalization.Conclusion the study showed that patients treated with primary percutaneous coronary intervention had better mean steps count and mean stepping time per day between weeks 2 and 6 after hospitalization in comparison with other treatment modalities.These findings could be used for development of effective intervention in the future.Further research using different research methods such as longitudinal studies among different cultures to confirm the finding of this study is recommended.

Journal: Dimensions of critical care nursing : DCCN (2019)
Publication types: Journal Article
Urinary Biomarkers for Kidney Allograft Injury.

The current standard of serum creatinine and biopsy to monitor allograft health has many limitations.The most significant drawback of the current standard is the lack of sensitivity and specificity to allograft injuries, which are diagnosed only after significant damage to the allograft.Thus, it is of critical need to identify a biomarker that is sensitive and specific to the early detection of allograft injuries.Urine, as the direct renal ultrafiltrate that can be obtained noninvasively, directly reflects intrarenal processes in the allograft at greater accuracy than analysis of peripheral blood.We review transcriptomic, metabolomic, genomic, and proteomic discovery-based approaches to identifying urinary biomarkers for the noninvasive detection of allograft injuries, as well as the use of urine cell-free dna in the qsant urine assay as a sensitive surrogate for the renal allograft biopsy for rejection diagnosis.

Journal: Transplantation (2022)
Publication types: Journal Article;Review
Kinetics of RNA and RNA:DNA Hybrid Strand Displacement.

In nucleic acid nanotechnology, strand displacement is a widely used mechanism where one strand from a hybridized duplex is exchanged with an invading strand that binds to a toehold, a single-stranded region on the duplex.It is used to perform logic operations on a molecular level, initiate cascaded reactions, or even forin vivodiagnostics and treatments.While systematic experimental studies have been carried out to probe the kinetics of strand displacement in dna with different toehold lengths, sequences, and mismatch positions, there has not been a comparable investigation of rna or rna-dna hybrid systems.Here, we experimentally study how toehold length, toehold location (5' or 3' end of the strand), and mismatches influence the strand displacement kinetics.We observe reaction acceleration with increasing toehold length and placement of the toehold at the 5' end of the substrate.We find that mismatches closer to the interface of toehold and duplex slow down the reaction more than remote mismatches.A comparison of rna and dna displacement with hybrid displacement (rna invading dna or dna invading rna) is partly explainable by the thermodynamic stabilities of the respective toehold regions, but also suggests that the rearrangement from b-form to a-form helix in the case of rna invading dna might play a role in the kinetics.

Journal: ACS synthetic biology (2021)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Identifying the molecular basis of Jinhong tablets against chronic superficial gastritis via chemical profile identification and symptom-guided network pharmacology analysis.

Chronic superficial gastritis (csg) is a common disease of the digestive system that possesses a serious pathogenesis.Jinhong tablet (jht), a traditional chinese medicine (tcm) prescription, exerts therapeutic effects against csg.However, the molecular basis of its therapeutic effect has not been clarified.Herein, we employed ultra-performance liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry (uplc-q/tof-ms) based chemical profile identification to determine the chemical components in jht.Further, we applied network pharmacology to illustrate its molecular mechanisms.A total of 96 chemical constituents were identified in jht, 31 of which were confirmed using reference standards.Based on the bioinformatics analysis using the symptom-guided pharmacological networks of "chi," "blood," "pain," and "inflammation," and target screening through the interaction probabilities between compounds and targets, matrix metalloproteinase 2 (mmp2), dopamine d2 receptor (drd2), and aldo-keto reductase family 1 member b1 (akr1b1) were identified as key targets in the therapeutic effect exhibited by jht against csg.Moreover, according to the inhibitory activities presented in the literature and binding mode analysis, the structural types of alkaloids, flavonoids, organic acids, including chlorogenic acid (10), caffeic acid (13), (-)-corydalmine (33), (-)-isocorypalmine (36), isochlorogenic acid c (38), isochlorogenic acid a (41), quercetin-3-o-α-l-rhamnoside (42), isochlorogenic acid b (47), quercetin (63), and kaempferol (70) tended to show remarkable activities against csg.Owing to the above findings, we systematically identified the chemical components of jht and revealed its molecular mechanisms based on the symptoms associated with csg.

Journal: Journal of pharmaceutical analysis (2022)
Publication types: Journal Article
Epilepsy Syndromes in the First Year of Life and Usefulness of Genetic Testing for Precision Therapy.

The high pace of gene discovery has resulted in thrilling advances in the field of epilepsy genetics.Clinical testing with comprehensive gene panels, exomes, or genomes are now increasingly available and have led to a significant higher diagnostic yield in early-onset epilepsies and enabled precision medicine approaches.These have been instrumental in providing insights into the pathophysiology of both early-onset benign and self-limited syndromes and devastating developmental and epileptic encephalopathies (dees).Genetic heterogeneity is seen in many epilepsy syndromes such as west syndrome and epilepsy of infancy with migrating focal seizures (eimfs), indicating that two or more genetic loci produce the same or similar phenotypes.At the same time, some genes such as scn2acan be associated with a wide range of epilepsy syndromes ranging from self-limited familial neonatal epilepsy at the mild end to ohtahara syndrome, eifms, west syndrome, lennox-gastaut syndrome, or unclassifiable dees at the severe end of the spectrum.The aim of this study was to review the clinical and genetic heterogeneity associated with epilepsy syndromes starting in the first year of life including: self-limited familial neonatal, neonatal-infantile or infantile epilepsies, genetic epilepsy with febrile seizures plus spectrum, myoclonic epilepsy in infancy, ohtahara syndrome, early myoclonic encephalopathy, west syndrome, dravet syndrome, eimfs, and unclassifiable dees.We also elaborate on the advantages and pitfalls of genetic testing in such conditions.Finally, we describe how a genetic diagnosis can potentially enable precision therapy in monogenic epilepsies and emphasize that early genetic testing is a cornerstone for such therapeutic strategies.

Journal: Genes (2021)
Publication types: Journal Article;Review
Efficient and Fast Production of Transgenic Rice Plants by Agrobacterium-Mediated Transformation.

Genetic transformation plays a key role in deciphering regulation of agronomic traits at molecular level in rice, a model monocot cereal crop.Here we describe an efficient and fast protocol for producing transgenic japonica rice plants using the agrobacterium-mediated transformation method.The protocol simplifies medium compositions and transformation steps and can be easily followed by a lab technician with little tissue culture experience.Using this protocol, we have transformed thousands of gene constructs in the past 10 years and edited hundreds of genes with the crispr-cas9 system recently.

Journal: Methods in molecular biology (Clifton, N.J.) (2019)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Alaska pollock gelatin sealant shows long-term efficacy and safety in a pulmonary air leakage rat model.

S postoperative prolonged air leakage is a frequent complication following lung resection.We have shown the high adhesive quality of a newly developed sealant based on a hydrophobically modified alaska pollock-derived gelatin (ap gltn) sealant in acute in vivo settings.The purpose of this study was to investigate the long-term efficacy and safety of ap gltn sealant using rats as a preclinical model.Methods an air leakage rat model with a 5-mm pleural defect was created, to which ap gltn sealant or fibrin sealant was applied.In both groups, the rats were evaluated on days 1, 7, 14 and 28.In the ap gltn sealant group, days 56 and 84 were added to evaluate absorption as sealant was still present on day 28.The number of rats in each subgroup was 4 (for a total of 40).Lung specimens and blood samples were obtained for histological and haematological assessment.Results no findings suggesting infection or air leakage were observed.Ap gltn sealant was absorbed from day 56 to day 84.Histologically, although neutrophil and lymphocyte infiltrations on the lung side did not differ between groups, those on the sealant side were significantly less in the ap gltn sealant group.Blood sample tests revealed no significant findings suggesting inflammation or organ damage in either group.Conclusions ap gltn sealant showed long-term sealing efficacy and safety with mild inflammation in a pulmonary air leakage rat model.Ap gltn sealant is expected to be a safe and effective sealant for clinical applications.

Journal: European journal of cardio-thoracic surgery : official journal of the European Association for Cardio-thoracic Surgery (2022)
Publication types: Journal Article
Resistance in marine cyanobacteria differs against specialist and generalist cyanophages.

Long-term coexistence between unicellular cyanobacteria and their lytic viruses (cyanophages) in the oceans is thought to be due to the presence of sensitive cells in which cyanophages reproduce, ultimately killing the cell, while other cyanobacteria survive due to resistance to infection.Here, we investigated resistance in marine cyanobacteria from the genera synechococcusand prochlorococcusand compared modes of resistance against specialist and generalist cyanophages belonging to the t7-like and t4-like cyanophage families.Resistance was extracellular in most interactions against specialist cyanophages irrespective of the phage family, preventing entry into the cell.In contrast, resistance was intracellular in practically all interactions against generalist t4-like cyanophages.The stage of intracellular arrest was interaction-specific, halting at various stages of the infection cycle.Incomplete infection cycles proceeded to various degrees of phage genome transcription and translation as well as phage genome replication in numerous interactions.In a particularly intriguing case, intracellular capsid assembly was observed, but the phage genome was not packaged.The cyanobacteria survived the encounter despite late-stage infection and partial genome degradation.We hypothesize that this is tolerated due to genome polyploidy, which we found for certain strains of both synechococcusand prochlorococcus our findings unveil a heavy cost of promiscuous entry of generalist phages into nonhost cells that is rarely paid by specialist phages and suggests the presence of unknown mechanisms of intracellular resistance in the marine unicellular cyanobacteria.Furthermore, these findings indicate that the range for virus-mediated horizontal gene transfer extends beyond hosts to nonhost cyanobacterial cells.

Journal: Proceedings of the National Academy of Sciences of the United States of America (2019)
Publication types: Journal Article;Research Support, Non-U.S. Gov't