syedzayyan/paper_mill_benchmark huggingface dataset:
Espial: Electrochemical Soil pH Sensor for In Situ Real-Time Monitoring.

We present a first-of-its-kind electrochemical sensor that demonstrates direct real-time continuous soil p h measurement without any soil pre-treatment.The sensor functionality, performance, and in-soil dynamics have been reported.The sensor coating is a composite matrix of alizarin and nafion applied by drop casting onto the working electrode.Electrochemical impedance spectroscopy (eis) and squarewave voltammetry (swv) studies were conducted to demonstrate the functionality of each method in accurately detecting soil p h.The studies were conducted on three different soil textures (clay, sandy loam, and loamy clay) to cover the range of the soil texture triangle.Squarewave voltammetry showed p h-dependent responses regardless of soil texture (while electrochemical impedance spectroscopy's p h detection range was limited and dependent on soil texture).The linear models showed a sensitivity range from -50 m v/p h up to -66 m v/p h with r2> 0.97 for the various soil textures in the p h range 3-9.The validation of the sensor showed less than a 10% error rate between the measured p h and reference p h for multiple different soil textures including ones that were not used in the calibration of the sensor.A 7-day in situ soil study showed the capability of the sensor to measure soil p h in a temporally dynamic manner with an error rate of less than 10%.The test was conducted using acidic and alkaline soils with p h values of 5.05 and 8.36, respectively.

Journal: Micromachines (2023)
Publication types: Journal Article
Multiple lipid binding sites determine the affinity of PH domains for phosphoinositide-containing membranes.

Association of peripheral proteins with lipid bilayers regulates membrane signaling and dynamics.Pleckstrin homology (ph) domains bind to phosphatidylinositol phosphate (pip) molecules in membranes.The effects of local pip enrichment on the interaction of ph domains with membranes is unclear.Molecular dynamics simulations allow estimation of the binding energy of grp1 ph domain to pip3-containing membranes.The free energy of interaction of the ph domain with more than two pip3molecules is comparable to experimental values, suggesting that ph domain binding involves local clustering of pip molecules within membranes.We describe a mechanism of ph binding proceeding via an encounter state to two bound states which differ in the orientation of the protein relative to the membrane, these orientations depending on the local pip concentration.These results suggest that nanoscale clustering of pip molecules can control the strength and orientation of ph domain interaction in a concentration-dependent manner.

Journal: Science advances (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Transplantation outcomes in patients with primary hyperoxaluria: a systematic review.

Primary hyperoxaluria type 1 (ph1) is characterized by hepatic overproduction of oxalate and often results in kidney failure.Liver-kidney transplantation is recommended, either combined (clkt) or sequentially performed (slkt).The merits of slkt and the place of an isolated kidney transplant (kt) in selected patients are unsettled.We systematically reviewed the literature focusing on patient and graft survival rates in relation to the chosen transplant strategy.Methods we searched medline and embase using a broad search string, consisting of the terms 'transplantation' and 'hyperoxaluria'.Studies reporting on at least four transplanted patients were selected for quality assessment and data extraction.Results we found 51 observational studies from 1975 to 2020, covering 756 clkt, 405 kt and 89 slkt, and 51 pre-emptive liver transplantations (plt).Meta-analysis was impossible due to reported survival probabilities with varying follow-up.Two individual high-quality studies showed an evident kidney graft survival advantage for clkt versus kt (87% vs.14% at 15 years, p<0.05) with adjusted hr for graft failure of 0.14 (95% confidence interval: 0.05-0.41), while patient survival was similar.Three other high-quality studies reported 5-year kidney graft survival rates of 48-89% for clkt and 14-45% for kt.Plt and slkt yielded 1-year patient and graft survival rates up to 100% in small cohorts.Conclusions our study suggests that clkt leads to superior kidney graft survival compared to kt.However, evidence for merits of slkt or for kt in pyridoxine-responsive patients was scarce, which warrants further studies, ideally using data from a large international registry.

Journal: Pediatric nephrology (Berlin, Germany) (2021)
Publication types: Journal Article;Meta-Analysis;Systematic Review
Translation of genomic epidemiology of infectious pathogens: Enhancing African genomics hubs for outbreaks.

Deadly emerging infectious pathogens pose an unprecedented challenge to health systems and economies, especially across africa, where health care infrastructure is weak, and poverty rates remain high.Genomic technologies are vital for enhancing the understanding and development of intervention approaches against these pathogens, including ebola and the novel coronavirus disease 2019 (covid-19).Discussion africa has contributed few genomes of severe acute respiratory syndrome-coronavirus 2 (sars-co v-2) to the global pool in growing open access repositories.To bridge this gap, the africa centre for disease control and prevention (acdc) is coordinating continent-wide initiatives to establish genomic hubs in selected well-resourced african centres of excellence.This will allow for standardisation and efficient and rapid data generation and curation.However, the strategy to ensure capacity for high-throughput genomics at selected hubs should not overshadow the deployment of portable, field-friendly and technically less demanding genomics technologies in all affected countries.This will enhance small-scale local genomic surveillance in outbreaks, leaving validation and large-scale approaches to be taken at central genomic hubs.Conclusion the acdc needs to scale-up its campaign for government support across african union countries to ensure the sustainable financing of its strategy for increased pathogen genomic intelligence and other interventions in current and inevitable future epidemics in africa.

Journal: International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases (2020)
Publication types: Journal Article
Genetic variants associated with the occurrence and progression of adolescent idiopathic scoliosis: a systematic review protocol.

Adolescent idiopathic scoliosis (ais) is a structural lateral spinal curvature of ≥ 10° with rotation.Approximately 2-3% of children in most populations are affected with ais, and this condition is responsible for approximately $1.1 billion in surgical costs to the us healthcare system.Although a genetic factor for ais has been demonstrated for decades, with multiple potentially contributory loci identified across populations, treatment options have remained limited to bracing and surgery.Methods the databases medline (via pub med), embase, google scholar, and ovid medline will be searched and limited to articles in english.We will conduct title and abstract, full-text, and data extraction screening through covidence, followed by data transfer to a custom redcap database.Quality assessment will be confirmed by multiple reviewers.Studies containing variant-level data (i.e., gwas, exome sequencing) for ais subjects and controls will be considered.Outcomes of interest will include presence/absence of ais, scoliosis curve severity, scoliosis curve progression, and presence/absence of nucleotide-level variants.Analyses will include odds ratios and relative risk assessments, and subgroup analysis (i.e., males vs.Females, age groups) may be applied.Quality assessment tools will include grade and q-genie for genetic studies.Discussion in this systematic review, we seek to evaluate the quality of genetic evidence for ais to better inform research efforts, to ultimately improve the quality of patient care and diagnosis.Systematic review registration prospero registration #crd42021243253.

Journal: Systematic reviews (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Investigating Cognitive Functions in Methadone Users in Comparison with Methadone and Methamphetamine Users and Control Group.

Cognitive impairment in drug users is a marker for predicting recurrence and poorer adherence to treatment.The purpose of this study was to compare the cognitive function in three groups of methadone users methadone maintenance treatment (mmt), compared to methadone and methamphetamine (mamp) users (mmt + mamp) and healthy people (control group).Methods three groups of 90 people including 30 users of mmt, 30 users of mmt + mamp, and 30 healthy persons participated in this cross-sectional and purposeful study.The study was performed on outpatients of mmt clinic of psychiatric hospital in kerman, iran.The demographic and related data questionnaire was filled out.In addition, persian version of the brief assessment of cognition in schizophrenia (bacs) was used to assess cognitive function.Findings the mean of total number of scores and all bacs subscales were significantly better in control group than the other two groups of patients.Moreover, not only the mean of total number of bacs was significantly different between two substance abuser groups, but also there was a significant difference between them on verbal memory, digit sequencing, and token motor test, with mmt + mamp group performing worse than mmt group.Conclusion concomitant use of opioids and stimulant substance such as mamp results in cumulative toxic effect of them on brain and cognitive functions.

Journal: Addiction & health (2022)
Publication types: Journal Article
Racial disparities in bariatric surgery postoperative weight loss and patient satisfaction.

A growing body of evidence has demonstrated racial disparities in bariatric surgery (bs) outcomes.We aimed to investigate the impact of race on postoperative percent excess weight loss (%ewl) and patient satisfaction.Methods single center retrospective study of patients who underwent bs january 2012 to november 2017.Statistical analysis utilized chi-squared, anova and multivariable regression.Results a total of 378 patients were included.African american patients lost significantly less weight compared to caucasian and hispanic patients (39.0 %ewl, 53.4 %ewl and 52.3 %ewl, respectively).A significant difference remained after adjustment for possible confounders.No difference in postoperative satisfaction was found.Conclusions our study adds to the existing literature demonstrating racial disparities in bs postoperative ewl, despite adjusting for possible confounders, while contributing to the limited literature examining hispanic patients.Furthermore, we examined an understudied outcome in postoperative patient satisfaction and found no racial disparity despite disparity in ewl.

Journal: American journal of surgery (2022)
Publication types: Journal Article
Bidirectional Chemotherapy in Advanced Colorectal Cancer Peritoneal Metastases.

Colorectal cancer (crc) patients with extensive peritoneal metastases who are not candidates for crs-hipec have poor prognoses.We evaluated the role of systemic and intra-peritoneal (ip) chemotherapy in these patients.Crc patients with confirmed peritoneal metastasis were enrolled.After implantation of ip chemoport patients received weekly ip paclitaxel in incremental doses of 20 mg/m2with systemic chemotherapy.The primary end-points were the feasibility, safety, and tolerance (perioperative complications), and the secondary end-point was the clinico-radiological response.Patients included in the study were registered between january 2018 and november 2021.Ip chemoport was implanted in 18 patients of which 14 patients underwent successful instillation of ip chemotherapy.Four patients did not receive ip chemotherapy in view of port-site infection for which ip ports were removed.The median age was 39 years (range: 19-61 years).The site of the primary tumor was equal in the colon and rectum.Fifty percent of patients had signet ring-cell adenocarcinoma, and 21% had poorly differentiated adenocarcinoma.The median serum of cea level was 12.27 ng/m l (1.63-116.16 ng/m l).The median pci score was 25 (18-35).The median number of ip chemotherapy cycles (weekly) was 3.5 (1-12 cycles).In 14.3% of patients, ip chemoport had to be removed due to block and infection.Three, five, and four patients had clinico-radiologically disease progression, stable disease, and partial response, respectively.One patient underwent subsequent successful crs-hipec.There were no grade 3-5 (ctcae 3.0) complications.Incremental doses of ip paclitaxel with systemic chemotherapy is safe and feasible in selected colorectal adenocarcinoma patients with peritoneal metastases without any serious adverse events.

Journal: Indian journal of surgical oncology (2023)
Publication types: Journal Article
TSOL18 vaccine and oxfendazole for control of Taenia solium cysticercosis in pigs: A field trial in endemic areas of Tanzania.

A field trial was conducted in tanzania to determine the effectiveness of tsol18 vaccine used concurrently with oxfendazole (ofz), and of ofz alone, on t.Solium cysticercosis determined by organ and half carcase dissection of slaughter age pigs.This study followed a quasi-experimental group design.Suitable trial sites were randomly allocated to either treatment group t1 (ofz treatment alone [30mg/kg, paranthic 10%]) or t2 (tsol18 [1ml, cysvax] plus ofz).Three 4-monthly treatments were administered to eligible pigs.A random selection of pigs were necropsied at baseline and at endline, 2-3.5 months after the final treatment.Additionally, untreated pigs from t1 and t2 areas were necropsied at endline to provide contemporaneous comparisons with t1 and t2 pigs.Baseline prevalence of viable t.Solium cysticerci for t1 was 25.5% (exact 95% ci: 13.9, 40.3; n = 12/47), and for t2 was 12.0% (ci: 6.4, 20.0; n = 12/100).At endline, prevalence was 2.8% for t1 (ci: 0.1, 14.5, n = 1/36) and 0% for t2 (ci: 0, 4.7, n = 0/77).Among untreated pigs, three had viable cysticerci, one from t1 area (12.5%, ci: 0.3, 52.7; n = 1/8) and two from t2 area (5.7%, ci: 0.7, 19.2, n = 2/35).Fisher's exact test showed significant changes in prevalence from baseline to endline in both groups (t1: p = 0.005, t2: p = 0.001).Firth's penalized maximum likelihood method suggested the changes were not significant relative to their controls (t1: p = 0.245, t2: p = 0.076).These findings showed a significant reduction in the prevalence of viable cysticerci from baseline to endline after both interventions.However, the changes could not be definitively attributed to the interventions due, in part, to small numbers of control pigs.Concurrent administration of the tsol18 and ofz cleared infection among assessed pigs whereas infection remained after treatment with ofz only.Further studies including larger sample sizes would be required for more definitive conclusions.A one health approach is recommended for rapid and sustainable impact.

Journal: PLoS neglected tropical diseases (2020)
Publication types: Journal Article;Randomized Controlled Trial, Veterinary;Research Support, Non-U.S. Gov't
Oral cavity adjuvant therapy (OCAT) -a phase III, randomized controlled trial of surgery followed by conventional RT (5 fr/wk) versus concurrent CT-RT versus accelerated RT (6fr/wk) in locally advanced, resectable, squamous cell carcinoma of oral cavity.

Limited data exists regarding the impact of intensification of adjuvant therapy in resected oral cavity squamous cell carcinomas (ocscc) with adverse prognostic features on histopathology.Patients and methods this was a three-arm phase iii, randomised trial including patients with resected advanced ocscc.Randomisation was done in a 1:1:1 ratio: arm-a- standard adjuvant radiation therapy (rt) 60gy/30 fractions over 6 weeks versus arm-b-concurrent chemoradiation versus arm-c-accelerated radiation therapy (6 d a week).The trial was powered to detect an absolute difference of 10% in 5-year locoregional control (lrc).Results the trial was conducted between june 2005 and march 2013.Majority of the patients were males, had t3-t4 disease, had n2-n3 nodal status and had extra-capsular extension (ece) in nodes.The median follow-up was 95.9 months.There was no difference between the three arms (a versus b versus c) for 10-year locoregional control (lrc): 60.2% versus 61.4% versus 65.7%, p = 0.57; disease free survival (dfs): 37.4% versus 43.9% versus 39.6%, p = 0.40; or overall survival (os): 39.7% versus 46.6% versus 40.4%, p = 0.40.There was no benefit of intensification with either modality in patients with any single adverse pathological factor.A benefit of intensification could be seen in patients with a combination of high-risk features: t3-t4 primary tumours with n2-n3 nodes along with ece for dfs (arm b versus arm a hr) = 0.53, arm c versus arm a hr = 0.63) and os (arm b versus arm a hr = 0.58, arm c versus arm a hr = 0.60).Conclusions all optimally resected ocscc with adverse features did not benefit from intensification of adjuvant therapy.Only a cohort of patients with a combination of high-risk features are likely candidates for intensification.Clinical trial registration nct00193843.

Journal: European journal of cancer (Oxford, England : 1990) (2023)
Publication types: Randomized Controlled Trial;Clinical Trial, Phase III;Journal Article;Research Support, Non-U.S. Gov't
A Comparative Evaluation of the KDSQ-C, AD8, and SMCQ as a Cognitive Screening Test to Be Used in National Medical Check-ups in Korea.

Korea has a periodic general health check-up program that uses the korean dementia screening questionnaire-cognition (kdsq-c) as a cognitive dysfunction screening tool.The alzheimer disease 8 (ad8) and subjective memory complaints questionnaire (smcq) are also used in clinical practice.We compared the diagnostic ability of these screening questionnaires for cognitive impairment when completed by participants and their caregivers.Hence, we aimed to evaluate whether the smcq or ad8 is superior to the kdsq-c and can be used as its replacement.Methods a total of 420 participants over 65 years and their informants were recruited from 11 hospitals for this study.The patients were grouped into normal cognition, mild cognitive impairment, and dementia subgroups.The kdsq-c, ad8, and smcq were completed separately by participants and their informants.Results a receiver operating characteristic analysis of questionnaire scores completed by participants showed that the areas under the curve (aucs) for the kdsq-c, ad8, and smcq for diagnosing dementia were 0.75, 0.8, and 0.73, respectively.Regarding informant-completed questionnaires, the ad8 (auc of 0.93), kdsq-c (auc of 0.92), and smcq (auc of 0.92) showed good discriminability for dementia, with no differences in discriminability between the questionnaires.Conclusion when an informant-report is possible, we recommend that the kdsq-c continues to be used in national medical check-ups as its discriminability for dementia is not different from that of the ad8 or smcq.Moreover, consistent data collection using the same questionnaire is important.When an informant is not available, either the kdsq-c or ad8 may be used.However, in the cases of patient-reports, discriminability is lower than that for informant-completed questionnaires.

Journal: Journal of Korean medical science (2019)
Publication types: Journal Article
Myofascial trigger points alter the modular control during the execution of a reaching task: a pilot study.

Myofascial trigger points (tp) constitute a conundrum in research and clinical practice as their etiopathogenesis is debated.Several studies investigating one or few muscles have shown that both active and latent tp causes an increased muscle activity, however the influence of tp on modular motor control during a reaching task is still unclear.Electromyographic signals, recorded from the muscles of the shoulder girdle and upper arm during a reaching task, were decomposed with non-negative matrix factorization algorithm.The extracted matrices of motor modules and activation signals were used to label the muscles condition as dominant or non-dominant.The presence of latent and active tp was detected in each muscle with manual examination.Despite a similar muscle activity was observed, we found that muscles with active tp had increased weighting coefficients when labeled in the dominant condition.No influences were found when muscles were in the non-dominant condition.These findings suggest that tp altered the motor control without co-contraction patterns.As a preliminary evidence, the present results suggest that the increased weighting coefficients in presence of tps are associated with an alteration of the modular motor control without affecting the dimensionality of motor modules for each individual and reciprocal inhibition.

Journal: Scientific reports (2019)
Publication types: Clinical Trial;Journal Article
A Rasch Analysis of the School-Related Well-Being (SRW) Scale: Measuring Well-Being in the Transition from Primary to Secondary School.

Within educational systems, promoting well-being is an essential objective along with traditional aims focused on students' learning.However, scarce attention has been devoted to school-related well-being in the transition from primary to lower secondary school, also for the paucity of brief instruments deputed to measure it.We assessed well-being at school for fourth-graders and seventh-graders, by adapting and validating the italian version of the school-related well-being (srw) scale, using in sequence exploratory factor analysis (efa), confirmatory factor analysis (cfa), and rasch analysis.Through the rasch analysis, we transformed the srw scale into an instrument that respects the properties of the fundamental measurement.We measured well-being and achievement emotions at time 1 and grades at time 2.The srw scale correlated with another measure of well-being and with students' achievement emotions.Grade-level differences emerged, with a decrease of well-being that attested a maladaptive trend at increasing age; moreover, females reported higher well-being than males.Well-being at school was positively linked to achievement.Beyond its methodological relevance, this study highlights the need for developing interventions to support students in the transition from primary to lower secondary school, which is such a pivotal time in their learning path.

Journal: International journal of environmental research and public health (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't