syedzayyan/paper_mill_benchmark huggingface dataset:
Antibody array-based proteomic screening of novel biomarkers in malignant biliary stricture.

Distinguishing between benign and malignant bile duct strictures has long been a diagnostic challenge in clinical practice.Objective this study aimed to discover novel biomarkers in bile to improve the diagnostic accuracy of malignant biliary strictures.Methods bile samples were collected from 6 patients with malignant or benign biliary stricture, respectively.Protein profiles of the bile were analyzed with a semi-quantitative human antibody array of 440 proteins.Then the differential expressed proteins were screened by venn diagram analysis.Following this, the accuracy of these potential biomarkers for discriminating between malignant and non-malignant biliary strictures was validated in a larger (n= 40) group of patients using roc analysis and the best biomarker combination was further selected by lasso analysis.Results twenty proteins were found differentially expressed in malignant versus benign biliary strictures, 6 of which were identified by venn diagram analysis to be up-regulated regardless of the location of biliary strictures.Among the 6 biomarkers, bile lipocalin-2, p-cadherin, and adipsin showed better diagnostic utility than that of bile ca19-9.Lasso analysis identified that lipocalin-2, p-cadherin and ca19-9 as a group of makers best distinguished malignant from benign strictures.Conclusions lipocalin-2 and p-cadherin measurements in bile could be clinically useful for the detection of malignant biliary strictures.

Journal: Cancer biomarkers : section A of Disease markers (2022)
Publication types: Journal Article
A Byzantine Sensing Network Based on Majority-Consensus Data Aggregation Mechanism.

In the current internet of things era, digital devices form complex interconnections.The statuses of objects of interest are monitored using sensors, and distributed wireless sensor networks are formed from numerous sensor nodes.Many byzantine fault tolerance mechanisms in wireless sensor networks (wsns) were proposed from byzantine agreement which even with a few faulty nodes in a sensor network, most healthy nodes can reach a consensus, perform data transmission tasks, and maintain network operation.In this study, this mechanism was utilized together with the majority function technique; in particular, the proposed method uses original sensor signals to define a threshold to assert a binary value of one or zero, thereby performing data judgment and aggregation.This approach reduces node energy consumption and enables the nodes to quickly reach a consensus.Moreover, the operating performance of the network can be maintained even when problems such as node failure and faults occur within the fault tolerance range.Compared with existing algorithms, the proposed data aggregation mechanism exhibits a better network life cycle and can effectively extend the flexibility of network operations.

Journal: Sensors (Basel, Switzerland) (2021)
Publication types: Journal Article
Microfluidics for real-time direct monitoring of self- and co-assembly biomolecular processes.

Molecular self-assembly is a major approach for the fabrication of functional supramolecular nanomaterials.This dynamic, straightforward, bottom-up procedure may result in the formation of various architectures at the nano-scale, with remarkable physical and chemical characteristics.Biological and bio-inspired building blocks are especially attractive due to their intrinsic tendency to assemble into well-organized structures, as well as their inherent biocompatibility.To further expand the morphological diversity, co-assembly methods have been developed, allowing to produce alternative unique architectures, enhanced properties, and improved structural control.However, in many cases, mechanistic understanding of the self- and co-assembly processes is still lacking.Microfluidic techniques offer a set of exclusive tools for real-time monitoring of biomolecular self-organization, which is crucial for the study of such dynamic processes.Assembled nuclei, confined by micron-scale pillars, could be subjected to controlled environments aiming to assess the effect of different conditions on the assembly process.Other microfluidics setups can produce droplets at a rate of over 100 s-1, with volumes as small as several picoliters.Under these conditions, each droplet can serve as an individual pico/nano-reactor allowing nucleation and assembly.These processes can be monitored, analyzed and imaged, by various techniques including simple bright-field microscopy.Elucidating the mechanism of such molecular events may serve as a conceptual stepping-stone for the rational control of the resulting physicochemical properties.

Journal: Nanotechnology (2019)
Publication types: Journal Article;Review
Effect of Optic Nerve Disinsertion During Evisceration on Nonporous Implant Migration: A Comparative Case Series and a Review of Literature.

To determine whether evisceration with optic nerve disinsertion and nonporous implant placement increases the risk of implant migration.Methods this was a single-center, retrospective consecutive comparative interventional case series including patients undergoing evisceration with nonporous implant between january and december 2014.Patients were grouped into 2 groups: group i where the optic nerve was not disinserted (n = 37) and group ii with optic nerve disinsertion (n = 50).Implant migration was assessed clinically and on patient photographs.Migration was subclassified as decentration that did not affect the prosthetic outcome and displacement that affected the prosthetic outcome.The secondary outcome measures were the mean implant diameter, volume of the custom ocular prosthesis, and implant-related complications like exposure and extrusion between the 2 groups.Results at a mean follow up of 12.5 months, none of the sockets in group i and 3 (6%) sockets in group ii (p = 0.35) had evidence of implant decentration.There were no cases of implant displacement in both groups.The mean implant diameter in group i was 16.97 mm ± 0.65 mm and in group ii 19.2 mm ± 0.83 mm (p = 0.0001).Implant extrusion was not different between the 2 groups.The mean custom ocular prosthesis volume in group i was 3.86 ml ± 0.52 ml and in group ii 2.50 ml ± 0.68 ml (p < 0.0001).Conclusions the rate of nonporous implant migration due to optic nerve disinsertion is not statistically or clinically significant in evisceration with optic nerve disinsertion, allowing placement of a larger implant and fabrication of a custom ocular prosthesis with an ideal weight.

Journal: Ophthalmic plastic and reconstructive surgery (2018)
Publication types: Comparative Study;Journal Article;Research Support, Non-U.S. Gov't;Review
Activity-based occupational therapy intervention for delirium superimposed on dementia in nursing home setting: a feasibility study.

Multi-component interventions can reduce delirium incidence.Occupational therapy (ot) has been effective in the management of dementia.We designed a real-world feasibility study of an ot intervention in the management of delirium superimposed on dementia (dsd).Methods we included a convenient sample of 22 patients older than 65 years of age with delirium and moderate dementia admitted to a nursing home (nh).The ot procedures were standardized according to the level of agitation or sedation of the patient and based on a structured ot evaluation.The canadian occupational performance measure (copm) was used to evaluate the proxy perception of performance in the daily activities at baseline and at delirium resolution.Results the mean age was 86.45 ± 6.46 years.The first daily treatment was delivered in the entire sample, while the second was delivered in 63.46% on day 1, 72.72% on day 2, 25% on day 3, 66.67% on day 4, 100% on days 5 and 6.The main time of the first daily treatment varied, day 1 through day 6, from 14.8 ± 8.5 to 20 ± 0 min; while the second daily treatment, in the same period, from 3.9 ± 6.7 to 20.1 ± 0 min.The mean time of the first treatment varied day 1 through day 6 from 14.8 ± 8.5 to 20 ± 0 min, while the second treatment from 3.9 ± 6.7 to 20.1 ± 0 min.The copm proxy performance and proxy satisfaction increased from delirium onset to delirium resolution.Conclusions this is the first study to report the feasibility of an ot intervention for the management of dsd in a nh setting.The results are important to support future trials on delirium management in a setting often understudied and underrepresented.

Journal: Aging clinical and experimental research (2020)
Publication types: Journal Article
Resveratrol treatment during maturation enhances developmental competence of oocytes after prolonged ovary storage at 4 °C in the domestic cat model.

Resveratrol (resv; 3,4,5-trihydroxy-trans-stilbene) is a phytoalexin with antioxidant activity that modulates redox homeostasis in oocytes and improves in vitro embryo production.Cold storage of cat ovaries for a period longer than 24 h alters oxidative status of oocytes after in vitro maturation and reduces their developmental competence.The aim of this study was to evaluate the effect of resveratrol supplementation to the maturation medium on embryo development of oocytes after storage of domestic cat ovaries at 4 °c for 24 h or 48 h.Cumulus-oocyte complexes (cocs) were recovered from ovaries of domestic queens and cultured in maturation medium supplemented with (+) or without (-) 5 μm resveratrol for 24 h.Cocs collected from fresh ovaries were matured in vitro (ivm) in standard conditions as control.After ivm, oocytes were in vitro fertilized (ivf) and presumptive zygotes cultured for 7 days.Oocyte nuclear maturation, reactive oxygen species (ros) and glutathione (gsh) levels as well as cleavage, blastocyst formation and blastocyst cell number were determined.There were no differences in the maturation rates of oocytes between the control and stored groups, irrespective of resveratrol supplementation.Resveratrol treatment during ivm significantly increased the level of gsh and reduced the level of ros of oocytes recovered from ovaries stored for 48 h as compared to the non-treated group (48 h-).The rate of blastocyst formation from oocytes recovered from ovaries after 48 h storage that underwent ivm with resveratrol was higher (p < 0.05) than that of oocytes matured without resveratrol and similar to that of control oocytes.Resveratrol treatment increased (p < 0.05) cell number in blastocysts from 24 h + and 48 h + groups as compared to their respective counterparts.In conclusion, our results demonstrated that resveratrol supplementation during ivm can reverse the adverse effect of oxidative stress on oocytes, and enhances embryo development after ovary storage at 4 °c for 48 h.These results may provide a basis for improving culture conditions and extend the possibility of storage of cat ovaries for more than 24 h thus ensuring successful in vitro embryo production.

Journal: Theriogenology (2020)
Publication types: Journal Article
Monitoring seasonal and phenological variability of cover management factor for wheat cropping systems under semi-arid climate conditions.

In modeling studies, the use of spatial data derived from geographic information systems and remote sensing applications to simulate the impact of phenological and seasonal changes on soil loss has a promising effect on the accuracy of predictions.The objective of this work was to estimate the c-factor (cover management) as a dynamic-factor rusle (revised universal soil loss equation) model based on an ndvi (normalized difference vegetation index) approach derived from high-resolution landsat 8 and landsat etm7 satellite images for 140 different rain-fed wheat parcels in terms of seasonal and phenological-based by the integrated use of remote sensing and gis.Overall, it was found that the highest c values, an average of 0.70, were estimated for the emergence period of the wheat, while the lowest value of 0.06 was found in the booting period.Seasonally, the estimated average c values in these parcels were 0.69, 0.63, 0.13, and 0.44 for the autumn, winter, spring, and summer, respectively.Corresponding soil losses for those seasons were 1.70, 1.55, 0.28, and 1.13 t ha-1year-1respectively.Comparatively, without considering the phenological growing periods of wheat, the annual predicted soil loss rate was 11.5% higher than the conditions considered.The present study concluded that an assessment of seasonal and phenological changes in the c-factor for fragile ecosystems with weak crop-cover development could significantly improve the accuracy of the rusle model predictions and effectively manage limited soil and water resources.

Journal: Environmental monitoring and assessment (2022)
Publication types: Journal Article
Ultra-Narrow Linewidth Photo-Emitters in Polymorphic Selenium Nanoflakes.

Photoluminescence (pl) in state-of-the-art 2d materials suffers from narrow spectral coverage, relatively broad linewidths, and poor room-temperature (rt) functionality.The authors report ultra-narrow linewidth photo-emitters (ulps) across the visible to near-infrared wavelength at rt in polymorphic selenium nanoflakes (se nfs), synthesized via a hot-pressing strategy.Photo-emitters in nir exhibit full width at half maximum (γ) of 330 ± 90 μe v, an order of magnitude narrower than the reported ulps in 2d materials at 300 k, and decrease to 82 ± 70 μe v at 100 k, with coherence time (τc) of 21.3 ps.The capping substrate enforced spatial confinement during thermal expansion at 250 °c is believed to trigger a localized crystal symmetry breaking in se nfs, causing a polymorphic transition from the semiconducting trigonal (t) to quasi-metallic orthorhombic (orth) phase.Fine structure splitting in orth-se causes degeneracy in defect-associated bright excitons, resulting in ultra-sharp emission.Combined theoretical and experimental findings, an optimal biaxial compressive strain of -0.45% cm-1in t-se is uncovered, induced by the coefficient of thermal expansion mismatch at the selenium/sapphire interface, resulting in bandgap widening from 1.74 to 2.23 ± 0.1 e v.This report underpins the underlying correlation between crystal symmetry breaking induced polymorphism and rt ulps in se nfs, and their phase change characteristics.

Journal: Small (Weinheim an der Bergstrasse, Germany) (2022)
Publication types: Journal Article
Antioxidant Activity and Neuroprotective Role of Docosahexaenoic Acid (DHA) Supplementation in Eye Diseases That Can Lead to Blindness: A Narrative Review.

The objective of this narrative review is to provide updated evidence, based on data from experimental and clinical studies, of the prominent role of omega-3 polyunsaturated fatty acids (n-3 pufas) for a number of crucial mechanisms involved in counteracting cell damage induced by oxidative stress in eye diseases.This article is focused on the antioxidant and neuroprotective effects of docosahexaenoic acid (dha), which have been assessed in different experimental models and clinical studies, particularly in proliferative diabetic retinopathy, age-related macular degeneration and glaucoma that are the most common eye diseases leading to severe vision loss.The mechanisms involved in the role of dha in protecting human retinal pigment epithelial cells from oxidative stress as well as the interaction with glutathione (gsh) are also described.The review is intended to provide novel and salient findings supporting the rationale of the use of dietary supplementation with high-dose dha (1050 mg/day) in the form of triglyceride as a potent antioxidant compound for improving the eye health.However, the overall clinical evidence for the use of dietary strategies based on supplementation with n-3 pufas in eye diseases linked to oxidative stress other than high-dose dha triglyceride is both limited and inconsistent.

Journal: Antioxidants (Basel, Switzerland) (2021)
Publication types: Journal Article;Review
Integrating physical and mental healthcare: Facilitators and barriers to success.

Introduction effective and appropriate provision of mental healthcare has long been a struggle globally, resulting in significant disparity between prevalence of mental illness and access to care.One attempt to address such disparity was the patient protection and affordable care act (ppaca), 2010, mandate in the united states to integrate physical and mental healthcare in federally qualified health centers (fqhcs).The notion of integration is attractive, as it has demonstrated the potential to improve both access to mental healthcare and healthcare outcomes.However, while the ppaca mandate set this requirement for fqhcs, no clear process as to how these centers should achieve successful integration was identified.Methods this research employed case study methods to examine the implementation of this policy in two fqhcs in new england.Data were obtained from in-depth interviews with leadership, management, and frontline staff at two case study sites.Results study findings include multiple definitions of and approaches for integrating physical and mental healthcare, mental healthcare being subsumed into, rather than integrated with, the medical model and multiple facilitators of and barriers to integration.Conclusion this study asked questions about what integration means, how it occurs, and what factors facilitate or pose barriers to integration.Integration is facilitated by co-location of providers within the same department, a warm hand-off, collaborative collegial relationships, strong leadership support, and a shared electronic health record.However, interdisciplinary conflict, power differentials, job insecurity, communication challenges, and the subsumption of mental health into the medical model pose barriers to successful integration.

Journal: Medicine access @ point of care (2021)
Publication types: Journal Article
Mechanism of bio-macromolecule denaturation on solid-liquid surface of ion-exchange chromatographic media - A case study for inactivated foot-and-mouth disease virus.

Destruction of assembly structures has been identified as a major cause for activity loss of virus and virus-like particles during their chromatographic process.A deep insight into the denaturation process at the solid-liquid interfaces is important for rational design of purification.In this study, in-situ differential scanning calorimetry (dsc) was employed to study the dissociation process of inactivated foot-and-mouth disease virus (fmdv) during ion exchange chromatography (iec) at different levels of p h.The intact fmdv known as 146s and the dissociation products were quantified by high performance size exclusion chromatography (hpsec) and the thermo-stability of 146s on-column was monitored in-situ by dsc.Serious dissociation was found at p h 7.0 and p h 8.0, leading to low 146s recoveries of 12.3% and 43.7%, respectively.The elution profiles from iec and hpsec combined with the thermal transition temperatures of 146s dissociation (tm1) from dsc suggested two denaturation mechanisms that the 146s dissociation occurred on-column after adsorption at p h 7.0 and during elution step at p h 8.0.By appending different excipients including sucrose, the improvement of 146s recovery and reduced dissociation was found highly correlated to increment of 146s stability on-column detected by dsc.The highest recovery of 99.9% and the highest tm1of 54.49 °c were obtained at p h 9.0 with 20% (w/v) sucrose.According to chromatographic behaviors and tm1, three different dissociation processes in iec were discussed.The study provides a perspective to understand the denaturation process of assemblies during chromatography, and also supplies a strategy to improve assembly recovery.

Journal: Journal of chromatography. B, Analytical technologies in the biomedical and life sciences (2020)
Publication types: Journal Article
Effect of SARS-CoV-2 Infection on Pregnancy Outcomes in an Inner-City Black Patient Population.

While data have shown that black populations are disproportionately affected by covid-19, few studies have evaluated birth outcomes in these understudied populations.This study hypothesized that sars-co v-2 infection would confer worse maternal and neonatal outcomes in a predominantly black and underserved population in brooklyn, new york city.In particular, sars-co v-2 is associated with higher rates of preterm birth, cesarean delivery, postpartum hemorrhage, lower apgar scores, and neonatal resuscitation.Demographic factors and comorbidities were compared between the sars-co v-2 positive and negative groups.A retrospective cohort study was conducted in hospitalized patients who gave birth at kings county hospital from april 10 through june 10, 2020.Demographic and clinical data were obtained from the electronic medical record.Patients were categorized based on sars-co v-2 infection status and peripartum outcomes were analyzed.We used the fisher exact test for categorical variables and the wilcoxon rank-sum test for continuous variables.P < 0.05 was considered significant.There were no differences in obstetric or neonatal outcomes between the sars-co v-2 positive and negative cohorts.Most sars-co v-2 positive patients were asymptomatic on admission.The rates of maternal comorbidities were similar in the sars-co v-2 positive and negative groups.In this predominantly black population in brooklyn, sars-co v-2 infection did not confer increased risk of adverse obstetric or neonatal outcomes, despite the prevalence of comorbidities.The impact of sars-co v-2 infection on pregnancy outcomes is complex and may differ on a community level.Determining how covid-19 is associated with perinatal outcomes in this minoritized patient population will augment our understanding of health disparities in order to improve care.

Journal: Journal of community health (2021)
Publication types: Journal Article
Preliminary evidence on cigarette nicotine reduction with concurrent access to an e-cigarette: Manipulating cigarette nicotine content, e-liquid nicotine content, and e-liquid flavor availability.

The reinforcing characteristics of e-cigarettes could moderate the impact of reducing cigarette nicotine content.In this study, people who smoke daily were recruited from north carolina and pennsylvania (us) in 2018 and 2019.Within a randomized 2 × 2 × 2 factorial design, participants received investigational cigarettes and an e-cigarette for 12 weeks.Cigarette nicotine content was very low (0.4 mg/g of tobacco; vlnc) or normal (15.8 mg/g; nnc).E-liquids were 0.3% ("low") or 1.8% ("moderate") freebase nicotine, and available in tobacco flavors or tobacco, fruit, dessert and mint flavors.Study recruitment concluded before reaching the planned sample size (n = 480).Fifty participants were randomized and 32 completed the study.We found that randomization to vlnc, relative to nnc cigarettes, reduced self-reported cigarettes per day (cpd; mean difference: -12.96; 95% ci: -21.51, -4.41; p = 0.005); whereas e-liquid nicotine content and flavor availability did not have significant effects.The effect of cigarette nicotine content was larger in the moderate vs.Low nicotine e-liquid groups and in the all flavors versus tobacco flavors e-liquid groups; tests of the interaction between e-liquid characteristics and cigarette nicotine content were not significant.Biomarkers of smoke exposure at week 12 did not differ across conditions, which may reflect variability in adherence to only using vlnc cigarettes.In conclusion this study offers preliminary evidence that the extent to which cigarette nicotine reduction decreases smoking may depend on the reinforcing characteristics of alternative products, including the available nicotine contents and flavors of e-cigarettes.

Journal: Preventive medicine (2022)
Publication types: Randomized Controlled Trial;Journal Article;Research Support, U.S. Gov't, P.H.S.;Research Support, N.I.H., Extramural