syedzayyan/paper_mill_benchmark huggingface dataset:
Trans-Tubular Translaminar Microscopic-Assisted Nucleotomy for Lumbar Disc Herniations in the Hidden Zone.

Study design a prospective cohort study in a high-flow spine center in germany.Objectives this study aimed to evaluate clinical outcomes and complications of the trans-tubular translaminar microscopic-assisted percutaneous nucleotomy in cases of cranially migrated lumbar disc herniations (ldh).Methods between january 2013 and january 2018, 66 consecutive patients with cranio-laterally migrated ldh were operated upon.The following outcome measures were evaluated:(1)visual analog scale (vas) for leg and back pain;(2)oswestry disability index (odi) and macnab ́s criteria.All patients were operated upon with trans-tubular translaminar microscopic-assisted percutaneous nucleotomy (tl-mapn).Perioperative radiographic and clinical evaluations were reported.The mean follow-up period was 32 months.Results the mean age was 59 years.L4/l5 was the commonest affected level (27 patients).The mean preoperative vas for leg pain was 6.44 (±2.06), improved to 0,35 (±0.59) postoperatively.Dural injury occurred in 1 patient, treated with dural patch.Improved neurological function was reported in 41/44 patients (neurological improvement rate of 93%) at the final follow up.There was a significant improvement in the mean odi values, from 50.19 ± 4.92 preoperatively to 10.14 ± 2.22 postoperatively(p < 0.001).Sixty four out of 66 patients (96%) showed an excellent or good functional outcome according to macnab ́s criteria.No recurrent herniations were observed.Conclusion the translaminar approach is a viable minimal invasive technique for cranially migrated ldh.The preservation of the flavum ligament is one of the main advantages of this technique.It is an effective, safe and reproducible minimally invasive surgical alternative in treatment of cranially migrated ldhs.

Journal: Global spine journal (2022)
Publication types: Journal Article
Colloidal Crystal Films with Narrow Reflection Bands by Hot-Pressing of Polymer-Grafted Silica Particles.

Previous reports have shown that colloidal crystal (cc) films with visible bragg reflection characteristics can be fabricated by the surface modification of monodisperse silica particles (si ps) with poly(methyl methacrylate) (pmma) chains, followed by hot-pressing at 150 °c.However, the reflection bands of the cc films were very broad due to their relative disordering of si ps.In this report, we attempted to fabricate the cc films using si ps surface-modified with poly(n-octyl acrylate) (poa) chains by hot-pressing.When the cast films of poa-grafted si ps were prepared by hot-pressing at 100 °c, the reflection bands were narrow rather than those of cc films of pmma-grafted si ps.This can be ascribed to easy disentanglement of poa chains during the hot-pressing process, thereby enabling the formation of well-ordered cc structures.Moreover, the reflection colors of cc films could be easily tuned by controlling the molecular weight of poa chains grafted on the si p surface.

Journal: Polymers (2022)
Publication types: Journal Article
Histone editing elucidates the functional roles of H3K27 methylation and acetylation in mammals.

Posttranslational modifications of histones (ptms) are associated with specific chromatin and gene expression states1,2.Although studies in drosophila melanogaster have revealed phenotypic associations between chromatin-modifying enzymes and their histone substrates, comparable studies in mammalian models do not exist3-5.Here, we use crispr base editing in mouse embryonic stem cells (m escs) to address the regulatory role of lysine 27 of histone h3 (h3k27), a substrate for polycomb repressive complex 2 (prc2)-mediated methylation and cbp/ep300-mediated acetylation6,7.By generating pan-h3k27r (p k27r) mutant m escs, where all 28 alleles of h3.1, h3.2 and h3.3 have been mutated, we demonstrate similarity in transcription patterns of genes and differentiation to prc2-null mutants.Moreover, h3k27 acetylation is not essential for gene derepression linked to loss of h3k27 methylation, or de novo activation of genes during cell-fate transition to epiblast-like cells (epi lcs).In conclusion, our results show that h3k27 is an essential substrate for prc2 in m escs, whereas other ptms in addition to h3k27 acetylation are likely involved in mediating cbp/ep300 function.Our work demonstrates the feasibility of large-scale multicopy gene editing to interrogate histone ptm function in mammalian cells.

Journal: Nature genetics (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Research Support, N.I.H., Extramural
Assessing Fluorosis Incidence in Areas with Low Fluoride Content in the Drinking Water, Fluorotic Enamel Architecture, and Composition Alterations.

There is currently no consensus among researchers on the optimal level of fluoride for human growth and health.As drinking water is not the sole source of fluoride for humans, and fluoride can be found in many food sources, this work aimed to determine the incidence and severity of dental fluorosis in poland, in areas where a low fluoride content characterizes the drinking water, and to assess the impact of fluoride on the enamel composition and microstructure.The dental examination involved 696 patients (aged 15−25 years) who had since birth lived in areas where the fluoride concentration in drinking water did not exceed 0.25 mg/l.The severity of the condition was evaluated using the dean’s index.Both healthy teeth and teeth with varying degrees of fluorosis underwent laboratory tests designed to assess the total protein and fluoride content of the enamel.Protein amount was assessed spectrophotometrically while the level of fluoride ions was measured by dx-120 ion chromatography.The clinical study revealed 89 cases (12.8%) of dental fluorosis of varying severity.The enamel of teeth with mild and moderate fluorosis contained a significantly higher protein (p-value < 0.001 and 0.002, respectively) and fluoride level (p < 0.001) than those with no clinical signs of fluorosis.Sem images showed irregularities in the structure of the fluorotic enamel.An excessive fluoride level during amelogenesis leads to adverse changes in the chemical composition of tooth enamel and its structure.Moreover, dental fluorosis present in areas where drinking water is low in fluorides indicates a need to monitor the supply of fluoride from other possible sources, regardless of its content in the water.

Journal: International journal of environmental research and public health (2022)
Publication types: Journal Article
Impacts of Removal Compensation Effect on the Mercury Emission Inventories for Nonferrous Metal (Zinc, Lead, and Copper) Smelting in China.

Nonferrous metal smelting (nfms) is one of the key sources of mercury (hg) emissions to the air and cross-media hg transfer in china.In this study, a "hg removal compensation effect" between upstream and downstream air pollution control devices (apcds) in nfms was uncovered based on the investigation of field test data.The relationships between the hg concentration in flue gas and the hg removal efficiencies of typical apcds were established, and an advanced probabilistic mass flow model regarding this effect was developed.Model comparison shows that the probabilistic essence of the advanced model prevents the underestimation of the deterministic model caused by using the geometric means of the hg contents of metal concentrates, and the consideration of the removal compensation effect leads to more accurate estimation of the overall hg removal efficiency of cascaded apcds.The hg emission abatement in the nfms sector from 2010 to 2017 was evaluated to be 55.6 t, which was 13.5% higher than the estimate without considering the hg removal compensation effect.The overall uncertainty of the improved model was reduced.This study provides a new methodology for more accurate evaluation of the effectiveness of the national implementation plan for the minamata convention on mercury.

Journal: Environmental science & technology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
COVID and Animal Trials: A Systematic Review.

Extensive work is being done to form targeted drugs against severe acute respiratory syndrome coronavirus 2 (sars-co v-2) infection; however, it is imperative to have a safe and effective vaccine against the same to win the war against this pandemic.For creating an efficacious vaccine, a proper animal model needs to be selected which can have an acceptable similarity of response as well as effects when administered to humans.For the present research, extensive search was conducted in medline and bio rxiv and med rxiv servers which were published in the english language from january 1, 2020, to august 20, 2020.Search terms included animal models, sars-co v-2, covid-19, immune response against coronavirus, nonhuman primates, mice, ferrets, and macaques.In our study, creating an adequate immune response mimicking the response as in humans, as the endpoint, was considered as inclusion criterion while assessment of any additional therapies like safety as well as minimal tolerable dose using animal models as well as formation of adequate sample size of these models against covid-19 was not considered.In our search, 163 articles were shortlisted, of them only 20 articles were finally included in our study which addressed to our inclusion and exclusion criterion.Our research articles focused on nonhuman primates, mice, hamsters, ferrets, cats, and dogs, with the main goal to investigate the role of animal models in the pathogenesis of covid-19.It was evident in our research that animal models only mimic limited signs and symptoms experienced in covid infection as compared to infections in humans.However, they are still essential to understand the pathogenesis, transmissibility of viral particles, and vaccine testing.

Journal: Journal of pharmacy & bioallied sciences (2021)
Publication types: Journal Article;Review
A Novel Thyroid Ultrasound Proficiency Metric Designed Through a Multidisciplinary Delphi Approach.

Thyroid ultrasounds extend surgeons' outpatient capabilities and are essential for operative planning.However, most residents are not formally trained in thyroid ultrasound.The purpose of this study was to create a novel thyroid ultrasound proficiency metric through a collaborative delphi approach.Methods clinical faculty experienced in thyroid ultrasound participated on a delphi panel to design the thyroid ultrasound proficiency scale (ups-thyroid).Participants proposed items under the categories of positioning, technique, image capture, measurement, and interpretation.In subsequent rounds, participants voted to retain, revise, or exclude each item.The process continued until all items had greater than 70% consensus for retention.The ups-thyroid was pilot tested across 5 surgery residents with moderate ultrasound experience.Learning curves were assessed with cumulative sum.Results three surgeons and 4 radiologists participated on the delphi panel.Following 3 iterative delphi rounds, the panel arrived at >70% consensus to retain 14 items without further revisions or additions.The metric included the following items on a 3-point scale for a maximum of 42 points: positioning (1 item), technique (4 items), image capture (2 items), measurement (2 items), and interpretation (5 items).A pilot group of 5 residents was scored against a proficiency threshold of 36 points.Learning curve inflection points were noted at between 4 to 7 repetitions.Conclusions a multidisciplinary delphi approach generated consensus for a thyroid ultrasound proficiency metric (ups-thyroid).Among surgery residents with moderate ultrasound experience, basic proficiency at thyroid ultrasound is feasible within 10 repetitions.

Journal: The American surgeon (2023)
Publication types: Journal Article
A Cross-Sectional Examination of the Mental Wellbeing, Coping and Quality of Working Life in Health and Social Care Workers in the UK at Two Time Points of the COVID-19 Pandemic.

As the covid-19 pandemic continues to evolve around the world, it is important to examine its effect on societies and individuals, including health and social care (hsc) professionals.The aim of this study was to compare cross-sectional data collected from hsc staff in the uk at two time points during the covid-19 pandemic: phase 1 (may-july 2020) and phase 2 (november 2020-january 2021).The hsc staff surveyed consisted of nurses, midwives, allied health professionals, social care workers and social workers from across the uk (england, wales, scotland, northern ireland).Multiple regressions were used to examine the effects of different coping strategies and demographic and work-related variables on participants' wellbeing and quality of working life to see how and if the predictors changed over time.An additional multiple regression was used to directly examine the effects of time (phase 1 vs.Phase 2) on the outcome variables.Findings suggested that both wellbeing and quality of working life deteriorated from phase 1 to phase 2.The results have the potential to inform interventions for hsc staff during future waves of the covid-19 pandemic, other infectious outbreaks or even other circumstances putting long-term pressures on hsc systems.

Journal: Epidemiologia (Basel, Switzerland) (2021)
Publication types: Journal Article
Association of Race and Ethnicity With Medication Use for Pediatric Lupus in the Childhood Arthritis and Rheumatology Research Alliance Registry.

Black and hispanic children with pediatric lupus (p sle) have higher morbidity and mortality than non-hispanic white children.The extent to which differences in outcomes are due to treatment disparities, including medication use, is unknown.We aimed to determine whether medication use in p sle is associated with race and ethnicity in the childhood arthritis and rheumatology research alliance (carra) registry.Methods patients with p sle enrolled in the carra registry from 2017 to 2020 were included.Multivariable mixed-effect logistic regression, adjusted for site of care, was used to compare use of antimalarials, high-dose oral glucocorticoids, and rituximab in black and hispanic children.Results we identified 639 children with p sle, of whom 480 had at least 1 year of follow-up.At enrollment, 89% of patients were prescribed an antimalarial and 50% were on high-dose glucocorticoids.Of those with 1 year of follow-up, 12% received rituximab.Nephritis, shorter disease duration, and higher systemic lupus erythematosus disease activity index 2000 scores were associated with high-dose glucocorticoid use.Antimalarial use was higher among those with nephritis and lower in children with no insurance.Rituximab use was associated with black race in the fixed-effects model but not when adjusted for site of care.Conclusion we identified differences in medication use by race and insurance status.Site of care was associated with the racial differences observed in rituximab use.Further research is needed to optimize p sle treatments particularly where use is highly variable, including glucocorticoid dosing and use of rituximab, and understand the impact of practice variation on disparities in p sle outcomes.

Journal: ACR open rheumatology (2022)
Publication types: Journal Article
BEAR reveals that increased fidelity variants can successfully reduce the mismatch tolerance of adenine but not cytosine base editors.

Adenine and cytosine base editors (abe, cbe) allow for precision genome engineering.Here, base editor activity reporter (bear), a plasmid-based fluorescent tool is introduced, which can be applied to report on abe and cbe editing in a virtually unrestricted sequence context or to label base edited cells for enrichment.Using bear-enrichment, we increase the yield of base editing performed by nuclease inactive base editors to the level of the nickase versions while maintaining significantly lower indel background.Furthermore, by exploiting the semi-high-throughput potential of bear, we examine whether increased fidelity sp cas9 variants can be used to decrease sp cas9-dependent off-target effects of abe and cbe.Comparing them on the same target sets reveals that cbe remains active on sequences, where increased fidelity mutations and/or mismatches decrease the activity of abe.Our results suggest that the deaminase domain of abe is less effective to act on rather transiently separated target dna strands, than that of cbe explaining its lower mismatch tolerance.

Journal: Nature communications (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Investigating the Anatomy and Microstructure of the Dentato-rubro-thalamic and Subthalamo-ponto-cerebellar Tracts in Parkinson's Disease.

Cerebellar-thalamic connections play a central role in deep brain stimulation-based treatment of tremor syndromes.Here, we used diffusion magnetic resonance imaging (mri) tractography to delineate the main cerebellar peduncles as well as two main white matter tracts that connect the cerebellum with the thalamus, the dentato-rubro-thalamic tract (drtt) and the subthalamo-ponto-cerebellar tract (spct).We first developed a reconstruction protocol in young healthy adults with high-resolution diffusion imaging data and then demonstrate feasibility of transferring this protocol to clinical studies using standard diffusion mri data from a cohort of patients with parkinson's disease (pd) and their matched healthy controls.The tracts obtained closely corresponded to the previously described anatomical pathways and features of the drtt and the spct.Second, we investigated the microstructure of these tracts with fractional anisotropy (fa), radial diffusivity (rd), and hindrance modulated orientational anisotropy (hmoa) in patients with pd and healthy controls.By reducing dimensionality of both the microstructural metrics and the investigated cerebellar and cerebellar-thalamic tracts using principal component analyses, we found global differences between patients with pd and controls, suggestive of higher fractional anisotropy, lower radial diffusivity, and higher hindrance modulated orientational anisotropy in patients.However, separate analyses for each of the tracts did not yield any significant differences.Our findings contribute to the characterization of the distinct anatomical connections between the cerebellum and the diencephalon.Microstructural differences between patients and controls in the cerebellar pathways suggest involvement of these structures in pd, complementing previous functional and diffusion imaging studies.

Journal: Frontiers in neurology (2022)
Publication types: Journal Article
Brooding as moderator of depressive symptoms after a work accident: A longitudinal study.

This study analyzes the relationship between having experienced a work accident and developing depressive symptoms six months later, considering the subjective severity of accidents, the use of both positive and negative religious coping strategies, and brooding as predictors variables.Fifty seven women and 187 men were evaluated during the month following their accident (t1) and six months later (t2).The results show that after controlling for initial depressive symptoms, all predictors showed a statistically significant relationship with depression at six months, including the interaction between brooding and subjective severity of accident.Forty nine percent of resilient participants exhibited low symptoms at t1 and t2, 22% of recovered individuals showed high symptoms at t1 and low symptoms afterwards, 20% of depressive individuals had high symptoms at t1 and t2, and 8% exhibited high symptoms only at t2.High severity, brooding and religious coping at t1 differentiated those who exhibited stable symptoms from those who were resilient.Resilience was specifically predicted with a negative coefficient by the interaction of brooding with subjective severity of accident.We conclude that brooding is a variable that moderates the relationship between subjective severity of accident and the development and maintenance of depressive symptoms.Subjective severity of accident, brooding and negative religious coping are risk factors, while positive religious coping is not a sufficient protection factor.

Journal: Scandinavian journal of psychology (2018)
Publication types: Journal Article
Presepsin levels in neonatal cord blood are not influenced by maternal SARS-CoV-2 infection.

S coronavirus disease (covid-19) can present with various symptoms and can involve multiple organs.Women infected during pregnancy have a higher incidence of obstetrical complications and infants born to "positive" mothers may get the infection with different manifestations.Presepsin seems to be a promising sepsis biomarker in adults and neonates.The aim of this study was to assess if presepsin levels in neonatal cord blood could be influenced by maternal severe acute respiratory syndrome coronavirus 2 (sars-co v-2) infection.Methods a total of 119 neonates born from women with a confirmed diagnosis of sars-co v-2 infection were enrolled and presepsin levels of cord blood samples were collected.All neonates were tested for sars-co v-2 infection at birth and after 48-72 h.Results the median presepsin value in umbilical cord blood samples collected after birth was 455 pg/m l.Presepsin levels were not influenced by maternal symptoms of covid-19, weight for gestational age, or delivery mode, and did not significantly differ between infants with and without adverse neonatal outcomes.Infants hospitalized for more than 5 days had a significantly higher presepsin level at birth rather than those discharged up to 4 days of life.Three infants with positive nasopharyngeal swab at birth had higher presepsin levels than two infants tested positive at 48 h.Conclusions this is the first study reporting cord presepsin levels in term and preterm infants born to mothers with covid-19, that appeared to be not influenced by maternal clinical presentation.However, further studies are needed to explain the mechanisms of p-sep increase in neonates exposed to perinatal maternal sars-co v-2 infection or with an indeterminate/possible sars-co v-2 infection in the same neonates.

Journal: Clinical chemistry and laboratory medicine (2022)
Publication types: Journal Article
Metabolic Implications of Oxidative Stress and Inflammatory Process in SARS-CoV-2 Pathogenesis: Therapeutic Potential of Natural Antioxidants.

Covid-19 is a zoonotic disease with devastating economic and public health impacts globally.Being a novel disease, current research is focused on a clearer understanding of the mechanisms involved in its pathogenesis and viable therapeutic strategies.Oxidative stress and inflammation are intertwined processes that play roles in disease progression and response to therapyviainterference with multiple signaling pathways.The redox status of a host cell is an important factor in viral entry due to the unique conditions required for the conformational changes that ensure the binding and entry of a virus into the host cell.Upon entry into the airways, viral replication occurs and the innate immune system responds by activating macrophage and dendritic cells which contribute to inflammation.This review examines available literature and proposes mechanisms by which oxidative stress and inflammation could contribute to covid-19 pathogenesis.Further, certain antioxidants currently undergoing some form of trial in covid-19 patients and the corresponding required research gaps are highlighted to show how targeting oxidative stress and inflammation could ameliorate covid-19 severity.

Journal: Frontiers in cellular and infection microbiology (2021)
Publication types: Journal Article;Review