syedzayyan/paper_mill_benchmark huggingface dataset:
Analysis of the MILES cohort reveals determinants of disease progression and treatment response in lymphangioleiomyomatosis.

Introduction the multicenter international lymphangioleiomyomatosis (lam) efficacy of sirolimus (miles) trial revealed that sirolimus stabilised lung function in patients with moderately severe lam.The purpose of this study was to further examine the miles cohort for the effects of racial, demographic, clinical and physiological patient characteristics on disease progression and treatment response in lam.Methods miles subjects were stratified on the basis of menopausal status (pre-menopausal/post-menopausal), race (asian/caucasian), bronchodilator responsiveness (present/absent), initial forced expiratory volume in 1 s (fev1; 51-70%versus≤50% predicted) and tuberous sclerosis complex (tsc) association (yes/no).A linear mixed effects model was used to compare slope differences, and nonparametric tests were used to compare medians and proportions between treatment groups in each stratum.Results in the miles placebo group, pre-menopausal patients declined 5-fold faster than post-menopausal patients (mean±se fev1slope -17±3versus-3±3 m l·month-1; p=0.003).Upon treatment with sirolimus, both the pre-menopausal (-17±3versus-1±2 m l·month-1; p 600 pg·m l-1identified subgroups of patients who were more likely to decline on placebo and respond to treatment with sirolimus.Conclusions in lam patients, treatment with sirolimus is beneficial regardless of menopausal status, race, bronchodilator responsiveness, baseline fev1or tsc association.Serum vegf-d and menopausal status can help inform therapeutic decisions.

Journal: The European respiratory journal (2019)
Publication types: Comparative Study;Journal Article;Multicenter Study;Research Support, Non-U.S. Gov't
Usefulness of three-dimensional computed tomographic anatomy in endoscopic frontal recess surgery.

The endoscopic bidimensional vision offered by the endoscope during endoscopic sinus surgery involves difficulty in visualizing surgical field depth which makes it difficult to learn this surgical technique and makes it necessary for the endoscopic surgeon to mentally create a three-dimensional (3d) picture of the paranasal sinuses anatomy.In particular, frontal recess surgery requires good knowledge of its anatomic position, also since it is necessary to use angled endoscopes, which distort the view, and angular instruments which are difficult to use.Purpose of this project is to offer to the endoscopic surgeon a detailed 3d model of the nose and paranasal sinuses with particular attention to the frontal recess.Methods a 3d reconstruction of the frontal recess and its related structures, starting from computer tomography scans of the human skull, was realized using a professional 3d graphics software.Results a detailed reconstruction of the main structures which contribute to form the frontal recess was obtained.Particular attention was paid when reproducing the agger nasi cells, uncinate process, ethmoidal bulla, anterior ethmoidal cells, frontoethmoidal cells and their anatomic variants.Conclusions this is the first experience reported in literature regarding this new technique of iconographic didactics applied to endoscopic sinus surgery.It represents a new frontier, which surpasses and integrates the previous didactic techniques to help the surgeon to mentally create a 3d image of the paranasal sinuses.

Journal: Surgical and radiologic anatomy : SRA (2017)
Publication types: Journal Article
Comparison of the printed and online administration of the Behavioral Regulation in Exercise Questionnaire (BREQ-2).

To compare the traditional printed form of the behavioral regulation in exercise questionnaire with a proposed online form in terms of validity, reliability, and applicability.Methods a crossover design study was conducted with 157 undergraduate students.Half of the sample answered the printed questionnaire first and then answered the online questionnaire 7 days later, while the other half of the sample did the inverse.Cronbach's alpha was used to analyze the internal consistency of both the online and printed questionnaires.The construct validity was analyzed by confirmatory factor analysis, using a weighted least square mean and adjusted variance estimation and oblique rotation.The quality of the model was tested with fit indices.Results the confirmatory factor analysis showed the 19-item structure with five factors: χ2 of 230.718; degrees of freedom of 142; χ2/degrees of freedom of 1.625; comparative fit index of 0.978 and root mean square error of approximation of 0.073.All items presented factorial loads above 0.5.There was also excellent consistency between the formats of administration in all dimensions, with cronbach's alpha values above 0.70.The stability between the formats of administration varied between 0.78 (95%ci: 0.69-0.85) and 0.84 (95%ci: 0.77-0.89), suggesting desirable confidence between both formats of administration.Conclusion the five-factor model of the online behavioral regulation in exercise questionnaire shows internal consistency both in terms of the scale dimensions as well as in terms of the total items.

Journal: Einstein (Sao Paulo, Brazil) (2021)
Publication types: Journal Article
Progerin impairs 3D genome organization and induces fragile telomeres by limiting the dNTP pools.

Chromatin organization within the nuclear volume is essential to regulate many aspects of its function and to safeguard its integrity.A key player in this spatial scattering of chromosomes is the nuclear envelope (ne).The ne tethers large chromatin domains through interaction with the nuclear lamina and other associated proteins.This organization is perturbed in cells from hutchinson-gilford progeria syndrome (hgps), a genetic disorder characterized by premature aging features.Here, we show that hgps-related lamina defects trigger an altered 3d telomere organization with increased contact sites between telomeres and the nuclear lamina, and an altered telomeric chromatin state.The genome-wide replication timing signature of these cells is perturbed, with a shift to earlier replication for regions that normally replicate late.As a consequence, we detected a higher density of replication forks traveling simultaneously on dna fibers, which relies on limiting cellular d ntp pools to support processive dna synthesis.Remarkably, increasing d ntp levels in hgps cells rescued fragile telomeres, and improved the replicative capacity of the cells.Our work highlights a functional connection between ne dysfunction and telomere homeostasis in the context of premature aging.

Journal: Scientific reports (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Availability of food stores around Brazilian schools.

The aim of this study was to analyze the availability of food stores in the territory of schools.Ecological study conducted in viçosa, minas gerais, brazil, with all schools (n=42) and food stores (n=656).Data were collected through the objective evaluation of the environment, and the stores were categorized into healthy, unhealthy, mixed and supermarkets.Bivariate ripley ́s k function assessed the existence of clustering of categories of stores in the territory of schools.All the schools had at least one food store in their territory.Unhealthy stores were the most common and closest to the schools.There were more stores around private schools, offering high school education, located in the central region and in the highest per capita income tercile.The bivariate ripley ́s k function showed evidence of clustering of stores at all analyzed distances (400 to 1.5 km) with up to 3 times more establishments than would be expected if they were randomly distributed.Therefore, schoolchildren were likely exposed to unhealthy food environments, regardless of neighborhood income and location, which may contribute to inadequate food choices.

Journal: Ciencia & saude coletiva (2022)
Publication types: Journal Article
Using Smartphones for Clinical Assessment in Cervical Spondylotic Myelopathy a Feasibility Study.

Degenerative cervical myelopathy (dcm) is characterized by a progressive deterioration in spinal cord function.Its evaluation requires subjective clinical examination with wide interobserver variability.Objective quantification of spinal cord function remains imprecise, even though validated myelopathy-grading scales have emerged and are now widely used.We created a smartphone application, the n-outcome app, with the aim of quantifying accurately and reliably spinal cord dysfunction using a 5-minute test.A patient suffering from dcm was clinically evaluated before surgery, at 3 and 6 months follow-up after surgical decompression of the cervical spinal cord.Standard scores (nurick grade, modified japanese orthopedic association (m joa) score) were documented at these time points.A 5-minute motor and proprioceptive performance test aided by a smartphone with the n-outcome app was also performed.Motor performance in rapid alternating movements and finger tapping improved in correlation with improvements in standard grading scale scores.Clinical improvements were seen in maximum reflex acceleration and in romberg testing which showed less closed/open eyes variation, suggesting pyramidal and proprioceptive function recovery.We demonstrate that using the n-outcome app as an adjunct to clinical evaluation of compressive myelopathy is feasible and potentially useful.The results correlate with the results of clinical assessment obtained by standard validated myelopathy scores.

Journal: Journal of medical devices (2021)
Publication types: Journal Article
Assessment of the sustainable use of chemicals on a level playing field.

Misleading conclusions can result from applying tools beyond the purposes for which they were designed.A range of chemical assessment systems was compared against a set of principles germane to the sustainable use of chemicals relevant to the whole societal life cycles of finished products.These principles of sustainable use included: wider dimensions of sustainability, a foundation in science, consideration of life-cycle risk rather than simply intrinsic chemical properties, contributions to meeting human needs, open access, and peer review.A transparent basis in science is important for deriving objective, comparable, and replicable sustainability-based findings across materials and applications, and for guiding innovation.Few assessment systems currently identify how use of substances contributes to meeting human needs, a vital albeit often overlooked aspect of sustainable development, with most based largely on potential hazard without addressing wider life-cycle exposure and risk assessment.Qualitatively differing substances were illustratively assessed against the sustainability principles and life-cycle context of the additive sustainability footprint (asf), aspects of this analysis highlighting how differing material sourcing, manufacturing, and management in-use and at end-of-life can lead to widely divergent sustainability assessments.These illustrative asf assessments also demonstrate that material use challenges, assessed on a systemic basis, are common across materials, with no defensible automatic assumption that there are inherently "good" or "bad" materials; differing stewardship across whole product life cycles substantially influences sustainability credentials for all materials.It is therefore important that the sustainability performance of all materials is assessed on an objective "level playing field," which also highlights "hot spots" for sustainable innovation from supply-chain management through manufacturing, substance selection by material compounders, maintenance inputs in product use, and beyond product end-of-life.Chemical regulation must evolve to include and embed wider sustainability principles into operational practice and become applicable and enforced across increasingly global value chains.Integr environ assess manag 2023;19:1131-1146.© 2022 the authors.Integrated environmental assessment and management published by wiley periodicals llc on behalf of society of environmental toxicology & chemistry (setac).

Journal: Integrated environmental assessment and management (2023)
Publication types: Journal Article
Holding back the tears: is there a role for marsupialisation?

Medial eyelid tumours may result in the loss of the proximal lacrimal system during staged excision and delayed reconstruction, to achieve tumour margin clearance.The remnant canaliculus was marsupialised during reconstruction.The aim was to understand how many patients experienced symptomatic epiphora as a consequence of this.Methods and analysis a retrospective study including patients over a 15-year period with medial eyelid tumours, where the proximal lacrimal system was sacrificed to achieve tumour margin clearance.Included were all who had marsupialisation of the remnant distal stump as part of their delayed reconstruction.All who had pre-existing epiphora were excluded.The primary objective was the rate of epiphora following the procedure.A systematic literature review of postoperative epiphora occurring in patients with lid tumours requiring lacrimal system injury/sacrifice during tumour excision.Results there were 22 eyes (22 patients).All were basal cell carcinomas except for 1 (4.5%) tarsal conjunctival squamous cell carcinoma.All cases involved the lower lid.There were two (9.1%) patients who developed epiphora.One patient underwent a superior three-snip punctoplasty, botulinum toxin to the lacrimal gland and conjunctivodacryocystorhinostomy with lester jones tube insertion.The other patient was not overly troubled and did not require further treatment.The literature review showed the median postoperative rate of epiphora in these patients was 12.5% (range 0%-100%).Conclusion marsupialisation of the remnant canaliculus during delayed reconstruction is a straightforward and effective surgical option, which may help prevent postreconstruction epiphora when the proximal lacrimal system is sacrificed for tumour margin clearance.Trial registration number 10391.

Journal: BMJ open ophthalmology (2022)
Publication types: Journal Article;Systematic Review
Elevated Circulating LINC-P21 Serves as a Diagnostic Biomarker of Type 2 Diabetes Mellitus and Regulates Pancreatic β-cell Function by Sponging miR-766-3p to Upregulate NR3C2.

The purpose of this study was to evaluate the clinical value and biological function of long non-coding rna (lnc rna) linc-p21 in type 2 diabetes mellitus (t2dm), and explore the underlying mechanisms.Methods the expression of linc-p21 was estimated using quantitative real-time pcr.The functional role of linc-p21 was explored by gain- and loss-of-function experiments.Ins-1 cell proliferation was analyzed using a cell counting kit-8 (cck-8)assay, and the glucose-stimulated insulin secretion was measured using an elisa kit.The mi rnas that might be sponged by linc-p21 were analyzed, and the subsequent target genes were predicted and assessed in ins-1 cells.Results serum expression of linc-p21 was elevated in t2dm patients, which was correlated with fasting blood glucose levels and disease diagnosis.The glucose-stimulated insulin secretion and the proliferation of ins-1 cells were enhanced by linc-p21 knockdown, but the overexpression of linc-p21 led to opposite effects.Mi r-766-3p could be directly inhibited by linc-p21 in ins-1 cells and reverse the effects of linc-p21 on β-cell function.Additionally, nr3c2 was determined as a target of mi r-766-3p, which could be positively regulated by linc-p21 and had same effects with linc-p21 on ins-1 cell proliferation and insulin secretion.Conclusion all the data demonstrated that serum elevated linc-p21 and decreased mi r-766-3p serve as candidate diagnostic biomarkers in t2dm patients.Linc-p21 acts as a potential regulator in insulin secretion and proliferation of pancreatic β-cells through targeting mi r-766-3p to upregulate nr3c2.

Journal: Experimental and clinical endocrinology & diabetes : official journal, German Society of Endocrinology [and] German Diabetes Association (2022)
Publication types: Journal Article
Mechanisms of persistence and impact of ordinary heterotrophic organisms in aerobic granular sludge.

The stability of granules, contaminant removal and microbial structure of an aerobic granular sludge (ags) process were investigated with a focus on ordinary heterotrophic organisms (ohos).Long-term stable granules and high removals of cod (97 %), nh4+(98 %), p (85 %) and total n (77 %) were achieved.Sequencing analyses identified 6.6 % of phosphorus-accumulating organisms in the sludge, concordant with the observed bio-p removal capacity.However, ohos were the most abundant bacteria in the sludge (70-93 %) without resulting in unstable aggregates.Under current dogmas of microbial competition in activated sludge, it seemed contradictory that ohos could persist in the long term in the ags where cod was depleted beginning in the anaerobic phase.Microbial analyses showed that ohos could survive in granules by micropredation, proteolysis, fermentation and eps consumption.Heterotrophic-nitrification/ aerobic-denitrification was an active pathway in the ags.These findings contribute to a better understanding of microbial competition in ags and its stability.

Journal: Bioresource technology (2023)
Publication types: Journal Article
The impact of prophylactic ureteral stenting during kidney transplantation on postoperative surgical outcomes.

The aim of this study was to evaluate the safety and feasibility of prophylactic ureteric stenting during kidney transplantation (kt).Methods the authors retrospectively reviewed patients who underwent kt between june 2016 and june 2019.The prophylactic ureteral stenting group (double-j [dj]) and no-stent group (no-dj) were compared with respect to the clinical data and surgical outcomes.Results a total of 42 patients underwent kt; 17 patients were classified into the dj group and 25 patients into the no-dj group.Antithymocyte globulin induction and donor-specific antibody positivity were significantly higher in the dj group.There were no significant differences between the groups in terms of symptomatic urinary tract infection (uti).The time to postoperative uti was significantly shorter in the dj group than in the no-dj group (33.5±7.8 vs.105.3±71.6 days, p=0.013).The development of postoperative bk viremia was significantly higher in the no-dj group (0.0% vs.16.0%, p=0.035).Urologic complications were significantly higher in the no-dj group (0.0% vs.16.0%, p=0.035).In the no-dj group, urologic complications occurred in four patients ureteroneocystostomy stenosis in three patients and ureteroneocystostomy leakage in one patient.Percutaneous ureteral interventions were performed for all patients using percutaneous nephrostomy and reno-uretero-vesical stenting.However, there were no postoperative urologic complications in the dj group.Conclusions prophylactic ureteric stenting during kt may be safe and feasible without significantly increasing the incidence of uti and bk viremia.Additionally, prophylactic ureteric stenting may reduce urologic complications after kt.

Journal: Korean journal of transplantation (2021)
Publication types: Journal Article
Anatomical Importance Between Neural Structure and Bony Landmark: Clinical Importance for Posterior Endoscopic Cervical Foraminotomy.

Posterior endoscopic cervical foraminotomy (pecf) is a well-established, minimally invasive surgery for cervical radiculopathy, but have the more chances of neural structure damage due to the limited visibility and steeper learning curve.So, the anatomical understanding of the nerve associated with the bony structure will be an essential surgical guideline.Methods we measured the distance between the bilateral dura lateral edge and bilateral v-point on axial cuts of cervical magnetic resonance imaging and 3-dimensional spine computed tomography imaging, respectively, from 80 patients.We then calculate the distance and position between the dura lateral edge and the v-point as surgically critical width (scw).Transverse interdural distance (tidw), transverse inter-v-point distance, and anatomical facet joint width were measured.Results the mean tidw decreased as the levels down in the 40s-60s but increased at the c4-5, c5-6, and c6-7 levels in the 70s.Statistically significant difference was shown at the c6-7 level between the 40s and the 70s.The mean anatomical inter-v-point distance markedly decreased at c5-6 and continued till the c7-tl level at all age groups.Moreover, a statistically significant difference was shown at the c3-4 and c4-5 level between the 40s and the 70s.The mean negative values of scw increased from the 40s to 70s at the c5-6 and c6-7 levels (c5-6: -0.60 ± 1.10 mm to -1.63 ± 1.56 mm; c6-7: -0.90 ± 0.74 mm to -2.18 ± 1.25 mm).There were statistically significant differences between the 2 aged groups at the c3-4, c4-5, c5-6, and c6-7 levels.Conclusion a prediction of the correlated position between the lateral dura edge and the v-point is essential for the pecf not to injure the neural structure.In the case of a performing the pecf at the c5-6 and c6-7 level in the old-aged patient, it should be considered the laterally moved dura edge, and more extended bony remove is needed for less neural structure damage.

Journal: Neurospine (2021)
Publication types: Journal Article
Analysis of Cell Differentiation, Morphogenesis, and Patterning During Chicken Embryogenesis Using the Soaked-Bead Assay.

A multitude of genetic programs is activated during embryonic development that orchestrates cell differentiation to generate an astounding diversity of somatic cells, tissues, and organs.The precise activation of these genetic programs is regulated by morphogens, diffusible molecules that direct cell fate at different thresholds.Understanding how genetic activation coordinates morphogenesis requires the study of local interactions triggered by morphogens during development.The use of beads soaked in proteins or drugs implanted into distinct regions of the embryo enables studying the role of specific molecules in the establishment of digits and other developmental processes.This experimental technique provides information on the control of cell induction, cell fate, and pattern formation.Thus, this soaked bead assay is an extremely powerful and valuable experimental tool applicable to other embryonic models.

Journal: Journal of visualized experiments : JoVE (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Video-Audio Media