syedzayyan/paper_mill_benchmark huggingface dataset:
The effect of focus size and intensity on stone fragmentation in SWL on a piezoelectric lithotripter.

We aim to analyze the efficacy of different focus sizes and the influence of pulse pressure (intensity) during shock wave lithotripsy (swl) in terms of stone fragmentation.Methods combination of three focal sizes (f1 = 2 mm, f2 = 4 mm, f3 = 8 mm) and 11 output pressure settings (intensity 10-20) of a piezoelectric lithotripter (wolf piezo lith 3000) were tested on artificial stones (n = 99).The stones were placed within a 2 mm mesh cage.The needed number of shockwaves (sw) to first visible crack, 50% and 100% stone disintegration were recorded.Results similar number of sw's were observed until the first crack 10, 11 and 11 sw's for f1, f2, and f3, respectively (p > 0,05).The median number of sw needed for 50% stone disintegration was 245 for f1 group, 242 for f2 group and 656 for f3 group.F1 vs f2 p = 0.7, f1 vs f3 and f2 vs f3 p < 0.05.Similarly, with larger focus size a higher number of shockwaves were necessary for 100% stone disintegration.894, 877 and 1708 sw's for f1, f2 and f3, respectively.Only for f1 vs f3 and f2 vs f3 (all p < 0.05) a statistical difference was observed.These findings were consistent in all different power settings, with an increased difference in lower power levels (≤ 14).Conclusions a smaller focus size, as well as a higher peak pressure results in a more effective stone fragmentation.However, these results need to be confirmed in an in vivo setting with multiple parameters interfering the efficacy, like bmi, respiration or stone migration.

Journal: World journal of urology (2020)
Publication types: Journal Article
A simpler linear-time algorithm for the common refinement of rooted phylogenetic trees on a common leaf set.

The supertree problem, i.e., the task of finding a common refinement of a set of rooted trees is an important topic in mathematical phylogenetics.The special case of a common leaf set l is known to be solvable in linear time.Existing approaches refine one input tree using information of the others and then test whether the results are isomorphic.Results an o(k|l|) algorithm, lin cr, for constructing the common refinement t of k input trees with a common leaf set l is proposed that explicitly computes the parent function of t in a bottom-up approach.Conclusion lin cr is simpler to implement than other asymptotically optimal algorithms for the problem and outperforms the alternatives in empirical comparisons.Availability an implementation of lin cr in python is freely available at .

Journal: Algorithms for molecular biology : AMB (2021)
Publication types: Journal Article
Oesophageal atresia without major cardiovascular anomalies: Is management justified at a district paediatric surgical institution?

Oesophageal atresia lacks sufficiently documented treatment approach, as guidelines are based rather on the opinion of experts than on systematic data.We aimed to answer the question if treatment of patients without major cardiovascular anomalies could be justified at a peripheral paediatric surgical institution, by evaluating the outcome of surgical correction.Methods thirty-three neonates underwent surgery for correction of oesophageal atresia during a period of 20 years.They were categorised into two time-period groups, to follow-up the evolution of surgical intervention and complications through time.Evaluation of post-operative outcome and morbidity was performed.The results were related to those of our recent cross-sectional study on families having experienced oesophageal atresia performed years after repair, regarding the long-term quality of life.Results a shift from staged to primary repair occurred throughout time in the patients with a marginal long gap between proximal and distal oesophagus (p = 0.008).Anastomotic stenosis was the major short-term complication encountered, treated with post-operative dilation sessions.Dysphagia and reflux were the most common long-term complications.Conclusions oesophageal atresia without severe cardiovascular abnormalities could be treated at a peripheral paediatric surgical department with satisfactory outcomes.However, qualified paediatric surgeons, anaesthesiologists and neonatologists and the availability of neonatal intensive care unit should be definitively required.

Journal: African journal of paediatric surgery : AJPS (2021)
Publication types: Journal Article
Novelty promotes recognition memory persistence by D1 dopamine receptor and protein kinase A signalling in rat hippocampus.

Strategies for improving memory are increasingly studied, and exposure to a novel experience can be an efficient neuromodulator.Novelty effects on memory depend on d1-family dopamine receptors (d1rs) activation.Here, we evaluated the novelty effect on memory persistence of wistar rats and investigated the contribution of d1rs and their signalling pathways by protein kinase a (pka) and c (pkc).Animals with infusion cannulae inserted into the ca1 hippocampus area were trained on the novel object recognition (nor) task, which involved exploring two different objects.After training, some rats received intrahippocampal infusions of vehicle or d1rs agonist; others explored a novel environment for 5 min and were infused with a variety of drugs targeting d1rs and their signalling pathways.We demonstrated that pharmacological stimulation of d1rs or novelty exposure promoted nor memory persistence for 14 days and that the novelty effect depended on d1rs activation.To determine if the d1 and d5 receptor subtypes were necessary for the impact of novelty exposure on memory, we blocked or stimulated pka or pkc-protein kinases activated mainly by d1 and d5, respectively.Only pka inhibition impaired the effect of novelty on memory persistence.After novelty and d1rs blocking, pka but not pkc stimulation maintained the memory persistence effect.Thus, we concluded that novelty promoted memory persistence by a mechanism-dependent on activating hippocampal d1rs and pka pathway.

Journal: The European journal of neuroscience (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
The relationship between schizotypal personality features and mind wandering among college students during COVID-19 pandemic: A moderator of depression.

Introduction although the impact of the covid-19 pandemic on people's mental health has been well documented in many studies, the schizotypal personality features in the general population have not received sufficient attention.Methods study 1 is a longitudinal study tracking changes in schizotypal personality features among college students during the covid-19 pandemic.A total of 153 chinese college students were assessed using the schizotypal personality questionnaire.Study 2 explored the relationship between schizotypal personality features, mind wandering, and depression.A total of 557 college students completed the schizotypal personality questionnaire, the beck depression inventory, and the mind-wandering questionnaire during the covid-19 pandemic.Results study 1 results showed that the scores from later stages in the pandemic were significantly higher than those from the initial stages on each dimension of schizotypal personality, which means that the schizotypal personality features became more obvious during the covid-19 pandemic.Study 2 results showed that there was a positive correlation between schizotypal personality features, depression, and mind wandering.Discussion depression played a moderating role in the relationship between schizotypal personality features and mind wandering.The schizotypal personality features of college students increase during covid-19; it has a positive relationship with mind wandering; depression moderates the relationship.We discussed these findings and provided some suggestions about future research.

Journal: Frontiers in psychiatry (2022)
Publication types: Journal Article
Genetics of ANCA-associated vasculitis: role in pathogenesis, classification and management.

Anti-neutrophil cytoplasmic antibody (anca)-associated vasculitis (aav) comprises granulomatosis with polyangiitis (gpa), microscopic polyangiitis (mpa) and eosinophilic granulomatosis with polyangiitis (egpa), that share features of pauci-immune small-vessel vasculitis and the positivity of anca targeting proteinase-3 (pr3-anca) or myeloperoxidase (mpo-anca).Aav syndromes are rare, complex diseases and their aetio-pathogenesis is mainly driven by the interaction between environmental and genetic factors.In patients with gpa and mpa, the genetic associations are stronger with anca specificity (pr3- versus mpo-anca) than with the clinical diagnosis, which, in keeping with the known clinical and prognostic differences between pr3-anca-positive and mpo-anca-positive patients, supports an anca-based re-classification of these disorders.Egpa is also made up of genetically distinct subsets, which can be stratified on anca-status (mpo anca-positive versus anca-negative); these subsets differ in clinical phenotype and possibly in their response to treatment.Interestingly, mpo-anca-positive patients with either mpa or egpa have overlapping genetic determinants, thus strengthening the concept that this egpa subset is closely related to the other aav syndromes.The genetics of aav provides us with essential information to understand its varied phenotype.This review discusses the main findings of genetic association studies in aav, their pathogenic implications and their potential effect on classification, management and prognosis.

Journal: Nature reviews. Rheumatology (2022)
Publication types: Journal Article;Review
Development of a method for the detection of zinc in Brassica oleracea using solid phase extraction and size-exclusion chromatography inductively coupled plasma mass spectrometry (SEC-ICP-MS).

The aim of this work is the development of a suitable method to extract and detect zinc-bound compounds from cabbage, broccoli and kale (family brassicaceae, species oleracea) using solid phase extraction (spe) and size-exclusion chromatography inductively coupled plasma mass spectrometry (sec-icp-ms).Tris [2-amino-2-(hydroxymethyl)-1,3-propanediol]/hydrochloric acid (tris/hcl) or ammonium nitrate were used as extractants added to the freeze-dried samples, which were then sonicated and centrifuged.An enzymatic mixture was added to the extracts and then incubated for 5- and 18 h prior to analysis by sec-icp-ms.Results showed a good coefficient of variation (cv) of the elution time (0.06-0.9%), concentration (4.7-16.9%) and molecular size (0.4-5.4%).The limit of detection (lod) and the limit of quantitation (loq) were 0.9 μg l-1 and 2.8 μg l-1, respectively.The proposed method is reliable and robust and can be applied to samples with difficult matrices like vegetables and soil.•good precision, stability and reproducibility.•easy to execute and suitable for analysis of vegetables and other samples with complex matrices, eg.Soil.•this method contributed to good maintenance of the instrument and to minimal cleaning time.

Journal: MethodsX (2021)
Publication types: Journal Article
Refining the mandibular osteoradionecrosis rat model by in vivo longitudinal µCT analysis.

Osteoradionecrosis (orn) is one of the most feared side effects of radiotherapy following cancers of the upper aero-digestive tract and leading to severe functional defects in patients.Today, our lack of knowledge about the physiopathology restricts the development of new treatments.In this study, we refined the orn rat model and quantitatively studied the progression of the disease.We tested the impact of radiation doses from 20 to 40 gy, delivered with incident 4mv x-ray beams on the left mandible of the inbred lewis rat.We used micro-computed tomography (μct) to obtain in vivo images for longitudinal bone imaging and ex vivo images after animal perfusion with barium sulphate contrast agent for vessel imaging.We compared quantification methods by analyzing 3d images and 2d measurements to determine the most appropriate and precise method according to the degree of damage.We defined 25 gy as the minimum irradiation dose combined with the median molar extraction necessary to develop non-regenerative bone necrosis.Μct image analyses were correlated with clinical and histological analyses.This refined model and accurate methods for bone and vessel quantification will improve our knowledge of the progression of orn pathology and allow us to test the efficacy of new regenerative medicine procedures.

Journal: Scientific reports (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Liquid-liquid equilibrium measurements and computational study of salt-polymer aqueous two phase system for extraction of analgesic drugs.

In recent decades, aqueous two phase systems have gained a lot of attention for extraction of different materials.In this work, an aqueous two phase system was made by polyethylene glycol 600 and potassium hydroxide and phase diagram were determined for this system.The experimental binodal data were described using two empirical nonlinear three parameter expressions developed by merchuk and zafarani-moattar.The consistency of the experimental tie-line data was determined by utilizing the othmer-tobias, bancraft, and setschenow correlations.Also, the extraction of two analgesic drugs, namely ibuprofen and acetaminophen were investigated by the mentioned atps.For this purpose, partition coefficients and extraction efficiencies of each drug were calculated.The trend of extraction efficiencies indicated that the responsibility of extraction of the mentioned drugs into the polymer-rich top phase is related to their hydrophobicity.The diamond-hsu equation and its modified version were used to correlate the drugs experimental partition coefficients.Furthermore, the interaction of mentioned drugs with polyethylene glycol was investigated employing quantum computing techniques based upon density functional theory (dft).These results were in good agreement with the trend of extraction efficiencies of studied drugs.

Journal: Scientific reports (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Acinetobacter baumannii K13 and K73 capsular polysaccharides differ only in K-unit side branches of novel non-2-ulosonic acids: di-N-acetylated forms of either acinetaminic acid or 8-epiacinetaminic acid.

Structures of capsular polysaccharides of acinetobacter baumannii isolates carrying kl13 and kl73 gene clusters were established.The closely related kl73 and kl13 gene clusters differ only by one gene in the module responsible for synthesis of the non-2-ulosonic acids.The k13 and k73 polysaccharides differ only in a single side-chain sugar, which is either 5,7-diacetamido-3,5,7,9-tetradeoxy-l-glycero-l-altro- or -d-glycero-l-altro-non-2-ulosonic acid [di-n-acetylated forms of acinetaminic acid (aci5ac7ac) or 8-epiacinetaminic acid (8e aci5ac7ac), respectively].The kl13 also is closely related to the kl12 gene cluster, which contains a different wzy gene encoding the k unit polymerase.Accordingly, the otherwise near identical k units are linked differently via an α-d-fucp nac-(1 → 4)-d-galp linkage in k13 and k73 or an α-d-fucp nac-(1 → 3)-d-galp nac linkage in k12.This finding confirms the predicted substrate of the itr b3 initiating transferase as d-fucp nac.Glycosyltransferases predicted to catalyse the linkage of d-galp or d-galp nac to l-fucp nac in the growing k13 and k73 or k12 units, respectively, differ by only two amino acids.

Journal: Carbohydrate research (2017)
Publication types: Journal Article
Integration of genomic variants and bioinformatic-based approach to drive drug repurposing for multiple sclerosis.

Multiple sclerosis (ms) is a chronic autoimmune disease in the central nervous system (cns) marked by inflammation, demyelination, and axonal loss.Currently available ms medication is limited, thereby calling for a strategy to accelerate new drug discovery.One of the strategies to discover new drugs is to utilize old drugs for new indications, an approach known as drug repurposing.Herein, we first identified 421 ms-associated snps from the genome-wide association study (gwas) catalog (p-value 0.8.Ms risk genes were then prioritized using bioinformatics analysis to identify biological ms risk genes.The prioritization was performed based on six defined categories of functional annotations, namely missense mutation,cis-expression quantitative trait locus (cis-e qtl), molecular pathway analysis, protein-protein interaction (ppi), genes overlap with knockout mouse phenotype, and primary immunodeficiency (pid).A total of 144 biological ms risk genes were found and mapped into 194 genes within an expanded ppi network.According to the drug bank and the therapeutic target database, 27 genes within the list targeted by 68 new candidate drugs were identified.Importantly, the power of our approach is confirmed with the identification of a known approved drug (dimethyl fumarate) for ms.Based on additional data from clinical trials.gov, eight drugs targeting eight distinct genes are prioritized with clinical evidence for ms disease treatment.Notably,cd80and cd86pathways are promising targets for ms drug repurposing.Usingin silicodrug repurposing, we identified belatacept as a promising ms drug candidate.Overall, this study emphasized the integration of functional genomic variants and bioinformatic-based approach that reveal important biological insights for ms and drive drug repurposing efforts for the treatment of this devastating disease.

Journal: Biochemistry and biophysics reports (2022)
Publication types: Journal Article
'Physio-EndEA' Study: A Randomized, Parallel-Group Controlled Trial to Evaluate the Effect of a Supervised and Adapted Therapeutic Exercise Program to Improve Quality of Life in Symptomatic Women Diagnosed with Endometriosis.

The 'physio-end ea' study aims to explore the potential benefits of a therapeutic exercise program (focused on lumbopelvic stabilization and tolerance to exertion) on the health-related quality of life (hrqo l) of symptomatic endometriosis women.Design the present study will use a parallel-group randomized controlled trial design.Methods a total of 22 symptomatic endometriosis women will be randomized 1:1 to the physio-end ea or usual care groups.The 'physio-end ea' program will consist of a one-week lumbopelvic stabilization learning phase followed by an eight-week phase of stretching, aerobic and resistance exercises focused on the lumbopelvic area that will be sequentially instructed and supervised by a trained physiotherapist (with volume and intensity progression) and adapted daily to the potential of each participant.The primary outcome measure is hrqo l.The secondary outcome measures included clinician-reported outcomes (pressure pain thresholds, muscle thickness and strength, flexibility, body balance and cardiorespiratory fitness) and patient-reported outcomes (pain intensity, physical fitness, chronic fatigue, sexual function, gastrointestinal function and sleep quality).Discussion findings of this study will help to identify cost-effective non-pharmacological options (such as this exercise-based intervention) that may contribute to the improvement of hrqo l in symptomatic endometriosis women.

Journal: International journal of environmental research and public health (2022)
Publication types: Journal Article;Randomized Controlled Trial;Research Support, Non-U.S. Gov't
DNA Strand Displacement Driven by Host-Guest Interactions.

Base-pair-driven toehold-mediated strand displacement (bp-tmsd) is a fundamental concept employed for constructing dna machines and networks with a gamut of applications─from theranostics to computational devices.To broaden the toolbox of dynamic dna chemistry, herein, we introduce a synthetic surrogate termed host-guest-driven toehold-mediated strand displacement (hg-tmsd) that utilizes bioorthogonal, cucurbit[7]uril (cb[7]) interactions with guest-linked input sequences.Since control of the strand-displacement process is salient, we demonstrate how hg-tmsd can be finely modulated via changes to the structure of the input sequence (including synthetic guest head-group and/or linker length).Further, for a given input sequence, competing small-molecule guests can serve as effective regulators (with fine and coarse control) of hg-tmsd.To show integration into functional devices, we have incorporated hg-tmsd into machines that control enzyme activity and layered reactions that detect specific micro rna.

Journal: Journal of the American Chemical Society (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, U.S. Gov't, Non-P.H.S.
Intimate partner violence during pregnancy and maternal and child health outcomes: a scoping review of the literature from low-and-middle income countries from 2016 - 2021.

Intimate partner violence (ipv) during pregnancy is significantly associated with negative outcomes for both mother and child.Current evidence indicates an association between low levels of social support and ipv, however there is less evidence from low-and-middle income countries (lmic) than high-income countries.Globally, the covid-19 pandemic has radically altered how women can access social support.Hence since 2020, studies investigating ipv and pregnancy have occurred within the changing social context of the pandemic.Objective this scoping review summarizes the evidence from lmics about the effects of ipv during pregnancy on maternal and child health.The review includes the impact of the covid-19 pandemic on social support as mentioned in studies conducted since 2020.Design library databases were used to identify papers from 2016 to 2021.These studies reported the maternal and child health outcomes of ipv during pregnancy, and described how social support during pregnancy, and the covid-19 pandemic, were associated with rates of ipv during pregnancy.Observational study designs, qualitative and mixed methods studies were included.Results twenty - six studies from 13 lmics were included.Half (n = 13) were cross sectional studies which only collected data at one time-point.Ipv during pregnancy was significantly associated with higher odds of postpartum depression, low birth weight, preterm birth and less breastfeeding in the year after birth.Lower levels of social support increased the odds of experiencing ipv during pregnancy, whilst higher levels of social support reduced antenatal anxiety and depression in women experiencing ipv during pregnancy.Of the four studies that investigated ipv during pregnancy throughout the covid-19 pandemic, only one compared prevalence before and after the pandemic and unexpectedly reported a lower prevalence.Conclusions further research on the impact of ipv during pregnancy on maternal and child outcomes in lmics is required, especially evidence from longitudinal studies investigating a wider range of outcomes.To date, there is limited evidence on the impact of the covid-19 pandemic on ipv during pregnancy in lmics, and this should be prioritized as the pandemic continues to affect women's access to social support globally.

Journal: BMC pregnancy and childbirth (2022)
Publication types: Journal Article;Review