syedzayyan/paper_mill_benchmark huggingface dataset:
Topology-Aware Non-Rigid Point Cloud Registration.

In this paper, we introduce a non-rigid registration pipeline for pairs of unorganized point clouds that may be topologically different.Standard warp field estimation algorithms, even under robust, discontinuity-preserving regularization, tend to produce erratic motion estimates on boundaries associated with 'close-to-open' topology changes.We overcome this limitation by exploiting backward motion: in the opposite motion direction, a 'close-to-open' event becomes 'open-to-close', which is by default handled correctly.At the core of our approach lies a general, topology-agnostic warp field estimation algorithm, similar to those employed in recently introduced dynamic reconstruction systems from rgb-d input.We improve motion estimation on boundaries associated with topology changes in an efficient post-processing phase.Based on both forward and (inverted) backward warp hypotheses, we explicitly detect regions of the deformed geometry that undergo topological changes by means of local deformation criteria and broadly classify them as 'contacts' or 'separations'.Subsequently, the two motion hypotheses are seamlessly blended on a local basis, according to the type and proximity of detected events.Our method achieves state-of-the-art motion estimation accuracy on the mpi sintel dataset.Experiments on a custom dataset with topological event annotations demonstrate the effectiveness of our pipeline in estimating motion on event boundaries, as well as promising performance in explicit topological event detection.

Journal: IEEE transactions on pattern analysis and machine intelligence (2021)
Publication types: Journal Article
Optimization of a resazurin-based microplate assay for large-scale compound screenings againstKlebsiella pneumoniae.

A new resazurin-based assay was evaluated and optimized using a microplate (384-well) format for high-throughput screening of antibacterial molecules against klebsiella pneumoniae.Growth of the bacteria in 384-well plates was more effectively measured and had a > sixfold higher signal-to-background ratio using the resazurin-based assay compared with absorbance measurements at 600 nm.Determination of minimum inhibitory concentrations of the antibiotics revealed that the optimized assay quantitatively measured antibacterial activity of various antibiotics.An edge effect observed in the initial assay was significantly reduced using a 1-h incubation of the bacteria-containing plates at room temperature.There was an approximately 10% decrease in signal variability between the edge and the middle wells along with improvement in the assay robustness (z' = 0.99).This optimized resazurin-based assay is an efficient, inexpensive, and robust assay that can quantitatively measure antibacterial activity using a high-throughput screening system to assess a large number of compounds for discovery of new antibiotics against k.Pneumoniae.

Journal: 3 Biotech (2018)
Publication types: Journal Article
Proposed protocol for rate-limiting step determination during anaerobic digestion of complex substrates.

Anaerobic digestion is a complex process, involving various microorganism groups and, consequently, several reactions.An easy-to-use protocol for the rate-limiting step determination of the process is proposed.The hydrogen production, acetate production, and acetate consumption rates can be calculated, according to a structured algorithm.During the rate limiting step determination, several compounds (biopolymer and monomer representatives, as well as sodium acetate) were used, combined or not with the substrate, to draw the corresponding conclusions.Three substrates were tested, characterized by specific organic compound groups (carbohydrates, proteins, and fats).All three substrates followed the acetate-consuming pathway for the organic matter conversion to methane.In this study, the rate-limiting step for the pathway of acetate consumption was acetate production.Determining the rate-limiting step through the proposed protocol can point to the appropriate actions needed to boost methane production, like substrate pretreatment, using an acidogenic reactor, or checking for the presence of inhibitors.

Journal: Bioresource technology (2022)
Publication types: Journal Article
Do fear of COVID-19 and religious coping predict depression, anxiety, and stress among the Arab population during health crisis?

The roles of fear of covid-19 and religious coping were examined in relation to depression, anxiety, and stress.Participants (n= 259; 88% female;mage= 32.96,sd= 8.88) completed measures of fear of covid-19, religious coping, depression, anxiety, and stress.Results showed that fear of covid-19 was associated with depression, anxiety, and stress.Negative religious coping was associated with depression, anxiety, and stress while positive religious coping was only associated with depression and stress.Fear of covid-19 and negative religious coping may be detrimental to mental health while positive religious coping may reduce depression and stress.

Journal: Death studies (2022)
Publication types: Journal Article
Electronic and optical aspects of novel quinoxaline derivatives as electron donor materials for bulk heterojunction solar cells.

In this paper, we design new forms of organic conjugated compounds-based quinoxaline derivatives.Specifically, we exploit density functional theory and time-dependent-density functional theory in order to study the structure, the optic, the electronic, the reorganization energy and the photovoltaic features of such new molecules.Particularly, all engineered compounds have a narrow band gap in the range of 0.696-0.721 e v, high oscillator frequency and good optical properties.Moreover, the pcbm is employed as an electron acceptor.Employing global reactivity descriptors, we demonstrate that the molecules can efficiently emit electrons into the pcbm and the electrons are attracted to pcbm from molecules.In addition, the results show an appropriate open circuit voltage in the range of 0.338-0.362 v.The proposed compounds exhibit excellent electron transport and charge conduction from the donor to the acceptor.These new molecules show potential properties to develop bulk heterojunction organic photovoltaic cells.

Journal: Journal of molecular graphics & modelling (2023)
Publication types: Journal Article
Telehealth in Times of COVID-19: Spotlight on Austria.

Introduction with the spread of coronavirus disease 2019 (covid-19), the world has been experiencing an extraordinary state of emergency.As patients entering a doctor's practice can potentially infect medical staff and other patients, using digital alternatives wherever possible is a potential solution to avoiding face-to-face encounters.In these conditions, telemedicine is becoming increasingly relevant.Hence, the aim of this study was to examine telemedicine use and gathered experiences during the covid-19 pandemic in austria.Materials and methods in june 2020, a representative group of austrian respondents (n= 1000) was asked via online survey whether they had contacted a doctor during spring of 2020, and, if so, whether they had used a telemedical method to do so.The survey also reflected gathered experiences and degrees of satisfaction with the use of telemedicine.Results a third (33%) of those who contacted a doctor during the target period did so using telemedical tools.The majority of those with previous telehealth experience were satisfied with the help they received.Patients commonly used a telephone to contact their doctors.The overall assessment of telemedical aids tended to be positive, with more than half (53%) of those surveyed seeing significant advantages, and a 90% satisfaction rate among the respondents who used telehealth services.Conclusion the outcomes from this work hint at fairly high acceptance of telemedical communication tools in the studied group of the austrian population.Based on the high rate of satisfaction among patients who used telehealth, it is expected that the use of telehealth services will increase further in the near future.

Journal: Healthcare (Basel, Switzerland) (2021)
Publication types: Journal Article
Impact of visual impairment on balance and visual processing functions in students with special educational needs.

Introduction vision is critical for children's development.However, prevalence of visual impairment (vi) is high in students with special educational needs (sen).Other than vi, sen students are prone to having functional deficits.Whether visual problems relate to these functional deficits is unclear.This study aimed to assess the impact of vision on visual processing functions and balance in sen students through a community service.Methods visual acuity (va) and contrast sensitivity were measured in a total of 104 (aged 14.3±4.3) sen students as the visual outcomes, followed by retinoscopy.Visual processing function assessment included facial expression recognition by card matching examiner's facial expression matching, and visual orientation recognition.Dynamic balance, by timed up and go test, and static standing balance (postural sway in double-legged standing with feet-together and tandem-stance for open-eye and closed-eye conditions) were assessed.Static balance was presented in terms of the maximal medial-lateral and antero-posterior sways.Results of the 104 students, 62 (59.6%) were classified as visually impaired according to who classification of visual impairment based on presenting distance acuity.Ocular problems (e.g.Optic nerve anomaly, uncorrected/ under-corrected refractive errors) and neurological anomalies were the major causes of vision loss.Va was positively associated with visual processing functions (all p ≤ 0.01), as sen students with better vision tended to perform better in visual orientation and facial expression recognition tasks, as well as dynamic balance function (p = 0.04).For the static balance, postural sway and va showed a positive relationship under open-eye and tandem stance conditions.However, the relationship between postural sway and va became negative under closed-eye and tandem stance conditions.Conclusion this study found a high prevalence of sen students with visual impairment, in which many of them were undetected.Optometric examination is important to improve their visual function to minimize the effect of vision on functional performance.Vision is critical in visual processing as well as playing an important role in maintaining balance in sen students.

Journal: PloS one (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Identification of neurodevelopmental transition patterns from infancy to early childhood and risk factors predicting descending transition.

It is unclear whether neurodevelopmental progress from infancy to early childhood remains stable.Moreover, little is known about the risk factors, if any, affecting neurodevelopmental descending transition patterns and the relationship between these patterns and later childhood adaptive behaviours.We used data of 875 children from the hamamatsu birth cohort study in japan.Children's neurodevelopment at 18 and 32 months and adaptive behaviours at 40 months were evaluated.Perinatal factors and infant overweight status at 18 months were investigated to identify descending-transition-associated risk factors.In the latent transition analysis, ultimately, three classes were identified for each time-point, resulting in nine transition patterns; among them, 10.4% of children showed descending class shifts (normal to delayed class).Such decelerated growth was predicted by maternal pre-pregnancy overweight status (odds ratio [or] 2.49; 95% confidence interval [ci] 1.23, 5.02), low maternal educational history (or 1.20; 95% ci 1.04, 1.36), and infant overweight status at 18 months (or 5.89; 95% ci 1.26, 27.45).Children with descending transition showed poor functioning in adaptive behaviours at the age of 40 months.To prevent subsequent poor adaptive functioning, it may be necessary to consider that a certain percentage of children show decelerated growth.

Journal: Scientific reports (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Effects of rifampin on the pharmacokinetics and pharmacodynamics of milvexian, a potent, selective, oral small molecule factor XIa inhibitor.

Milvexian (bms-986177/jnj-70033093) is a potent, oral small molecule that inhibits the active form of factor xi with high affinity and selectivity.This study assessed the single-dose pharmacokinetic and pharmacodynamic properties of milvexian co-administered with rifampin, an organic anion transport protein (oatp) inhibitor and potent cytochrome p450 (cyp) 3a and p-glycoprotein (p-gp) inducer.In this open-label, nonrandomized, single-sequence study, healthy participants (n = 16) received single doses of milvexian on day 1 (100 mg), milvexian and rifampin (600 mg) on day 4, rifampin on days 5-11, milvexian and rifampin on day 12, and rifampin on days 13-14.Pharmacokinetic data were summarized using descriptive statistics.Administration of milvexian, alone or in combination with rifampin, was generally safe and well tolerated.Single-dose co-administration of rifampin and milvexian demonstrated no meaningful changes in milvexian exposure versus milvexian alone (cmax, 110%; auc[0-t], 102%; auc[inf], 101%).After multiple doses of rifampin and milvexian, peak and total milvexian exposure substantially decreased versus milvexian alone (cmax, 22%; auc[0-t], 15%; auc[inf], 15%).Results were consistent with preclinical data, indicating that milvexian is a substrate for cyp3a4/5 and p-gp but not oatp.The implications of these results on the need for dose adjustment of milvexian will be further elucidated following the completion of phase 2 and 3 trials.trial registration the study was registered with clinical trials.gov (nct02959060; submitted 7/11/2016, first posted 8/11/2016).

Journal: Scientific reports (2022)
Publication types: Clinical Trial;Journal Article;Research Support, Non-U.S. Gov't
Fatty Acids and Frailty: A Mendelian Randomization Study.

Observational studies have suggested that fatty acids such as higher levels of n-3 polyunsaturated fatty acids (pufas) may prevent frailty.By using mendelian randomization analysis, we examined the relationship between fatty acids and frailty.Methods we used summary statistics data for single-nucleotide polymorphisms associated with plasma levels of saturated fatty acids (palmitic acid, stearic acid), mono-unsaturated fatty acids (mufas) (palmitoleic acid, oleic acid), n-6 pufas (linoleic acid, arachidonic acid), and n-3 pufas (alpha-linolenic acid, eicosapentaenoic acid, docosapentaenoic acid, docosahexaenoic acid), and the corresponding data for frailty index (fi) in 356,432 individuals in the uk biobank.Results although there were no robust associations on the mufas or the pufas, genetically predicted higher plasma stearic acid level (one of saturated fatty acids) was statistically significantly associated with higher fi (β = 0.178; 95% confidence interval = -0.050 to 0.307;p= 0.007).Such a relationship was also observed in a multivariate mr (β = 0.361; 95% confidence interval = 0.155 to 0.567;p= 0.001).Genetically predicted higher palmitic acid was also significantly associated with higher fi (β = 0.288; 95% confidence interval = 0.128 to 0.447;p< 0.001) in the multivariate mr analysis.Conclusions the present mr study implies that saturated fatty acids, especially stearic acid, is a risk factor of frailty.

Journal: Nutrients (2021)
Publication types: Journal Article
Poor Functional Outcome in Patients with Voluntary Knee Instability after Anterior Cruciate Ligament Reconstruction.

Backgroud anterior cruciate ligament reconstruction (aclr) remains the gold standard treatment for anterior cruciate ligament (acl) injury.However, a good functional outcome even after a successful surgery depends on multiple factors.It has been observed that certain patients with a chronic acl injury demonstrate knee instability voluntarily.The authors observed that these patients might not perform well even after a successful surgery.This study aims to assess the outcome after acl and other ligament reconstruction in patients with voluntary knee instability.Methods from a total of 824 patients who underwent aclr, 13 patients with a history of voluntary knee instability were selected, and data of these patients (demographic and clinical profile) were obtained.Outcomes of surgery in this group of patients were evaluated by using lysholm score and tegner activity level.Results all patients were young men with a chronic acl injury and manifested instability.Associated injuries were lateral meniscus tear in 3 patients, medial meniscus tear in 2, and posterolateral corner (plc) injury in 3.Aclr was done using the semitendinosus-gracilis graft in all patients.Further, anterolateral ligament reconstruction was done in 2 patients and plc reconstruction, in 3 patients.The mean lysholm score was 54.76 (range, 48-62) preoperatively and 60.92 (range, 54-78) at a mean follow-up of 14.3 months (range, 11-26 months).The median tegner activity level was 6 (range, 5-7) before injury and 4 (range, 3-5) at the final follow-up.Twelve of the 13 patients were able to demonstrate instability voluntarily at the time of the final follow-up.Conclusions in patients with acl and other ligament injuries who demonstrated voluntary knee instability, the functional outcome even after successful ligament reconstruction was poor.

Journal: Clinics in orthopedic surgery (2020)
Publication types: Journal Article
Phenomenology and content of the inhaled N, N-dimethyltryptamine (N, N-DMT) experience.

Understanding the phenomenology and content of the inhaled n, n, dimethyltryptamine (n, n-dmt) experience is critical to facilitate and support ongoing research and therapeutic models targeting mental health conditions and central nervous system pathology.A qualitative analysis was conducted of all n, n-dmt experiences posted to the r/dmt reddit community over a 10-year period from 2009 to 2018.A total of 3778 experiences from 3305 posts were included in this study.A median dose of n, n-dmt of 40.0 mg [interquartile range (iqr), 27.5 to 50.0] and a median experience duration of 10 min (iqr, 5.0 to 15.0) were identified.The most common somatic effects were somaesthesias (n = 1415, 37.5%) and an auditory ringing (n = 583, 15.4%).Visualizations predominantly consisted of fractals, shapes, patterns (n = 1231, 32.6%) and vivid colours (n = 953, 25.2%).Entity encounters were reported in 45.5% (n = 1719) of the experiences and involved predominantly a feminine phenotype (n = 416, 24.2%); deities (n = 293, 17.0%); aliens (n = 281, 16.3%); creature-based entities (n = 158, 9.2%, including reptilian and insectoid beings); mythological beings (n = 144, 8.4%, including machine elves); and jesters (n = 112, 6.5%).Entity interactions were predominantly positive (n = 600, 34.9% of encounters) involving benevolent, comforting, protecting, or outwardly caring interactions.A companion-type, pedagogical, or guide-type interaction was identified 32.4% of encounters (n = 557).Common typology, architecture, and structural features of the "dmt world" included descriptions of alternate or higher dimensions (n = 952, 25.2%); rooms [n = 582, 15.4%, including the "waiting room" (n = 105, 2.8%)], and a tunnel (n = 390, 10.3%).Features of mystical and ego-dissolution experiences were common.Additional rewarding aspects were identified, including a sense of familiarity and the acceptance/removal of the fear of death.Challenging and difficult responses were less frequent but also documented.Statements of profundity were identified in 232 experiences (6.1%), including pronouncing the experience or an aspect of the experience as the most "beautiful" or feeling the most "beautiful" of their life (n = 47, 1.2%).This study identified common phenomenological themes and content of naturalistic inhaled n, n-dmt experiences.Major thematic domains included (1) physical and somatic experiences; (2) visualizations and imagery; (3) entity encounters including entity phenotype, descriptors, attributes, disposition, and characteristics of the interaction; (4) typology, architectural features, structural characteristics, and scenery of the "dmt world"; (5) alerations in consciousness (including mystical experiences, out-of-body experiences, and ego-dissolution); (6) emotional responses (including positive, rewarding, difficult, and challenging); and (7) statements of profundity.

Journal: Scientific reports (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Intrahepatic manifestation and distant extrahepatic disease in alveolar echinococcosis: a multicenter cohort study.

The main endemic areas of alveolar echinococcosis (ae) are in central europe and western china.The infiltration of intrahepatic vascular and bile ducts as well as extrahepatic disease can lead to complications and may increase morbidity in ae.Purpose to evaluate the vascular/biliary involvement of hepatic alveolar echinococcosis (hae) and distant extrahepatic disease at each of four locations in germany, france, and china.Material and methods contrast-enhanced abdominal magnetic resonance imaging (mri) scans of patients with hae, 200 in total, were evaluated by five examiners.Ae liver lesions were classified according to kodama's classification.Furthermore, distant extrahepatic manifestations were documented with additionally performed imaging modalities.Vascular/biliary involvement of hepatic manifestations as well as the presence of extrahepatic manifestations were correlated with the respective kodama type of the liver lesion.Results distant extrahepatic ae manifestations were significantly more frequent in china than in europe (12/100 vs.3/100; fisher's exact test:p=0.0286).A significant relationship exists between presence of distant extrahepatic disease manifestation and size of the ae liver lesion (132.53 ± 48.65 vs.92.49 ± 50.06;p= 0.0030).Vascular/biliary involvement is significantly more frequent in china than in europe (86/100 vs.65/100; χ2= 11.92;p= 0.0006).Vascular/biliary involvement depends on lesion size (111.10 ± 47.44 vs.47.36 ± 24.36;p<0.0001).Different types of ae liver lesions are associated with differences in vascular/biliary involvement and extrahepatic manifestations.Conclusion vascular/biliary involvement and presence of distant extrahepatic manifestations depend on size of the hae lesions and are more frequently detected in china.Different mri morphological patterns influence vascular/biliary involvement and the occurrence of distant extrahepatic manifestations.

Journal: Acta radiologica (Stockholm, Sweden : 1987) (2021)
Publication types: Journal Article;Multicenter Study