cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Toyz: A Framework for Scientific Analysis of Large Datasets and Astronomical Images
Creators: name: Moolekamp, Fred
name: Mamajek, Eric
Publisher: name: arXiv
Year: 2015
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: As the size of images and data products derived from astronomical data continues to increase, new tools are needed to visualize and interact with that data in a meaningful way. Motivated by our own astronomical images taken with the Dark Energy Camera (DECam) we present Toyz, an open source Python package for viewing and analyzing images and data stored on a remote server or cluster. Users connect to the Toyz web application via a web browser, making it an convenient tool for students to visualize and interact with astronomical data without having to install any software on their local machines. In addition it provides researchers with an easy-to-use tool that allows them to browse the files on a server and quickly view very large images ($>$ 2 Gb) taken with DECam and other cameras with a large FOV and create their own visualization tools that can be added on as extensions to the default Toyz framework.
description: 7 pages, 7 figures
Incremental Benefit of a Home Visit Following Discharge for Patients with Multiple Chronic Conditions Receiving Transitional Care
Creators: name: Williams, Christianna
name: Jackson, Carlos
name: DuBard, C. Annette
name: Kasper, Elizabeth W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Transitional care management is effective at reducing hospital readmissions among patients with multiple chronic conditions, but evidence is lacking on the relative benefit of the home visit as a component of transitional care. The sample included non-dual Medicaid recipients with multiple chronic conditions enrolled in Community Care of North Carolina (CCNC), with a hospital discharge between July 2010 and December 2012. Using claims data and care management records, this study retrospectively examined whether home visits reduced the odds of 30-day readmission compared to less intensive transitional care support, using multivariate logistic regression to control for demographic and clinical characteristics. Additionally, the researchers examined group differences within clinical risk strata on inpatient admissions and total cost of care in the 6 months following hospital discharge. Of 35,174 discharges receiving transitional care from a CCNC care manager, 21% (N = 7468) included a home visit. In multivariate analysis, home visits significantly reduced the odds of readmission within 30 days (odds ratio = 0.52, 95% confidence interval 0.48–0.57). At the 6-month follow-up, home visits were associated with fewer inpatient admissions within 4 of 6 clinical risk strata, and lower total costs of care for highest risk patients (average per member per month cost difference $970; P < 0.01). For complex chronic patients, home visits reduced the likelihood of a 30-day readmission by almost half compared to less intensive forms of nurse-led transitional care support. Higher risk patients experienced the greatest benefit in terms of number of inpatient admissions and total cost of care in the 6 months following discharge. (Population Health Management 2016;19:163–170)
Genomic profiling of murine mammary tumors identifies potential personalized drug targets for p53-deficient mammary cancers
Creators: name: Pfefferle, Adam D.
name: Perou, Charles M.
name: Mardis, Elaine R.
name: Kanchi, Krishna L.
name: Koboldt, Daniel C.
name: Agrawal, Yash N.
name: Rosen, Jeffrey M.
name: Herschkowitz, Jason I.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Targeted therapies against basal-like breast tumors, which are typically ‘triple-negative breast cancers (TNBCs)’, remain an important unmet clinical need. Somatic TP53 mutations are the most common genetic event in basal-like breast tumors and TNBC. To identify additional drivers and possible drug targets of this subtype, a comparative study between human and murine tumors was performed by utilizing a murine Trp53-null mammary transplant tumor model. We show that two subsets of murine Trp53-null mammary transplant tumors resemble aspects of the human basal-like subtype. DNA-microarray, whole-genome and exome-based sequencing approaches were used to interrogate the secondary genetic aberrations of these tumors, which were then compared to human basal-like tumors to identify conserved somatic genetic features. DNA copy-number variation produced the largest number of conserved candidate personalized drug targets. These candidates were filtered using a DNA-RNA Pearson correlation cut-off and a requirement that the gene was deemed essential in at least 5% of human breast cancer cell lines from an RNA-mediated interference screen database. Five potential personalized drug target genes, which were spontaneously amplified loci in both murine and human basal-like tumors, were identified: Cul4a, Lamp1, Met, Pnpla6 and Tubgcp3. As a proof of concept, inhibition of Met using crizotinib caused Met-amplified murine tumors to initially undergo complete regression. This study identifies Met as a promising drug target in a subset of murine Trp53-null tumors, thus identifying a potential shared driver with a subset of human basal-like breast cancers. Our results also highlight the importance of comparative genomic studies for discovering personalized drug targets and for providing a preclinical model for further investigations of key tumor signaling pathways.
Nonequilibrium dynamical mean-field theory for the charge-density-wave phase of the Falicov-Kimball model
Creators: name: Matveev, O. P.
name: Shvaika, A. M.
name: Devereaux, T. P.
name: Freericks, J. K.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Nonequilibrium dynamical mean-field theory (DMFT) is developed for the case of the charge-density-wave ordered phase. We consider the spinless Falicov-Kimball model which can be solved exactly. This strongly correlated system is then placed in an uniform external dc electric field. We present a complete derivation for nonequilibrium dynamical mean-field theory Green's functions defined on the Keldysh-Schwinger time contour. We also discuss numerical issues involved in solving the coupled equations.
description: 4 pages, 2 figures, submitted to the proceedings of "Superstripes 2015"
A classification system for zebrafish adipose tissues
Creators: name: Rawls, John F.
name: Minchin, James E.N.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: The zebrafish model system offers significant utility for in vivo imaging of adipose tissue (AT) dynamics and for screening to identify chemical and genetic modifiers of adiposity. In particular, AT can be quantified accurately in live zebrafish using fluorescent lipophilic dyes. Although this methodology offers considerable promise, the comprehensive identification and classification of zebrafish ATs has not been performed. Here, we use fluorescent lipophilic dyes and in vivo imaging systematically to identify, classify and quantify the zebrafish AT pool. We identify 34 regionally distinct zebrafish ATs, including five visceral ATs and 22 subcutaneous ATs. For each of these ATs, we describe detailed morphological characteristics to aid their identification in future studies. Furthermore, we quantify the areas for each AT and construct regression models to allow prediction of expected AT size and variation across a range of developmental stages. Finally, we demonstrate the utility of this resource for identifying effects of strain variation and high-fat diet on AT growth. Altogether, this resource provides foundational information on the identity, dynamics and expected quantities of zebrafish ATs for use as a reference for future studies.
The frequency of snowline-region planets from four-years of OGLE-MOA-Wise second-generation microlensing
Creators: name: Shvartzvald, Y.
name: Maoz, D.
name: Udalski, A.
name: Sumi, T.
name: Friedmann, M.
name: Kaspi, S.
name: Poleski, R.
name: Szymański, M. K.
name: Skowron, J.
name: Kozłowski, S.
name: Wyrzykowski, Ł.
name: Mróz, P.
name: Pietrukowicz, P.
name: Pietrzyński, G.
name: Soszyński, I.
name: Ulaczyk, K.
name: Abe, F.
name: Barry, R. K.
name: Bennett, D. P.
name: Bhattacharya, A.
name: Bond, I. A.
name: Freeman, M.
name: Inayama, K.
name: Itow, Y.
name: Koshimoto, N.
name: Ling, C. H.
name: Masuda, K.
name: Fukui, A.
name: Matsubara, Y.
name: Muraki, Y.
name: Ohnishi, K.
name: Rattenbury, N. J.
name: Saito, To.
name: Sullivan, D. J.
name: Suzuki, D.
name: Tristram, P. J.
name: Wakiyama, Y.
name: Yonehara, A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: We present a statistical analysis of the first four seasons from a "second-generation" microlensing survey for extrasolar planets, consisting of near-continuous time coverage of 8 deg$^2$ of the Galactic bulge by the OGLE, MOA, and Wise microlensing surveys. During this period, 224 microlensing events were observed by all three groups. Over 12% of the events showed a deviation from single-lens microlensing, and for $\sim$1/3 of those the anomaly is likely caused by a planetary companion. For each of the 224 events we have performed numerical ray-tracing simulations to calculate the detection efficiency of possible companions as a function of companion-to-host mass ratio and separation. Accounting for the detection efficiency, we find that $55^{+34}_{-22}\%$ of microlensed stars host a snowline planet. Moreover, we find that Neptunes-mass planets are $\sim10$ times more common than Jupiter-mass planets. The companion-to-host mass ratio distribution shows a deficit at $q\sim10^{-2}$, separating the distribution into two companion populations, analogous to the stellar-companion and planet populations, seen in radial-velocity surveys around solar-like stars. Our survey, however, which probes mainly lower-mass stars, suggests a minimum in the distribution in the super-Jupiter mass range, and a relatively high occurrence of brown-dwarf companions.
description: 24 pages, 13 figures, 2 tables. 2016, MNRAS, 457, 4089
Semantic Learning Preregistration
Creators: name: Leshinskaya, Anna
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Social and Behavioral Sciences
subject: Cognitive Neuroscience
subject: Episodic Memory
subject: fMRI
subject: Learning
subject: MTG
subject: MTL
subject: Semantic Memory

description: Preregistration for research project entitled Semantic Learning, investigating neural mechanisms supporting relational learning and generalization from experience.
Responsible research and innovation training programs: implementation and evaluation
Creators: name: Tokalić, Ružica
name: Marusic, Ana
name: Buljan, Ivan
name: Mejlgaard, Niels
name: Revuelta, Gema
name: Lang, Alexander
name: Carrió, Mar
Publisher: name: Open Science Framework
Year: 2022

description: A Registry for Research on the Responsible Conduct of Research designed to enable researchers to share information on six key aspects of RCR research: Problem, Impact, Intervention, Hypothesis, Assessment and Data sharing.
Patient-Reported Roles, Preferences, and Expectations Regarding Treatment of Stage I Rectal Cancer in the Cancer Care Outcomes Research and Surveillance Consortium
Creators: name: Charlton, Mary E.
name: Stitzenberg, Karyn B.
name: Tyler Ellis,
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Historically, stage I rectal cancer was treated with total mesorectal excision. However, there has been growing use of local excision, with and without adjuvant therapy to treat these early rectal cancers. Little is known about how patients and providers choose amongst the various treatment approaches.
Automated Synchronization of Driving Data Using Vibration and Steering Events
Creators: name: Fridman, Lex
name: Brown, Daniel E
name: Angell, William
name: Abdić, Irman
name: Reimer, Bryan
name: Noh, Hae Young
Publisher: name: arXiv
Year: 2015
Subjects: subject: Robotics (cs.RO)
subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: FOS: Computer and information sciences

description: We propose a method for automated synchronization of vehicle sensors useful for the study of multi-modal driver behavior and for the design of advanced driver assistance systems. Multi-sensor decision fusion relies on synchronized data streams in (1) the offline supervised learning context and (2) the online prediction context. In practice, such data streams are often out of sync due to the absence of a real-time clock, use of multiple recording devices, or improper thread scheduling and data buffer management. Cross-correlation of accelerometer, telemetry, audio, and dense optical flow from three video sensors is used to achieve an average synchronization error of 13 milliseconds. The insight underlying the effectiveness of the proposed approach is that the described sensors capture overlapping aspects of vehicle vibrations and vehicle steering allowing the cross-correlation function to serve as a way to compute the delay shift in each sensor. Furthermore, we show the decrease in synchronization error as a function of the duration of the data stream.
description: Accepted for Publication in Elsevier Pattern Recognition Letters
Portfolio of EELISA Clusters
Creators: name: Gallerani, Simona
name: Giua, Claudia
name: Pucci, Barbara
name: Oddo, Calogero M.
name: Barsanti, Sara
name: Salgueiro, Isabel
name: Muñoz-Guijosa, Juan Manuel
name: Domokos Esztergár-Kiss
name: Gheorghe, Dana
name: Huber, Charlotte
name: Gamero, Roberto Martínez
name: Erden, Hamza Salih
name: Börte Köse Mutlu
name: Catalin Negru
Publisher: name: Zenodo
Year: 2023

description: In this document, the EELISA Alliance presents the first portfolio of EELISA Clusters (Deliverable 5.2). This document describes how Clusters are included in the EELISA InnoCORE strategy for the R&I dimension of the EELISA alliance, it provides their definition and explains their aim and purpose in the context of the EELISA InnoCORE project. The document further outlines the methodology used so far for identifying Clusters and how it will change when the EELISA InnoCORE Platform will be delivered. Connections between Clusters and EELISA communities, as well as links between EELISA Erasmus and EELISA InnoCORE projects are highlighted. We finally propose key performance indicators that allow us measuring the success of creating and putting in place Clusters.
description: This version of the document has not yet been approved by the European Commission.
Effects of preceding endoscopic mucosal resection on the efficacy and safety of radiofrequency ablation for treatment of Barrett's esophagus: results from the United States Radiofrequency Ablation Registry: Effect of prior EMR on RFA efficacy
Creators: name: Li,
name: Bulsiewicz,
name: Chang,
name: Corbett,
name: Shaheen,
name: Chmielewski,
name: Wolfsen,
name: Pasricha,
name: Komanduri,
name: Pruitt,
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: The effects of preceding endoscopic mucosal resection (EMR) on the efficacy and safety of radiofrequency ablation (RFA) for treatment of nodular Barrett’s esophagus (BE) is poorly understood. Prior studies have been limited to case series from individual tertiary care centers. We report the results of a large, multicenter registry. We assessed the effects of preceding EMR on the efficacy and safety of RFA for nodular BE with advanced neoplasia (high-grade dysplasia or intramucosal carcinoma) using the US RFA Registry, a nationwide study of BE patients treated with RFA at 148 institutions. Safety outcomes included stricture, gastrointestinal bleeding, and hospitalization. Efficacy outcomes included complete eradication of intestinal metaplasia (CEIM), complete eradication of dysplasia (CED), and number of RFA treatments needed to achieve CEIM. Analyses comparing patients with EMR before RFA to patients undergoing RFA alone were performed with Student’s t-test, Chi-square test, logistic regression, and Kaplan–Meier analysis. Four hundred six patients were treated with EMR before RFA for nodular BE, and 857 patients were treated with RFA only for non-nodular BE. The total complication rates were 8.4% in the EMR-before-RFA group and 7.2% in the RFA-only group (P = 0.48). Rates of stricture, bleeding, and hospitalization were not significantly different between patients treated with EMR before RFA and patients treated with RFA alone. CEIM was achieved in 84% of patients treated with EMR before RFA, and 84% of patients treated with RFA only (P = 0.96). CED was achieved in 94% and 92% of patients in EMR-before-RFA and RFA-only group, respectively (P = 0.17). Durability of eradication did not differ between the groups. EMR-before-RFA for nodular BE with advanced neoplasia is effective and safe. The preceding EMR neither diminished the efficacy nor increased complication rate of RFA treatment compared to patients with advanced neoplasia who had RFA with no preceding EMR. Preceding EMR is not associated with poorer outcomes in RFA.
Enhancement of Real Time EPICS IOC PV Management for Data Archiving System
Creators: name: Kim, Jae-ha
Publisher: name: arXiv
Year: 2015
Subjects: subject: Accelerator Physics (physics.acc-ph)
subject: FOS: Physical sciences

description: For operating a 100MeV linear proton accelerator, the major driving values and experimental data need to be archived. According to the experimental conditions, different data are required. It is necessary to implement functions that can add new data and delete data in real time. In an experimental physics and industrial control system (EPICS) input output controller (IOC), the process variable (PV) values are matched with the driving values and data. The PV values are archived in text file format using the Channel Archiver. There is no need to create a database (DB) server, just need a large hard disk. Through the web, the archived data can be loaded and new PV values can be archived without stopping the archive engine. Implementation of a Data Archiving System with Channel Archiver is presented and some preliminary results are reported.
description: 6 pages, 4 figures
Tuning Physical Properties of La0.7Sr0.3MnO3-δ via Oxygen Off-Stoichiometry Using Thermal Annealing and Ionic Liquid Gating
Creators: name: Yin, C.
name: Cao, L.
name: He, S.
name: Duchon, T.
name: Zhou, Y.
name: Brückel, T.
name: Petracic, O.
name: Fernandez Diaz, M.
Publisher: name: Forschungzentrum Jülich
Year: 2023

description: 13th Joint European Magnetic Symposia, JEMS, Faculty of Medicine in the main campus of Universidad Complutense de Madrid, Spain, 27 Aug 2023 - 1 Sep 2023
High rate of galactose-alpha-1,3-galactose sensitization in both eosinophilic esophagitis and patients undergoing upper endoscopy: Alpha-gal sensitization
Creators: name: Burk,
name: Beitia,
name: Dellon,
name: Lund,
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Eosinophilic esophagitis (EoE) is an antigen/allergy-mediated chronic inflammatory condition. The rapid rise in the number of cases of EoE suggests an as-yet discovered environmental trigger. This study tested the hypothesis that IgE to galactose-alpha-1,3-galactose (alpha-gal), a newly recognized sensitization induced by a tick bite that causes mammalian meat allergy, is a risk factor for eosinophilic esophagitis. We conducted a case-control study using prospectively collected and stored samples in the University of North Carolina EoE Patient Registry and Biobank. Serum from 50 subjects with a new diagnosis of EoE and 50 non-EoE subjects (either with gastroesophageal reflux disease or dysphagia from non-EoE etiologies) was tested for alpha-gal-specific IgE using an ImmunoCAP-based method. Specific IgE >0.35 kUA/L was considered a positive result. Subjects with EoE were a mean of 35 years old, 68% where male, and 94% were white. Non-EoE controls were a mean of 42 years, 50% were male, and 78% were white. A total of 22 (22%) subjects overall had alpha-gal-specific IgE >0.35 kUA/L. Of these, 12 (24%) were EoE cases and 10 (20%) were non-EoE controls (p=0.63). Neither the proportion sensitized nor the absolute values differed between EoE and non-EoE subjects. We found a similar but high rate of alpha-gal sensitization in patients with EoE as found in non-EoE controls who were undergoing endoscopy. While our data do not support alpha-gal sensitization as a risk factor for EoE, the high rates of sensitization observed in patients undergoing upper endoscopy for symptoms of esophageal dysfunction is a new finding.
Asymptotic Freedom in Quantum Antiferromagnet TlCuCl3
Creators: name: Scammell, Harley
name: Sushkov, Oleg
Publisher: name: arXiv
Year: 2015
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: Phase transitions in isotropic quantum antiferromagnets are described by an O(3) nonlinear quantum field theory. In three dimensions, the fundamental property of this theory is logarithmic scaling of the coupling constant. At the quantum critical point the coupling asymptotically vanishes and the quasiparticles become free. This logarithmic decay of the coupling constant has never been ob- served. In this paper, we derive finite temperature properties of the field theory and use our results to analyze the existing data on the real antiferromagnet TlCuCl3. Including finite temperatures into the theory, we find that agreement between theory and experiment is sufficiently sensitive to unambiguously identify the asymptotic decay of the coupling constant. We also comment on the unique possibility to study Landau pole-physics in quantum magnets.
An age-period-cohort analysis of obesity and incident esophageal adenocarcinoma among white males
Creators: name: Yang, Y. Claire
name: Sandler, Robert S.
name: Shaheen, Nicholas J.
name: Murphy, Caitlin C.
name: Hofstetter, Wayne L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: The incidence of esophageal adenocarcinoma (EAC) has increased in recent decades. Increases in incidence have been attributed to changes in the prevalence of risk factors for EAC; however, the extent to which these changes explain increases in EAC incidence has not been studied in detail. We used age-period-cohort analysis to estimate changes in the incidence of EAC among white males by age, time period, and birth cohort. Incidence rates per 100,000 individuals were analyzed from 1973 to 2012. Hierarchical Poisson models were used to estimate age, period, and cohort effects, whereby age-specific incidence rates were nested within periods and cohorts. The prevalence of obesity for each time period and birth cohort was included in the model as a fixed-effect. Incidence increased with advancing age (β = 0.12, P <0.01). There were significant period and birth cohort effects, although the period effect was much larger than the cohort effect. The period effect decreased dramatically when obesity was included as a fixed effect, while the small cohort effect remained unchanged. Results suggest much of the increase in the incidence of EAC can be attributed to a period effect, which may be due to changes in the prevalence of obesity over time.
Realizability Semantics for Quantified Modal Logic: Generalizing Flagg's 1985 Construction
Creators: name: Rin, Benjamin G.
name: Walsh, Sean
Publisher: name: arXiv
Year: 2015
Subjects: subject: Logic (math.LO)
subject: FOS: Mathematics
subject: 03B45, 03F55, 03B40

description: A semantics for quantified modal logic is presented that is based on Kleene's notion of realizability. This semantics generalizes Flagg's 1985 construction of a model of a modal version of Church's Thesis and first-order arithmetic. While the bulk of the paper is devoted to developing the details of the semantics, to illustrate the scope of this approach, we show that the construction produces (i) a model of a modal version of Church's Thesis and a variant of a modal set theory due to Goodman and Scedrov, (ii) a model of a modal version of Troelstra's generalized continuity principle together with a fragment of second-order arithmetic, and (iii) a model based on Scott's graph model (for the untyped lambda calculus) which witnesses the failure of the stability of non-identity.
description: Forthcoming in The Review of Symbolic Logic
Nonhomologous end joining of complex DNA double-strand breaks with proximal thymine glycol and interplay with base excision repair
Creators: name: Bafail, Duaa
name: Povirk, Lawrence F.
name: Akopiants, Konstantin
name: Ramsden, Dale A.
name: Yannone, Steven M.
name: Hartman, Matthew C.T.
name: Chalasani, Sri Lakshmi
name: Zhou, Tong
name: Almohaini, Mohammed
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: DNA double-strand breaks induced by ionizing radiation are often accompanied by ancillary oxidative base damage that may prevent or delay their repair. In order to better define the features that make some DSBs repair-resistant, XLF-dependent nonhomologous end joining of blunt-ended DSB substrates having the oxidatively modified nonplanar base thymine glycol at the first (Tg1), second (Tg2), third (Tg3) or fifth (Tg5) positions from one 3' terminus, was examined in human whole-cell extracts. Tg at the third position had little effect on end-joining even when present on both ends of the break. However, Tg as the terminal or penultimate base was a major barrier to end joining (>10-fold reduction in ligated products) and an absolute barrier when present at both ends. Dideoxy trapping of base excision repair intermediates indicated that Tg was excised from Tg1, Tg2 and Tg3 largely if not exclusively after DSB ligation. However, Tg was rapidly excised from the Tg5 substrate, resulting in a reduced level of DSB ligation, as well as slow concomitant resection of the opposite strand. Ligase reactions containing only purified Ku, XRCC4, ligase IV and XLF showed that ligation of Tg3 and Tg5 was efficient and only partially XLF-dependent, whereas ligation of Tg1 and Tg2 was inefficient and only detectable in the presence of XLF. Overall, the results suggest that promoting ligation of DSBs with proximal base damage may be an important function of XLF, but that Tg can still be a major impediment to repair, being relatively resistant to both trimming and ligation. Moreover, it appears that base excision repair of Tg can sometimes interfere with repair of DSBs that would otherwise be readily rejoined.
Assistive devices for SMA type 1: scoping review protocol
Creators: name: Livingstone, Roslyn
name: Paleg, Ginny
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Physiotherapy
subject: Occupational Therapy
subject: Medicine and Health Sciences
subject: Rehabilitation and Therapy
subject: Physical Therapy

description: Scoping review to map evidence supporting use of assistive devices and equipment to enhance participation, mobility, function and posture in lying, sitting and standing positions.
N-acetylglucosamine-phosphatidylinositol de-N-acetylase as a novel target for probing potential inhibitor against Leishmania donovani
Creators: name: Kumar, Mukesh
name: Tripathi, Manish Kumar
name: Gupta, Deepali
name: Kumar, Sanjit
name: Biswas, Nihar Ranjan
name: Ethayathulla, A. S.
name: Kaur, Punit
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences

description: Leishmania donavani is the causative agent of leishmaniasis, responsible for social and economic disruption, especially in developing countries. Lack of effective drugs with few side effects have necessitated the discovery of newer therapeutic solutions for leishmaniasis. Glycophosphatidylinositol (GPI) synthesis plays a vital role in protozoan cell membranes structural formation and antigenic modification. Hence, any disruption in its biosynthesis can prove fatal to the parasitic protozoans. N-acetylglucosamine-phosphatidylinositol de-N-acetylase (NAGP-deacetylase) is an enzyme from the GPI biosynthetic pathway that catalyzes the deacetylation of N-acetylglucosaminylphosphatidylinositol to glucosaminylphosphatidylinositol, a step essential for the proper functioning of the enzyme. In the quest for novel scaffolds as anti-leishmaniasis agents, we have executed in silico virtual screening, density function theory, molecular dynamics and MM-GBSA based energy calculations with a natural product library and a diverse library set from Chembridge database. Two compounds, 14671 and 4610, were identified at the enzyme's active site and interacted with catalytic residues, Asp43, Asp44, His41, His147, His 150, Arg80 and Arg231. Both molecules exhibited stable conformation in their protein-ligand complexes with binding free energies for compound-14671 and compound-4610 of −54 ± 4 and −50 ± 4 kcal/mol, respectively. These scaffolds can be incorporated in future synthetic determinations, focusing on developing druggable inhibitor support, increasing potency, and introducing species selectivity. Communicated by Ramaswamy H. Sarma
Direct numerical simulation of Taylor-Couette flow with grooved walls: torque scaling and flow structure
Creators: name: Zhu, Xiaojue
name: Mónico, Rodolfo Ostilla
name: Verzicco, Roberto
name: Lohse, Detlef
Publisher: name: arXiv
Year: 2015
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: We present direct numerical simulations of Taylor-Couette flow with grooved walls at a fixed radius ratio $η=r_i/r_o=0.714$ with inner cylinder Reynolds number up to $Re_i=3.76\times10^4$, corresponding to Taylor number up to $Ta=2.15\times10^9$. The grooves are axisymmetric V-shaped obstacles attached to the wall with a tip angle of $90^\circ$. Results are compared to the smooth wall case in order to investigate the effects of grooves on Taylor-Couette flow. We focus on the effective scaling laws for the torque, flow structures, and boundary layers. It is found that, when the groove height is smaller than the boundary layer thickness, the torque is the same as that of the smooth wall cases. With increasing $Ta$, the boundary layer thickness becomes smaller than the groove height. Plumes are ejected from the tips of the grooves and secondary circulations between the latter are formed. This is associated to a sharp increase of the torque and thus the effective scaling law for the torque vs. $Ta$ becomes much steeper. Further increasing $Ta$ does not result in an additional slope increase. Instead, the effective scaling law saturates to the "ultimate" regime effective exponents seen for smooth walls. It is found that even though after saturation the slope is the same as for the smooth wall case, the absolute value of torque is increased, and the more the larger size of the grooves.
description: Accepted by JFM, 27 pages, 23 figures
Regulation of human polλ by ATM-mediated phosphorylation during non-homologous end joining
Creators: name: Sastre-Moreno, Guillermo
name: Herrero-Ruiz, Andrés M.
name: Moreno-Oñate, Marta
name: Ramsden, Dale A.
name: Ruiz, Jose F.
name: Cortés-Ledesma, Felipe
name: Pryor, John M.
name: Blanco, Luis
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: DNA double strand breaks (DSBs) trigger a variety of cellular signaling processes, collectively termed the DNA-damage response (DDR), that are primarily regulated by protein kinase ataxia-telangiectasia mutated (ATM). Among DDR activated processes, the repair of DSBs by non-homologous end joining (NHEJ) is essential. The proper coordination of NHEJ factors is mainly achieved through phosphorylation by an ATM-related kinase, the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), although the molecular basis for this regulation has yet to be fully elucidated. In this study we identify the major NHEJ DNA polymerase, DNA polymerase lambda (Polλ), as a target for both ATM and DNA-PKcs in human cells. We show that Polλ is efficiently phosphorylated by DNA-PKcs in vitro and predominantly by ATM after DSB induction with ionizing radiation (IR) in vivo. We identify threonine 204 (T204) as a main target for ATM/DNA-PKcs phosphorylation on human Polλ, and establish that its phosphorylation may facilitate the repair of a subset of IR-induced DSBs and the efficient Polλ-mediated gap-filling during NHEJ. Molecular evidence suggests that Polλ phosphorylation might favor Polλ interaction with the DNA-PK complex at DSBs. Altogether, our work provides the first demonstration of how Polλ is regulated by phosphorylation to connect with the NHEJ core machinery during DSB repair in human cells.
Similarities and differences in dynamic symptom networks in individuals at different levels of risk for psychosis
Creators: name: van der Tuin, Sara
name: Groen, Robin
name: Castro-Alvarez, Sebastian
name: Oldehinkel, Albertine
name: Booij, Sanne
name: Wigman, Hanneke
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Social and Behavioral Sciences
subject: Psychology
subject: FOS: Psychology

description: Improving our understanding of how symptoms interact in early clinical stages that represent different levels of risk for psychosis may reveal important insights in underlying mechanisms in early illness development. When studying these dynamics, it is important to acknowledge the heterogeneity in the population. One way of doing so is by assessing the extent to which dynamics between symptoms reflect a universal, clinical stage-specific or person-specific process. To this end we aim to answer three research questions: Research question 1: which connections between daily reports of psychological symptoms and resilience are stage independent (i.e., are found at group-level), which connections are stage specific (i.e, are found at subgroup-level) and which reflect heterogeneity in the sample (i.e., are found at the individual-level) in a sample of individuals at different levels of risk for psychosis? Research question 2: To what extent are subgroups defined by the clinical staging model, with subgroup membership determined mostly on severity of psychotic symptomatology, similar to subgroups when subgroup membership is determined based on symptom dynamics (i.e. connections between symptoms)? Research question 3: This research question is conditional on the previous research question. If we find differences between the two approaches, we will explore if the subgroups that represent different symptom dynamics additionally differ on other factors like age, gender, psychopathology, well-being and social functioning.
Evidence of Ising pairing in superconducting NbSe$_2$ atomic layers
Creators: name: Xi, Xiaoxiang
name: Wang, Zefang
name: Zhao, Weiwei
name: Park, Ju-Hyun
name: Law, Kam Tuen
name: Berger, Helmuth
name: Forró, László
name: Shan, Jie
name: Mak, Kin Fai
Publisher: name: arXiv
Year: 2015
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Two-dimensional transition metal dichalcogenides with strong spin-orbit interactions and valley-dependent Berry curvature effects have attracted tremendous recent interests. Although novel single-particle and excitonic phenomena related to spin-valley coupling have been extensively studied, effects of spin-momentum locking on collective quantum phenomena remain unexplored. Here we report an observation of superconducting monolayer NbSe$_2$ with an in-plane upper critical field over six times of the Pauli paramagnetic limit by magneto-transport measurements. The effect can be understood in terms of the competing Zeeman effect and large intrinsic spin-orbit interactions in non-centrosymmetric NbSe$_2$ monolayers, where the electronic spin is locked to the out-of-plane direction. Our results provide a strong evidence of unconventional Ising pairing protected by spin-momentum locking and open up a new avenue for studies of non-centrosymmetric superconductivity with unique spin and valley degrees of freedom in the exact two-dimensional limit.
Discovery of new 1,4-disubstituted 1,2,3-triazoles: in silico ADME profiling, molecular docking and biological evaluation studies
Creators: name: Şahin, İrfan
name: Çeşme, Mustafa
name: Yüce, Neslihan
name: Tümer, Ferhan
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biochemistry
subject: Medicine
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer

description: In this work, eight new 1,2,3-triazoles (6a–h) were synthesized from acetylenes’ “click” reaction with p-substituted azide derivatives. The structures of the compounds were characterized using standard analytical and spectroscopic methods (elemental analysis, FT-IR, 1H(13C)NMR). The anticancer, antioxidant, α-amylase, ADME, molecular docking studies of synthesized triazoles were investigated. According to α -amylase enzyme inhibition results, all compounds except 6c (IC50: 2299 μg/mL) were found to have a higher IC50 value than the standard drug acarbose (IC50: 891 μg/mL). Compound 6g (IC50: 68 μg/mL) exhibited 13 times higher activity than standard acarbose. All compounds, except 6e, have been shown to have greater DPPH radical scavenging capabilities than BHT and β-carotene standards. According to ABTS radical scavenging studies, all compounds showed higher scavenging activity than ascorbic acid and Trolox. To determine the anticancer activity of the synthesized compounds, they were screened against the Hela cell line, and the results were compared with standard cisplatin (IC50: 16.30 μg/mL). Compound 6a (IC50: 49.03 μg/mL) was determined to have moderate activity relative to cisplatin. The compounds were examined comprehensively for ADME characteristics and did not violate any drug-likeness rule. ADME data showed that all physicochemical and pharmacological parameters of the compounds remained within defined limits as specified in Lipinski's rules (RO5) and put forth a high bioavailability profile. The molecular docking findings show that all molecules have a high affinity by exhibiting polar and apolar contact with essential residues in the binding pocket of α-amylase. Communicated by Ramaswamy H. Sarma
Locally conformally Berwald manifolds and compact quotients of reducible manifolds by homotheties
Creators: name: Matveev, Vladimir S.
name: Nikolayevsky, Yuri
Publisher: name: arXiv
Year: 2015
Subjects: subject: Differential Geometry (math.DG)
subject: FOS: Mathematics
subject: 53C60, 53C22, 53B40, 53C29

description: We study locally conformally Berwald metrics on closed manifolds which are not globally conformally Berwald. We prove that the characterization of such metrics is equivalent to characterizing incomplete, simply-connected, Riemannian manifolds with reducible holonomy group whose quotient by a group of homotheties is closed. We further prove a de Rham type splitting theorem which states that if such a manifold is analytic, it is isometric to the Riemannian product of a Euclidean space and an incomplete manifold.
description: 15 pages
A benzimidazole scaffold as a promising inhibitor against SARS-CoV-2
Creators: name: Mudi, Prafullya Kumar
name: Mahanty, Ayan Kumar
name: Kotakonda, Muddukrishnaiah
name: Prasad, Sunnapu
name: Bhattacharyya, Subires
name: Biswas, Bhaskar
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: The manuscript reports the green-chemical synthesis of a new diindole-substituted benzimidazole compound, B1 through a straightforward route in coupling between indolyl-3-carboxaldehyde and o-phenylenediamine in water medium under the aerobic condition at 75 ºC. The single crystal X-ray structural analysis of B1 suggests that the disubstituted benzimidazole compound crystallizes in a monoclinic system and the indole groups exist in a perpendicular fashion with respect to benzimidazole moiety. The SARS-CoV-2 screening activity has been studied against 1 × 10e4 VeroE6 cells in a dose-dependent manner following Hoechst 33342 and nucleocapsid staining activity with respect to remdesivir. The compound exhibits 92.4% cell viability for 30 h and 35.1% inhibition against VeroE6 cells at non-cytotoxic concentration. Molecular docking studies predict high binding propensities of B1 with the main protease (Mpro) and non-structural (nsp2 and nsp7-nsp8) proteins of SARS-CoV-2 through a number of non-covalent interactions. Molecular dynamics (MD) simulation analysis for 100 ns confirms the formation of stable conformations of B1-docked proteins with significant changes of binding energy, attributing the potential inhibition properties of the synthetic benzimidazole scaffold against SARS-CoV-2. Communicated by Ramaswamy H. Sarma
Optically controlled periodical chain of quantum rings
Creators: name: Hasan, M.
name: Iorsh, I. V.
name: Kibis, O. V.
name: Shelykh, I. A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We demonstrated theoretically that a circularly polarized electromagnetic field substantially modifies electronic properties of a periodical chain of quantum rings. Particularly, the field opens band gaps in the electron energy spectrum of the chain, generates edge electron currents and induces the Fano-like features in the electron transport through the finite chain. These effects create physical prerequisites for the development of optically controlled nanodevices based on a set of coupled quantum rings.
description: Published version
Leptogium milligranum Sierk 1964
Creators: name: Kitaura, Marcos J.
name: Bernardo, Caique M.
name: Koch, Natália M.
name: Rodrigues, Andressa S.
name: Torres, Jean-Marc
name: Barbosa, Thiago D.
name: Canêz, Luciana Da S.
name: Spielmann, Adriano A.
name: Honda, Neli K.
name: Fleig, Mariana
name: Lorenz, Aline P.
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Fungi
Ascomycota
Lecanoromycetes
Peltigerales
Collemataceae
Leptogium
Leptogium milligranum

description: Leptogium milligranum Sierk (1964: 290). (Figure 3C)
 Holotype:— USA. New Jersey: Pasadena, on bark, G.G. Nearing s/n (F!).
Description: Sierk (1964) and Kitaura (2012).
 Notes: Leptogium milligranum is characterized by the ridged thallus, covered by granular isidia. The isidia are darker than the thallus and coralloid.
Fertile specimens were not found in Mato Grosso do Sul, but, when present, the apothecia have thick proper exciple composed by paraplectenchymatous tissue and fusiform ascospores (Sierk 1964).
 Distribution in Brazil: First record to Mato Grosso do Sul state, but the species was recently reported to São Paulo (Kitaura et al. 2017).
 Examined material: BRAZIL. Mato Grosso do Sul: Aquidauana, Rodovia MS 450, on branch, 20°27’27.40”S 55°29’12.00” 188 m elev., 29 November 2014, S. R. Ramalho, F.M. R. Godoy, M.M. Morelli, P.P. Oliveira, A.A. Spielmann 44 (CGMS 47810); Campo Grande, Jardim Itatiaia, on cortex, 13 March 1991, I. Riquelme 0283 pr. min. p. (No. EQL 0454, CGMS); Vila da Base Aérea, on cortex, 19 June 1991, I. Riquelme 0288 pr. p. (No. EQL 0457, CGMS).
description: Published as part of Kitaura, Marcos J., Bernardo, Caique M., Koch, Natália M., Rodrigues, Andressa S., Torres, Jean-Marc, Barbosa, Thiago D., Canêz, Luciana Da S., Spielmann, Adriano A., Honda, Neli K., Fleig, Mariana & Lorenz, Aline P., 2019, Leptogium (Collemataceae, Peltigerales) from Mato Grosso do Sul state, Brazil: nine new records, three new taxa and a key for the species, pp. 127-146 in Phytotaxa 399 (2) on page 139, DOI: 10.11646/phytotaxa.399.2.3, http://zenodo.org/record/13714341
Synthesis, characterizations of aryl-substituted dithiodibenzothioate derivatives, and investigating their anti-Alzheimer's properties
Creators: name: Çalışır, Ümit
name: Camadan, Yasemin
name: Çiçek, Baki
name: Akkemik, Ebru
name: Eyüpoğlu, Volkan
name: Adem, Şevki
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Physiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer

description: The main objective of the present study was to synthesize potential inhibitor/activators of AChE and hCA I-II enzymes, which are thought to be directly related to Alzheimer's disease. Dithiodibenzothioate compounds were synthesized by thioesterification. Six different thiolate compounds produced were characterized by 1H-, 13C-NMR, FT-IR, LC-MS/MS methods. HOMO-LUMO calculations and electronic properties of all synthesized compounds were comprehensively illuminated with a semi-empirical molecular orbital (SEMO) package for organic and inorganic systems using Austin Model 1 (AM1)-Hamiltonian as implemented in the VAMP module of Materials Studio. In addition, the inhibition effects of these compounds for AChE and hCA I-II in vitro conditions were investigated. It was revealed that TE-1, TE-2, TE-3, TE-4, TE-5, and TE-6 compounds inhibited the AChE under in vitro conditions. TE-1 compound activated the enzyme hCA I while TE-2, TE-3 TE-4 compounds inhibited it. TE-5 and TE-6, on the other hand, did not exhibit a regular inhibition profile. Similarly, TE-1 activated the hCA II enzyme whereas TE-2, TE-3, TE-4, and TE-5 compounds inhibited it. TE-6 compound did not have a consistent inhibition profile for hCA II. Docking studies were performed with the compounds against AChE and hCA I-II receptors using induced-fit docking method. Molecular Dynamics (MD) simulations for best effective three protein-ligand couple were conducted to explore the binding affinity of the considered compounds in semi-real in-silico conditions. Along with the MD results, TE-1-based protein complexes were found more stable than TE-5. Based on these studies, TE-1 compound could be considered as a potential drug candidate for AD. Communicated by Ramaswamy H. Sarma
Genetic variation in FAAH is associated with cannabis use disorders in a young adult sample of Mexican Americans
Creators: name: Wilhelmsen, Kirk C.
name: Ehlers, Cindy L.
name: Melroy-Greif, Whitney E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Cannabis is a commonly used drug and studies have shown that a significant portion of the variation in cannabis use disorders (CUDs) is heritable. Five genes known to play a role in the endocannabinoid system and CUDs were examined in a community sample of young adult Mexican Americans (MAs): CNR1, MGLL, FAAH, DAGLA, and DAGLB.