cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Association between genetic polymorphisms of cadherin 23 and noise-induced hearing loss: a meta-analysis
Creators: name: Wu, Zhi-Dan
name: Lu, Jun-Qi
name: Du, Wen-Jing
name: Wu, Shan
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: Science Policy

description: NIHL is one of the most common occupational diseases induced by gene-environment interaction. The CDH23 gene is a candidate gene related to NIHL susceptibility. However, the relationship between CDH23 gene and NIHL is still inconclusive. To clarify the association between CDH23 gene and NIHL, a meta-analysis was performed. A search in MEDLINE, PubMed, Web of Science, EBSCO, China National Knowledge Infrastructure (CNKI), and Wanfang Data was implemented to collect data. Six studies were eventually included and all the subjects were Chinese. The results showed that rs1227051, rs1227049, and rs3752752 were not associated with NIHL susceptibility under five genetic models. But rs3802711 reduced the risk of NIHL under the recessive model, and the BB genotype and B allele of rs3802711 were significantly linked to NIHL under recessive, super-dominant, homozygote, and allele genetic models when stratified by the HWE result. Moreover, when not conform to HWE, the BB + AB genotypes and B allele of Exon7 in dominant, super-dominant, homozygote, and allele genetic model increased the risk of NIHL. CDH23 may be a potential gene marker for the prevention and early screening of NIHL in Chinese. Further large and well-designed studies are needed to confirm this association.
Local Guidance of Emerging Vessel Sprouts Requires Soluble Flt-1
Creators: name: Chappell, John C.
name: Bautch, Victoria L.
name: Ferrara, Napoleone
name: Taylor, Sarah M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Blood vessel networks form via sprouting of endothelial cells from parent vessels. Extrinsic cues guide sprouts once they leave the initiation site, but these cues are likely insufficient to regulate initial outward movement, and many embryonic vessel networks form in the absence of a strong extrinsic gradient. We hypothesized that nascent sprouts are guided by spatial cues produced along their own vessels, and that soluble Flt-1 (sFlt-1) participates in this guidance. Analysis of developing vessels with perturbed flt-1 function revealed mis-guided emerging sprouts, and transgenic sFlt-1 rescued sprout guidance parameters. sFlt-1 activity in endothelial cells immediately adjacent to the emerging sprout significantly improved local sprout guidance. Thus we propose that a vessel-intrinsic system initially guides emerging sprouts away from the parent vessel, utilizing spatially regulated expression of sFlt-1 in conjunction with exogenous VEGF. Local sprout guidance defects are predicted to contribute to vessel dysmorphogenesis during perturbed development and disease.
Scripts
Creators: name: Ruiz-Rizzo, Adriana L.
name: Polegre, Daniela Marrero
Publisher: name: Open Science Framework
Year: 2023
Subjects: subject: R
subject: Data analysis
subject: Correlations
subject: Descriptive statistics

description: R code used to describe and analyze the data of the manuscript Lower Visual Processing Speed Relates to Greater Subjective Cognitive Complaints in Community-Dwelling Healthy Older Adults by Marrero-Polegre et al.
title: Investigating the Pathology of Endometriosis through the use of Bioinformatics
Creators: name: Sajjad, Usman
Publisher: name: University of Liverpool Repository
Year: 2012

description: BACKGROUND Endometriosis is a common gynecological disease with unknown pathogenesis. There is a lack of clear understanding towards the pathogenesis and etiology of the disease, and as a result, a deficiency of effective treatment methods. Past theories and approaches have ignored interactions between genes on cellular level and how processes such as the immune system genetically can influence the development of the disease. HYPOTHESIS Bioinformatics, an evolving form of computational technology, can be used to systematically and methodically collate available information on gene expression and relevant transcription factors with aim of identifying the key players in the disease process. METHODS Genomic/Proteomic information was inputted into software programs such as Ingenuity IPA, GenEvestigator and Opossum. The software was able to produce network maps of biological pathways and meta-analysis plots of genes/proteins differentially expressed during endometriosis. Common regulatory transcription factors were subsequently identified for these up-regulated genes. Immunohistochemistry (IHC) work was conducted to validate and analyze the expressional pattern of FOXD3 in endometrial samples of 20 patients (n=20). The expression in 10 normal fertile control endometrial samples (n=10) was compared to 10 endometrial samples from women with active peritoneal endometriosis at two different stages of the menstrual cycle (proliferative phase and window of implantation). The same sets of samples were used to compare any changes in expression of Androgen receptors (AR) and Progesterone receptors (PR), based on findings we obtained from our bioinformatics work. RESULTS We found FOXD3 to be the most common transcription involved in endometriosis, controlling 16 out of 38 up-regulated genes. SPP1, PTGS2, IL-8, StAR and CXCR4 were found to be strongly up regulated in patients with endometriosis. The same pattern of up-regulation genes was seen in gastric cancer. AR and PR were seen to interact centrally with other genes/proteins in the Ingenuity IPA network map. From the IHC work, we found FOXD3 to be expressed in the luminal epithelium and glandular compartments of the normal proliferative endometrium. In patients with endometriosis, there was an increase in expression of FOXD3 in the luminal epithelium and glands of secretory endometrium. There was no significant difference between the expressional pattern of AR and PR in the endometrium of normal fertile control women and endometriosis patients. DISCUSSION We concluded FOXD3 to be a key player in the pathogenesis of endometriosis. The transcription factor was able to control up-regulated genes on a cellular level in various pathological processes, which contribute to the development of endometriosis. We propose future work is needed to extend the investigative measures of FOXD3 in the pathogenesis of endometriosis and elucidate how it can be a therapeutic target for treatment purposes in a clinical setting.
Nuclear Bodies: Random Aggregates of Sticky Proteins or Crucibles of Macromolecular Assembly?
Creators: name: Rajendra, T.K.
name: Matera, A. Gregory
name: Izaguire-Sierra, Mario
name: Praveen, Kavita
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: The principles of self-assembly and self-organization are major tenets of molecular and cellular biology. Governed by these principles, the eukaryotic nucleus is composed of numerous subdomains and compartments, collectively described as nuclear bodies. Emerging evidence reveals that associations within and between various nuclear bodies and genomic loci are dynamic and can change in response to cellular signals. This review will discuss recent progress in our understanding of how nuclear body components come together, what happens when they form, and what benefit these subcellular structures may provide to the tissues or organisms in which they are found.
Identification of potential inhibitors of HER2 targeting breast cancer—a structure-based drug design approach
Creators: name: Singh, Gagandeep
name: Al-Fahad, Dhurgham
name: Al-Zrkani, Mrtatha K.
name: Chaudhuri, Tapan K.
name: Soni, Hemant
name: Tandon, Smriti
name: Narasimhaji, Cheemalapati Venkata
name: Azam, Faizul
name: Patil, Rajesh
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biophysics
Biochemistry
Pharmacology
Biotechnology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Information Systems not elsewhere classified
Cancer

description: Breast cancer is one of the most prevalent and malignant cancers in women. Most breast cancer patients show overexpression of the HER2 protein. The current study focused on identifying potent inhibitors of HER2 using a structure-based drug design approach. Prefiltered compounds from the Drugbank and the ZINC database were docked on HER2 protein using the FlexX docking tool of LeadIT. The docking study identified the 12 best molecules that interacted strongly with the active site of HER2 and also fulfilled the ADMET parameters. The complexes of these compounds with HER2 were further subjected to molecular dynamics simulation using GROMACS 2021.4, followed by the end-state MMGBSA binding energy calculations. The RMSD analysis was conducted to study the conformational changes, which revealed stability throughout the 100 ns simulation period. The local flexibility and dynamics of the simulated ligand-protein complexes were studied using RMSF analysis. The values of the radius of gyration were computed to analyze the compactness of HER2. The MMGBSA analysis provided insights into the energetic aspects of the system. The compound DB15187 emerged as the most potent candidate, showing MMGBSA-computed binding energy of −63.60 ± 3.39 kcal/mol. The study could help develop targeted therapies for HER2-positive breast cancer. Communicated by Ramaswamy H. Sarma
title: Nuclear structure studies of 159Er up to high spin
Creators: name: Mohammed Mustafa, Mohammed
Publisher: name: University of Liverpool Repository
Year: 2013

description: In the current work a detailed spectroscopic investigations of the gamma-decays from the excited states of the rare-earth nucleus 159Er has been performed to study the structural properties up to possible ultrahigh spins. The nucleus of 159Er had been populated by the reaction 116Cd(48Ca,5n ) at beam energy of 215-MeV in an experiment at Argonne National Laboratory using the Gammashphere array. Following a hypercube analysis of the collected data, new rotational bands were observed and the previously reported bands were extended up to possible spin through observation of new gamma-ray transitions in coincidence with the existing sequences. Possible angular intensity-ratio, B(M1)/B(E2)-ratios, measurements have been performed to confirm the nature of previously observed transitions and to assign multipolarites of the new ones. The band structures are discussed within the framework of cranked shell model calculations, revealing a diverse range of quasiparticle configurations. At spins of around 50¯h, there is evidence for a change from dominant prolate collective motion in the yrast band and its signature partner to oblate non-collective structures via the mechanism of band termination. A possible strongly deformed triaxial band occurs at these high spins, which indicate collectivity beyond 50¯h. The high-spin structures of data are interpreted within the framework of cranked Nilsson-Strutinsky calculations.
Differential Regulation of Protrusion and Polarity by PI(3)K during Neutrophil Motility in Live Zebrafish
Creators: name: Huttenlocher, Anna
name: Wu, Yi I.
name: Hahn, Klaus M.
name: Cavnar, Peter J.
name: Yoo, Sa Kan
name: Deng, Qing
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Cell polarity is crucial for directed migration. Here we show that phosphoinositide 3-kinase (PI(3)K) mediates neutrophil migration in vivo by differentially regulating cell protrusion and polarity. The dynamics of PI(3)K products PI(3,4,5)P3-PI(3,4)P2 during neutrophil migration were visualized in living zebrafish, revealing that PI(3)K activation at the leading edge is critical for neutrophil motility in intact tissues. A genetically encoded photoactivatable Rac was used to demonstrate that localized activation of Rac is sufficient to direct migration with precise temporal and spatial control in vivo. Similar stimulation of PI(3)K-inhibited cells did not direct migration. Localized Rac activation rescued membrane protrusion but not anteroposterior polarization of F-actin dynamics of PI(3)K-inhibited cells. Uncoupling Rac-mediated protrusion and polarization suggests a paradigm of two-tiered PI(3)K-mediated regulation of cell motility. This work provides new insight into how cell signaling at the front and back of the cell is coordinated during polarized cell migration in intact tissues within a multicellular organism.
Energy gap for Yang-Mills connections, I: Four-dimensional closed Riemannian manifolds
Creators: name: Feehan, Paul M. M.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Differential Geometry (math.DG)
subject: Mathematical Physics (math-ph)
subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics
subject: FOS: Physical sciences
subject: Primary 58E15, 57R57, secondary 37D15, 58D27, 70S15, 81T13

description: We extend an $L^2$ energy gap result due independently to Min-Oo and Parker (1982) for Yang-Mills connections on principal $G$-bundles, $P$, over closed, connected, four-dimensional, oriented, smooth manifolds, $X$, from the case of positive Riemannian metrics to the more general case of good Riemannian metrics, including metrics that are generic and where the topologies of $P$ and $X$ obey certain mild conditions and the compact Lie group, $G$, is $\mathrm{SU}(2)$ or $\mathrm{SO}(3)$.
description: 24 pages, incorporating final galley proof corrections. Background and analytical results provided by arXiv:1409.1525v2; the proof of Proposition 34.14 from arXiv:1409.1525v2 is included by request
Indexes and Rankings for Indicators of Social Well-Being for U.S. Counties -- Statistical Supplement for Rural Development Research Report No. 10
Creators: name: Ross, Peggy J.
name: Bluestone, Herman
name: Hines, Fred K.
name: Ross, Peggy J.
name: Bluestone, Herman
name: Hines, Fred K.
Publisher: name: Unknown
Year: 1979
Subjects: subject: Community/Rural/Urban Development
subject: Financial Economics
subject: Health Economics and Policy
subject: Research Methods/ Statistical Methods
subject: Alienation
subject: Health
subject: Indexes (ratio)
subject: Population (statistics)
subject: Ranking
subject: Ratings
subject: Samples
subject: Socioeconomic status
subject: Sociology
subject: FOS: Sociology
subject: Statistical analysis

description: This Statistical supplement provides indexes of social well-being and rankings for 3,097 U.S. counties. This detailed information supplements research reported in RDRR-10 INDICATORS OF SOCIAL WELL-BEING FOR U.S. COUNTIES. In that study, Census and vital statistics data (circa 1970) were used to produce composite indicators of socioeconomic, health, and family status, and alienation. National patterns of these composites were depicted in U. S. county maps and through mean index scores of counties grouped by metro-nonmetro status and rural-urban orientation.
A PLCβ/PI3Kγ-GSK3 Signaling Pathway Regulates Cofilin Phosphatase Slingshot2 and Neutrophil Polarization and Chemotaxis
Creators: name: Sondek, John
name: Zhang, Yong
name: Li, Lin
name: Harden, T. Kendall
name: Tang, Wenwen
name: Xu, Wenwen
name: Sun, Le
name: Wu, Dianqing
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Neutrophils, in response to a chemoattractant gradient, undergo dynamic F actin remodeling, a process important for their directional migration or chemotaxis. However, signaling mechanisms for chemoattractants to regulate the process are incompletely understood. Here, we characterized chemoattractant-activated signaling mechanisms that regulate cofilin dephosphorylation and actin cytoskeleton reorganization and are critical for neutrophil polarization and chemotaxis. In neutrophils, chemoattractants induced phosphorylation and inhibition of GSK3 via both PLCβ-PKC and PI3Kγ-AKT pathways, leading to the attenuation of GSK3-mediated phosphorylation and inhibition of the cofilin phosphatase slingshot2 and an increase in dephosphorylated, active cofilin. The relative contribution of this GSK3-mediated pathway to neutrophil chemotaxis regulation depended on neutrophil polarity preset by integrin-induced polarization of PIP5K1C. Therefore, our study characterizes a signaling mechanism for chemoattractant-induced actin cytoskeleton remodeling and elucidates its context-dependent role in regulating neutrophil polarization and chemotaxis.
Ras Effector Switching Promotes Divergent Cell Fates in C. elegans Vulval Patterning
Creators: name: Zand, Tanya P.
name: Reiner, David J.
name: Der, Channing J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: The C. elegans vulva is patterned by epidermal growth factor (EGF) activation of Ras to control 1° fate, and 1° fate induces antagonistic Notch-dependent 2° fate. Furthermore, a spatial EGF gradient, in addition to inducing 1° fate, directly contributes to 2° fate via an unknown pathway. We find that in addition to its canonical effector, Raf, vulval Ras utilizes an exchange factor for the Ral small GTPase (RalGEF), such that Ras-RalGEF-Ral antagonizes Ras-Raf pro-1° fate activity. Consistent with its restricted expression pattern, Ral participates in EGF pro-2° activity. Thus, we have delineated a Ras effector-switching mechanism whereby position within the morphogen gradient dictates that Ras effector usage is switched to RalGEF from Raf to promote 2° instead of 1° fate. Our observations define the utility of Ras effector switching during normal development, and may provide a possible mechanistic basis for cell and cancer type differences in effector dependency and activation.
Conformal Field Theory, Tensor Categories and Operator Algebras
Creators: name: Kawahigashi, Yasuyuki
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mathematical Physics (math-ph)
subject: High Energy Physics - Theory (hep-th)
subject: Operator Algebras (math.OA)
subject: Quantum Algebra (math.QA)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: This is a set of lecture notes on the operator algebraic approach to 2-dimensional conformal field theory. Representation theoretic aspects and connections to vertex operator algebras are emphasized. No knowledge on operator algebras or quantum field theory is assumed.
description: Lectures notes, 66 pages: references and explanations added, typos fixed
Data
Creators: name: Ruiz-Rizzo, Adriana L.
name: Polegre, Daniela Marrero
Publisher: name: Open Science Framework
Year: 2023
Subjects: subject: Older adults
subject: Visual attention functions
subject: Neuropsychological tests
subject: Cognitive functions

description: Tabular data on which the results and conclusions of the manuscript Lower Visual Processing Speed Relates to Greater Subjective Cognitive Complaints in Community-Dwelling Healthy Older Adults by Marrero-Polegre et al. are based.
Solution structure of the N-terminal extension domain of a Schistosoma japonicum asparaginyl-tRNA synthetase
Creators: name: Peck, Yoshimi
name: Pickering, Darren
name: Mobli, Mehdi
name: Liddell, Michael J.
name: Wilson, David T.
name: Ruscher, Roland
name: Ryan, Stephanie
name: Buitrago, Geraldine
name: McHugh, Connor
name: Love, Nicholas C.
name: Pinlac, Theresa
name: Haertlein, Michael
name: Kron, Michael A.
name: Loukas, Alex
name: Daly, Norelle L.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Hematology
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Several secreted proteins from helminths (parasitic worms) have been shown to have immunomodulatory activities. Asparaginyl-tRNA synthetases are abundantly secreted in the filarial nematode Brugia malayi (BmAsnRS) and the parasitic flatworm Schistosoma japonicum (SjAsnRS), indicating a possible immune function. The suggestion is supported by BmAsnRS alleviating disease symptoms in a T-cell transfer mouse model of colitis. This immunomodulatory function is potentially related to an N-terminal extension domain present in eukaryotic AsnRS proteins but few structure/function studies have been done on this domain. Here we have determined the three-dimensional solution structure of the N-terminal extension domain of SjAsnRS. A protein containing the 114 N-terminal amino acids of SjAsnRS was recombinantly expressed with isotopic labelling to allow structure determination using 3D NMR spectroscopy, and analysis of dynamics using NMR relaxation experiments. Structural comparisons of the N-terminal extension domain of SjAsnRS with filarial and human homologues highlight a high degree of variability in the β-hairpin region of these eukaryotic N-AsnRS proteins, but similarities in the disorder of the C-terminal regions. Limitations in PrDOS-based intrinsically disordered region (IDR) model predictions were also evident in this comparison. Empirical structural data such as that presented in our study for N-SjAsnRS will enhance the prediction of sequence-homology based structure modelling and prediction of IDRs in the future. Communicated by Ramaswamy H. Sarma
Arl13b in Primary Cilia Regulates the Migration and Placement of Interneurons in the Developing Cerebral Cortex
Creators: name: Caspary, Tamara
name: Higginbotham, Holden
name: Bachleda, Amelia
name: Hirt, Joshua
name: Anton, E.S.
name: Cusack, Corey L.
name: Eom, Tae-Yeon
name: Gukassyan, Vladimir
name: Mariani, Laura E.
name: Lai, Cary
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Coordinated migration and placement of interneurons and projection neurons lead to functional connectivity in the cerebral cortex; defective neuronal migration and the resultant connectivity changes underlie the cognitive defects in a spectrum of neurological disorders. Here we show that primary cilia play a guiding role in the migration and placement of postmitotic interneurons in the developing cerebral cortex, and that this process requires the ciliary protein, Arl13b. Through live imaging of interneuronal cilia we show migrating interneurons display highly dynamic primary cilia and we correlate cilia dynamics with the interneuron’s migratory state. We demonstrate that the guidance cue receptors essential for interneuronal migration localize to interneuronal primary cilia, but their concentration and dynamics are altered in the absence of Arl13b. Expression of Arl13b variants known to cause Joubert syndrome induce defective interneuronal migration, suggesting that defects in cilia-dependent interneuron migration may underlie the neurological defects in Joubert syndrome patients.
Six2 and Wnt Regulate Self-Renewal and Commitment of Nephron Progenitors through Shared Gene Regulatory Networks
Creators: name: Park, Joo-Seop
name: Ma, Wenxiu
name: Chung, Eunah
name: McMahon, Andrew P.
name: Wong, Wing Hung
name: Valerius, M. Todd
name: O'Brien, Lori L.
name: Cheng, Jr-Gang
name: McMahon, Jill A.
name: Guo, Jin-Jin
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: A balance between Six2-dependent self-renewal and canonical Wnt signaling-directed commitment regulates mammalian nephrogenesis. Intersectional studies using chromatin immunoprecipitation and transcriptional profiling identified direct target genes shared by each pathway within nephron progenitors. Wnt4 and Fgf8 are essential for progenitor commitment; cis-regulatory modules flanking each gene are co-bound by Six2 and β-catenin, and dependent on conserved Lef/Tcf binding sites for activity. In vitro and in vivo analyses suggest that Six2 and Lef/Tcf factors form a regulatory complex that promotes progenitor maintenance while entry of β-catenin into this complex promotes nephrogenesis. Alternative transcriptional responses associated with Six2 and β-catenin co-binding events occur through non-Lef/Tcf DNA binding mechanisms highlighting the regulatory complexity downstream of Wnt signaling in the developing mammalian kidney.
Dynamics of a scalar field, with a double exponential potential, interacting with dark matter
Creators: name: Gupta, Vartika
name: Kabir, Rakesh
name: Mukherjee, Amitabha
name: Lohiya, Daksh
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We study the interaction between dark matter and dark energy, with dark energy described by a scalar field having a double exponential effective potential. We discover conditions under which such a scalar field driven solution is a late time attractor. We observe a realistic cosmological evolution which consists of sequential stages of dominance of radiation, matter and dark energy, respectively.
description: 10 pages, 2 figures; v2: few typo corrected; to be communicated to JCAP, comments welcome
Determining the ability for universal quantum computing: Testing controllability via dimensional expressivity
Creators: name: Gago-Encinas, Fernando
name: Hartung, Tobias
name: Reich, Daniel M.
name: Jansen, Karl
name: Koch, Christiane P.
Publisher: name: Deutsches Elektronen-Synchrotron, DESY, Hamburg
Year: 2023
Subjects: qubit
quantum device
unitarity
hybrid
scaling
quantum circuit

description: Operator controllability refers to the ability to implement an arbitrary unitary in SU(N) and is a prerequisite for universal quantum computing. Controllability tests can be used in the design of quantum devices to reduce the number of external controls. Their practical use is hampered, however, by the exponential scaling of their numerical effort with the number of qubits. Here, we devise a hybrid quantum-classical algorithm based on a parametrized quantum circuit. We show that controllability is linked to the number of independent parameters, which can be obtained by dimensional expressivity analysis. We exemplify the application of the algorithm to qubit arrays with nearest-neighbour couplings and local controls. Our work provides a systematic approach to the resource-efficient design of quantum chips.
title: Acoustic testing on engineering materials
Creators: name: Dong, Yishan
Publisher: name: The Open University
Year: 2023

description: This thesis provides the findings from a project to investigate if a mechanical property of a material can be defined through an acoustic recording method which would be conducted in a non-destructive testing manner. This project has found two successful acoustic recording methods to define viscosity in a fluid mixture, and surface roughness in a solid substrate. The dynamic viscosity of a fluid mixture is found to be defined by a steady-state sound recording when the fluid is contained within a conical flask and is stirred by a ferrous stirring device inside the fluid mixture which is induced to spin at a set rate. The sound is processed into the Frequency Domain for assessment and resonant frequencies are observed to change in amplitude for different fluid mixtures up to a ceiling viscosity threshold, thereby enabling the classification of fluid mixture by viscosity. The surface roughness of a solid substrate is classified through an impact sound recording when a solid nylon sphere contacts the substrate. The impact sound is processed using analysis of the decay constant which is the reduction of sound pressure level over time. It has been found that the decay constant varies in a predictable manner for aluminium substrates from 1 mm to 5 mm thickness when surface roughness is between 0.8 µm to 1.6 µm, thus facilitating material property definition through acoustic recording.
Bioinformatics and systems biology analysis revealed PMID26394986-Compound-10 as potential repurposable drug against covid-19
Creators: name: Nisar, Haseeb
name: Wajid, Bilal
name: Anwar, Faria
name: Ahmad, Ashfaq
name: Javaid, Anum
name: Attique, Syed Awais
name: Nisar, Wardah
name: Saeed, Amir
name: Shahid, Samiah
name: Sadaf, Saima
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: The global health pandemic known as COVID-19, which stems from the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a significant concern worldwide. Several treatment methods exist for COVID-19; however, there is an urgent demand for previously established drugs and vaccines to effectively combat the disease. Since, discovering new drugs poses a significant challenge, making the repurposing of existing drugs can potentially reduce time and costs compared to developing entirely new drugs from scratch. The objective of this study is to identify hub genes and associated repurposed drugs targeting them. We analyzed differentially expressed genes (DEGs) by analyzing RNA-seq transcriptomic datasets and integrated with genes associated with COVID-19 present in different databases. We detected 173 Covid-19 associated genes for the construction of a protein-protein interaction (PPI) network which resulted in the identification of the top 10 hub genes/proteins (STAT1, IRF7, MX1, IRF9, ISG15, OAS3, OAS2, OAS1, IRF3, and IRF1). Hub genes were subjected to GO functional and KEGG pathway enrichment analyses, which indicated some key roles and signaling pathways that were strongly related to SARS-CoV-2 infections. We conducted drug repurposing analysis using CMap, TTD, and DrugBank databases with these 10 hub genes, leading to the identification of Piceatannol, CKD-712, and PMID26394986-Compound-10 as top-ranked candidate drugs. Finally, drug–gene interactions analysis through molecular docking and validated via molecular dynamic simulation for 80 ns suggests PMID26394986-Compound-10 as the only potential drug. Our research demonstrates how in silico analysis might produce repurposing candidates to help respond faster to new disease outbreaks. Communicated by Ramaswamy H. Sarma
Sox2 in the Dermal Papilla Niche Controls Hair Growth by Fine-Tuning BMP Signaling in Differentiating Hair Shaft Progenitors
Creators: name: Zemla, Roland
name: Ma'ayan, Avi
name: Barros, Rita
name: Clavel, Carlos
name: Rendl, Michael
name: Nicolis, Silvia
name: Grisanti, Laura
name: Pevny, Larysa
name: Mazloom, Amin Reza
name: Sennett, Rachel
name: Rezza, Amelie
name: Cai, Chen-Leng
name: Cai, Xiaoqiang
name: Chung, Chi-Yeh
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: How dermal papilla (DP) niche cells regulate hair follicle progenitors to control hair growth remains unclear. Using Tbx18Cre to target embryonic DP precursors, we ablate the transcription factor Sox2 early and efficiently, resulting in diminished hair shaft outgrowth. We find that DP niche expression of Sox2 controls the migration rate of differentiating hair shaft progenitors. Transcriptional profiling of Sox2 null DPs reveals increased Bmp6 and decreased Bmp inhibitor Sostdc1, a direct Sox2 transcriptional target. Subsequently, we identify upregulated Bmp signaling in knockout hair shaft progenitors and demonstrate that Bmps inhibit cell migration, an effect that can be attenuated by Sostdc1. A shorter and Sox2-negative hair type lacks Sostdc1 in the DP and shows reduced migration and increased Bmp activity of hair shaft progenitors. Collectively, our data identify Sox2 as a key regulator of hair growth that controls progenitor migration by fine-tuning Bmp-mediated mesenchymal-epithelial crosstalk.
TGF-β Type II Receptor/MCP-5 Axis: At the Crossroad between Joint and Growth Plate Development
Creators: name: O'Rear, Lynda
name: Contaldo, Clara
name: Ozkan, Huseyin
name: Li, Tieshi
name: Longobardi, Lara
name: Spagnoli, Anna
name: Myers, Timothy J.
name: Li, Ying
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Despite its clinical significance, the mechanisms of joint morphogenesis are still elusive. Here, we show by combining laser-capture microdissection for RNA sampling with microarray analysis, that the setting in which joint-forming interzone cells develop is distinct from adjacent growth plate chondrocytes and is characterized by down-regulation of chemokines, such as monocyte-chemoattractant protein-5 (MCP-5). Using in-vivo, ex-vivo and in-vitro approaches, we showed that low levels of interzone-MCP-5 are essential for joint formation and contribute to proper growth plate organization. Mice lacking the TGF-β-type-II-receptor (TβRII) in their limbs (Tgfbr2Prx1KO), which lack joint development and fail chondrocyte hypertrophy, showed up-regulation of interzone-MCP-5. In-vivo and ex-vivo blockade of the sole MCP-5 receptor, CCR2, in Tgfbr2Prx1KO led to rescue of joint formation and growth plate maturation; while in control mice determined an acceleration of endochondral growth plate mineralization. Taken together, we characterized the TβRII/MCP-5 axis as an essential crossroad for joint development and endochondral growth.
A Common Set of DNA Regulatory Elements Shapes Drosophila Appendages
Creators: name: Lieb, Jason D.
name: McKay, Daniel J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Animals have body parts made of similar cell types located at different axial positions, such as limbs. The identity and distinct morphology of each structure is often specified by the activity of different "master regulator" transcription factors. Although similarities in gene expression have been observed between body parts made of similar cell types, how regulatory information in the genome is differentially utilized to create morphologically diverse structures in development is not known. Here, we use genome-wide open chromatin profiling to show that among the Drosophila appendages, the same DNA regulatory modules are accessible throughout the genome at a given stage of development, except at the loci encoding the master regulators themselves. In addition, open chromatin profiles change over developmental time, and these changes are coordinated between different appendages. We propose that master regulators create morphologically distinct structures by differentially influencing the function of the same set of DNA regulatory modules.
Thiadiazine thione derivatives as anti-leishmanial agents: synthesis, biological evaluation, structure activity relationship, ADMET, molecular docking and molecular dynamics simulation studies
Creators: name: Tamanna
name: Fu, Chaoping
name: Qadir, Meshil
name: Shah, Muhammad Ishaq Ali
name: Shtaiwi, Amneh
name: Khan, Rasool
name: Khan, Shafi Ullah
name: Htar, Thet Thet
name: Zada, Amir
name: Lodhi, Muhammad Arif
name: Ateeq, Muhammad
name: Ali, Arif
name: Naeem, Mohammad
name: Ibrahim, Mohammad
name: Khan, Sher Wali
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biochemistry
Physical Sciences not elsewhere classified
Medicine
Pharmacology
Environmental Sciences not elsewhere classified
Chemical Sciences not elsewhere classified
Science Policy
Biological Sciences not elsewhere classified

description: During last decades, 3,5-disubstituted-tetrahydro-2H-thiadiazine-2-thione scaffold remains the center of interest due to their ease of preparation, diverse range substituents at N-3 and N-5 positions, and profound biological activities. In the current study, a series of 3,5-disubstituted-tetrahydro-2H-thiadiazine-2-thiones were synthesized in good to excellent yield, and the structure of the compounds were confirmed by various spectroscopic techniques such as FTIR, 1H-NMR, 13C-NMR and Mass spectrometry, and finally evaluated against Leishmania major. Whereas, all the evaluated compounds (1-33), demonstrate potential leishmanicidal activities with IC50 values in the range of (1.30- 149.98 uM). Among the evaluated compounds such as 3, 4, 6, and 10 exhibited excellent leishmanicidal activities with IC50 values of (2.17 μM), (2.39 μM), (2.00 μM), and (1.39 μM), respectively even better than the standard amphotericin B (IC50 = 0.50) and pentamidine (IC50 = 7.52). In order to investigate binding interaction of the most active compounds, molecular docking study was conducted with Leishmania major. Further molecular dynamic simulation study was also carried out to assess the stability and correct binding of the most active compound 10, within active site of the Leishamania major. Likewise, the physiochemical properties, drug likeness, and ADMET of the most active compounds were investigated, it was found that none of the compounds violate Lipiniski’s rule of five, which show that this class of compounds had enough potential to be used as drug candidate in near future. Communicated by Ramaswamy H. Sarma
Nonlinearity and nonclassicality in a nanomechanical resonator
Creators: name: Teklu, Berihu
name: Ferraro, Alessandro
name: Paternostro, Mauro
name: Paris, Matteo G. A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We address quantitatively the relationship between the nonlinearity of a mechanical resonator and the nonclassicality of its ground state. In particular, we analyze the nonclassical properties of the nonlinear Duffing oscillator (being driven or not) as a paradigmatic example of a nonlinear nanomechanical resonator. We first discuss how to quantify the nonlinearity of this system and then show that the nonclassicality of the ground state, as measured by the volume occupied by the negative part of the Wigner function, monotonically increases with the nonlinearity in all the working regimes addressed in our study. Our results show quantitatively that nonlinearity is a resource to create nonclassical states in mechanical systems.
description: 6 pages; 7 figures; RevTeX4-1
title: Image classification : a study in age-related macular degeneration screening
Creators: name: Ahmad Hijazi, Mohd Hanafi
Publisher: name: University of Liverpool Repository
Year: 2013

description: This thesis presents research work conducted in the field of image mining. More specifically, the work is directed at the employment of image classification techniques to classify images where features of interest are very difficult to distinguish. In this context, three distinct approaches to image classification are proposed. The first is founded on a time series based image representation, whereby each image is defined in terms of histograms that in turn are presented as "time series" curves. A Case Based Reasoning (CBR) mechanism, coupled with a Time Series Analysis (TSA) technique, is then applied to classify new "unseen" images. The second proposed approach uses statistical parameters that are extracted from the images either directly or indirectly. These parameters are then represented in a tabular form from which a classifier can be built on. The third is founded on a tree based representation, whereby a hierarchical decomposition technique is proposed. The images are successively decomposed into smaller segments until each segment describes a uniform set of features. The resulting tree structures allow for the application of weighted frequent sub-graph mining to identify feature vectors representing each image. A standard classifier generator is then applied to this feature vector representation to produce the desired classifier. The presented evaluation, applied to all three approaches, is directed at the classification of retinal colour fundus images; the aim is to screen for an eye condition known as Age-related Macular Degeneration (AMD). Of all the approaches considered in this thesis, the tree based representation coupled with weighted frequent sub-graph mining produced the best performance. The evaluation also indicated that a sound foundation has been established for future potential AMD screening programmes.
A derivation (and quantification) of the third law of thermodynamics
Creators: name: Masanes, Lluis
name: Oppenheim, Jonathan
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: Quantum Gases (cond-mat.quant-gas)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: The third law of thermodynamics has a controversial past and a number of formulations due to Planck, Einstein, and Nernst. It's most accepted version, the unattainability principle, states that "any thermodynamic process cannot reach the temperature of absolute zero by a finite number of steps and within a finite time." Although formulated in 1912, there has been no general proof of the principle, and the only evidence we have for it is that particular cooling methods become less efficient as the temperature decreases. Here we provide the first derivation of a general unattainability principle, which applies to arbitrary cooling processes, even those exploiting the laws of quantum mechanics or involving an infinite-dimensional reservoir. We quantify the resources needed to cool a system to any particular temperature, and translate these resources into a minimal time or number of steps by considering the notion of a Thermal Machine which obeys similar restrictions to universal computers. We generally find that the obtainable temperature can scale as an inverse power of the cooling time. Our argument relies on the heat capacity of the bath being positive, and we show that if this is not the case then perfect cooling in finite time is in principle possible. Our results also clarify the connection between two versions of the third law (the Unattainability Principle and the Heat Theorem), and place ultimate bounds on the speed at which information can be erased.
description: Substantial improvement of the third law derivation, which now only relies on a single assumption: the positivity of the heat capacity. 7 pages+appendix, 2 figures
A Sequence in the Drosophila H3-H4 Promoter Triggers Histone Locus Body Assembly and Biosynthesis of Replication-Coupled Histone mRNAs
Creators: name: McDaniel, Stephen L.
name: Salzler, Harmony R.
name: Duronio, Robert J.
name: Tatomer, Deirdre C.
name: Malek, Pamela Y.
name: Marzluff, William F.
name: Orlando, Anna N.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Compartmentalization of RNA biosynthetic factors into nuclear bodies (NBs) is a ubiquitous feature of eukaryotic cells. How NBs initially assemble and ultimately affect gene expression remains unresolved. The histone locus body (HLB) contains factors necessary for replication-coupled histone mRNA transcription and processing and associates with histone gene clusters. Using a transgenic assay for ectopic Drosophila HLB assembly, we show that a sequence located between, and transcription from, the divergently transcribed H3-H4 genes nucleates HLB formation and activates other histone genes in the histone gene cluster. In the absence of transcription from the H3-H4 promoter, “proto-HLBs”, containing only a subset of HLB components, form and the adjacent histone H2a-H2b genes are not expressed. Proto-HLBs also transiently form in mutant embryos with the histone locus deleted. We conclude that HLB assembly occurs through a stepwise process involving stochastic interactions of individual components that localize to a specific sequence in the H3-H4 promoter.
International Forum on Quality and Safety in Healthcare. Session L1: A dynamic, interactive platform for assessing urban health services' accessibility and equity. Tuesday, May 16, 2023. 12:30 to 13:00. Bella Center, Copenhagen, Auditorium C1M3. Organized by the Institute of Healthcare Improvement and BMJ. Presented by Luis Gabriel Cuervo, Doctoral student, Universitat Autònoma de Barcelona.
Creators: name: CUERVO, Luis Gabriel
Publisher: name: figshare
Year: 2023
Subjects: Transport engineering
Cartography and digital mapping
Geospatial information systems and geospatial data modelling
Urban planning and health
Health and community services
Health services and systems not elsewhere classified
Health equity
Social determinants of health
Applications in health
Spatial data and applications
Public participation and community engagement
Strategic, metropolitan and regional planning

description: Presentation notes and handout used at session L1 on Tuesday, May 16, 2023. Bella Center, Copenhagen, Room C1M3, 12:30 - 13:00. https://internationalforum.bmj.com/handouts-copenhagen-2023
 Programme
 Speaker's biography
title: Investigating the genetic basis of pyrethroid resistance in two members of the Anopheles gambiae complex
Creators: name: Witzig, Claudia
Publisher: name: University of Liverpool Repository
Year: 2013

description: Chemical control of mosquito vectors, via indoor residual spraying or insecticide treated bed nets, is an integral component of malaria control strategies. Limited availability of insecticides licensed for public health and the rapid development of resistance in mosquito populations to these insecticides, in particular to some pyrethroids, may compromise vector control efforts. With the exception of mutations in the insecticide target sites, relatively little is known about the genetics of pyrethroid resistance in malaria vectors. In some populations candidate effector genes, e.g. cyp6p3 or cyp6m2 in An. gambiae s.s. from Akron, Benin, have been identified as being over expressed in resistant strains but the underlying mechanisms responsible for the increased expression remain unknown. In this study, a combination of quantitative PCR, genetic mapping and microarray tools were used to investigate the mechanisms responsible for pyrethroid resistance in two African major malaria vectors, Anopheles gambiae and An. arabiensis. The current work was unable to confirm an association of these known candidates in either a laboratory colony established from Akron or in recent field caught material. Therefore a genetic mapping approach was adopted using field collected mated females to generate F2 isofemale lines. A major QTL on chromosome 3R was identified which coincides with a genomic region previously implicated in pyrethroid resistance in East African populations. This is the first genetic mapping of insecticide resistance using natural out-bred populations of Anopheles and the advantages and limitations of this approach are discussed. In a second experiment, genetic loci involved in permethrin resistance in An. arabiensis were mapped by establishing genetic crosses between a permethrin resistant strain from Chad and a susceptible strain from Mozambique. A single QTL on chromosome 2R was identified in the F2 progeny that accounts for ~24% of the phenotypic variance. This QTL coincides with a large cluster of detoxification genes. Pyrethroid resistance is not associated with target-site mutations in this population. Finally, microarrays were used to identify genes differentially expressed between a backcross population, generated by crossing the F1 population from the resistant Chad strain and the susceptible Mozambique strain of An. arabiensis back to the parental resistant strain, with the susceptible strain. A number of candidate genes were identified, including the P450 genes cyp4h24 and cyp9j5, but neither of these were located within the boundaries of the QTL on 2R. These findings support the presence of metabolic resistance in this population and fine mapping of the identified QTL as well as further investigation of the microarray hits is warranted.