cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
A case-control collapsing analysis identifies epilepsy genes implicated in trio sequencing studies focused on de novo mutations
Creators: name: Zhu, Xiaolin
name: Padmanabhan, Raghavendra
name: Copeland, Brett
name: Bridgers, Joshua S.
name: Ren, Zhong
name: Kamalakaran, Sitharthan
name: O’Driscoll-Collins, Ailbhe
name: Berkovic, Samuel F.
name: Scheffer, Ingrid E.
name: Poduri, Annapurna
name: Mei, Davide
name: Guerrini, Renzo
name: Lowenstein, Daniel H.
name: Allen, Andrew S.
name: Heinzen, Erin L.
name: Goldstein, David B.
Publisher: name: Columbia University
Year: 2017
Subjects: subject: Epilepsy--Genetic aspects
subject: Mutation (Biology)
subject: Nucleotide sequence
subject: Genetics
subject: FOS: Biological sciences

description: Trio exome sequencing has been successful in identifying genes with de novo mutations (DNMs) causing epileptic encephalopathy (EE) and other neurodevelopmental disorders. Here, we evaluate how well a case-control collapsing analysis recovers genes causing dominant forms of EE originally implicated by DNM analysis. We performed a genome-wide search for an enrichment of "qualifying variants" in protein-coding genes in 488 unrelated cases compared to 12,151 unrelated controls. These "qualifying variants" were selected to be extremely rare variants predicted to functionally impact the protein to enrich for likely pathogenic variants. Despite modest sample size, three known EE genes (KCNT1, SCN2A, and STXBP1) achieved genome-wide significance (p<2.68×10−6). In addition, six of the 10 most significantly associated genes are known EE genes, and the majority of the known EE genes (17 out of 25) originally implicated in trio sequencing are nominally significant (p<0.05), a proportion significantly higher than the expected (Fisher’s exact p = 2.33×10−17). Our results indicate that a case-control collapsing analysis can identify several of the EE genes originally implicated in trio sequencing studies, and clearly show that additional genes would be implicated with larger sample sizes. The case-control analysis not only makes discovery easier and more economical in early onset disorders, particularly when large cohorts are available, but also supports the use of this approach to identify genes in diseases that present later in life when parents are not readily available.
Ultrasound speech training for Japanese adults learning English as a second language
Creators: name: Tsui, Haley May-Lai
Publisher: name: University of British Columbia
Year: 2012

description: Japanese adults learning English as a second language often have difficulty perceiving and producing English /l/ and /ɹ/ due to specific acoustic and articulatory characteristics of these speech sounds and their absence in Japanese phonology. The current study investigated the effectiveness of using two-dimensional tongue ultrasound to teach pronunciation of these sounds to six adult native Japanese speakers. Each participant had four 45-minute training sessions over a two-week period where visual feedback from ultrasound was used to support the teaching of lingual configurations for /l/ and /ɹ/ in a variety of vowel contexts and word positions. Speech samples from participants were taken prior to training and at a two-week follow-up session. All participants were rated by expert listeners as having more accurate productions of /l/ and /ɹ/ post-training, with the most accuracy seen in word-initial clusters and as word-initial segments. The lateral /l/ showed greater improvement than /ɹ/. Acoustic and visual analyses revealed frequencies and components of tongue positioning closer to native English speaker production in words perceived to be greatly improved between pre- and post-training productions. The effect of training on perception was exploratory and did not yield analyzable results. All participants gave very positive feedback regarding the use of ultrasound for speech training, as determined by a participant questionnaire. The results suggest that incorporating lingual ultrasound in speech training can be beneficial for Japanese adults learning English liquids.
Topological Change in Mean Convex Mean Curvature Flow
Creators: name: White, Brian
Publisher: name: arXiv
Year: 2011
Subjects: subject: Differential Geometry (math.DG)
subject: FOS: Mathematics
subject: 53C44

description: Consider the mean curvature flow of an (n+1)-dimensional, compact, mean convex region in Euclidean space (or, if n<7, in a Riemannian manifold). We prove that elements of the m-th homotopy group of the complementary region can die only if there is a shrinking S^k x R^(n-k) singularity for some k less than or equal to m. We also prove that for each m from 1 to n, there is a nonempty open set of compact, mean convex regions K in R^(n+1) with smooth boundary for which the resulting mean curvature flow has a shrinking S^m x R^(n-m) singularity.
description: 19 pages. This version includes a new section proving that certain kinds of mean curvature flow singularities persist under arbitrary small perturbations of the initial surface. Newest update (Oct 2013) fixes some bibliographic references
Computational Methods for Haplotype-aware De Novo Genome Assembly from Long Reads
Creators: name: Luo, Xiao
Publisher: name: Universität Bielefeld
Year: 2023
Subjects: subject: 570

description: Genomes of the same species usually show high diversity due to genetic variations. Most eukaryotes involve multiple copies of genomes, each of which is inherited from one of the ancestors. Whereas prokaryotes, such as virus and bacteria, are prone to form a collection of closely related strains which differ by small amounts of variants in the infected hosts or environment. Determining the DNA sequence of each genome copy and strain (together are called haplotype here), which is referred to as haplotype-aware genome assembly, plays a crucial role in genomics, medicine, and many other disciplines, because biological functionalities or phenotypic appearance can differ substantially across different haplotypes. Over the last few years, long-read sequencing technologies such as Pacific Biosciences and Oxford Nanopore Technologies, have greatly improved haplotype phasing and genome assembly because of the tremendous advantages in terms of read length. Nevertheless, the vast majority of existing long-read haplotype phasing or genome assembly tools rely on a pre-known high-quality reference as a backbone, or collapse homologous sequences into one consensus sequence, respectively, which introduces disturbing biases or fails to capture the haplotype diversity of heterogeneous genomes.

 In this dissertation, several novel computational approaches are proposed to haplotype-aware de novo genome assembly by only using long-read sequencing data, which are particularly applied in diploid genome, viral quasispecies, polyploid genome and metagenome, respectively. Briefly, these methods firstly perform haplotype-aware sequencing error correction using different strategies, and subsequently construct haplotype-aware sequence graphs to generate haplotype-specific assemblies, which together enable to avoid reference biases on one hand and preserve haplotype diversity on the other. Benchmarking experiments on simulated and real datasets of varying complexity and diversity demonstrate that these methods drastically outperforms other state-of-the-art tools in terms of various evaluation criteria related to genome assembly, especially haplotype completeness and accuracy. In addition, these approaches presented in the thesis have been implemented as easy-to-use open-source tools.
Additional file 3 of How many mosquito nets are needed to maintain universal coverage: an update
Creators: name: Koenker, Hannah
name: Yukich, Josh
name: Erskine, Marcy
name: Opoku, Robert
name: Sternberg, Eleanore
name: Kilian, Albert
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Biotechnology
classificationCode: 19999
subject: Mathematical Sciences not elsewhere classified
subject: Cancer
classificationCode: 110309
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Additional file 3: Frontier plots of Person-years of ITN access vs Total nets delivered.
Interaction of IL-6 and TNF-α contributes to endothelial dysfunction in type 2 diabetic mouse hearts
Creators: name: Lee, Jonghae
name: Lee, Sewon
name: Zhang, Hanrui
name: Hill, Michael A.
name: Zhang, Cuihua
name: Park, Yoonjung
Publisher: name: Columbia University
Year: 2017
Subjects: Vascular endothelium
Cytokines
Mice as laboratory animals
Cardiology

description: Objectives:
Inflammatory cytokines, such as tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6), are individually considered as important contributors to endothelial dysfunction in obesity and type 2 diabetes (T2D). However, their interactions in coronary arteriole endothelial dysfunction are uncertain. Therefore, this study aimed to determine the effects of TNF-α and IL-6 interactions on coronary endothelial dysfunction in experimental T2D.

Methods:
The studies used wild type (WT), diabetic mice (db/db), db/db null for TNF (dbTNF-/dbTNF-), and db/db mice treated with neutralizing antibody to IL-6 (anti-IL-6). Endothelium-dependent (acetylcholine [ACh], or luminal flow-induced shear stress) and endothelium-independent (sodium nitroprusside [SNP]) vasodilation of isolated and pressurized coronary arterioles were determined. Quantitative PCR, Western blot, and immunofluorescence staining were utilized for mechanistic studies.

Results:
Relative to WT, arteriolar dilation to both ACh and flow was attenuated in db/db mice and dbTNF-/dbTNF-. Treatment of dbTNF-/dbTNF- and db/db mice with anti-IL-6 improved arteriolar dilation compared to db/db mice. Immunofluorescence staining illustrated localization of IL-6 within the endothelial cells of coronary arterioles. In db/db mice, mRNA and protein expression of IL-6 and superoxide (O2-) production were higher, but reduced by anti-IL-6 treatment. Also, in db/db mice, mRNA and protein expression of TNF-α suppressed by the anti-IL-6 treatment and the reduced expression of mRNA and protein expression of IL-6 by the genetic deletion of TNF-α both supported a reciprocal regulation between TNF-α and IL-6. Superoxide dismutase 2 (SOD2) expression and phosphorylation of eNOS (p-eNOS/eNOS) were lower in db/db mice coronary arterioles and were restored in db/db+Anti-IL-6 and dbTNF-/dbTNF- mice.

Conclusion:
The interactions between TNF-α and IL-6 exacerbate oxidative stress and reduce phosphorylation of eNOS, thereby contributing to coronary endothelial dysfunction in T2D mice.
Magnetic charge and ordering in kagome spin ice
Creators: name: Chern, Gia-Wei
name: Tchernyshyov, Oleg
Publisher: name: arXiv
Year: 2011
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We present a numerical study of magnetic ordering in spin ice on kagome, a two-dimensional lattice of corner-sharing triangles. The magnet has six ground states and the ordering occurs in two stages, as one might expect for a six-state clock model. In spin ice with short-range interactions up to second neighbors, there is an intermediate critical phase separated from the paramagnetic and ordered phases by Kosterlitz-Thouless transitions. In dipolar spin ice, the intermediate phase has long-range order of staggered magnetic charges. The high and low-temperature phase transitions are of the Ising and 3-state Potts universality classes, respectively. Freeze-out of defects in the charge order produces a very large spin correlation length in the intermediate phase. As a result of that, the lower-temperature transition appears to be of the Kosterlitz-Thouless type.
description: 20 pages, 12 figures, accepted version with minor changes
Siphonophoridae Newport 1844
Creators: name: Wesener, Thomas
name: Moritz, Leif
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Diplopoda
Siphonophorida
Siphonophoridae

description: Family Siphonophoridae Newport, 1844 (35) Literature record. 4?, AMNH (Grimaldi et al. 2002). New records. 1 F, RO my130; 1?, RO my330; 1 F, BuB1030; 1 F, BuB2243; 1 F (broken), BuB644; 1? (broken), BuB73; 1?, BuB828; 1 F, BuB978; 1 F, BuB981; 1?, BuB984; 1?, BuB986; 1 F, BuB1143; 1 F, BuB1159; 1 F, BuB2963; 1 F, BuB2973; 1?, BuB2986;1 M, BuB2989; 1?, BuB2997; 1 M, BuB3006; 1 M, BuB3007; 1?, BuB3010; 1 M, BuB3034; 1?, BuB3047; 1 F, BuB3052;1 F, BuB3239; 1?, BuB3245; 2 F, BuB3261; 1 F, BuB3262; 1?, Wu F3149/Bu/CJW; 1?, Wu F3393/Bu/CJW. Identification. Members of the family Siphonophoridae can be easily identified based on the head characteristics (Enghoff et al. 2015): the antennae is straight, with large sensory pits on the antennomeres 5 and 6. The antennomere 2 is as long as the others.
description: Published as part of Wesener, Thomas & Moritz, Leif, 2018, Checklist of the Myriapoda in Cretaceous Burmese amber and a correction of the Myriapoda identified by Zhang (2017), pp. 1131-1140 in Check List 14 (6) on page 1134, DOI: 10.15560/14.6.1131
description: {"references": ["Grimaldi DA, Engel MS, Nascimbene PC (2002) Fossiliferous Cretaceous amber from Myanmar (Burma): its rediscovery, biotic diversity, and paleontological significance. American Museum Novitates 3361: 1 - 71.", "Enghoff H, Golovatch S, Short M, Stoev P, Wesener T (2015) Diplopoda - taxonomic overview. In: Minelli A (Ed.) Treatise on Zoology - Anatomy, Taxonomy, Biology. The Myriapoda, Vol. 2. Brill, Leiden, 363 - 453. https: // doi. org / 10.1163 / 9789004188273"]}
Natural Supersymmetry and b -> s gamma constraints
Creators: name: Ishiwata, Koji
name: Nagata, Natsumi
name: Yokozaki, Norimi
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We investigate constraints from the observed branching ratio for b -> s gamma and fine-tuning in the framework of natural supersymmetry. The natural supersymmetry requires the large trilinear coupling of the stop sector, light higgsinos (a small mu parameter) and light stops, in order to reduce the fine-tuning in the Higgs sector while avoiding the LEP constraint. It is found that in such a scenario 5% (10%) level of fine-tuning is inevitable due to the b -> s gamma constraint even if the messenger scale is as low as 10^5 GeV (10^4 GeV), provided that the gaugino masses satisfy the GUT relation.
description: 13 pages, 4 figures; version to be published in PLB
Siphonorhinidae Cook 1895
Creators: name: Wesener, Thomas
name: Moritz, Leif
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Diplopoda
Siphonophorida
Siphonorhinidae

description: Family Siphonorhinidae Cook, 1895 (12) New records. 1 M, BuB1086; 1 M, BuB997; 1 F, BuB1123; 1 F, BuB1150; 1 F, BuB1822; 1 F, BuB1838; 1 F, BuB1842; 1 F, BuB1845; 1?, BuB1851; 1?, BuB2979; 1 F, BuB3243; 1?, BuB3283. Identification. Members of the order Siphonorhinidae can be easily identified based on the head characteristics (Enghoff et al. 2015): the antennae is elbowed, the antennomere 2 is twice as long as antennomere 3, lacking any large sensory pits.
description: Published as part of Wesener, Thomas & Moritz, Leif, 2018, Checklist of the Myriapoda in Cretaceous Burmese amber and a correction of the Myriapoda identified by Zhang (2017), pp. 1131-1140 in Check List 14 (6) on page 1134, DOI: 10.15560/14.6.1131
description: {"references": ["Enghoff H, Golovatch S, Short M, Stoev P, Wesener T (2015) Diplopoda - taxonomic overview. In: Minelli A (Ed.) Treatise on Zoology - Anatomy, Taxonomy, Biology. The Myriapoda, Vol. 2. Brill, Leiden, 363 - 453. https: // doi. org / 10.1163 / 9789004188273"]}
Additional file 1 of Priorities in Chronic nonbacterial osteomyelitis (CNO) – results from an international survey and roundtable discussions
Creators: name: Mohanna, M.
name: Roberts, E.
name: Whitty, L.
name: Gritzfeld, J. F.
name: Pain, C. E.
name: Girschick, H. J.
name: Preston, J.
name: Hadjittofi, M.
name: Anderson, C.
name: Ferguson, P. J.
name: Theos, A.
name: Hedrich, C. M.
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Cell Biology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Science Policy
classificationCode: 111714
subject: Mental Health
subject: Hematology
classificationCode: 110309
subject: Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1.
Additional file 1 of Aligned nanofibrous collagen membranes from fish swim bladder as a tough and acid-resistant suture for pH-regulated stomach perforation and tendon rupture
Creators: name: Luan, Zhaohui
name: Liu, Shuang
name: Wang, Wei
name: Xu, Kaige
name: Ye, Shaosong
name: Dan, Ruijue
name: Zhang, Hong
name: Shu, Zhenzhen
name: Wang, Tongchuan
name: Fan, Chaoqiang
name: Xing, Malcolm
name: Yang, Shiming
Publisher: name: figshare
Year: 2022
Subjects: subject: Biophysics
subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Pharmacology
subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1: Supplementary Fig. S1. PGA with highly complex structure under SEM. Supplementary Fig. S2. Two other crosslinking methods. Supplementary Fig. S3. The detailed process of fabricating DCDS suture with standardization. Supplementary Fig. S4. The tensile strength of double-layers swim bladder with and without crosslinking.
Sexual assault incidents among college undergraduates: Prevalence and factors associated with risk
Creators: name: Mellins, Claude
name: Walsh, Kate
name: Sarvet, Aaron L.
name: Wall, Melanie M.
name: Gilbert, Louisa
name: Santelli, John S.
name: Thompson, Martie
name: Wilson, Patrick A.
name: Khan, Shamus
name: Benson, Stephanie
name: Bah, Karimata
name: Kaufman, Kathy A.
name: Reardon, Leigh J.
name: Hirsch, Jennifer S.
Publisher: name: Columbia University
Year: 2017
Subjects: College students--Health and hygiene
Sexual harassment in universities and colleges
Rape in universities and colleges
Epidemiology
Social surveys

description: Sexual assault on college campuses is a public health issue. However varying research methodologies (e.g., different sexual assault definitions, measures, assessment timeframes) and low response rates hamper efforts to define the scope of the problem. To illuminate the complexity of campus sexual assault, we collected survey data from a large population-based random sample of undergraduate students from Columbia University and Barnard College in New York City, using evidence based methods to maximize response rates and sample representativeness, and behaviorally specific measures of sexual assault to accurately capture victimization rates. This paper focuses on student experiences of different types of sexual assault victimization, as well as sociodemographic, social, and risk environment correlates. Descriptive statistics, chi-square tests, and logistic regression were used to estimate prevalences and test associations. Since college entry, 22% of students reported experiencing at least one incident of sexual assault (defined as sexualized touching, attempted penetration [oral, anal, vaginal, other], or completed penetration). Women and gender nonconforming students reported the highest rates (28% and 38%, respectively), although men also reported sexual assault (12.5%). Across types of assault and gender groups, incapacitation due to alcohol and drug use and/or other factors was the perpetration method reported most frequently (> 50%); physical force (particularly for completed penetration in women) and verbal coercion were also commonly reported. Factors associated with increased risk for sexual assault included non-heterosexual identity, difficulty paying for basic necessities, fraternity/sorority membership, participation in more casual sexual encounters (“hook ups”) vs. exclusive/monogamous or no sexual relationships, binge drinking, and experiencing sexual assault before college. High rates of re-victimization during college were reported across gender groups. Our study is consistent with prevalence findings previously reported. Variation in types of assault and methods of perpetration experienced across gender groups highlight the need to develop prevention strategies tailored to specific risk groups.
The growth index of matter perturbations and modified gravity
Creators: name: Basilakos, Spyros
name: Pouri, Athina
Publisher: name: arXiv
Year: 2012
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We place tight constraints on the growth index $γ$ by using the recent growth history results of 2dFGRS, SDSS-LRG, VIMOS-VLT deep Survey (VVDS) and {\em WiggleZ} datasets. In particular, we investigate several parametrizations of the growth index $γ(z)$, by comparing their cosmological evolution using observational growth rate data at different redshifts. Utilizing a standard likelihood analysis we find that the use of the combined growth data provided by the 2dFGRS, SDSS-LRG, VVDS and {\em WiggleZ} galaxy surveys, puts the most stringent constraints on the value of the growth index. As an example, assuming a constant growth index we obtain that $γ=0.602\pm 0.055$ for the concordance $Λ$CDM expansion model. Concerning the Dvali-Gabadadze-Porrati gravity model, we find $γ=0.503\pm 0.06$ which is lower, and almost $3σ$ away, from the theoretically predicted value of $γ_{DGP}\simeq 11/16$. Finally, based on a time varying growth index we also confirm that the combined growth data disfavor the DGP gravity.
description: 8 pages, 5 figures. Revised version accepted in MNRAS. arXiv admin note: text overlap with arXiv:1202.1637
Труды Кольского научного центра РАН, Выпуск 92018
Creators: name: Кольский научный центр Российской академии наук
Publisher: name: Труды Кольского научного центра РАН
Year: 2018

description: , Выпуск 92018
description: В 2010-м году президиум КНЦ РАН принял решение о возвращении к уже имевшейся в предыдущие годы практике издания «Трудов Кольского научного центра РАН» в виде специализированных тематических научных журналов по основным направлениям научно-исследовательской деятельности учреждений Центра.
Siphonotidae Cook 1895
Creators: name: Wesener, Thomas
name: Moritz, Leif
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Diplopoda
Polyzoniida
Siphonotidae

description: Family Siphonotidae Cook, 1895 (67) New records. 1?, BuB612; 1 F, BuB825; 1 F, BuB837; 1 F, BuB817; 1 F, BuB824; 1 F, BuB831; 1 F, BuB826;; 1 F, BuB836; 1 F, BuB840; 1 F, BuB925; 1 F, BuB979; 1 F, BuB1130; 1 F, BuB1034; 1 F, BuB1087;1 F, BuB1161; 3?, BuB1162; 1 F, BuB1163; 1 F, BuB1164; 1 F, BuB1166; 1 F, BuB1167; 1 F, BuB1834; 2 F, BuB1837; 1 F, BuB1853; 1 F, BuB1854; 1 F, BuB1855; 2 F, BuB1856; 1 F, BuB1956; 1 F, BuB1966; 1 F, BuB1972; 1 F, BuB1976; 1 F, BuB1983; 2?, BuB1984; 1 F, BuB1993; 1 F, BuB2607; 1 F, BuB2608; 1 F, BuB2609; 1 F, BuB2610; 1 F, BuB2611; 1?, BuB2615; 1?, BuB2656; 1?, BuB2657; 1 F, BuB3266; 1 F, BuB3268; 1 F, BUB3270; 2 F, BuB3272; 1 F; BuB3273; 1 juv., BuB3280; 5 F, BuB3281; 5 F, BuB3284; 1 F, ZFMK MYR06122; 1 F, ZFMK MYR06124; 1 F, ZFMK MYR07374; 1 F, ZFMK MYR07381. Figure 1D Identification. Members of the Siphonotidae have the following characters (Enghoff et al. 2015): the posterior tergal margins is “normal”, not upturned. The telson is surrounding the anal valves in ventral view. The head is free, not covered by the first tergite. The leg claws carry a paronychium.
description: Published as part of Wesener, Thomas & Moritz, Leif, 2018, Checklist of the Myriapoda in Cretaceous Burmese amber and a correction of the Myriapoda identified by Zhang (2017), pp. 1131-1140 in Check List 14 (6) on page 1134, DOI: 10.15560/14.6.1131
description: {"references": ["Enghoff H, Golovatch S, Short M, Stoev P, Wesener T (2015) Diplopoda - taxonomic overview. In: Minelli A (Ed.) Treatise on Zoology - Anatomy, Taxonomy, Biology. The Myriapoda, Vol. 2. Brill, Leiden, 363 - 453. https: // doi. org / 10.1163 / 9789004188273"]}
Additional file 2 of Genetic diversity and genetic relatedness in Plasmodium falciparum parasite population in individuals with uncomplicated malaria based on microsatellite typing in Eastern and Western regions of Uganda, 2019–2020
Creators: name: Bosco, Agaba B.
name: Anderson, Karen
name: Gresty, Karryn
name: Prosser, Christiane
name: Smith, David
name: Nankabirwa, Joaniter I.
name: Nsobya, Sam
name: Yeka, Adoke
name: Namubiru, Rhoda
name: Arinaitwe, Emmanuel
name: Mbaka, Paul
name: Kissa, John
name: Lim, Chae Seung
name: Karamagi, Charles
name: Nakayaga, Joan K.
name: Kamya, Moses R.
name: Cheng, Qin
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2: Table S2. Sequence length and unique sequence type of pfhrp2 exon 2.
Uniform description of bulk observables in the hydrokinetic model of A+A collisions at RHIC and LHC
Creators: name: Karpenko, Iu. A.
name: Sinyukov, Yu. M.
name: Werner, K.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Nuclear Theory (nucl-th)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: A simultaneous description of hadronic yields; pion, kaon, and proton spectra; elliptic flows; and femtoscopy scales in the hydrokinetic model of A+A collisions is presented at different centralities for the top BNL Relativistic Heavy Ion Collider (RHIC) and CERN Large Hadron Collider (LHC) 2.76-TeV energies. The initial conditions are based on the Glauber Monte-Carlo simulations. When going from RHIC to LHC energy in the model, the only parameters changed are the normalization of the initial entropy defined by the number of all charged particles in most central collisions, contribution to entropy from binary collisions and baryonic chemical potential. The hydrokinetic model is used in its hybrid version (hHKM), which provides the correct match (at the isochronic hypersurface) of the decaying hadron matter evolution with hadronic ultrarelativistic quantum molecular dynamics cascade. The results are compared with the standard hybrid models where hydrodynamics and hadronic cascade are matching just at the non-space-like hypersurface of chemical freeze-out or on the isochronic hypersurface. The modification of the particle number ratios at LHC caused, in particular, by the particle annihilations at the afterburn stage is also analyzed.
description: 14 pages, 7 figures. Version accepted for publication in Phys.Rev. C
APOE Genotype Influences Functional Status among Elderly without Dementia
Creators: name: Albert, Steven M.
name: Gurland, Barry J.
name: Maestre, Gladys
name: Jacobs, Diane
name: Stern, Yaakov
name: Mayeux, Richard Paul
Publisher: name: Columbia University
Year: 1995
Subjects: Medical genetics
Apolipoprotein E
Cognition--Age factors
Aging

description: The presence of apolipoprotein-ϵ4 (APOE-ϵ4) significantly increases the risk of Alzheimer's disease (AD). The association between APOE-ϵ4 status and functional abilities was explored further in a multicultural sample of community-dwelling, non-demented elders. The sample was limited to cognitively-intact, community-dwelling elders, who were free of stroke or other neurologic disability. In 218 elders who met research criteria, the presence of APO-ϵ4 was associated with poorer functional status, apart from the effects of neuropsychological performance, gender, age, and education (OR = 2.5, 95% CI: 1.3, 4.9). In 158 subjects without an APOE-ϵ4 allele, 50% reported no functional limitation; in the 60 subjects with an ϵ4 allele, only 28% reported no functional limitation (P < .01). The relationship was not explained by the distribution of co-morbidities. The association between poorer function and the presence of an APOE-ϵ4 allele was evident in each ethnic group. In path analyses, the presence of an APOE-ϵ4 allele was associated with decreased functional ability in non-demented elders not simply through an association with poorer cognitive status, but also independently. These results suggest that the APOE-ϵ4 genotype is associated with functional deficit in people with normal neuropsychological profiles.
Reconstructing Seesaws
Creators: name: Davidson, Sacha
name: Elmer, Martin
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We explore some aspects of "reconstructing" the heavy singlet sector of supersymmetric type I seesaw models, for two, three or four singlets. We work in the limit where one light neutrino is massless. In an ideal world, where selected coefficients of the TeV-scale effective Lagrangian could be measured with arbitrary accuracy, the two-singlet case can be reconstructed, two three or more singlets can be differentiated, and an inverse seesaw with four singlets can be reconstructed. In a more realistic world, we estimate $\ell_\a \to \ell_\b γ$ expectations with a "Minimal-Flavour-Violation-like" ansatz, which gives a relation between ratios of the three branching ratios. The two singlet model predicts a discrete set of ratios.
description: 14 pages
Additional file 1 of The expression profiles and prognostic values of HSP70s in hepatocellular carcinoma
Creators: name: Wang, Ben
name: Lan, Tian
name: Xiao, Han
name: Chen, Zhong-Huo
name: Wei, Chao
name: Chen, Lei-Feng
name: Guan, Jia-Fu
name: Yuan, Rong-Fa
name: Yu, Xin
name: Hu, Zhi-Gang
name: Wu, Hua-Jun
name: Dai, Zhi
name: Wang, Kai
Publisher: name: figshare
Year: 2021
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer

description: Additional file 1: Table S1. The specific primers used for PCR amplification.
Unifying model of driven polymer translocation
Creators: name: Ikonen, Timo
name: Bhattacharya, Aniket
name: Ala-Nissila, Tapio
name: Sung, Wokyung
Publisher: name: arXiv
Year: 2011
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Biological Physics (physics.bio-ph)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: We present a Brownian dynamics model of driven polymer translocation, in which non-equilibrium memory effects arising from tension propagation (TP) along the cis side subchain are incorporated as a time-dependent friction. To solve the effective friction, we develop a finite chain length TP formalism, expanding on the work of Sakaue [Sakaue, PRE 76, 021803 (2007)]. The model, solved numerically, yields results in excellent agreement with molecular dynamics simulations in a wide range of parameters. Our results show that non-equilibrium TP along the cis side subchain dominates the dynamics of driven translocation. In addition, the model explains the different scaling of translocation time w.r.t chain length observed both in experiments and simulations as a combined effect of finite chain length and pore-polymer interactions.
description: 7 pages, 3 figures
Participation in Clinical Trials and Long-Term Outcomes in Alzheimer's Disease
Creators: name: Albert, Steven M.
name: Sano, Mary
name: Marder, Karen
name: Jacobs, Diane
name: Brandt, Jason
name: Albert, Marilyn
name: Stern, Yaakov
Publisher: name: Columbia University
Year: 1997
Subjects: Neurology
Alzheimer's disease--Patients
Clinical trials--Evaluation
Dementia

description: The objective of this study was to determine whether participation in clinical trials affects long-term outcomes in Alzheimer's disease (AD). Participation in clinical trials for persons with dementia is often justified on the grounds that patients benefit from the medical oversight typical of trials, even when experimental agents do not demonstrate short-term benefits. This claim has not been rigorously assessed. Of 215 community-resident subjects enrolled in a prospective study of outcomes in AD, 101 participated in randomized clinical trials (RCTs) during the first 2 years of follow-up. These subjects were compared with subjects who met eligibility requirements for RCTs but did not participate (N = 57) and with subjects who were ineligible (N = 57), over a total of 3.5 years of follow-up. Survival analyses assessed risk of death, nursing home placement, and incident functional deficit end points, adjusting for baseline differences. Subjects who participated in RCTs were younger and more highly educated. Mortality, risk of hospitalization, number of medical examinations conducted by study physicians, and onset of severe functional deficit did not differ between the groups, but risk of nursing home admission was significantly lower among RCT participants compared with eligible nonparticipants and ineligible subjects (16.8% versus 36.8% and 31.6%, respectively [p = 0.01]). The difference in risk of nursing home placement may represent a long-term, drug-related benefit to patients, a selection effect (caregivers of patients who participate in RCTs differ from caregivers of patients who do not), or a positive effect on caregivers (greater contact with a medical service may be associated with better care-giving outcomes). Further research is required to assess these effects.
Letter from Jose Melena to Emmett L. Bennett Jr., November 19, 1977
Creators: name: Melena, Jose
Publisher: name: The University of Texas at Austin
Year: 1977
Subjects: Emmett L. Bennett, Jr. Collection
Emmett L. Bennett, Jr. Collection--Correspondence
Emmett L. Bennett, Jr. Collection--Correspondence--Jose Melena
Spanish Universities
Greek Linguistics
employment

description: Melena asks Bennett of openings for Mycenologists in the United States as he observes employment is difficult in Spain as one.
A class of exposed indecomposable positive maps
Creators: name: Sarbicki, Gniewomir
name: Chruściński, Dariusz
Publisher: name: arXiv
Year: 2012
Subjects: subject: Quantum Physics (quant-ph)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: Exposed positive maps in matrix algebras define a dense subset of extremal maps. We provide a class of indecomposable positive maps in the algebra of 2n x 2n complex matrices with n>1. It is shown that these maps are exposed and hence define the strongest tool in entanglement theory to discriminate between separable and entangled states.
description: 15 pages; slightly improved version
Additional file 2 of Priorities in Chronic nonbacterial osteomyelitis (CNO) – results from an international survey and roundtable discussions
Creators: name: Mohanna, M.
name: Roberts, E.
name: Whitty, L.
name: Gritzfeld, J. F.
name: Pain, C. E.
name: Girschick, H. J.
name: Preston, J.
name: Hadjittofi, M.
name: Anderson, C.
name: Ferguson, P. J.
name: Theos, A.
name: Hedrich, C. M.
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Cell Biology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Science Policy
classificationCode: 111714
subject: Mental Health
subject: Hematology
classificationCode: 110309
subject: Infectious Diseases
subject: FOS: Health sciences

description: Additional file 2.
SOS : sharing online stories
Creators: name: Cameron, Brett Charles
Publisher: name: University of British Columbia
Year: 2012

description: Social network sites (Facebook, Twitter, MySpace, etc.) provide opportunities to millions of users to share themselves with an online global community. Youth enter adolescence eager to explore and experiment with the world as they learn about and negotiate through identity forming and decision-making. Youth use social network sites as a tool to develop their public and private selves. As guides for youth, teachers need to integrate social network sites into their classroom practices to facilitate and aid adolescent development and formal learning. This study employs grounded theory methodology and a focus group of nine thirteen and fourteen year-old research participants to discuss and investigate adolescent use of social network sites to better understand how they make decisions, share, and learn on these websites. These learnings around adolescent social network site use are then applied to my own teaching practice to establish and organize a new strategy for the introduction of social network sites to teaching. The exploration and research generates three fundamental categories – choosing, sharing, and learning. Choosing, sharing, and learning are synthesized and demonstrate that sharing on social network sites influences adolescent identity forming, decision-making, and informal and formal learning.
Letter from Jose Melena to Emmett L. Bennett Jr., September 22, 1982
Creators: name: Melena, Jose
Publisher: name: The University of Texas at Austin
Year: 1982
Subjects: Emmett L. Bennett, Jr. Collection
Emmett L. Bennett, Jr. Collection--Correspondence
Emmett L. Bennett, Jr. Collection--Correspondence--Jose Melena
PY Un 1320

description: Melena sends Bennett thoughts on Pylos tablet PY Un 1320.
Quality of Life in Patients with Alzheimer's Disease as Reported by Patient Proxies
Creators: name: Albert, Steven M.
name: Del Castillo-Castaneda, Caridad
name: Sano, Mary
name: Jacobs, Diane
name: Marder, Karen
name: Bell, Karen L.
name: Bylsma, Fred
name: Lafleche, Ginette
name: Brandt, Jason
name: Albert, Marilyn
name: Stern, Yaakov
Publisher: name: Columbia University
Year: 1996
Subjects: Neurology
Alzheimer's disease--Patients
Quality of life
Geriatrics

description: OBJECTIVE: To measure behaviors indicative of quality of life (QOL) in patients with Alzheimer's disease and to examine correlates of patient QOL. DESIGN: Cross-sectional investigation. SETTING: Multi-center study. PARTICIPANTS: Sample of 130 diagnosed patients. PRINCIPAL OUTCOME MEASURES: Proxy ratings of (1) the frequency, opportunity, and enjoyment of 15 non-ADL activities potentially within the capacity of a demented person, and (2) the frequency of a series of positive and negative affects, evident in clearly demarcated facial and bodily expressions. RESULTS: QOL ratings were reliably elicited. Family and institutional caregivers differed only in reports of opportunity for patient activity. Frequency of activities declined with increasing severity of dementia. The frequency of negative affects increased and positive affects declined with increasing severity of dementia, but correlations were weak. High QOL, defined by frequent activity and positive affect, was evident in a quarter of the sample. In multivariate models, functional and cognitive status independently predicted QOL among community-resident older adults; only absence of antipsychotics was related to QOL among older people in nursing homes. Patient education, a marker of premorbid state, independently predicted some activity patterns. CONCLUSIONS: Although the subjective world of the demented patient is not directly accessible, readily observable behaviors offer a basis for assessing QOL.
Andrognathidae Cope 1869
Creators: name: Wesener, Thomas
name: Moritz, Leif
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Diplopoda
Platydesmida
Andrognathidae

description: Family Andrognathidae Cope, 1869 (8) New records. 1 M, Wu F3391/Bu/CJW; 1 F, BuB1413; 1 M, BuB2670; 1 M, BuB2991; 1 M, BuB3237; 1 F, BuB3291; 1 M, BuB3307; 1 F, BuB3308. Figure 1E Identification. Members of the order Platydesmida are morphologically variable, the head is only weakly elongated, lacking eyes. The tergites and pleurites are fused, but have dorsally a clearly evident suture (Blanke and Wesener 2014).
description: Published as part of Wesener, Thomas & Moritz, Leif, 2018, Checklist of the Myriapoda in Cretaceous Burmese amber and a correction of the Myriapoda identified by Zhang (2017), pp. 1131-1140 in Check List 14 (6) on page 1134, DOI: 10.15560/14.6.1131
description: {"references": ["Blanke A, Wesener T (2014) Revival of forgotten characters and modern imaging techniques help to produce a robust phylogeny of the Dip- lopoda (Arthropoda, Myriapoda). Arthropod Structure & Development 43 (1): 63 - 75. https: // doi. org / 10.1016 / j. asd. 2013.10.003"]}
Chagas disease vector control and Taylor's law
Creators: name: Cohen, Joel E.
name: Rodriguez-Planes, Lucia I.
name: Gaspe, Maria S.
name: Cecere, María C.
name: Cardinal, Marta V.
name: Gürtler, Ricardo E.
Publisher: name: Columbia University
Year: 2017
Subjects: Chagas' disease
Insect population density
Vector control
Triatoma

description: Background:
Large spatial and temporal fluctuations in the population density of living organisms have profound consequences for biodiversity conservation, food production, pest control and disease control, especially vector-borne disease control. Chagas disease vector control based on insecticide spraying could benefit from improved concepts and methods to deal with spatial variations in vector population density.

Methodology/Principal findings:
We show that Taylor's law (TL) of fluctuation scaling describes accurately the mean and variance over space of relative abundance, by habitat, of four insect vectors of Chagas disease (Triatoma infestans, Triatoma guasayana, Triatoma garciabesi and Triatoma sordida) in 33,908 searches of people's dwellings and associated habitats in 79 field surveys in four districts in the Argentine Chaco region, before and after insecticide spraying. As TL predicts, the logarithm of the sample variance of bug relative abundance closely approximates a linear function of the logarithm of the sample mean of abundance in different habitats. Slopes of TL indicate spatial aggregation or variation in habitat suitability. Predictions of new mathematical models of the effect of vector control measures on TL agree overall with field data before and after community-wide spraying of insecticide.

Conclusions/Significance:
A spatial Taylor's law identifies key habitats with high average infestation and spatially highly variable infestation, providing a new instrument for the control and elimination of the vectors of a major human disease.
Additional figures and Raw data tables from Migratory birds are able to choose the appropriate migratory direction under dim yellow narrowband light
Creators: name: Romanova, Nadezhda
name: Utvenko, Gleb
name: Prokshina, Anisia
name: Cellarius, Fyodor
name: Fedorishcheva, Aleksandra
name: Pakhomov, Alexander
Publisher: name: The Royal Society
Year: 2023
Subjects: classificationCode: 310901
subject: Animal behaviour
classificationCode: 419999
subject: Other environmental sciences not elsewhere classified

description: This EMS contains tables with raw data of all experiments, pictures of the experimental setups and visialisation of the bootstrap analysis' results.
Renormalization of Polyakov loops in different representations and the large-N limit
Creators: name: Mykkanen, Anne
name: Panero, Marco
name: Rummukainen, Kari
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: High Energy Physics - Theory (hep-th)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We study the renormalization of Polyakov loops in different irreducible representations of SU(N) Yang-Mills theories at finite temperature, and investigate their behavior in the large-N limit.
description: 7 pages, 5 figures, talk presented at the 29th International Symposium on Lattice Field Theory "Lattice 2011" (10-16 July 2011, Squaw Valley, CA, USA); v2: added references
Using iterative learning to improve understanding during the informed consent process in a South African psychiatric genomics study
Creators: name: Campbell, Megan M.
name: Susser, Ezra S.
name: Mall, Sumaya
name: Mqulwana, Sibonile G.
name: Mndini, Michael M.
name: Ntola, Odwa A.
name: Nagdee, Mohamed
name: Zingela, Zukiswa
name: Van Wyk, Stephanus
name: Stein, Dan
Publisher: name: Columbia University
Year: 2017
Subjects: Medical ethics
Public health--Research
Informed consent (Medical law)
Learning
Psychiatry

description: Obtaining informed consent is a great challenge in global health research. There is a need for tools that can screen for and improve potential research participants’ understanding of the research study at the time of recruitment. Limited empirical research has been conducted in low and middle income countries, evaluating informed consent processes in genomics research. We sought to investigate the quality of informed consent obtained in a South African psychiatric genomics study. A Xhosa language version of the University of California, San Diego Brief Assessment of Capacity to Consent Questionnaire (UBACC) was used to screen for capacity to consent and improve understanding through iterative learning in a sample of 528 Xhosa people with schizophrenia and 528 controls. We address two questions: firstly, whether research participants’ understanding of the research study improved through iterative learning; and secondly, what were predictors for better understanding of the research study at the initial screening? During screening 290 (55%) cases and 172 (33%) controls scored below the 14.5 cut-off for acceptable understanding of the research study elements, however after iterative learning only 38 (7%) cases and 13 (2.5%) controls continued to score below this cut-off. Significant variables associated with increased understanding of the consent included the psychiatric nurse recruiter conducting the consent screening, higher participant level of education, and being a control. The UBACC proved an effective tool to improve understanding of research study elements during consent, for both cases and controls. The tool holds utility for complex studies such as those involving genomics, where iterative learning can be used to make significant improvements in understanding of research study elements. The UBACC may be particularly important in groups with severe mental illness and lower education levels. Study recruiters play a significant role in managing the quality of the informed consent process.
Understanding the core density profile in TCV H-mode plasmas
Creators: name: Wágner, Dávid
name: Fable, Emiliano
name: Pitzschke, Andreas
name: Sauter, Olivier
name: Weisen, Henri
Publisher: name: arXiv
Year: 2012
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: Results from a database analysis of H-mode electron density profiles on the Tokamak à Configuration Variable (TCV) in stationary conditions show that the logarithmic electron density gradient increases with collisionality. By contrast, usual observations of H-modes showed that the electron density profiles tend to flatten with increasing collisionality. In this work it is reinforced that the role of collisionality alone, depending on the parameter regime, can be rather weak and in these, dominantly electron heated TCV cases, the electron density gradient is tailored by the underlying turbulence regime, which is mostly determined by the ratio of the electron to ion temperature and that of their gradients. Additionally, mostly in ohmic plasmas, the Ware-pinch can significantly contribute to the density peaking. Qualitative agreement between the predicted density peaking by quasi-linear gyrokinetic simulations and the experimental results is found. Quantitative comparison would necessitate ion temperature measurements, which are lacking in the considered experimental dataset. However, the simulation results show that it is the combination of several effects that influences the density peaking in TCV H-mode plasmas.
description: 23 pages, 12 figures