cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Bothrops mattogrossensis Amaral 1925
Creators: name: Fischer, Wagner
name: Faria de Godoi, Raquel
name: Conceição Paranhos Filho, Antonio
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Reptilia
Squamata
Viperidae
Bothrops
Bothrops mattogrossensis

description: Bothrops mattogrossensis Amaral, 1925 Records. Table 2. The Cerrado Lancehead was identified by its size (TL = 101.5 cm ± 20.5; n = 2) and color pattern. The supralabial scales were dark and uniformly pigmented and more conspicuous on the anterior half of the mouth. The dorsolateral blotches of the body had well-defined contours, standing out from the background color. The postocular stripes were well defined. The keels always had the same coloration as the dorsal scales. There were blotches in the interspaces between 2 consecutive blotches. We used several specimens for identifications (e.g. ZUFMS-REP00005, REP00058, REP00286, REP00342, REP01333, REP01530, REP01726, REP01869, REP02137).
description: Published as part of Fischer, Wagner, Faria de Godoi, Raquel & Conceição Paranhos Filho, Antonio, 2018, Roadkill records of reptiles and birds in Cerrado and Pantanal landscapes, pp. 845-876 in Check List 14 (5) on page 865, DOI: 10.15560/14.5.845
Fluorescence quenching in graphene: a fundamental ruler and evidence for transverse plasmons
Creators: name: Gómez-Santos, G.
name: Stauber, T.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Graphene's fluorescence quenching is studied as a function of distance. Transverse decay channels, full retardation and graphene-field coupling to all orders are included, extending previous instantaneous results. For neutral graphene, a virtually exact analytical expression for the fluorescence yield is derived, valid for arbitrary distances and only based on the fine structure constant $α$, the fluorescent wavelength $λ$, and distance $z$. Thus graphene's fluorescence quenching measurements provide a fundamental distance ruler. For doped graphene and at appropriate energies, the fluorescence yield at large distances is dominated by transverse plasmons, providing a platform for their detection.
description: 6 pages, 2 figures
Bothrops moojeni Hoge 1966
Creators: name: Fischer, Wagner
name: Faria de Godoi, Raquel
name: Conceição Paranhos Filho, Antonio
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Reptilia
Squamata
Viperidae
Bothrops
Bothrops moojeni

description: Bothrops moojeni Hoge, 1966 Records. Table 2. The Brazilian Lancehead was identified by size (TL = 89.5 cm ± 6.0; n = 4) and grayish brown background color, with a series of dark hourglass-shaped bands that are narrowest dorsally with paler centers and borders, the top of the head matched the background color, and the face was pale with a post ocular stripe. We vouchered all 4 specimens found (ZUFMS-REP01864, REP02720, REP02718, REP02719).
description: Published as part of Fischer, Wagner, Faria de Godoi, Raquel & Conceição Paranhos Filho, Antonio, 2018, Roadkill records of reptiles and birds in Cerrado and Pantanal landscapes, pp. 845-876 in Check List 14 (5) on page 865, DOI: 10.15560/14.5.845
Genetic Susceptibility and Head Injury as Risk Factors for Alzheimer's Disease among Community-Dwelling Elderly Persons and Their First-Degree Relatives
Creators: name: Mayeux, Richard Paul
name: Ottman, Ruth
name: Tang, Mingxin
name: Noboa-Bauza, Lourdes
name: Marder, Karen
name: Gurland, Barry J.
name: Stern, Yaakov
Publisher: name: Columbia University
Year: 1993
Subjects: Neurology
Alzheimer's disease
Older people
Medical genetics
Head--Wounds and injuries--Complications

description: We performed a community-based study to investigate the relationship of genetic susceptibility and head injury to Alzheimer's disease(AD) in 138 patients with AD and 193 healthy elderly control subjects. Data concerning presence or absence of dementia and certain exposures were also obtained from 799 first-degree relatives of the patients and 1,238 first-degree relatives of the control subjects. Adjusting for age, gender, and other risk factors, the odds ratio for AD associated with head injury was 3.7 (95% confidence interval [CI], 1.4–9.7). The association was highest for head injuries that occurred after age 70. The risk of AD was higher in first-degree relatives of patients with onset prior to age 70 than in relatives of control subjects (risk ratio [RR] = 2.5; 95% CI, 1.1–5.6). The risk was not increased for relatives of patients with onset of AD at age 70 or older. Compared with relatives without head injury, the risk of AD was increased among both head-injured relatives of patients (RR = 5.9; 95% CI, 2.3–14.8) and head-injured relatives of control subjects (RR = 6.9; 95% CI, 2.5–18.9). Our results are consistent with the hypothesis that severe head injury and genetic susceptibility are associated with AD. Both associations concur with current concepts regarding the role of amyloid in AD. Although we regard head injury, like genetic susceptibility, to be a putative risk factor for AD, the temporal relationship between head injury and AD warrants further investigation.
Rhea americana
Creators: name: Fischer, Wagner
name: Faria de Godoi, Raquel
name: Conceição Paranhos Filho, Antonio
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Aves
Rheiformes
Rheidae
Rhea
Rhea americana

description: Rhea americana (Linnaeus, 1758) Records. Table 3. The Greater Rhea is the largest flightless bird species in Brazil (Fig. 11), and is easily recognized by its size (TL ca 1.5 m), long neck and legs, no tail, and brown-gray plumage. The males have a black breast and neck.
description: Published as part of Fischer, Wagner, Faria de Godoi, Raquel & Conceição Paranhos Filho, Antonio, 2018, Roadkill records of reptiles and birds in Cerrado and Pantanal landscapes, pp. 845-876 in Check List 14 (5) on page 866, DOI: 10.15560/14.5.845
Could any black holes be produced at the LHC?
Creators: name: Mureika, Jonas
name: Nicolini, Piero
name: Spallucci, Euro
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We introduce analytical quantum gravity modifications of the production cross section for terascale black holes by employing an effective ultraviolet cut off $l$. We find the new cross sections approach the usual "black disk" form at high energy, while they differ significantly near the fundamental scale from the standard increase with respect to $s$. We show that the heretofore discontinuous step function used to represent the cross section threshold can realistically be modeled by two functions representing the incoming and final parton states in a high energy collision. The growth of the cross section with collision energy is thus a unique signature of $l$ and number of spatial dimensions $d$. Contrary to the classical black disk result, our cross section is able to explain why black holes might not be observable in LHC experiments while they could be still at the reach of ultra-high energy cosmic ray events.
description: v1: 10 pages, 1 figure; v2: 11 pages, 1 figure, additional references, minor modifications; v3: new title, expanded discussion with updated production estimates, additional references, 4 figures, 19 pages, version accepted for publication on Physical Review D
Convergence towards an asymptotic shape in first-passage percolation on cone-like subgraphs of the integer lattice
Creators: name: Ahlberg, Daniel
Publisher: name: arXiv
Year: 2011
Subjects: subject: Probability (math.PR)
subject: FOS: Mathematics
subject: 60K35, 60F15, 60F10

description: In first-passage percolation on the integer lattice, the Shape Theorem provides precise conditions for convergence of the set of sites reachable within a given time from the origin, once rescaled, to a compact and convex limiting shape. Here, we address convergence towards an asymptotic shape for cone-like subgraphs of the $\Z^d$ lattice, where $d\ge2$. In particular, we identify the asymptotic shapes associated to these graphs as restrictions of the asymptotic shape of the lattice. Apart from providing necessary and sufficient conditions for $L^p$- and almost sure convergence towards this shape, we investigate also stronger notions such as complete convergence and stability with respect to a dynamically evolving environment.
description: 23 pages. Together with arXiv:1305.6260, this version replaces the old. The main results have been strengthened and an earlier error in the statement corrected. To appear in J. Theoret. Probab
Further Examination of the Candidate Genes in Chromosome 12p13 Locus for Late-Onset Alzheimer Disease
Creators: name: Lee, Joseph H.
name: Cheng, Rong
name: Rogaeva, Ekaterina
name: Meng, Yan
name: Stern, Yaakov
name: Santana, Vincent
name: Lantigua, Rafael Antonio
name: Medrano, Martin
name: Jimenez-Velazquez, Ivonne Z.
name: Farrer, Lindsay
name: St. George-Hyslop, Peter
name: Mayeux, Richard Paul
Publisher: name: Columbia University
Year: 2008
Subjects: subject: Neurogenetics
subject: Alzheimer's disease--Genetic aspects
subject: Neurology
subject: Genetics
subject: FOS: Biological sciences

description: A broad region on chromosome 12p13 has been intensely investigated for novel genetic variants associated with Alzheimer disease (AD). We examined this region with 23 microsatellite markers using 124 North European (NE) families and 209 Caribbean Hispanic families with late-onset AD (FAD). Significant evidence for linkage was present in a 5-cM interval near 20 cM in both the NE FAD (LOD = 3.5) and the Caribbean Hispanic FAD (LOD = 2.2) datasets. We further investigated these families and an independent NE case-control dataset using 14 single nucleotide polymorphisms (SNPs). The initial screening of the region at approximately 20 cM in the NE case-control dataset revealed significant association between AD and seven SNPs in several genes, with the strongest result for rs2532500 in TAPBPL (p = 0.006). For rs3741916 in GAPDH, the C allele, rather than the G allele as was observed by Li et al. (Proc Natl Acad Sci U S A 101(44):15688-15693, 2004), was the risk allele. When the two family datasets were examined, none of the SNPs were significant in NE families, but two SNPs were associated with AD in Caribbean Hispanics: rs740850 in NCAPD2 (p = 0.0097) and rs1060620 in GAPDH (p = 0.042). In a separate analysis combining the Caribbean Hispanic families and NE cases and controls, rs740850 was significant after correcting for multiple testing (empirical p = 0.0048). Subsequent haplotype analyses revealed that two haplotype sets-haplotype C-A at SNPs 6-7 within NCAPD2 in Caribbean Hispanics, and haplotypes containing C-A-T at SNPs 8-10 within GAPDH in Caribbean Hispanic family and NE case-control datasets-were associated with AD. Taken together, these SNPs may be in linkage disequilibrium with a pathogenic variant(s) on or near NCAPD2 and GAPDH
Clinical Characteristics and Longitudinal Changes of Informal Cost of Alzheimer's Disease in the Community
Creators: name: Zhu, Carolyn W.
name: Scarmeas, Nikolaos
name: Torgan, Rebecca L.
name: Albert, Marilyn
name: Brandt, Jason
name: Blacker, Deborah
name: Sano, Mary
name: Stern, Yaakov
Publisher: name: Columbia University
Year: 2006
Subjects: Neurology
Alzheimer's disease--Patients
Medical care, Cost of
Geriatrics

description: Most estimates of the cost of informal caregiving in patients with Alzheimer's disease (AD) remain cross-sectional. Longitudinal estimates of informal caregiving hours and costs are less frequent and are from assessments covering only short periods of time. The objectives of this study were to estimate long-term trajectories of the use and cost of informal caregiving for patients with AD and the effects of patient characteristics on the use and cost of informal caregiving. The sample is drawn from the Predictors Study, a large, multicenter cohort of patients with probable AD, prospectively followed annually for up to 7 years in three university-based AD centers in the United States (n=170). Generalized linear mixed models were used to estimate the effects of patient characteristics on use and cost of informal caregiving. Patients' clinical characteristics included cognitive status (Mini-Mental State Examination), functional capacity (Blessed Dementia Rating Scale (BDRS)), comorbidities, psychotic symptoms, behavioral problems, depressive symptoms, and extrapyramidal signs. Results show that rates of informal care use and caregiving hours (and costs) increased substantially over time but were related differently to patients' characteristics. Use of informal care was significantly associated with worse cognition, worse function, and higher comorbidities. Conditional on receiving informal care, informal caregiving hours (and costs) were mainly associated with worse function. Each additional point on the BDRS increased informal caregiving costs 5.4%. Average annual informal cost was estimated at $25,381 per patient, increasing from $20,589 at baseline to $43,030 in Year 4.
Explicit Dehn filling and Heegaard splittings
Creators: name: Futer, David
name: Purcell, Jessica S.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Geometric Topology (math.GT)
subject: Differential Geometry (math.DG)
subject: FOS: Mathematics
subject: 57M50, 53A10

description: We prove an explicit, quantitative criterion that ensures the Heegaard surfaces in Dehn fillings behave "as expected." Given a cusped hyperbolic manifold X, and a Dehn filling whose meridian and longitude curves are longer than 2pi(2g-1), we show that every genus g Heegaard splitting of the filled manifold is isotopic to a splitting of the original manifold X. The analogous statement holds for fillings of multiple boundary tori. This gives an effective version of a theorem of Moriah-Rubinstein and Rieck-Sedgwick.
description: 17 pages. v3 contains minor revisions and cleaner arguments, incorporating referee comments. To appear in Communications in Analysis and Geometry
Wave propagation across acoustic / Biot's media: a finite-difference method
Creators: name: Chiavassa, Guillaume
name: Lombard, Bruno
Publisher: name: arXiv
Year: 2011
Subjects: subject: Classical Physics (physics.class-ph)
subject: Numerical Analysis (math.NA)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: Numerical methods are developed to simulate the wave propagation in heterogeneous 2D fluid / poroelastic media. Wave propagation is described by the usual acoustics equations (in the fluid medium) and by the low-frequency Biot's equations (in the porous medium). Interface conditions are introduced to model various hydraulic contacts between the two media: open pores, sealed pores, and imperfect pores. Well-possedness of the initial-boundary value problem is proven. Cartesian grid numerical methods previously developed in porous heterogeneous media are adapted to the present context: a fourth-order ADER scheme with Strang splitting for time-marching; a space-time mesh-refinement to capture the slow compressional wave predicted by Biot's theory; and an immersed interface method to discretize the interface conditions and to introduce a subcell resolution. Numerical experiments and comparisons with exact solutions are proposed for the three types of interface conditions, demonstrating the accuracy of the approach.
description: Communications in Computational Physics (2012) XXX
Accidental exposure of pregnant patients to ionizing radiation during radiation therapy planning and treatment in British Columbia cancer centers
Creators: name: Goddard, Karen Jane
Publisher: name: University of British Columbia
Year: 2012

description: This project was an interdisciplinary study of a specific medical error - inadvertent radiation therapy (RT) in the treatment of female cancer patients during early pregnancy in British Columbia. RT is very damaging to the fetus during the first trimester of pregnancy and this is a very undesirable adverse event (or medical error). I explored why this error could occur by reviewing the types and causes of medical errors in general and then studying potential errors specific to RT planning and treatment. I created and administered a questionnaire of all health care professionals (HCPs) in cancer centers across British Columbia to assess if this error had occurred. I also asked if HCPs thought this error was a significant problem and asked for their opinions regarding solutions. I examined the potential for HCP legal liability as a result of this error and existing Canadian case law regarding the inadvertent use of teratogenic agents in early pregnancy. I examined different methods for gathering data about and documenting medical errors in general and then specifically for this particular problem. I looked at the barriers to improving patient safety and how the risk of making this medical error could be reduced. As a result of my work, policy has been changed in all British Columbia Cancer Centers. A program now exists which involves check lists, signage and patient education to address this problem.
Method for classifying multiqubit states via the rank of the coefficient matrix and its application to four-qubit states
Creators: name: Li, Xiangrong
name: Li, Dafa
Publisher: name: arXiv
Year: 2012
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We construct coefficient matrices of size 2^l by 2^{n-l} associated with pure n-qubit states and prove the invariance of the ranks of the coefficient matrices under stochastic local operations and classical communication (SLOCC). The ranks give rise to a simple way of partitioning pure n-qubit states into inequivalent families and distinguishing degenerate families from one another under SLOCC. Moreover, the classification scheme via the ranks of coefficient matrices can be combined with other schemes to build a more refined classification scheme. To exemplify we classify the nine families of four qubits introduced by Verstraete et al. [Phys. Rev. A 65, 052112 (2002)] further into inequivalent subfamilies via the ranks of coefficient matrices, and as a result, we find 28 genuinely entangled families and all the degenerate classes can be distinguished up to permutations of the four qubits. We also discuss the completeness of the classification of four qubits into nine families.
Functional Status in the Young-Old: Establishing a Working Prototype of an Extended-Instrumental Activities of Daily Living Scale
Creators: name: Fieo, Robert A.
name: Manly, Jennifer J.
name: Schupf, Nicole
name: Stern, Yaakov
Publisher: name: Columbia University
Year: 2014
Subjects: Neurology
Cognition--Age factors
Aging
Gerontology
Dementia

description: BACKGROUND: Instrumental activities of daily living (IADLs) exhibit strong predictive power for the presence of dementia and mild cognitive impairment. However, IADLs are often less effective in younger cohorts or in healthy community-dwelling samples, presenting with large ceiling effects. This study aimed to construct an IADL scale with an extended range. An effort was made to incorporate leisure activity tasks that were more stimulating, and potentially more challenging, into a set of traditional IADLs. METHODS: Beginning with a set of IADL and leisure activity items, nonparametric item response theory methodology was used to construct a scale with appropriate dimensionality, monotonicity, item discrimination power, and scalability within a large cohort of young-old (aged 65-75). Dimensionality was further scrutinized by principal component analysis of the residuals. The predictive validity of the resulting scale for poor cognitive performance was evaluated using logistic regression. RESULTS: A reliable (rho = .73) unidimensional construct was established, meeting the Mokken item response theory criteria of medium scalability. Excluding demented participants, the adjusted model proved sensitive to relatively subtle cognitive deficits; each additional task endorsed (nine-item scale) significantly decreased the odds of being in the bottom quarter of composite domains relating to processing speed (odds ratio = 0.73 [confidence interval: 0.56-0.97], p < .05) and visuospatial ability (odds ratio = 0.70 [confidence interval: 0.73-0.87], p < .01). CONCLUSIONS: A reliable extended-IADL scale was constructed meeting item response theory assumptions relating to unidimensionality, monotonicity, and invariant item ordering. The range of measurement extends well beyond traditional IADL scales. Finally, the scale appears to be sensitive to cognitive differences within the normal spectrum.
Tilting modules in category O and sheaves on moment graphs
Creators: name: Kübel, Johannes
Publisher: name: arXiv
Year: 2012
Subjects: subject: Representation Theory (math.RT)
subject: FOS: Mathematics

description: We describe tilting modules of the deformed category O over a semisimple Lie algebra as certain sheaves on a moment graph associated to the corresponding block of category O. We prove that they map to Braden-MacPherson sheaves constructed along the reversed Bruhat order under Fiebig's localization functor. By this means, we get character formulas for tilting modules and explain how Soergel's result about the Andersen filtration gives a Koszul dual proof of the semisimplicity of subquotients of the Jantzen filtration.
description: 18 pages; minor typos and changes in chapter 5.1
Cosmology and perturbations in massive gravity
Creators: name: D'Amico, Guido
Publisher: name: arXiv
Year: 2012
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We study perturbations around some cosmological backgrounds in the dRGT theory of massive gravity. We develop a general formalism to calculate the perturbations around any background. We derive the Lagrangian for fluctuations in the small scale limit, and for the open FRW solution we repeat the analysis around the full background. We find that the perturbations display similar properties: the longitudinal modes of the massive graviton are instantaneous at quadratic level, but they acquire a time-kinetic term at cubic order.
description: 17 pages. v2: references added, minor changes to match PRD published version
The basis for calcium regulation of the cardiac sodium channel
Creators: name: Sarhan, Maen Fuad
Publisher: name: University of British Columbia
Year: 2012

description: Voltage-gated sodium channels underlie the rapid regenerative upstroke of action potentials and are potently modulated by cytoplasmic calcium ions resulting in an increase in the availability of channels available for a depolarization. Characterization of calmodulin (CaM) and Ca²⁺ binding to the C-terminus have failed to identify a mechanism due to data which is inconsistent and difficult to interpret. We examined the possibility of whether CaM interactions with the inactivation gate of the sodium channel between domains three and four (DIII-IV linker) and C-terminus could possibly explain how the channel is modulated by Ca²⁺. We employ highly purified recombinant proteins for X-ray crystallography and Isothermal titration calorimetry (ITC) to identify tyrosine 1494 as an aromatic anchor for the C-terminal lobe of Ca²⁺/CaM binding to the DIII-IV linker. Through crystallographic insight, and confirmation by ITC, we incorporate mutations in the DIII-IV linker that enhance or diminish Ca²⁺/CaM binding, which sensitize or abolish Ca²⁺ regulation of full-length channels in whole-cell electrophysiological experiments. The single lobe interaction with the DIII-IV linker opens the possibility that the N-terminal lobe interacts with another region of the sodium channel. To examine this possibility we used ITC to examine how CaM interacts with the C-terminus and found that in the absence of Ca²⁺, CaM interacts with its C-lobe with very high affinity, allowing it to act as a resident Ca2+ sensor. As Ca²⁺ levels rise, lobe switching occurs, and preferential N-lobe binding to the C-terminus followed by C-lobe binding to the DIII-IV linker. The Ca²⁺/CaM DIII-IV crystal structure we obtained harbors the positive of five disease mutations involved in deadly arrhythmias. We find that two of these mutations altered both Ca²⁺/CaM binding as well as Ca²⁺ regulation in full length channels suggesting that calcium dysregulation may be involved in cardiac arrhythmia. We conclude that Ca²⁺ regulation of the cardiac voltage gated sodium channel occurs through CaM bridging of the C-terminus and the inactivation gate and that dysfunction of this process may result in cardiac arrhythmia.
Information gain versus coupling strength in quantum measurements
Creators: name: Zhu, Xuanmin
name: Zhang, Yuxiang
name: Liu, Quanhui
name: Wu, Shengjun
Publisher: name: arXiv
Year: 2012
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We investigate the relationship between the information gain and the interaction strength between the quantum system and the measuring device. A strategy is proposed to calculate the information gain of the measuring device as the coupling strength is a variable. For qubit systems, we prove that the information gain increases monotonically with the coupling strength. It is obtained that the information gain of the projective measurement along the x-direction reduces with the increasing of the measurement strength along the z-direction, and a complementarity of information gain in the measurements along those two directions is presented.
description: 7 pages, 1 figures
Crypturellus parvirostris
Creators: name: Fischer, Wagner
name: Faria de Godoi, Raquel
name: Conceição Paranhos Filho, Antonio
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Aves
Tinamiformes
Tinamidae
Crypturellus
Crypturellus parvirostris

description: Crypturellus parvirostris (Wagler, 1827) Record. Table 3. The Small-billed Tinamou was recognized by its size (almost 20.0 cm long), ratite-like shape (small wingspan; no tail), dark brown upperparts, grey to brownish underparts and head, and red bill and legs.
description: Published as part of Fischer, Wagner, Faria de Godoi, Raquel & Conceição Paranhos Filho, Antonio, 2018, Roadkill records of reptiles and birds in Cerrado and Pantanal landscapes, pp. 845-876 in Check List 14 (5) on page 866, DOI: 10.15560/14.5.845
A new, precise measurement of the primordial abundance of Deuterium
Creators: name: Pettini, Max
name: Cooke, Ryan
Publisher: name: arXiv
Year: 2012
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: The metal-poor damped Lyman alpha (DLA) system at z = 3.04984 in the QSO SDSSJ1419+0829 has near-ideal properties for an accurate determination of the primordial abundance of deuterium, (D/H)_p. We have analysed a high-quality spectrum of this object with software specifically designed to deduce the best fitting value of D/H and to assess comprehensively the random and systematic errors affecting this determination. We find (D/H)_DLA = (2.535 +/-0.05) x 10^(-5), which in turn implies Omega_b h^2 = 0.0223 +/- 0.0009, in very good agreement with Omega_b h^2 (CMB) = 0.0222 +/- 0.0004 deduced from the angular power spectrum of the cosmic microwave background. If the value in this DLA is indeed the true (D/H)_p produced by Big-Bang nucleosynthesis (BBN), there may be no need to invoke non-standard physics nor early astration of D to bring together Omega_b h^2 (BBN) and Omega_b h^2 (CMB). The scatter between most of the reported values of (D/H)_p in the literature may be due largely to unaccounted systematic errors and biases. Further progress in this area will require a homogeneous set of data comparable to those reported here and analysed in a self-consistent manner. Such an endeavour, while observationally demanding, has the potential of improving our understanding of BBN physics, including the relevant nuclear reactions, and the subsequent processing of 4He and 7Li through stars.
description: 11 pages, 7 figures, Accepted for publication in Monthly Notices of the Royal Astronomical Society
Functional Network Mediates Age-Related Differences in Reaction Time: A Replication and Extension Study
Creators: name: Gazes, Yunglin
name: Habeck, Christian G.
name: O'Shea, Deirdre
name: Razlighi, Qolamreza R.
name: Steffener, Jason
name: Stern, Yaakov
Publisher: name: Columbia University
Year: 2015
Subjects: Neurology
Aging
Reaction time
Cognitive neuroscience

description: INTRODUCTION: A functional activation (i.e., ordinal trend) pattern was previously identified in both young and older adults during task-switching performance, the expression of which correlated with reaction time. The current study aimed to (1) replicate this functional activation pattern in a new group of fMRI activation data, and (2) extend the previous study by specifically examining whether the effect of aging on reaction time can be explained by differences in the activation of the functional activation pattern. METHOD: A total of 47 young and 50 older participants were included in the extension analysis. Participants performed task-switching as the activation task and were cued by the color of the stimulus for the task to be performed in each block. To test for replication, two approaches were implemented. The first approach tested the replicability of the predictive power of the previously identified functional activation pattern by forward applying the pattern to the Study II data and the second approach was rederivation of the activation pattern in the Study II data. RESULTS: Both approaches showed successful replication in the new data set. Using mediation analysis, expression of the pattern from the first approach was found to partially mediate age-related effects on reaction time such that older age was associated with greater activation of the brain pattern and longer reaction time, suggesting that brain activation efficiency (defined as "the rate of activation increase with increasing task difficulty" in Neuropsychologia 47, 2009, 2015) of the regions in the Ordinal trend pattern directly accounts for age-related differences in task performance. DISCUSSION: The successful replication of the functional activation pattern demonstrates the versatility of the Ordinal Trend Canonical Variates Analysis, and the ability to summarize each participant's brain activation map into one number provides a useful metric in multimodal analysis as well as cross-study comparisons.
Axial anomaly and the three-flavor Nambu--Jona-Lasinio model with confinement: Constructing the QCD phase diagram
Creators: name: Powell, Philip D.
name: Baym, Gordon
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We investigate the phase structure of massless three-flavor QCD by extending the Nambu-Jona- Lasinio model to include the effects of confinement and the axial anomaly. We study the interplay between the chiral and diquark condensates induced by the axial anomaly, as well as their relationship with the Polyakov loop, which parameterizes confinement. By minimizing the thermodynamic potential we construct the QCD phase diagram and investigate the possibility of realizing a recently discovered low temperature critical point and an associated BEC-BCS crossover. We also perform a Ginzburg-Landau expansion of the thermodynamic potential, comparing our results to a prior analysis based purely on symmetry considerations, in order to assess the lowest-order effects of the condensate-confinement couplings.
description: 13 pages, 14 figures
Change in Body Mass Index before and after Alzheimer's Disease Onset
Creators: name: Gu, Yian
name: Scarmeas, Nikolaos
name: Cosentino, Stephanie
name: Brandt, Jason
name: Albert, Marilyn
name: Blacker, Deborah
name: Dubois, Bruno
name: Stern, Yaakov
Publisher: name: Columbia University
Year: 2014
Subjects: Neurology
Alzheimer's disease
Body mass index

description: OBJECTIVES: A high body mass index (BMI) in middle-age or a decrease in BMI at late-age has been considered a predictor for the development of Alzheimer's disease (AD). However, little is known about the BMI change close to or after AD onset. METHODS: BMI of participants from three cohorts, the Washington Heights and Inwood Columbia Aging Project (WHICAP; population-based) and the Predictors Study (clinic-based), and National Alzheimer's Coordinating Center (NACC; clinic-based) were analyzed longitudinally. We used generalized estimating equations to test whether there were significant changes of BMI over time, adjusting for age, sex, education, race, and research center. Stratification analyses were run to determine whether BMI changes depended on baseline BMI status. RESULTS: BMI declined over time up to AD clinical onset, with an annual decrease of 0.21 (p=0.02) in WHICAP and 0.18 (p=0.04) kg/m2 in NACC. After clinical onset of AD, there was no significant decrease of BMI. BMI even increased (b=0.11, p=0.004) among prevalent AD participants in NACC. During the prodromal period, BMI decreased over time in overweight (BMI>/=25 and <30) WHICAP participants or obese (BMI>/=30) NACC participants. After AD onset, BMI tended to increase in underweight/normal weight (BMI<25) patients and decrease in obese patients in all three cohorts, although the results were significant in NACC study only. CONCLUSIONS: Our study suggests that while BMI declines before the clinical AD onset, it levels off after clinical AD onset, and might even increase in prevalent AD. The pattern of BMI change may also depend on the initial BMI.
CoFold : an RNA structure prediction method that takes co-transcriptional folding into account
Creators: name: Proctor, Jeffrey Ryan
Publisher: name: University of British Columbia
Year: 2013

description: RNA has a diverse array of cellular functions, and relies on molecular structure to carry them out. The vast majority of current methods for prediction of RNA secondary structure (i.e. the set of base pairs in the molecule) consider the minimum free energy structure (i.e. the most thermodynamically stable structure), and thus disregard the process of structural formation. There exists substantial evidence that the process of structure formation is important, and that it does impact the resulting functional RNA structure. Several methods currently exist that explicitly simulate the kinetic folding pathway as a time-ordered sequence of structural changes. However, these methods not only suffer from a long list of limiting assumptions about the cellular environment, but also are restricted to short sequences. In this thesis, we explore the idea of capturing the effects of kinetic folding rather than simulating in detail the process over time, and propose that accounting for kinetic effects of structural formation is crucial to further improve non-comparative RNA secondary structure prediction methods. During transcription, RNA structure begins to form immediately as the molecule emerges from the polymerase (i.e. co-transcriptionally). Long-range base pairs suffer a disadvantage during this process, as quickly forming short-range base pairs act to block their formation (i.e. due to kinetic barriers). We propose a novel method, CoFold, that captures the reachability of potential pairing partners during co-transcriptional folding. We show that it significantly improves prediction accuracy over free energy minimization alone, particularly for long sequences. CoFold depends on only two free parameters that are highly correlated, and we demonstrate robust training. Furthermore, the resulting structures predicted by CoFold have a free energy measurement that does not significantly differ from that of the respective RNAfold prediction, indicating that they are indeed stable secondary structures. We propose that consideration of kinetics in RNA secondary structure prediction is crucial, and we hope that this work encourages further exploration of its effect on biological RNA structure.
Social Cognition in Alzheimer's Disease: A Separate Construct Contributing to Dependence
Creators: name: Cosentino, Stephanie
name: Zahodne, Laura B.
name: Brandt, Jason
name: Blacker, Deborah
name: Albert, Marilyn
name: Dubois, Bruno
name: Stern, Yaakov
Publisher: name: Columbia University
Year: 2014
Subjects: Social perception
Alzheimer's disease
Cognition

description: The extent to which social cognitive changes reflect a discrete constellation of symptoms dissociable from general cognitive changes in Alzheimer's disease (AD) is unclear. Moreover, whether social cognitive symptoms contribute to disease severity and progression is unknown. The current multicenter study investigated cross-sectional and longitudinal associations between social cognition measured with six items from the Blessed Dementia Rating Scale, general cognition, and dependence in 517 participants with probable AD. Participants were monitored every 6 months for 5.5 years. Results from multivariate latent growth curve models adjusted for sex, age, education, depression, and recruitment site revealed that social cognition and general cognition were unrelated cross-sectionally and throughout time. However, baseline levels of each were related independently to dependence, and change values of each were related independently to change in dependence. These findings highlight the separability of social and general cognition in AD. Results underscore the relevance of considering social cognition when modeling disease and estimating clinical outcomes related to patient disability.
Cooling of young neutron stars in GRB associated to Supernova
Creators: name: Negreiros, Rodrigo
name: Ruffini, Remo
name: Bianco, Carlo Luciano
name: Rueda, Jorge A.
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: Recent observations of the late ($t=10^8$--$10^9$ s) emission of supernovae (SNe) associated to GRBs (GRB-SN) show a distinctive emission in the X-ray regime consistent with temperatures $10^7$--$10^8$ K. Similar features have been also observed in the two Type Ic SNe SN 2002ap and SN 1994I that are not associated to GRBs. We advance the possibility that the late X-ray emission observed in GRB-SN and in isolated SN is associated to a hot neutron star (NS) just formed in the SN event, here defined as a neo-NS. We discuss the thermal evolution of neo-NS in the age regime that spans from $\sim 1$ minute (just after the proto-NS phase) up to ages <10-100 yr. We examine the key factor governing the neo-NS cooling emphasizing on the neutrino emission. A phenomenological heating source and new boundary conditions are introduced to mimic the high-temperature atmosphere of young NSs. We match the neo-NS luminosity to the late X-ray emission of the GRB-SN events URCA-1 in GRB980425-SN1998bw, URCA-2 in GRB030329-SN2003dh, and URCA-3 in GRB031203-SN2003lw. By calibrating our additional heating source at early times to $\sim 10^{12}$--$10^{15}$ erg/g/s, we find a striking agreement of the luminosity obtained from the cooling of neo-NSs with the late ($t=10^{8}$--$10^{9}$ s) X-ray emission observed in GRB-SN. It is therefore appropriate to revise the boundary conditions used in the cooling theory of NSs, to match the proper conditions of the atmosphere at young ages. Additional heating processes that are still not studied within this context, such as e+e- pair creation by overcritical fields and nuclear fusion and fission energy release, might also take place under such conditions and deserve further analysis. Observation of GRB-SN has shown the possibility of witnessing the thermal evolution of neo-NSs. A new campaign of dedicated observations is recommended both of GRB-SN and of isolated Type Ic SN.
description: Version to be published by Astronomy & Astrophysics. Abstract reduced with respect to the one to be published in A&A due to arXiv system constraint of 300 words
Nothura maculosa
Creators: name: Fischer, Wagner
name: Faria de Godoi, Raquel
name: Conceição Paranhos Filho, Antonio
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Aves
Tinamiformes
Tinamidae
Nothura
Nothura maculosa

description: Nothura maculosa (Temminck, 1815) Records. Table 3. Spotted Nothura individuals were recognized by their size (ca 25 cm long), ratite-like shape, brown upper parts with beige streaks, under parts with beige-streaks, black and brown on the breast, barring on the flanks, a black crown with beige streaks, white throat, and dull yellowish-brown legs.
description: Published as part of Fischer, Wagner, Faria de Godoi, Raquel & Conceição Paranhos Filho, Antonio, 2018, Roadkill records of reptiles and birds in Cerrado and Pantanal landscapes, pp. 845-876 in Check List 14 (5) on page 866, DOI: 10.15560/14.5.845
Rhynchotus rufescens
Creators: name: Fischer, Wagner
name: Faria de Godoi, Raquel
name: Conceição Paranhos Filho, Antonio
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Aves
Tinamiformes
Tinamidae
Rhynchotus
Rhynchotus rufescens

description: Rhynchotus rufescens (Temminck, 1815) Record. Table 3. The Red-winged Tinamou was recognized by its relatively large size (ca. 40 cm long), ratite-like shape, black crown, rufous primary feathers, and light gray underneath. This species has black bars on the flanks, abdomen and vent, a whitish throat, a bronze fore-neck and breast, and dark patch behind the eyes.
description: Published as part of Fischer, Wagner, Faria de Godoi, Raquel & Conceição Paranhos Filho, Antonio, 2018, Roadkill records of reptiles and birds in Cerrado and Pantanal landscapes, pp. 845-876 in Check List 14 (5) on page 866, DOI: 10.15560/14.5.845
K^- nuclear potentials from in-medium chirally motivated models
Creators: name: Cieplý, A.
name: Friedman, E.
name: Gal, A.
name: Gazda, D.
name: Mareš, J.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Nuclear Theory (nucl-th)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Experiment (nucl-ex)
subject: FOS: Physical sciences

description: A self consistent scheme for constructing K^- nuclear optical potentials from subthreshold in-medium Kbar-N s-wave scattering amplitudes is presented and applied to analysis of kaonic atoms data and to calculations of K^- quasibound nuclear states. The amplitudes are taken from a chirally motivated meson-baryon coupled-channel model, both at the Tomozawa-Weinberg leading order and at the next to leading order. Typical kaonic atoms potentials are characterized by a real part -Re V(K^-;chiral)=(85+/-5) MeV at nuclear matter density, in contrast to half this depth obtained in some derivations based on in-medium Kbar-N threshold amplitudes. The moderate agreement with data is much improved by adding complex rho- and rho^2-dependent phenomenological terms, found to be dominated by rho^2 contributions that could represent Kbar-NN -> YN absorption and dispersion, outside the scope of meson-baryon chiral models. Depths of the real potentials are then near 180 MeV. The effects of p-wave interactions are studied and found secondary to those of the dominant s-wave contributions. The in-medium dynamics of the coupled-channel model is discussed and systematic studies of K^- quasibound nuclear states are presented.
description: extension of Phys. Lett. B 702, 402 (2011) by the same authors; v2: minor corrections, matching PRC version
title: InChI Isotopologue and Isotopomer Specifications
Creators: name: Hunter N.B. Moseley
name: Philippe Rocca-Serra
name: Reza M. Salek
name: Masanori Arita
name: Emma Schymanski
Publisher: name: LCSB
Year: 2023

description: We present an approved extension to the International Union of Pure and Applied Chemistry (IUPAC) International Chemical Identifier (InChI) standard that allows the representation of isotopically-resolved chemical entities at varying levels of ambiguity in isotope location. This extension includes an improved interpretation of the current isotopic layer within the InChI standard and a new isotopologue layer specification for representing chemical intensities with ambiguous isotope localization. Both improvements support the unique isotopically-resolved chemical identification of features detected and measured in analytical instrumentation, specifically nuclear magnetic resonance and mass spectrometry. This new extension to the InChI standard enables improved annotation of analytical datasets characterizing chemical entities, supporting the FAIR (Findable, Accessible, Interoperable, and Reusable) guiding principles of data stewardship for chemical datasets, ultimately promoting Open Science in chemistry.
Penelope superciliaris Temminck 1815
Creators: name: Fischer, Wagner
name: Faria de Godoi, Raquel
name: Conceição Paranhos Filho, Antonio
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Aves
Galliformes
Cracidae
Penelope
Penelope superciliaris

description: Penelope superciliaris Temminck, 1815 Records. Table 3. The Rusty-margined Guan was easily identified by its large size (> 50 cm long), its naked red barbel and rudimentary tuft, wing plumage with rusty edges, a whitish design on the chest, and light grayish brown eyebrows.
description: Published as part of Fischer, Wagner, Faria de Godoi, Raquel & Conceição Paranhos Filho, Antonio, 2018, Roadkill records of reptiles and birds in Cerrado and Pantanal landscapes, pp. 845-876 in Check List 14 (5) on page 866, DOI: 10.15560/14.5.845
Full counting statistics in a disordered free fermion system
Creators: name: Levine, G. C.
name: Bantegui, M. J.
name: Burg, J. A.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: FOS: Physical sciences

description: The Full Counting Statistics (FCS) is studied for a one-dimensional system of non-interacting fermions with and without disorder. For two unbiased $L$ site lattices connected at time $t=0$, the charge variance increases as the natural logarithm of $t$, following the universal expression $ \approx \frac{1}{π^2}\log{t}$. Since the static charge variance for a length $l$ region is given by $ \approx \frac{1}{π^2}\log{l}$, this result reflects the underlying relativistic or conformal invariance and dynamical exponent $z=1$ of the disorder-free lattice. With disorder and strongly localized fermions, we have compared our results to a model with a dynamical exponent $z \ne 1$, and also a model for entanglement entropy based upon dynamical scaling at the Infinite Disorder Fixed Point (IDFP). The latter scaling, which predicts $ \propto \log\log{t}$, appears to better describe the charge variance of disordered 1-d fermions. When a bias voltage is introduced, the behavior changes dramatically and the charge and variance become proportional to $(\log{t})^{1/ψ}$ and $\log{t}$, respectively. The exponent $ψ$ may be related to the critical exponent characterizing spatial/energy fluctuations at the IDFP.
description: 10 pages, 14 figures; fixed typos; added references; added IDFP scaling based upon reference [1]; added finite bias section; fixed typos