cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Trans effects of chromosome aneuploidies on DNA methylation patterns in human Down syndrome and mouse models
Creators: name: Mendioroz, Maite
name: Do, Catherine
name: Jiang, Xiaoling
name: Liu, Chunhong
name: Darbary, Huferesh
name: Lang, Charles F.
name: Lin, John
name: Thomas, Anna
name: Abu-Amero, Sayeda
name: Stanier, Philip
name: Temkin, Alexis
name: Yale, Alexander
name: Liu, Meng-Min
name: Li, Yang
name: Salas, Martha C.
name: Kerkel, Kristi
name: Capone, George
name: Silverman, Wayne
name: Yu, Y. Eugene
name: Moore, Gudrun
name: Wegiel, Jerzy
name: Tycko, Benjamin
Publisher: name: Columbia University
Year: 2015
Subjects: subject: Epigenetics
subject: Chromosomes
subject: Down syndrome
subject: Genetics
subject: FOS: Biological sciences
subject: Biomechanics

description: Background
Trisomy 21 causes Down syndrome (DS), but the mechanisms by which the extra chromosome leads to deficient intellectual and immune function are not well understood.

Results
Here, we profile CpG methylation in DS and control cerebral and cerebellar cortex of adults and cerebrum of fetuses. We purify neuronal and non-neuronal nuclei and T lymphocytes and find biologically relevant genes with DS-specific methylation (DS-DM) in each of these cell types. Some genes show brain-specific DS-DM, while others show stronger DS-DM in T cells. Both 5-methyl-cytosine and 5-hydroxy-methyl-cytosine contribute to the DS-DM. Thirty percent of genes with DS-DM in adult brain cells also show DS-DM in fetal brains, indicating early onset of these epigenetic changes, and we find early maturation of methylation patterns in DS brain and lymphocytes. Some, but not all, of the DS-DM genes show differential expression. DS-DM preferentially affected CpGs in or near specific transcription factor binding sites (TFBSs), implicating a mechanism involving altered TFBS occupancy. Methyl-seq of brain DNA from mouse models with sub-chromosomal duplications mimicking DS reveals partial but significant overlaps with human DS-DM and shows that multiple chromosome 21 genes contribute to the downstream epigenetic effects.

Conclusions
These data point to novel biological mechanisms in DS and have general implications for trans effects of chromosomal duplications and aneuploidies on epigenetic patterning.
Chamber Surface Roughness and Electron Cloud for the Advanced Photon Source Superconducting Undulator
Creators: name: Boon, Laura
name: Harkay, Katherine
Publisher: name: arXiv
Year: 2013
Subjects: subject: Accelerator Physics (physics.acc-ph)
subject: Instrumentation and Detectors (physics.ins-det)
subject: FOS: Physical sciences

description: The electron cloud is a possible heat source in the superconducting undulator (SCU) designed for the Advanced Photon Source (APS), a 7-GeV electron synchrotron radiation source at Argonne National Laboratory. In electron cloud generation extensive research has been done, and is continuing, to understand the secondary electron component. However, little work has been done to understand the parameters of photoemission in the accelerator environment. To better understand the primary electron generation in the APS; a beamline at the Australian Light Source synchrotron was used to characterize two samples of the Al APS vacuum chamber. The total photoelectron yield and the photoemission spectra were measured. Four parameters were varied: surface roughness, sample temperature, incident photon energy, and incident photon angle, with their results presented here.
description: presented at ECLOUD'12: Joint INFN-CERN-EuCARD-AccNet Workshop on Electron-Cloud Effects, La Biodola, Isola d'Elba, Italy, 5-9 June 2012
Galea Meyen 1832
Creators: name: Honacki, James H.
name: Kinman, Kenneth E.
name: Koeppl, James W.
Publisher: name: Zenodo
Year: 1982
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Rodentia
Caviidae
Galea

description: Galea Meyen, 1832. Nouv. Acta Acad. Caes. Leop.-Carol., 16: 597. COMMENT: Reviewed by Huckinghaus, 1961, Z. Wiss. Zool., 166:58-72, and Cabrera, 1961:573-575. ISIS NUMBER: 5301410019002000000.
description: Published as part of James H. Honacki, Kenneth E. Kinman & James W. Koeppl, 1982, Order Rodentia (Part 6), pp. 560-594 in Mammal Species of the World (1 st Edition), Lawrence, Kansas, USA :Alien Press, Inc. & The Association of Systematics Collections on page 574, DOI: 10.5281/zenodo.7353039
description: {"references": ["Huckinghaus, F. 1961. Vergleichende Untersuchungen uber die Formenmannigfaltigkeit der Unterfamilie Caviinae Murray 1886. (Ergebnisse der Sudamerikaexpedition Herre / Rohrs 1956 - 1957). Zeitschrift fur Wissenschaftliche Zoologie, 166: 1 - 98, 62 pls."]}
Feasibility and safety of continuous retrograde administration of Del Nido cardioplegia: a case series.
Creators: name: Najjar, Marc
name: George, Isaac
name: Akashi, Hirokazu
name: Nishimura, Takashi
name: Yerebakan, Halit
name: Mongero, Linda B.
name: Beck, James
name: Hill, Stephen C.
name: Takayama, Hiroo
name: Williams, Mathew R.
Publisher: name: Columbia University
Year: 2015
Subjects: Heart--Surgery
Cardiac arrest, Induced
Muscle cells
Intracellular calcium
Medicine
Medical sciences

description: Background
Del Nido (DN) cardioplegia, a calcium-free, hyperkalemic solution containing lidocaine and magnesium has been developed to help reduce intracellular calcium influx and the resulting myocyte damage in the immediate postischemic period following cardiac arrest. DN cardioplegia has been used for pediatric cardiac surgery but its use in complex reoperative surgery has not been studied. We specifically report the outcomes of patients undergoing reoperative cardiac surgery after previous coronary artery bypass grafting with a patent internal mammary artery (IMA).

Methods
Patients undergoing reoperative cardiac surgery with prior coronary bypass grafting surgery were studied between 2010 and 2013. Fourteen patients were identified who required continued retrograde cardioplegia administration. In all cases, an initial antegrade dose was given, followed by continuous retrograde administration. Demographics, co-morbidities, intra-operative variables including cardioplegia volumes, post-operative complications, and patient outcomes were collected.

Results
The mean age of all patients was 73.3+/−6.7 years, and 93 % were male. Aortic cross clamp time and cardiopulmonary bypass times were 81+/−35 and 151+/−79 mins, respectively. Antegrade, retrograde and total cardioplegia doses were 1101+/−398, 3096+/−3185 and 4367+/−3751 ml, respectively. An average of 0.93+/−0.92 inotropes and 1.50+/−0.76 pressors were used on ICU admission after surgery. ICU and total hospital lengths of stay were 5.5+/−7.4 and 9.6+/−8.0 days, respectively. Complications occurred in two patients (14 %) (pneumonia and prolonged mechanical ventilation) and new arrhythmias occurred in five patients (36 %) (four new-onset atrial fibrillation and one pulseless electrical activity requiring 2 min of chest compression). No perioperative myocardial infarctions were noted based on electrocardiograms and cardiac serum markers. Postoperatively, left ventricular function was preserved in all patients whereas two patients (14 %) had mild decrease in right ventricular function as assessed by echocardiography. No mortality was observed.

Conclusion
Del Nido cardioplegia solution provides acceptable myocardial protection for cardiac surgery that requires continuous retrograde cardioplegia administration. DN cardioplegia’s administration in a continuous retrograde fashion with a patent IMA is believed to provide adequate myocardial protection while avoiding injuring the IMA through dissection and clamping.
Galea flavidens
Creators: name: Honacki, James H.
name: Kinman, Kenneth E.
name: Koeppl, James W.
Publisher: name: Zenodo
Year: 1982
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Rodentia
Caviidae
Galea
Galea flavidens

description: Galea flavidens (Brandt, 1835). Mem. Acad. Imp. Sci. St. Petersb., ser. 6, 3:439. TYPE LOCALITY: Unknown; possibly Minas Gerais, Brazil. DISTRIBUTION: Brazil. COMMENT: Couto, 1950, Mem. Paleontol. Bras., p. 232, considered flavidens synonymous with spixii, but see Cabrera, 1961:573, who considered both to be distinct species and discussed type locality. ISIS NUMBER: 5301410019002001001.
description: Published as part of James H. Honacki, Kenneth E. Kinman & James W. Koeppl, 1982, Order Rodentia (Part 6), pp. 560-594 in Mammal Species of the World (1 st Edition), Lawrence, Kansas, USA :Alien Press, Inc. & The Association of Systematics Collections on page 574, DOI: 10.5281/zenodo.7353039
description: {"references": ["Paula Couto, C. 1950. Footnote number 249. P. 232, in Memorias sobre a Paleontologia Brasileira (P. W. Lund with notes and comments by C. Paula Couto). Instituto Nacional do Livro, Rio de Janeiro, 589 pp., 56 pls."]}
title: Bey dem Grabe Friedrichs des Zweyten; 1786
title: Eine Elegie
titleType: Subtitle
Creators: name: Karsch, Anna Luise
Publisher: name: Universitätsbibliothek der Ludwig-Maximilians-Universität München
Year: 2015

description: Vorlageform des Erscheinungsvermerks: Berlin, 1786. Bey C. F. Matzdorf, unter der Stechbahn. - In Fraktur. - Verf. ermittelt
Galea musteloides Meyen 1832
Creators: name: Honacki, James H.
name: Kinman, Kenneth E.
name: Koeppl, James W.
Publisher: name: Zenodo
Year: 1982
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Rodentia
Caviidae
Galea
Galea musteloides

description: Galea musteloides Meyen, 1832. Nouv. Acta Acad. Caes. Leop.-Carol., 16: 597. TYPE LOCALITY: Peru, Paso de Tacna, on road to Lake Titicaca. DISTRIBUTION: S. Peru; Bolivia; Argentina; N. Chile. COMMENT: Reviewed by Mann, 1950, Invest. Zool. Chil., 1:2. ISIS NUMBER: 5301410019002002001.
description: Published as part of James H. Honacki, Kenneth E. Kinman & James W. Koeppl, 1982, Order Rodentia (Part 6), pp. 560-594 in Mammal Species of the World (1 st Edition), Lawrence, Kansas, USA :Alien Press, Inc. & The Association of Systematics Collections on page 574, DOI: 10.5281/zenodo.7353039
description: {"references": ["Mann, G. 1950. Nuevos mamiferos de Tarapaca. Investigacions Zoologicas Chilenas, 1: 2."]}
Transcriptomic profiles of aging in purified human immune cells
Creators: name: Reynolds, Lindsay M.
name: Ding, Jingzhong
name: Taylor, Jackson R.
name: Lohman, Kurt
name: Soranzo, Nicola
name: De La Fuente, Alberto
name: Liu, Tie Fu
name: Johnson, Craig
name: Barr, R. Graham
name: Register, Thomas C.
name: Donohue, Kathleen M.
name: Talor, Monica V.
name: Cihakova, Daniela
name: Gu, Charles
name: Divers, Jasmin
name: Siscovick, David
name: Burke, Gregory
name: Post, Wendy
name: Shea, Steven
name: Jacobs Jr., David R.
name: Hoeschele, Ina
name: McCall, Charles E.
name: Kritchevsky, Stephen B.
name: Herrington, David
name: Tracy, Russell P.
name: Liu, Yongmei
Publisher: name: Columbia University
Year: 2015
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Aging

description: Background:
Transcriptomic studies hold great potential towards understanding the human aging process. Previous transcriptomic studies have identified many genes with age-associated expression levels; however, small samples sizes and mixed cell types often make these results difficult to interpret.

Results:
Using transcriptomic profiles in CD14+ monocytes from 1,264 participants of the Multi-Ethnic Study of Atherosclerosis (aged 55–94 years), we identified 2,704 genes differentially expressed with chronological age (false discovery rate, FDR ≤ 0.001). We further identified six networks of co-expressed genes that included prominent genes from three pathways: protein synthesis (particularly mitochondrial ribosomal genes), oxidative phosphorylation, and autophagy, with expression patterns suggesting these pathways decline with age. Expression of several chromatin remodeler and transcriptional modifier genes strongly correlated with expression of oxidative phosphorylation and ribosomal protein synthesis genes. 17% of genes with age-associated expression harbored CpG sites whose degree of methylation significantly mediated the relationship between age and gene expression (p
Algebraic properties of Indigenous semirings
Creators: name: Behzadipour, Hussein
name: Koppelaar, Henk
name: Nasehpour, Peyman
Publisher: name: arXiv
Year: 2024
Subjects: subject: Commutative Algebra (math.AC)
subject: Discrete Mathematics (cs.DM)
subject: Rings and Algebras (math.RA)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences
subject: 16Y60, 13A15, 01A07

description: In this paper, we introduce Indigenous semirings and show that they are examples of information algebras. We also attribute a graph to them and discuss their diameters, girths, and clique numbers. On the other hand, we prove that the Zariski topology of any Indigenous semiring is the Sierpiński space. Next, we investigate their algebraic properties (including ideal theory). In the last section, we characterize units and idempotent elements of formal power series over Indigenous semirings.
description: Minor revision. Some examples and explanations added to the paper
Electromagnetic polarizabilities of the spin-$\frac{1}{2}$ singly heavy baryons in heavy baryon chiral perturbation theory
Creators: name: Chen, Yan-Ke
name: Wen, Liang-Zhen
name: Meng, Lu
name: Zhu, Shi-Lin
Publisher: name: arXiv
Year: 2024
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: We calculate the electromagnetic polarizabilities of the spin-$\frac{1}{2}$ singly heavy baryons in the heavy baryon chiral perturbation theory up to $\mathcal{O}(p^3)$. We estimate the low-energy constants using the magnetic moments of singly charmed baryons from lattice QCD simulations and the experimental decay widths of $Σ_c$ and $Σ_c^*$. Our results indicate that the long-range chiral corrections make significant contributions to the polarizabilities. Additionally, the magnetic dipole transitions $\mathcal{B}_6^* \to \mathcal{B}_6 +γ$ also provide large contribution to the magnetic polarizabilities.
description: 17 pages, 1 figure, 6 tables. Version accepted by PRD
Risk factors for loss to follow-up prior to ART initiation among patients enrolling in HIV care with CD4+ cell count ≥200 cells/μL in the multi-country MTCT-Plus Initiative
Creators: name: Gwynn, R. Charon
name: Fawzy, Ashraf
name: Viho, Ida
name: Wu, Yingfeng
name: Abrams, Elaine J.
name: Nash, Denis
Publisher: name: Columbia University
Year: 2015
Subjects: Highly active antiretroviral therapy
AIDS (Disease)--Patients--Death
Medical sciences

description: Background:

In resource-limited settings, many HIV-infected patients are lost to follow-up (LTF) before starting ART; risk factors among those not eligible for ART at enrollment into care are not well described.
Methods:

We examined data from 4,278 adults (3,613 women, 665 men) enrolled in HIV care through March 2007 in the MTCT-Plus Initiative with a CD4 count ≥200 cells/mm3 and WHO stage ≤ 2 at enrollment. Patients were considered LTF if > 12 months elapsed since their last clinic visit. Gender-specific Cox regression models were used to assess LTF risk factors.
Results:

The proportion LTF was 8.2 % at 12 months following enrollment, and was higher among women (8.4 %) than men (7.1 %). Among women, a higher risk of LTF was associated with younger age (adjusted hazard ratio [AHR]15–19/30+: 2.8, 95 % CI:2.1-3.6; AHR20–24/30+:1.9, 95 % CI:1.7-2.2), higher baseline CD4 count (AHR350–499/200–349:1.5; 95 % CI:1.0-2.1; AHR500+/200–349:1.5; 95 % CI:1.0-2.0), and being pregnant at the last clinic visit (AHR:1.9, 95 % CI:1.4-2.5). Factors associated with a lower risk of LTF included, employment outside the home (AHR:0.73, 95 % CI:0.59-0.90), co-enrollment of a family/household member (AHR:0.40, 95 % CI:0.26-0.61), and living in a household with ≥4 people (AHR:0.74, 95 % CI:0.64-0.85). Among men, younger age (AHR15–19/30+: 2.1, 95 % CI:1.2-3.5 and AHR30–34/35+:1.5, 95 % CI:1.0-2.4) had a higher risk of LTF. Electricity in the home (AHR:0.61, 95 % CI:0.41-0.91) and living in a household with ≥4 people (AHR:0.58, 95 % CI:0.39-0.85) had a lower risk of LTF.
Conclusions:

Socio-economic status and social support may be important determinants of retention in patients not yet eligible for ART. Among women of child-bearing age, strategies around sustaining HIV care during and after pregnancy require attention.
Keywords
HIV AIDS Anti-retroviral therapy Pre-ART, Lost to follow up Risk factors Social support
Galea spixii
Creators: name: Honacki, James H.
name: Kinman, Kenneth E.
name: Koeppl, James W.
Publisher: name: Zenodo
Year: 1982
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Rodentia
Caviidae
Galea
Galea spixii

description: Galea spixii (Wagler, 1831). Isis, 24: 512. TYPE LOCALITY: Brazil, Minas Gerais, Lagoa Santa. DISTRIBUTION: Brazil; Bolivia, east of the Andes. COMMENT: Includes wellsi; see Corbet and Hill, 1980:190; also see Cabrera, 1961:575, who fixed the type locality. Huckinghaus, 1961, Z. Wiss. Zool., 166:71, considered wellsi a distinct species. ISIS NUMBER: 5301410019002003001.
description: Published as part of James H. Honacki, Kenneth E. Kinman & James W. Koeppl, 1982, Order Rodentia (Part 6), pp. 560-594 in Mammal Species of the World (1 st Edition), Lawrence, Kansas, USA :Alien Press, Inc. & The Association of Systematics Collections on page 574, DOI: 10.5281/zenodo.7353039
description: {"references": ["Corbet, G. B., and J. E. Hill. 1980. A world list of mammalian species. British Museum (Natural History), London, 226 pp.", "Huckinghaus, F. 1961. Vergleichende Untersuchungen uber die Formenmannigfaltigkeit der Unterfamilie Caviinae Murray 1886. (Ergebnisse der Sudamerikaexpedition Herre / Rohrs 1956 - 1957). Zeitschrift fur Wissenschaftliche Zoologie, 166: 1 - 98, 62 pls."]}
A meta-analysis of parton distribution functions
Creators: name: Gao, Jun
name: Nadolsky, Pavel
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: A "meta-analysis" is a method for comparison and combination of nonperturbative parton distribution functions (PDFs) in a nucleon obtained with heterogeneous procedures and assumptions. Each input parton distribution set is converted into a "meta-parametrization" based on a common functional form. By analyzing parameters of the meta-parametrizations from all input PDF ensembles, a combined PDF ensemble can be produced that has a smaller total number of PDF member sets than the original ensembles. The meta-parametrizations simplify the computation of the PDF uncertainty in theoretical predictions and provide an alternative to the 2010 PDF4LHC convention for combination of PDF uncertainties. As a practical example, we construct a META ensemble for computation of QCD observables at the Large Hadron Collider using the next-to-next-to-leading order PDF sets from CTEQ, MSTW, and NNPDF groups as the input. The META ensemble includes a central set that reproduces the average of LHC predictions based on the three input PDF ensembles and Hessian eigenvector sets for computing the combined PDF+$α_s$ uncertainty at a common QCD coupling strength of 0.118.
description: version to appear on JHEP
Development of somites and their derivatives in amphioxus, and implications for the evolution of vertebrate somites
Creators: name: Mansfield, Jennifer H.
name: Haller, Edward
name: Holland, Nicholas D.
name: Brent, Ava E.
Publisher: name: Columbia University
Year: 2015
Subjects: Transmission electron microscopy
Evolution (Biology)
Somite
Biology

description: Background:
Vertebrate somites are subdivided into lineage compartments, each with distinct cell fates and evolutionary histories. Insights into somite evolution can come from studying amphioxus, the best extant approximation of the chordate ancestor. Amphioxus somites have myotome and non-myotome compartments, but development and fates of the latter are incompletely described. Further, while epithelial to mesenchymal transition (EMT) is important for most vertebrate somitic lineages, amphioxus somites generally have been thought to remain entirely epithelial. Here, we examined amphioxus somites and derivatives, as well as extracellular matrix of the axial support system, in a series of developmental stages by transmission electron microscopy (TEM) and in situ hybridization for collagen expression.

Results:
The amphioxus somite differentiates medially into myotome, laterally into the external cell layer (a sub-dermal mesothelium), ventrally into a bud that forms mesothelia of the perivisceral coelom, and ventro-medially into the sclerotome. The sclerotome forms initially as a monolayered cell sheet that migrates between the myotome and the notochord and neural tube; subsequently, this cell sheet becomes double layered and encloses the sclerocoel. Other late developments include formation of the fin box mesothelia from lateral somites and the advent of isolated fibroblasts, likely somite derived, along the myosepta. Throughout development, all cells originating from the non-myotome regions of somites strongly express a fibrillar collagen gene, ColA, and thus likely contribute to extracellular matrix of the dermal and axial connective tissue system.

Conclusions:
We provide a revised model for the development of amphioxus sclerotome and fin boxes and confirm previous reports of development of the myotome and lateral somite. In addition, while somite derivatives remain almost entirely epithelial, limited de-epithelialization likely converts some somitic cells into fibroblasts of the myosepta and dermis. Ultrastructure and collagen expression suggest that all non-myotome somite derivatives contribute to extracellular matrix of the dermal and axial support systems. Although amphioxus sclerotome lacks vertebrate-like EMT, it resembles that of vertebrates in position, movement to surround midline structures and into myosepta, and contribution to extracellular matrix of the axial support system. Thus, many aspects of the sclerotome developmental program evolved prior to the origin of the vertebrate mineralized skeleton.

Keywords:

Somite evolution Sclerotome Skeleton Connective tissue Tendon Amphioxus Chordate
High incidence and remission of reported food hypersensitivity in Swedish children followed from 8 to 12 years of age – a population based cohort study
Creators: name: Winberg, Anna
name: Strinnholm, Åsa
name: Hedman, Linnea
name: West, Christina E.
name: Perzanowski, Matthew S.
name: Rönmark, Eva
Publisher: name: Columbia University
Year: 2014
Subjects: Food allergy in children
Food intolerance
Food--Analysis
Public health

description: Background:
Few population-based cohort studies have examined reported food hypersensitivity longitudinally. We investigated prevalence, incidence and remission of perceived food hypersensitivity among schoolchildren from 8 to 12 years of age, and risk factors associated with incidence and remission.

Methods:
A population-based cohort including all 7–8 year-old children in three Swedish towns was recruited in 2006. A total of 2,585 (96% of invited) children participated in a parental questionnaire. The children in two of the towns, n = 1,700 (90% of invited) also participated in skin-prick-testing with airborne allergens. The cohort was followed using the same methods at 11–12 years of age. At study follow up, specific IgE to foods was analyzed in a randomized subset of children (n = 652).

Results:
The prevalence of perceived food hypersensitivity increased from 21% at 8 years to 26% at 12 years of age. During this four-year-period, the cumulative incidence of food hypersensitivity was high (15%), as was remission (33%). This pattern was particularly evident for hypersensitivity to cow´s milk, while the incidence of hypersensitivity to other foods was lower. Female sex, allergic heredity, current rhinitis and allergic sensitization were associated with the incidence of food hypersensitivity and allergic sensitization was negatively associated with remission. Risk-factor-patterns for both incidence and remission were different for hypersensitivity to milk compared with hypersensitivity to other foods. Generally, the agreement between reported food hypersensitivity and IgE-sensitization to the implicated food was poor.

Conclusions:
In this longitudinal, population-based cohort-study perceived food hypersensitivity was common among children between ages 8 and 12, often transient and not well correlated with food-specific IgE. While these findings suggest an overestimated prevalence of food hypersensitivity, the public-health-significance remains high as they reflect the perceived reality to which the children adapt their life and food intakes.

Keywords:

Food hypersensitivity Incidence Remission Risk factors Sensitization
Development and validation of a classification approach for extracting severity automatically from electronic health records
Creators: name: Boland, Mary Regina
name: Tatonetti, Nicholas P.
name: Hripcsak, George
Publisher: name: Columbia University
Year: 2015
Subjects: subject: Phenotype
subject: Data mining
subject: Health status indicators
subject: Medical records--Data processing
subject: Bioinformatics
subject: FOS: Computer and information sciences

description: Background:
Electronic Health Records (EHRs) contain a wealth of information useful for studying clinical phenotype-genotype relationships. Severity is important for distinguishing among phenotypes; however other severity indices classify patient-level severity (e.g., mild vs. acute dermatitis) rather than phenotype-level severity (e.g., acne vs. myocardial infarction). Phenotype-level severity is independent of the individual patient’s state and is relative to other phenotypes. Further, phenotype-level severity does not change based on the individual patient. For example, acne is mild at the phenotype-level and relative to other phenotypes. Therefore, a given patient may have a severe form of acne (this is the patient-level severity), but this does not effect its overall designation as a mild phenotype at the phenotype-level.

Methods:
We present a method for classifying severity at the phenotype-level that uses the Systemized Nomenclature of Medicine – Clinical Terms. Our method is called the Classification Approach for Extracting Severity Automatically from Electronic Health Records (CAESAR). CAESAR combines multiple severity measures – number of comorbidities, medications, procedures, cost, treatment time, and a proportional index term. CAESAR employs a random forest algorithm and these severity measures to discriminate between severe and mild phenotypes.

Results:
Using a random forest algorithm and these severity measures as input, CAESAR differentiates between severe and mild phenotypes (sensitivity = 91.67, specificity = 77.78) when compared to a manually evaluated reference standard (k = 0.716).

Conclusions:
CAESAR enables researchers to measure phenotype severity from EHRs to identify phenotypes that are important for comparative effectiveness research.

Keywords:
Electronic Health Records Phenotype Health status indicators Data mining Outcome assessment (Health Care)
Full Field Supercritical Angle Fluorescence Microscopy for live cell imaging
Creators: name: Barroca, Thomas
name: Balaa, Karla
name: Delahaye, Julie
name: Lévêque-Fort, Sandrine
name: Fort, Emmanuel
Publisher: name: arXiv
Year: 2013
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We introduce a full field fluorescence imaging technique with axial confinement of about 100 nm at the sample/substrate interface. Contrary to standard surface imaging techniques, this confinement is obtained through emission filtering. This technique is based on supercritical emission selectivity. It can be implemented on any epifluorescence microscope with a commercial high numerical aperture objective and offers a real time surface imaging capability. This technique is of particular interest for live cell membrane and adhesion studies. Using HEK cells, we show that one can observe simultaneously the surface and in-depth cell phenomena.
Kerodon F. Cuvier 1825
Creators: name: Honacki, James H.
name: Kinman, Kenneth E.
name: Koeppl, James W.
Publisher: name: Zenodo
Year: 1982
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Rodentia
Caviidae
Kerodon

description: Kerodon F. Cuvier, 1825. Des Dentes des Mammiferes, p. 151. REVIEWED BY: T. E. Lacher, Jr. (TEL); M. R. Willig (MRW). COMMENT: Reviewed by Huckinghaus, 1961, Z. Wiss. Zool., 166:12- 14, 33. J. Moojen and M. Locks are describing a new species in this genus, from Brazil (MRW and TEL). ISIS NUMBER: 5301410019003000000.
description: Published as part of James H. Honacki, Kenneth E. Kinman & James W. Koeppl, 1982, Order Rodentia (Part 6), pp. 560-594 in Mammal Species of the World (1 st Edition), Lawrence, Kansas, USA :Alien Press, Inc. & The Association of Systematics Collections on page 574, DOI: 10.5281/zenodo.7353039
description: {"references": ["Huckinghaus, F. 1961. Vergleichende Untersuchungen uber die Formenmannigfaltigkeit der Unterfamilie Caviinae Murray 1886. (Ergebnisse der Sudamerikaexpedition Herre / Rohrs 1956 - 1957). Zeitschrift fur Wissenschaftliche Zoologie, 166: 1 - 98, 62 pls."]}
White dwarfs constraints on dark sector models with light particles
Creators: name: Ubaldi, Lorenzo
Publisher: name: arXiv
Year: 2013
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: The white dwarf luminosity function is well understood in terms of standard model physics and leaves little room for exotic cooling mechanisms related to the possible existence of new weakly interacting light particles. This puts significant constraints on the parameter space of models that contain a massive dark photon and light dark sector particles.
description: CETUP*2013 proceedings
Haploinsufficiency of Bcl11b suppresses the progression of ATM-deficient T cell lymphomas
Creators: name: Pinkney, Kerice A.
name: Jiang, Wenxia
name: Lee, Brian J.
name: Loredan, Denis G.
name: Li, Chen
name: Bhagat, Govind
name: Zha, Shan
Publisher: name: Columbia University
Year: 2015
Subjects: subject: Transcription factors
subject: Leukemia--Genetic aspects
subject: T cells
subject: Immunology
subject: FOS: Clinical medicine
subject: Oncology

description: Bcl11b is a transcription factor important for T cell development and also a tumor-suppressor gene that is hemizygously inactivated in ~10 % human T cell acute lymphoblastic leukemia (T-ALL) and several murine T-ALL models, including ATM−/− thymic lymphomas. Here we report that heterozygous loss of Bcl11b (Bcl11b+/−) unexpectedly reduced lethal thymic lymphoma in ATM−/− mice by suppressing lymphoma progression, but not initiation. The suppression was associated with a T cell-mediated immune response in ATM−/−Bcl11b+/− mice, revealing a haploid insufficient function of Bcl11b in immune modulation against lymphoma and offering an explanation for the complex relationship between Bcl11b status with T-ALL prognosis.
British Columbia Legislative Assembly sessional clipping book (1891-04)
Creators: name: :Unav
Publisher: name: University of Victoria Libraries
Year: 2022
Subjects: subject: Law
valueUri: http://id.worldcat.org/fast/993678
subject: FOS: Law
subject: Politics and government
valueUri: http://id.worldcat.org/fast/1919741
subject: British Columbia. Legislative Assembly
valueUri: http://id.worldcat.org/fast/600765

description: These Sessional Clippings books cover the period 1891 to 1972, and include newspaper accounts written by various legislative reporters who covered debates occurring in the British Columbia Legislative Assembly. Transcripts of debates of the Legislative Assembly (Hansard) were not published in B.C. until 1970; hence these "Sessional Clipping Books" augment the "Journals", the record of daily proceedings of the Legislative Assembly. Selected clippings from various newspapers including the Vancouver Sun, the Vancouver Province, the Colonist, and the Times newspapers, relating to the newspaper reports concerning activities of the Legislature. The original sessional clippings books comprise 351 ledger size print volumes, held at the Legislative Library in Victoria BC. The print volumes were microfilmed onto 26 reels in 1977 under a Tri University Libraries (TRIUL) project by Precision Micrographic Services (Vancouver, B.C.), with the permission of the Legislative Library, Victoria, British Columbia. This digital collection was created by scanning the 26 microfilm reels.
Designing quantum dots for solotronics
Creators: name: Kobak, J.
name: Smoleński, T.
name: Goryca, M.
name: Papaj, M.
name: Gietka, K.
name: Bogucki, A.
name: Koperski, M.
name: Rousset, J. -G.
name: Suffczyński, J.
name: Janik, E.
name: Nawrocki, M.
name: Golnik, A.
name: Kossacki, P.
name: Pacuski, W.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Solotronics, optoelectronics based on solitary dopants, is an emerging field of research and technology reaching the ultimate limit of miniaturization. It aims at exploiting quantum properties of individual ions or defects embedded in a semiconductor matrix. As already shown, optical control of a spin of a magnetic ion is feasible employing photo-generated carriers confined in a quantum dot. A non-radiative recombination, regarded as a severe problem, limited development of quantum dots with magnetic ions. Our photoluminescence studies on, so far unexplored, individual CdTe dots with single cobalt ions and individual CdSe dots with single manganese ions show, however, that even if energetically allowed, the single ion related non-radiative recombination is negligible in such zero-dimensional structures. This opens solotronics for a wide range of even not yet considered systems. Basing on the results of our single spin relaxation experiments and on the material trends, we identify optimal magnetic ion-quantum dot systems for implementation of a single-ion based spin memory.
description: Main text and supplementary information: 15 pages, 6 figures, 3 tables
Improving DRAM Performance, Security, and Reliability by Understanding and Exploiting DRAM Timing Parameter Margins
Creators: name: Kim, Jeremie
Publisher: name: Carnegie Mellon University
Year: 2020
Subjects: Computer Engineering

description: Characterization of real DRAM devices has enabled findings in DRAM device properties, which has led to proposals that significantly improve overall system performance by reducing DRAM access latency and power consumption. In addition to improving system performance, a deeper understanding of DRAM technology via characterization can also improve device reliability and security. These can beseen with the recent discoveries of 1) DRAM-based true random number generators (TRNGs), a method for generating true random numbers using DRAM devices which can be used in many applications, 2) DRAM-based physical unclonable functions (PUFs), a method for generating unique device-dependent keys for identification and authentication, and 3) the RowHammer vulnerability, a phenomenon where repeatedly accessing a DRAM row can cause failures in unaccessed neighboring DRAM rows.To advance DRAM-based discoveries and mechanisms, this dissertation rigorously characterizes many modern commodity DRAM devices and shows that by exploitingDRAM access timing margins within manufacturer-recommended DRAM timing specifications, we can significantly improve system performance, reduce power consumption, and improve device reliability and security. First, we characterize DRAM timing parameter margins and find that certain regions of DRAM can be accessed faster than other regions due to DRAM cell process manufacturing variation. We exploit this by enabling variable access times depending on the DRAM cells being accessed, whichnot only improves overall system performance, but also decreases power consumption. Second, we find that we can uniquely identify DRAM devices by the locations offailures that result when we access DRAM with timing parameters reduced below specification values. Because we induce these failures with DRAM accesses, we cangenerate these unique identifiers significantly more quickly than prior work. Third, we propose a random number generator that is based on our observation that timingfailures in certain DRAM cells are randomly induced and can thus be repeatedly polled to very quickly generate true random values. Finally, we characterize the RowHammersecurity vulnerability on a wide range of modern DRAM chips while violating the DRAM refresh requirement in order to directly characterize the underlying DRAM technology without the interference of refresh commands. We demonstrate with our characterization of real chips, that existing RowHammer mitigation mechanisms eitherare not scalable or suffer from prohibitively large performance overheads in projected future devices and it is critical to research more effective solutions to RowHammer.Overall, our studies build a new understanding of modern DRAM devices to improve computing system performance, reliability and security all at the same time.
Proof of the Formula of Cachazo, He and Yuan for Yang-Mills Tree Amplitudes in Arbitrary Dimension
Creators: name: Dolan, Louise
name: Goddard, Peter
Publisher: name: arXiv
Year: 2013
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: A proof is given of the formula, recently proposed by Cachazo, He and Yuan (CHY) for gluon tree amplitudes in pure Yang-Mills theory in arbitrary dimension. The approach is to first establish the corresponding result for massless $ϕ^3$ theory using the BCFW recurrence relation and then to extend this to the gauge theory case. Additionally, it is shown that the scattering equations introduced by CHY can be generalized to massive particles, enabling the description of tree amplitudes for massive $ϕ^3$ theory.
description: 27 pp
Kerodon rupestris
Creators: name: Honacki, James H.
name: Kinman, Kenneth E.
name: Koeppl, James W.
Publisher: name: Zenodo
Year: 1982
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Rodentia
Caviidae
Kerodon
Kerodon rupestris

description: Kerodon rupestris (Wied, 1820). Isis, 6:43. TYPE LOCALITY: Brazil, Bahia, Rio Belmonte. DISTRIBUTION: E. Brazil. COMMENT: MRW and TEL give the type locality as Rio Pardo and Moojen, 1952, Os Roedores do Brasil, as Rio Grande de Belmonte, Rio Pardo, Rio San Francisco; but see Cabrera, 1961:580. ISIS NUMBER: 5301410019003001001.
description: Published as part of James H. Honacki, Kenneth E. Kinman & James W. Koeppl, 1982, Order Rodentia (Part 6), pp. 560-594 in Mammal Species of the World (1 st Edition), Lawrence, Kansas, USA :Alien Press, Inc. & The Association of Systematics Collections on page 574, DOI: 10.5281/zenodo.7353039
description: {"references": ["Moojen, J. 1952. Os roedores do Brasil. Biblioteca Cientifica Brasileira, ser. A, 2: 1 - 214."]}
On integral forms for vertex algebras associated with affine Lie algebras and lattices
Creators: name: McRae, Robert
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Algebra (math.QA)
subject: Representation Theory (math.RT)
subject: FOS: Mathematics
subject: 17B69 (primary), 17B67 (secondary)

description: We revisit the construction of integral forms for vertex (operator) algebras $V_L$ based on even lattices $L$ using generators instead of bases, and we construct integral forms for $V_L$-modules. We construct integral forms for vertex (operator) algebras based on highest-weight modules for affine Lie algebras and we exhibit natural generating sets. For vertex operator algebras in general, we give conditions showing when an integral form contains the standard conformal vector generating the Virasoro algebra. Finally, we study integral forms in contragredients of modules for vertex algebras.
description: 25 pages, minor corrections and references added, now published online in the Journal of Pure and Applied Algebra
Soft Electronic Materials for Stretchable Circuits & Devices
Creators: name: Chengfeng Pan
Publisher: name: Carnegie Mellon University
Year: 2020
Subjects: subject: 91299 Materials Engineering not elsewhere classified
subject: FOS: Materials engineering

description: Stretchable electronics have shown great potential for emerging applications in mechanically deformable displays, soft robotics, wearable computing, bio-integrated devices for human health monitoring, and energy storage and harvesting. Compared to traditional silicon based electrical system, stretchable electronics enables devices to remain functional under mechanical deformation such as twisting, bending, compressing, and stretching. Future progress in stretchable circuits and devices depends on high performance soft and stretchable electronic materials. Efforts in soft and stretchable electronic materials have been largely focused on improving two essential performances, including electrical property (e.g. electrical conductivity, dielectric permittivity) and mechanical property (e.g. stretchability, compliance). My dissertation focuses on developing high performance soft and elastic conductive and high dielectric materials to expand the material selection domain for the development of stretchable electronics.In this dissertation, a materials architecture of liquid metal (LM) elastomer nanocomposites are designed to enhance the dielectric permittivity without degrading mechanical properties (stretchability and softness) and dielectric breakdown strength significantly for stretchable dielectric materials. I also introduce a phase segregated silver-silicone (PS3) materials architecture that is designed for soft, stretchable, and thermally stable conductor. PS3 composites are enabled with core-shell silver coated PDMS beads and silver flakes embedded in PDMS matrix. In addition to these composites, I also introduce two classes of soft and stretchable multifunctional electronic materials, i.e. a transparent, stretchable conductive film composed of liquid metal traces that are patterned using direct laser writing technology, and is a sediment liquid metal (SLM) elastomer composite for stretchable and wearable triboelectric nanogenerators (TENGs). A series of applications, including dielectric elastomer actuators, dielectric generators, strain sensors, RFID antennas, TENGs, and soft display, are presented to demonstrate these materials.
British Columbia Legislative Assembly sessional clipping book (1891-03)
Creators: name: :Unav
Publisher: name: University of Victoria Libraries
Year: 2022
Subjects: subject: British Columbia. Legislative Assembly
valueUri: http://id.worldcat.org/fast/600765
subject: Law
valueUri: http://id.worldcat.org/fast/993678
subject: FOS: Law
subject: Politics and government
valueUri: http://id.worldcat.org/fast/1919741

description: These Sessional Clippings books cover the period 1891 to 1972, and include newspaper accounts written by various legislative reporters who covered debates occurring in the British Columbia Legislative Assembly. Transcripts of debates of the Legislative Assembly (Hansard) were not published in B.C. until 1970; hence these "Sessional Clipping Books" augment the "Journals", the record of daily proceedings of the Legislative Assembly. Selected clippings from various newspapers including the Vancouver Sun, the Vancouver Province, the Colonist, and the Times newspapers, relating to the newspaper reports concerning activities of the Legislature. The original sessional clippings books comprise 351 ledger size print volumes, held at the Legislative Library in Victoria BC. The print volumes were microfilmed onto 26 reels in 1977 under a Tri University Libraries (TRIUL) project by Precision Micrographic Services (Vancouver, B.C.), with the permission of the Legislative Library, Victoria, British Columbia. This digital collection was created by scanning the 26 microfilm reels.
Magnetospheric accretion on the fully-convective classical T Tauri star DN Tau
Creators: name: Donati, JF
name: Gregory, SG
name: Alencar, SHP
name: Hussain, G
name: Bouvier, J
name: Jardine, MM
name: Menard, F
name: Dougados, C
name: Romanova, MM
name: collaboration, the MaPP
Publisher: name: arXiv
Year: 2013
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We report here results of spectropolarimetric observations of the classical T Tauri star DN Tau carried out (at 2 epochs) with ESPaDOnS at the Canada-France-Hawaii Telescope within the `Magnetic Protostars and Planets' programme. We infer that DN Tau, with a photospheric temperature of 3,950+-50 K, a luminosity of 0.8+-0.2 Lsun and a rotation period of 6.32 d, is a ~2Myr-old fully-convective 0.65+-0.05 Msun star with a radius of 1.9+-0.2 Dsun, viewed at an inclination of 35+-10degr. Clear circularly-polarized Zeeman signatures are detected in both photospheric and accretion-powered emission lines, probing longitudinal fields of up to 1.8 kG (in the He1 D3 accretion proxy). Rotational modulation of Zeeman signatures, detected both in photospheric and accretion lines, is different between our 2 runs, providing further evidence that fields of cTTSs are generated by non-stationary dynamos. Using tomographic imaging, we reconstruct maps of the large-scale field, of the photospheric brightness and of the accretion-powered emission at the surface of DN Tau at both epochs. We find that the magnetic topology is mostly poloidal, and largely axisymmetric, with an octupolar component (of polar strength 0.6-0.8 kG) 1.5-2.0x larger than the dipolar component (of polar strength 0.3-0.5 kG). DN Tau features dominantly poleward accretion at both epochs. The large-scale dipole component of DN Tau is however too weak to disrupt the surrounding accretion disc further than 65-90% of the corotation radius (at which the disc Keplerian period matches the stellar rotation period), suggesting that DN Tau is already spinning up despite being fully convective.
description: MNRAS in press (18 pages, 11 figures, 1 table)
Whole genome capture of vector-borne pathogens from mixed DNA samples: a case study of Borrelia burgdorferi
Creators: name: Carpi, Giovanna
name: Walter, Katharine S.
name: Bent, Stephen J.
name: Hoen, Anne Gatewood
name: Diuk-Wasser, Maria
name: Caccone, Adalgisa
Publisher: name: Columbia University
Year: 2015
Subjects: subject: Lyme disease
subject: Communicable diseases--Epidemiology
subject: Nucleotide sequence
subject: Genetics
subject: FOS: Biological sciences

description: Background:
Rapid and accurate retrieval of whole genome sequences of human pathogens from disease vectors or animal reservoirs will enable fine-resolution studies of pathogen epidemiological and evolutionary dynamics. However, next generation sequencing technologies have not yet been fully harnessed for the study of vector-borne and zoonotic pathogens, due to the difficulty of obtaining high-quality pathogen sequence data directly from field specimens with a high ratio of host to pathogen DNA.

Results:
We addressed this challenge by using custom probes for multiplexed hybrid capture to enrich for and sequence 30 Borrelia burgdorferi genomes from field samples of its arthropod vector. Hybrid capture enabled sequencing of nearly the complete genome (~99.5 %) of the Borrelia burgdorferi pathogen with 132-fold coverage, and identification of up to 12,291 single nucleotide polymorphisms per genome.

Conclusions:
The proprosed culture-independent method enables efficient whole genome capture and sequencing of pathogens directly from arthropod vectors, thus making population genomic study of vector-borne and zoonotic infectious diseases economically feasible and scalable. Furthermore, given the similarities of invertebrate field specimens to other mixed DNA templates characterized by a high ratio of host to pathogen DNA, we discuss the potential applicabilty of hybrid capture for genomic study across diverse study systems.

Keywords:
Hybrid capture Whole-genome sequencing SNPs Tick-borne pathogens Lyme disease