cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Clustering and principal-components approach based on heritability for mapping multiple gene expressions
Creators: name: Wang, Yuanjia
name: Fang, Yixin
name: Wang, Shuang
Publisher: name: Columbia University
Year: 2007
Subjects: subject: Phenotype
subject: Gene expression
subject: Biometry
subject: Genetics
subject: FOS: Biological sciences

description: When the number of phenotypes in a genetic study is on the scale of thousands, such as in studies concerning thousands of gene expression levels, the single-trait analysis is computationally intensive, and heavy adjustment of multiple comparisons is required. Traditional multivariate genetic linkage analysis for quantitative traits focuses on mapping only a few phenotypes and is not feasible for a large number of traits. To cope with high-dimensional phenotype data, clustering analysis and principal-component analysis (PCA) are proposed to reduce the data dimensionality and to map shared genetic contributions for multiple traits. However, standard clustering analysis and PCA are applicable for independent observations. In most genetic studies, where family data are collected, these standard analyses can only be applied to founders and can lead to the loss of information. Here, we proposed a clustering method that can exploit family structure information and applied the method to 29 gene expression levels mapped to a reported hot spot on chromosome 14. We then used a PCA approach based on heritability applicable to small number of traits to combine phenotypes in the clusters. Lastly, we used a penalized PCA approach based on heritability applicable to arbitrary number of traits to combine 150 gene expression levels with the highest heritability. Genome-wide multipoint linkage analysis was carried out on the individual traits and on the combined traits. Two previously reported peaks on chromosomes 14 and 20 were identified. Linkage evidence was stronger for traits derived from methods that incorporate family structure information.
Additional file 3 of Molecular surveillance of the Plasmodium vivax multidrug resistance 1 gene in Peru between 2006 and 2015
Creators: name: Villena, Fredy E.
name: Maguiña, Jorge L.
name: Meddly L. Santolalla
name: Edwar Pozo
name: Salas, Carola J.
name: Ampuero, Julia S.
name: Lescano, Andres G.
name: Danett K. Bishop
name: Valdivia, Hugo O.
Publisher: name: figshare
Year: 2020
Subjects: subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: 60506 Virology

description: Additional file 3: Table S3. Prevalence of haplotypes consisting of synonymous and nonsynonymousmutation.
Logarithmic operator intervals in the boundary theory of critical percolation
Creators: name: Simmons, Jacob J H
Publisher: name: arXiv
Year: 2013
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: We consider the sub-sector of the $c=0$ logarithmic conformal field theory (LCFT) generated by the boundary condition changing (bcc) operator in two dimensional critical percolation. This operator is the zero weight Kac operator $ϕ_{1,2}$, identified with the growing hull of the SLE$_6$ process. We identify percolation configurations with the significant operators in the theory. We consider operators from the first four bcc operator fusions: the identity and bcc operator; the stress tensor and its logarithmic partner; the derivative of the bcc operator and its logarithmic partner; and the pre-logarithmic operator $ϕ_{1,3}$. We construct several intervals in the percolation model, each associated to one of the LCFT operators we consider, allowing us to calculate crossing probabilities and expectation values of crossing cluster numbers. We review the Coulomb gas, which we use as a method of calculating these quantities when the number of bcc operator makes a direct solution to the system of differential equations intractable. Finally we discuss the case of the six-point correlation function, which applies to crossing probabilities between the sides of a conformal hexagon. Specifically we introduce an integral result that allows one to identify the probability that a single percolation cluster touches three alternating sides a hexagon with free boundaries. We give results of the numerical integration for the case of a regular hexagon.
description: 32 pages, 20 figures
SModelS v2.3: enabling global likelihood analyses
Creators: name: Altakach, Mohammad Mahdi
name: Kraml, Sabine
name: Lessa, Andre
name: Narasimha, Sahana
name: Pascal, Timothée
name: Waltenberger, Wolfgang
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: We present version 2.3 of SModelS, a public tool for the fast reinterpretation of LHC searches for new physics on the basis of simplified-model results. The main new features are a database update with the latest available experimental results for full Run 2 luminosity, comprising in particular a large variety of electroweak-ino searches, and the ability to combine likelihoods from different analyses. This enables statistically more rigorous constraints and opens the way for global likelihood analyses for LHC searches. The physics impact is demonstrated for the electroweak-ino sector of the minimal supersymmetric standard model.
description: 34 pages, 13 figures, 3 tables. The program and an extensive online documentation are available at https://smodels.github.io/. The dataset used in section 4 is available at https://doi.org/10.5281/zenodo.8086949
Proechimys urichi
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
Echimyidae
Proechimys
Proechimys urichi

description: Proechimys urichi (J. A. Allen, 1899). Bull. Am. Mus. Nat. Hist., 12: 199. TYPE LOCALITY: Venezuela, Sucre, Quebrada Seca. DISTRIBUTION: N. Venezuela. COMMENT: Formerly included in guyannensis; see Reig et al., 1980:291-312, in Voronstov and Van Brink, eds., Animal genetics and evolution, Junk, The Hague.
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 591, DOI: 10.5281/zenodo.7353039
description: {"references": ["Reig, O. A., M. Aguilera, M. A. Barros, and M. Useche. 1980. Chromosomal speciation in a Rassenkreis of Venezuelan spiny rats (genus Proechimys; Rodentia: Echimyidae). Genetica, 52 / 53: 291 - 312."]}
Additional file 2 of Molecular surveillance of the Plasmodium vivax multidrug resistance 1 gene in Peru between 2006 and 2015
Creators: name: Villena, Fredy E.
name: Maguiña, Jorge L.
name: Meddly L. Santolalla
name: Edwar Pozo
name: Salas, Carola J.
name: Ampuero, Julia S.
name: Lescano, Andres G.
name: Danett K. Bishop
name: Valdivia, Hugo O.
Publisher: name: figshare
Year: 2020
Subjects: subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: 60506 Virology

description: Additional file 2: Table S1. Primers for conventional PCR, Nested PCR and sequencing ofpvmdr1 gene.
A Critical Assessment of Photometric Redshift Methods: A CANDELS Investigation
Creators: name: Dahlen, Tomas
name: Mobasher, Bahram
name: Faber, Sandra M.
name: Ferguson, Henry C.
name: Barro, Guillermo
name: Finkelstein, Steven L.
name: Finlator, Kristian
name: Fontana, Adriano
name: Gruetzbauch, Ruth
name: Johnson, Seth
name: Pforr, Janine
name: Salvato, Mara
name: Wiklind, Tommy
name: Wuyts, Stijn
name: Acquaviva, Viviana
name: Dickinson, Mark E.
name: Guo, Yicheng
name: Huang, Jiasheng
name: Huang, Kuang-Han
name: Newman, Jeffrey A.
name: Bell, Eric F.
name: Conselice, Christopher J.
name: Galametz, Audrey
name: Gawiser, Eric
name: Giavalisco, Mauro
name: Grogin, Norman A.
name: Hathi, Nimish
name: Kocevski, Dale
name: Koekemoer, Anton M.
name: Koo, David C.
name: Lee, Kyoung-Soo
name: McGrath, Elizabeth J.
name: Papovich, Casey
name: Peth, Michael
name: Ryan, Russell
name: Somerville, Rachel
name: Weiner, Benjamin
name: Wilson, Grant
Publisher: name: arXiv
Year: 2013
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We present results from the Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey (CANDELS) photometric redshift methods investigation. In this investigation, the results from eleven participants, each using a different combination of photometric redshift code, template spectral energy distributions (SEDs) and priors, are used to examine the properties of photometric redshifts applied to deep fields with broad-band multi-wavelength coverage. The photometry used includes U-band through mid-infrared filters and was derived using the TFIT method. Comparing the results, we find that there is no particular code or set of template SEDs that results in significantly better photometric redshifts compared to others. However, we find codes producing the lowest scatter and outlier fraction utilize a training sample to optimize photometric redshifts by adding zero-point offsets, template adjusting or adding extra smoothing errors. These results therefore stress the importance of the training procedure. We find a strong dependence of the photometric redshift accuracy on the signal-to-noise ratio of the photometry. On the other hand, we find a weak dependence of the photometric redshift scatter with redshift and galaxy color. We find that most photometric redshift codes quote redshift errors (e.g., 68% confidence intervals) that are too small compared to that expected from the spectroscopic control sample. We find that all codes show a statistically significant bias in the photometric redshifts. However, the bias is in all cases smaller than the scatter, the latter therefore dominates the errors. Finally, we find that combining results from multiple codes significantly decreases the photometric redshift scatter and outlier fraction. We discuss different ways of combining data to produce accurate photometric redshifts and error estimates.
description: 26 pages, 15 figures, ApJ in press
A Method of Drusen Measurement Based on the Geometry of Fundus Reflectance
Creators: name: Smith, R. Theodore
name: Nagasaki, Takayuki
name: Sparrow, Janet R.
name: Barbazetto, Irene
name: Klaver, Caroline
name: Chan, Jackie
Publisher: name: Columbia University
Year: 2003
Subjects: Blindness
Retinal degeneration
Ophthalmology
Medical sciences

description: Background: The hallmarks of age-related macular degeneration, the leading cause of blindness in the developed world, are the subretinal deposits known as drusen. Drusen identification and measurement play a key role in clinical studies of this disease. Current manual methods of drusen measurement are laborious and subjective. Our purpose was to expedite clinical research with an accurate, reliable digital method. Methods: An interactive semi-automated procedure was developed to level the macular background reflectance for the purpose of morphometric analysis of drusen. 12 color fundus photographs of patients with age-related macular degeneration and drusen were analyzed. After digitizing the photographs, the underlying background pattern in the green channel was leveled by an algorithm based on the elliptically concentric geometry of the reflectance in the normal macula: the gray scale values of all structures within defined elliptical boundaries were raised sequentially until a uniform background was obtained. Segmentation of drusen and area measurements in the central and middle subfields (1000 μm and 3000 μm diameters) were performed by uniform thresholds. Two observers using this interactive semi-automated software measured each image digitally. The mean digital measurements were compared to independent stereo fundus gradings by two expert graders (stereo Grader 1 estimated the drusen percentage in each of the 24 regions as falling into one of four standard broad ranges; stereo Grader 2 estimated drusen percentages in 1% to 5% intervals). Results: The mean digital area measurements had a median standard deviation of 1.9%. The mean digital area measurements agreed with stereo Grader 1 in 22/24 cases. The 95% limits of agreement between the mean digital area measurements and the more precise stereo gradings of Grader 2 were -6.4 % to +6.8 % in the central subfield and -6.0 % to +4.5 % in the middle subfield. The mean absolute differences between the digital and stereo gradings 2 were 2.8 +/- 3.4% in the central subfield and 2.2 +/- 2.7% in the middle subfield. Conclusions: Semi-automated, supervised drusen measurements may be done reproducibly and accurately with adaptations of commercial software. This technique for macular image analysis has potential for use in clinical research.
Quantum State Assignment Flows
Creators: name: Schwarz, Jonathan
name: Cassel, Jonas
name: Boll, Bastian
name: Gärttner, Martin
name: Albers, Peter
name: Schnörr, Christoph
Publisher: name: arXiv
Year: 2023
Subjects: subject: Dynamical Systems (math.DS)
subject: Neural and Evolutionary Computing (cs.NE)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences

description: This paper introduces assignment flows for density matrices as state spaces for representing and analyzing data associated with vertices of an underlying weighted graph. Determining an assignment flow by geometric integration of the defining dynamical system causes an interaction of the non-commuting states across the graph, and the assignment of a pure (rank-one) state to each vertex after convergence. Adopting the Riemannian Bogoliubov-Kubo-Mori metric from information geometry leads to closed-form local expressions which can be computed efficiently and implemented in a fine-grained parallel manner. Restriction to the submanifold of commuting density matrices recovers the assignment flows for categorial probability distributions, which merely assign labels from a finite set to each data point. As shown for these flows in our prior work, the novel class of quantum state assignment flows can also be characterized as Riemannian gradient flows with respect to a non-local non-convex potential, after proper reparametrization and under mild conditions on the underlying weight function. This weight function generates the parameters of the layers of a neural network, corresponding to and generated by each step of the geometric integration scheme. Numerical results indicates and illustrate the potential of the novel approach for data representation and analysis, including the representation of correlations of data across the graph by entanglement and tensorization.
Disentangling the two sub-populations of early Herbig Be stars using VLT/X-Shooter spectra
Creators: name: Shridharan, B.
name: Mathew, Blesson
name: Arun, R.
name: Cysil, T. B.
name: Subramaniam, A.
name: Manoj, P.
name: Maheswar, G.
name: Sudheesh, T. P.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Early Herbig Be (HBe) stars are massive, young stars accreting through the Boundary Layer mechanism. However, given the rapid ($<$ 2 Myr) evolution of early Herbig stars to the main-sequence phase, studying the evolution of the circumstellar medium around these stars can be a cumbersome exercise. In this work, we study the sample of early (B0-B5) HBe stars using the correlation between H$α$ emission strength and near--infrared excess, complemented by the analysis of various emission features in the X-Shooter spectra. We segregate the sample of 37 early HBe stars based on the median values of H$α$ equivalent width (EW) and near--infrared index (n(J$-$H)) distributions. The stars with |H$α$ EW| $>$ 50 Å and n(J$-$H) $>$ -2 are classified as intense HBe stars and stars with |H$α$ EW| $<$ 50 Å and n(J$-$H) $<$ -2 as weak HBe stars. Using the VLT/X--Shooter spectra of five intense and eight weak HBe stars, we visually checked for the differences in intensity and profiles of various H{\sc I} and metallic emission lines commonly observed in Herbig stars. We propose that the intense HBe stars possess an inner disk close to the star (as apparent from the high near-infrared excess) and an active circumstellar environment (as seen from high H$α$ EW value and presence of emission lines belonging to Fe{\sc II}, Ca{\sc II}, O{\sc I} and [O{\sc I}]). However, for weak HBe stars, the inner disk has cleared, and the circumstellar environment appears more evolved than for intense HBe stars. Furthermore, we compiled a sample of $\sim$58,000 emission-line stars published in \textit{Gaia DR3} to identify more intense HBe candidates. Further spectroscopic studies of these candidates will help us to understand the evolution of the inner ($\sim$a few au) disk in early HBe stars.
description: Accepted for publication in Astronomy & Astrophysics journal. 14 pages, 7 figures and 2 tables
Little Rip and Pseudo Rip Phenomena from Coupled Dark Energy
Creators: name: Brevik, I.
name: Timoshkin, A. V.
name: Rabochaya, Y.
Publisher: name: arXiv
Year: 2013
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We consider Little Rip (LR) and Pseudo Rip (PR) cosmological models with two interacting ideal fluids, corresponding to dark energy and dark matter. The interaction between the dark energy and the dark matter fluid components is described in terms of the parameters in the equations of state for the LR and PR universes. In contrast to a model containing only a pure dark energy, the presence of the interaction term between the fluid components in the gravitational equations leads to a modification of the equation of state parameters. The properties of the early universe in this formalism are pointed out.
description: 11 pages, Latex2e, no figures. To appear in Modern Physics Letters A
Major surgery delegation to mid-level health practitioners in Mozambique: health professionals' perceptions
Creators: name: Cumbi, Amelia
name: Pereira, Caetano
name: Malalane, Raimundo
name: Vaz, Fernando
name: McCord, Colin
name: Bacci, Alberta
name: Bergström, Staffan
Publisher: name: Columbia University
Year: 2007
Subjects: Surgeons
Public health
Medicine

description: Background: This study examines the opinions of health professionals about the capacity and performance of the 'técnico de cirurgia', a surgically trained assistant medical officer in the Mozambican health system. Particular attention is paid to the views of medical doctors and maternal and child health nurses. Methods: The results are derived from a qualitative study using both semi-structured interviews and group discussions. Health professionals (n = 71) were interviewed at both facility and system level. Eight group discussion sessions of about two hours each were run in eight rural hospitals with a total of 48 participants. Medical doctors and district officers were excluded from group discussion sessions due to their hierarchical position which could have prevented other workers from expressing opinions freely. Results: Health workers at all levels voiced satisfaction with the work of the "técnicos de cirurgia". They stressed the life-saving skills of these cadres, the advantages resulting from a reduction in the need for patient referrals and the considerable cost reduction for patients and their families. Important problems in the professional status and remuneration of "técnicos de cirurgia" were identified. Conclusion: This study, the first one to scrutinize the judgements and attitudes of health workers towards the "técnico de cirurgia", showed that, despite some shortcomings, this cadre is highly appreciated and that the health delivery system does not recognize and motivate them enough. The findings of this study can be used to direct efforts to improve motivation of health workers in general and of técnicos de cirurgia in particular.
Data-driven Predictive Latency for 5G: A Theoretical and Experimental Analysis Using Network Measurements
Creators: name: Skocaj, Marco
name: Conserva, Francesca
name: Grande, Nicol Sarcone
name: Orsi, Andrea
name: Micheli, Davide
name: Ghinamo, Giorgio
name: Bizzarri, Simone
name: Verdone, Roberto
Publisher: name: arXiv
Year: 2023
Subjects: subject: Networking and Internet Architecture (cs.NI)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: The advent of novel 5G services and applications with binding latency requirements and guaranteed Quality of Service (QoS) hastened the need to incorporate autonomous and proactive decision-making in network management procedures. The objective of our study is to provide a thorough analysis of predictive latency within 5G networks by utilizing real-world network data that is accessible to mobile network operators (MNOs). In particular, (i) we present an analytical formulation of the user-plane latency as a Hypoexponential distribution, which is validated by means of a comparative analysis with empirical measurements, and (ii) we conduct experimental results of probabilistic regression, anomaly detection, and predictive forecasting leveraging on emerging domains in Machine Learning (ML), such as Bayesian Learning (BL) and Machine Learning on Graphs (GML). We test our predictive framework using data gathered from scenarios of vehicular mobility, dense-urban traffic, and social gathering events. Our results provide valuable insights into the efficacy of predictive algorithms in practical applications.
Implementing academic detailing for breast cancer screening in underserved communities
Creators: name: Gorin, Sherri
name: Ashford, Alfred
name: Lantigua, Rafael Antonio
name: Desai, Manisha
name: Troxel, Andrea
name: Gemson, Donald
Publisher: name: Columbia University
Year: 2007
Subjects: Poor
Breast--Cancer
Medical sciences
Medicine

description: Background: African American and Hispanic women, such as those living in the northern Manhattan and the South Bronx neighborhoods of New York City, are generally underserved with regard to breast cancer prevention and screening practices, even though they are more likely to die of breast cancer than are other women. Primary care physicians (PCPs) are critical for the recommendation of breast cancer screening to their patients. Academic detailing is a promising strategy for improving PCP performance in recommending breast cancer screening, yet little is known about the effects of academic detailing on breast cancer screening among physicians who practice in medically underserved areas. We assessed the effectiveness of an enhanced, multi-component academic detailing intervention in increasing recommendations for breast cancer screening within a sample of community-based urban physicians. Methods: Two medically underserved communities were matched and randomized to intervention and control arms. Ninety-four primary care community (i.e., not hospital based) physicians in northern Manhattan were compared to 74 physicians in the South Bronx neighborhoods of the New York City metropolitan area. Intervention participants received enhanced physician-directed academic detailing, using the American Cancer Society guidelines for the early detection of breast cancer. Control group physicians received no intervention. We conducted interviews to measure primary care physicians' self-reported recommendation of mammography and Clinical Breast Examination (CBE), and whether PCPs taught women how to perform breast self examination (BSE). Results: Using multivariate analyses, we found a statistically significant intervention effect on the recommendation of CBE to women patients age 40 and over; mammography and breast self examination reports increased across both arms from baseline to follow-up, according to physician self-report. At post-test, physician involvement in additional educational programs, enhanced self-efficacy in counseling for prevention, the routine use of chart reminders, computer- rather than paper-based prompting and tracking approaches, printed patient education materials, performance targets for mammography, and increased involvement of nursing and other office staff were associated with increased screening. Conclusion: We found some evidence of improvement in breast cancer screening practices due to enhanced academic detailing among primary care physicians practicing in urban underserved communities.
Supersingular distribution on average for congruence classes of primes
Creators: name: Walji, Nahid
Publisher: name: arXiv
Year: 2013
Subjects: subject: Number Theory (math.NT)
subject: FOS: Mathematics
subject: 11G05, 14H52

description: We demonstrate the existence of a congruence class bias in the distribution of supersingular primes on average for elliptic curves over $\Q$. For example, we show that on average there are twice as many supersingular primes congruent to 2 mod 3 as there are congruent to 1 mod 3. Our result is obtained using the averaging approach of Fouvry-Murty along with ideas of David-Pappalardi.
description: Preprint of an old paper
Proechimys warreni Thomas 1905
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
Echimyidae
Proechimys
Proechimys warreni

description: Proechimys warreni Thomas, 1905. Ann. Mag. Nat. Hist., ser. 7, 16:312 -313. TYPE LOCALITY: Guyana, 80 mi. (129 km) up the Demerara River, Comackka. DISTRIBUTION: Guyana; Surinam; exact limits not known. COMMENT: Considered a distinct species by Husson, 1978:436; considered a subspecies of guyannensis by Cabrera, 1961: 520.
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 591, DOI: 10.5281/zenodo.7353039
description: {"references": ["Husson, A. M. 1978. The mammals of Suriname. E. J. Brill, Leiden, 569 pp., 160 pls."]}
Viewing of Internet-Based Sexually Explicit Media as a Risk Factor for Condomless Anal Sex among Men Who Have Sex with Men in Four U.S. Cities
Creators: name: Schrimshaw, Eric W.
name: Antebi-Gruszka, Nadav
name: Downing Jr., Martin J.
Publisher: name: Columbia University
Year: 2016
Subjects: subject: Pornographic films
subject: Gay men--Sexual behavior
subject: Condom use
subject: Sociology
subject: FOS: Sociology
subject: Medical sciences
subject: Public health

description: The last decade has seen a dramatic increase in the availability of sexually explicit media (SEM) on the Internet. Men who have sex with men (MSM) report near universal use of SEM. However, this widespread use of SEM among MSM may contribute to more condomless anal sex. To examine the association of viewing SEM on the Internet and the number of condomless anal sex encounters among MSM, in 2012, an online survey was conducted of 265 MSM from New York, Philadelphia, Baltimore, or Washington D.C. who reported viewing SEM online in the past 3 months. Analyses were performed using negative binomial regression. Nearly all men reported viewing SEM featuring anal sex with (91%) or without (92%) condoms in the past 3 months. Neither viewing more hours of SEM per week or compulsively viewing SEM were associated with more condomless anal sex encounters. Rather, viewing a greater proportion of SEM containing condomless anal sex was associated with engaging in more condomless anal encounters (IRR = 1.25), while viewing a greater proportion of SEM containing anal sex where condoms were used was associated with fewer condomless anal sex encounters (IRR = 0.62). MSM reported that viewing SEM caused changes in their sexual fantasies, desires, and behaviors. These findings provide important insights for health policy and the design of interventions addressing SEM and condomless sex among MSM. The findings suggest that condom use by SEM performers may benefit not only actor health, but also have health implications for SEM viewers.
Dissecting complex transcriptional responses using pathway-level scores based on prior information
Creators: name: Bussemaker, Harmen J.
name: Ward, Lucas
name: Boorsma, Andre
Publisher: name: Columbia University
Year: 2007
Subjects: subject: Messenger RNA
subject: DNA microarrays
subject: Biology
subject: Genetics
subject: FOS: Biological sciences

description: Background: The genomewide pattern of changes in mRNA expression measured using DNA microarrays is typically a complex superposition of the response of multiple regulatory pathways to changes in the environment of the cells. The use of prior information, either about the function of the protein encoded by each gene, or about the physical interactions between regulatory factors and the sequences controlling its expression, has emerged as a powerful approach for dissecting complex transcriptional responses. Results: We review two different approaches for combining the noisy expression levels of multiple individual genes into robust pathway-level differential expression scores. The first is based on a comparison between the distribution of expression levels of genes within a predefined gene set and those of all other genes in the genome. The second starts from an estimate of the strength of genomewide regulatory network connectivities based on sequence information or direct measurements of protein-DNA interactions, and uses regression analysis to estimate the activity of gene regulatory pathways. The statistical methods used are explained in detail. Conclusion: By avoiding the thresholding of individual genes, pathway-level analysis of differential expression based on prior information can be considerably more sensitive to subtle changes in gene expression than gene-level analysis. The methods are technically straightforward and yield results that are easily interpretable, both biologically and statistically.
Bipolar spin blockade and coherent state superpositions in a triple quantum dot
Creators: name: Busl, M.
name: Granger, G.
name: Gaudreau, L.
name: Sánchez, R.
name: Kam, A.
name: Pioro-Ladrière, M.
name: Studenikin, S. A.
name: Zawadzki, P.
name: Wasilewski, Z. R.
name: Sachrajda, A. S.
name: Platero, G.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Spin qubits based on interacting spins in double quantum dots have been successfully demonstrated. Readout of the qubit state involves a conversion of spin to charge information, universally achieved by taking advantage of a spin blockade phenomenon resulting from Pauli's exclusion principle. The archetypal spin blockade transport signature in double quantum dots takes the form of a rectified current. Currently more complex spin qubit circuits including triple quantum dots are being developed. Here we show both experimentally and theoretically (a) that in a linear triple quantum dot circuit, the spin blockade becomes bipolar with current strongly suppressed in both bias directions and (b) that a new quantum coherent mechanism becomes relevant. Within this mechanism charge is transferred non-intuitively via coherent states from one end of the linear triple dot circuit to the other without involving the centre site. Our results have implications in future complex nano-spintronic circuits.
description: 21 pages, 7 figures
A Poincaré formula for differential forms and applications
Creators: name: Ginoux, Nicolas
name: Habib, Georges
name: Raulot, Simon
Publisher: name: arXiv
Year: 2023
Subjects: subject: Differential Geometry (math.DG)
subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics
subject: 53C21, 53C24, 58J32, 58J50

description: We prove a new general Poincaré-type inequality for differential forms on compact Riemannian manifolds with nonempty boundary. When the boundary is isometrically immersed in Euclidean space, we derive a new inequality involving mean and scalar curvatures of the boundary only and characterize its limiting case in codimension one. A new Ros-type inequality for differential forms is also derived assuming the existence of a nonzero parallel form on the manifold.
Landen transforms as families of (commuting) rational self-maps of projective space
Creators: name: Joyce, Michael
name: Kawaguchi, Shu
name: Silverman, Joseph H.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Algebraic Geometry (math.AG)
subject: Dynamical Systems (math.DS)
subject: Number Theory (math.NT)
subject: FOS: Mathematics
subject: Primary: 14E05, Secondary: 37P05

description: The classical (m,k)-Landen transform F_{m,k} is a self-map of the field of rational functions C(z) obtained by forming a weighted average of a rational function over twists by m'th roots of unity. Identifying the set of rational maps of degree d with an affine open subset of P^{2d+1}, we prove that F_{m,0} induces a dominant rational self-map R_{d,m,0} of P^{2d+1} of algebraic degree m, and for 0 < k < m, the transform F_{m,k} induces a dominant rational self-map R_{d,m,k} of algebraic degree m of a certain hyperplane in P^{2d+1}. We show in all cases that R_{d,m,k} extends nicely to a map of P^{2d+1} over Spec(Z), and that {R_{d,m,0} : m \ge 0} is a commuting family of maps.
description: 35 pages
Thrichomys Trouessart 1880
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
Echimyidae
Thrichomys

description: Thrichomys Trouessart, 1880. Cat. Mamm. Bull. Soc. Etudes Sci. Angers, 1881: 179. COMMENT: Formerly referred to as Cercomys which was based on Cercomys cunicularius, a composite; see Petter, 1973, Mammalia, 37:422-426. ISIS NUMBER: 5301410029002000000 as Cercomys.
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 591, DOI: 10.5281/zenodo.7353039
Spin-superflow turbulence in spin-1 ferromagnetic spinor Bose-Einstein condensates
Creators: name: Fujimoto, Kazuya
name: Tsubota, Makoto
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: Spin-superflow turbulence (SST) in spin-1 ferromagnetic spinor Bose-Einstein condensates is theoretically and numerically studied by using the spinor Gross-Pitaevskii (GP) equations. SST is turbulence in which the disturbed spin and superfluid velocity fields are coupled. Applying the Kolmogorov-type dimensional scaling analysis to the hydrodynamic equations of spin and velocity fields, we theoretically find that the -5/3 and -7/3 power laws appear in spectra of the superflow kinetic and the spin-dependent interaction energy, respectively. Our numerical calculation of the GP equations confirms SST with the coexistence of disturbed spin and superfluid velocity field with two power laws.
description: 7 pages, 5 figures
Additional file 1 of Designing a chimeric subunit vaccine for influenza virus, based on HA2, M2e and CTxB: a bioinformatics study
Creators: name: Davod Jafari
name: Malih, Sara
name: Gomari, Mohammad Mahmoudi
name: Safari, Marzieh
name: Rasool Jafari
name: Farajollahi, Mohammad Morad
Publisher: name: figshare
Year: 2020
Subjects: subject: Biochemistry
subject: Molecular Biology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1: Table S1. Sequences for the different antigenic and adjuvant fragments used in this study. Table S2. The Tm and Ti of antigens and vaccines. Table S3. Information and sequence of linear epitopes found for B cells by Bepipred. Table S4. Linear B cell epitopes from BepiPred confirmed by VaxiJene. Table S5. Confirmation of linear B cell epitopes from BepiPred by IEDB. Table S6. Linear epitopes predicted by Ellipro. Table S7. Confirmation of linear epitopes from Ellipro by VaxiJen. Table S. Linear epitopes from Ellipro confirmed by IEDB for MCH and MCH-LR5. Table S9. Amino acid residues involved in the conformational epitopes of linker-containing structure (MCH-Lr5) and linker-free structure (MCH), predicted by ellipro and analyzed by vaxijen. Table S10. Epitope prediction for MHC class II by NetMHCIIpan for MCH and MCH-LR. Table S11. Epitopes found for CTL cells. Table S12. MHC restriction of epitopes found for CTL cells. Table S13. Codon optimized sequences of MCH-LR5 vaccine candidate for expression in different hosts. Figure S1. O-glycosylation site prediction. Using NetOGlyC server, the potential O-glycosylation sites predicted for a) MCH-LR and b) MCH. Figure S2. N-glycosylation site prediction. Using NetNGlyC server, the potential N-glycosylation sites predicted for a) MCH-LR and b) MCH. Figure S3. Phosphorylation site prediction. Using NetPhos server, the potential phosphorylation sites predicted for a) MCH-LR and b) MCH. Table S14. Proteinases that potentially can cut the vaccine.
Cooperative Multibeamforming in Ad Hoc Networks
Creators: name: Li, Chuxiang
name: Wang, Xiaodong
Publisher: name: Columbia University
Year: 2008
Subjects: Ad hoc networks (Computer networks)
Beamforming
Electrical engineering

description: We treat the problem of cooperative multiple beamforming in wireless ad hoc networks. The basic scenario is that a cluster of source nodes cooperatively forms multiple data-carrying beams toward multiple destination nodes. To resolve the hidden node problem, we impose a link constraint on the receive power at each unintended destination node. Then the problem becomes
to optimize the transmit powers and beam weights at the source cluster subject to the maximal transmit power constraint, the minimal receive signal-to-interference-plus-noise ratio (SINR) constraints at the destination nodes, and the minimal receive power constraints at the unintended destination nodes. We first propose an iterative transmit power allocation algorithm under fixed beamformers subject to the maximal transmit power constraint, as well as the minimal receive SINR and receive power constraints. We then develop a joint optimization algorithm to iteratively optimize the powers and the beamformers based on the duality analysis. Since channel state information (CSI) is required by the sources to perform the above optimization, we further propose a cooperative scheme to implement a simple CSI estimation and feedback mechanism based on the subspace tracking principle. Simulation results are provided to demonstrate the performance of the proposed algorithms.
Slow-roll inflation and growth of perturbations in Kaniadakis modification of Friedmann cosmology
Creators: name: Lambiase, Gaetano
name: Luciano, Giuseppe Gaetano
name: Sheykhi, Ahmad
Publisher: name: arXiv
Year: 2023
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Kaniadakis entropy is a one-parameter deformation of the classical Boltzmann-Gibbs-Shannon entropy, arising from a self-consistent relativistic statistical theory. Assuming a Kaniadakis-type generalization of the entropy associated with the apparent horizon of Friedmann-Robertson-Walker (FRW) Universe and using the gravity-thermodynamics conjecture, a new cosmological scenario is obtained based on the modified Friedmann equations. By employing such modified equations, we analyze the slow-roll inflation, driven by a scalar field with power-law potential, at the early stages of the Universe. We explore the phenomenological consistency of this model by computation of the scalar spectral index and tensor-to-scalar ratio. Comparison with the latest Planck data allows us to constrain Kaniadakis parameter to $κ\lesssim\mathcal{O}(10^{-12}\div10^{-11})$, which is discussed in relation to other observational bounds in the past literature. We also disclose the effects of Kaniadakis correction term on the growth of perturbations at the early stages of the Universe by employing the spherically symmetric collapse formalism in the linear regime of density perturbations. We find out that the profile of density contrast is non-trivially affected in this scenario. Interestingly enough, we observe that increasing Kaniadakis parameter $κ$ corresponds to a faster growth of perturbations in a Universe governed by the corrected Friedmann equations. Finally, we comment on the consistency of the primordial power spectrum for scalar perturbations with the best data-fit provided by Planck.
description: Discussion added on the primordial power spectrum for scalar perturbations
Disorder effects on superconducting tendencies in the checkerboard Hubbard model
Creators: name: Smith, Peter M.
name: Kennett, Malcolm P.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: The question of whether spatially inhomogeneous hopping in the two dimensional Hubbard model can lead to enhancement of superconductivity has been tackled by a number of authors in the context of the checkerboard Hubbard model (CHM). We address the effects of disorder on superconducting properties of the CHM by using exact diagonalization calculations for both potential and hopping disorder. We characterize the superconducting tendencies of the model by focusing on the pair binding energy, the spin gap, and d-wave pairing order parameter. We find that superconducting tendencies, particularly the pair binding energy, are more robust to disorder when there is inhomogeneous hopping than for the uniform Hubbard model. We also study all possible staggered potentials for an eight site CHM cluster and relate the behaviour of these configurations to the disordered system.
description: 13 pages, 29 figures
Thrichomys apereoides Lund 1839
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
Echimyidae
Thrichomys
Thrichomys apereoides

description: Thrichomys apereoides Lund, 1839. Afh. Kongl. Danske Vid. Selsk., p. 38. TYPE LOCALITY: Brazil, Minas Gerais, Lagoa Santa. DISTRIBUTION: E. Brazil; Paraguay. COMMENT: Formerly referred to as Cercomys cunicularius, a composite; see Petter, 1973, Mammalia, 37:422-426, and Mares et al., 1981, Ann. Carnegie Mus., 50(4): 120. ISIS NUMBER: 5301410029002001001 as Cercomys cunicularis (sic).
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 591, DOI: 10.5281/zenodo.7353039
K-theory of weight varieties
Creators: name: Leung, Ho-Hon
Publisher: name: arXiv
Year: 2013
Subjects: subject: K-Theory and Homology (math.KT)
subject: Symplectic Geometry (math.SG)
subject: FOS: Mathematics
subject: 19L64 (Primary) 53D20 (Secondary)

description: Let $T$ be a compact torus and $(M,ω)$ a Hamiltonian $T$-space. We give a new proof of the $K$-theoretic analogue of the Kirwan surjectivity theorem in symplectic geometry by using the equivariant version of the Kirwan map introduced in one of R. Goldin's papers. We compute the kernel of this equivariant Kirwan map, and hence give a computation of the kernel of the Kirwan map. As an application, we find the presentation of the kernel of the Kirwan map for the $T$-equivariant $K$-theory of flag varieties $G/T$ where $G$ is a compact, connected and simply-connected Lie group. In the last section, we find explicit formulae for the $K$-theory of weight varieties.
description: 16 pages
Stationary state of harmonic chains driven by boundary resetting
Creators: name: Sarkar, Ritwick
name: Roy, Pritam
Publisher: name: arXiv
Year: 2023
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: We study the nonequilibrium steady state (NESS) of an ordered harmonic chain of $N$ oscillators connected to two walls which undergo diffusive motion with stochastic resetting. The intermittent resettings of the walls effectively emulate two nonequilibrium reservoirs that exert temporally correlated forces on the boundary oscillators. These reservoirs are characterized by the diffusion constant and resetting rates of the walls. We find that, for any finite $N$, the velocity distribution remains non-Gaussian, as evidenced by a non-zero bulk kurtosis that decays $\sim N^{-1}$. We calculate the spatio-temporal correlation of the velocity of the oscillators $\langle v_l(t) v_{l'}(t') \rangle$ both analytically as well as using numerical simulation. The signature of the boundary resetting is present at the bulk in terms of the two-time velocity correlation of a single oscillator and the equal-time spatial velocity correlation. For the resetting driven chain, the two-time velocity correlation decay as $t^{-\frac{1}{2}}$ at the large time, and there exists a non-zero equal-time spatial velocity correlation $\langle v_l(t) v_{l'}(t') \rangle$ when $l \neq l'$. A non-zero average energy current will flow through the system when the boundary walls reset to their initial position at different rates. This average energy current can be computed exactly in the thermodynamic limit. Numerically we show that the distribution of the instantaneous energy current at the boundary is independent of the system size. However, the distribution of the instantaneous energy current in the bulk approaches a stationary distribution in the thermodynamic limit.
description: 24 pages. Comments are welcome