cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
MOESM2 of Development and characterization of a CRISPR/Cas9n-based multiplex genome editing system for Bacillus subtilis
Creators: name: Liu, Dingyu
name: Huang, Can
name: Guo, Jiaxin
name: Zhang, Peiji
name: Chen, Tao
name: Wang, Zhiwen
name: Zhao, Xueming
Publisher: name: figshare
Year: 2019
Subjects: subject: Biophysics
subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Pharmacology
subject: Evolutionary Biology
subject: Biological Sciences not elsewhere classified
subject: Hematology
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Additional file 2: Figure S2. Strategy for the construction of plasmids expressing multiple gRNA sequences. Figure S3. CRISPR-Cas9/Cas9n mediated inducible plasmid curing. Figure S4. The influence of ligD knockout on cell growth. Figure S5. The secondary structures in the 5′-UTR regions of the mRNA of riboflavin operon genes in strain BS89. Figure S6. The secondary structures in the 5′-UTR regions of the mRNA of riboflavin operon genes in strain CY46. Figure S7. The secondary structures in the 5′-UTR regions of the mRNA of riboflavin operon genes in strain CY124. Figure S8. The secondary structures in the 5′-UTR regions of the mRNA of riboflavin operon genes in strain CY79. Figure S9. The secondary structures in the 5′-UTR regions of the mRNA of riboflavin operon genes in strain CY49. Table S1. Primers and gRNA sequences used in this study.
Properties of spectrally-defined red QSOs at z = 0.3-1.2
Creators: name: Tsai, An-Li
name: Hwang, Chorng-Yuan
Publisher: name: arXiv
Year: 2017
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We investigated the properties of a sample of red Quasi-stellar Objects (QSOs) using optical, radio, and infrared data. These QSOs were selected from the Sloan Digital Sky Survey Data Release 7 (SDSS DR7) quasar catalog. We only selected sources with sky coverage of the Very Large Array Faint Images of the Radio Sky at Twenty-centimeters (VLA FIRST) survey, and searched for sources with Wide-field Infrared Survey Explorer (WISE) counterparts. We defined the spectral color of the QSOs based on the flux ratio of the rest frame 4000$Å$ to 3000$Å$ continuum emission to select red QSOs and typical QSOs. In accordance with this criterion, only QSOs with redshifts between 0.3 and 1.2 could be selected. We found that the red QSOs have stronger infrared emission than the typical QSOs do. We noted that the number ratios of the red QSOs to the typical QSOs decrease with increasing redshifts, although the number of the typical QSOs increase with redshifts. Furthermore, at high redshifts, the luminosity distributions of the typical QSOs and the red QSOs seem to have similar luminosity distribution peaks; however, at low redshifts, the luminosities of the red QSOs seem to be lower than those of the typical QSOs. These findings suggest that there might be at least two types of red QSOs in our QSO samples.
description: 12 pages, 11 figures, 9 tables, ApJ accepted
title: Maturation characteristics in Norwegian spring-spawning herring before, during, and after a major population collapse
Creators: name: Engelhard, Georg H.
name: Heino, Mikko
Publisher: name: ASC 2002 - Y - Theme session
Year: 2024
Subjects: Fisheries and aquaculture
Pressures, impacts, conservation, and management

description: No abstracts are to be cited without prior reference to the author.The immense Norwegian spring-spawning herring (Clupea harengus) population collapsed to the state of commercial extinction in the late 1960s, probably largely due to overfishing; the stock has fully recovered since the 1980s. It is known that the collapse strongly affected maturation characteristics. However, the long-term patterns of maturation in this stock have remained largely undescribed. Using discriminant analysis and artificial neural networks, the age at maturation for individual fish can be predicted fromroutine scale measurements. We applied these methods to historical data on herring scales available from 1935 up to the present, in order to (1) describe the long-term variability in both age and length at 50% maturity, and (2) compute new, revised maturity ogives for the stock over the same period with temporal resolution of one year. This new information, with improved temporal resolution, enables comparisons of maturation characteristics before, during, and after the population collapse. As a further step, in order to increase our understanding of the potential impact of commercial fisheries on the genetic composition of fish stocks, we aim to disentangle genetic from phenotypic aspects of maturation.
GUB Covers and Power-Indexed formulations for Wireless Network Design
Creators: name: D'Andreagiovanni, Fabio
name: Mannino, Carlo
name: Sassano, Antonio
Publisher: name: arXiv
Year: 2017
Subjects: subject: Optimization and Control (math.OC)
subject: Discrete Mathematics (cs.DM)
subject: Data Structures and Algorithms (cs.DS)
subject: Networking and Internet Architecture (cs.NI)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences

description: We propose a pure 0-1 formulation for the wireless network design problem, i.e. the problem of configuring a set of transmitters to provide service coverage to a set of receivers. In contrast with classical mixed integer formulations, where power emissions are represented by continuous variables, we consider only a finite set of powers values. This has two major advantages: it better fits the usual practice and eliminates the sources of numerical problems which heavily affect continuous models. A crucial ingredient of our approach is an effective basic formulation for the single knapsack problem representing the coverage condition of a receiver. This formulation is based on the GUB cover inequalities introduced by Wolsey (1990) and its core is an extension of the exact formulation of the GUB knapsack polytope with two GUB constraints. This special case corresponds to the very common practical situation where only one major interferer is present. We assess the effectiveness of our formulation by comprehensive computational results over realistic instances of two typical technologies, namely WiMAX and DVB-T.
description: This is the authors' final version of the paper published in Management Science 59(1), 142-156, 2013. DOI: 10.1287/mnsc.1120.1571. The final publication is available at INFORMS via http://pubsonline.informs.org/doi/abs/10.1287/mnsc.1120.1571
Additional file 2 of Genome-wide characterization of PEBP family genes in nine Rosaceae tree species and their expression analysis in P. mume
Creators: name: Zhang, Man
name: Li, Ping
name: Yan, Xiaolan
name: Wang, Jia
name: Cheng, Tangren
name: Zhang, Qixiang
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Plant Biology

description: Additional file2: Fig. S2. Exon-intron distributions of PEBP family genes from nine Rosaceae species and A. thaliana.
Do joint CMB and HST data support a scale invariant spectrum?
Creators: name: Benetti, Micol
name: Graef, Leila L.
name: Alcaniz, Jailson S.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We combine current measurements of the local expansion rate, $H_0$, and Big Bang Nucleosynthesis (BBN) estimates of helium abundance with the latest cosmic microwave background (CMB) data from the Planck Collaboration to discuss the observational viability of the scale invariant Harrison-Zeldovch-Peebles (HZP) spectrum. We also analyze some of its extensions, namely, HZP + $Y_P$ and HZP + $N_{eff}$, where $Y_P$ is the primordial helium mass fraction and $N_{eff}$ is the effective number of relativistic degrees of freedom. We perform a Bayesian analysis and show that the latter model is favored with respect to the standard cosmology for values of $N_{eff}$ lying in the interval $3.70 \pm 0.13$ ($1σ$), which is currently allowed by some independent analyses.
description: 4 pages, Letter
Additional file 1: Figure S1. of Melting phase relations in the MgSiO3–CaSiO3 system at 24 GPa
Creators: name: Nomura, Ryuichi
name: Youmo Zhou
name: Irifune, Tetsuo
Publisher: name: figshare
Year: 2017
Subjects: subject: Biophysics
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Microbiology
subject: FOS: Biological sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Pressure calibrations at room temperature (RT) and high temperatures. Fo, Mg2SiO4, forsterite; Wd, Mg2SiO4 wadsleyite; Rw, Mg2SiO4 ringwoodite; Ak, MgSiO3 akimotoite; Bdg, MgSiO3 bridgmanite; Pc, MgO periclase. Pressures of the phase transitions at high temperatures were taken from Morishima et al. (1994), Suzuki et al. (2000), and Fei et al. (2004). The red point at 790 ton, 23 GPa, and 2273 K is 0.55 GPa away from the green curve of 1873 K, which is comparable to the standard deviation of the fitting curves, 0.4 GPa. Figure S2: Heating power-temperature relationships. Figure S3: Melting temperatures of MgO. The black line represents the melting temperatures calculated in this study, and the dashed gray line represents those by de Koker and Stixrude (2009). The melting temperatures determined by high-pressure experiments and ab initio calculations are also plotted: orange squares, Zerr and Boehler (1994); green triangles, Alfe (2005); blue circles, Zhang and Fei (2008); purple squares, Du and Lee (2014); and red squares, Kimura et al. (2017). Figure S4: Melting phase diagram in the MgO–MgSiO3 system at 24 GPa. The black line represents the phase boundary calculated in this study, and the gray line represents that by Liebske and Frost (2012). The experimental data by Liebske and Frost (2012) are also plotted, where the red circle represents the composition of liquid above liquidus, the green squares represent liquid coexisting with periclase (Pc), the orange squares represent liquid coexisting with bridgmanite (Bdg), and the diamonds represent subsolidus phases. Interaction parameter updated by Ohnishi et al. (2017) was used to calculate the phase relations. Figure S5: X-ray diffraction patterns of the run products. The black short bars beneath the curves denote the peak positions of bridgmanite (Bdg) and rhenium (Re). (PDF 1046 kb)
Quantum chemical exploration of the binding motifs and binding energies of neutral molecules, radicals and ions with small water clusters: characterisation and astrochemical implications
Creators: name: Hendrix, Josie
name: Bera, Partha P.
name: Lee, Timothy J.
name: Head-Gordon, Martin
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Computational Biology

description: Accurate binding energies of molecules to water clusters are relevant for understanding intermolecular interactions and various chemical applications. They enter models of interstellar chemical processes, as binding to icy grains influences surface reactions and thus affects calculated gas-phase abundances. Unfortunately, many astrochemical molecules (especially radicals and ions) are incompletely characterised in these models. To address this, we report computational searches for optimal structures and benchmark binding and condensation energies for sets of neutral, radical, cationic, and anionic molecules of astrochemical relevance with clusters of N=1−4 water molecules. These calculations utilised reliable density functionals for geometry optimisation, and coupled cluster (CCSD(T)) single point calculations with large basis sets. Four energetic binding motifs (weak, intermediate, strong or covalently bonded) were observed depending on the chemical nature of the guest molecule. Neutral closed and open-shell molecules with strong dipoles and a greater potential for hydrogen bonding are more tightly bound to water clusters compared to non-polar ones. For closed-shell cationic and anionic species, barrier-less reactions with water clusters occur, which reveals radical-free routes to molecular processing in the gas phase and on amorphous ice surfaces.
Pseudo-Majoron as Light Mediator of Singlet Scalar Dark Matter
Creators: name: Ma, Ernest
name: Maniatis, Markos
Publisher: name: arXiv
Year: 2017
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: In the singlet-triplet majoron model of neutrino mass, lepton number is spontaneously broken. If it is also softly broken, then a naturally light pseudoscalar particle $η_I$ exists. It may then act as a light mediator for a real singlet scalar $χ$ with odd dark parity. It is itself unstable, but decays dominantly to two neutrinos through its triplet scalar component, thereby not disturbing the cosmic microwave background (CMB). It also mixes with the standard-model Higgs boson only in one loop, thereby not contributing significantly to the elastic scattering of $χ$ off nuclei in dark-matter direct-search experiments.
description: 10 pages
title: Selective Fishing And Phenotypic Evolution: Past, Present And Future
Creators: name: Law, Richard
Publisher: name: ASC 2002 - Y - Theme session
Year: 2024
Subjects: Fisheries and aquaculture
Pressures, impacts, conservation, and management

description: No abstracts are to be cited without prior reference to the author.There is accumulating evidence for genetic change caused by fishing. Selection differentials generated by fishing are detectable within year classes in certain major exploited stocks. Breeding experiments in the aquaculture industry demonstrate the existence of genetic variation in production-related traits. Genetic change in growth rates due to fishing has been found in experimental systems. There is evidence that changes in maturation taking place in fish stocks have a genetic component. This paper is therefore a call for action on the part of fisheries science adopt a precautionary approach to fishing-induced evolutionary change, and to develop a Darwinian perspective to fisheries management.
Additional file 4: Table S3. of Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes
Creators: name: Bhavya Papudeshi
name: J. Haggerty
name: Doane, Michael
name: Morris, Megan
name: Walsh, Kevin
name: Beattie, Douglas
name: Dnyanada Pande
name: Zaeri, Parisa
name: Genivaldo Silva
name: Thompson, Fabiano
name: Edwards, Robert
name: Dinsdale, Elizabeth
Publisher: name: figshare
Year: 2017
Subjects: subject: Space Science
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Genetics
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Marine Biology
subject: Computational Biology

description: Assembly statistics. QUAST results for the 12 Contigs files assembled using the three assemblers; IDBA, MetaVelvet, SPAdes. (DOCX 16Â kb)
Use of neurostimulation to localize and anesthetize the brachia! plexus of calves undergoing metacarpal surgery
Creators: name: Lardé, H.
name: Nichols, S.
name: Desrochers, A.
name: Bussières, G.
name: Kopal, M.
Publisher: name: American Association of Bovine Practitioners  Proceedings of the Annual Conference
Year: 2012

description: In cattle, locoregional anesthesia is usually effective for surgery distal to the metacarpophalangealjoint. However, for proximal interventions, general anesthesia is often required. The aim of this study was to assess the usefulness of brachial plexus anesthesia for orthopedic surgery in calves. We hypothesized that this locoregional block, combined with sedation, would be sufficient for interventions on the metacarpal bones in calves.
description: American Association of Bovine Practitioners Proceedings of the Annual Conference, 2012
Ga-polar (In,Ga)N/GaN quantum wells vs. N-polar (In,Ga)N quantum disks in GaN nanowires: Comparative analysis of carrier recombination, diffusion, and radiative efficiency
Creators: name: Feix, F.
name: Flissikowski, T.
name: Sabelfeld, K. K.
name: Kaganer, V. M.
name: Wölz, M.
name: Geelhaar, L.
name: Grahn, H. T.
name: Brandt, O.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We investigate the radiative and nonradiative recombination processes in planar (In,Ga)N/GaN(0001) quantum wells and (In,Ga)N quantum disks embedded in GaN$(000\bar{1})$ nanowires using photoluminescence spectroscopy under both continuous-wave and pulsed excitation. The photoluminescence intensities of these two samples quench only slightly between 10 and 300 K, which is commonly taken as evidence for high internal quantum efficiencies. However, a side-by-side comparison shows that the absolute intensity of the Ga-polar quantum wells is two orders of magnitude higher than that of the N-polar quantum disks. A similar difference is observed for the initial decay time of photoluminescence transients obtained by time-resolved measurements, indicating the presence of a highly efficient nonradiative decay channel for the quantum disks. In apparent contradiction to this conjecture, the decay of both samples is observed to slow down dramatically after the initial rapid decay. Independent of temperature, the transients approach a power law for longer decay times, reflecting that recombination occurs between individual electrons and holes with varying spatial separation. Employing a coupled system of stochastic integro-differential equations taking into account both radiative and nonradiative Shockley-Read-Hall recombination of spatially separate electrons and holes as well as their diffusion, we obtain simulated transients matching the experimentally obtained ones. The results reveal that even dominant nonradiative recombination conserves the power law decay for (In,Ga)N/GaN{0001} quantum wells and disks.
An evaluation of the prevalence of BHV-1 abortions based on diagnostic submissions to five U.S. veterinary diagnostic laboratories
Creators: name: Gould, S.
name: O'Connor, A. M.
name: Cooper, V.
Publisher: name: American Association of Bovine Practitioners  Proceedings of the Annual Conference
Year: 2012

description: This retrospective study used data on bovine abortion submissions from 5 U.S. veterinary diagnostic laboratories (VDLs) from 2000-2011. Objectives of this study were to describe the prevalence and patterns of BHV-1-associated abortion in submissions at VDLs. There were three specific aims: 1) examine the proportion of BHV-1-associated abortions with the introduction of new diagnostic assays, 2) evaluate the agreement of the histopathology report of the abortion submissions and the result of the assay used, and 3) evaluate the association between farm history of vaccination against BHV-1 and BHV-1-positive abortion submissions.
description: American Association of Bovine Practitioners Proceedings of the Annual Conference, 2012
Additional file 3: Table S3. of Serum concentrations of active tamoxifen metabolites predict long-term survival in adjuvantly treated breast cancer patients
Creators: name: Helland, Thomas
name: Henne, Nina
name: Bifulco, Ersilia
name: Naume, Bjørn
name: Borgen, Elin
name: Kristensen, Vessela
name: Kvaløy, Jan
name: Lash, Timothy
name: Alnæs, Grethe
name: Schaik, Ron Van
name: Janssen, Emiel
name: Hustad, Steinar
name: Lien, Ernst
name: Mellgren, Gunnar
name: Søiland, Håvard
Publisher: name: figshare
Year: 2017
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer
subject: Plant Biology

description: Imprecision and accuracy. (DOCX 16 kb)
Real-time PCR assay for trichomonosis on pooled direct preputial samples
Creators: name: Guerra, A. Garcia
name: Hill, J. E.
name: Campbell, J.
name: Waldner, C.
name: Hendrick, S.
Publisher: name: American Association of Bovine Practitioners  Proceedings of the Annual Conference
Year: 2012

description: Tritrichomonas foetus is recognized as important cause of reproductive loss in beef herds. Strategies for the control of trichomonosis (trich) in beef herds are based on identifying and eliminating infected bulls. The sensitivity of conventional PCR methods is sufficient for use of detecting trich in pooled preputial samples from up to five bulls. Areal-time PCR (RT-PCR) assay for trich detection has shown improved sensitivity, compared with that of the conventional PCR assay. Previous research from our group demonstrated that pools of samples from up to 25 bulls, enriched by culture, could be tested for trich with the RT-PCR assay without a significant decrease in sensitivity. The objective of the present study was to evaluate the sensitivity of a commercially available RT-PCR assay for the detection of trich in pooled samples of direct preputial samples from five or 10 bulls.
description: American Association of Bovine Practitioners Proceedings of the Annual Conference, 2012
Influence of spin ordering on superconducting correlations in the spin-one-half Falicov-Kimball model with Hund and Hubbard coupling
Creators: name: Farkasovsky, Pavol
Publisher: name: arXiv
Year: 2017
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: The generalized spin-one-half Falicov-Kimball model with Hund and Hubbard coupling is used to examine effects of spin ordering on superconducting correlations in the strongly correlated electron and spin systems. It is found that the ferromagnetic spin clusters (lines, bands, domains) suppress the superconducting correlations in the d-wave chanel, while the antiferromagnetic ones have the fully opposite effect. The enhancement of the superconducting correlations due to the antiferromagnetic spin ordering is by factor 3 in the axial striped phase and even by the factor 8 in the phase segregated phase.
description: Journal of Superconductivity and Novel Magnetism, 15 pages, 6 figures. arXiv admin note: substantial text overlap with arXiv:1611.04890
Clinical sensitivity and specificity of a quantitative PCR assay for bovine genital campylobacteriosis in bulls
Creators: name: Guerra, A. Garcia
name: Chaban, B.
name: Hill, J. E.
name: Waldner, C.
name: Hendrick, S.
Publisher: name: American Association of Bovine Practitioners  Proceedings of the Annual Conference
Year: 2012

description: Bovine genital campylobacteriosis occurs worldwide wherever natural service is used. The disease is transmitted by carrier bulls and characterized by early pregnancy loss and infertility. Despite the challenge of maintaining viability of the Campylobacter fetus subsp venerealis (Cfv) during transport and avoiding overgrowth of contaminants, culture remains the "gold standard". Several PCR tests have been developed for the detection of Cfv, and primers VenSF/VenSR have been extensively tested and recognized worldwide. Recently, our research group at WCVM adapted these primers to a SYER Green qPCR platform. This assay presents a high analytical sensitivity and provides a fast and effective technique, suitable to be used as a screening test for the detection of carrier bulls. The objective of the present study was to determine the clinical sensitivity and specificity of the RT-PCR assay in direct preputial samples.
description: American Association of Bovine Practitioners Proceedings of the Annual Conference, 2012
MOESM1 of The miR-141/neuropilin-1 axis is associated with the clinicopathology and contributes to the growth and metastasis of pancreatic cancer
Creators: name: Ma, Lixin
name: Zhai, Bo
name: Zhu, Huaqiang
name: Li, Weidong
name: Jiang, Wenjing
name: Lei, Liwang
name: Zhang, Shujun
name: Qiao, Haiquan
name: Jiang, Xian
name: Sun, Xueying
Publisher: name: figshare
Year: 2019
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Cancer

description: Additional file 1. Supplementary information containing Table S1–2, Materials S1 and Figure S1–8.
Bovine coronaviruses from the respiratory tract
Creators: name: Fulton, R. W.
name: Ridpath, J. F.
name: Burge, L. J.
Publisher: name: American Association of Bovine Practitioners  Proceedings of the Annual Conference
Year: 2012

description: Bovine coronaviruses (BoCV) have been associated with bovine respiratory diseases (BRD) in cattle pulled for treatment in feedlots and from healthy cattle in the US with BoCV identified by virus isolation from nasal swab and bronchoalveolar lavage (BAL) samples, and also by seroconversions for the detection of active infections. Bovine coronaviruses have been identified in pneumonic lungs from field cases, often in combination with other viruses and bacteria including Mycoplasma spp. Experimentally, BoCV infections have caused respiratory tract lesions. It has been suggested there is a dual tropism of BoCV for the respiratory and enteric tracts. Historically, BoCV was associated with neonatal enteric disease and adult winter dysentery. Respiratory isolates were identified later and focused on post-weaning cattle entering feedlots. Control measures are limited. There are USDA-licensed killed and modified live virus (MLV) vaccines for BoCV; however, these are for control of the enteric disease in cattle. There are no USDA-licensed vaccines for control of BoCV associated BRD in cattle. The purpose of the study was to compare BoCVisolates from the respiratory tract of cattle in Oklahoma to reference respiratory tract and enteric strains via antigenic and genetic procedures.
description: American Association of Bovine Practitioners Proceedings of the Annual Conference, 2012
title: Fisheries-induced long-term effects on age-at-maturation in mixed fisheries
Creators: name: Gårdmark, Anna
Publisher: name: ASC 2002 - Y - Theme session
Year: 2024
Subjects: Fisheries and aquaculture
Pressures, impacts, conservation, and management

description: No abstracts are to be cited without prior reference to the author.Theoretical and experimental studies show that fishing can change the genetic composition of exploited species. In particular, selective fishing of older and larger individuals can cause maturation at an earlier age and smaller size. These predictions, however, are all based on single-species considerations. Our recent studies show that in the presence of species-interactions, the potential evolutionary response to fishing is ambiguous: fishing can cause either earlier or later maturation depending on the type of interaction and its strength relative to the fishing pressure. Moreover, interactions between the target species and other species provide a mechanism whereby fisheries can induce long-term genetic effects also in unexploited and non-target species. Here, I review our findings and discuss their implications for the long-term genetic effects of mixed fisheries on age-at-maturation.
A computational and spectroscopic study of MgCCH (X2Σ+): towards characterizing MgCCH+
Creators: name: Burns, Joseph E.
name: Cheng, Qianyi
name: Fortenberry, Ryan C.
name: Sun, Ming
name: Zack, Lindsay N.
name: Zaveri, Trishal
name: DeYonker, Nathan J.
name: Ziurys, Lucy M.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biophysics
Biochemistry
Space Science
Medicine
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Cancer

description: New computational and experimental studies have been carried out for the MgCCH radical in its X2Σ+ state. Coupled cluster theory [CCSD(T)], was used in conjunction with post-CCSD(T) and scalar relativistic additive corrections to compute vibrational quartic force fields for MgCCH and its cation. From the quartic force fields, higher-order spectroscopic properties, including rotational constants, were obtained. In tandem, the five lowest energy rotational transitions for MgCCH, N = 1→0 through N = 5→4, were measured for the first time using Fourier transform microwave/millimetre wave methods in the frequency range 9–50 GHz. The radical was created in the Discharge Assisted Laser Ablation Source (DALAS) developed in the Ziurys group. A combined fit of these data with previous millimetre direct absorption measurements have yielded the most accurate rotational constants for MgCCH to date. The computed principle rotational constant lies within −1.51 to +1.65 MHz of the experimental one, validating the computational approach. High-level theory was then applied to produce rovibrational spectroscopic constants for MgCCH+, including a rotational constant of B0 = 5354.5–5359.5 MHz. These new predictions will further the experimental study of MgCCH+, and aid in the low-temperature characterisation of MgCCH in the interstellar medium.
Additional file 1: of Modulation of innate immune responses at birth by prenatal malaria exposure and association with malaria risk during the first year of life
Creators: name: Natama, Hamtandi
name: Moncunill, Gemma
name: Rovira-Vallbona, Eduard
name: Sanz, Héctor
name: Sorgho, Hermann
name: Aguilar, Ruth
name: Coulibaly-Traoré, Maminata
name: Somé, M.
name: Scott, Susana
name: Valéa, Innocent
name: Mens, Petra
name: Schallig, Henk
name: Kestens, Luc
name: Tinto, Halidou
name: Dobaño, Carlota
name: Rosanas-Urgell, Anna
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Infectious Diseases
subject: FOS: Health sciences

description: Boxplots showing variation in cytokine responses by stimulation. Figure S1. Boxplots generated using log10 of crude concentrations (pg/mL). Figure S2. Boxplots generated using log10 of ratios (TLR/unstimulated). (PDF 287 kb)
MOESM2 of Toxicological investigation of acute and chronic treatment with Gnidia stenophylla Gilg root extract on some blood parameters and histopathology of spleen, liver and kidney in mice
Creators: name: Tilahun Nigatu
name: Mekbeb Afework
name: Kelbessa Urga
name: Wondwossen Ergete
name: Eyasu Makonnen
Publisher: name: figshare
Year: 2017
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Marine Biology
subject: Plant Biology

description: Additional file 2. Histomicrograph of kidney.
The GTC exoplanet transit spectroscopy survey. VII. Detection of sodium in WASP-52b's cloudy atmosphere
Creators: name: Chen, G.
name: Palle, E.
name: Nortmann, L.
name: Murgas, F.
name: Parviainen, H.
name: Nowak, G.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: We report the first detection of sodium absorption in the atmosphere of the hot Jupiter WASP-52b. We observed one transit of WASP-52b with the low-resolution Optical System for Imaging and low-Intermediate-Resolution Integrated Spectroscopy (OSIRIS) at the 10.4 m Gran Telescopio Canarias (GTC). The resulting transmission spectrum, covering the wavelength range from 522 nm to 903 nm, is flat and featureless, except for the significant narrow absorption signature at the sodium doublet, which can be explained by an atmosphere in solar composition with clouds at 1 mbar. A cloud-free atmosphere is stringently ruled out. By assessing the absorption depths of sodium in various bin widths, we find that temperature increases towards lower atmospheric pressure levels, with a positive temperature gradient of 0.88 +/- 0.65 K/km, possibly indicative of upper atmospheric heating and a temperature inversion.
description: 6 pages, 5 figures, accepted for publication in A&A Letter
Identifying changes in stress regulation and organisation within the messenger RNA metabolism in myotonic dystrophy type 1 disease models
Creators: name: Gulyurtlu, Selma Melis Cabrita
Publisher: name: The University of St Andrews
Year: 2021
Subjects: subject: QP623.G8
subject: RNA--Metabolism
subject: Myotonia atrophica

description: Myotonic dystrophy is an RNA-mediated multi-systemic disease, and the most common form of muscular dystrophy in adults. This project focussed on type 1 (DM1), characterised by a CTG trinucleotide repeat expansion on the 3’UTR of the DMPK gene. This expansion when transcribed forms an elongated metastable stem loop structure, with mutant transcripts accumulating into nuclear foci resulting in toxic gain-of-effects. This causes a shift in activities of antagonistic alternative splicing regulators MBNL1 and CUGBP1. MBNL1 is attracted to and believed to sequester in the foci, whereas CUGBP1 experiences an increase of activity. It is deemed that the shift in splicing patterns caused by their altered activities, gives rise to the DM1 phenotype. Cataracts are the most prevalent DM1 symptom. The human eye lens epithelium contains the majority of nucleated cells. The foci in these epithelial cells in vitro are smaller than in other tissues, with little MBNL1 recruitment. It was suggested that other mechanisms apart from MBNL1 sequestration are likely to be contributing to the DM1 phenotype. Here, the RNA metabolism was investigated, observing different RNA-rich bodies and MBNL1/CUGBP1’s relationship to them in human lens epithelial cells (HLECs). Importantly, it was investigated whether these bodies or MBNL1/CUGBP1’s relationship to them changed in DM1 HLECs. It was found that altered intracellular bodies in DM1 HLECs had a common theme of stress sensing and regulation. This implies that these cells may be experiencing an impairment in responding to stress. It was suggested that these changes may be attributed to altered autophagy levels. This is important because lens epithelial cells differentiate into fiber cells, a process involving denucleation and organelle loss and regulated partly by autophagy. Additionally, changes in MBNL1 expression patterns and increased formation of solid bodies were also observed. Hence, additional contributions to the cellular DM1 phenotype were suggested in HLECs, apart from altered splicing patterns.
Additional file 10: of Modeling, validation and verification of three-dimensional cell-scaffold contacts from terabyte-sized images
Creators: name: Bajcsy, Peter
name: Soweon Yoon
name: Florczyk, Stephen
name: Hotaling, Nathan
name: Mylene Simon
name: Szczypinski, Piotr
name: Schaub, Nicholas
name: Simon, Carl
name: Brady, Mary
name: Sriram, Ram
Publisher: name: figshare
Year: 2017
Subjects: subject: Space Science
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Developmental Biology
subject: Marine Biology

description: Validation steps based on 2D SEM and 3D CLSM data of Single Fibers. (DOCX 34Â kb)
title: Maintenance of genetic diversity: challenges for management of marine resources
Creators: name: Kenchington, Ellen
name: Heino, Mikko
Publisher: name: ASC 2002 - Y - Theme session
Year: 2024
Subjects: Fisheries and aquaculture
Pressures, impacts, conservation, and management

description: No abstracts are to be cited without prior reference to the author.There are three general classes of threat to biodiversity at the gene level: 1) extinction, which results in complete and irreversible loss of genes; 2) hybridization, which may cause re-arrangement of co-adapted genes and loss of adaptability to local conditions, and 3) reduction of genetic variability within populations. While extinction avoidance is a fundamental management objective and hybridization can usually be dismissed in marine populations, the reduction of genetic variability within populations is a plausible threat and can occur in two ways. First, a decrease in population size may result in inbreeding. Normally, marine fish have very large population sizes, and commercial extinction is likely to occur long before populations are reduced to the level required for losses of genetic diversity due to inbreeding. However, when populations are very severely over-fished to small numbers, concerns associated with small population sizes and disruptions of migration between populations may become prominent. In particular, undetected populations within management units may be fished to this level before the situation is properly evaluated and remedied. Second, a reduction of genetic variability within populations may occur in a directed way, due to, e.g., selective fishing. Fishing is expected to generate selection on life history traits such as age and size at maturation; changes in life history traits influence the dynamics of fish populations, energy flows in the ecosystem, and ultimately, sustainable yield. We discuss management objectives designed to ameliorate genetic complications associated with small population size and fisheries-induced selection, and outline a management approach that may be useful when developing advice for maintaining genetic diversity
Long period helical structures and twist-grain boundary phases induced by non magnetic ion doping in Mn$_{1-x}$(Co,Rh)$_{x}$Ge chiral magnet
Creators: name: Martin, N.
name: Deutsch, M.
name: Chaboussant, G.
name: Damay, F.
name: Bonville, P.
name: Fomicheva, L. N.
name: Tsvyashchenko, A. V.
name: Rössler, U. K.
name: Mirebeau, I.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We study the evolution of helical magnetism in MnGe chiral magnet upon partial substitution of Mn for non magnetic 3d-Co and 4d-Rh ions. At high doping levels, we observe spin helices with very long periods -more than ten times larger than in the pure compound- and sizable ordered moments. This behavior calls for a change in the energy balance of interactions leading to the stabilization of the observed magnetic structures. Strikingly, neutron scattering unambiguously shows a double periodicity in the observed spectra at $x \gtrsim 0.45$ and $\gtrsim 0.25$ for Co- and Rh-doping, respectively. In analogy with observations made in cholesteric liquid crystals, we suggest that it reveals the presence of magnetic twist-grain-boundary phases, involving a dense short-range correlated network of screw dislocations. The dislocation cores are described as smooth textures made of non-radial double-core skyrmions.
description: 6 pages, 6 figures
title: ADCO, Sixième cartulaire de Saint-Étienne de Dijon (1662), Cart. 30 (G 133), 441 folios, f. 798
Creators: name: de la Côte d'Or, Archives départementales
name: Archives Départementales De La Côte-D'Or
name: Petot, Frédérique
name: Projet CBMA
name: CG21/F.PETOT/2012
name: Petot, Frédéric
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020
Subjects: subject: Corpus Burgundiae Medii Aevi
subject: Chartes de la Bourgogne du Moyen Âge
subject: cartulaire
subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris

description: Sixième cartulaire de Saint-Étienne de Dijon (1662), Archives départementales de la Côte-d'Or, Cart. 30 (G 133), 441 folios, f. 798, Numérisation en mode image.
description: Relation: http://www.cbma-project.eu/
description: Bibliographic citation: Sixième cartulaire de Saint-Étienne de Dijon (1662), Archives départementales de la Côte-d'Or, Cart. 30 (G 133), 441 folios, f. 798, in Projet CBMA - Corpus Burgundiae Medii Aevi [Ressource en ligne], https://manuscrits.cbma-project.eu/
description: Provenance: abbaye Saint-Étienne de Dijon
description: Provenance: http://www.wikidata.org/entity/Q15945019
MOESM1 of Firmicutes-enriched IS1447 represents a group of IS3-family insertion sequences exhibiting unique + 1 transcriptional slippage
Creators: name: Liu, Ya-Jun
name: Qi, Kuan
name: Zhang, Jie
name: Chen, Chao
name: Cui, Qiu
name: Feng, Yingang
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Biotechnology
subject: Evolutionary Biology
subject: Ecology
subject: Developmental Biology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1: Table S1. Primers used in this study. Table S2. Bacterial strains and plasmids used in this study. Figure S1. Evolutionary relationships of representative IS1447_like OrfAB protein sequences from non-Firmicutes strains. The evolutionary history was inferred using the Neighbor-Joining method [60]. The optimal tree with the sum of branch length = 13.53466248 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) is shown next to the branches [38]. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The bar indicates 0.1 estimated changes per amino acid. Sequences from Firmicutes species are clustered into one branch as shown in Fig. 2, which is compressed as a black triangle in this figure. The accession numbers of corresponding nucleotide sequences are given in front of the species names. The strains with OrfAB proteins that are translated via no or − 1 frameshifting are marked by an asterisk or pound sign, respectively. Figure S2. Sequencing results of the colonies containing partial IS1447 sequences amplified from cDNA of C. thermocellum DSM1313. The potential slippage-prone regions with − 1, + 1 or no transcriptional rearrangement are yellow highlighted. Figure S3. Identification of OrfABt protein by mass spectrometry analysis. The protein produced by BL21(DE3)::pET21a-OrfABt-A8 with the size of ~18.8 kDa was investigated (Fig. 5b). Peptides detected by mass spectrometry are in red.
A performance evaluation of CCS QCD Benchmark on the COMA (Intel(R) Xeon Phi$^{TM}$, KNC) system
Creators: name: Boku, Taisuke
name: Ishikawa, Ken-Ichi
name: Kuramashi, Yoshinobu
name: Meadows, Lawrence
name: D`Mello, Michael
name: Troute, Maurice
name: Vemuri, Ravi
Publisher: name: arXiv
Year: 2016
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: The most computationally demanding part of Lattice QCD simulations is solving quark propagators. Quark propagators are typically obtained with a linear equation solver utilizing HPC machines. The CCS QCD Benchmark is a benchmark program solving the Wilson-Clover quark propagator, and is developed at the Center for Computational Sciences (CCS), University of Tsukuba. We optimized the benchmark program for a \Intel \XeonPhi (Knights Corner, KNC) system named "COMA (PACS-IX)" at CCS Tsukuba under the Intel Parallel Computing Center program. A single precision BiCGStab solver with the overlapped Restricted Additive Schwarz (RAS) preconditioner was implemented using SIMD intrinsics, OpenMP and MPI in the offload mode. With the reverse-offloading technique, we could reduce the communication and offloading overheads. We observed a performance of $\sim 200$ GFlops sustained for the Wilson-Clover hopping matrix multiplication on the lattice sizes larger than $24^3\times 32$ on a sinlge card of the COMA system. A good weak scaling perofmace was observed on the local lattice sizes larger than $24^3\times 32$.
description: 7 pages, 6 figures, talk presented at the 34th International Symposium on Lattice Field Theory, 24-30 July 2016, University of Southampton, UK
Quark matter with strong magnetic field and possibility of the third family of compact stars
Creators: name: Sotani, Hajime
name: Tatsumi, Toshitaka
Publisher: name: arXiv
Year: 2017
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We consider the possibility for the existence of the third family of compact objects, considering the effect of strong magnetic fields inside the hybrid stars. As a result, we demonstrate such new sequences of stable equilibrium configurations for some hadronic equations of state. Through the analysis of the adiabatic index inside stars, we find the conditions for appearing the third family of compact objects, i.e., for hadronic stars without quarks, that the maximum mass should be small, the central density for the maximum mass should be also small, and the radius for the the maximum mass should be large. Even for soft hadronic equations of state, the two solar-mass stars might survive as the third family of compact objects, once quark matter with strong magnetic field, such as $\sim {\cal O}(10^{19} {\rm G})$, is taken into account. It might give a hint to solve the so-called hyperon puzzle in nuclear physics.
description: accepted for publication in MNRAS
Comparison of crossbred and purebred Holstein cows during the transition period
Creators: name: Mendonça, L. G. D.
name: Litherland, N. B.
name: Ballou, M. A.
name: Chebel, R. C.
Publisher: name: American Association of Bovine Practitioners  Proceedings of the Annual Conference
Year: 2012

description: Since the early 1900s, scientists have been comparing phenotypic characteristics of purebred and crossbred dairy cows in an attempt to determine the advantages of heterosis. However, the benefit of heterosis on the immune system has not been investigated during the transition period in lactating dairy cows. Innate immunity during the transition period (three weeks pre- to three weeks postpartum) plays a critical role on the postparturient health of dairy cows. The objectives of this study were to compare dry matter intake (DMI), metabolite concentration, innate immunity, and postpartum health of purebred Holstein (HO) and Montbeliarde-sired crossbred (MS) cows.
description: American Association of Bovine Practitioners Proceedings of the Annual Conference, 2012