cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges
Creators: name: Schupp, Peter J.
name: Tsai, Peter
name: Webster, Nicole
name: Rodrigo, Allen
name: Lindquist, Niels
name: Schmitt, Susanne
name: Perez, Thierry
name: Bell, James
name: Hentschel, Ute
name: Fromont, Jane
name: Vacelet, Jean
name: Ilan, Micha
name: Taylor, Michael W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Marine sponges are well known for their associations with highly diverse, yet very specific and often highly similar microbiota. The aim of this study was to identify potential bacterial sub-populations in relation to sponge phylogeny and sampling sites and to define the core bacterial community. 16S ribosomal RNA gene amplicon pyrosequencing was applied to 32 sponge species from eight locations around the world's oceans, thereby generating 2567 operational taxonomic units (OTUs at the 97% sequence similarity level) in total and up to 364 different OTUs per sponge species. The taxonomic richness detected in this study comprised 25 bacterial phyla with Proteobacteria, Chloroflexi and Poribacteria being most diverse in sponges. Among these phyla were nine candidate phyla, six of them found for the first time in sponges. Similarity comparison of bacterial communities revealed no correlation with host phylogeny but a tropical sub-population in that tropical sponges have more similar bacterial communities to each other than to subtropical sponges. A minimal core bacterial community consisting of very few OTUs (97%, 95% and 90%) was found. These microbes have a global distribution and are probably acquired via environmental transmission. In contrast, a large species-specific bacterial community was detected, which is represented by OTUs present in only a single sponge species. The species-specific bacterial community is probably mainly vertically transmitted. It is proposed that different sponges contain different bacterial species, however, these bacteria are still closely related to each other explaining the observed similarity of bacterial communities in sponges in this and previous studies. This global analysis represents the most comprehensive study of bacterial symbionts in sponges to date and provides novel insights into the complex structure of these unique associations.
A new species of Polycirridae (Annelida: Terebellida) and three new reports for Cantabrian and Mediterranean Seas
Creators: name: CEPEDA, Diego
name: LATTIG, Patricia
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 2016

description: Several polychaetes species from the central Cantabrian (NE Atlantic Ocean) and western Mediterranean Seas were studied. The Fabriciidae species Parafabricia mazzellae and Pseudofabricia aberrans are recorded for the first time in the western Mediterranean Sea and Novafabricia infratorquata in the northeast Atlantic Ocean (Cantabrian Sea). A new species of Polycirridae, Polycirrus asturiensis sp. nov., is described for the Cantabrian Sea; it is characterized by having two types of buccal tentacles, a transverse prostomium covering segment 1, a trilobed upper lip, notopodial lobes equally long, notochaetigerous segments with broadly winged chaetae of different lengths and widths, up to segment 12, and type- 1 neurochaetae beginning on segment 6. New habitat information for the fabricids Novafabricia infratorquata, Parafabricia mazzellae and Pseudofabricia aberrans is also provided.
Bosonic seesaw mechanism in a classically conformal extension of the Standard Model
Creators: name: Haba, Naoyuki
name: Ishida, Hiroyuki
name: Okada, Nobuchika
name: Yamaguchi, Yuya
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We suggest the so-called bosonic seesaw mechanism in the context of a classically conformal $U(1)_{B-L}$ extension of the Standard Model with two Higgs doublet fields. The $U(1)_{B-L}$ symmetry is radiatively broken via the Coleman-Weinberg mechanism, which also generates the mass terms for the two Higgs doublets through quartic Higgs couplings. Their masses are all positive but, nevertheless, the electroweak symmetry breaking is realized by the bosonic seesaw mechanism. Analyzing the renormalization group evolutions for all model couplings, we find that a large hierarchy among the quartic Higgs couplings, which is crucial for the bosonic seesaw mechanism to work, is dramatically reduced toward high energies. Therefore, the bosonic seesaw is naturally realized with only a mild hierarchy, if some fundamental theory, which provides the origin of the classically conformal invariance, completes our model at some high energy, for example, the Planck scale. We identify the regions of model parameters which satisfy the perturbativity of the running couplings and the electroweak vacuum stability as well as the naturalness of the electroweak scale.
description: 5 pages, 2 figures, published version in PLB
Increased rectal microbial richness is associated with the presence of colorectal adenomas in humans
Creators: name: Galanko, Joseph
name: McCoy, Amber
name: Legge, Ryan M.
name: Rawls, John F.
name: Fodor, Anthony A.
name: Keku, Temitope O.
name: Benson, Andrew
name: Sanapareddy, Nina
name: Randall, Thomas A.
name: Araujo-Perez, Felix
name: Burcal, Lauren
name: Sandler, Robert S.
name: Abdo, Zaid
name: Jovov, Biljana
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Differences in the composition of the gut microbial community have been associated with diseases such as obesity, Crohn's disease, ulcerative colitis and colorectal cancer (CRC). We used 454 titanium pyrosequencing of the V1–V2 region of the 16S rRNA gene to characterize adherent bacterial communities in mucosal biopsy samples from 33 subjects with adenomas and 38 subjects without adenomas (controls). Biopsy samples from subjects with adenomas had greater numbers of bacteria from 87 taxa than controls; only 5 taxa were more abundant in control samples. The magnitude of the differences in the distal gut microbiota between patients with adenomas and controls was more pronounced than that of any other clinical parameters including obesity, diet or family history of CRC. This suggests that sequence analysis of the microbiota could be used to identify patients at risk for developing adenomas.
Hydrocarbon-degrading bacteria enriched by the Deepwater Horizon oil spill identified by cultivation and DNA-SIP
Creators: name: Berry, David
name: Aitken, Michael D.
name: Gutierrez, Tony
name: Yang, Tingting
name: Teske, Andreas
name: Singleton, David R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: The massive influx of crude oil into the Gulf of Mexico during the Deepwater Horizon (DWH) disaster triggered dramatic microbial community shifts in surface oil slick and deep plume waters. Previous work had shown several taxa, notably DWH Oceanospirillales, Cycloclasticus and Colwellia, were found to be enriched in these waters based on their dominance in conventional clone and pyrosequencing libraries and were thought to have had a significant role in the degradation of the oil. However, this type of community analysis data failed to provide direct evidence on the functional properties, such as hydrocarbon degradation of organisms. Using DNA-based stable-isotope probing with uniformly 13C-labelled hydrocarbons, we identified several aliphatic (Alcanivorax, Marinobacter)- and polycyclic aromatic hydrocarbon (Alteromonas, Cycloclasticus, Colwellia)-degrading bacteria. We also isolated several strains (Alcanivorax, Alteromonas, Cycloclasticus, Halomonas, Marinobacter and Pseudoalteromonas) with demonstrable hydrocarbon-degrading qualities from surface slick and plume water samples collected during the active phase of the spill. Some of these organisms accounted for the majority of sequence reads representing their respective taxa in a pyrosequencing data set constructed from the same and additional water column samples. Hitherto, Alcanivorax was not identified in any of the previous water column studies analysing the microbial response to the spill and we discuss its failure to respond to the oil. Collectively, our data provide unequivocal evidence on the hydrocarbon-degrading qualities for some of the dominant taxa enriched in surface and plume waters during the DWH oil spill, and a more complete understanding of their role in the fate of the oil.
(4088) Lucy Knight
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Constraining fundamental parameters in modified gravity using Gaia-DR2 massive white dwarf observation
Creators: name: Kalita, Surajit
name: Uniyal, Akhil
Publisher: name: arXiv
Year: 2023
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Various experiments and observations have led researchers to suggest different bounds on fundamental constants like the fine-structure constant and the proton-to-electron mass ratio. These bounds differ mostly due to the energy scale of the systems where the experiments are performed. In this article, we obtain bounds on these parameters in the modified gravity context using the Gaia-DR2 massive white dwarf data and show that the bounds alter as the gravity theory changes. This exploration not only indicates strong support for non-negligible influences of modified gravity in astrophysical scenarios in high-density regimes but also reveals that the bounds on fundamental parameters can be much stronger under alternate gravity theories.
description: 9 pages with 3 figures; accepted for publication in ApJ
Data tables from Managing fisheries in a World with more Sea turtles
Creators: name: Putman, Nathan F.
name: Hawkins, Jesse
name: Gallaway, Benny J.
Publisher: name: The Royal Society
Year: 2020
Subjects: subject: Ecology
subject: FOS: Biological sciences

description: Tables of managment actions, fishery effort, harvest, sea turtle bycatch, and indices of sea turtle abundance.
An Infinite Family of Elliptic Ladder Integrals
Creators: name: McLeod, Andrew
name: Morales, Roger
name: von Hippel, Matt
name: Wilhelm, Matthias
name: Zhang, Chi
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We identify two families of ten-point Feynman diagrams that generalize the elliptic double box, and show that they can be expressed in terms of the same class of elliptic multiple polylogarithms to all loop orders. Interestingly, one of these families can also be written as a dlog form. For both families of diagrams, we provide new 2l-fold integral representations that are linearly reducible in all but one variable and that make the above properties manifest. We illustrate the simplicity of this integral representation by directly integrating the three-loop representative of both families of diagrams. These families also satisfy a pair of second-order differential equations, making them ideal examples on which to develop bootstrap techniques involving elliptic symbol letters at high loop orders.
description: 27 pages, 2 figures; v2: typo in ancillary file fixed, matches journal version
Stochastic changes over time and not founder effects drive cage effects in microbial community assembly in a mouse model
Creators: name: Mühlbauer, Marcus
name: Arthur, Janelle C.
name: McCafferty, Jonathan
name: Gharaibeh, Raad Z.
name: Fodor, Anthony A.
name: Jobin, Christian
name: Sha, Wei
name: Perez-Chanona, Ernesto
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Maternal transmission and cage effects are powerful confounding factors in microbiome studies. To assess the consequences of cage microenvironment on the mouse gut microbiome, two groups of germ-free (GF) wild-type (WT) mice, one gavaged with a microbiota harvested from adult WT mice and another allowed to acquire the microbiome from the cage microenvironment, were monitored using Illumina 16S rRNA sequencing over a period of 8 weeks. Our results revealed that cage effects in WT mice moved from GF to specific pathogen free (SPF) conditions take several weeks to develop and are not eliminated by the initial gavage treatment. Initial gavage influenced, but did not eliminate a successional pattern in which Proteobacteria became less abundant over time. An analysis in which 16S rRNA sequences are mapped to the closest sequenced whole genome suggests that the functional potential of microbial genomes changes significantly over time shifting from an emphasis on pathogenesis and motility early in community assembly to metabolic processes at later time points. Functionally, mice allowed to naturally acquire a microbial community from their cage, but not mice gavaged with a common biome, exhibit a cage effect in Dextran Sulfate Sodium-induced inflammation. Our results argue that while there are long-term effects of the founding community, these effects are mitigated by cage microenvironment and successional community assembly over time, which must both be explicitly considered in the interpretation of microbiome mouse experiments.
Additional file 1 of Guided imagery for treatment (GIFT): protocol of a pilot trial of guided imagery versus treatment as usual to address radiotherapy-related distress in head and neck cancer
Creators: name: Kolva, Elissa
name: Karam, Sana D.
name: Carr, Alaina L.
name: Roberts, Sydneyjane
name: Torkko, Kathleen
name: Lanning, Ryan
name: Cox-Martin, Emily
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 1.
Interaction between Bicycles and Automated Delivery Droids. Results from GNSS Measurements and a Survey
Creators: name: Mattas, Konstantinos
name: Dubos, Louison
name: Damy, Sophie
name: Cepolina, Elvezia
name: Silani, Enrico
name: Alonso Raposo, Maria
name: Ciuffo, Biagio
Publisher: name: Zenodo
Year: 2023
Subjects: Automated Guided Vehicles
Last-Mile delivery
Bicycle safety
Vulnerable Road Users

description: Small autonomous vehicles (droids, automated guided vehicles), already used for logistics operations in industrial environments, are also attracting interest for last mile logistics, in particular for short-distance deliveries in urban areas where the circulation of traditional vans is limited and alternative transport modes (motorcycle and cycle delivery services) resulted extremely dangerous. In these contexts, the use of small autonomous vehicles on roadways is extremely complicated due to regulatory and permit-related issues mainly linked to safety. This research focuses on the potential use of small autonomous vehicles on cycle paths. The paper concerns an empirical analysis of the behaviour of cyclists and droids sharing the same physical space (cycle lane). The data collected is both quantitative and qualitative, via GNSS and a via survey. From the first data source the distribution of cyclists' speeds, both in free flow conditions and in following conditions, the median distance and the minimum Time To Collision (TTC) were studied. From the survey instead, we obtained information on opinions and attitudes towards the experience with the droid. The results obtained are valuable for assessing the conditions under which droids can use cycle paths without posing a danger to cyclists and without limiting the level of service of the cycle path too much.
New contributions to the marine hypotrichous ciliate, Pseudokeronopsis qingdaoensis Hu & Song, 2000 (Protozoa: Ciliophora: Stichotrichida)
Creators: name: SONG, Weibo
name: WILBERT, Norbert
name: HU, Xiaozhong
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 2004

description: A reinvestigation on the morphology and classification of Pseudokeronopsis qingdaoensis Hu & Song, 2000, a
 large and unique marine ciliate collected from the coastal water near Qingdao, China, was performed using living observa-
 tion and silver impregnation methods. Based on previous and the current studies, a redescription and an updated diagnosis
 are supplied: marine Pseudokeronopsis; 150-300 x 40-70 µm in vivo; body colourless, flexible, and contractile. Bicorona
 comprising about 15 pairs of frontal cirri; 6-13 buccal and 2 (rarely 4) frontoterminal cirri; transverse row with 25-45 cirri
 extending to anterior 2/5 of cell; midventral complex consisting of two conspicuously separated rows with c. 40 pairs of
 cirri; distal end of adoral zone curved posteriorly to about cytostome level; constantly 3 dorsal kineties. Two kinds of cor-
 tical granules: one tiny and colourless; another one large and about 2 µm across, brownish to brown-reddish, blood-cell-
 shaped, distributed sparsely. Contractile vacuole positioned in anterior 1/3 of body. More than 100 macronuclear segments.
Construction and Optimization of the Quantum Analog of Carnot Cycles
Creators: name: Xiao, Gaoyang
name: Gong, Jiangbin
Publisher: name: arXiv
Year: 2015
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The quantum analog of Carnot cycles in few-particle systems consists of two quantum adiabatic steps and two isothermal steps. This construction is formally justified by use of a minimum work principle. It is then shown, without relying on any microscopic interpretations of work or heat, that the heat-to-work efficiency of the quantum Carnot cycle thus constructed may be further optimized, provided that two conditions regarding the expectation value of some generalized force operators evaluated at equilibrium states are satisfied. In general the optimized efficiency is system-specific, lower than the Carnot efficiency, and dependent upon both temperatures of the cold and hot reservoirs. Simple computational examples are used to illustrate our theory. The results should be an important guide towards the design of favorable working conditions of a realistic quantum heat engine.
description: 5+ pages, two figures. Comments are most welcome
Composition and enzymatic function of particle-associated and free-living bacteria: a coastal/offshore comparison
Creators: name: Teske, Andreas
name: Ziervogel, Kai
name: Macgregor, Barbara
name: Arnosti, Carol
name: D'Ambrosio, Lindsay
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: We compared the function and composition of free-living and particle-associated microbial communities at an inshore site in coastal North Carolina and across a depth profile on the Blake Ridge (offshore). Hydrolysis rates of six different polysaccharide substrates were compared for particle-associated (>3 μm) and free-living (<3 to 0.2 μm) microbial communities. The 16S rRNA- and rDNA-based clone libraries were produced from the same filters used to measure hydrolysis rates. Particle-associated and free-living communities resembled one another; they also showed similar enzymatic hydrolysis rates and substrate preferences. All six polysaccharides were hydrolyzed inshore. Offshore, only a subset was hydrolyzed in surface water and at depths of 146 and 505 m; just three polysaccharides were hydrolyzed at 505 m. The spectrum of bacterial taxa changed more subtly between inshore and offshore surface waters, but changed greatly with depth offshore. None of the OTUs occurred at all sites: 27 out of the 28 major OTUs defined in this study were found either exclusively in a surface or in a mid-depth/bottom water sample. This distinction was evident with both 16S rRNA and rDNA analyses. At the offshore site, despite the low community overlap, bacterial communities maintained a degree of functional redundancy on the whole bacterial community level with respect to hydrolysis of high-molecular-weight substrates.
RawHash: Enabling Fast and Accurate Real-Time Analysis of Raw Nanopore Signals for Large Genomes
Creators: name: Firtina, Can
name: Ghiasi, Nika Mansouri
name: Lindegger, Joel
name: Singh, Gagandeep
name: Cavlak, Meryem Banu
name: Mao, Haiyu
name: Mutlu, Onur
Publisher: name: arXiv
Year: 2023
Subjects: subject: Genomics (q-bio.GN)
subject: FOS: Biological sciences

description: Nanopore sequencers generate electrical raw signals in real-time while sequencing long genomic strands. These raw signals can be analyzed as they are generated, providing an opportunity for real-time genome analysis. An important feature of nanopore sequencing, Read Until, can eject strands from sequencers without fully sequencing them, which provides opportunities to computationally reduce the sequencing time and cost. However, existing works utilizing Read Until either 1) require powerful computational resources that may not be available for portable sequencers or 2) lack scalability for large genomes, rendering them inaccurate or ineffective. We propose RawHash, the first mechanism that can accurately and efficiently perform real-time analysis of nanopore raw signals for large genomes using a hash-based similarity search. To enable this, RawHash ensures the signals corresponding to the same DNA content lead to the same hash value, regardless of the slight variations in these signals. RawHash achieves an accurate hash-based similarity search via an effective quantization of the raw signals such that signals corresponding to the same DNA content have the same quantized value and, subsequently, the same hash value. We evaluate RawHash on three applications: 1) read mapping, 2) relative abundance estimation, and 3) contamination analysis. Our evaluations show that RawHash is the only tool that can provide high accuracy and high throughput for analyzing large genomes in real-time. When compared to the state-of-the-art techniques, UNCALLED and Sigmap, RawHash provides 1) 25.8x and 3.4x better average throughput and 2) significantly better accuracy for large genomes, respectively. Source code is available at https://github.com/CMU-SAFARI/RawHash.
description: To appear in proceedings of ISMB/ECCB 2023
Updated High-Temperature Opacities for the Dartmouth Stellar Evolution Program and their Effect on the Jao Gap Location
Creators: name: Boudreaux, Emily M.
name: Chaboyer, Brian C.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: The Jao Gap, a 17 percent decrease in stellar density at $M_G \sim10$ identified in both Gaia DR2 and EDR3 data, presents a new method to probe the interior structure of stars near the fully convective transition mass. The Gap is believed to originate from convective kissing instability wherein asymmetric production of $^{3}$He causes the core convective zone of a star to periodically expand and contract and consequently the stars' luminosity to vary. Modeling of the Gap has revealed a sensitivity in its magnitude to a population's metallicity primarily through opacity. Thus far, models of the Jao Gap have relied on OPAL high-temperature radiative opacities. Here we present updated synthetic population models tracing the Gap location modeled with the Dartmouth stellar evolution code using the OPLIB high-temperature radiative opacities. Use of these updated opacities changes the predicted location of the Jao Gap by $\sim0.05$ mag as compared to models which use the OPAL opacities. This difference is likely too small to be detectable in empirical data.
description: 15 pages, 13 figures; Accepted for publication in The Astrophysical Journal
Role of methylotrophs in the degradation of hydrocarbons during the Deepwater Horizon oil spill
Creators: name: Gutierrez, Tony
name: Aitken, Michael D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: The role of methylotrophic bacteria in the fate of the oil and gas released into the Gulf of Mexico during the Deepwater Horizon oil spill has been controversial, particularly in relation to whether organisms such as Methylophaga had contributed to the consumption of methane. Whereas methanotrophy remains unqualified in these organisms, recent work by our group using DNA-based stable-isotope probing coupled with cultivation-based methods has uncovered hydrocarbon-degrading Methylophaga. Recent findings have also shown that methylotrophs, including Methylophaga, were in a heightened state of metabolic activity within oil plume waters during the active phase of the spill. Taken collectively, these findings suggest that members of this group may have participated in the degradation of high-molecular-weight hydrocarbons in plume waters. The discovery of hydrocarbon-degrading Methylophaga also highlights the importance of considering these organisms in playing a role to the fate of oil hydrocarbons at oil-impacted sites.
A new genus and three new species of free-living marine nematodes (Nematoda: Enoplida: Enchelidiidae) from the Yellow Sea, China
Creators: name: HUANG, Yong
name: ZHANG, Zhinan
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 2004

description: A new genus, Abelbolla gen. nov. and three new species of free-living marine nematodes in this genus, Abelbolla
 boucheri sp. nov., Abelbolla huanghaiensis sp. nov. and Abelbolla warwicki sp. nov. from the Yellow Sea, China, are
 described and illustrated. Abelbolla gen.nov. is characterized by tapered anterior end of the body, buccal cavity divided in
 two parts, precloacal supplements more or less visible and the absence of differentiated oesophageal bulbs. A. boucheri can
 be separated from other species of Abelbolla by thin spicules with an elongated capitulum and rather short and massive
 gubernacular apophysis. A. huanghaiensis can be separated from A. boucheri by the presence of spicules with a small hook
 at distal end, and by gubernaculums with longer dorsal apophysis. A. warwicki is characterized by a large buccal cavity and
 no winged precloacal supplements. The types are deposited in the College of Marine Life Sciences, Ocean University of
 China.
(4087) george Smyth
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Calcite-accumulating large sulfur bacteria of the genus Achromatium in Sippewissett Salt Marsh
Creators: name: Berben, Tom
name: Angert, Esther
name: Salman, Verena
name: Yang, Tingting
name: Klein, Frieder
name: Teske, Andreas
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Large sulfur bacteria of the genus Achromatium are exceptional among Bacteria and Archaea as they can accumulate high amounts of internal calcite. Although known for more than 100 years, they remain uncultured, and only freshwater populations have been studied so far. Here we investigate a marine population of calcite-accumulating bacteria that is primarily found at the sediment surface of tide pools in a salt marsh, where high sulfide concentrations meet oversaturated oxygen concentrations during the day. Dynamic sulfur cycling by phototrophic sulfide-oxidizing and heterotrophic sulfate-reducing bacteria co-occurring in these sediments creates a highly sulfidic environment that we propose induces behavioral differences in the Achromatium population compared with reported migration patterns in a low-sulfide environment. Fluctuating intracellular calcium/sulfur ratios at different depths and times of day indicate a biochemical reaction of the salt marsh Achromatium to diurnal changes in sedimentary redox conditions. We correlate this calcite dynamic with new evidence regarding its formation/mobilization and suggest general implications as well as a possible biological function of calcite accumulation in large bacteria in the sediment environment that is governed by gradients. Finally, we propose a new taxonomic classification of the salt marsh Achromatium based on their adaptation to a significantly different habitat than their freshwater relatives, as indicated by their differential behavior as well as phylogenetic distance on 16S ribosomal RNA gene level. In future studies, whole-genome characterization and additional ecophysiological factors could further support the distinctive position of salt marsh Achromatium.
Electronic Supplementary Material for Freitas et al. 'Benthic-pelagic coupling in the Barents Sea: an integrated data-model framework'.
Creators: name: Freitas, Felipe S.
name: Hendry, Katharine R.
name: Henley, Sian F.
name: Faust, Johan C.
name: Tessin, Allyson C.
name: Stevenson, Mark A.
name: Abbott, Geoffrey D.
name: März, Christian
name: Arndt, Sandra
Publisher: name: The Royal Society
Year: 2020
Subjects: subject: Geochemistry
subject: FOS: Earth and related environmental sciences
subject: Oceanography
subject: 80110 Simulation and Modelling
subject: FOS: Computer and information sciences

description: The Barents Sea is experiencing long-term climate-driven changes, e.g. modification in oceanographic conditions and extensive sea ice loss, which can lead to large, yet unquantified disruptions to ecosystem functioning. This key region hostsa large fraction of Arctic primary productivity. However, processes governing benthic and pelagic coupling are not mechanistically understood, limiting our ability to predict the impacts of future perturbations. We combine field observations with a reaction-transport model approach to quantify organic matter (OM) processing and disentangle its drivers. Sedimentary OM reactivity patterns show no gradients relative to sea ice extent, being mostly driven by seafloor spatial heterogeneity. Burial of high reactivity, marine-derived OM is evident at sites influenced by Atlantic Water (AW), whereas low reactivity material is linked to terrestrial inputs on the central shelf. Degradation rates are mainly driven by aerobic respiration (40–75%), being greater at sites where highly reactive material is buried. Similarly, ammonium and phosphate fluxes are greater at those sites. The present-day AW-dominated shelf might represent the future scenario for the entire Barents Sea. Our results represent a baseline systematic understanding of seafloor geochemistry, allowing us to anticipate changes that could be imposed on the pan-Arctic in the future if climate-driven perturbations persist.This article is part of the theme issue ‘The changing Arctic Ocean: consequences for biological communities, biogeochemical processes and ecosystems’.
A case study on catch characteristics of European hake gillnet fishery in the southern Sea of Marmara, Turkey
Creators: name: GÖKTÜRK, Didem
name: DENIZ, Tomris
name: ATEŞ, Celal
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 2016

description: The focus of the present study was to provide information on European hake gillnet fishery in the southern Sea of Marmara (Turkey) based on samples collected during in high fishery season between April and May 2013 with experimental gillnets of different mesh sizes. European hake gillnets of three mesh sizes 28, 30, and 32 mm (nominal bar length) were set at between the 50 and 70 m depth water to test the effects of mesh size on the species composition, size of fish, catch rates, catch composition, bycatch and discard ratios and CPUE estimates. Cluster analysis was used to examine the stability of the results. Multi-dimensional scaling (MDS) was also applied to assess catch species aggregation patterns in the catch. The results showed that, 1062 specimens (182.79 kg) belonging to 8 species were caught and Merluccius merluccius and Solea solea were two dominant species of the catches with all studied mesh sizes with the percentage of 76.57, 19.54% in biomass and 48.96, 39.36% in number of specimens, respectively. The size frequency distribution of M. merluccius and S. solea are determined with the length range of 23.5 to 41.0 cm TL (mean 31.9 ± 0.14 cm) and 18.5 to 35.5 cm TL (mean 22.2 ± 0.09), respectively. The highest CPUE estimates by number and biomass of European hake was determined in 30 mm mesh size as 0.093 n.m-1 and 25.153 g.m-1, respectively. The similarity levels found by cluster analyses indicated that 32 mm mesh size is different from 28 and 30 mm mesh size with 85.67 and 85.55% respectively, for number of specimens and biomass based on standardized data. Since the present study reported here is the first concerning European hake gillnet fisheries and these findings will help to improve the management and conservation of this fishery.
A Study of Correlations in the Stock Market
Creators: name: Sharma, Chandradew
name: Banerjee, Kinjal
Publisher: name: arXiv
Year: 2015
Subjects: subject: Statistical Finance (q-fin.ST)
subject: Data Analysis, Statistics and Probability (physics.data-an)
subject: Mathematical Finance (q-fin.MF)
subject: FOS: Economics and business
subject: FOS: Physical sciences

description: We study the various sectors of the Bombay Stock Exchange(BSE) for a period of 8 years from April 2006 - March 2014. Using the data of daily returns of a period of eight years we make a direct model free analysis of the pattern of the sectorial indices movement and the correlations among them. Our analysis shows significant auto correlation among the individual sectors and also strong cross-correlation among sectors. We also find that auto correlations in some of the sectors persist in time. This is a very significant result and has not been reported so far in Indian context These findings will be very useful in model building for prediction of price movement of equities, derivatives and portfolio management. We show that the Random Walk Hypothesis is not applicable in modeling the Indian market and Mean-Variance-Skewness-Kurtosis based portfolio optimization might be required. We also find that almost all sectors are highly correlated during large fluctuation periods and have only moderate correlation during normal periods.
description: 12 pages, 10 figures
Marine diatom proteorhodopsins and their potential role in coping with low iron availability
Creators: name: Ellis, Kelsey
name: Catlett, Dylan
name: Marchetti, Adrian
name: Hopkinson, Brian M.
name: Cassar, Nicolas
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Proteorhodopsins (PR) are retinal-binding membrane proteins that function as light-driven proton pumps to generate energy for metabolism and growth. Recently PR-like genes have been identified in some marine eukaryotic protists, including diatoms, dinoflagellates, haptophytes and cryptophytes. These rhodopsins are homologous to green-light-absorbing, ATP-generating PRs present within bacteria. Here we show that in the oceanic diatom Pseudo-nitzschia granii, PR-like gene and protein expressions increase appreciably under iron limitation. In a survey of available transcriptomes, PR-like genes in diatoms are generally found in isolates from marine habitats where seasonal to chronic growth limitation by the micronutrient iron is prevalent, yet similar biogeographical patterns are not apparent in other phytoplankton taxa. We propose that rhodopsin-based phototrophy could account for a proportion of energy synthesis in marine eukaryotic photoautotrophs, especially when photosynthesis is compromised by low iron availability. This alternative ATP-generating pathway could have significant effects on plankton community structure and global ocean carbon cycling.
Additional file 1 of Oxytocin impacts top-down and bottom-up social perception in adolescents with ASD: a MEG study of neural connectivity
Creators: name: Korisky, Adi
name: Gordon, Ilanit
name: Goldstein, Abraham
Publisher: name: figshare
Year: 2022
Subjects: subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 1. Medication information.
title: Financial disclosure for diversified operations : a critique of the orthodox model, and some tentative proposals
Creators: name: Rutherford, B. A.
Publisher: name: University of Kent
Year: 2023

description: The aggregative information disclosed by all entities will represent a lower quality of reporting in the case of diversified organisations because it will be more difficult to place the information in context. However, the boundaries of industrial activity are poorly defined and this will cause cause substantial difficulties for any attempt to restore the quality of information disclosed by diversified organisations. This study is based on the view that financial reports should be veritable (ie be shown to have real-world referents). The orthodox model for reporting the results of diversified operations requires that allocations be made according to the criterion of benefit. In the, almost inevitable, presence of interaction, such allocations cannot have real-world referents and thus reports drawn up using the orthodox model cannot be veritable. Empirical evidence suggests that the attempt to require the publication of such reports in the UK has yielded uneven and inconsistent information. The treatment of interaction in the literature dealing with the orthodox model is confused. If interaction effects can be identified and measured, they can be disclosed separately or summarised by means of the range of ambiguity. Reports incorporating this information are likely to be highly complex and difficult to interpret. A variety of proposals for dealing with the problems of allocation In financial reports is examined in the context of diversified operations, but the proposals are found to be unsatisfactory. Some tentative suggestions concerning the search for a veridical reporting scheme are made. Finally, the boundary condition management model is developed. Since diversification causes a loss of quality ox Information available to outside parties, it is argued that such parties should be given some control over the process, together with the necessary information. Internal boundary condition management should provide some scope for improving performance' and disclosures relating to this improvement should be made.
Electronic Supplementary Material for Freitas et al. 'Benthic-pelagic coupling in the Barents Sea: an integrated data-model framework'
Creators: name: Freitas, Felipe S.
name: Hendry, Katharine R.
name: Henley, Sian F.
name: Faust, Johan C.
name: Tessin, Allyson C.
name: Stevenson, Mark A.
name: Abbott, Geoffrey D.
name: März, Christian
name: Arndt, Sandra
Publisher: name: The Royal Society
Year: 2020
Subjects: subject: Geochemistry
subject: FOS: Earth and related environmental sciences
subject: Oceanography
subject: 80110 Simulation and Modelling
subject: FOS: Computer and information sciences

description: The Barents Sea is experiencing long-term climate-driven changes, e.g. modification in oceanographic conditions and extensive sea ice loss, which can lead to large, yet unquantified disruptions of ecosystem functioning. This key region hosts large fraction of Arctic primary productivity. However, processes governing benthic and pelagic coupling are not mechanistically understood, limiting our ability to predict the impacts of future perturbations. We combine field observations with a reaction-transport model approach to quantify organic matter (OM) processing and disentangle its drivers. Sedimentary OM reactivity patterns show no gradients relative to sea ice extent, being mostly driven by seafloor spatial heterogeneity. Burial of high reactivity, marine-derived OM is evident at sites influenced by Atlantic Water (AW), whereas low reactivity material is linked to terrestrial inputs on the central shelf. Degradation rates are mainly driven by aerobic respiration (40–75%), being greater at sites where highly reactive material is buried. Similarly, ammonium and phosphate fluxes are greater at those sites. The present-day AW-dominated shelf might represent the future scenario for the entire Barents Sea. Our results represent a baseline systematic understanding of seafloor geochemistry, allowing anticipating changes that could be imposed to the pan-Arctic in the future if climate-driven perturbations persist.This article is part of the theme issue ‘The changing Arctic Ocean: consequences for biological communities, biogeochemical processes and ecosystems’.
(4089) Lucy Elizabeth Little
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Polymer Quantization predicts radiation in inertial frames
Creators: name: Kajuri, Nirmalya
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We investigate the response of an Unruh-DeWitt detector coupled to a polymer quantized massless scalar field in flat spacetime, using the propagator obtained by Hossain, Husain and Seahra. As this propagator violates Lorentz invariance, frames moving at different constant velocities are no longer equivalent. This means that it is possible in principle for even an observer moving at constant velocity to detect radiation. We show that such an observer indeed detects radiation. Remarkably, we show that the rate of this radiation does not decrease with the decrease in the characteristic length scale of polymer quantization. Thus the radiation cannot be suppressed by making the polymer length scale arbitrarily small. Our results should bring this theory within the ambit of low-energy experiments and place a lower limit on the characteristic polymer length scale.
description: 18 pages, 2 figures, published version
Headache and Health-Related Job Loss Among Disadvantaged Women
Creators: name: Beeber, Linda L.
name: Linnan, Laura A.
name: Kneipp, Shawn M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: AbstractHeadache is a significant public health issue and a major cause of work-related disability. Given that lower-income groups suffer more frequent and more severe headaches, this study examined the associations between headaches, comorbid conditions, symptom management, and health-related job loss in 432 low-income women. The presence of headaches, headaches and allergy symptoms combined, and a higher number of comorbid conditions were significantly associated with health-related job loss. Medication use and emergency department use patterns suggest further research related to day-to-day headache symptom management strategies, and role functioning among this vulnerable group is needed.
Externalizing symptoms among children of alcoholic parents: Entry points for an antisocial pathway to alcoholism.
Creators: name: Chassin, L. A.
name: Wirth, R. J.
name: Edwards, M. C.
name: Curran, P. J.
name: Zucker, R. A.
name: Hussong, A. M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: We examined heterogeneity in risk for externalizing symptoms in children of alcoholic parents as it may inform the search for entry points into an antisocial pathway to alcoholism. Specifically, we tested whether the number of alcoholic parents in a family, the comorbid subtype of parent alcoholism, and the gender of the child predicted trajectories of externalizing symptoms over the early life course as assessed in high-risk samples of children of alcoholic parents and matched controls. Through integrative analyses of two independent, longitudinal studies, we showed that children with either antisocial alcoholic parents or two alcoholic parents were at greatest risk for externalizing symptoms. Moreover, children with a depressed alcoholic parent did not differ from those with an antisocial alcoholic parent in reported symptoms. These findings were generally consistent across mother-, father- and adolescent-reports of symptoms, child gender and child age (ages 2 through 17), and the two independent studies examined. Multi-alcoholic and comorbid-alcoholic families may thus convey a genetic susceptibility to dysregulation along with environments that both exacerbate this susceptibility and provide few supports to offset it.
Characterization of azimuthal and radial velocity fields induced by rotors in flows with a low Reynolds number
Creators: name: Köhler, Jannis
name: Friedrich, Jan
name: Ostendorf, Andreas
name: Gurevich, Evgeny
Publisher: name: arXiv
Year: 2015
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: We theoretically and experimentally investigate the flow field that emerges from a rod-like microrotor rotating about its center in a non-axisymmetric manner. A simple theoretical model is proposed that uses a superposition of two rotlets as a fundamental solution to the Stokes equation. The predictions of this model are compared to measurements of the azimuthal and radial microfluidic velocity field components that are induced by a rotor composed of fused microscopic spheres. The rotor is driven magnetically and the fluid flow is measured with the help of a probe particle fixed by an optical tweezer. We find considerable deviations of the mere azimuthal flow pattern induced by a single rotating sphere as it has been reported by Di Leonardo \textit{et al.} [Phys. Rev. Lett. 96, 134502 (2006)]. Notably, the presence of a radial velocity component that manifests itself by an oscillation of the probe particle with twice the rotor frequency is observed. These findings open up a way to discuss possible radial transport in microfluidic devices.
description: 7 pages, 7 figures