bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site
Authors: Chakraborty Romy , Woo Hannah , Dehal Paramvir , Walker Robert , Zemla Marcin , Auer Manfred , Goodwin Lynne A. , Kazakov Alexey , Novichkov Pavel , Arkin Adam P. , Hazen Terry C. 
Published: February 2017

AbstractHexavalent Chromium [Cr(VI)] is a widespread contaminant found in soil, sediment, and ground water in several DOE sites, including Hanford 100 H area. In order to stimulate microbially mediated reduction of Cr(VI) at this site, a poly-lactate hydrogen release compound was injected into the chromium contaminated aquifer. Targeted enrichment of dominant nitrate-reducing bacteria post injection resulted in the isolation of Pseudomonas stutzeri strain RCH2. P. stutzeri strain RCH2 was isolated using acetate as the electron donor and is a complete denitrifier. Experiments with anaerobic washed cell suspension of strain RCH2 revealed it could reduce Cr(VI) and Fe(III). The genome of strain RCH2 was sequenced using a combination of Illumina and 454 sequencing technologies and contained a circular chromosome of 4.6 Mb and three plasmids. Global genome comparisons of strain RCH2 with six other fully sequenced P. stutzeri strains revealed most genomic regions are conserved, however strain RCH2 has an additional 244 genes, some of which are involved in chemotaxis, Flp pilus biogenesis and pyruvate/2-oxogluturate complex formation.
Pore types, pore-network analysis, and pore quantification of the lacustrine shale-hydrocarbon system in the Late Triassic Yanchang Formation in the southeastern Ordos Basin, China
Authors: Loucks Robert G. , Ruppel Stephen C. , Wang Xiangzeng , Ko Lucy , Peng Sheng , Zhang Tongwei , Rowe Harry D. , Smith Patrick 
Published: February 2017

Continental Upper Triassic Yanchang “black shales” in the southeastern Ordos Basin have been proven to be unconventional gas reservoirs. Organic-matter-lean and organic-matter-rich argillaceous mudstones form reservoirs that were deposited in a deeper water lacustrine setting during lake highstands. In the stratified lake, the bottom waters were dysaerobic to anoxic. This low-energy and low-oxygen lake-bottom setting allowed types II and III organic matter to accumulate. Interbedded with the argillaceous mudstones are argillaceous arkosic siltstones deposited by gravity-flow processes. Rock samples from the Yanchang Chang 7–9 members are very immature mineralogically. Mineral grains are predominantly composed of relatively equal portions of quartz and feldspar. The high clay-mineral content, generally greater than 40%, has promoted extensive compaction of the sediments, permitting the ductile material to deform and occlude interparticle pores. Furthermore, this high clay-mineral content does not favor hydraulic fracturing of the mudstone reservoir. The pore network within the mudstones is dominated by intraparticle pores and a lesser abundance of organic-matter pores. Interparticle pores are rare. The mean Gas Research Institute (GRI) crushed-rock porosity is 4.2%. Because the pore network is dominated by poorly connected intraparticle pores, permeability is very low (the GRI-calculated geometric mean permeability = 9.9 nd). The dominance of intraparticle pores creates a very poor correlation between GRI porosity and GRI permeability. Several methods of porosity analysis (GRI crushed rock, nitrogen adsorption, and point count) were conducted on each samples, and the results were compared. There is no significant correlation between the three methods, implying that each method measures different pore sizes or types. There is also no relationship between the porosity and permeability and total organic carbon. Much of the mature (peak oil window) organic matter is nonporous, suggesting that it is of type III. Most of the organic-matter pores are in migrated solid bitumen. Overall, the samples analyzed have low porosity and permeability for mudrocks.
Geochemical evidence for oil and gas expulsion in Triassic lacustrine organic-rich mudstone, Ordos Basin, China
Authors: Zhang Tongwei , Wang Xiangzeng , Zhang Jianfeng , Sun Xun , Milliken Kitty L. , Ruppel Stephen C. , Enriquez Daniel 
Published: February 2017

Forty-six core samples were collected from a deep well that penetrated organic-rich layers of the Chang 7, 8, and 9 members of the Yanchang Formation (Fm) in the Ordos Basin. Tests for total organic content (TOC), Rock-Eval pyrolysis, X-ray diffraction (XRD) mineralogy, and molecular composition of gases released from rock crushing were conducted. Analytical results indicate that TOC and clay contents are elevated. The organic matter (OM)-rich mudstone in the Triassic Yanchang Fm suggests good-to-excellent source potential for oil generation. Its thermal maturity is in the oil window. Strong petroleum expulsion occurred from the upper part of the approximately 13 m (42.6 ft) thick Chang 7 member, and for the Chang 8 and Chang 9 members, resulting in low free oil and low methane ([Formula: see text]) concentration in these OM-rich intervals. A combination of sandstone and thin organic-rich mudstone layers is a perfect hybrid lithology stacking pattern for petroleum expulsion. The thickness for effective source rock, approximately 10–12 m (32.8–39.3 ft), varied with sandstone/mudstone lithology stacking pattern. In contrast, limited or no oil expulsion occurred in the lower part of Chang 7 member, a 25 m (82 ft) thick organic-rich interval, which is indicated by high free oil and high [Formula: see text] concentration. A [Formula: see text]-TOC plot can be used to differentiate generated gas, retained gas in OM-rich mudstones, and migrated gas in permeable sandstone beds. We have developed a conceptual model for petroleum expulsion from OM-rich thin versus OM-rich thick layers. Compaction and thermal volume expansion of oil generated from OM may play an important role in petroleum expulsion in OM-rich mudstones. The estimated petroleum expulsion efficiency is approximately 70% and 35% for thin and thick OM-rich mudstone layers, respectively. The redistributed OM in clay-dominated rock assemblage likely forms the preferred migration path to petroleum expulsion.
Theoretical Clarification of the Coexistence of Cl Effects on Au/TiO2: The Interaction between Au Clusters and the TiO2 Surface, and the Aggregation of Au Clusters on the TiO2 Surface
Authors: Tada Kohei , Koga Hiroaki , Hayashi Akihide , Kondo Yudai , Kawakami Takashi , Yamanaka Shusuke , Okumura Mitsutaka 
Published: February 2017

Abstract
Interactions between nanosized Au cluster models (Au rods, ribbons, and film) and rutile TiO2 (110) modeled surfaces (stoichiometric: sTiO2, reduced: rTiO2, and Cl-adsorbed: Cl-rTiO2) were determined using density functional theory. The Au–Au bonds are weakened and the Au–Ti bonds are strengthened because the oxygen defect sites in rTiO2 donate electrons to the nanosized Au models. These interactions suppress the aggregation of the nanosized Au models on the rTiO2 surface. However, Cl atoms are more strongly adsorbed at the oxygen defect site of rTiO2 than Au. The amount of transferred electrons from Cl-rTiO2 to the nanosized Au models is smaller than that of rTiO2. Notably, the Au/Cl-rTiO2 interactions are smaller than the Au/sTiO2 interactions in two- and three-dimensional Au clusters. Thus, Cl atom adsorption onto the oxygen defect site decreases the Au/TiO2 interaction, and the aggregation of the nanosized Au models easily proceeds on Cl-rTiO2. Hence, the Cl atom adsorption onto the oxygen defect site of the TiO2 surface can be assumed as a reason for the residual Cl enhancement of Au aggregation on the TiO2 surface during Au/TiO2 catalyst preparation.
Lectotypification of five Linnaean names in Lonicera (Caprifoliaceae)
Authors: Ferrer-Gallego P. Pablo 
Published: February 2017

AbstractThe lectotypification of five Linnaean names in the genus Lonicera (L. alpigena, L. caerulea, L. dioica, L. nigra, L. tatarica) is discussed. The names are lectotypified using specimens preserved at LINN and UPS (Burser’s collection) herbaria.
Out‐of‐India dispersal of Paliurus (Rhamnaceae) indicated by combined molecular phylogenetic and fossil evidence
Authors: Chen Yong-Sheng , Meseguer Andrea S. , Godefroid Martin , Zhou Zhuo , Zhang Jian-Wen , Deng Tao , Kim Joo-Hwan , Nie Ze-Long , Liu Yu-Sheng (Christopher) , Sun Hang 
Published: February 2017

AbstractPaliurus (Rhamnaceae) is a small genus with a narrow and disjunct distribution in East Asia and the Mediterranean. Fossil evidence from the Late Cretaceous to the present suggests it once had a broad geographic distribution, encompassing parts of India, North America, Asia, and Europe. To reconstruct the evolutionary history of Paliurus and understand the origin of the disjunction observed today in the Northern Hemisphere, phylogenetic and biogeographical reconstructions were performed based on ITS, trnL‐F, and rbcL sequences. Paliurus is shown to be a monophyletic genus, which could be divided into two clades as suggested by previous studies. Biogeographical inference integrated with fossil information indicates that the origin and dispersal pattern of the genus coincide with the “Out‐of‐India” hypothesis. The genus may have originated in India or other parts of Gondwana and then dispersed to East Asia after the collision of the Indian subcontinent with Eurasia, and to North America via the Bering land bridge. Paliurus appears to have reached the Mediterranean region in the late Oligocene following closure of the Turgai Strait. The uplift of the Qinghai‐Tibet Plateau and the advent of drying and cooling climates during the Miocene may have fragmented the distribution of the genus, shaping the biogeographical patterns observed today. Paliurus populations in different regions either became extinct or adapted to changes in local ecological conditions following global climatic shifts through geological time.
Different speciation types meet in a Mediterranean genus: The biogeographic history ofCymbalaria(Plantaginaceae)
Authors: Carnicero Pau , Sáez Llorenç , Garcia-Jacas Núria , Galbany-Casals Mercè 
Published: February 2017

AbstractCymbalariacomprises ten species and six subspecies growing in rocky habitats in the Mediterranean Basin. Several features, such as the genus’ highly fragmented distribution as well as noticeable ecological differentiation between partially sympatric species and presence of ploidy barriers between species suggest the involvement of different speciation types in its evolution. The aims of this study were to test the monophyly ofCymbalariaand to reconstruct infrageneric phylogenetic relationships, to infer the genus’ biogeographic history by estimating divergence times and ancestral distribution areas of lineages, and to disentangle the role of different speciation types. To address these issues, we constructed a phylogeny with a complete taxon sampling based on ITS, 3′ETS,ndhFandrpl32‐trnLsequences. We used the nuclear ribosomal DNA data to produce a time‐calibrated phylogeny, which served as basis for estimating ploidy level evolution and biogeographic history.Cymbalariawas resolved as monophyletic. The genus originated ca. 4 Ma and three lineages segregated rapidly, one comprising solelyC. microcalyxsubsp.microcalyxand the other two corresponding to western and central‐eastern species, respectively. The main diversification events occurred after the onset of the Mediterranean climate and during Pleistocene climate oscillations. Both founder‐event speciation linked to long‐distance dispersal events and sympatric speciation were supported by the biogeographic analyses. In addition, at least two polyploid speciation events were inferred. Finally, conflicts between current taxonomy and the phylogeny at the species and subspecies level clearly show the need of more detailed integrative taxonomic studies.
From healthcare assistant to student nurse
Authors: Adair Fiona M 
Published: February 2017

This article discusses research undertaken to investigate the journey that student nurses make who have previously worked as healthcare assistants (HCAs). It briefly identifies the research process, followed by in-depth discussion of one of the themes that emerged from the study: the difference between a student nurse and a healthcare assistant. The author chose to explore this theme in depth because more and more HCAs are undertaking the undergraduate degree programme to become a registered nurse. This article should help to inform them of the changes in role they can expect before embarking on their career progression.
Drivers for and barriers to the continued development of assistant practitioner roles
Authors: Wheeler Ian 
Published: February 2017

The role of assistant practitioner (AP) was defined around 14 years ago. It is widely regarded as an innovative role, with the ability to work semi-autonomously and across conventional health boundaries, and between both the health and social care sectors. APs are non-registered, so are not subject to regulation like nurses. Their accountability, however, comes through working to locally agreed and defined protocols. They are able to undertake a wide range of technical tasks and work with a high degree of autonomy within a specified care plan. The role is often cited as an effective means of helping the sector meet the productivity challenges that it is confronted with. APs are credited with being able to take on a wide range of tasks that are traditionally, but not necessarily, undertaken by registered professionals. It is a role which many are happy to treat as a destination in its own right, and which others view as a stepping stone to move up to registered roles. Our own research at Skills for Health has seen that APs have become more successful in some areas than others. And while the role has had some successes, there is a case for significant and ongoing action to improve not only training and development for support workers, but also to clarify and develop high-quality support worker roles, of which the AP is an important aspiration and legitimate channel.
Withdrawal of ICS treatment in primary care: A practical guide
Authors: Chalmers James , Bobak Alex , Scullion Jane , Murphy Anna 
Published: February 2017

Inhaled corticosteroids (ICS) are frequently inappropriately prescribed for patients with COPD resulting in up to 70% of patients in current practice receiving them. ICS (prescribed as a combination inhaler with a long-acting beta2-agonist (LABA)) are primarily indicated for patients with an FEV1<50% predicted and a history of frequent exacerbations. There is a consensus that they provide no benefit for patients with preserved lung function and no history of exacerbations. Safety concerns, particularly with regard to pneumonia, osteoporosis, bruising, adrenal suppression and diabetes have been reported in ICS users. Withdrawal of ICS in these patients may therefore promote cost-effective prescribing, and reduce the risk of adverse effects. Nevertheless, in the absence of recognised national guidelines, removing a longstanding therapy from patients with COPD can be challenging. Concerns and barriers reported by clinicians include the risk that patients may subsequently exacerbate or experience a worsening of symptoms, the risk of inadvertently removing ICS from patients with a diagnosis of asthma, and the risks of adrenal insufficiency. Recent randomised controlled trials clearly demonstrate it is possible to remove ICS in a subgroup of patients with COPD and replace with bronchodilator therapies, and that such withdrawal does not result in clinically important increases in exacerbations or worsening of symptoms. In this article, we provide practical advice about when and how to withdraw ICS in patients with COPD.
Developing awareness and use of compliments in the Chinese homestay: A longitudinal case study
Authors: Lee Sheng-Hsun 
Published: February 2017

Abstract
The study abroad homestay enjoys a widespread reputation as a key context for language learning. However, a homestay advantage has been difficult to prove in large-scale quantitative studies. Few qualitative studies examine the long-term developmental processes that can take place in homestays at the micro-ethnographic level. This paper focuses on how one participant, John, gradually developed awareness of the role of compliments and ability to use them for various purposes. Drawing on Vygotskian sociocultural theory, this study analyzes qualitative changes in John’s use of compliments from informal interaction in two homestays across a year. Over time, John learned to use compliments for an array of purposes: expressing appreciation for food, maintaining his hosts’ positive face, developing cordial relationships, and defusing potential conflict. Development in John’s case is evident as he internalized this speech act that he once grappled with, and used it to mediate the behavior of the others when confronted with interactionally and emotionally challenging situations. This process led to John’s ability to participate appropriately as a guest at the Chinese homestay dinner table and to appreciate the subtleties of interpersonal communication that includes unstated expressions of affection.
Carbon Dioxide Adsorption Using High Surface Area Activated Carbons from Local Coals Modified by KOH, NaOH and ZnCl2 Agents
Authors: Toprak Atakan , Kopac Turkan 
Published: February 2017

Abstract
Activated carbons of various features were produced by the impregnation of local coal samples that were taken from Kilimli region of Zonguldak (Turkey) with chemical agents KOH, NaOH and ZnCl2 at different temperatures (600–800 °C) and concentrations (1:1–6:1 agent:coal), for their evaluation in CO2 adsorption studies. BET, DR, t-plot and DFT methods were used for the characterization of carbon samples based on N2 adsorption data obtained at 77 K. The pore sizes of activated carbons produced were generally observed to be in between 13–25 Å, containing highly micropores. Mesopore formations were higher in samples treated with ZnCl2. The highest value for the BET surface area was found as 2,599 m2 g−1 for the samples treated with KOH at 800 °C with a KOH to coal ratio of 4:1. It was observed that the CO2 adsorption capacities obtained at atmospheric pressure and 273 K were considerably affected by the micropore volume and surface area. The highest CO2 adsorption capacities were found as 9.09 mmol/g (28.57 % wt) and 8.25 mmol g−1 (26.65 % wt) for the samples obtained with KOH and NaOH treatments, respectively, at ratio of 4:1. The activated carbons produced were ordered as KOH>NaOH>ZnCl2, according to their surface areas, micropore volumes and CO2 adsorption capacities. The low-cost experimental methods developed by the utilization of local coals in this study enabled an effective capture of CO2 before its emission to atmosphere.
Hetereogeneity in Neuronal Intrinsic Properties: A Possible Mechanism for Hub-Like Properties of the Rat Anterior Cingulate Cortex during Network Activity
Authors: Adams Natalie E. , Sherfey Jason S. , Kopell Nancy J. , Whittington Miles A. , LeBeau Fiona E.N. 
Published: February 2017

AbstractThe anterior cingulate cortex (ACC) is vital for a range of brain functions requiring cognitive control and has highly divergent inputs and outputs, thus manifesting as a hub in connectomic analyses. Studies show diverse functional interactions within the ACC are associated with network oscillations in the β (20–30 Hz) and γ (30-80 Hz) frequency range. Oscillations permit dynamic routing of information within cortex, a function that depends on bandpass filter–like behavior to selectively respond to specific inputs. However, a putative hub region such as ACC needs to be able to combine inputs from multiple sources rather than select a single input at the expense of others. To address this potential functional dichotomy, we modeled local ACC network dynamics in the rat in vitro. Modal peak oscillation frequencies in the β- and γ-frequency band corresponded to GABAAergic synaptic kinetics as seen in other regions; however, the intrinsic properties of ACC principal neurons were highly diverse. Computational modeling predicted that this neuronal response diversity broadened the bandwidth for filtering rhythmic inputs and supported combination—rather than selection—of different frequencies within the canonical γ and β electroencephalograph bands. These findings suggest that oscillating neuronal populations can support either response selection (routing) or combination, depending on the interplay between the kinetics of synaptic inhibition and the degree of heterogeneity of principal cell intrinsic conductances.
Resting-State Network Topology Differentiates Task Signals across the Adult Life Span
Authors: Chan Micaela Y. , Alhazmi Fahd H. , Park Denise C. , Savalia Neil K. , Wig Gagan S. 
Published: February 2017

Brain network connectivity differs across individuals. For example, older adults exhibit less segregated resting-state subnetworks relative to younger adults (Chan et al., 2014). It has been hypothesized that individual differences in network connectivity impact the recruitment of brain areas during task execution. While recent studies have described the spatial overlap between resting-state functional correlation (RSFC) subnetworks and task-evoked activity, it is unclear whether individual variations in the connectivity pattern of a brain area (topology) relates to its activity during task execution. We report data from 238 cognitively normal participants (humans), sampled across the adult life span (20–89 years), to reveal that RSFC-based network organization systematically relates to the recruitment of brain areas across two functionally distinct tasks (visual and semantic). The functional activity of brain areas (network nodes) were characterized according to their patterns of RSFC: nodes with relatively greater connections to nodes in their own functional system (“non-connector” nodes) exhibited greater activity than nodes with relatively greater connections to nodes in other systems (“connector” nodes). This “activation selectivity” was specific to those brain systems that were central to each of the tasks. Increasing age was accompanied by less differentiated network topology and a corresponding reduction in activation selectivity (or differentiation) across relevant network nodes. The results provide evidence that connectional topology of brain areas quantified at rest relates to the functional activity of those areas during task. Based on these findings, we propose a novel network-based theory for previous reports of the “dedifferentiation” in brain activity observed in aging.SIGNIFICANCE STATEMENTSimilar to other real-world networks, the organization of brain networks impacts their function. As brain network connectivity patterns differ across individuals, we hypothesized that individual differences in network connectivity would relate to differences in brain activity. Using functional MRI in a group of individuals sampled across the adult life span (20–89 years), we measured correlations at rest and related the functional connectivity patterns to measurements of functional activity during two independent tasks. Brain activity varied in relation to connectivity patterns revealed by large-scale network analysis. This relationship tracked the differences in connectivity patterns accompanied by older age, providing important evidence for a link between the topology of areal connectivity measured at rest and the functional recruitment of these areas during task performance.