bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioturbation as a key driver behind the dominance of Bacteria over Archaea in near-surface sediment
Authors: Chen Xihan , Andersen Thorbjørn Joest , Morono Yuki , Inagaki Fumio , Jørgensen Bo Barker , Lever Mark Alexander 
Published: May 2017

AbstractThe factors controlling the relative abundances of Archaea and Bacteria in marine sediments are poorly understood. We determined depth distributions of archaeal and bacterial 16S rRNA genes by quantitative PCR at eight stations in Aarhus Bay, Denmark. Bacterial outnumber archaeal genes 10–60-fold in uppermost sediments that are irrigated and mixed by macrofauna. This bioturbation is indicated by visual observations of sediment color and faunal tracks, by porewater profiles of dissolved inorganic carbon and sulfate, and by distributions of unsupported 210Pb and 137Cs. Below the depth of bioturbation, the relative abundances of archaeal genes increase, accounting for one third of 16S rRNA genes in the sulfate zone, and half of 16S rRNA genes in the sulfate-methane transition zone and methane zone. Phylogenetic analyses reveal a strong shift in bacterial and archaeal community structure from bioturbated sediments to underlying layers. Stable isotopic analyses on organic matter and porewater geochemical gradients suggest that macrofauna mediate bacterial dominance and affect microbial community structure in bioturbated sediment by introducing fresh organic matter and high-energy electron acceptors from overlying seawater. Below the zone of bioturbation, organic matter content and the presence of sulfate exert key influences on bacterial and archaeal abundances and overall microbial community structure.
A Bioactive Chemical Markers Based Strategy for Quality Assessment of Botanical Drugs: Xuesaitong Injection as a Case Study
Authors: Yang Zhenzhong , Shao Qing , Ge Zhiwei , Ai Ni , Zhao Xiaoping , Fan Xiaohui 
Published: May 2017

AbstractCurrent chemical markers based quality assessment methods largely fail to reflect intrinsic chemical complexity and multiple mechanisms of action of botanical drugs (BD). The development of novel quality markers is greatly needed. Here we propose bioactive chemical markers (BCM), defined as a group of chemo-markers that exhibit similar pharmacological activities comparable to the whole BD, which can therefore be used to effectively assess the quality of BD. As a proof-of-concept, a BCM-based strategy was developed and applied to Xuesaitong Injection (XST) for assessing the efficacy and consistency of different batches. Firstly, systemic characterization of chemical profile of XST revealed a total number of 97 compounds. Secondly, notoginsenoside R1, ginsenoside Rg1, Re, Rb1 and Rd were identified as BCM of XST on treating cardiovascular and cerebrovascular diseases according to Adjusted Efficacy Score following an in vivo validation. Analytical method for quantification of BCM was then developed to ensure the efficacy of XST. Finally, chemical fingerprinting was developed and used to evaluate the batch-to-batch consistency. Our present case study on XST demonstrates that BCM-based strategy offers a rational approach for quality assessment of BD and provides a workflow for chemistry, manufacturing, and controls (CMC) study of BD required by regulatory authority.
Autocatalytic Time-Dependent Evolution of Metastable Two-Component Supramolecular Assemblies to Self-Sorted or Coassembled State
Authors: Fukui Tomoya , Takeuchi Masayuki , Sugiyasu Kazunori 
Published: May 2017

AbstractDespite substantial effort devoted in the history of supramolecular chemistry, synthetic supramolecular systems still lag behind biomolecular systems in terms of complexity and functionality. This is because biomolecular systems function in a multicomponent molecular network under out-of-equilibrium conditions. Here we report two-component supramolecular assemblies that are metastable and thus show time-dependent evolution. We found that the systems undergo either self-sorting or coassembly in time depending on the combination of components. Interestingly, this outcome, which had been previously achievable only under specific conditions, emerged from the two-component systems as a result of synergistic or reciprocal interplay between the coupled equilibria. We believe that this study sheds light on the similarity between synthetic and biomolecular systems and promotes better understanding of their intricate kinetic behaviors.
Classification of Paediatric Inflammatory Bowel Disease using Machine Learning
Authors: Mossotto E. , Ashton J. J. , Coelho T. , Beattie R. M. , MacArthur B. D. , Ennis S. 
Published: May 2017

AbstractPaediatric inflammatory bowel disease (PIBD), comprising Crohn’s disease (CD), ulcerative colitis (UC) and inflammatory bowel disease unclassified (IBDU) is a complex and multifactorial condition with increasing incidence. An accurate diagnosis of PIBD is necessary for a prompt and effective treatment. This study utilises machine learning (ML) to classify disease using endoscopic and histological data for 287 children diagnosed with PIBD. Data were used to develop, train, test and validate a ML model to classify disease subtype. Unsupervised models revealed overlap of CD/UC with broad clustering but no clear subtype delineation, whereas hierarchical clustering identified four novel subgroups characterised by differing colonic involvement. Three supervised ML models were developed utilising endoscopic data only, histological only and combined endoscopic/histological data yielding classification accuracy of 71.0%, 76.9% and 82.7% respectively. The optimal combined model was tested on a statistically independent cohort of 48 PIBD patients from the same clinic, accurately classifying 83.3% of patients. This study employs mathematical modelling of endoscopic and histological data to aid diagnostic accuracy. While unsupervised modelling categorises patients into four subgroups, supervised approaches confirm the need of both endoscopic and histological evidence for an accurate diagnosis. Overall, this paper provides a blueprint for ML use with clinical data.
Proximity Effect induced transport Properties between MBE grown (Bi1−xSbx)2Se3 Topological Insulators and Magnetic Insulator CoFe2O4
Authors: Huang Shun-Yu , Chong Cheong-Wei , Tung Yi , Chen Tzu-Chin , Wu Ki-Chi , Lee Min-Kai , Huang Jung-Chun-Andrew , Li Z. , Qiu H. 
Published: May 2017

AbstractIn this study, we investigate the proximity effect in topological insulator (TI) and magnetic insulator bilayer system. (Bi1−xSbx)2Se3/CoFe2O4 (CFO) heterostructure was fabricated using molecular beam epitaxy and pulsed laser deposition system respectively. As revealed from the magnetoresistance measurement, the weak anti-localization (WAL) is strongly suppressed by proximity effect in (Bi1−xSbx)2Se3/CFO interface. Modified Hikama-Larkin-Nagaoka equation was used to fit the WAL results so that the size of surface state gap can be extracted successfully. The temperature-dependent resistance of the heterostructures at small and large perpendicular magnetic fields were also measured and analyzed. The results indicate that the surface band gap can be induced in TI and continuously enlarged up to 9 T, indicating the gradual alignment of the magnetic moment in CFO under perpendicular magnetic field. The approaches and results accommodated in this work show that CFO can effectively magnetize (Bi1−xSbx)2Se3 and the heterostructures are promising for TI-based spintronic device applications.
Probing the Roles of Calcium-Binding Sites during the Folding of Human Peptidylarginine Deiminase 4
Authors: Liu Yi-Liang , Lee Chien-Yun , Huang Yu-Ni , Chen Hui-Yi , Liu Guang-Yaw , Hung Hui-Chih 
Published: May 2017

AbstractOur recent studies of peptidylarginine deiminase 4 (PAD4) demonstrate that its non-catalytic Ca2+-binding sites play a crucial role in the assembly of the correct geometry of the enzyme. Here, we examined the folding mechanism of PAD4 and the role of Ca2+ ions in the folding pathway. Multiple mutations were introduced into the calcium-binding sites, and these mutants were termed the Ca1_site, Ca2_site, Ca3_site, Ca4_site and Ca5_site mutants. Our data indicate that during the unfolding process, the PAD4 dimer first dissociates into monomers, and the monomers then undergo a three-state denaturation process via an intermediate state formation. In addition, Ca2+ ions assist in stabilizing the folding intermediate, particularly through binding to the Ca3_site and Ca4_site to ensure the correct and active conformation of PAD4. The binding of calcium ions to the Ca1_site and Ca2_site is directly involved in the catalytic action of the enzyme. Finally, this study proposes a model for the folding of PAD4. The nascent polypeptide chains of PAD4 are first folded into monomeric intermediate states, then continue to fold into monomers, and ultimately assemble into a functional and dimeric PAD4 enzyme, and cellular Ca2+ ions may be the critical factor governing the interchange.
Elevated baseline potassium level within reference range is associated with worse clinical outcomes in hospitalised patients
Authors: Park Sehoon , Baek Seon Ha , Lee Sung Woo , Lee Anna , Chin Ho Jun , Na Ki Young , Kim Yon Su , Chae Dong-Wan , Han Jin Suk , Kim Sejoong 
Published: May 2017

AbstractThe clinical significance of elevated baseline serum potassium (K+) levels in hospitalised patients is rarely described. Hence, we performed a retrospective study assessing the significance of elevated K+ levels in a one-year admission cohort. Adult patients without hypokalaemia or end-stage renal disease were included. Adverse outcomes were all-cause mortality, hospital-acquired acute kidney injury, and events of arrhythmia. In total, 17,777 patients were included in the study cohort, and a significant difference (P < 0.001) was observed in mortality according to baseline serum K+ levels. The adjusted hazard ratios (HRs) and associated 95% confidence intervals (CIs) of all-cause mortality for K+ levels above the reference range of 3.6–4.0 mmol/L were as follows: 4.1–4.5 mmol/L, adjusted HR 1.075 (95% CI 0.981–1.180); 4.6–5.0 mmol/L, adjusted HR 1.261 (1.105–1.439); 5.1–5.5 mmol/L, adjusted HR 1.310 (1.009–1.700); >5.5 mmol/L, adjusted HR 2.119 (1.532–2.930). Moreover, the risks of in-hospital acute kidney injury and arrhythmia were higher in patients with serum K+ levels above 4.0 mmol/L and 5.5 mmol/L, respectively. In conclusion, increased serum K+ levels, including mild elevations may be related to worse prognosis. Close monitoring and prompt correction of underlying causes or hyperkalaemia itself is warranted for admitted patients.
Potential decline in carbon carrying capacity under projected climate-wildfire interactions in the Sierra Nevada
Authors: Liang Shuang , Hurteau Matthew D. , Westerling Anthony LeRoy 
Published: May 2017

AbstractEcosystem carbon carrying capacity (CCC) is determined by prevailing climate and natural disturbance regimes, conditions that are projected to change significantly. The interaction of changing climate and its effects on disturbance regimes is expected to affect forest regeneration and growth, which may diminish forest carbon (C) stocks and uptake. We modeled landscape C dynamics over 590 years along the latitudinal gradient of the U.S. Sierra Nevada Mountains under climate and area burned by large wildfires projected by late 21stcentury. We assumed climate and wildfire stabilize at late-21stcentury conditions (2090–2100) to facilitate analysis of lags between warming and changing CCC. We show that compared with historical (1980–2010) climate and wildfire conditions, projected scenarios would drive a significant decrease of up to 73% in mean total ecosystem carbon (TEC) by the end of the 590-year simulation. Tree regeneration failure due to intensified growing season dryness and increased area burned would substantially decrease forested area, transitioning the system from C sink to source. Our results demonstrate the potential for a lower CCC in the system due to extensive vegetation type conversion from forest to non-forest types, and suggest a decline in the contribution of Sierra Nevada forests to U.S. C sink.
Local cryotherapy minimally impacts the metabolome and transcriptome of human skeletal muscle
Authors: Sarver Dylan C. , Sugg Kristoffer B. , Disser Nathaniel P. , Enselman Elizabeth R. Sibilsky , Awan Tariq M. , Mendias Christopher L. 
Published: May 2017

AbstractCryotherapy is commonly used in the treatment of skeletal muscle injuries. However, the data to support the use of cryotherapy is inconclusive, and the biochemical etiology of cryotherapy in human skeletal muscle remains largely unknown. We therefore sought to determine how a clinically-relevant dose of cryotherapy would impact the transcriptome and metabolome of skeletal muscle. Eight healthy male subjects (age 24.7 ± 4.5 years, BMI 22.2 ± 1.6) received a 15 minute bout of local cryotherapy, delivered via ice cup massage over the anterolateral thigh. This resulted in an 85% decrease in skin temperature and a predicted 27% reduction in intramuscular temperature. The contralateral side served as a non-treated control. Two hours after cryotherapy, muscle biopsies were obtained to analyze changes in the transcriptome, metabolome, and activation of p38 MAPK, ERK1/2, Akt, and p70S6K proteins. No changes were detected in the transcriptome between control and cooled muscles. Cryotherapy reduced levels of hexose sugars and hypoxanthine by 1.3%, but no statistically different changes were observed in 60 additional metabolites. Overall, no differences in phosphorylated p38 MAPK, ERK1/2, Akt, and p70S6K were observed. A clinically relevant dose of cryotherapy produced negligible acute biochemical and molecular changes in the skeletal muscle of human subjects.
Glioblastoma-derived cells in vitro unveil the spectrum of drug resistance capability – comparative study of tumour chemosensitivity in different culture systems
Authors: Witusik-Perkowska Monika , Zakrzewska Magdalena , Sikorska Beata , Papierz Wielislaw , Jaskolski Dariusz J. , Szemraj Janusz , Liberski Pawel P. 
Published: May 2017

Resistance to cancer drugs is a complex phenomenon which could be influenced by in vitro conditions. However, tumour-derived cell cultures are routinely used for studies related to mechanisms of drug responsiveness or the search for new therapeutic approaches. The purpose of our work was to identify the potential differences in drug resistance and response to treatment of glioblastoma with the use of three in vitro models: traditional adherent culture, serum-free spheroid culture and novel adherent serum-free culture.
The experimental models were evaluated according to ‘stemness state‘ and epithelial-to-mesenchymal transition (EMT) status, invasion capability and their expression pattern of genes related to the phenomenon of tumour drug resistance. Additionally, the response to drug treatments of three different culture models was compared with regard to the type of cell death.
Multi-gene expression profiling revealed differences between examined culture types with regard to the expression pattern of the selected genes. Functionally, the examined genes were related to drug resistance and metabolism, DNA damage and repair and cell cycle control, and included potential therapeutic targets.
Cytotoxicity analyses confirmed that environmental factors can influence not only the molecular background of glioblastoma drug-resistance and efficiency of treatment, but also the mechanisms/pathways of cell death, which was reflected by a distinct intensification of apoptosis and autophagy observed in particular culture models. Our results suggest that parallel exploitation of different in vitro experimental models can be used to reveal the spectrum of cancer cell resistance capability, especially regarding intra-heterogeneous glioblastomas.
Role of Endoscopic Third Ventriculostomy in Shunt Malfunction
Authors: Sobti Shivender , Choudhary Ajay , Bhaskar Suryanaraynam , Gupta Laxmi 
Published: May 2017

Background Shunt placement was a standard treatment for patients with hydrocephalus. The risk of shunt malfunction is quite high. Endoscopic third ventriculostomy (ETV) for hydrocephalus is an important advancement for patients with hydrocephalus. The aim is to study the role of ETV in patients with ventriculoperitoneal shunt malfunction.
Methods A prospective study of 21 patients with shunt malfunction, who underwent secondary ETV instead of shunt revision, was conducted in Department of Neurosurgery, PGIMER, and Dr. RML Hospital, New Delhi. Patients data included age, cause of hydrocephalus, number of previous shunt surgeries, and outcome after ETV. Shunt was removed in all patients at the time of ETV. Success was defined as shunt independence till the last follow-up.
Results There were 17 males and 4 females. The age range was 2 months to 53 years. Eleven patients had communicating and 10 patients had noncommunicating hydrocephalus. Overall success rate of ETV was 61.90% with 80% (8/10) in noncommunicating and 45.45% (5/11) in communicating hydrocephalus. None of the possible contributing factors for successful ETV, including age (p = 0.088), the etiology of hydrocephalus (p = 0.296), and number of previous shunt surgeries (p = 0.399), were statistically significantly correlated with outcome in our series. Overall complication rate was 14.2%. No death was reported.
Conclusion ETV is an effective alternative for patients who present with shunt malfunction. Age, etiology, type of hydrocephalus, and number of shunt revisions did not have a significant impact on outcome of ETV.
Epilepsy Surgery in Children and Adolescents
Authors: Ramantani Georgia , Zentner Josef 
Published: May 2017

AbstractEpilepsy surgery has been established in recent years as an effective treatment option for children and adolescents with pharmacoresistant structural epilepsies. Thanks to advances in neurosurgery, anesthesia and intensive care, epilepsy surgery is also possible in infants with excellent results. Epilepsy surgery should be considered in children with structural epilepsies and presurgical evaluation should be initiated at the latest when the criteria for pharmacoresistance are met. Focal cortical dysplasia and glioneuronal tumors are the most common etiologies in pediatric cohorts. Postoperative seizure-freedom depends on completeness of resection. In childhood, multilobular and hemispheric interventions predominate, whereas adults commonly undergo temporal resections. The extent of resections decreases with age. Younger children often require larger resections, but have higher capacities to compensate for neurological deficits, due to functional plasticity. Postoperative seizure freedom depends on the epilepsy syndrome, underlying etiology and accurate demarcation of the epileptogenic zone. Postoperatively, two-thirds of the children remain seizure-free in the long-term. Significant improvements in cognitive development are observed with seizure control. In addition to the development of non-invasive methods for presurgical evaluation, it is crucial to reduce the latency between the establishment of pharmacoresistance, presurgical evaluation and surgical treatment in suitable candidates. Multicentric studies with longer observation intervals are urgently needed in order to identify predictors of seizure freedom and favorable developmental trajectories, to facilitate the selection of optimal candidates and to improve counseling of patients and their families.
Initial Economic Impacts of the U.S. Pacific Coast Groundfish Fishery Individual Fishing Quota Program
Authors: Leonard Jerry , Steiner Erin 
Published: May 2017

Abstract
In 2011, management of the limited-entry groundfish trawl fishery on the Pacific coast switched from a system of vessel entry restrictions, gear restrictions, seasonal closures, and bimonthly catch limits to an individual fishing quota (IFQ) program. In addition to advancing a profitable and efficient groundfish fishery, the Pacific Fishery Management Council's objectives for the IFQ program included minimizing the adverse effects on fishing communities and promoting measurable economic and employment benefits. We developed counterfactual revenues and costs for the fleet and used an input–output model to estimate the change in income and employment for the West Coast as a whole and for 12 different port areas. Our results indicated that alternative assumptions regarding the distribution of quota payments substantially changed conclusions about the economic impacts of the IFQ program. Under an assumption that payments to lease quota were distributed to homeports of vessels reporting revenue from the lease or sale of quota, income in most port areas and across the West Coast increased. Alternatively, assuming that there were no quota payments, about half the port areas and the West Coast overall experienced an increase in income. Lastly, assuming that payments to lease quota were a leakage, income decreased in most port areas and across the West Coast. Regardless of the assumption on the distribution of lease payments, the employment in most port areas and throughout the West Coast has declined due to a direct reduction in the number of employee positions on participating vessels. Although increased income resulted in a boost to employment in some areas, it was usually not enough to completely offset the reduction in the number of vessel employees.
Received July 25, 2016; accepted May 9, 2017Published online July 11, 2017
Between innovation and industrial policy: how Washington succeeds and fails at renewable energy
Authors: MacNeil Robert 
Published: May 2017

Abstract
During its eight years in office, the Obama administration undertook an ambitious effort to transition the US economy towards the use of renewable energy technologies, and promote American leads in the global ‘cleantech’ industry. While many of the strategies selected to achieve these goals rendered positive results, others proved unproductive and/or politically toxic. Approaching the issue from a critical innovation framework (which focuses on the political and economic conditions under which the federal government is best able to promote technological change), this paper argues that the administration ignored some of the key conditions that have historically allowed Washington to succeed in promoting the uptake of new technologies. The paper describes the nature of these mistakes, and suggests an alternative way forward based on historical precedent.
Public-private partnerships in sexual and reproductive healthcare provision: establishing a gender analysis
Authors: Gideon Jasmine , Hunter Benjamin M. , Murray Susan F. 
Published: May 2017

AbstractThe past few decades have seen the growing popularity of public-private partnerships (PPPs) across the health sector – a catch all term used to encompass diverse activities involving both public and private sector entities in areas of global and domestic health. In the article we consider the factors that have led to this proliferation of PPPs in the healthcare delivery field and consider the link to the process of ‘scientization’ of healthcare. With a focus on sexual and reproductive health the article also considers two commonly used mechanisms employed in SRH service delivery that have been used in PPPs – social franchise and health voucher schemes. We then reprise key points from the existing critical literature on gendered health systems and go on to consider their application to such service provision-oriented PPPs, using an exploratory analysis of a case study of the use of maternal health vouchers in India.