bluuebunny/crossref_metadata_2025_split huggingface dataset:
A probabilistic approach to discovering dynamic full-brain functional connectivity patterns
Authors: Manning Jeremy R. , Zhu Xia , Willke Theodore L. , Ranganath Rajesh , Stachenfeld Kimberly , Hasson Uri , Blei David M. , Norman Kenneth A. 
Published: February 2017

AbstractRecent research shows that the covariance structure of functional magnetic resonance imaging (fMRI) data - commonly described asfunctional connectivity- can change as a function of the participant’s cognitive state (for review see [35]). Here we present a Bayesian hierarchical matrix factorization model, termedhierarchical topographic factor analysis(HTFA), for efficiently discovering full-brain networks in large multi-subject neuroimaging datasets. HTFA approximates each subject’s network by first re-representing each brain image in terms of the activities of a set of localized nodes, and then computing the covariance of the activity time series of these nodes. The number of nodes, along with their locations, sizes, and activities (over time) are learned from the data. Because the number of nodes is typically substantially smaller than the number of fMRI voxels, HTFA can be orders of magnitude more efficient than traditional voxel-based functional connectivity approaches. In one case study, we show that HTFA recovers the known connectivity patterns underlying a collection of synthetic datasets. In a second case study, we illustrate how HTFA may be used to discover dynamic full-brain activity and connectivity patterns in real fMRI data, collected as participants listened to a story. In a third case study, we carried out a similar series of analyses on fMRI data collected as participants viewed an episode of a television show. In these latter case studies, we found that the HTFA-derived activity and connectivity patterns can be used to reliably decode which moments in the story or show the participants were experiencing. Further, we found that these two classes of patterns contained partially non-overlapping information, such that decoders trained on combinations of activity-based and dynamic connectivity-based features performed better than decoders trained on activity or connectivity patterns alone. We replicated this latter result with two additional (previously developed) methods for efficiently characterizing full-brain activity and connectivity patterns.
Free energy calculations suggest a mechanism for Na+/K+-ATPase ion selectivity
Authors: Razavi Asghar M. , Delemotte Lucie , Berlin Joshua R. , Carnevale Vincenzo , Voelz Vincent A. 
Published: February 2017

AbstractNa+/K+-ATPase transports Na+and K+ions across the cell membrane via an ion binding site made alternatively accessible to the intra- and extracellular milieu by conformational transitions that confer marked changes in ion binding stoichiometry and selectivity. To probe the mechanism of these changes, we used molecular simulation approaches to identify the protonation state of Na+and K+coordinating residues in E1P and E2P conformations. Further analysis of these simulations revealed a novel molecular mechanism responsible for the change in protonation state: the conformation-dependent binding of an anion (a chloride ion in our simulations) to a previously unrecognized cytoplasmic site in the loop between transmembrane helices 8 and 9, which influences the electrostatic potential of the crucial Na+-coordinating residue D926. This mechanistic model is consistent with experimental observations and provides a molecular-level picture of how E1P to E2P enzyme conformational transitions are coupled to changes in ion binding stoichiometry and selectivity.
Reduced protein expression in a virus attenuated by codon deoptimization
Authors: Jack Benjamin R. , Boutz Daniel R. , Paff Matthew L. , Smith Bartram L. , Bull James J. , Wilke Claus O. 
Published: February 2017

AbstractThe engineering of hundreds of synonymous codon changes into a viral genome appears to provide a general means of achieving attenuation. The mechanistic underpinnings of this approach remain enignmatic, however. Using quantitative proteomics and RNA sequencing, we explore the molecular basis of attenuation in a strain of bacteriophage T7 whose major capsid gene was engineered to carry 182 suboptimal codons. As expected, there was no evident effect of the recoding on transcription. Proteomic observations revealed that translation is halved for the recoded major capsid gene, and a smaller reduction applies to a few genes downstream, potentially caused by translational coupling. Viral burst size is also approximately halved, and the fitness drop accompanying attenuation is compatible with the reduced burst size. Overall, the fitness effect and molecular basis of attenuation by codon deoptimization are compatible with a relatively simple model of reduced translation of a few genes and a consequent diminished virion assembly. This mechanism is simpler than that operating in eukaryotic viruses.
Increased habitat connectivity homogenizes freshwater communities: historical and landscape perspectives
Authors: Strecker Angela L. , Brittain Jeffrey T. 
Published: February 2017

Summary

Increases in habitat connectivity can have consequences for taxonomic, functional, and genetic diversity of communities. Previously isolated aquatic habitats were connected with canals and pipelines in the largest water development project in the US history, the Columbia Basin Project (CBP; eastern Washington, USA), which also altered environmental conditions; however, the ecological consequences are largely unknown.

Using a historical dataset, we examined long‐term patterns in zooplankton communities, water chemistry and clarity, testing the hypothesis that increased connectivity will result in taxonomic homogenization. Further, we tested contemporary drivers of communities using a comprehensive set of environmental and landscape variables.

Waterbodies were sampled for zooplankton community composition as well as physical and chemical variables inside and outside the CBP using methods consistent with historical studies.

We found significant declines in salinity inside the CBP, whereas changes in water clarity were prevalent across all waterbodies. Increased connectivity via canals homogenized zooplankton communities over time, as well as increasing regional richness. Other long‐term changes in zooplankton communities may be related to climate change, invasive species, and land‐use changes.

Synthesis and applications. Though canals may offer species spatial refugia, homogenization may decrease resilience to environmental stressors. These new hybrid aquatic landscapes, or hydroscapes, should be considered carefully in future water development, including specific plans for monitoring of species and environmental conditions, as well as mitigation of undesirable conditions and/or non‐native species.
Comparison of the Antimicrobial and Sanitizer Resistance of Salmonella Isolates from Chicken Slaughter Processes in Korea
Authors: Youn So Youn , Jeong Ok Mi , Choi Byung Kook , Jung Suk Chan , Kang Min Su 
Published: February 2017

AbstractSalmonella is a foodborne pathogen worldwide. Outbreaks of Salmonella are commonly associated with consumption of contaminated foods such as poultry products. Therefore, the objective of this study was to determine the occurrence, biofilm formation, antibiotic resistance, and sanitizer resistance of Salmonella enterica isolated from chicken carcasses. A total of 318 samples were collected from 15 chicken slaughterhouses in 8 provinces of Korea. They were then examined for Salmonella contamination. S. enterica isolates were tested for their susceptibilities to 15 antimicrobials by broth microdilution method. Their biofilm formation ability and resistance to sanitizers were also evaluated. Eighty‐two isolates of S. enterica were obtained from the 318 samples. There were 14 serotypes and 2 untypable isolates. Fifty‐seven (69.5%) isolates were resistant to at least one antibiotic while 30 (36.6%) isolates were resistant to 5 or more antibiotics. Two S. Senftenberg and 3 S. Montevideo isolates exhibited considerable biofilm formation ability (A600>0.2) following incubation in Luria‐Bertani (LB) broth for 48 h. Biofilm cell survival and recovery growth assay after sanitization showed that most isolates were highly susceptible to 2.5% lactic acid and 0.1% cetylpyridinium chloride. Therefore, lactic acid and cetylpyridinium chloride might be alternatively or additionally used in addition to chlorine‐based sanitizers that are frequently used to reduce Salmonella contamination of chicken carcasses. Our results provide basic information on the distribution of Salmonella serotypes in chicken slaughterhouses. This study also highlights the necessity to improve farming practices and use antimicrobial agents cautiously. This study also suggests that sanitization during the slaughtering process might be necessary to reduce Salmonella contamination of chicken carcasses.
Mega‐Regional Trade Agreements and the Future of the WTO
Authors: Bown Chad P. 
Published: February 2017

AbstractMajor economies such as the United States, European Union, Japan, and even China have shifted trade negotiating emphasis toward ‘mega‐regional’ agreements, including the Trans‐Pacific Partnership (TPP), the Transatlantic Trade and Investment Partnership (TTIP), and the Regional Comprehensive Economic Partnership (RCEP). This paper explores why countries have chosen to pursue mega‐regionals, what is likely to be contained in the agreements, and some of their potential implications for the multilateral trading system under the World Trade Organization (WTO). I call for revisiting the historical approach of introducing plurilateral and critical mass agreements – that would cover some of the mega‐regionals’ new provisions – into the WTO so as to avoid a more substantial, long‐run erosion of the relevance of the nondiscriminatory system. I also highlight potential reforms to the WTO's dispute settlement procedure that are required to strengthen its already prominent role.
Competition and Complementarity between Global and Regional Human Rights Institutions
Authors: Voeten Erik 
Published: February 2017

AbstractFragmentation and competition between global and regional institutions are not among the major issues that threaten the regime. There are three ways in which tensions nonetheless arise. First, consistent with the universalist aspirations of human rights, global conventions have played a focal role in verbally defining rights. This masks considerable cross‐regional and intra‐regional differences in how rights should be interpreted. Second, judicialization of human rights has mostly occurred at the regional level. This occasionally creates inconsistencies with the global regime. Third, rights concerns often encroach on other areas of international cooperation, including security, trade, and development. This raises similar issues of forum shopping as in the other issue areas, for example because some governments may shop for trade agreements or development loans with fewer rights conditions.
New Multilateral Development Banks: Opportunities and Challenges for Global Governance
Authors: Wang Hongying 
Published: February 2017

AbstractIs the creation of the New Development Bank (NDB) and the Asian Infrastructure Investment Bank (AIIB) a challenge for the World Bank and other traditional multilateral development banks (MDBs)? This paper provides an initial assessment of the potential benefits and risks of NDB and AIIB by examining their motivations, scale, structures, rules and first projects. It identifies areas in which the new MDBs can complement the World Bank and other traditional MDBs and discusses ways in which they can undermine the latter. It suggests ways in which the two types of MDBs can further their cooperation in development financing.
Factors associated with the diagnostic yield of computed tomography‐guided transbronchial lung biopsy
Authors: Park Seon Cheol , Kim Cheong Ju , Han Chang Hoon , Lee Sun Min 
Published: February 2017

BackgroundComputed tomography (CT) may be useful for increasing the diagnostic yield of transbronchial lung biopsy (TBLB). However, only a few studies with small sample sizes have reported the diagnostic utility of CT‐guided TBLB and the factors affecting the diagnostic accuracy of CT‐guided TBLB are not well known. We evaluated the diagnostic yield of CT‐guided TBLB and associated factors.Methods
CT‐guided TBLB was performed in 59 patients. Both conventional fluoroscopy and CT were used in all patients for TBLB. The biopsy forceps were advanced toward the lesion under conventional fluoroscopic guidance. CT was used to check whether the forceps were in the correct position.ResultsThe average diameter of the lesions was 3.1 ± 1.0 cm. The biopsy forceps correctly reached the lesion in 43 patients by real‐time CT. A diagnosis was made in 42 patients, and the overall diagnostic yield was 71.2%. The sensitivity for malignancy was 85.7%. In multivariate analysis, the only factor associated with diagnostic yield was forceps position assessed by CT scan (adjusted odds ratio 53.31; 95% confidence interval 5.31, 535.27; P = 0.001).Conclusion
CT‐guided TBLB is a useful diagnostic tool for pulmonary nodules or masses. The correct positioning of biopsy forceps using CT is valuable for successful CT‐guided TBLB.
Ketamine as an Adjunct to Opioids for Acute Pain in the Emergency Department: A Randomized Controlled Trial
Authors: Bowers Karen J. , McAllister Kelly B. , Ray Meredith , Heitz Corey 
Published: February 2017

AbstractObjectivesThis study had five objectives: 1) to measure and compare total opioid use and number of opioid doses in patients treated with opioids versus ketamine in conjunction with opioids; 2) to measure pain scores up to 2 hours after presentation in the ED patient with pain, comparing standard opioid pain control to ketamine in conjunction with opioids; 3) to compare patient satisfaction with pain control using opioids alone versus ketamine in conjunction with opioids; 4) to monitor and compare side effects in patients treated with opioids versus ketamine in conjunction with opioids; and 5) to identify effect variation between different subgroups of patients, with the purpose of focusing future research. We hypothesized that low‐dose ketamine, compared to placebo, as an adjunctive treatment to opioids would result in better pain control over 2 hours and greater patient satisfaction with pain control; further, this protocol will result in a lower opioid dosage over 2 hours.MethodsThis was a randomized, double‐blinded, placebo‐controlled trial at a single academic emergency department evaluating the use of ketamine versus placebo in conjunction with opioids for moderate to severe pain. Subjects with a continued high level of pain after an initial dose of opioid analgesia were randomized to receive either 0.1 mg/kg ketamine or placebo prior to protocol‐based dosing of additional opioid analgesia, if required. Over 120 minutes, subjects were assessed for pain level (0–10), satisfaction with pain control (0–4), side effects, sedation level, and need for additional pain medication. Total opioid dose, including the initial dose, was compared between groups.ResultsSixty‐three subjects were randomized to the placebo group and 53 to the ketamine group. No significant differences were found in demographics between the groups. Patients receiving ketamine reported lower pain scores over 120 minutes than patients receiving placebo (p = 0.015). Total opioid dose was lower in the ketamine group (mean ± SD = 9.95 ± 4.83 mg) compared to placebo (mean ± SD = 12.81 ± 6.81 mg; p = 0.02). Satisfaction did not differ between groups. Fewer patients in the ketamine group required additional opioid doses. More patients reported light‐headedness and dizziness in the ketamine group.ConclusionsKetamine, as an adjunct to opioid therapy, was more effective at reducing pain over 120 minutes and resulted in a lower total opioid dose as well as fewer repeat doses of analgesia. More side effects were reported in the ketamine group (51% vs. 19%), but the side effect profile appears tolerable.
Emergency Department Triage of Traumatic Head Injury Using a Brain Electrical Activity Biomarker: A Multisite Prospective Observational Validation Trial
Authors: Hanley Daniel , Prichep Leslie S. , Bazarian Jeffrey , Huff J. Stephen , Naunheim Rosanne , Garrett John , Jones Elizabeth B. , Wright David W. , O'Neill John , Badjatia Neeraj , Gandhi Dheeraj , Curley Kenneth C. , Chiacchierini Richard , O'Neil Brian , Hack Dallas C. 
Published: February 2017

AbstractObjectivesA brain electrical activity biomarker for identifying traumatic brain injury (TBI) in emergency department (ED) patients presenting with high Glasgow Coma Scale (GCS) after sustaining a head injury has shown promise for objective, rapid triage. The main objective of this study was to prospectively evaluate the efficacy of an automated classification algorithm to determine the likelihood of being computed tomography (CT) positive, in high‐functioningTBIpatients in the acute state.MethodsAdult patients admitted to theEDfor evaluation within 72 hours of sustaining a closed head injury withGCS12 to 15 were candidates for study. A total of 720 patients (18–85 years) meeting inclusion/exclusion criteria were enrolled in this observational, prospective validation trial, at 11 U.S.EDs.GCSwas 15 in 97%, with the first and third quartiles being 15 (interquartile range = 0) in the study population at the time of the evaluation. Standard clinical evaluations were conducted and 5 to 10 minutes of electroencephalogram (EEG) was acquired from frontal and frontal–temporal scalp locations. Using an a priori derivedEEG‐based classification algorithm developed on an independent population and applied to this validation population prospectively, the likelihood of each subject beingCT+ was determined, and performance metrics were computed relative to adjudicatedCTfindings.ResultsSensitivity of the binary classifier (likelyCT+ orCT–) was 92.3% (95% confidence interval [CI] = 87.8%–95.5%) for detection of any intracranial injury visible onCT(CT+), with specificity of 51.6% (95%CI = 48.1%–55.1%) and negative predictive value (NPV) of 96.0% (95%CI = 93.2%–97.9%). Using ternary classification (likelyCT+, equivocal, likelyCT–) demonstrated enhanced sensitivity to traumatic hematomas (≥1 mLof blood), 98.6% (95%CI = 92.6%–100.0%), andNPVof 98.2% (95%CI = 95.5%–99.5%).ConclusionUsing anEEG‐based biomarker high accuracy of predicting the likelihood of beingCT+ was obtained, with highNPVand sensitivity to any traumatic bleeding and to hematomas. Specificity was significantly higher than standardCTdecision rules. The short time to acquire results and the ease of use in theEDenvironment suggests thatEEG‐based classifier algorithms have potential to impact triage and clinical management of head‐injured patients.
Culture and the commodification of water in Samoa
Authors: Macpherson Cluny , Macpherson La'avasa 
Published: February 2017

AbstractWhile ‘solutions’ to challenges of water supply in the Pacific may seem obvious to hydrologists, engineers and planners, their implementation may not be straightforward. Water is embedded in cultural, religious and political contexts, and what seems obvious to planners may seem neither obvious, nor acceptable, to citizens. However, these contexts change continuously, and opportunities arise for changes in narratives around ownership, supply and management of water. Citizens' beliefs about the state's ‘rights’ will vary with societal context, and will shape the ways in which ownership and management of water is worked out in specific locations. This paper outlines thinking and discourses around ownership and management of fresh water in Samoa, and the constraints which culture has imposed on water supply over time. Water discourses have shifted from questions about ownership of specific sources to general discussions about conservation and management of natural resources. This shift has resulted, in part, from the ways in which government has managed the process and, in part, from growing public awareness of water within the larger environmental context. The paper focuses on Samoan material, but some of the generic issues have wider significance in the Pacific because similar variables combine in similar ways.
Intra‐household constraints on educational attainment in rural households in Papua New Guinea
Authors: Ryan Sean , Koczberski Gina , Curry George Nicolas , Germis Emmanuel 
Published: February 2017

AbstractThis paper examines intra‐household and socio‐cultural factors leading to differential outcomes in educational attainment by gender and birth order amongst smallholder oil palm households in Papua New Guinea. Not all children share equitably in the household resources allocated to education: females have lower average education levels than males, and high birth order children have higher education attainment than lower birth order siblings, indicating preferential parental investment in sons and early born children. The findings demonstrate that despite households having regular access to relatively high incomes from oil palm and residing in close proximity to schools, primary school net enrolment rates remain significantly lower than those for East Asia and the Pacific region, and the millennium development goal of universal primary education has not been met. This finding is likely to be the result of a combination of intra‐household factors including gender power imbalances, low parental education levels, the agency of youth in educational decision‐making and the weakening attraction of education as a means of improving income‐earning potential.
Successful laparoscopic distal pancreatectomy for a large solid pseudopapillary neoplasm: A case report
Authors: Tada Seiichiro , Iida Taku , Anazawa Takayuki , Yagi Shintaro , Seo Satoru , Masui Toshihiko , Kaido Toshimi , Takaori Kyoichi , Uemoto Shinji 
Published: February 2017

AbstractA 30‐year‐old Japanese woman presented at our hospital with a pancreatic tumor. Contrast‐enhanced CT revealed a tumor with a 12‐cm diameter in the pancreatic body and tail. In the preoperative setting, endoscopic ultrasound‐guided fine‐needle aspiration permitted a histopathological diagnosis of solid pseudopapillary neoplasm. Twhe patient underwent laparoscopic distal pancreatectomy with splenectomy. Our procedure involved three steps. Firstly, the splenic artery was occluded to block inflow of blood to the tumor. Then, we transected the neck of the pancreas using radical antegrade modular pancreatosplenectomy. Finally, hand‐assisted laparoscopic surgery allowed us to secure the operating field and easily handle the large tumor. This enabled us to accomplish laparoscopic distal pancreatectomy, and en‐bloc resection was completed. The patient was discharged without major complications. Laparoscopic distal pancreatectomy for huge solid pancreatic tumors can be completed safely.