bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inferring protein-protein interaction networks from inter-protein sequence co-evolution
Authors: Feinauer Christoph , Szurmant Hendrik , Weigt Martin , Pagnani Andrea 
Published: December 2015

AbstractInteraction between proteins is a fundamental mechanism that underlies virtually all biological processes. Many important interactions are conserved across a large variety of species. The need to maintain interaction leads to a high degree of co-evolution between residues in the interface between partner proteins. The inference of protein-protein interaction networks from the rapidly growing sequence databases is one of the most formidable tasks in systems biology today. We propose here a novel approach based on theDirect-Coupling Analysisof the co-evolution between inter-protein residue pairs. We use ribosomal and trp operon proteins as test cases: For the small resp. large ribosomal subunit our approach predicts protein-interaction partners at a true-positive rate of 70% resp. 90% within the first 10 predictions, with areas of 0.69 resp. 0.81 under the ROC curves for all predictions. In the trp operon, it assigns the two largest interaction scores to the only two interactions experimentally known. On the level of residue interactions we show that for both the small and the large ribosomal subunit our approach predicts interacting residues in the system with a true positive rate of 60% and 85% in the first 20 predictions. We use artificial data to show that the performance of our approach depends crucially on the size of the joint multiple sequence alignments and analyze how many sequences would be necessary for a perfect prediction if the sequences were sampled from the same model that we use for prediction. Given the performance of our approach on the test data we speculate that it can be used to detect new interactions, especially in the light of the rapid growth of available sequence data.
SPECtre: a spectral coherence-based classifier of actively translated transcripts from ribosome profiling sequence data
Authors: Chun Sang Y. , Rodriguez Caitlin M. , Todd Peter K. , Mills Ryan E. 
Published: December 2015

AbstractSummary:Active protein translation can be assessed and measured using ribosome profiling sequencing strategies. Existing analytical approaches applied to this technology make use of sequence fragment length or frame occupancy to differentiate between active translation and background noise, however they do not consider additional characteristics inherent to the technology which limits their overall accuracy. Here, we present an analytical tool that models the overall tri-nucleotide periodicity of ribosomal occupancy using a classifier based on spectral coherence. Our software, SPECtre, examines the relationship of normalized ribosome profiling read coverage over a rolling series of windows along a transcript against an idealized reference signal. A comparison of SPECtre against current methods on existing and new data shows a marked improvement in accuracy for detecting active translation and exhibits overall high sensitivity at a low false discovery rate.Availability and Implementation:SPECtre source code is available for download athttps://github.com/mills-lab/spectre.Contact:remills@med.umich.edu
Exchange Rate Dynamics and the Skill Structure of Labor Demand in Tunisian Manufacturing Industries
Authors: Zmami Mourad , Ben‐Salha Ousama 
Published: December 2015

AbstractThis paper provides empirical evidence on the effects of exchange rates movements on the demand for labor by skill in Tunisia. Using a panel of manufacturing industries from 1990 to 2010, findings suggest that only the demand for skilled labor positively responds to effective exchange rates depreciation. When the focus is shifted to bilateral exchange rates, it is shown that contrary to the USD/TND exchange rate, the EUR/TND exchange rate significantly affects the demand for the skilled labor force. The disaggregation of industries according to the technological intensity reveals that the effects of exchange rates on the demand for skilled labor are more important in medium‐high technology industries than in low technology industries. On the contrary, the effects on the demand for unskilled labor remain not significant in the two categories of industries.
What Drives Foreign Direct Investment in Africa? An Empirical Investigation with Panel Data
Authors: Mijiyawa Abdoul’ Ganiou 
Published: December 2015

AbstractThis paper analyzes factors that drive foreign direct investment (FDI) in Africa. To do so, for the first time in the literature, the paper uses 5‐year panel data and the system‐GMM technique over the period 1970–2009. The main results are as follows: (a) larger countries attract more FDI; (b) regardless of their size, however, more open countries, politically stable countries, and countries offering higher return to investment also attract FDI; (c) FDI inflows are persistent in Africa. This suggests that countries that manage to attract FDI today are likely to attract more FDI in the future.
Private Capital Flows and Economic Growth of Sub‐Saharan African Countries
Authors: Alley Ibrahim 
Published: December 2015

AbstractIn theory, private capital flows (PCF) augment domestic capital for economic growth. In sub‐Saharan African (SSA) economies, foreign direct investment per capita (FDIC), portfolio investment per capita (PIC) and bank lending per capita (BLC) components of PCF grew inversely to gross domestic product per capita (GDPC). Previous studies have attributed this problem largely to recipient economies' structural features, with little attention paid to PCF shocks (sharp fluctuations from the equilibrium path). Employing annual data on 14 SSA countries from 1990 to 2013, this study estimated a neoclassical growth model to evaluate the effects of PCF shocks on the SSA countries' economic output and growth. The results showed that private capital flows positively affected economic output and growth, as hypothesized in theory. The effects of PCF shocks were negative, however, and are thus culpable for poor response of the region's economic performance to inflows of private capital.
Applying Statistical Causal Analyses to Agricultural Conservation: A Case Study Examining P Loss Impacts
Authors: Qian Song S. , Harmel R. Daren 
Published: December 2015

AbstractEstimating the effect of agricultural conservation practices on reducing nutrient loss using observational data can be confounded by factors such as differing crop types and management practices. As we may not have the full knowledge of these confounding factors, conventional statistical meta‐analysis methods can be misleading. We discuss the use of two statistical causal analysis methods for quantifying the effects of water and soil conservation practices in reducing P loss from agricultural fields. With the propensity score method, a subset of data was used to form a treatment group and a control group with similar distributions of confounding factors. With the multilevel modeling method, data were stratified based on important confounding factors, and the conservation practice effect was evaluated for each stratum. Both methods resulted in similar estimates of the conservation practice effect (total P load reduction avg. ~70%). In addition, both methods show evidence of conservation practices reducing the incremental increase in total P export per unit increase in fertilizer application. These results are presented as examples of the types of outcomes provided by statistical causal analyses, not to provide definitive estimates of P loss reduction. The enhanced meta‐analysis methods presented within are applicable for improved assessment of agricultural practices and their effects and can be used for providing realistic parameter values for watershed‐scale modeling.
Effect of the acute general surgical unit: a regional perspective
Authors: Pritchard Natasha , Newbold Ryan , Robinson Kerian , Ooi Wei Ming 
Published: December 2015

AbstractBackgroundAcute surgical units have gained favour in Australia and New Zealand. However, there is a lack of evidence regarding their effectiveness in regional centres. We aim to investigate the effect of the introduction of the Acute General Surgical Unit (AGSU) on the outcomes for patients undergoing emergency appendicectomies or cholecystectomies in a regional hospital.MethodsAGSU was introduced in March 2012. We conducted a retrospective comparison analysis of patients admitted 2 years prior to and 2 years after the introduction of AGSU. Primary outcomes included length of stay, time to theatre, after hours and overnight operating. Secondary outcomes included negative appendicectomy rate, conversion to open cholecystectomy and bile duct injuries.ResultsNo difference was seen between pre and post‐AGSU introduction in median time to theatre in the appendicectomy group (8.00 h versus 9.24 h) or cholecystectomy group (17.63 h versus 17.75 h). Additionally, there was no difference between median length of stay in the appendicectomy group (47.52 h versus 48.00 h) or the cholecystectomy group (71.50 h versus 70.67 h). Night operating was significantly reduced in the positive appendicectomy group (4.4% versus 9.1%, P = 0.027) and the overall cholecystectomy group (0.43% versus 3.4%, P = 0.035), however overall after hours operating remained equivalent.ConclusionsThe introduction of the AGSU unit led to a significant reduction in overnight operating, which may improve patient outcomes and surgeon satisfaction. Length of stay and time to theatre did not change. Future directions include further research into the impact of theatre access on emergency surgery outcomes.
Combined liver mobilization and retraction: A novel technique to obtain the optimal surgical field during laparoscopic total gastrectomy
Authors: Yoshikawa Kozo , Shimada Mitsuo , Higashijima Jun , Nakao Toshihiro , Nishi Masaaki , Takasu Chie , Kashihara Hideya , Eto Syohei 
Published: December 2015

AbstractIntroductionDuring laparoscopic gastrectomy, it is important to establish a good operative field and ensure an adequate working space. The combined liver mobilization and retraction method is used to get a safe and optimal view.MethodsWe retrospectively analyzed 32 consecutive patients who underwent laparoscopic total gastrectomy for gastric cancer. The patients were divided into two groups: the mobilization (+) group (n = 12) and the mobilization (−) group (n = 20). Hepatic function tests were performed in all patients.ResultsMobilization provided a satisfactory view of the working field, especially the gastroesophageal junction and the angle of His during laparoscopic total gastrectomy, and no complications were observed during liver retraction. On postoperative hepatic function testing, there was no significant difference between the two groups on any day.ConclusionsCombined liver mobilization and retraction may be helpful in laparoscopic total gastrectomy.
Resveratrol preserves the function of human platelets stored for transfusion
Authors: Lannan Katie L. , Refaai Majed A. , Ture Sara K. , Morrell Craig N. , Blumberg Neil , Phipps Richard P. , Spinelli Sherry L. 
Published: December 2015

SummaryStored platelets undergo biochemical, structural and functional changes that lead to decreased efficacy and safety of platelet transfusions. Not only do platelets acquire markers of activation during storage, but they also fail to respond normally to agonists post‐storage. We hypothesized that resveratrol, a cardioprotective antioxidant, could act as a novel platelet storage additive to safely prevent unwanted platelet activation during storage, while simultaneously preserving normal haemostatic function. Human platelets treated with resveratrol and stored for 5 d released less thromboxane B2 and prostaglandin E2 compared to control platelets. Resveratrol preserved the ability of platelets to aggregate, spread and respond to thrombin, suggesting an improved ability to activate post‐storage. Utilizing an in vitro model of transfusion and thromboelastography, clot strength was improved with resveratrol treatment compared to conventionally stored platelets. The mechanism of resveratrol's beneficial actions on stored platelets was partly mediated through decreased platelet apoptosis in storage, resulting in a longer half‐life following transfusion. Lastly, an in vivo mouse model of transfusion demonstrated that stored platelets are prothrombotic and that resveratrol delayed vessel occlusion time to a level similar to transfusion with fresh platelets. We show resveratrol has a dual ability to reduce unwanted platelet activation during storage, while preserving critical haemostatic function.
Livelihoods Limitations: The Political Economy of Urban Poverty in Dhaka, Bangladesh
Authors: Banks Nicola 
Published: December 2015

ABSTRACTResearch in Bangladesh reveals the limitations of actor‐oriented frameworks for understanding urban poverty that assess household livelihoods on the basis of a household's portfolio of assets or capitals. The narrow focus of these frameworks on households and their depoliticized definition of social capital overlook the political roots of urban poverty. The informal systems of governance that dominate resource distribution within low‐income settlements ensure that the social resources necessary for long‐term household improvement are confined to a small elite. Only through extending our analysis beyond the household level, to explore their position within this local political economy of employment and enterprise, can we recognize the limitations placed on household efforts to improve their livelihoods.
Quantifying the erosion effect on current carbon budget of European agricultural soils at high spatial resolution
Authors: Lugato Emanuele , Paustian Keith , Panagos Panos , Jones Arwyn , Borrelli Pasquale 
Published: December 2015

AbstractThe idea of offsetting anthropogenic CO2 emissions by increasing global soil organic carbon (SOC), as recently proposed by French authorities ahead of COP21 in the ‘four per mil’ initiative, is notable. However, a high uncertainty still exits on land C balance components. In particular, the role of erosion in the global C cycle is not totally disentangled, leading to disagreement whether this process induces lands to be a source or sink of CO2. To investigate this issue, we coupled soil erosion into a biogeochemistry model, running at 1 km2 resolution across the agricultural soils of the European Union (EU). Based on data‐driven assumptions, the simulation took into account also soil deposition within grid cells and the potential C export to riverine systems, in a way to be conservative in a mass balance. We estimated that 143 of 187 Mha have C erosion rates <0.05 Mg C ha−1 yr−1, although some hot‐spot areas showed eroded SOC >0.45 Mg C ha−1 yr−1. In comparison with a baseline without erosion, the model suggested an erosion‐induced sink of atmospheric C consistent with previous empirical‐based studies. Integrating all C fluxes for the EU agricultural soils, we estimated a net C loss or gain of −2.28 and +0.79 Tg yr−1 of CO2eq, respectively, depending on the value for the short‐term enhancement of soil C mineralization due to soil disruption and displacement/transport with erosion. We concluded that erosion fluxes were in the same order of current carbon gains from improved management. Even if erosion could potentially induce a sink for atmospheric CO2, strong agricultural policies are needed to prevent or reduce soil erosion, in order to maintain soil health and productivity.
N fertilizer and harvest impacts on bioenergy crop contributions to SOC
Authors: Stewart Catherine E. , Follett Ronald F. , Pruessner Elizabeth G. , Varvel Gary E. , Vogel Kenneth P. , Mitchell Robert B. 
Published: December 2015

AbstractBelowground root biomass is infrequently measured and simply represented in models that predict landscape‐level changes to soil carbon stocks and greenhouse gas balances. Yet, crop‐specific responses to N fertilizer and harvest treatments are known to impact both plant allocation and tissue chemistry, potentially altering decomposition rates and the direction and magnitude of soil C stock changes and greenhouse gas fluxes. We examined switchgrass (Panicum virgatum L.) and corn (Zea mays L.,) yields, belowground root biomass, C, N and soil particulate organic matter‐C (POM‐C) in a 9‐year rainfed study of N fertilizer rate (0, 60, 120 and 180 kg N ha−1) and harvest management near Mead, NE, USA. Switchgrass was harvested with one pass in either August or postfrost, and for no‐till (NT) corn, either 50% or no stover was removed. Switchgrass had greater belowground root biomass C and N (6.39, 0.10 Mg ha−1) throughout the soil profile compared to NT‐corn (1.30, 0.06 Mg ha−1) and a higher belowground root biomass C:N ratio, indicating greater recalcitrant belowground root biomass C input beneath switchgrass. There was little difference between the two crops in soil POM‐C indicating substantially slower decomposition and incorporation into SOC under switchgrass, despite much greater root C. The highest N rate decreased POM‐C under both NT‐corn and switchgrass, indicating faster decomposition rates with added fertilizer. Residue removal reduced corn belowground root biomass C by 37% and N by 48% and subsequently reduced POM‐C by 22% compared to no‐residue removal. Developing productive bioenergy systems that also conserve the soil resource will require balancing fertilization that maximizes aboveground productivity but potentially reduces SOC sequestration by reducing belowground root biomass and increasing root and soil C decomposition.
Somatosensory temporal discrimination is prolonged during migraine attacks
Authors: Boran H. Evren , Cengiz Bülent , Bolay Hayrunnisa 
Published: December 2015

Background and ObjectiveSymptoms and signs of sensorial disturbances are characteristic features of a migraine headache. Somatosensory temporal discrimination measures the temporal threshold to perceive two separate somaesthetic stimuli as clearly distinct. This study aimed to evaluate somaesthetic perception in migraine patients by measuring the somatosensory temporal discrimination thresholds.MethodsThe study included 12 migraine patients without aura and 12 volunteers without headache. Somatosensory temporal discrimination threshold (STDT) values were measured in the face (V3) and hands (C7) during a lateralized headache attack and the headache‐free interictal period. The disease duration, pain intensity, phonophobia, photophobia, nausea, vomiting, and brush allodynia were also recorded during the migraine attack.ResultsSTDT values were within normal limits and not different between the control group and the interictal period in migraine patients. Compared to the headache‐free period, STDT values during the attack were significantly prolonged in the contralateral hand (C7) (155.7 ± 84.2 vs 40.6 ± 16.1 ms [P < .001]), ipsilateral hand (C7) (88.6 ± 51.3 vs 31.4 ± 14.2 ms [P < 0.001]), contralateral face (V3) (65.5 ± 35.4 vs 37.6 ± 22.2 ms [P = .006]) and ipsilateral face (V3) (104.1 ± 44.5 vs 37.5 ± 21.4 ms [P < 0.001]) according to the lateralization of the headache. Ictal STDT values of the contralateral hand and ipsilateral face were significantly increased compared to that of the ipsilateral hand and contralateral face (155.7 ± 84.2 ms vs 88.6 ± 5.1.3 ms [P = .001], 104.1 ± 44.5 ms vs 65.5 ± 35.4 ms [P = 0.001]). No allodynia was detected in the areas that were tested for somatosensory temporal discrimination. The visual analog scale scores were correlated with the somatosensory temporal discrimination thresholds of the contralateral hand (r = 0.602, P = .038), whereas no correlation was detected between the somatosensory temporal discrimination thresholds and disease duration, brush allodynia in the forehead, phonophobia, photophobia, nausea and vomiting.ConclusionThe study demonstrates for the first time that somatosensory temporal discrimination thresholds are elevated during migraine attacks. A transient disruption of the central processing of somaesthetic stimuli during the lateralized migraine attack may provide additional information to understand the mechanisms of the cognitive and sensory perception impairment associated with migraine headache and may have diagnostic value.
Rituximab for subcutaneous delivery: Clinical management principles from a nursing perspective
Authors: Carlson Julia , Cox Keith , Bedwell Kylie , Ku Mathew 
Published: December 2015

Nurses play an integral role in administering treatments to patients with non‐Hodgkin's lymphomas. Intravenous (IV) rituximab was approved by the Australian Therapeutic Goods Administration in 1998, and a novel subcutaneous (SC) formulation was approved in 2014. Fixed‐dose SC rituximab is highly concentrated; co‐formulation with a fully human recombinant vorhyaluronidase alfa enzyme helps overcome the physiological barriers of the SC space, facilitating drug dispersion. Despite a different pharmacokinetic profile to the IV preparation, SC rituximab demonstrates a comparable efficacy/safety profile. Most frequently occurring rituximab‐related adverse events include neutropenia, nausea and constipation, and administration‐related reactions are more frequent with the SC preparation. Compared with IV, SC delivery reduces treatment times and nurse workload, and patients report greater comfort and convenience.This article sets out nursing considerations for optimal administration of SC rituximab, including premedication, drug handling/preparation, injection technique, after‐care and management of adverse events, particularly administration‐related reactions.
Melatonin: the dawning of a treatment for fibrosis?
Authors: Hu Wei , Ma Zhiqiang , Jiang Shuai , Fan Chongxi , Deng Chao , Yan Xiaolong , Di Shouyin , Lv Jianjun , Reiter Russel J. , Yang Yang 
Published: December 2015

AbstractFibrosis is a common occurrence following organ injury and failure. To date, there is no effective treatment for this condition. Melatonin targets numerous molecular pathways, a consequence of its antioxidant and anti‐inflammatory actions that reduce excessive fibrosis. Herein, we review the multiple protective effects of melatonin against fibrosis. There exist four major phases of the fibrogenic response including primary injury to the organ, activation of effector cells, the elaboration of extracellular matrix (ECM) and dynamic deposition. Melatonin regulates each of these phases. Additionally, melatonin reduces fibrosis levels in numerous organs. Melatonin exhibits its anti‐fibrosis effects in heart, liver, lung, kidney, and other organs. In addition, adhesions which occur following surgical procedures are also inhibited by melatonin. The information reviewed here should be significant to understanding the protective role of melatonin against fibrosis, contribute to the design of further experimental studies related to melatonin and the fibrotic response and shed light on a potential treatment for fibrosis.