bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell activity of freshwater aerobic anoxygenic phototrophic bacteria and their contribution to biomass production
Authors: Garcia-Chaves Maria C , Cottrell Matthew T , Kirchman David L , Ruiz-González Clara , del Giorgio Paul A 
Published: January 2016

Abstract
Aerobic anoxygenic phototrophic (AAP) bacteria are photoheterotrophs that despite their low abundances have been hypothesized to play an ecologically and biogeochemically important role in aquatic systems. Characterizing this role requires a better understanding of the in situ dynamics and activity of AAP bacteria. Here we provide the first assessment of the single-cell activity of freshwater AAP bacteria and their contribution to total bacterial production across lakes spanning a wide trophic gradient, and explore the role of light in regulating AAP activity. The proportion of cells that were active in leucine incorporation and the level of activity per cell were consistently higher for AAP than for bulk bacteria across lakes. As a result, AAP bacteria contributed disproportionately more to total bacterial production than to total bacterial abundance. Interestingly, although environmentally driven patterns in activity did not seem to differ largely between AAP and bulk bacteria, their response to light did, and exposure to light resulted in increases in the proportion of active AAP bacteria with no clear effect on their cell-specific activity. This suggests that light may play a role in the activation of AAP bacteria, enabling these photoheterotrophs to contribute more to the carbon cycle than suggested by their abundance.
Segregating metabolic processes into different microbial cells accelerates the consumption of inhibitory substrates
Authors: Lilja Elin E , Johnson David R 
Published: January 2016

Abstract
Different microbial cell types typically specialize at performing different metabolic processes. A canonical example is substrate cross-feeding, where one cell type consumes a primary substrate into an intermediate and another cell type consumes the intermediate. While substrate cross-feeding is widely observed, its consequences on ecosystem processes is often unclear. How does substrate cross-feeding affect the rate or extent of substrate consumption? We hypothesized that substrate cross-feeding eliminates competition between different enzymes and reduces the accumulation of growth-inhibiting intermediates, thus accelerating substrate consumption. We tested this hypothesis using isogenic mutants of the bacterium Pseudomonas stutzeri that either completely consume nitrate to dinitrogen gas or cross-feed the intermediate nitrite. We demonstrate that nitrite cross-feeding eliminates inter-enzyme competition and, in turn, reduces nitrite accumulation. We further demonstrate that nitrite cross-feeding accelerates substrate consumption, but only when nitrite has growth-inhibiting effects. Knowledge about inter-enzyme competition and the inhibitory effects of intermediates could therefore be important for deciding how to best segregate different metabolic processes into different microbial cell types to optimize a desired biotransformation.
Isotope dependence of the Zeeman effect in lithium-like calcium
Authors: Köhler Florian , Blaum Klaus , Block Michael , Chenmarev Stanislav , Eliseev Sergey , Glazov Dmitry A. , Goncharov Mikhail , Hou Jiamin , Kracke Anke , Nesterenko Dmitri A. , Novikov Yuri N. , Quint Wolfgang , Minaya Ramirez Enrique , Shabaev Vladimir M. , Sturm Sven , Volotka Andrey V. , Werth Günter 
Published: January 2016

AbstractThe magnetic moment μ of a bound electron, generally expressed by the g-factor μ=−g μBs ħ−1 with μB the Bohr magneton and s the electron’s spin, can be calculated by bound-state quantum electrodynamics (BS-QED) to very high precision. The recent ultra-precise experiment on hydrogen-like silicon determined this value to eleven significant digits, and thus allowed to rigorously probe the validity of BS-QED. Yet, the investigation of one of the most interesting contribution to the g-factor, the relativistic interaction between electron and nucleus, is limited by our knowledge of BS-QED effects. By comparing the g-factors of two isotopes, it is possible to cancel most of these contributions and sensitively probe nuclear effects. Here, we present calculations and experiments on the isotope dependence of the Zeeman effect in lithium-like calcium ions. The good agreement between the theoretical predicted recoil contribution and the high-precision g-factor measurements paves the way for a new generation of BS-QED tests.
An evaluation of the accuracy and speed of metagenome analysis tools
Authors: Lindgreen Stinus , Adair Karen L. , Gardner Paul P. 
Published: January 2016

AbstractMetagenome studies are becoming increasingly widespread, yielding important insights into microbial communities covering diverse environments from terrestrial and aquatic ecosystems to human skin and gut. With the advent of high-throughput sequencing platforms, the use of large scale shotgun sequencing approaches is now commonplace. However, a thorough independent benchmark comparing state-of-the-art metagenome analysis tools is lacking. Here, we present a benchmark where the most widely used tools are tested on complex, realistic data sets. Our results clearly show that the most widely used tools are not necessarily the most accurate, that the most accurate tool is not necessarily the most time consuming and that there is a high degree of variability between available tools. These findings are important as the conclusions of any metagenomics study are affected by errors in the predicted community composition and functional capacity. Data sets and results are freely available from http://www.ucbioinformatics.org/metabenchmark.html
Alcohol drinking as an unfavorable prognostic factor for male patients with nasopharyngeal carcinoma
Authors: Chen Yu-Pei , Zhao Bing-Cheng , Chen Chen , Lei Xin-Xing , Shen Lu-Jun , Chen Gang , Yan Fang , Wang Guan-Nan , Chen Han , Jiang Yi-Quan , Xia Yun-Fei 
Published: January 2016

AbstractThe relationship between alcohol drinking and the prognosis of nasopharyngeal carcinoma (NPC) is unknown. To investigate the prognostic value of alcohol drinking on NPC, this retrospective study was conducted on 1923 male NPC patients. Patients were classified as current, former and non-drinkers according to their drinking status. Furthermore, they were categorized as heavy drinkers and mild/none drinkers based on the intensity and duration of alcohol drinking. Survival outcomes were compared using Kaplan–Meier analysis and Cox proportional hazards model. We found that current drinkers had significantly lower overall survival (OS) rate (5-year OS: 70.2% vs. 76.4%, P < 0.001) and locoregional recurrence-free survival (LRFS) rate (5-year LRFS: 69.3% vs. 77.5%, P < 0.001) compared with non-drinkers. Drinking ≥14 drinks/week and drinking ≥20 years were both independent unfavorable prognostic factors for OS (hazard ratio [HR] = 1.38, 95% confidence interval [CI] 1.05–1.81, P = 0.022; HR = 1.38, 95% CI 1.09–1.75, P = 0.007). Stratified analyses further revealed that the negative impacts of alcohol were manifested mainly among older patients and among smokers. In conclusion, alcohol drinking is a useful predictor of prognosis in male NPC patients; drinkers, especially heavy drinkers have poorer prognosis.
Role of Carbonyl Modifications on Aging-Associated Protein Aggregation
Authors: Tanase Maya , Urbanska Aleksandra M. , Zolla Valerio , Clement Cristina C. , Huang Liling , Morozova Kateryna , Follo Carlo , Goldberg Michael , Roda Barbara , Reschiglian Pierluigi , Santambrogio Laura 
Published: January 2016

AbstractProtein aggregation is a common biological phenomenon, observed in different physiological and pathological conditions. Decreased protein solubility and a tendency to aggregate is also observed during physiological aging but the causes are currently unknown. Herein we performed a biophysical separation of aging-related high molecular weight aggregates, isolated from the bone marrow and splenic cells of aging mice and followed by biochemical and mass spectrometric analysis. The analysis indicated that compared to younger mice an increase in protein post-translational carbonylation was observed. The causative role of these modifications in inducing protein misfolding and aggregation was determined by inducing carbonyl stress in young mice, which recapitulated the increased protein aggregation observed in old mice. Altogether our analysis indicates that oxidative stress-related post-translational modifications accumulate in the aging proteome and are responsible for increased protein aggregation and altered cell proteostasis.
Enhancement of human sodium iodide symporter gene therapy for breast cancer by HDAC inhibitor mediated transcriptional modulation
Authors: Kelkar Madhura G. , Senthilkumar Kalimuthu , Jadhav Smita , Gupta Sudeep , Ahn Beyong-Cheol , De Abhijit 
Published: January 2016

AbstractThe aberrant expression of human sodium iodide symporter (NIS) in breast cancer (BC) has raised the possibility of using targeted radioiodide therapy. Here we investigate modulation of endogenous, functional NIS expression by histone deacetylase inhibitors (HDACi) in vitro and in vivo. Luciferase reporter based initial screening of six different HDACi shows 2–10 fold enhancement of NIS promoter activity in majority of the cell types tested. As a result of drug treatment, endogenous NIS transcript and protein shows profound induction in BC cells. To get an insight on the mechanism of such transcriptional activation, role of Stat4, CREB and other transcription factors are revealed by transcription factor profiling array. Further, NIS-mediated intracellular iodide uptake also enhances substantially (p < 0.05) signifying functional relevance of the transcriptional modulation strategy. Gamma camera imaging confirms 30% higher uptake in VPA or NaB treated BC tumor xenograft. Corroborating with such functional impact of NIS, significant reduction in cell survival (p < 0.005) is observed in VPA, NaB or CI994 drug and 131I combination treatment in vivo indicating effective radioablation. Thus, for the first time this study reveals the mechanistic basis and demonstrates functional relevance of HDACi pre-treatment strategy in elevating NIS gene therapy approach for BC management in clinic.
The episodic ataxia type 1 mutation I262T alters voltage-dependent gating and disrupts protein biosynthesis of human Kv1.1 potassium channels
Authors: Chen Szu-Han , Fu Ssu-Ju , Huang Jing-Jia , Tang Chih-Yung 
Published: January 2016

AbstractVoltage-gated potassium (Kv) channels are essential for setting neuronal membrane excitability. Mutations in human Kv1.1 channels are linked to episodic ataxia type 1 (EA1). The EA1-associated mutation I262T was identified from a patient with atypical phenotypes. Although a previous report has characterized its suppression effect, several key questions regarding the impact of the I262T mutation on Kv1.1 as well as other members of the Kv1 subfamily remain unanswered. Herein we show that the dominant-negative effect of I262T on Kv1.1 current expression is not reversed by co-expression with Kvβ1.1 or Kvβ2 subunits. Biochemical examinations indicate that I262T displays enhanced protein degradation and impedes membrane trafficking of Kv1.1 wild-type subunits. I262T appears to be the first EA1 mutation directly associated with impaired protein stability. Further functional analyses demonstrate that I262T changes the voltage-dependent activation and Kvβ1.1-mediated inactivation, uncouples inactivation from activation gating and decelerates the kinetics of cumulative inactivation of Kv1.1 channels. I262T also exerts similar dominant effects on the gating of Kv1.2 and Kv1.4 channels. Together our data suggest that I262T confers altered channel gating and reduced functional expression of Kv1 channels, which may account for some of the phenotypes of the EA1 patient.
Ptychographic Imaging of Branched Colloidal Nanocrystals Embedded in Free-Standing Thick Polystyrene Films
Authors: De Caro Liberato , Altamura Davide , Arciniegas Milena , Siliqi Dritan , Kim Mee R. , Sibillano Teresa , Manna Liberato , Giannini Cinzia 
Published: January 2016

AbstractResearch on composite materials is facing, among others, the challenging task of incorporating nanocrystals and their superstructures, in polymer matrices. Electron microscopy can typically image nanometre-scale structures embedded in thin polymer films, but not in films that are micron size thick. Here, X-ray Ptychography was used to visualize, with a resolution of a few tens of nanometers, how CdSe/CdS octapod-shaped nanocrystals self-assemble in polystyrene films of 24 ± 4 μm, providing a unique means for non-destructive investigation of nanoparticles distribution and organization in thick polymer films.
Gel electrophoresis in a polyvinylalcohol coated fused silica capillary for purity assessment of modified and secondary-structured oligo- and polyribonucleotides
Authors: Barciszewska Martyna , Sucha Agnieszka , Bałabańska Sandra , Chmielewski Marcin K. 
Published: January 2016

AbstractApplication of a polyvinylalcohol-coated (PVA-coated) capillary in capillary gel electrophoresis (CGE) enables the selective separation of oligoribonucleotides and their modifications at high resolution. Quality assessment of shorter oligomers of small interfering RNA (siRNA) is of key importance for ribonucleic acid (RNA) technology which is increasingly being applied in medical applications. CGE is a technique of choice for calculation of chemically synthesized RNAs and their modifications which are frequently obtained as a mixture including shorter oligoribonucleotides. The use of CGE with a PVA-coated capillary to analyze siRNA mixtures presents an alternative to conventionally employed techniques. Here, we present study on identification of the length and purity of RNA mixture ingredients by using PVA-coated capillaries. Also, we demonstrate the use of PVA-coated capillaries to identify and separate phosphorylated siRNAs and secondary structures (e.g. siRNA duplexes).
Structural understanding of the recycling of oxidized ascorbate by dehydroascorbate reductase (OsDHAR) from Oryza sativa L. japonica
Authors: Do Hackwon , Kim Il-Sup , Jeon Byoung Wook , Lee Chang Woo , Park Ae Kyung , Wi Ah Ram , Shin Seung Chul , Park Hyun , Kim Young-Saeng , Yoon Ho-Sung , Kim Han-Woo , Lee Jun Hyuck 
Published: January 2016

AbstractDehydroascorbate reductase (DHAR) is a key enzyme involved in the recycling of ascorbate, which catalyses the glutathione (GSH)-dependent reduction of oxidized ascorbate (dehydroascorbate, DHA). As a result, DHAR regenerates a pool of reduced ascorbate and detoxifies reactive oxygen species (ROS). In previous experiments involving transgenic rice, we observed that overexpression of DHAR enhanced grain yield and biomass. Since the structure of DHAR is not available, the enzymatic mechanism is not well-understood and remains poorly characterized. To elucidate the molecular basis of DHAR catalysis, we determined the crystal structures of DHAR from Oryza sativa L. japonica (OsDHAR) in the native, ascorbate-bound and GSH-bound forms and refined their resolutions to 1.9, 1.7 and 1.7 Å, respectively. These complex structures provide the first information regarding the location of the ascorbate and GSH binding sites and their interacting residues. The location of the ascorbate-binding site overlaps with the GSH-binding site, suggesting a ping-pong kinetic mechanism for electron transfer at the common Cys20 active site. Our structural information and mutagenesis data provide useful insights into the reaction mechanism of OsDHAR against ROS-induced oxidative stress in rice.
A network analysis of cofactor-protein interactions for analyzing associations between human nutrition and diseases
Authors: Scott-Boyer Marie Pier , Lacroix Sébastien , Scotti Marco , Morine Melissa J. , Kaput Jim , Priami Corrado 
Published: January 2016

AbstractThe involvement of vitamins and other micronutrients in intermediary metabolism was elucidated in the mid 1900’s at the level of individual biochemical reactions. Biochemical pathways remain the foundational knowledgebase for understanding how micronutrient adequacy modulates health in all life stages. Current daily recommended intakes were usually established on the basis of the association of a single nutrient to a single, most sensitive adverse effect and thus neglect interdependent and pleiotropic effects of micronutrients on biological systems. Hence, the understanding of the impact of overt or sub-clinical nutrient deficiencies on biological processes remains incomplete. Developing a more complete view of the role of micronutrients and their metabolic products in protein-mediated reactions is of importance. We thus integrated and represented cofactor-protein interaction data from multiple and diverse sources into a multi-layer network representation that links cofactors, cofactor-interacting proteins, biological processes and diseases. Network representation of this information is a key feature of the present analysis and enables the integration of data from individual biochemical reactions and protein-protein interactions into a systems view, which may guide strategies for targeted nutritional interventions aimed at improving health and preventing diseases.
A transcriptional signature of hub connectivity in the mouse connectome
Authors: Fulcher Ben D. , Fornito Alex 
Published: January 2016

Significance
Some brain regions are highly connected with other areas, designating them as network hubs. These hubs are also heavily interconnected with each other, forming a dense core that integrates information across different neural systems. Here, we show that the functionally important projections linking hub areas of the mouse brain have a distinct genetic signature that is characterized by the tightly coupled expression of genes regulating the synthesis and metabolism of ATP, the primary energy source for neural activity. Our findings establish a direct link between molecular function and the large-scale organization of neuronal connectivity and suggest that coordinated gene expression between hub areas is closely related to the metabolic demands of these highly active and functionally important regions.
Changes in Treatment Patterns and Overall Survival in Patients With Early-Stage Non–Small Cell Lung Cancer in the United States After the Incorporation of Stereotactic Ablative Radiation Therapy
Authors: Haque Waqar , Szeja Sean , Tann Anne , Kalra Sarathi , Teh Bin S. 
Published: January 2016

Purpose:
Technologic developments have made radiation therapy (RT) more effective and have introduced new treatment options, such as stereotactic ablative radiation therapy (SABR). This study sought to determine changes in practice patterns for treatment of stage IA non–small cell lung cancer (NSCLC) after the introduction of SABR into the United States. This population-based study also examined changes in survival during this time period for all patients and specifically for patients treated with RT, surgery, or observation.

Methods:
We included patients in the Surveillance, Epidemiology, and End Results database diagnosed with stage IA NSCLC diagnosed between 2004 and 2012. Changes in treatment patterns were assessed. Outcomes were compared across 2 time periods: 2004 to 2008 (pre-SABR) and 2009 to 2012 (post-SABR). Kaplan-Meier and Cox regression were performed to compare overall survival (OS) for patients treated with surgery, RT, or observation.

Results:
A total of 32,249 patients met the specified criteria. Comparing patients diagnosed in 2004 to those diagnosed in 2012, RT use increased from 13% to 29% (P<0.001), surgery use decreased from 76% to 61% (P<0.001), and patients observed decreased from 11% to 10% (P=0.3). There was no significant OS improvement in all patients or those patients who were observed; there were significant improvements in OS for patients treated with RT (hazard ratio=0.768; 95% confidence interval, 0.711-0.829) and those patients treated with surgery (hazard ratio=0.9; 95% confidence interval, 0.855-0.962).

Conclusions:
There has been an increase in RT utilization and decrease in surgical utilization after the incorporation of SABR by radiation oncologists within the United States. In addition, there has been an improvement in OS for patients treated with definitive RT for early-stage NSCLC between 2004 and 2012 that may be associated with increased utilization of SABR.
Prevalence of Functional Gastrointestinal Disorders in Schoolchildren in Ecuador
Authors: Játiva Edgar , Velasco‐Benítez Carlos A. , Koppen Ilan J.N. , Játiva‐Cabezas Zahira , Saps Miguel 
Published: January 2016

ABSTRACTThe prevalence of functional gastrointestinal disorders (FGIDs) in children in Ecuador is unknown. We describe a survey study in 2 schools in Quito, Ecuador, using a Spanish translation of the Questionnaire on Pediatric Gastrointestinal Symptoms‐Rome III Version (QPGS‐RIII). A total of 417 children (51% boys) with a mean age of 12.0 years were included. FGIDs were present in 95 children (22.8%) and occurred in 25% of girls and in 20.7% of boys (P = 0.296). Functional defecation disorders were found in 12.0% of children, 9.4% had an abdominal pain‐related FGID and 3.8% was diagnosed with a vomiting or aerophagia FGID.
Embedding components in voltage converter PCB for size reduction and heat management
Authors: Wojcik Mariusz , Witek Dariusz , Klej Tomasz , Ramotowski Edward 
Published: January 2016

Purpose
– The purpose of this paper was to show physical limitation of embedding standard packaging components into printed circuit board (PCB) which is more reasonable technology for small series productions which is popular in industrial products. Embedding electronic components inside a PCB FR-4 substrate leads to significant size reduction and better heat management. Embedded chip technology is already known in many consumer electronics applications, but it is focused on high volumes and required to order components ready to be embedded.

Design/methodology/approach
– Highly integrated DC/DC converter with standard-package electronic parts (passive and active) was embedded inside a PCB structure. The design and the manufacturing process was based on standard PCB FR-4 technology. Sandwich solution was used to integrate all layers together; one of the main investigations was to focus on how to fill space around components to keep internal stresses on very low level.

Findings
– There were few considerations during choosing the right concept. The first, which occurred during the first producing round, was the distance between thick copper and inner layer. The second one was the way how to fill space between mounted components on inner layer and isolation laminate. A few trials took place and it is decided that it is impossible to fill this space with resin from prepregs; therefore, a casting compound was used.

Originality/value
– Design and manufacturing process which brings 37 per cent of size reduction of complete DC/DC voltage converter PCB with 28.5 W output power comparing to a reference design with standard surface mounted devices (SMD) and copper layout implementation has been achieved during research project.