bluuebunny/crossref_metadata_2025_split huggingface dataset:
Life on the edge: functional genomic response of Ignicoccus hospitalis to the presence of Nanoarchaeum equitans
Authors: Giannone Richard J , Wurch Louie L , Heimerl Thomas , Martin Stanton , Yang Zamin , Huber Harald , Rachel Reinhard , Hettich Robert L , Podar Mircea 
Published: July 2014

Abstract
The marine hyperthermophilic crenarchaeon Ignicoccus hospitalis supports the propagation on its surface of Nanoarchaeum equitans, an evolutionarily enigmatic archaeon that resembles highly derived parasitic and symbiotic bacteria. The cellular and molecular mechanisms that enable this interarchaea relationship and the intimate physiologic consequences to I. hospitalis are unknown. Here, we used concerted proteomic and transcriptomic analyses to probe into the functional genomic response of I. hospitalis as N. equitans multiplies on its surface. The expression of over 97% of the genes was detected at mRNA level and over 80% of the predicted proteins were identified and their relative abundance measured by proteomics. These indicate that little, if any, of the host genomic information is silenced during growth in the laboratory. The primary response to N. equitans was at the membrane level, with increases in relative abundance of most protein complexes involved in energy generation as well as that of several transporters and proteins involved in cellular membrane stabilization. Similar upregulation was observed for genes and proteins involved in key metabolic steps controlling nitrogen and carbon metabolism, although the overall biosynthetic pathways were marginally impacted. Proliferation of N. equitans resulted, however, in selective downregulation of genes coding for transcription factors and replication and cell cycle control proteins as I. hospitalis shifted its physiology from its own cellular growth to that of its ectosymbiont/parasite. The combination of these multiomic approaches provided an unprecedented level of detail regarding the dynamics of this interspecies interaction, which is especially pertinent as these organisms are not genetically tractable.
New insights into iron acquisition by cyanobacteria: an essential role for ExbB-ExbD complex in inorganic iron uptake
Authors: Jiang Hai-Bo , Lou Wen-Jing , Ke Wen-Ting , Song Wei-Yu , Price Neil M , Qiu Bao-Sheng 
Published: July 2014

Abstract
Cyanobacteria are globally important primary producers that have an exceptionally large iron requirement for photosynthesis. In many aquatic ecosystems, the levels of dissolved iron are so low and some of the chemical species so unreactive that growth of cyanobacteria is impaired. Pathways of iron uptake through cyanobacterial membranes are now being elucidated, but the molecular details are still largely unknown. Here we report that the non-siderophore-producing cyanobacterium Synechocystis sp. PCC 6803 contains three exbB-exbD gene clusters that are obligatorily required for growth and are involved in iron acquisition. The three exbB-exbDs are redundant, but single and double mutants have reduced rates of iron uptake compared with wild-type cells, and the triple mutant appeared to be lethal. Short-term measurements in chemically well-defined medium show that iron uptake by Synechocystis depends on inorganic iron (Fe′) concentration and ExbB-ExbD complexes are essentially required for the Fe′ transport process. Although transport of iron bound to a model siderophore, ferrioxamine B, is also reduced in the exbB-exbD mutants, the rate of uptake at similar total [Fe] is about 800-fold slower than Fe′, suggesting that hydroxamate siderophore iron uptake may be less ecologically relevant than free iron. These results provide the first evidence that ExbB-ExbD is involved in inorganic iron uptake and is an essential part of the iron acquisition pathway in cyanobacteria. The involvement of an ExbB-ExbD system for inorganic iron uptake may allow cyanobacteria to more tightly maintain iron homeostasis, particularly in variable environments where iron concentrations range from limiting to sufficient.
Virtual finger boosts three-dimensional imaging and microsurgery as well as terabyte volume image visualization and analysis
Authors: Peng Hanchuan , Tang Jianyong , Xiao Hang , Bria Alessandro , Zhou Jianlong , Butler Victoria , Zhou Zhi , Gonzalez-Bellido Paloma T. , Oh Seung W. , Chen Jichao , Mitra Ananya , Tsien Richard W. , Zeng Hongkui , Ascoli Giorgio A. , Iannello Giulio , Hawrylycz Michael , Myers Eugene , Long Fuhui 
Published: July 2014

AbstractThree-dimensional (3D) bioimaging, visualization and data analysis are in strong need of powerful 3D exploration techniques. We develop virtual finger (VF) to generate 3D curves, points and regions-of-interest in the 3D space of a volumetric image with a single finger operation, such as a computer mouse stroke, or click or zoom from the 2D-projection plane of an image as visualized with a computer. VF provides efficient methods for acquisition, visualization and analysis of 3D images for roundworm, fruitfly, dragonfly, mouse, rat and human. Specifically, VF enables instant 3D optical zoom-in imaging, 3D free-form optical microsurgery, and 3D visualization and annotation of terabytes of whole-brain image volumes. VF also leads to orders of magnitude better efficiency of automated 3D reconstruction of neurons and similar biostructures over our previous systems. We use VF to generate from images of 1,107 Drosophila GAL4 lines a projectome of a Drosophila brain.
Cell-secreted Flavins Bound to Membrane Cytochromes Dictate Electron Transfer Reactions to Surfaces with Diverse Charge and pH
Authors: Okamoto Akihiro , Kalathil Shafeer , Deng Xiao , Hashimoto Kazuhito , Nakamura Ryuhei , Nealson Kenneth H. 
Published: July 2014

AbstractThe variety of solid surfaces to and from which microbes can deliver electrons by extracellular electron transport (EET) processes via outer-membrane c-type cytochromes (OM c-Cyts) expands the importance of microbial respiration in natural environments and industrial applications. Here, we demonstrate that the bifurcated EET pathway of OM c-Cyts sustains the diversity of the EET surface in Shewanella oneidensis MR-1 via specific binding with cell-secreted flavin mononucleotide (FMN) and riboflavin (RF). Microbial current production and whole-cell differential pulse voltammetry revealed that RF and FMN enhance EET as bound cofactors in a similar manner. Conversely, FMN and RF were clearly differentiated in the EET enhancement by gene-deletion of OM c-Cyts and the dependency of the electrode potential and pH. These results indicate that RF and FMN have specific binding sites in OM c-Cyts and highlight the potential roles of these flavin-cytochrome complexes in controlling the rate of electron transfer to surfaces with diverse potential and pH.
Limits of Predictability in Commuting Flows in the Absence of Data for Calibration
Authors: Yang Yingxiang , Herrera Carlos , Eagle Nathan , González Marta C. 
Published: July 2014

AbstractThe estimation of commuting flows at different spatial scales is a fundamental problem for different areas of study. Many current methods rely on parameters requiring calibration from empirical trip volumes. Their values are often not generalizable to cases without calibration data. To solve this problem we develop a statistical expression to calculate commuting trips with a quantitative functional form to estimate the model parameter when empirical trip data is not available. We calculate commuting trip volumes at scales from within a city to an entire country, introducing a scaling parameter α to the recently proposed parameter free radiation model. The model requires only widely available population and facility density distributions. The parameter can be interpreted as the influence of the region scale and the degree of heterogeneity in the facility distribution. We explore in detail the scaling limitations of this problem, namely under which conditions the proposed model can be applied without trip data for calibration. On the other hand, when empirical trip data is available, we show that the proposed model's estimation accuracy is as good as other existing models. We validated the model in different regions in the U.S., then successfully applied it in three different countries.
Profiling of the Tox21 10K compound library for agonists and antagonists of the estrogen receptor alpha signaling pathway
Authors: Huang Ruili , Sakamuru Srilatha , Martin Matt T. , Reif David M. , Judson Richard S. , Houck Keith A. , Casey Warren , Hsieh Jui-Hua , Shockley Keith R. , Ceger Patricia , Fostel Jennifer , Witt Kristine L. , Tong Weida , Rotroff Daniel M. , Zhao Tongan , Shinn Paul , Simeonov Anton , Dix David J. , Austin Christopher P. , Kavlock Robert J. , Tice Raymond R. , Xia Menghang 
Published: July 2014

AbstractThe U.S. Tox21 program has screened a library of approximately 10,000 (10K) environmental chemicals and drugs in three independent runs for estrogen receptor alpha (ERα) agonist and antagonist activity using two types of ER reporter gene cell lines, one with an endogenous full length ERα (ER-luc; BG1 cell line) and the other with a transfected partial receptor consisting of the ligand binding domain (ER-bla; ERα β-lactamase cell line), in a quantitative high-throughput screening (qHTS) format. The ability of the two assays to correctly identify ERα agonists and antagonists was evaluated using a set of 39 reference compounds with known ERα activity. Although both assays demonstrated adequate (i.e. >80%) predictivity, the ER-luc assay was more sensitive and the ER-bla assay more specific. The qHTS assay results were compared with results from previously published ERα binding assay data and showed >80% consistency. Actives identified from both the ER-bla and ER-luc assays were analyzed for structure-activity relationships (SARs) revealing known and potentially novel ERα active structure classes. The results demonstrate the feasibility of qHTS to identify environmental chemicals with the potential to interact with the ERα signaling pathway and the two different assay formats improve the confidence in correctly identifying these chemicals.
Comparative RNA-sequencing analysis of myocardial and circulating small RNAs in human heart failure and their utility as biomarkers
Authors: Akat Kemal Marc , Moore-McGriff D’Vesharronne , Morozov Pavel , Brown Miguel , Gogakos Tasos , Correa Da Rosa Joel , Mihailovic Aleksandra , Sauer Markus , Ji Ruiping , Ramarathnam Aarthi , Totary-Jain Hana , Williams Zev , Tuschl Thomas , Schulze P. Christian 
Published: July 2014

Significance
Heart failure (HF) has a high morbidity and mortality and its incidence is increasing worldwide. While protein biomarkers have been established for diagnostic and prognostic evaluation of patients with HF, there is currently no systematic assessment of RNA biomarkers. We determined the composition of myocardial tissue and circulating microRNAs (miRNAs) in a large cohort of patients with stable and advanced HF and compared it to the composition of normal adult and fetal samples. The advanced HF patients underwent mechanical unloading with left ventricular assist devices and samples were collected at different postoperative time points. Our findings provide the underpinning for miRNA-based therapies and emphasize the usefulness of circulating miRNAs as biomarkers for heart injury performing similar to established diagnostic protein biomarkers.
Diversity in organic and agroecological farming systems for mitigation of climate change impact, with examples from Latin America.
Authors: Rossing W. A. H. , Modernel P. , Tittonell P. A. 
Published: July 2014

Abstract

This chapter reviews the impact of climate change on, and the adaptation potential of, ecologically intensive systems such as those known in different parts of the world as organic farming, or agroecology. To fit into the rationale of this book, this chapter focuses on Latin America, and on the array of organic and agroecological farming systems (OAFS) that coexist in the region. The chapter starts by defining the farming systems focused on in the chapter. Then climate change predictions for Latin America are reviewed and their impacts assessed. Next, recent evidence from global meta-analyses on the performance of OAFS is summarized. Information from OAFS from Latin America is included in the reviews but is too scant to warrant a specific section. Instead, two specific OAFS from Latin America are focused on: coffee production systems and natural grassland systems. Their current status, challenges in view of climate change predictions and adaptation options proposed in the literature are reviewed. The chapter ends by discussing the key features and impediments of OAFS and how they can help to build farming systems in the face of global and climate change.
Climate change and integrated crop-livestock systems in temperate-humid regions of North and South America: mitigation and adaptation.
Authors: Franzluebbers A. J. 
Published: July 2014

Abstract

This chapter focuses on the types of integrated crop-livestock systems in North and South America and reviews soil organic C sequestration and greenhouse gas emissions in integrated crop-livestock systems. The impact of climate change on integrated crop-livestock systems are discussed and prospects for developing greater resilience to climate extremes are presented.
Structural deformation of longitudinal arches during running in soccer players with medial tibial stress syndrome
Authors: Noh Byungjoo , Masunari Akihiko , Akiyama Kei , Fukano Mako , Fukubayashi Toru , Miyakawa Shumpei 
Published: July 2014

AbstractThe purpose of this study was to compare angular change and translational motion from the medial longitudinal arch (MLA) and lateral longitudinal arch (LLA) during running between medial tibial stress syndrome (MTSS) and non‐MTSS subjects. A total of 10 subjects volunteered, comprising 5 subjects with MTSS and 5 subjects without injury (non‐MTSS) as the control group. All subjects performed the test movement that simulated running. Fluoroscopic imaging was used to investigate bone movement during landing in running. Sagittal motion was defined as the angular change and translational motion of the arch. A Mann‐Whitney U‐test was performed to determine the differences in the measured values between the MTSS and non‐MTSS groups. The magnitude of angular change for the MLA and LLA was significantly greater for subjects with MTSS than for control subjects. Translational motion of the MLA and LLA of the MTSS group was also significantly greater than that of the non‐MTSS group (all p < 0.05). Soccer players with MTSS have an abnormal structural deformation of foot during support (or stance) phase of running, with a large decrease in both the MLA and LLA. This abnormal motion could be a risk factor for the development of MTSS in these subjects.
Ultrasonographic Diagnosis of Midgut Volvulus With Malrotation in Children
Authors: Esposito Francesco , Vitale Valerio , Noviello Domenico , Di Serafino Marco , Vallone Gianfranco , Salvatore Marco , Oresta Patrizia 
Published: July 2014

ABSTRACTObjectives:Midgut volvulus with malrotation is typical in newborns. We present our experience to emphasize the importance of suspecting midgut volvulus as a cause of abdominal pain also beyond infancy, particularly in relation to malrotation, and the relevance of ultrasonographic (US) signs in its diagnosis.Methods:A total of 34 patients (10 boys, 24 girls; ages between 1 day and 12 years) diagnosed as having malrotation or malrotation with volvulus, surgically confirmed, between 2006 and 2013 were retrospectively selected among all of the patients referred to our institution for acute abdomen and bilious vomiting. All of them underwent US and color Doppler examination before surgery. The US examinations were performed with 6 to 10 MHz microconvex and 7.5 to 10 Mhz linear transducer. The transducer was placed under xiphoid, and, with axial projection, the presence of anatomic position reversed between superior mesenteric vein (SMV) and superior mesenteric artery (SMA), as a sign of malrotation, and the presence of “whirlpool sign” (WS) (wrapping of the SMV and the mesentery around the SMA), as a sign of midgut volvulus, were evaluated.Results:In 27 of these 34 patients, midgut volvulus was present; 7 patients had intestinal malrotation. In 2 of 7 (28%) patients with malrotation, SMA and SMV were inverted. Among the patients with volvulus, 2 showed reversed vessel position and 22 patients presented the WS in association with SMA/SMV inversion (22/27, 81%).Conclusions:Midgut volvulus with malrotation can appear beyond the neonatal age group as demonstrated in our case. The WS sign is sufficiently sensitive for its diagnosis and should be routinely researched at all ages of pediatric population. Anatomic inversion between SMV and SMA seems to be not enough sensitive in isolated malrotation diagnosis.
Insights into the Localization and Function of the Membrane Trafficking Regulator GNOM ARF-GEF at the Golgi Apparatus inArabidopsis
Authors: Naramoto Satoshi , Otegui Marisa S. , Kutsuna Natsumaro , de Rycke Riet , Dainobu Tomoko , Karampelias Michael , Fujimoto Masaru , Feraru Elena , Miki Daisuke , Fukuda Hiroo , Nakano Akihiko , Friml Jiří 
Published: July 2014

AbstractGNOM is one of the most characterized membrane trafficking regulators in plants, with crucial roles in development. GNOM encodes an ARF-guanine nucleotide exchange factor (ARF-GEF) that activates small GTPases of the ARF (ADP ribosylation factor) class to mediate vesicle budding at endomembranes. The crucial role of GNOM in recycling of PIN auxin transporters and other proteins to the plasma membrane was identified in studies using the ARF-GEF inhibitor brefeldin A (BFA). GNOM, the most prominent regulator of recycling in plants, has been proposed to act and localize at so far elusive recycling endosomes. Here, we report the GNOM localization in context of its cellular function in Arabidopsis thaliana. State-of-the-art imaging, pharmacological interference, and ultrastructure analysis show that GNOM predominantly localizes to Golgi apparatus. Super-resolution confocal live imaging microscopy identified GNOM and its closest homolog GNOM-like 1 at distinct subdomains on Golgi cisternae. Short-term BFA treatment stabilizes GNOM at the Golgi apparatus, whereas prolonged exposures results in GNOM translocation to trans-Golgi network (TGN)/early endosomes (EEs). Malformed TGN/EE in gnom mutants suggests a role for GNOM in maintaining TGN/EE function. Our results redefine the subcellular action of GNOM and reevaluate the identity and function of recycling endosomes in plants.
Machinery transportation management: case study of “plant-trailer” H&S incidents
Authors: D. Holt Gary , J. Edwards David 
Published: July 2014

Purpose
– The purpose of this paper is to investigate causal agents of health and safety (H&S) incidents among “plant-trailers” (as used by construction and utility contractors to transport mechanical machinery); including the relationship(s) of such incidents to routine safety inspections and, plant maintenance functions.

Design/methodology/approach
– H&S plant-trailer incident data, from a collaborating UK-based case study utility company are analysed using inductive, interpretative and descriptive statistical methods.

Findings
– Principal incident occurrences relate to trailer wheels, wheel bearings, tyres and braking systems. All forms of incidents observed harbour significant risk and especially, if they occur during travel on public highways. Derived recommendations for incident mitigation and control, suggest a requirement for improved human behaviour, machinery inspection regimes and maintenance systems.

Research limitations/implications
– The findings will be valuable to academia as a basis for advancing this new research subject, both empirically and internationally. Direction is offered in this respect.

Practical implications
– Recommendations will be of practical relevance to machinery management practitioners generally and to plant-trailer stakeholders more specifically. For the latter, the study encourages introspective consideration of plant-trailer H&S systems.

Originality/value
– No previous research has targeted these issues relating to plant-trailers.
Perceived claim sources in the Nigerian construction industry
Authors: A. Olanrewaju AbdulLateef , J. Anavhe Paul 
Published: July 2014

Purpose– With the increase in the cases of construction claims in Nigeria, many projects have remained uncompleted, while many of those completed receive poor client satisfaction. The purpose of this paper is to investigate how construction claims are managed.Design/methodology/approach– In total, 58 claim factors were identified and addressed to construction professionals through survey to indicate the extent at which the factors contributed to claims. A case study was conducted to illustrate claim management.Findings– In total, 37 factors were the major source of claims. Late payment, delayed approval of change order and delay cost were the extremely influential while the least were storage charges, loss of productivity, and costs of preparing claims. Evidences revealed that all stakeholders should play active roles to deliver “claim free” projects.Practical implications– The findings will be useful to practitioners in the effort to improve project delivery by providing some guidance on claim minimization. It is hoped that this study will encourage academics to conduct more research on this issue.Originality/value– There is no known conclusive empirical study on construction claim factors in Nigeria. In light of this, the findings offer greater opportunities for claim minimization/avoidance.