bluuebunny/crossref_metadata_2025_split huggingface dataset:
A GIS Toolbox for Measuring and Mapping Person‐Based Space‐Time Accessibility
Authors: Charleux Laure 
Published: August 2014

AbstractThis article presents a toolbox to compute and map person‐based accessibility indicators, based on classical time geography concepts. The intent is to provide GIS and urban planning practitioners with a user‐friendly and easily customizable tool. While it relies on well‐known concepts, the toolbox implements a major innovation in person‐based accessibility assessment by taking into account opening hours when measuring the accessibility of urban facilities. The toolbox can be downloaded from http://bit.ly/1h6yg5Z.
Two Arabidopsis proteins synthesize acetylated xylan in vitro
Authors: Urbanowicz Breeanna R. , Peña Maria J. , Moniz Heather A. , Moremen Kelley W. , York William S. 
Published: August 2014

SummaryXylan is the third most abundant glycopolymer on earth after cellulose and chitin. As a major component of wood, grain and forage, this natural biopolymer has far‐reaching impacts on human life. This highly acetylated cell wall polysaccharide is a vital component of the plant cell wall, which functions as a molecular scaffold, providing plants with mechanical strength and flexibility. Mutations that impair synthesis of the xylan backbone give rise to plants that fail to grow normally because of collapsed xylem cells in the vascular system. Phenotypic analysis of these mutants has implicated many proteins in xylan biosynthesis; however, the enzymes directly responsible for elongation and acetylation of the xylan backbone have not been unambiguously identified. Here we provide direct biochemical evidence that two Arabidopsis thaliana proteins, IRREGULAR XYLEM 10–L (IRX10‐L) and ESKIMO1/TRICOME BIREFRINGENCE 29 (ESK1/TBL29), catalyze these respective processes in vitro. By identifying the elusive xylan synthase and establishing ESK1/TBL29 as the archetypal plant polysaccharide O‐acetyltransferase, we have resolved two long‐standing questions in plant cell wall biochemistry. These findings shed light on integral steps in the molecular pathways used by plants to synthesize a major component of the world's biomass and expand our toolkit for producing glycopolymers with valuable properties.
UBC13, an E2 enzyme for Lys63‐linked ubiquitination, functions in root development by affecting auxin signaling and Aux/IAA protein stability
Authors: Wen Rui , Wang Sheng , Xiang Daoquan , Venglat Prakash , Shi Xianzong , Zang Yuepeng , Datla Raju , Xiao Wei , Wang Hong 
Published: August 2014

SummaryUnlike conventional lysine (K) 48–linked polyubiquitination, K63‐linked polyubiquitination plays signaling roles in yeast and animals. Thus far, UBC13 is the only known ubiquitin‐conjugating enzyme (E2) specialized in K63‐linked polyubiquitination. Previous identification of Arabidopsis genes encoding UBC13 as well as its interacting partner UEV1 indicates that the UBC13‐mediated ubiquitination pathway is conserved in plants; however, little is known about functions and signaling mediated through K63‐linked polyubiquitination in plants. To address the functions of UBC13‐mediated ubiquitination in plants, we created Arabidopsis ubc13 null mutant lines in which the two UBC13 genes were disrupted. The double mutant displayed altered root development, including shorter primary root, fewer lateral roots and only a few short root hairs in comparison with the wild type and single mutant plants, indicating that UBC13 activity is critical for all major aspects of root development. The double mutant plants were insensitive to auxin treatments, suggesting that the strong root phenotypes do not simply result from a reduced level of auxin. Instead, the ubc13 mutant had a reduced auxin response, as indicated by the expression of an auxin‐responsive DR5 promoter‐GFP. Furthermore, both the enzymatic activity and protein level of an AXR3/IAA17‐GUS reporter were greatly increased in the ubc13 mutant, whereas the induction of many auxin‐responsive genes was suppressed. Collectively, these results suggest that Aux/IAA proteins accumulate in the ubc13 mutant, resulting in a reduced auxin response and defective root development. Hence, this study provides possible mechanistic links between UBC13‐mediated protein ubiquitination, root development and auxin signaling.
HISTONE DEACETYLASE 9 represses seedling traits in Arabidopsis thaliana dry seeds
Authors: van Zanten Martijn , Zöll Christian , Wang Zhi , Philipp Christina , Carles Annaick , Li Yong , Kornet Noortje G. , Liu Yongxiu , Soppe Wim J. J. 
Published: August 2014

SummaryPlant life is characterized by major phase changes. We studied the role of histone deacetylase (HDAC) activity in the transition from seed to seedling in Arabidopsis. Pharmacological inhibition of HDAC stimulated germination of freshly harvested seeds. Subsequent analysis revealed that histone deacetylase 9 (hda9) mutant alleles displayed reduced seed dormancy and faster germination than wild‐type plants. Transcriptome meta‐analysis comparisons between the hda9 dry seed transcriptome and published datasets demonstrated that transcripts of genes that are induced during imbibition in wild‐type prematurely accumulated in hda9‐1 dry seeds. This included several genes associated with photosynthesis and photoautotrophic growth such as RuBisCO and RuBisCO activase (RCA). Chromatin immunoprecipitation experiments demonstrated enhanced histone acetylation levels at their loci in young hda9‐1 seedlings. Our observations suggest that HDA9 negatively influences germination and is involved in the suppression of seedling traits in dry seeds, probably by transcriptional repression via histone deacetylation. Accordingly, HDA9 transcript is abundant in dry seeds and becomes reduced during imbibition in wild‐type seeds. The proposed function of HDA9 is opposite to that of its homologous genes HDA6 and HDA19, which have been reported to repress embryonic properties in germinated seedlings.
Thrombocytopenia in late preterm and term neonates after perinatal asphyxia
Authors: Christensen Robert D. , Baer Vickie L. , Yaish Hassan M. 
Published: August 2014

BackgroundA recent NHLBI conference concluded that platelet (PLT) transfusions of neonates must become more evidence based. One neonatal disorder for which transfusions are given is a poorly defined entity, the “thrombocytopenia of perinatal asphyxia.” To expand the evidence base for this entity, we performed a multicentered, retrospective analysis of neonates with perinatal asphyxia.Study Design and MethodsWe analyzed records of term and late preterm neonates with perinatal asphyxia defined by a cord blood pH of not more than 6.99 and/or base deficit of at least 16 mmol/L. From these we identified neonates with at least two PLT counts of fewer than 150 × 109/L in the first week of life and described the severity, nadir, and duration of the thrombocytopenia.ResultsThrombocytopenia occurred in 31% (117/375) of neonates with asphyxia versus 5% of matched nonasphyxiated controls admitted to a neonatal intensive care unit (p < 0.0001). Twenty‐one of the 117 asphyxiated neonates were excluded from the remaining analysis due to disseminated intravascular coagulation or extracorporeal membrane oxygenation. Nadir PLT counts of the remaining 96 were on Day 3 (75 × 109/L; 90% confidence interval, 35.7 × 109‐128.6 × 109/L) and normalized by Days 19 to 21. PLT counts after asphyxia roughly correlated inversely with elevated nucleated red blood cell count (NRBC) counts at birth. Thirty of the 96 received at least one PLT transfusion, all given prophylactically, none for bleeding.ConclusionsWe maintain that the thrombocytopenia of perinatal asphyxia is an authentic entity. Its association with elevated NRBC counts suggests that hypoxia is involved in the pathogenesis. Because PLT counts are only moderately low, the condition is transient, and bleeding problems seem rare, we speculate that PLT transfusions should not be needed for most neonates with this condition.
Linear algebra over and related rings
Authors: Caruso Xavier , Lubicz David 
Published: August 2014

AbstractLet $\mathfrak{R}$ be a complete discrete valuation ring, $S=\mathfrak{R}[[u]]$ and $d$ a positive integer. The aim of this paper is to explain how to efficiently compute usual operations such as sum and intersection of sub-$S$-modules of $S^d$. As $S$ is not principal, it is not possible to have a uniform bound on the number of generators of the modules resulting from these operations. We explain how to mitigate this problem, following an idea of Iwasawa, by computing an approximation of the result of these operations up to a quasi-isomorphism. In the course of the analysis of the $p$-adic and $u$-adic precisions of the computations, we have to introduce more general coefficient rings that may be interesting for their own sake. Being able to perform linear algebra operations modulo quasi-isomorphism with $S$-modules has applications in Iwasawa theory and $p$-adic Hodge theory. It is used in particular in Caruso and Lubicz (Preprint, 2013, arXiv:1309.4194) to compute the semi-simplified modulo $p$ of a semi-stable representation.
Using computer‐extracted image features for modeling of error‐making patterns in detection of mammographic masses among radiology residents
Authors: Zhang Jing , Lo Joseph Y. , Kuzmiak Cherie M. , Ghate Sujata V. , Yoon Sora C. , Mazurowski Maciej A. 
Published: August 2014

Purpose:Mammography is the most widely accepted and utilized screening modality for early breast cancer detection. Providing high quality mammography education to radiology trainees is essential, since excellent interpretation skills are needed to ensure the highest benefit of screening mammography for patients. The authors have previously proposed a computer‐aided education system based on trainee models. Those models relate human‐assessed image characteristics to trainee error. In this study, the authors propose to build trainee models that utilize features automatically extracted from images using computer vision algorithms to predict likelihood of missing each mass by the trainee. This computer vision‐based approach to trainee modeling will allow for automatically searching large databases of mammograms in order to identify challenging cases for each trainee.Methods:The authors’ algorithm for predicting the likelihood of missing a mass consists of three steps. First, a mammogram is segmented into air, pectoral muscle, fatty tissue, dense tissue, and mass using automated segmentation algorithms. Second, 43 features are extracted using computer vision algorithms for each abnormality identified by experts. Third, error‐making models (classifiers) are applied to predict the likelihood of trainees missing the abnormality based on the extracted features. The models are developed individually for each trainee using his/her previous reading data. The authors evaluated the predictive performance of the proposed algorithm using data from a reader study in which 10 subjects (7 residents and 3 novices) and 3 experts read 100 mammographic cases. Receiver operating characteristic (ROC) methodology was applied for the evaluation.Results:The average area under the ROC curve (AUC) of the error‐making models for the task of predicting which masses will be detected and which will be missed was 0.607 (95% CI,0.564‐0.650). This value was statistically significantly different from 0.5 (p < 0.0001). For the 7 residents only, the AUC performance of the models was 0.590 (95% CI,0.537‐0.642) and was also significantly higher than 0.5 (p = 0.0009). Therefore, generally the authors’ models were able to predict which masses were detected and which were missed better than chance.Conclusions:The authors proposed an algorithm that was able to predict which masses will be detected and which will be missed by each individual trainee. This confirms existence of error‐making patterns in the detection of masses among radiology trainees. Furthermore, the proposed methodology will allow for the optimized selection of difficult cases for the trainees in an automatic and efficient manner.
Physical Demands of Match Play in Successful and Less-Successful Elite Rugby League Teams
Authors: Hulin Billy T. , Gabbett Tim J. , Kearney Simon , Corvo Alex 
Published: August 2014

Purpose:
To quantify activity profiles in approximately 5-min periods to determine if the intensity of rugby league match play changes after the most intense period of play and to determine if the intensity of activity during predefined periods of match play differ between successful and less-successful teams playing at an elite standard.

Methods:
Movement was recorded using a MinimaxX global positioning system (GPS) unit sampling at 10 Hz during 25 rugby league matches, equating to 200 GPS files. Data for each half of match play were separated into 8 equal periods. These periods represented the most intense phase of match play (peak period), the period after the most intense phase of match play (subsequent period), and the average demands of all other periods in a match (mean period). Two rugby league teams were split into a high-success and a low-success group based on their success rates throughout their season.

Results:
Compared with their less-successful counterparts, adjustables and hit-up forwards from the high-success team covered less total distance (P < .01) and less high-intensity-running distance (P < .01) and were involved in a greater number of collisions (P < .01) during the mean period of match play.

Conclusions:
Although a greater number of collisions during match play is linked with a greater rate of success, greater amounts of high-intensity running and total distance are not related to competitive success in elite rugby league. These results suggest that technical and tactical differences, rather than activity profiles, may be the distinguishing factor between successful and less-successful rugby league teams.
Varying planetary heat sink led to global-warming slowdown and acceleration
Authors: Chen Xianyao , Tung Ka-Kit 
Published: August 2014

Deep-sea warming slows down global warming
Global warming seems to have paused over the past 15 years while the deep ocean takes the heat instead. The thermal capacity of the oceans far exceeds that of the atmosphere, so the oceans can store up to 90% of the heat buildup caused by increased concentrations of greenhouse gases such as carbon dioxide. Chen and Tung used observational data to trace the pathways of recent ocean heating. They conclude that the deep Atlantic and Southern Oceans, but not the Pacific, have absorbed the excess heat that would otherwise have fueled continued warming.

Science
, this issue p.
897
Fusion Protein Comprising Factor H Domains 6 and 7 and Human IgG1 Fc as an Antibacterial Immunotherapeutic
Authors: Shaughnessy Jutamas , Vu David M. , Punjabi Rahi , Serra-Pladevall Judit , DeOliveira Rosane B. , Granoff Dan M. , Ram Sanjay 
Published: August 2014

ABSTRACT

The emergence of antimicrobial resistance among several medically important pathogens represents a serious threat to human health globally and necessitates the development of novel therapeutics. Complement forms a key arm of innate immune defenses against invading pathogens. A mechanism of complement evasion employed by many pathogens is binding of complement inhibitors, including factor H (FH), a key downregulator of the alternative pathway. Most FH-binding bacteria engage FH through regions in FH spanned by domains 6 and 7 and/or 18 through 20. We created a chimeric protein that comprised human FH domains 6 and 7 fused to human IgG1 Fc (FH6,7/HuFc) and tested its activity as an immunotherapeutic against
Neisseria meningitidis
, which binds FH through domains 6 and 7. FH6,7/HuFc bound to meningococci and effectively blocked FH binding to bacteria. FH6,7/HuFc enhanced human C3 and C4 deposition and facilitated complement-mediated killing in a dose-responsive manner; complement activation and killing were classical pathway dependent. To investigate
in vivo
efficacy, infant Wistar rats were treated intraperitoneally (IP) with different doses of FH6,7/HuFc and challenged 2 h later with serogroup C strain 4243 given IP. At 8 to 9 h after the challenge, the FH6,7/HuFc-treated rats had >100-fold fewer CFU per ml of blood than control animals pretreated with phosphate-buffered saline (PBS) or FH18–20/HuFc, which does not bind to meningococci (
P
< 0.0001). These data provide proof of concept of the utility of FH/Fc fusion proteins as anti-infective immunotherapeutics. Because many microbes share a common binding region(s) in FH, FH/Fc chimeric proteins may be a promising candidate for adjunctive therapy against drug-resistant pathogens.
Precision of Vancomycin and Daptomycin MICs for Methicillin-Resistant Staphylococcus aureus and Effect of Subculture and Storage
Authors: Charlton Carmen L. , Hindler Janet A. , Turnidge John , Humphries Romney M. 
Published: August 2014

ABSTRACT

The reproducibility of vancomycin and daptomycin MICs, measured by broth microdilution (BMD) and Etest, was prospectively assessed for 10 methicillin-resistant
Staphylococcus aureus
(MRSA) isolates from the blood samples from patients on vancomycin therapy. The isolates were tested at the time of isolation from blood and following 5, 10, and 20 subcultures and at 1, 3, 6, and 12 months of storage at −70°C. The MICs were determined by Etest and BMD using two different manufacturers (BBL and Difco) of cation-adjusted Mueller-Hinton broth (CA-MHB), and using three different drug powders: vancomycin from Sigma, vancomycin from Novation, and daptomycin from Cubist. The antimicrobial concentrations tested were 0.25, 0.5, 0.75, 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, and 4.0 μg/ml. Two isolates were vancomycin intermediate and daptomycin nonsusceptible, and two isolates had reduced susceptibility to vancomycin (BMD MIC, 1.5 or 2.0 μg/ml). The vancomycin MICs were significantly higher in the BBL CA-MHB than those in the Difco CA-MHB, and with Sigma versus Novation vancomycin powder. The daptomycin MICs were also significantly higher in the BBL CA-MHB. The Etest MICs were significantly higher than those obtained by BMD for vancomycin but not for daptomycin. The average precision of the vancomycin BMD MICs when analyzing 20 results was ±1.10-fold log
2
dilutions, and it was ±1.67-fold for daptomycin (10 results). The average precision for Etest was ±1.11-fold for vancomycin and ±1.16-fold for daptomycin. No significant change in MICs was noted following 5, 10, or 20 subcultures or at up to 6 months of frozen storage. However, the vancomycin MICs alone were significantly lower (0.74-fold) following 12 months of frozen storage. From these data, despite variations in CA-MHB and antimicrobial powder, the MIC result precision was <0.5 log
2
dilutions in a single laboratory, suggesting that testing interdilution MICs (e.g., MICs between serial 2-fold dilutions) is a possibility. A more accurate method for measuring vancomycin MIC results is thus possible, but further standardization of BMD testing would be required to achieve this goal.
Immunodeficient Mouse Models with Different Disease Profiles byIn VivoInfection with the Same Clinical Isolate of Enterovirus 71
Authors: Liao Chun-Che , Liou An-Ting , Chang Ya-Shu , Wu Szu-Yao , Chang Chih-Shin , Lee Chien-Kuo , Kung John T. , Tu Pang-Hsien , Yu Ya-Yen , Lin Chi-Yung , Lin Jen-Shiou , Shih Chiaho 
Published: August 2014

ABSTRACTLike poliovirus infection, severe infection with enterovirus 71 (EV71) can cause neuropathology. Unlike poliovirus, EV71 is often associated with hand-foot-and-mouth disease (HFMD). Here we established three mouse models for experimental infection with the same clinical isolate of EV71. The NOD/SCID mouse model is unique for the development of skin rash, an HFMD-like symptom. While the NOD/SCID mice developed limb paralysis and death at near-100% efficiency, the gamma interferon receptor knockout (ifngrKO) andstat-1knockout mice exhibited paralysis and death rates near 78% and 30%, respectively. Productive infection with EV71 depends on the viral dose, host age, and inoculation route. Levels of infectious EV71, and levels of VP1-specific RNA and protein in muscle, brain, and spinal cord, were compared side by side between the NOD/SCID andstat-1knockout models before, during, and after disease onset. Spleen fibrosis and muscle degeneration are common in the NOD/SCID andstat-1knockout models. The main differences between these two models include their disease manifestations and cytokine/chemokine profiles. The pathology of the NOD/SCID model includes (i) inflammation and expression of viral VP1 antigen in muscle, (ii) increased neutrophil levels and decreased eosinophil and lymphocyte levels, and (iii) hair loss and skin rash. The characteristic pathology of thestat-1knockout model includes (i) a strong tropism of EV71 for the central nervous system, (ii) detection of VP1 protein in the Purkinje layer of cerebellar cortex, pons, brain stem, and spinal cord, (iii) amplification of microglial cells, and (iv) dystrophy of intestinal villi. Our comparative studies on these new models with oral or intraperitoneal (i.p.) infection underscored the contribution of host immunity, including the gamma interferon receptor, to EV71 pathogenesis.IMPORTANCEIn the past decade, enterovirus 71 (EV71) has emerged as a major threat to public health in the Asia-Pacific region. Disease manifestations include subclinical infection, common-cold-like syndromes, hand-foot-and-mouth disease (HFMD), uncomplicated brain stem encephalitis, severe dysregulation of the autonomic nerve system, fatal pulmonary edema, and cardiopulmonary collapse. To date, no effective vaccine or treatment is available. A user-friendly and widely accessible animal model for researching EV71 infection and pathogenesis is urgently needed by the global community, both in academia and in industry.
Autographa californica Multiple Nucleopolyhedrovirus
orf132
Encodes a Nucleocapsid-Associated Protein Required for Budded-Virus and Multiply Enveloped Occlusion-Derived Virus Production
Authors: Yang Ming , Wang Shuo , Yue Xiu-Li , Li Lu-Lin 
Published: August 2014

ABSTRACT

Autographa californica
multiple nucleopolyhedrovirus
orf132
(named
ac132
) has homologs in all genome-sequenced group I nucleopolyhedroviruses. Its role in the viral replication cycle is unknown. In this study,
ac132
was shown to express a protein of around 28 kDa, which was determined to be associated with the nucleocapsids of both occlusion-derived virus and budded virus. Confocal microscopy showed that AC132 protein appeared in central region of the nucleus as early as 12 h postinfection with the virus. It formed a ring zone at the periphery of the nucleus by 24 h postinfection. To investigate its role in virus replication,
ac132
was deleted from the viral genome by using a bacmid system. In the Sf9 cell culture transfected by the
ac132
knockout bacmid, infection was restricted to single cells, and the titer of infectious budded virus was reduced to an undetectable level. However, viral DNA replication and the expression of late genes
vp39
and
odv-e25
and a reporter gene under the control of the very late gene
p10
promoter were unaffected. Electron microscopy showed that nucleocapsids, virions, and occlusion bodies were synthesized in the cells transfected by an
ac132
knockout bacmid, but the formation of the virogenic stroma and occlusion bodies was delayed, the numbers of enveloped nucleocapsids were reduced, and the occlusion bodies contained mainly singly enveloped nucleocapsids. AC132 was found to interact with envelope protein ODV-E18 and the viral DNA-binding protein P6.9. The data from this study suggest that
ac132
possibly plays an important role in the assembly and envelopment of nucleocapsids.

IMPORTANCE
To our knowledge, this is the first report on a functional analysis of
ac132
. The data presented here demonstrate that
ac132
is required for production of the budded virus and multiply enveloped occlusion-derived virus of
Autographa californica
multiple nucleopolyhedrovirus. This article reveals unique phenotypic changes induced by
ac132
deletion on the virus and multiple new findings on
ac132
.