bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating the Vehicle‐Miles‐Traveled Implications of Alternative Metropolitan Growth Scenarios: A Boston Example
Authors: Ferreira Joseph , Diao Mi , Xu Jingsi 
Published: May 2013

AbstractThis study demonstrates the potential value, and difficulties, in utilizing large‐scale, location aware, administrative data together with urban modeling to address current policy issues in a timely fashion. We take advantage of a unique dataset of millions of odometer readings from annual safety inspections of all private passenger vehicles in Metropolitan Boston to estimate the vehicle‐miles‐traveled (VMT) implication of alternative metropolitan growth scenarios: a sprawl‐type “let‐it‐be” scenario and a smart‐growth‐type “winds‐of‐change” scenario. The data are georeferenced to 250 × 250 m grid cells developed by MassGIS. We apply a greedy algorithm to assign Traffic Analysis Zone (TAZ) level household growth projections to grid cells and then use spatial interpolation tools to estimate VMT‐per‐vehicle surfaces for the region. If new growth households have similar VMT behavior as their neighbors, then the let‐it‐be scenario will generate 12–15% more VMT per household compared to the winds‐of‐change scenario. However, even the “wind‐of‐change” scenario, will result in new households averaging higher VMT per household than the Metro Boston average observed in 2005. The implication is that urban growth management can significantly reduce GHG but, by itself, will not be sufficient to achieve the GHG emission reduction targets set by the State for the transportation sector.
Potential uses of small unmanned aircraft systems (UAS) in weed research
Authors: Rasmussen J , Nielsen J , Garcia‐Ruiz F , Christensen S , Streibig J C 
Published: May 2013

SummarySmall unmanned aerial systems (UAS) with cameras have not been adopted in weed research, but offer low‐cost sensing with high flexibility in terms of spatial resolution. A small rotary‐wing UAS was tested as part of a search for an inexpensive, user‐friendly and reliable aircraft for practical applications in UAS imagery weed research. In two experiments with post‐emergence weed harrowing in barley, the crop resistance parameter, which reflects the crop response to harrowing, was unaffected by image capture altitude in the range from 1 to 50 m. This corresponded to image spatial resolution in the range from 0.3 to 17.1 mm per pixel. This finding is important because spatial resolution is inversely related to sensing capacity. We captured 20 plots comprising a total of about 0.2 ha in one image at 50 m altitude without losing information about the cultivation impacts on vegetation compared with ground truth data. UAS imagery also gave excellent results in logarithmic sprayer experiments in oilseed rape, where we captured 37 m long plots in each image from an altitude of 35 m. Furthermore, perennial weeds could be mapped from UAS images. These first experiences with a small rotary‐wing UAS show that it is relatively easy to integrate as a tool in weed research and offers great potential for site‐specific weed management.
Self-dual integral normal bases and Galois module structure
Authors: Pickett Erik Jarl , Vinatier Stéphane 
Published: May 2013

AbstractLet $N/ F$ be an odd-degree Galois extension of number fields with Galois group $G$ and rings of integers ${\mathfrak{O}}_{N} $ and ${\mathfrak{O}}_{F} = \mathfrak{O}$. Let $ \mathcal{A} $ be the unique fractional ${\mathfrak{O}}_{N} $-ideal with square equal to the inverse different of $N/ F$. B. Erez showed that $ \mathcal{A} $ is a locally free $\mathfrak{O}[G] $-module if and only if $N/ F$ is a so-called weakly ramified extension. Although a number of results have been proved regarding the freeness of $ \mathcal{A} $ as a $ \mathbb{Z} [G] $-module, the question remains open. In this paper we prove that $ \mathcal{A} $ is free as a $ \mathbb{Z} [G] $-module provided that $N/ F$ is weakly ramified and under the hypothesis that for every prime $\wp $ of $\mathfrak{O}$ which ramifies wildly in $N/ F$, the decomposition group is abelian, the ramification group is cyclic and $\wp $ is unramified in $F/ \mathbb{Q} $. We make crucial use of a construction due to the first author which uses Dwork’s exponential power series to describe self-dual integral normal bases in Lubin–Tate extensions of local fields. This yields a new and striking relationship between the local norm-resolvent and the Galois Gauss sum involved. Our results generalise work of the second author concerning the case of base field $ \mathbb{Q} $.
Companion forms in parallel weight one
Authors: Gee Toby , Kassaei Payman 
Published: May 2013

AbstractLet $p\gt 2$ be prime, and let $F$ be a totally real field in which $p$ is unramified. We give a sufficient criterion for a $\mathrm{mod} \hspace{0.167em} p$ Galois representation to arise from a $\mathrm{mod} \hspace{0.167em} p$ Hilbert modular form of parallel weight one, by proving a ‘companion forms’ theorem in this case. The techniques used are a mixture of modularity lifting theorems and geometric methods. As an application, we show that Serre’s conjecture for $F$ implies Artin’s conjecture for totally odd two-dimensional representations over $F$.
Complete Genome Sequences of Four Virulent Rabies Virus Strains Isolated from Rabid Animals in Russia
Authors: Poleshchuk E. M. , Deviatkin A. A. , Dedkov V. G. , Sidorov G. N. , Ochkasova J. V. , Hodjakova I. A. , Schukina I. A. , Savel'ev S. I. , Golenskih A. G. , Shipulin G. A. 
Published: May 2013

ABSTRACT

Rabies virus (RABV) strains Rus(Lipetsk)-8052f, Rus(Lipetsk)-8053c, Rus(Lipetsk)-8054f, and Rus(Lipetsk)-8057f were isolated from foxes (
Vulpes vulpes
) and a cat (
Felis catus
) in the Lipetsk region of Russia in 2011. Close relationships between these strains and the members of the “Cosmopolitan” group from Russia (98% homology) and from Europe (95% homology) were estimated.
Complete Genome Sequence of a Newly Emerging Newcastle Disease Virus Isolated in China
Authors: Sun Minhua , Dong Jiawen , Wang Zhaoxiong , Li Linlin , Yuan Jianfeng , Jiao Peirong , Hu Qilin , Ren Tao 
Published: May 2013

ABSTRACT
Goose/GD/2010 is a newly emerging Newcastle disease virus (NDV) isolated from a sick goose flock in southern China. Here, we report the complete genome sequence of this isolate, which belongs to NDV subgenotype VIIb. This is the first report about the complete genome information of an isolate of subgenotype VIIb in China.
Genome Sequence of Klebsiella pneumoniae HSL4, a New Strain Isolated from Mangrove Sediment for Biosynthesis of 1,3-Propanediol
Authors: Zhou Sheng , Li Lili , Wei Jingguang , Qin Qiwei 
Published: May 2013

ABSTRACT

Klebsiella pneumoniae
HSL4 is a 1,3-propanediol-producing bacterium strain isolated from mangrove sediment. We present here a 5,221,448-bp assembly of its genome sequence. Genome analysis revealed that it contains 10 coding sequences (CDSs) responsible for glycerol fermentation to 1,3-propanediol, 19 CDSs encoding glycerol utilization, and 140 CDSs related to its virulence.
Draft Genome Sequence of Lactobacillus pobuzihii E100301
T
Authors: Chiu Chi-ming , Chang Chi-huan , Pan Shwu-fen , Wu Hui-chung , Li Shiao-wen , Chang Chuan-hsiung , Lee Yun-shien , Chiang Chih-ming , Chen Yi-sheng 
Published: May 2013

ABSTRACT

Lactobacillus pobuzihii
E100301
T
is a novel
Lactobacillus
species previously isolated from pobuzihi (fermented cummingcordia) in Taiwan. Phylogenetically, this strain is closest to
Lactobacillus acidipiscis
, but its phenotypic characteristics can be clearly distinguished from those of
L. acidipiscis
. We present the draft genome sequence of strain
L. pobuzihii
E100301
T
.
Complete Genome Sequence of a Newly Emerging Newcastle Disease Virus
Authors: Wang Jing-Yu , Liu Wan-Hua , Ren Juan-Juan , Tang Pan , Wu Ning , Liu Hung-Jen 
Published: May 2013

ABSTRACT
The complete genome sequence of a newly emerging Newcastle disease virus, isolated in China, was determined. A phylogenetic analysis based on the F gene revealed that the isolate is phylogenetically related to Newcastle disease virus genotype VIId. Sequence analysis indicated that amino acid residue substitutions occur at neutralizing epitopes on the hemagglutinin-neuraminidase (HN) protein.
Draft Genome Sequence of Methylophaga lonarensis MPL
T
, a Haloalkaliphilic (Non-Methane-Utilizing) Methylotroph
Authors: Shetty Sudarshan A. , Marathe Nachiket P. , Munot Hitendra , Antony Chakkiath Paul , Dhotre Dhiraj P. , Murrell J. Colin , Shouche Yogesh S. 
Published: May 2013

ABSTRACT

Methylophaga lonarensis
strain MPL
T
is a haloalkaliphilic methylotroph isolated from Lonar Lake, a saline and alkaline lake in Maharashtra, India. Strain MPL
T
utilizes methanol as its sole carbon and energy source. Here, we present the draft genome sequence of
M. lonarensis
MPL
T
(VKM B-2684
T
= MCC 1002
T
).
Genome Sequences of
Pseudomonas
spp. Isolated from Cereal Crops
Authors: Gardiner Donald M. , Stiller Jiri , Covarelli Lorenzo , Lindeberg Magdalen , Shivas Roger G. , Manners John M. 
Published: May 2013

ABSTRACT
Compared to those of dicot-infecting bacteria, the available genome sequences of bacteria that infect wheat and barley are limited. Herein, we report the draft genome sequences of four pseudomonads originally isolated from these cereals. These genome sequences provide a useful resource for comparative analyses within the genus and for cross-kingdom analyses of plant pathogenesis.
Whole-Genome Sequences of Four Salmonella enterica Serotype Newport Strains from Humans
Authors: Zhang Jianmin , Cao Guojie , Xu Xuebin , Jin Huiming , Zhang Qiong , Chen Jianwei , Yang Xiaowei , Pan Haijian , Zhang Xiuli , Allard Marc , Brown Eric , Meng Jianghong 
Published: May 2013

ABSTRACT

Salmonellosis contributes significantly to the public health burden globally.
Salmonella enterica
serotype Newport is among
Salmonella
serotypes most associated with food-borne illness in the United States and China. It was thought to be polyphyletic and to contain different lineages. We report draft genomes of four
S
. Newport strains isolated from humans in China.
Draft Genome Sequence of Myxococcus xanthus Wild-Type Strain DZ2, a Model Organism for Predation and Development
Authors: Müller Susanne , Willett Jonathan W. , Bahr Sarah M. , Darnell Cynthia L. , Hummels Katherine R. , Dong Carolyn K. , Vlamakis Hera C. , Kirby John R. 
Published: May 2013

ABSTRACT

Myxococcus xanthus
is a member of the
Myxococcales
order within the
Deltaproteobacteria
subdivision. The myxobacteria reside in soil, have relatively large genomes, and display complex life cycles. Here, we report the whole-genome shotgun sequence of strain DZ2, which includes unique genes not found previously in strain DK1622.
Complete Genome Sequences of Two Sweet Potato Chlorotic Stunt Virus Isolates from China
Authors: Qin Yanhong , Zhang Zhenchen , Qiao Qi , Zhang Desheng , Tian Yuting , Wang Yongjiang , Wang Shuang 
Published: May 2013

ABSTRACT
Sweet potato chlorotic stunt virus (SPCSV) was first detected in China in 2010, and several partial sequences have been determined for Chinese SPCSV isolates. This report describes the complete genome sequences of two SPCSV isolates from the Guangdong and Jiangsu provinces and will be valuable for understanding the characteristics of SPCSVs in China.
Genome Sequence of Hydrothermal Arsenic-Respiring Bacterium Marinobacter santoriniensis NKSG1
T
Authors: Handley Kim M. , Upton Mathew , Beatson Scott A. , Héry Marina , Lloyd Jonathan R. 
Published: May 2013

ABSTRACT

Marinobacter santoriniensis
NKSG1
T
originates from metalliferous marine sediment. It can respire and redox cycle arsenic species and perform mixotrophic, nitrate-dependent Fe(II) oxidation. The genome sequence, reported here, will help further elucidate the genetic mechanisms underlying these and other potential biogeochemically relevant functions, such as arsenic and mercury resistance and hydrocarbon degradation.
MECHANICAL LOADING MODULATES ANGIOGENIC FACTORS IN TENDON CELLS
Authors: Mousavizadeh R , Duronio V , McCormack B , Khosravi S , Scott A 
Published: May 2013

IntroductionTendon disorders are a significant cause of pain and morbidity amongst athletes, workers and the general public.1 2 Tendinopathy is often viewed as the result of failed or inadequate healing response through repetitive overuse.3 The clinical symptoms of tendinopathy are activity–related pain, focal tenderness, and intratendinous imaging changes. Previous authors have suggested there may be an association between pain and neurovascular changes resulting from tendon overuse in tendinopathy patients.4 5 In order to examine the effects of repetitive overuse on the expression of angiogenic genes which regulate neovascularization in tendinopathy, primary human tendon cells were subjected to cyclic strain.MethodsBy using Flexcell Tension Systems, the isolated tendon cells from human hamstring tendons (excess ACL autograft material) were exposed to cyclic tension (1 Hz frequency and 10% strain). RNA samples were isolated at different time points and gene expression was evaluated by qPCR and qPCR array. Zymography assay was also conducted in order to measure the activity of MMP-2 in the supernatant of tendon cell culture.ResultsInitial experiments show that cyclic strain of two-dimensional primary tenocyte cell cultures (1 Hz) promotes increased expression of VEGF, bFGF, Cox-2 and IL-6 genes, and increased activity of MMP-2. But, by increasing the time course (∼after 4 h), bFGF, Cox-2 and VEGF are progressively downregulated. Our preliminary results of qPCR array for angiogenic profiling of tendon cells also led to the discovery of other genes (ANGPTL4, FGF-1, TGFα, VEGF-C, PROK2 and SPHK1) that may respond to tensile loading following a similar pattern.ConclusionIt seems that the early response of the tendon cell to overuse tensile loading leads to upregulation of some angiogenic factors which may play an important role in tissue homeostasis following periods of overuse.
AGING UNIQUELY INFLUENCES TISSUE INHIBITOR OF METALLOPROTEINASE-2 (TIMP-2) EXPRESSION IN NORMAL TENDON
Authors: Thornton G M , Reno C R , Lo I K Y , Hart D A 
Published: May 2013

IntroductionThe incidence of tendinopathy increases with aging. Alterations to the balance between matrix metalloproteinases (MMPs) and the tissue inhibitors of metalloproteinases (TIMPs) may play a role in the degenerative changes seen in tendinopathy.1 In addition, aging may have an effect on the expression of these molecules in tendon, as was found in skin.2 Our purpose in this study was to examine the effect of aging on patellar tendons from 1-year-old and 3-year-old rabbits comparing molecular expression of MMPs and TIMPs. Our hypothesis was that patellar tendons from 3-year-old rabbits would have increased MMP expression and decreased TIMP expression compared to patellar tendons from 1-year-old rabbits.MethodsPatellar tendons from 1-year-old (n=8) and 3-year-old (n=6) female New Zealand White rabbits underwent RT-qPCR using rabbit specific primers for MMPs (MMP-1, MMP-3, MMP-13) and TIMPs (TIMP-1, TIMP-2, TIMP-3), and the housekeeping gene 18S. Data were compared using Mann Whitney U tests.ResultsComparing patellar tendons from 3-year-old to 1-year-old rabbits, the expression of MMP-1, MMP-3 and MMP-13 did not change with aging. The expression of TIMP-2 was decreased comparing patellar tendons from 3-year-old to 1-year-old rabbits (p=0.02; figure 1). TIMP-1 and TIMP-3 expression were not affected by aging.Figure 1.MMP and TIMP Expression in Patellar Tendons from 1-year-old and 3-year-old rabbits. Expression of TIMP-2 was decreased comparing patellar tendons from 3-year-old to 1-year-old rabbits (p=0.02).DiscussionAging significantly decreased TIMP-2 expression in patellar tendon with no changes in the other TIMPs and MMPs investigated. This suggests a change in the balance of MMP/TIMP expression towards degradation in tendon with aging, or a significant shift in the MMP-independent activities of TIMP-2.3 In human skin, TIMP-2 expression was decreased with aging.2 Despite no change in TIMP-2 expression in degenerated human patellar4 and Achilles1 tendons compared to normal tendons, TIMP-2 expression was decreased in ruptured human Achilles1 and rotator cuff5 tendons compared to normal tendons.
MOLECULAR GENETICS AN IMPORTANT TOOL IN ELUCIDATING THE MOLECULAR MECHANISMS UNDERLYING TENDINOPATHIES
Authors: Collins M 
Published: May 2013

The causation of tendinopathy is multifactorial and there is increasing evidence that genetic factors play an important role in its aetiology. Some of the genes implicated encode: (i) structural components of connective tissue (collagens and glycoproteins); (ii) extracellular matrix (ECM) proteinases (MMPs); and (iii) cytokines and growth factors.1 2 Although several genes have been implicated to date, variants within the 3′-untranslated region (UTR) ofCOL5A1were shown to associate with chronic Achilles tendinopathy3 4 and lower limb range of motion measurements,5 6 an additional intrinsic risk factor for chronic Achilles tendinopathy.COL5A1encodes the α1 chain of type V collagen, a quantitatively minor fibrillar collagen that regulates type I fibrillogenesis.We have recently described two major functional forms of theCOL5A13′-UTR, namely the C- and T-forms, which contained a set of seven strongly linked sequence variants that showed significant differences in mRNA stability.7 Four of theseCOL5A1variants are associated with Achilles tendinopathy and appear to alter the predicted mRNA secondary structure of the 3′-UTR. We propose that this change in secondary structure causes the alteredCOL5A1mRNA stability and, by implication, type V collagen production.In addition theCOL5A13′-UTR contains several putative cis-acting elements including a functional microRNA binding site for Hsa-miR-608.7 Two forms of the mature Hsa-miR-608, which are produced by the polymorphicMIR608gene, can potentially bind this miRNA binding site (http://www.ncbi.nlm.nih.gov). This variant within theMIR608gene is also independently associated with chronic Achilles tendinopathy. These genetic association studies of theCOL5A1andMIR608genes, together with the functional studies of theCOL5A13′-UTR, suggest that type V collagen synthesis is involved in the molecular mechanisms of, at least, chronic Achilles tendinopathy.We hypothesise that the T-functional form of theCOL5A13′-UTR, which is associated with chronic Achilles tendinopathy, results in increased type V collagen production, decreased mean fibril diameter, and increased fibril density. These structural changes in the fibril result in changes to the mechanical properties of tendons. More specifically, we hypothesise that the changes in mechanical properties associated with the T-functional form result in (i) a reduced tensile strength and (ii) increased creep inhibition and/or stiffness. However, future work is required to test this hypothesis.8
AN ASSOCIATION BETWEEN COMPONENTS OF THE APOPTOSIS PATHWAY AND THE GENETIC PREDISPOSITION TO ACHILLES TENDINOPATHY
Authors: Nell E , van der Merwe L , Cook J , Handley C J , Collins M , September A V 
Published: May 2013

IntroductionAchilles tendinopathy is a degenerative condition for which several risk factors have been implicated including components of the inflammatory pathway. The aims of this study was to evaluate (i) several functional variants within genes encoding components of the apoptosis signalling cascade and (ii) the effectiveness of a polygenic apoptosis profile to capture Achilles tendinopathy (TEN) risk.MethodsA total of 358 unaffected control (CON) participants (159 South Africa (SA CON) and 199 Australia (AUS CON)) and 166 affected TEN participants (87 SA TEN and 79 AUS TEN) were genotyped for four variants (CASP8(rs384129),CASP8(rs1045485), NOS3(rs1799983) andNOS2(rs2779249)). Logistic regression was used to derive risk models for TEN and a receiver operator characteristic (ROC) curve was plotted to determine the effectiveness of the models to capture TEN risk.ResultsAn independent association ofCASP8_rs1045485 andCASP8_rs3834129, together with their haplotype was observed with TEN risk. The optimal risk model identified from the study included the two CASP8 genetic loci investigated (CASP8_rs384129 andCASP8_rs1045485) together with sex to capture TEN risk in both SA and AUS participants collectively.ConclusionsThese findings further implicate the apoptosis signalling cascade as one of the important biological pathways involved in the development of Achilles tendinopathy.
TENDINOPATHY: MORE QUESTIONS THAN ANSWERS
Authors: Langberg H 
Published: May 2013

Tendinopathy is a big problem for athletes, ordinary people and clinicians. At present neither the aetiology and pathology, nor the rehabilitations is well understood, and good evidence is lacking within all these areas.During the last 10 years substantial research has been performed. New data indicate that in the chronic state, tendinopathy in humans is characterised by focal changes in the expression of matrix proteins, increased collagen turnover, smaller collagen fibrils and increased microvascular volume. These changes are attenuated with increased loading as during running. Despite this new knowledge, models for investigating the development of tendinopathy are still lacking and the complex nature of tendinopathy is still a great challenge. However, by developing novel human and animal models, hopefully a thorough understanding of human tendinopathy will be possible within the near future.In relation to treatment, new methods such as injection of platelet rich plasma (PRP) and large quantities of isotonic saline (HVI) have been developed based on sound rationales, but with only minor scientific evidence. More research is needed in this area too.