bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immunology of experimental and natural human hookworm infection
Authors: Gaze S. , Bethony J. M. , Periago M. V. 
Published: November 2013

SummaryHuman hookworm infection is one amongst the most prevalent of the neglected tropical diseases. An informative experimental animal model, that is, one that parallels a human infection, is not available for the study of human hookworm infection. Much of our current understanding of the human immune response during hookworm infection relies on the studies from experimental infection of hookworm‐naïve individuals or the natural infections from individuals residing in hookworm‐endemic areas. The experimental human infections tend to be acute, dose‐controlled infections, often with a low larval inoculum so that they are well tolerated by human volunteers. Natural hookworm infections usually occur in areas where hookworm transmission is constant and infection is chronic. In cases where there has been drug administration in an endemic area, re‐infection often occurs quickly even amongst those who were treated. Hence, although many of the characteristics of experimental and natural hookworm infection differ, both models have elements in common: mainly an intense Th2 response with the production of total and specific IgE as well as elevated levels of eosinophilia, IL‐5, IL‐10 and TNF. While hookworm infection affects millions of individuals worldwide, much of the human immunology of this infection still needs to be studied and understood.
Does proximity to a mature forest contribute to the seed rain and recovery of an abandoned agriculture area in a semiarid climate?
Authors: Souza J. T. , Ferraz E. M. N. , Albuquerque U. P. , Araújo E. L. 
Published: November 2013

AbstractProximity to forests contributes to the recolonisation of anthropogenic‐disturbed areas through seed input. We evaluated the role of proximity to a mature forest in the recolonisation of an agricultural area that has been abandoned for 18 years and is currently a young forest. Seed rain was monitored at fixed distances from the mature forest. The type of surface recolonisation (germinationversusresprouting) and the reproductive season were measured in both forests. The majority of plants recolonising the young forest originated from seed germination. Proximity to the mature forest contributed to the seed rain in the young forest; however, 18 years has not provided sufficient time for the recolonisation of 80 species present in the mature forest. Some species shared between forests differed in their fruiting season and seed dispersal. The seed rain had a total species richness of 56, a total density of 2270 seeds·m−2·year−1and predominance of self‐ and wind dispersal. A significant reduction in seed rain with increasing distance from the mature forest was observed. The young forest contained 35 species not observed in the mature forest, and the floristic similarity between the two forests was 0.5, indicating that the two forests are floristically distinct.
Gravity‐dependent differentiation and root coils in Arabidopsis thaliana wild type and phospholipase‐A‐I knockdown mutant grown on the International Space Station
Authors: Scherer G. F. E. , Pietrzyk P. 
Published: November 2013

AbstractArabidopsis roots on 45° tilted agar in 1‐g grow in wave‐like figures. In addition to waves, formation of root coils is observed in several mutants compromised in gravitropism and/or auxin transport. The knockdown mutant ppla‐I‐1 of patatin‐related phospholipase‐A‐I is delayed in root gravitropism and forms increased numbers of root coils. Three known factors contribute to waving: circumnutation, gravisensing and negative thigmotropism. In microgravity, deprivation of wild type (WT) and mutant roots of gravisensing and thigmotropism and circumnutation (known to slow down in microgravity, and could potentially lead to fewer waves or increased coiling in both WT and mutant). To resolve this, mutant ppla‐I‐1 and WT were grown in the BIOLAB facility in the International Space Station. In 1‐g, roots of both types only showed waving. In the first experiment in microgravity, the mutant after 9 days formed far more coils than in 1‐g but the WT also formed several coils. After 24 days in microgravity, in both types the coils were numerous with slightly more in the mutant. In the second experiment, after 9 days in microgravity only the mutant formed coils and the WT grew arcuated roots. Cell file rotation (CFR) on the mutant root surface in microgravity decreased in comparison to WT, and thus was not important for coiling. Several additional developmental responses (hypocotyl elongation, lateral root formation, cotyledon expansion) were found to be gravity‐influenced. We tentatively discuss these in the context of disturbances in auxin transport, which are known to decrease through lack of gravity.
Risk of Transmission of Bovine Herpesvirus‐1 (BHV‐1) by Infected Semen to Embryo Recipients and Offspring
Authors: Bielanski A , Algire J , Lalonde A , Garceac A 
Published: November 2013

ContentsInfection with bovine herpesvirus‐1 (BHV‐1), also called infectious bovine rhinotracheitis/infectious pustular vulvovaginitis virus, is associated with a variety of respiratory, neurological and infertility health problems causing worldwide economic losses and trading restrictions to the livestock industry. Although there is a considerable amount of information about the risk of BHV‐1 transmission through contaminated semen used for artificial insemination, there is no available evidence to indicate whether the resulting embryos, when used for embryo transfer (ET), can lead to the transmission of BHV‐1 to recipients and offspring. For this study, cryopreserved bull semen contaminated with BHV‐1 was used for artificial insemination (AI) of seronegative, superovulated heifers (N = 43). Embryos were collected post‐mortem at 7 days post‐insemination and were washed according to the International Embryo Transfer Society (IETS) guidelines. BHV‐1 was detected in all samples of follicular fluid, oviductal epithelial cells, endometrium and corpora lutea tissues and a proportion of unwashed (52 of 120, 43%) and washed oocytes and embryos (7 of 113, 6%) collected from embryo donors. Of the 396 collected, unfertilized oocytes and embryos, only 29 (7%) were of ET quality. Most of the embryos and oocytes were degenerated (N = 224, 57%) or unfertilized (N = 143, 36%). The 13 heifers, which each received a single morula‐stage washed embryo, maintained seronegative status, but only two (15%) became pregnant and delivered BHV‐1‐free calves. In conclusion, results suggest that embryos fertilized with BHV‐1‐contaminated semen may not result in disease transmission to embryo recipients or their offspring when embryos are processed according to IETS and the World Organization for Animal Health (OIE) guidelines. However, due to the transmission of BHV‐1 via AI to embryo donors and the apparent adverse effect of BHV‐1 on the quality of the embryos, it is unlikely that the procedure can be justified for a commercial application.
Information Structure, Syntax and Intonational Properties of MultipleWh‐Questions
Authors: Hosono Mayumi 
Published: November 2013

AbstractI discuss multiplewh‐questions from the perspective of information structure. I argue that information‐structural effects differ between multiplewh‐questions with a pair‐list answer reading and ones with a single‐answer reading, thus the way of deriving them in narrow syntax differs too. I claim that the spelled‐out positions ofwh‐phrases are solely determined in the phonological component, specifically by the intonational properties of individual languages. I also argue that the Superiority Effect is derived from a conflicting pitch pattern caused by in‐situ monosyllabicwh‐subjects and no longer problematic in the current phase framework.
Successful high‐level accumulation of fish oil omega‐3 long‐chain polyunsaturated fatty acids in a transgenic oilseed crop
Authors: Ruiz‐Lopez Noemi , Haslam Richard P. , Napier Johnathan A. , Sayanova Olga 
Published: November 2013

SummaryOmega‐3 (also called n‐3) long‐chain polyunsaturated fatty acids (≥C20; LC‐PUFAs) are of considerable interest, based on clear evidence of dietary health benefits and the concurrent decline of global sources (fish oils). Generating alternative transgenic plant sources of omega‐3 LC‐PUFAs, i.e. eicosapentaenoic acid (20:5 n‐3, EPA) and docosahexaenoic acid (22:6 n‐3, DHA) has previously proved problematic. Here we describe a set of heterologous genes capable of efficiently directing synthesis of these fatty acids in the seed oil of the crop Camelina sativa, while simultaneously avoiding accumulation of undesirable intermediate fatty acids. We describe two iterations: RRes_EPA in which seeds contain EPA levels of up to 31% (mean 24%), and RRes_DHA, in which seeds accumulate up to 12% EPA and 14% DHA (mean 11% EPA and 8% DHA). These omega‐3 LC‐PUFA levels are equivalent to those in fish oils, and represent a sustainable, terrestrial source of these fatty acids. We also describe the distribution of these non‐native fatty acids within C. sativa seed lipids, and consider these data in the context of our current understanding of acyl exchange during seed oil synthesis.
Impact of the MLC on the MRI field distortion of a prototype MRI‐linac
Authors: Kolling Stefan , Oborn Brad , Keall Paul 
Published: November 2013

Purpose:To cope with intrafraction tumor motion, integrated MRI‐linac systems for real‐time image guidance are currently under development. The multileaf collimator (MLC) is a key component in every state‐of‐the‐art radiotherapy treatment system, allowing for accurate field shaping and tumor tracking. This work quantifies the magnetic impact of a widely used MLC on the MRI field homogeneity for such a modality.Methods:The finite element method was employed to model a MRI‐linac assembly comprised of a split‐bore MRI magnet and the key ferromagnetic components of a Varian Millennium 120 MLC, namely, the leaves and motors. Full 3D magnetic field maps of the system were generated. From these field maps, the peak‐to‐peak distortion within the MRI imaging volume was evaluated over a diameter sphere volume (DSV) around the isocenter and compared to a maximum preshim inhomogeneity of . Five parametric studies were performed: (1) The source‐to‐isocenter distance (SID) was varied from 100 to , to span the range of a compact system to that with lower magnetic coupling. (2) The MLC model was changed from leaves only to leaves with motors, to determine the contribution to the total distortion caused by MLC leaves and motors separately. (3) The system was configured in the inline or perpendicular orientation, i.e., the linac treatment beam was oriented parallel or perpendicular to the magnetic field direction. (4) The treatment field size was varied from 0 × 0 to , to span the range of clinical treatment fields. (5) The coil currents were scaled linearly to produce magnetic field strengths B0 of 0.5, 1.0, and , to estimate how the MLC impact changes with B0.Results:(1) The MLC‐induced MRI field distortion fell continuously with increasing SID. (2) MLC leaves and motors were found to contribute to the distortion in approximately equal measure. (3) Due to faster falloff of the fringe field, the field distortion was generally smaller in the perpendicular beam orientation. The peak‐to‐peak DSV distortion was below at (perpendicular) and (inline) for the design. (4) The simulation of different treatment fields was identified to cause dynamic changes in the field distribution. However, the estimated residual distortion was below geometric distortion at (perpendicular) and (inline) for a frequency‐encoding gradient. (5) Due to magnetic saturation of the MLC materials, the field distortion remained constant at .Conclusions:This work shows that the MRI field distortions caused by the MLC cannot be ignored and must be thoroughly investigated for any MRI‐linac system. The numeric distortion values obtained for our magnet may vary for other magnet designs with substantially different fringe fields, however the concept of modest increases in the SID to reduce the distortion to a shimmable level is generally applicable.
Constancy of built‐in luminance meter measurements in diagnostic displays
Authors: Silosky M. , Marsh R. M. 
Published: November 2013

Purpose:Liquid crystal displays used to interpret medical images are often equipped with built‐in luminance meters to evaluate luminance response and Grayscale Standard Display Function conformance. This work evaluates agreement between luminance reported by the built‐in meters and external measurements.Methods:The white level luminance was measured using a built‐in meter and an external meter for 93 primary review workstations (Models MFGD 3420 and MDCG 3120‐CB) with between 117 and 49 336 backlight hours (BLH). Measured luminance values were compared viat‐test for displays with less than 25 000 BLH and those with more than 25 000 BLH. Bias between meters was also evaluated. Changes in luminance uniformity with increasing backlight hours were explored by determining the maximum luminance deviation (MLD) for subsets of these displays with less than 800 BLH and greater than 35 000 BLH.Results:The mean difference between built‐in and external luminance measurements was 5.84% and 38.92% for displays with less than 25 000 and greater than 25 000 BLH, respectively, with a statistically significant difference in the means (p < 0.001). For displays with low BLH, a statistically significant bias was observed (p < 0.001) between built‐in and external measurements. A high degree of correlation was observed between measurements made with two separate external meters (r = 0.999). The mean MLD was 9.5% and 11.2% for MDCG 3120‐CB displays with less than 800 and greater than 35 000 BLH, respectively. The difference in the mean values was not statistically significant (p < 0.001).Conclusions:Disagreement between the white level luminance measured using the built‐in and external meter increased with BLH. Consequently, reliance on values reported by the built‐in luminance meter may result in a reduction in image contrast with time. Recommendations have been proposed regarding luminance response testing and corrective action for failing displays.
Molecular Architecture of a Eukaryotic Translational Initiation Complex
Authors: Fernández Israel S. , Bai Xiao-Chen , Hussain Tanweer , Kelley Ann C. , Lorsch Jon R. , Ramakrishnan V. , Scheres Sjors H. W. 
Published: November 2013

Introduction

Initiation of protein synthesis is a key step in the control of gene expression. In eukaryotes, initiation is a highly complex process that requires almost a dozen protein factors. The last step involves joining of the large and small subunits of the ribosome to form the 80
S
initiation complex with the transfer RNA (tRNA) in the P-site base paired to the start codon. This step is catalyzed by the guanosine triphosphatase (GTPase) factor eIF5B. In addition, eIF5B is thought to play a role in ensuring that translation initiation takes place only on mature ribosomes.

Methods
The development of fast, direct electron detectors and new methods of image analysis for cryo–electron microscopy allow high-resolution reconstructions from much smaller numbers of particles than previously possible. We used these new methods to provide feedback to improve the biochemical preparation of samples for structure determination of the eukaryotic translation initiation complex with initiator tRNA and eIF5B, which was trapped on the ribosome with the nonhydrolyzable GTP analog GDPCP.

Results
Although the structure of the fully assembled complex was calculated from only 5143 particles, representing just 3% of the population in the sample, it was possible to obtain a resolution of 6.6 Å. This allowed us to propose a molecular model for the initiation complex. The structure shows that the subunits of the ribosome are rotated relative to the canonical state after initiation. The long helix and C-terminal domain of eIF5B have changed conformation and moved into the ribosome, where the C-terminal domain interacts with the initiator tRNA. The tRNA is stabilized in a distorted conformation, with its 3′-CCA end out of the peptidyl transferase center.

Discussion

The conformational change in eIF5B may be induced upon binding to the small (40
S
) subunit when it specifically recognizes initiator tRNA. In its altered conformation, eIF5B interacts simultaneously with the initiator tRNA and the GTPase center of the ribosome, thus coupling GTP hydrolysis with tRNA recognition in the ribosome. The large number of contacts made by eIF5B with the ribosomal subunits and tRNA is consistent with its role in subunit joining. A close contact with the eukaryote-specific ribosomal protein L40 would not be possible in the immature ubiquitinated form of L40, thus precluding the recruitment of immature 60
S
subunits. A comparison with previous work on the bacterial homolog IF2 suggests that the mechanism of this step of initiation is conserved across kingdoms. Finally, the use of recent advances in cryo-EM to determine a relatively high-resolution structure of the eIF5B-ribosome complex from a very small fraction of a sample could be a general approach for the study of other dynamic or transient biological complexes.
Complete Sequence of a New Bipartite Begomovirus Infecting Cotton Plants in Brazil
Authors: de Almeida Mariana Martins Severo , Jain Sona , Barroso Paulo Augusto Vianna , Hoffmann Lúcia Vieira , de Lucena Monaliza Gomes , Resende Renato de Oliveira , Inoue-Nagata Alice Kazuko 
Published: November 2013

ABSTRACT
Begomoviruses are plant viruses responsible for severe losses in important crops, such as beans, cassavas, tomatoes, and cotton, around the world. Here, we report the first full-genome sequence of a bipartite begomovirus species collected from cotton plants in Brazil.
Draft Genome Sequence of the Antibiotic-Producing Epiphytic Isolate Pantoea ananatis BRT175
Authors: Smith Derek D. N. , Kirzinger Morgan W. B. , Stavrinides John 
Published: November 2013

ABSTRACT

Pantoea
is a member of the
Enterobacteriaceae
, whose members have been shown to produce novel antibiotics. Here, we report the 4.8-Mb genome sequence of
Pantoea ananatis
strain BRT175, an epiphytic isolate from strawberries that produces an antibiotic that is effective against the fire blight pathogen,
Erwinia amylovora
.
Complete Genome Sequence of Leifsonia xyli subsp.
cynodontis
Strain DSM46306, a Gram-Positive Bacterial Pathogen of Grasses
Authors: Monteiro-Vitorello Claudia Barros , Zerillo Marcelo Marques , Van Sluys Marie-Anne , Camargo Luis Eduardo Aranha , Kitajima João Paulo 
Published: November 2013

ABSTRACT

We announce the complete genome sequence of
Leifsonia xyli
subsp.
cynodontis
, a vascular pathogen of Bermuda grass. The species also comprises
Leifsonia xyli
subsp.
xyli
, a sugarcane pathogen. Since these two subspecies have genome sequences available, a comparative analysis will contribute to our understanding of the differences in their biology and host specificity.
Draft Genome Sequence of the Fish Pathogen Piscirickettsia salmonis
Authors: Eppinger Mark , McNair Katelyn , Zogaj Xhavit , Dinsdale Elizabeth A. , Edwards Robert A. , Klose Karl E. 
Published: November 2013

ABSTRACTPiscirickettsia salmonisis a Gram-negative intracellular fish pathogen that has a significant impact on the salmon industry. Here, we report the genome sequence ofP. salmonisstrain LF-89. This is the first draft genome sequence ofP. salmonis, and it reveals interesting attributes, including flagellar genes, despite this bacterium being considered nonmotile.
Draft Genome Sequence of
Nitrosospira
sp. Strain APG3, a Psychrotolerant Ammonia-Oxidizing Bacterium Isolated from Sandy Lake Sediment
Authors: Garcia Juan C. , Urakawa Hidetoshi , Le Vang Q. , Stein Lisa Y. , Klotz Martin G. , Nielsen Jeppe L. 
Published: November 2013

ABSTRACT

Bacteria in the genus
Nitrosospira
play vital roles in the nitrogen cycle.
Nitrosospira
sp. strain APG3 is a psychrotolerant betaproteobacterial ammonia-oxidizing bacterium isolated from freshwater lake sediment. The draft genome revealed that it represents a new species of cluster 0
Nitrosospira
, which is presently not represented by described species.
Targeted exome capture and sequencing identifies novel PRPF31 mutations in autosomal dominant retinitis pigmentosa in Chinese families
Authors: Yang Liping , Yin Xiaobei , Wu Lemeng , Chen Ningning , Zhang Huirong , Li Genlin , Ma Zhizhong 
Published: November 2013

ObjectivesTo identify disease-causing mutations in two Chinese families with autosomal dominant retinitis pigmentosa (adRP).DesignProspective analysis.PatientsTwo Chinese adRP families underwent genetic diagnosis. A specific hereditary eye disease enrichment panel (HEDEP) based on targeted exome capture technology was used to collect the protein coding regions of targeted 371 hereditary eye disease genes; high throughput sequencing was done with the Illumina HiSeq 2000 platform. The identified variants were confirmed with Sanger sequencing.SettingAll experiments were performed in a large laboratory specialising in genetic studies in the Department of Ophthalmology, Peking University Third Hospital.ResultsTwo novel mutations, including one splice site mutation (Int10 c.1074-2 A>T; p.Y359SfsX29) and one insertion (c.824_825insA; p.Y275X) of PRPF31 were identified in the two families. The two mutations segregated with the disease phenotype in their respective families.ConclusionsOur findings broaden the spectrum of PRPF31 mutations causing adRP and the phenotypic spectrum of the disease in Chinese patients. The HEDEP based on targeted exome capture technology is an efficient method for molecular diagnosis in adRP patients.
Transcervical access in acute ischemic stroke
Authors: Jadhav Ashutosh P , Ribo Marc , Grandhi Ramesh , Linares Guillermo , Aghaebrahim Amin , Jovin Tudor G , Jankowitz Brian T 
Published: November 2013

BackgroundLarge vessel occlusive disease portends a poor prognosis unless recanalization is rapidly achieved. Endovascular treatment is typically performed via a transfemoral approach, but catheterization of the occluded vessel can be problematic in cases of extensive vessel tortuosity.MethodsA retrospective review of a prospectively maintained database identified 7 patients who underwent acute endovascular reperfusion therapy via transcervical approach.ResultsWe identified 7 patients. Admission NIHSS ranged from 8–27 and recanalization occurred between 7–49 min of carotid access. Prior to carotid access, 20–90 min were spent attempting target vessel catheterization via the transfemoral approach. All occlusions were in the left MCA. In 87.5% of patient, TICI2b/3 recanalization was achieved. Neck hematoma formation occurred in one case requiring elective intubation. At 2 months followup, all patients had survived with mRS 0–4 except for one patient who had a large infarct despite recanalization.ConclusionsTranscervical access for acute ischemic stroke leads to rapid and high quality recanalization. Future studies will focus on improved hemostasis and early identification of patients who would benefit the most from direct carotid access for acute stroke.
Feller evolution systems: Generators and approximation
Authors: Böttcher Björn 
Published: November 2013

A time and space inhomogeneous Markov process is a Feller evolution process, if the corresponding evolution system on the continuous functions vanishing at infinity is strongly continuous. We discuss generators of such systems and show that under mild conditions on the generators a Feller evolution can be approximated by Markov chains with Lévy increments.The result is based on the approximation of the time homogeneous spacetime process corresponding to a Feller evolution process. In particular, we show that a d-dimensional Feller evolution corresponds to a (d + 1)-dimensional Feller process. It is remarkable that, in general, this Feller process has a generator with discontinuous symbol.