bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transfer of the methicillin resistance genomic island among staphylococci by conjugation
Authors: Ray M. D. , Boundy S. , Archer G. L. 
Published: January 2016

SummaryMethicillin resistance creates a major obstacle for treatment of Staphylococcus aureus infections. The resistance gene, mecA, is carried on a large (20 kb to > 60 kb) genomic island, staphylococcal cassette chromosome mec (SCCmec), that excises from and inserts site‐specifically into the staphylococcal chromosome. However, although SCCmec has been designated a mobile genetic element, a mechanism for its transfer has not been defined. Here we demonstrate the capture and conjugative transfer of excised SCCmec. SCCmec was captured on pGO400, a mupirocin‐resistant derivative of the pGO1/pSK41 staphylococcal conjugative plasmid lineage, and pGO400::SCCmec (pRM27) was transferred by filter‐mating into both homologous and heterologous S. aureus recipients representing a range of clonal complexes as well as S. epidermidis. The DNA sequence of pRM27 showed that SCCmec had been transferred in its entirety and that its capture had occurred by recombination between IS257/431 elements present on all SCCmec types and pGO1/pSK41 conjugative plasmids. The captured SCCmec excised from the plasmid and inserted site‐specifically into the chromosomal att site of both an isogenic S. aureus and a S. epidermidis recipient. These studies describe a means by which methicillin resistance can be environmentally disseminated and a novel mechanism, IS‐mediated recombination, for the capture and conjugative transfer of genomic islands.
Bone metabolism in epilepsy patients: An analysis of 30 cases taking classic anti‐epileptic drugs
Authors: Yokota Ichiro , Kuga Atsushi , Uenishi Kazuhiro , Ishihara Hiroyuki , Kageyama Yasushi , Fujino Masahiro , Nagao Mitsushiro , Kanda Fumio , Toda Tatsushi 
Published: January 2016

AbstractBackgroundThe majority of classic anti‐epileptic drugs can decrease bone mineral density through the acceleration of vitamin D metabolism by cytochrome P450.AimWe tried to investigate the bone metabolism. in adult patients with epilepsy.MethodsBone mineral density was measured in 30 patients (18 men and 12 women, age 24–76 years) treated with classic anti‐epileptic drugs for more than 5 years. Dietary intake of nutrients and laboratory data were assessed in patients, and age‐ and sex‐matched healthy controls.ResultsUsing T‐scores measured at the lumbar spine, seven patients (23%) were diagnosed as osteopenia and two patients (6%) as osteoporosis. Serum 25‐hydroxyvitamin D levels were significantly decreased in patients taking phenytoin, but were unchanged in patients taking valproic acid, compared with those on other prescription anti‐epileptic drugs. Dietary intake of vitamin D, assessed by a nutritionist, did not differ among patients. Bone mineral density score was not correlated with serum 25‐hydroxyvitamin D, but it was significantly correlated with serum under‐carboxylated osteocalcin and serum tartrate‐resistant acid phosphatase isoform 5b. Serum under‐carboxylated osteocalcin levels were significantly higher in patients with decreased bone mineral density compared with age‐ and sex‐matched healthy controls. Dietary intake of vitamin K did not differ between patients and controls.ConclusionThese results suggest that vitamin D plays a pivotal role in the altered bone metabolism in patients taking classic anti‐epileptic drugs. With the use of bone mineral density scores and biomarkers, neurologists in Japan might be able to evaluate bone health in the management of patients with epilepsy.
Altitude and arteriolar hyalinosis after kidney transplantation
Authors: Cippà Pietro E , Grebe Scott O , Fehr Thomas , Wüthrich Rudolf P , Mueller Thomas F 
Published: January 2016

AbstractThe kidney is very susceptible to hypoxic injury. Calcineurin inhibitors (CNIs) induce vasoconstriction and might reduce renal tissue oxygenation. We aimed to investigate if the synergistic deleterious effects of CNI‐treatment and hypoxia of high altitude living might accelerate the development of arteriolar hyalinosis in kidney allografts. We stratified all patients who received a kidney graft from 2000 to 2010 in our centre (n = 477) in three groups according to the residential elevation (below 400, between 400 to 600 and above 600 m above sea level) and we retrospectively re‐evaluated all transplant biopsies performed during follow‐up, specifically looking at the degree of arteriolar hyalinosis, the hallmark of chronic CNI nephrotoxicity. Living at high altitude was markedly associated with a higher degree of arteriolar hyalinosis (P < 0.001). Haemoglobin levels confirmed the functional relevance of different arterial oxygenation among the groups (P = 0.01). Thus, patients living at high altitude seem to be more susceptible to the development of arteriolar hyalinosis after kidney transplantation.
Pressure topography metrics for high‐resolution pharyngeal‐esophageal manofluorography—a normative study of younger and older adults
Authors: Nativ‐Zeltzer N. , Logemann J. A. , Zecker S. G. , Kahrilas P. J. 
Published: January 2016

AbstractBackgroundWe aimed to define normative values for novel pressure topography metrics for high‐resolution pharyngeal‐esophageal manofluorography. The effects of age, gender, and bolus properties were examined.MethodsConcurrent high‐resolution manometry (HRM) and videofluoroscopy data were collected from 22 younger (aged 21–40) and 22 older (aged 60–80) healthy subjects. Pressure topography was analyzed by correlating pressure domains with videofluoroscopic events. Nine pressure topography metrics of the pharyngeal and proximal esophageal swallow were extracted; four of these were also compared with previously obtained esophageal HRM studies to assess the effects of catheter diameter.Key ResultsOlder individuals exhibited more vigorous contractility in the pharynx than did younger subjects with all bolus types, but the greatest values for both groups were with effortful swallow and on that measure the age groups were similar. Upper esophageal sphincter (UES) intrabolus pressure during sphincter opening was also greater in the older subjects. Some gender differences were observed, particularly related to proximal esophageal contractile vigor. Bolus consistency had no consistent effect. Studies using the larger catheter diameter resulted in significantly greater contractile vigor in the UES and proximal esophagus.Conclusions & InferencesOlder adults exhibited more vigorous pharyngeal contractions than young adults, albeit within a similar range of capacity, perhaps reflecting a compensatory response to other age‐related physiological changes. Greater UES intrabolus pressures observed during bolus transit in the older group likely reflect reduced UES compliance with age. Normative data on novel HRM metrics collected in this study can serve as a reference for future clinical studies.
Subcutaneous Fat Necrosis of the Neonate with a Delayed Second Eruption
Authors: Thomas Justyn M. , Bhandari Jasjit , Rytina Ed , Gass Julia K. , Williams Rachel M. , Burrows Nigel P. 
Published: January 2016

AbstractSubcutaneous fat necrosis (SCFN) of the neonate is a rare panniculitis of early life that occurs in association with gestational diabetes and preeclampsia, as well as perinatal asphyxia, hypothermia, and trauma. A characteristic feature of this condition is its self‐limiting and monophasic nature. We report a highly unusual case of delayed SCFN in a male neonate involving an anatomically discrete eruption, reminiscent of erythema nodosum, occurring many weeks after his original eruption had resolved.
Low serum biotin in Japanese children fed with hydrolysate formula
Authors: Sato Yasuhiro , Wakabayashi Kenji , Ogawa Eishin , Kodama Hiroko , Mimaki Masakazu 
Published: January 2016

AbstractBackgroundGiven that nutritional biotin deficiency in Japanese infants has been reported, a straightforward method for estimating biotin level is needed. The biotin content in infant formula, breast milk, and the sera of infants fed with various types of formula were measured using avidin‐binding assay.MethodsA commercially available ELISA kit was used for the measurement of biotin in 54 types of formula, including hydrolysate formulas for milk allergy, as well as in breast milk and in the sera of 27 infants fed with these formulas.ResultsThe biotin content reached the recommended value in only five formulas. All of the hydrolysate formulas and more than half of the special formulas contained biotin <0.1 μg/dL. Serum biotin was low in infants fed only with the hydrolysate formulas, and one of them had alopecia related to biotin deficiency.ConclusionWhile many were asymptomatic, infants fed with formulas lacking biotin are at risk of developing symptomatic disease. The addition of biotin to breast milk substitutes was finally approved in the middle of 2014, however pediatricians in Japan should still be vigilant with regard to nutritional biotin deficiency in infants for the time being.
Three‐dimensional organization of flagellar basal apparatus inEctocarpusgametes
Authors: Kinoshita Nana , Fu Gang , Ito Toshiaki , Motomura Taizo 
Published: January 2016

SummaryThe flagellar basal apparatus of the brown algaEctocarpus siliculosuswas re‐investigated in details using transmission electron microscopy and electron tomography. As a result, three‐dimensional structures with spatial arrangement of bands and microtubular flagellar rootlets were observed. Fibrous structures linking the anterior flagellar basal body to the major anterior rootlet (R3) or the bypassing rootlet was newly discovered in this study. A direct attachment from the minor anterior rootlet (R4) to the anterior and posterior basal bodies was also discovered, as were attachments from the minor posterior rootlet (R1) to the deltoid striated band and from the major posterior rootlet (R2) to the posterior fibrous band. The microtubular flagellar rootlets were connected to the bands and to the anterior or posterior basal body. These bands may have a role in maintaining the spatial arrangement of the anterior and posterior flagellar basal bodies and the microtubular flagellar rootlets. A numbering system of the basal body triplets was established by tracing axonemal doublets in the serial sections. From these observations, the precise position of two flagellar basal bodies, bands, and flagellar rootlets was determined.
China's Labor Market Integration and the Effect of Economic Openness
Authors: Yi Miao , Zhou Shen 
Published: January 2016

AbstractThis research theoretically and empirically studies China's labor market integration and the effect of economic openness. We introduce an open parameter to the previous theoretical framework and, based on that, we carry out an empirical study of China's labor market integration measurement from 1987 to 2006, and focus on the impact of economic openness. Research indicates that economic openness has an obvious effect on promoting China's labor market integration. The labor market integration progress differs between regions, with labor markets of coastal areas such as North China, East China and South China, which have one or two labor market centers, being better integrated than those of other interior areas.
Managing donors and donation sessions to improve donor service and session productivity
Authors: Nyberg‐Oksanen E. , Morgan S. , Sydenham V. , Georgsen J. , Jansen E. ,   the EBA Benchmarking Group
Published: January 2016

Background and ObjectivesThe European Blood Alliance's Benchmarking group (EBA BMG) has facilitated three collection productivity workshops (2008–15). Productivity improvements are evident in some European blood services, but fewer than anticipated. European blood services sometimes lack data, experience and state of the art technology to implement opportunities to improve productivity. With the decline in red cell demand across the developed world alongside constrained healthcare budgets and the changing expectations of the evolving donor base, as countries see a need to recruit younger donors, the challenge is balancing increasing donor expectations with higher productivity targets.Materials and MethodsAgainst each identified key element, we have collected key performance indicators (KPIs) and benchmarked them across European blood services. We have also identified technologies, which we call enablers that could help blood services improve performance.ResultsThe analysis performed by the EBA BMG identifies the key elements associated with efficient management of donors and donation sessions.ConclusionsWith these best practices and KPIs, it is possible for blood services to increase session productivity and donor satisfaction through low deferrals, low end‐to‐end donation time and smooth, consistent, yet ‘tailored’ individual service inside the session.
Powerful tools for resolving antibody problems
Authors: Hamilton J. R. 
Published: January 2016

BackgroundIdentifying the specificity of antibodies in a patient's plasma can be as straightforward as testing selected reagent red cells on the basis of the antibody detection results. Many investigations, however, require the use of additional methods or supplemental tests for resolution.AimsSpecifics related to performance of these procedures, their interpretations and their limitations were reviewed.DiscussionGel microcolumn or solid phase methods, polyethylene glycol or low‐ionic strength saline enhancement media or unenhanced tests have appropriate uses for detecting or avoiding antibody reactivity. Useful red cell treatments include enzymes or thiol compounds to destroy antigens or enhance the antigen–antibody interaction and EDTA–glycine acid or chloroquine diphosphate to remove bound IgG from autologous cells. Separating autologous red cells from transfused donor cells for phenotyping or testing with plasma or eluate is critical. Alloantibodies or autoantibodies can be removed or separated by appropriate adsorption tests. Inhibition of antibody reactivity by a known soluble blood group substance confirms specificity or neutralizes interfering reactivity.ConclusionCombined into a logical investigation, these additional tests will aid in resolution of most antibody‐containing samples.
A new approach to the discrete logarithm problem with auxiliary inputs
Authors: Cheon Jung Hee , Kim Taechan 
Published: January 2016

The aim of the discrete logarithm problem with auxiliary inputs is to solve for ${\it\alpha}$, given the elements $g,g^{{\it\alpha}},\ldots ,g^{{\it\alpha}^{d}}$ of a cyclic group $G=\langle g\rangle$, of prime order $p$. The best-known algorithm, proposed by Cheon in 2006, solves for ${\it\alpha}$ in the case where $d\mid (p\pm 1)$, with a running time of $O(\sqrt{p/d}+d^{i})$ group exponentiations ($i=1$ or $1/2$ depending on the sign). There have been several attempts to generalize this algorithm to the case of ${\rm\Phi}_{k}(p)$ where $k\geqslant 3$. However, it has been shown by Kim, Cheon and Lee that a better complexity cannot be achieved than that of the usual square root algorithms.We propose a new algorithm for solving the DLPwAI. We show that this algorithm has a running time of $\widetilde{O}(\sqrt{p/{\it\tau}_{f}}+d)$ group exponentiations, where ${\it\tau}_{f}$ is the number of absolutely irreducible factors of $f(x)-f(y)$. We note that this number is always smaller than $\widetilde{O}(p^{1/2})$.In addition, we present an analysis of a non-uniform birthday problem.
Complete Genome Sequence Analysis of Acute and Mild Strains of Classical Swine Fever Virus Subgenotype 3.2
Authors: Lim Seong-In , Han Song-Hee , Hyun HyeSook , Lim Ji-Ae , Song Jae-Young , Cho In-Soo , An Dong-Jun 
Published: January 2016

ABSTRACT
We report the complete genome sequences of two classical swine fever virus strains (JJ9811 and YI9908). Both belong to subgenotype 3.2. Strain JJ9811 causes mild symptoms and strain YI9908 causes acute symptoms. The sequences were 95.7% homologous at the nucleotide level and 95.6% homologous at the amino acid level.
Draft Genome Assembly of a Filamentous Euendolithic (True Boring) Cyanobacterium,
Mastigocoleus testarum
Strain BC008
Authors: Guida Brandon S. , Garcia-Pichel Ferran 
Published: January 2016

ABSTRACT

Mastigocoleus testarum
strain BC008 is a model organism used to study marine photoautotrophic carbonate dissolution. It is a multicellular, filamentous, diazotrophic, euendolithic cyanobacterium ubiquitously found in marine benthic environments. We present an accurate draft genome assembly of 172 contigs spanning 12,700,239 bp with 9,131 annotated genes with an average G+C% of 37.3.
Complete Genome Sequence of Nonhemolytic Streptococcus agalactiae Serotype V Strain 1, Isolated from the Buccal Cavity of a Canine
Authors: Harden Leeanne K. , Morales Karina M. , Hughey Jeffery R. 
Published: January 2016

ABSTRACT

The complete genome sequence from a nonhemolytic strain of
Streptococcus agalactiae
from the oral cavity of a canine was assembled. The genome is 2,165,968 bp, contains 2,055 genes, and is classified as group B streptococcus (GBS) serotype V, strain 1. A comparison to other
S. agalactiae
sequences shows high gene synteny with human and bovine strains.
Draft Genome Sequence of Probiotic Enterococcus faecium Strain L-3
Authors: Karaseva Alena , Tsapieva Anna , Pachebat Justin , Suvorov Alexander 
Published: January 2016

ABSTRACT

We report here the draft genome sequence of the bacteriocin producer
Enterococcus faecium
strain L-3, isolated from a probiotic preparation, Laminolact, which is widely used in the Russian Federation. The draft genome sequence is composed of 74 contigs for a total of 2,643,001 bp, with 2,646 coding genes. Five clusters for bacteriocin production were found.
Complete Genome Sequence of Porcine Parvovirus 2 Recovered from Swine Sera
Authors: Campos F. S. , Kluge M. , Franco A. C. , Giongo A. , Valdez F. P. , Saddi T. M. , Brito W. M. E. D. , Roehe P. M. 
Published: January 2016

ABSTRACT
A complete genomic sequence of porcine parvovirus 2 (PPV-2) was detected by viral metagenome analysis on swine sera. A phylogenetic analysis of this genome reveals that it is highly similar to previously reported North American PPV-2 genomes. The complete PPV-2 sequence is 5,426 nucleotides long.
Complete Genome Sequence of Corynebacterium pseudotuberculosis Viscerotropic Strain N1
Authors: Loureiro Dan , Portela Ricardo W. , Sousa Thiago J. , Rocha Flávia , Pereira Felipe L. , Dorella Fernanda A. , Carvalho Alex F. , Menezes Nildo , Macedo Eduardo S. , Moura-Costa Lilia F. , Meyer Roberto , Leal Carlos A. G. , Figueiredo Henrique C. , Azevedo Vasco 
Published: January 2016

ABSTRACT

We present the complete genome sequence of
Corynebacterium pseudotuberculosis
strain N1. The sequencing was performed with the Ion Torrent Personal Genome Machine system. The genome is a circular chromosome with 2,337,845 bp, a G+C content of 52.85%, and a total of 2,045 coding sequences, 12 rRNAs, 49 tRNAs, and 58 pseudogenes.
Draft Genome Sequence of Pannonibacter phragmitetus Strain CGMCC9175, a Halotolerant Polycyclic Aromatic Hydrocarbon-Degrading Bacterium
Authors: Wang Xinxin , Jin Decai , Zhou Lisha , Zhang Zhuo 
Published: January 2016

ABSTRACT

Pannonibacter phragmitetus
CGMCC9175 is a halotolerant polycyclic aromatic hydrocarbon (PAH)-degrading bacterium isolated from PAH-contaminated intertidal zone sediment. Here, we report the 5.7-Mb draft genome sequence of this strain, which will provide insights into the diversity of
Pannonibacter
and the mechanism of PAH degradation in sediments.
Draft Genome Sequences of Acinetobacter baumannii Strains Harboring the
bla
NDM-1
Gene Isolated in Lebanon from Civilians Wounded during the Syrian Civil War
Authors: Tokajian Sima , Eisen Jonathan A. , Jospin Guillaume , Hamze Monzer , Rafei Rayane , Salloum Tamara , Ibrahim Joe , Coil David A. 
Published: January 2016

ABSTRACT

We present here the draft genome sequences of multidrug-resistant
bla
NDM-1
-positive
Acinetobacter baumannii
strains ACMH-6200 and ACMH-6201, isolated in north Lebanon from civilians wounded during the Syrian civil war. The draft genomes were contained in 217 contigs for ACMH-6200 and 83 contigs for ACMH-6201, including a combined 3,997,237 bases for ACMH-6200 and 3,983,110 bases for ACMH-6201, with 39% and 38.9% G+C content, respectively.
Characterization of a Pathogenic Full-Length cDNA Clone and Transmission Model for Porcine Epidemic Diarrhea Virus Strain PC22A
Authors: Beall Anne , Yount Boyd , Lin Chun-Ming , Hou Yixuan , Wang Qiuhong , Saif Linda , Baric Ralph 
Published: January 2016

ABSTRACT

Porcine epidemic diarrhea virus (PEDV) is a highly pathogenic alphacoronavirus. In the United States, highly virulent PEDV strains cause between 80 and 100% mortality in suckling piglets and are rapidly transmitted between animals and farms. To study the genetic factors that regulate pathogenesis and transmission, we developed a molecular clone of PEDV strain PC22A. The infectious-clone-derived PEDV (icPEDV) replicated as efficiently as the parental virus in cell culture and in pigs, resulting in lethal disease
in vivo
. Importantly, recombinant PEDV was rapidly transmitted to uninoculated pigs via indirect contact, demonstrating virulence and efficient transmission while replicating phenotypes seen in the wild-type virus. Using reverse genetics, we removed open reading frame 3 (ORF3) and replaced this region with a red fluorescent protein (RFP) gene to generate icPEDV-ΔORF3-RFP. icPEDV-ΔORF3-RFP replicated efficiently
in vitro
and
in vivo
, was efficiently transmitted among pigs, and produced lethal disease outcomes. However, the diarrheic scores in icPEDV-ΔORF3-RFP-infected pigs were lower than those in wild-type-virus- or icPEDV-infected pigs, and the virus formed smaller plaques than those of PC22A. Together, these data describe the development of a robust reverse-genetics platform for identifying genetic factors that regulate pathogenic outcomes and transmission efficiency
in vivo
, providing key infrastructural developments for developing and evaluating the efficacy of live attenuated vaccines and therapeutics in a clinical setting.

IMPORTANCE
Porcine epidemic diarrhea virus (PEDV) emerged in the United States in 2013 and has since killed 10% of U.S. farm pigs. Though the disease has been circulating internationally for decades, the lack of a rapid reverse-genetics platform for manipulating PEDV and identifying genetic factors that impact transmission and virulence has hindered the study of this important agricultural disease. Here, we present a DNA-based infectious-clone system that replicates the pathogenesis of circulating U.S. strain PC22A both
in vitro
and in piglets. This infectious clone can be used both to study the genetics, virulence, and transmission of PEDV coronavirus and to inform the creation of a live attenuated PEDV vaccine.