bluuebunny/crossref_metadata_2025 huggingface dataset:
Overexpression of BpAP1 induces early flowering and produces dwarfism in Betula platyphylla × Betula pendula
Authors: Huang Haijiao , Wang Shan , Jiang Jing , Liu Guifeng , Li Huiyu , Chen Su , Xu Huanwen
Published: November 2013

The involvement of APETALA1 (AP1) in the flowering transition has been the focus of much research. Here, we produced Betula platyphylla × Betula pendula (birch) lines that overexpressed BpAP1 using Agrobacterium‐mediated transformation; we obtained five independent 35S::BpAP1 transgenic lines. Polymerase chain reaction (PCR), Southern, northern and western analyses were used to identify the transformants. As determined by quantitative real‐time PCR (qRT‐PCR), BpAP1 expression in roots, shoots, leaves and terminal buds of 35S::BpAP1 transgenic lines was significantly higher than that in the wild type (WT, P < 0.01). The average height of 2‐year‐old 35S::BpAP1 plants was significantly lower (41.17%) than that of non‐transgenic plants. In the 35S::BpAP1 lines, inflorescences emerged successively beginning 2 months after transplanting. In addition, the length–diameter ratio of fully developed male and female inflorescences were both significantly less than those of the WT (P < 0.05), i.e. the morphological characteristic was stubby. The male inflorescences emerged early, with empty, draped anthers, and pollen was rarely produced, whereas the female floret structure was not different from WT. The pistils developed normally and could accept pollen, leading to the production of hybrid progeny (F1). F1 plants completed flowering within only 1 year after sowing. We demonstrate that BpAP1 can be inherited through sexual reproduction. Overexpression of BpAP1 caused early flowering and dwarfism; these lines had an obviously shortened juvenile phase. These results greatly increase our understanding of the mechanisms underlying the flowering transition and enhance genetic studies of birch traits, and they open up new possibilities for the breeding of birch and other woody plants.
Physiological and molecular characterization of Si uptake in wild rice species
Authors: Mitani‐Ueno Namiki , Ogai Hisao , Yamaji Naoki , Ma Jian Feng
Published: November 2013

Cultivated rice (Oryza sativa) accumulates high concentration of silicon (Si), which is required for its high and sustainable production. High Si accumulation in cultivated rice is achieved by a high expression of both influx (Lsi1) and efflux (Lsi2) Si transporters in roots. Herein, we physiologically investigated Si uptake, isolated and functionally characterized Si transporters in six wild rice species with different genome types. Si uptake by the roots was lower in Oryza rufipogon, Oryza barthii (AA genome), Oryza australiensis (EE genome) and Oryza punctata (BB genome), but similar in Oryza glumaepatula and Oryza meridionalis (AA genome) compared with the cultivated rice (cv. Nipponbare). However, all wild rice species and the cultivated rice showed similar concentration of Si in the shoots when grown in a field. All species with AA genome showed the same amino acid sequence of both Lsi1 and Lsi2 as O. sativa, whereas species with EE and BB genome showed several nucleotide differences in both Lsi1 and Lsi2. However, proteins encoded by these genes also showed transport activity for Si in Xenopus oocyte. The mRNA expression of Lsi1 in all wild rice species was lower than that in the cultivated rice, whereas the expression of Lsi2 was lower in O. rufipogon and O. barthii but similar in other species. Similar cellular localization of Lsi1 and Lsi2 was observed in all wild rice as the cultivated rice. These results indicate that superior Si uptake, the important trait for rice growth, is basically conserved in wild and cultivated rice species.
High Dimensional Thresholded Regression and Shrinkage Effect
Authors: Zheng Zemin , Fan Yingying , Lv Jinchi
Published: November 2013

High dimensional sparse modelling via regularization provides a powerful tool for analysing large-scale data sets and obtaining meaningful interpretable models. The use of non-convex penalty functions shows advantage in selecting important features in high dimensions, but the global optimality of such methods still demands more understanding. We consider sparse regression with a hard thresholding penalty, which we show to give rise to thresholded regression. This approach is motivated by its close connection with L0-regularization, which can be unrealistic to implement in practice but of appealing sampling properties, and its computational advantage. Under some mild regularity conditions allowing possibly exponentially growing dimensionality, we establish the oracle inequalities of the resulting regularized estimator, as the global minimizer, under various prediction and variable selection losses, as well as the oracle risk inequalities of the hard thresholded estimator followed by further L2-regularization. The risk properties exhibit interesting shrinkage effects under both estimation and prediction losses. We identify the optimal choice of the ridge parameter, which is shown to have simultaneous advantages to both the L2-loss and the prediction loss. These new results and phenomena are evidenced by simulation and real data examples.
On Estimation Efficiency of the Central Mean Subspace
Authors: Ma Yanyuan , Zhu Liping
Published: November 2013

We investigate the estimation efficiency of the central mean subspace in the framework of sufficient dimension reduction. We derive the semiparametric efficient score and study its practical applicability. Despite the difficulty caused by the potential high dimension issue in the variance component, we show that locally efficient estimators can be constructed in practice. We conduct simulation studies and a real data analysis to demonstrate the finite sample performance and gain in efficiency of the proposed estimators in comparison with several existing methods.
Optimal Sampling Ratios in Comparative Diagnostic Trials
Authors: Dong Ting , Tang Liansheng Larry , Rosenberger William F.
Published: November 2013

A subjective sampling ratio between the case and the control groups is not always an efficient choice to maximize the power or to minimize the total required sample size in comparative diagnostic trials. We derive explicit expressions for an optimal sampling ratio based on a common variance structure shared by several existing summary statistics of the receiver operating characteristic curve. We propose a two-stage procedure to estimate adaptively the optimal ratio without pilot data. We investigate the properties of the proposed method through theoretical proofs, extensive simulation studies and a real example in cancer diagnostic studies.
Cultivating Back‐to‐the‐Landers: Networks of Knowledge in Rural Northern Italy
Authors: Wilbur Andrew
Published: November 2013

Back‐to‐the‐land migration offers a unique and insightful opportunity to explore how individuals from non‐agricultural backgrounds adopt, adapt and perceive the demands of farming. There is considerable variation in the forms of study and methods of preparation that back‐to‐the‐landers undertake before trying to create a livelihood from the land, not to mention highly disparate results from their efforts. This article considers the value that new farmers in Italy attach to different forms of knowledge, in particular the discrepancies between formal scientific and local knowledges. The utility of different forms is discussed in relation to the individual experiences of farmers, as well as formal networks that exist to impart technical knowledge of agriculture. Two case‐study organisations, Worldwide Opportunities on Organic Farms (WWOOF) and Associazione per Esperienze (APE) are analysed with regard to their abilities to assemble and transmit specific forms of knowledge to new and aspiring farmers, thus strengthening the viability of back‐to‐the‐land as a lifestyle choice and farming as a vocation.
Description and molecular modeling of four novel HLA‐B alleles identified in Brazilian individuals
Authors: Fabreti‐Oliveira R. A. , Nascimento E. , Santos M. A.
Published: November 2013

Four novel HLA‐B alleles, B*42:20, B*51:151, B*57:64 and B*58:42 were identified in Brazilian individuals.
A new HLA‐C allele, C*06:99, identified by sequence‐based typing in a Korean individual
Authors: Kim S. H. , Yoon C. E. , Kwon O. J. , Cho D. , Shin M. G.
Published: November 2013

The C*06:99 allele substitutes one nucleotide of C*06:02:01:01 at codon 50 (CCG→CTG), Pro to Leu.
Extruding the Borborema Province (NE‐Brazil): a two‐stage Neoproterozoic collision process
Authors: Ganade de Araujo Carlos E. , Weinberg Roberto F. , Cordani Umberto G.
Published: November 2013

We propose that the development of the Borborema Province from 620 to 570 Ma resulted from two discrete collisional events. Collision I, along the West Gondwana Orogen on the west side of the Province, took place at c. 620–610 Ma as the result of collision between the Parnaíba Block, as the forefront of the much larger Amazonian‐West Africa Craton, and the old basement of the Borborema Province. The suture zone related to this collision was reactivated by a dextral transform zone (the Transbrasiliano Lineament), allowing the Borborema Province to approach and collide against the São Francisco Craton in the south at c. 590–580 Ma marking collision II along the Sergipano Orogen. The combined stresses related to eastward push from collision I and northward push from the cratonic indentation into a thickened lithosphere gave rise to an extensive network of strike‐slip shear zones across the Province, forcing its northeastward extrusion.
Map Width Enhancement Technique for a Turbocharger Compressor
Authors: Sivagnanasundaram Subenuka , Spence Stephen , Early Juliana
Published: November 2013

This paper presents an investigation of map width enhancement and the performance improvement of a turbocharger compressor using a series of static vanes in the annular cavity of a classical bleed slot system. The investigation has been carried out using both experimental and numerical analysis. The compressor stage used for this study is from a turbocharger unit used in heavy duty diesel engines of approximately 300 kW. Two types of vanes were designed and added to the annular cavity of the baseline classical bleed slot system. The purpose of the annular cavity vane technique is to remove some of the swirl that can be carried through the bleed slot system, which would influence the pressure ratio. In addition to this, the series of cavity vanes provides a better guidance to the slot recirculating flow before it mixes with the impeller main inlet flow. Better guidance of the flow improves the mixing at the inducer inlet in the circumferential direction. As a consequence, the stability of the compressor is improved at lower flow rates and a wider map can be achieved. The impact of two cavity vane designs on the map width and performance of the compressor was highlighted through a detailed analysis of the impeller flow field. The numerical and experimental study revealed that an effective vane design can improve the map width and pressure ratio characteristic without an efficiency penalty compared to the classical bleed slot system without vanes. The comparison study between the cavity vane and noncavity vane configurations presented in this paper showed that the map width was improved by 14.3% due to a significant reduction in surge flow and the peak pressure ratio was improved by 2.25% with the addition of a series of cavity vanes in the annular cavity of the bleed slot system.
Kinetic study on hot-wire-assisted atomic layer deposition of nickel thin films
Authors: Yuan Guangjie , Shimizu Hideharu , Momose Takeshi , Shimogaki Yukihiro
Published: November 2013

High-purity Ni films were deposited using hot-wire-assisted atomic layer deposition (HW-ALD) at deposition temperatures of 175, 250, and 350 °C. Negligible amount of nitrogen or carbon contamination was detected, even though the authors used NH2 radical as the reducing agent and nickelocene as the precursor. NH2 radicals were generated by the thermal decomposition of NH3 with the assist of HW and used to reduce the adsorbed metal growth precursors. To understand and improve the deposition process, the kinetics of HW-ALD were analyzed using a Langmuir-type model. Unlike remote-plasma-enhanced atomic layer deposition, HW-ALD does not lead to plasma-induced damage. This is a significant advantage, because the authors can supply sufficient NH2 radicals to deposit high-purity metallic films by adjusting the distance between the hot wire and the substrate. NH2 radicals have a short lifetime, and it was important to use a short distance between the radical generation site and substrate. Furthermore, the impurity content of the nickel films was independent of the deposition temperature, which is evidence of the temperature-independent nature of the NH2 radical flux and the reactivity of the NH2 radicals.
High-Speed Force Spectroscopy Unfolds Titin at the Velocity of Molecular Dynamics Simulations
Authors: Rico Felix , Gonzalez Laura , Casuso Ignacio , Puig-Vidal Manel , Scheuring Simon
Published: November 2013

Bridging the Titin Gap

The muscle protein titin is a molecular spring that has been extensively studied by single-molecule unfolding experiments and by molecular simulation. However, experimental and simulated unfolding could not be compared directly because they differ by orders of magnitude in pulling velocity.

Rico
et al.

(p
741
) developed high-speed force spectroscopy to pull titin molecules at speeds that reach the lower limits of molecular dynamics simulations. Bridging the gap between simulation and experiment clarified the mechanism of conformational changes in titin.
Cold-Atom Thermoelectrics
Authors: Heikkilä Tero T.
Published: November 2013

Two coupled reservoirs of cold atoms can be used as a model system to study the thermoelectric effect.

[Also see Report by

Brantut
et al.

]
Vertebral Aspergillosis in a Patient with Autosomal-Dominant Hyper-IgE Syndrome
Authors: Ma Hong , Kuang Lei , Lv Guohua , Wang Bing , Lian Zhesi
Published: November 2013

We present a report of an autosomal-dominant hyper-IgE syndrome patient with vertebral aspergillosis. Early diagnosis and antifungal therapy with surgery are crucial for improving the outcome of this aggressive condition.
Draft Genome Sequence ofSphingobiumsp. Strain KK22, a High-Molecular-Weight Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Isolated from Cattle Pasture Soil
Authors: Maeda Allyn H. , Nishi Shinro , Ozeki Yasuhiro , Ohta Yukari , Hatada Yuji , Kanaly Robert A.
Published: November 2013

Sphingobiumsp. strain KK22 was isolated from a bacterial consortium that originated from cattle pasture soil from Texas. Strain KK22 grows on phenanthrene and has been shown to biotransform the high-molecular-weight (HMW) polycyclic aromatic hydrocarbon (PAH) benz[a]anthracene. The genome of strain KK22 was sequenced to investigate the genes involved in aromatic pollutant biotransformation.
Draft Genome Sequence of Enterococcus raffinosus Strain CFTRI 2200, Isolated from Infant Fecal Material
Authors: Rajagopal Kammara
Published: November 2013

The complete genome sequence of
Enterococcus raffinosus
strain CFTRI 2200, isolated from the fecal material of a 7-month-old infant, is reported. The complete genome consists of 4.237 Mbp with a G+C content of 39.47% and 4,242 protein-coding genes, 54 tRNAs, and 46 rRNAs.
Characterization of Rough and Smooth Morphotypes of Mycobacterium abscessus Isolates from Clinical Specimens
Authors: Rüger Kai , Hampel Annegret , Billig Sandra , Rücker Nadine , Suerbaum Sebastian , Bange Franz-Christoph
Published: November 2013

Mycobacterium abscessus
, which consists of the two subspecies
M. abscessus
subspecies
abscessus
and
M. abscessus
subspecies
bolletii
, can produce rough or smooth colony morphologies. Here we analyzed 50
M. abscessus
isolates cultured from the respiratory specimens of 34 patients, 28 (82%) of whom had cystic fibrosis (CF), with respect to their colony morphologies and antibiotic susceptibilities. The overall proportions of occurrences of the two morphotypes were similar, with specimens from 50% of the patients showing a rough and 38% showing a smooth morphotype. A total of 12% of the specimens from the patients showed both morphotypes simultaneously. At the subspecies level, the proportions of rough and smooth morphotypes differed substantially; 88% of rough morphotypes belonged to
M. abscessus
subspecies
abscessus
, and 85% of smooth morphotypes belonged
M. abscessus
subspecies
bolletii
. Inducible clarithromycin resistance due to the Erm(41) methylase, as well as high-level resistance to clarithromycin due to mutations within the
rrl
gene, occurred independently of the morphotype. The MIC
50
s of amikacin and cefoxitin were identical for the two morphotypes, whereas the MIC
50
s of tigecycline were 0.25 μg/ml for the rough morphotype and 2.0 μg/ml for the smooth morphotype. Our results show that the smooth morphotype was more dominant in respiratory specimens from CF patients than previously thought. With respect to resistance, colony morphology did not affect the susceptibility of
Mycobacterium abscessus
to the first-line antibiotics clarithromycin, amikacin, and cefoxitin.
Comparison of Human Papillomavirus Detections in Urine, Vulvar, and Cervical Samples from Women Attending a Colposcopy Clinic
Authors: Sahasrabuddhe Vikrant V. , Gravitt Patti E. , Dunn S. Terence , Brown David , Allen Richard A. , Eby Yolanda J. , Smith Katie , Zuna Rosemary E. , Zhang Roy R. , Gold Michael A. , Schiffman Mark , Walker Joan L. , Castle Philip E. , Wentzensen Nicolas
Published: November 2013

While urine-based sampling for human papillomavirus (HPV) is being explored as a simple and noninvasive approach for cervical cancer screening, data comparing HPV genotyping in urine and those in cellular sampling of the cervix and vulva, and their correlation with rigorously confirmed cervical disease status, are sparse. We performed HPV genotyping on voided-urine and clinician-collected vulvar and cervical samples from 72 women undergoing colposcopy. Although urine-based HPV carcinogenic HPV detection was lower (58.3%) than cervical (73.6%) and vulvar (72.1%) detection (
P
= 0.05 and 0.07, respectively), the agreement of urine HPV with cervical and vulvar HPV was moderate (kappa = 0.55) and substantial (kappa = 0.62), respectively. Urine-based carcinogenic HPV detection had a clinical sensitivity of 80.8% (95% confidence interval [CI] = 60.7 to 93.5) and a specificity of 53.3% (95% CI = 37.9 to 68.3) for diagnosing cervical intraepithelial neoplasia grades 2/3 (CIN2/3) on histology; 90.0% of CIN3 was positive for urine HPV. The corresponding sensitivity and specificity values for vulvar sampling were 92% (95% CI = 74 to 99) and 40.5% (95% CI = 25.6 to 56.7), and those for cervical sampling were 96.2% (95% CI = 80.4 to 99.9) and 40% (95% CI = 25.7 to 55.7), respectively. HPV16 was the most common carcinogenic genotype detectable in 25% of urine, 33.8% of vulvar, and 31.9% of cervical samples overall, with prevalence increasing with cervical disease grade, regardless of the sampling method. Stronger cervical HPV PCR signal strengths were associated with increased frequency of urine HPV detection. In summary, the relatively lower detection rates but comparable clinical performance of urine-based HPV sampling underscore the need for larger studies to evaluate urine-based sampling for cervical cancer screening, epidemiologic studies, and postvaccination HPV disease surveillance.
Rapid Detection of Staphylococcus aureus Strains with Reduced Susceptibility to Vancomycin by Isothermal Microcalorimetry
Authors: Entenza J. M. , Bétrisey B. , Manuel O. , Giddey M. , Sakwinska O. , Laurent F. , Bizzini A.
Published: November 2013

Methicillin-resistant
Staphylococcus aureus
(MRSA) usually harbors a vancomycin-susceptible phenotype (VSSA) but can exhibit reduced vancomycin susceptibility phenotypes that can be heterogeneous-intermediate (hVISA), intermediate (VISA), or fully resistant (VRSA). Current detection techniques (e.g., Etest and population analysis profiles [PAPs]) are slow and time-consuming. We investigated the potential of microcalorimetry to detect reduced susceptibilities to vancomycin in MRSA strains. Representative MSSA, VSSA, hVISA, VISA, and VRSA reference strains, as well as clinical isolates, were used. PAPs were performed by standard methods. Microcalorimetry was performed by inoculating 5 × 10
7
CFU of overnight cultures into 3-ml vials of brain heart infusion broth supplemented with increasing concentrations of vancomycin, and growth-related heat production was measured at 37°C. For the reference strains, no heat production was detected in the VSSA isolates at vancomycin concentrations of >3 μg/ml during the 72 h of incubation. The hVISA and VISA strains showed heat production with concentration-proportional delays of up to 6 μg/ml in 48 h and up to 12 μg/ml in 72 h, respectively. The VRSA strain showed heat production at concentrations up to 16 μg/ml in 12 h. The testing of clinical strains indicated an excellent negative predictive value, allowing us to rule out a decreased vancomycin susceptibility phenotype in <8 h of incubation. Sequential isolates from a patient undergoing vancomycin therapy showed evolving microcalorimetric profiles up to a VISA phenotype. Microcalorimetry was able to detect strains with reduced susceptibilities to vancomycin in <8 h. The measurement of bacterial heat production might represent a simple and rapid method for the detection of reduced susceptibilities to vancomycin in MRSA strains.
Virological Diagnosis of Central Nervous System Infections by Use of PCR Coupled with Mass Spectrometry Analysis of Cerebrospinal Fluid Samples
Authors: Lévêque Nicolas , Legoff Jérôme , Mengelle Catherine , Mercier-Delarue Séverine , N'guyen Yohan , Renois Fanny , Tissier Fabien , Simon François , Izopet Jacques , Andréoletti Laurent
Published: November 2013

Viruses are the leading cause of central nervous system (CNS) infections, ahead of bacteria, parasites, and fungal agents. A rapid and comprehensive virologic diagnostic testing method is needed to improve the therapeutic management of hospitalized pediatric or adult patients. In this study, we assessed the clinical performance of PCR amplification coupled with electrospray ionization-time of flight mass spectrometry analysis (PCR-MS) for the diagnosis of viral CNS infections. Three hundred twenty-seven cerebrospinal fluid (CSF) samples prospectively tested by routine PCR assays between 2004 and 2012 in two university hospital centers (Toulouse and Reims, France) were retrospectively analyzed by PCR-MS analysis using primers targeted to adenovirus, human herpesviruses 1 to 8 (HHV-1 to -8), polyomaviruses BK and JC, parvovirus B19, and enteroviruses (EV). PCR-MS detected single or multiple virus infections in 190 (83%) of the 229 samples that tested positive by routine PCR analysis and in 10 (10.2%) of the 98 samples that tested negative. The PCR-MS results correlated well with herpes simplex virus 1 (HSV-1), varicella-zoster virus (VZV), and EV detection by routine PCR assays (kappa values [95% confidence intervals], 0.80 [0.69 to 0.92], 0.85 [0.71 to 0.98], and 0.84 [0.78 to 0.90], respectively), whereas a weak correlation was observed with Epstein-Barr virus (EBV) (0.34 [0.10 to 0.58]). Twenty-six coinfections and 16 instances of uncommon neurotropic viruses (HHV-7 [
n
= 13], parvovirus B19 [
n
= 2], and adenovirus [
n
= 1]) were identified by the PCR-MS analysis, whereas only 4 coinfections had been prospectively evidenced using routine PCR assays (
P
< 0.01). In conclusion, our results demonstrated that PCR-MS analysis is a valuable tool to identify common neurotropic viruses in CSF (with, however, limitations that were identified regarding EBV and EV detection) and may be of major interest in better understanding the clinical impact of multiple or neglected viral neurological infections.
Comparison of Commercial Hybridization and Automated Transcription-Mediated Amplification Modalities for Detection of High-Risk Human Papillomavirus Nucleic Acid
Authors: Munson Erik , Kroeger Lynn , Balzer Sandra , Amrhein Robert , Munson Kimber L. , Napierala Maureen , Hudspeth Richard , Dillon Patrick J.
Published: November 2013

Assessment of 4,056 cytology collections by Cervista HPV HR and APTIMA HPV yielded 88.7% concordance, with increased detection by Cervista in patients with atypical squamous cells of undetermined significance (ASC-US) and patients negative for intraepithelial lesions and malignancy (NILM) (
P
≤ 0.02). Both assays detected ≥91.7% of cervical intraepithelial neoplasia grade 2+ (CIN2+) lesions. A total of 262 specimens demonstrated luminescence within all three Cervista oligonucleotide mixtures (triple positive). APTIMA HPV and PCR-based microarray confirmed triple-positive results at rates of 7.3% and 5.9%, respectively.
New Small Molecule Entry Inhibitors Targeting Hemagglutinin-Mediated Influenza A Virus Fusion
Authors: Basu Arnab , Antanasijevic Aleksandar , Wang Minxiu , Li Bing , Mills Debra M. , Ames Jessica A. , Nash Peter J. , Williams John D. , Peet Norton P. , Moir Donald T. , Prichard Mark N. , Keith Kathy A. , Barnard Dale L. , Caffrey Michael , Rong Lijun , Bowlin Terry L.
Published: November 2013

Influenza viruses are a major public health threat worldwide, and options for antiviral therapy are limited by the emergence of drug-resistant virus strains. The influenza virus glycoprotein hemagglutinin (HA) plays critical roles in the early stage of virus infection, including receptor binding and membrane fusion, making it a potential target for the development of anti-influenza drugs. Using pseudotype virus-based high-throughput screens, we have identified several new small molecules capable of inhibiting influenza virus entry. We prioritized two novel inhibitors, MBX2329 and MBX2546, with aminoalkyl phenol ether and sulfonamide scaffolds, respectively, that specifically inhibit HA-mediated viral entry. The two compounds (i) are potent (50% inhibitory concentration [IC50] of 0.3 to 5.9 μM); (ii) are selective (50% cytotoxicity concentration [CC50] of >100 μM), with selectivity index (SI) values of >20 to 200 for different influenza virus strains; (iii) inhibit a wide spectrum of influenza A viruses, which includes the 2009 pandemic influenza virus A/H1N1/2009, highly pathogenic avian influenza (HPAI) virus A/H5N1, and oseltamivir-resistant A/H1N1 strains; (iv) exhibit large volumes of synergy with oseltamivir (36 and 331 μM2% at 95% confidence); and (v) have chemically tractable structures. Mechanism-of-action studies suggest that both MBX2329 and MBX2546 bind to HA in a nonoverlapping manner. Additional results from HA-mediated hemolysis of chicken red blood cells (cRBCs), competition assays with monoclonal antibody (MAb) C179, and mutational analysis suggest that the compounds bind in the stem region of the HA trimer and inhibit HA-mediated fusion. Therefore, MBX2329 and MBX2546 represent new starting points for chemical optimization and have the potential to provide valuable future therapeutic options and research tools to study the HA-mediated entry process.
Newly Identified Minor Phosphorylation Site Threonine-279 of Measles Virus Nucleoprotein Is a Prerequisite for Nucleocapsid Formation
Authors: Sugai Akihiro , Sato Hiroki , Hagiwara Kyoji , Kozuka-Hata Hiroko , Oyama Masaaki , Yoneda Misako , Kai Chieko
Published: November 2013

Measles virus nucleoprotein is the most abundant viral protein and tightly encapsidates viral genomic RNA to support viral transcription and replication. Major phosphorylation sites of nucleoprotein include the serine residues at locations 479 and 510. Minor phosphorylation residues have yet to be identified, and their functions are poorly understood. In our present study, we identified nine putative phosphorylation sites by mass spectrometry and demonstrated that threonine residue 279 (T279) is functionally significant. Minigenome expression assays revealed that a mutation at the T279 site caused a loss of activity. Limited proteolysis and electron microscopy suggested that a T279A mutant lacked the ability to encapsidate viral RNA but was not denatured. Furthermore, dephosphorylation of the T279 site by alkaline phosphatase treatment caused deficiencies in nucleocapsid formation. Taken together, these results indicate that phosphorylation at T279 is a prerequisite for successful nucleocapsid formation.
Hepatitis E Virus Genotype 1 Infection of Swine Kidney Cells
In Vitro
Is Inhibited at Multiple Levels
Authors: Nguyen H. T. , Shukla P. , Torian U. , Faulk K. , Emerson S. U.
Published: November 2013

Genotype 1 hepatitis E viruses (HEVs) are restricted to primate hosts, whereas genotype 3 HEVs predominantly infect swine, in addition to primates. In order to identify possible determinants of the host range, infectious recombinant viruses and chimeras of a genotype 1 isolate and a genotype 3 isolate were compared for their ability to infect versus transfect cultured human HepG2/C3A cells and swine LLC-PK cells. The patterns of luciferase expression from virus replicons containing the
Gaussia
luciferase gene in place of the viral ORF2 or ORF3 genes demonstrated that translation of the ORF2 capsid gene of genotype 1 virus is severely inhibited in swine kidney cells compared to its translation in rhesus macaque kidney or human liver cells. Therefore, this virus may produce insufficient capsid protein for optimal assembly in swine cells. Infectivity assays with a virus containing a chimeric capsid protein confirmed that amino acids 456 to 605 of the virus capsid protein comprised the virus receptor-binding region and suggested that genotype 1 viruses may be prevented from infecting swine because genotype 1 viruses are unable to enter swine cells. Rhesus macaque cells appeared to be better than human cells for growing the genotype 1 virus. These cell and virus combinations may serve as a useful
in vitro
model with which to study determinants of the natural host range of this virus.
Differential Role for Host Translation Factors in Host and Viral Protein Synthesis during Human Cytomegalovirus Infection
Authors: Lenarcic Erik M. , Ziehr Ben , De Leon Gabe , Mitchell Duane , Moorman Nathaniel J.
Published: November 2013

The host eIF4F translation initiation complex plays a critical role the translation of capped mRNAs. Although human cytomegalovirus (HCMV) infection increases the abundance and activity of the host eIF4F complex, the requirement for eIF4F components in HCMV replication and mRNA translation has not been directly tested. In this study, we found that decreasing the abundance or activity of eIF4F from the start of infection inhibits HCMV replication. However, as infection progresses, viral mRNA translation and replication becomes increasingly resistant to eIF4F inhibition. During the late stage of infection the association of representative immediate-early, early, and late mRNAs with polysomes was not affected by eIF4F disruption. In contrast, eIF4F inhibition decreased the translation of representative host eIF4F-dependent mRNAs during the late stage of infection. A global analysis of the translation efficiency of HCMV mRNAs during the late stage of infection found that eIF4F disruption had a minimal impact on the association of HCMV mRNAs with polysomes but significantly diminished the translation efficiency of eIF4F-dependent host transcripts. Together, our data show that the translation of host eIF4F-dependent mRNAs remains dependent on eIF4F activity during HCMV infection. However, during the late stage of infection the translation efficiency of viral mRNAs does not correlate with the abundance or activity of the host eIF4F complex.
Neisseria gonorrhoeae Filamentous Phage NgoΦ6 Is Capable of Infecting a Variety of Gram-Negative Bacteria
Authors: Piekarowicz Andrzej , Kłyż Aneta , Majchrzak Michał , Szczêsna Ewa , Piechucki Marcin , Kwiatek Agnieszka , Maugel Timothy K. , Stein Daniel C.
Published: November 2013

We constructed a phagemid consisting of the whole genome of the
Neisseria gonorrhoeae
bacteriophage NgoΦ6 cloned into a pBluescript plasmid derivative lacking the
f1
origin of replication (named pBS::Φ6).
Escherichia coli
cells harboring pBS::Φ6 were able to produce a biologically active phagemid, NgoΦ6fm, capable of infecting, integrating its DNA into the chromosome of, and producing progeny phagemids in, a variety of taxonomically distant Gram-negative bacteria, including
E. coli
,
Haemophilus influenzae
,
Neisseria sicca
,
Pseudomonas
sp., and
Paracoccus methylutens
. A derivative of pBS::Φ6 lacking the phage
orf7
gene, a positional homolog of filamentous phage proteins that mediate the interaction between the phage and the bacterial pilus, was capable of producing phagemid particles that were able to infect
E. coli
,
Haemophilus influenzae
,
N. sicca
,
Pseudomonas
sp., and
Paracoccus methylutens
, indicating that NgoΦ6 infects cells of these species using a mechanism that does not involve the Orf7 gene product and that NgoΦ6 initiates infection through a novel process in these species. We further demonstrate that the establishment of the lysogenic state does not require an active phage integrase. Since phagemid particles were capable of infecting diverse hosts, this indicates that NgoΦ6 is the first broad-host-range filamentous bacteriophage described.
Infection of Pericytes
In Vitro
by Japanese Encephalitis Virus Disrupts the Integrity of the Endothelial Barrier
Authors: Chen Chun-Jung , Ou Yen-Chuan , Li Jian-Ri , Chang Cheng-Yi , Pan Hung-Chuan , Lai Ching-Yi , Liao Su-Lan , Raung Shue-Ling , Chang Chen-Jung
Published: November 2013

Though the compromised blood-brain barrier (BBB) is a pathological hallmark of Japanese encephalitis-associated neurological sequelae, the underlying mechanisms and the specific cell types involved are not understood. BBB characteristics are induced and maintained by cross talk between brain microvascular endothelial cells and neighboring elements of the neurovascular unit. In this study, we show a potential mechanism of disruption of endothelial barrier integrity during the course of Japanese encephalitis virus (JEV) infection through the activation of neighboring pericytes. We found that cultured brain pericytes were susceptible to JEV infection but were without signs of remarkable cytotoxicity. JEV-infected pericytes were found to release biologically active molecules which activated ubiquitin proteasome, degraded zonula occludens-1 (ZO-1), and disrupted endothelial barrier integrity in cultured brain microvascular endothelial cells. Infection of pericytes with JEV was found to elicit elevated production of interleukin-6 (IL-6), which contributed to the aforementioned endothelial changes. We further demonstrated that ubiquitin-protein ligase E3 component
n
-recognin-1 (Ubr 1) was a key upstream regulator which caused proteasomal degradation of ZO-1 downstream of IL-6 signaling. During JEV central nervous system trafficking, endothelial cells rather than pericytes are directly exposed to cell-free viruses in the peripheral bloodstream. Therefore, the results of this study suggest that subsequent to primary infection of endothelial cells, JEV infection of pericytes might contribute to the initiation and/or augmentation of Japanese encephalitis-associated BBB breakdown in concerted action with other unidentified barrier disrupting factors.
Corticosteroid and platelet-rich plasma injection therapy in tennis elbow (lateral epicondylalgia): a survey of current UK specialist practice and a call for clinical guidelines
Authors: Titchener Andrew G , Booker Simon J , Bhamber Nivraj S , Tambe Amol A , Clark David I
Published: November 2013

Background

Tennis elbow is a common condition with a variety of treatment options, but little is known about which of these options specialists choose most commonly. Corticosteroid injections in tennis elbow may reduce pain in the short-term but delay long-term recovery. We have undertaken a UK-wide survey of upper limb specialists to assess current practice.

Methods

Cross-sectional electronic survey of current members of the British Elbow and Shoulder Society (BESS) and the British Society for Surgery of the Hand (BSSH).

Results

271 of 1047 eligible members responded (25.9%); consultant surgeons constituted the largest group (232/271, 85%). 131 respondents (48%) use corticosteroid injections as their first-line treatment for tennis elbow. 206 respondents (77%) believed that corticosteroid injections are not potentially harmful in the treatment of tennis elbow, while 31 (11%) did not use them in their current practice. In light of recent evidence of the potential harmful effects of corticosteroid therapy, 136 (50%) had not changed their practice while 108 (40.1%) had reduced or discontinued their use. 43 respondents (16%) reported having used platelet-rich plasma injections.

Conclusions

Recent high-quality evidence that corticosteroids may delay recovery in tennis elbow appears to have had a limited effect on current practice. Treatment is not uniform among specialists and a proportion of them use platelet-rich plasma injections.
Factors associated with vitamin D deficiency in a Norwegian population: the HUNT Study
Authors: Larose Tricia L , Chen Yue , Camargo Carlos A , Langhammer Arnulf , Romundstad Pål , Mai Xiao-Mei
Published: November 2013

Vitamin D deficiency occurs worldwide. Winter season and high Body Mass Index (BMI) are associated with low levels of serum 25-hydroxyvitamin D (25(OH)D). We estimated the prevalence of vitamin D deficiency in a Norwegian adult population and examined factors associated with vitamin D deficiency. A cohort of 25 616 adults (19–55 years) who participated in both the second and third Nord-Trøndelag Health Study (HUNT 2 (1995–1997) and HUNT 3 (2006–2008)) was established in a previous study. A 10% random sample of the cohort population was recruited for serum 25(OH)D measurements (n=2584), which was used for the current cross-sectional study. Vitamin D deficiency was defined as serum 25(OH)D level <50 nmol/L. The overall prevalence of vitamin D deficiency was 40%, but varied by season (winter: 64%; summer: 20%). Winter season (adjusted prevalence ratio (PR): 3.16, 95% CI 2.42 to 4.12) and obesity (BMI ≥30.0 kg/m2) (PR: 1.74, 95% CI 1.45 to 2.10) were strongly associated with prevalent vitamin D deficiency. Current smoking also demonstrated an increased PR (1.41, 95% CI 1.21 to 1.65). Daily intake of cod liver oil (PR: 0.60, 95% CI 0.41 to 0.77), increased physical activity (PR: 0.80, 95% CI 0.68 to 0.95) and more frequent alcohol consumption (PR: 0.76, 95% CI 0.60 to 0.95) were associated with a reduced PR. The prevalence of vitamin D deficiency was high in Norwegian adults. Winter season, high BMI and current smoking were positively associated, and intake of cod liver oil, increased physical activity and more frequent alcohol consumption were inversely associated with vitamin D deficiency.
Clinical governance development: learning from the New Zealand experience
Authors: Gauld Robin
Published: November 2013

The development of clinical governance in New Zealand has been pivotal to the country’s health policy since 2009. Some of the key findings from one component of a national assessment project, which involved interviews with health professionals and managers at 19 of the country’s 20 district health boards, are reviewed here. Key lessons for clinical governance are that: clinical governance needs to be clearly defined; it requires robust management–clinical partnerships along with a multi-layered developmental strategy and investment in training; and it also requires organisational arrangements such as a clinical board. The New Zealand emphasis on clinical governance has been positive for health professionals but, at this stage, it is not possible to assess its broader impact.
Forensic cases of bruises in pigs
Authors: Barington K. , Jensen H. E.
Published: November 2013

Bruises in pigs inflicted by blunt trauma are a significant animal welfare problem, and affected skin and underlying muscle are regularly submitted for forensic investigation. Central to the evaluation is an assessment of the age of the bruises. This paper presents cases of bruises in pigs sent for forensic investigation that were collected retrospectively. Data comprised photographs of the gross lesions, slides for histology, and written reports. The time from collecting the animals at the farms and delivery to the slaughterhouse was recorded together with the time of slaughter. Since 2005 there has been an increase in cases, with a peak in 2008 and 2009 of 40 cases for each year. At gross examination, the pattern of bruises often reflected the type of object which caused them. Histologically, haemorrhage and cellular infiltrations were frequently present. Currently, the age of bruises may be estimated to be more or less than four hours based on a porcine bruise model. In bruises more than four hours old, estimations of two‐hour intervals are used based on studies of wound healing. The time from collecting the pigs at the farms until slaughter was between one and four hours in 44.1 per cent of cases, during which time the pigs had been handled by several people. In addition, in 22.0 per cent of cases of bruising an inflammatory response was absent, making it impossible to estimate the age of the bruise.
Synthesis and catalytic properties of trans-A2B2-type metalloporphyrins in cyclohexane oxidation
Authors: Xie Yujia , Zhang Fengyong , Liu Pingle , Hao Fang , Luo He’an
Published: November 2013

A new efficient and mild protocol for synthesizing a series of trans-A2B2-porphyrins through a TFA-catalyzed condensation reaction between various aldehydes and dipyrromethanes has been developed. Several trans-A2B2-metalloporphyrins (cobalt, nickel) were synthesized and used to catalyze cyclohexane oxidation C–H bonds with dioxygen in the absence of additives and solvents. The results show that the catalytic activities were relative to the nature of the substituted groups and the central metal ions of trans-A2B2-metalloporphyrin. Cobalt metalloporphyrin presents better catalytic performance in the conversion of cyclohexane than the nickel metalloporphyrin under the same reaction conditions.
Random DNA libraries from three species of the stick insect genus Bacillus (Insecta: Phasmida): repetitive DNA characterization and first observation of polyneopteran MITEs
Authors: Ricci Marco , Luchetti Andrea , Bonandin Livia , Mantovani Barbara
Published: November 2013

The repetitive DNA content of the stick insect species Bacillus rossius (facultative parthenogenetic), Bacillus grandii (gonochoric), and Bacillus atticus (obligate parthenogenetic) was analyzed through the survey of random genomic libraries roughly corresponding to 0.006% of the genome. By repeat masking, 19 families of transposable elements were identified (two LTR and six non-LTR retrotransposons; 11 DNA transposons). Moreover, a de novo analysis revealed, among the three libraries, the first MITE family observed in polyneopteran genomes. On the whole, transposable element abundance represented 23.3% of the genome in B. rossius, 22.9% in B. atticus, and 18% in B. grandii. Tandem repeat content in the three libraries is much lower: 1.32%, 0.64%, and 1.86% in B. rossius, B. grandii, and B. atticus, respectively. Microsatellites are the most abundant in all species. Minisatellites were only found in B. rossius and B. atticus, and five monomers belonging to the Bag320 satellite family were detected in B. atticus. Assuming the survey provides adequate representation of the relative genome, the obligate parthenogenetic species (B. atticus), compared with the other two species analyzed, does not show a lower transposable element content, as expected from some theoretical and empirical studies.
TRIGONOMETRIC sℓ(2) GAUDIN MODEL WITH BOUNDARY TERMS
Authors: CIRILO ANTÓNIO N. , MANOJLOVIĆ N. , NAGY Z.
Published: November 2013

We review the derivation of the Gaudin model with integrable boundaries. Starting from the non-symmetric R-matrix of the inhomogeneous spin-½ XXZ chain and generic solutions of the reflection equation and the dual reflection equation, the corresponding Gaudin Hamiltonians with boundary terms are calculated. An alternative derivation based on the so-called classical reflection equation is discussed.
PRESSURE OF DEGENERATE AND RELATIVISTIC ELECTRONS IN A SUPERHIGH MAGNETIC FIELD
Authors: GAO ZHI FU , WANG NA , PENG QIU HE , LI XIANG DONG , DU YUAN JIE
Published: November 2013

Based on our previous work, we deduce a general formula for pressure of degenerate and relativistic electrons, Pe, which is suitable for superhigh magnetic fields, discuss the quantization of Landau levels of electrons, and consider the quantum electrodynamic (QED) effects on the equations of states (EOSs) for different matter systems. The main conclusions are as follows: Pe is related to the magnetic field B, matter density ρ, and electron fraction Ye; the stronger the magnetic field, the higher the electron pressure becomes; the high electron pressure could be caused by high Fermi energy of electrons in a superhigh magnetic field; compared with a common radio pulsar, a magnetar could be a more compact oblate spheroid-like deformed neutron star (NS) due to the anisotropic total pressure; and an increase in the maximum mass of a magnetar is expected because of the positive contribution of the magnetic field energy to the EOS of the star.
WHY X(3915) IS SO NARROW AS A χc0(2P) STATE?
Authors: JIANG YUE , WANG GUO-LI , WANG TIANHONG , JU WAN-LI
Published: November 2013

New resonance X(3915) was identified as the charmonium χc0(2P) by BaBar Collaboration, but there still seems an open question of this assignment: why its full width is so narrow? To answer this question, we calculate the Okubo–Zweig–Iizuka (OZI)-allowed strong decays [Formula: see text], where X(3915) is assigned as a χc0(2P) state, and estimate its full width in the cooperating framework of 3P0 model and the Bethe–Salpeter (BS) method using the Mandelstam formalism, during which nonperturbative quantum chromodynamics (QCD) effects of the hadronic matrix elements are well-considered by overlapping integral over the relativistic Salpeter wave functions of the initial and final states. We find the node structure of χc0(2P) wave function resulting in the narrow width of X(3915) and show the dependence of the decay width on the variation of the initial mass of X(3915). We point out that the rate of [Formula: see text] is crucial to confirm whether X(3915) is the χc0(2P) state or not.
INTRINSIC RESONANT TUNNELING PROPERTIES OF THE ONE-DIMENSIONAL SCHRÖDINGER OPERATOR WITH A DELTA DERIVATIVE POTENTIAL
Authors: ZOLOTARYUK A. V. , ZOLOTARYUK Y.
Published: November 2013

Restricting ourselves to a simple rectangular approximation but using properly a two-scale regularization procedure, additional resonant tunneling properties of the one-dimensional Schrödinger operator with a delta derivative potential are established, which appear to be lost in the zero-range limit. These "intrinsic" properties are complementary to the main already proved result that different regularizations of Dirac's delta function produce different limiting self-adjoint operators. In particular, for a given regularizing sequence, a one-parameter family of connection condition matrices describing bound states is constructed. It is proposed to consider the convergence of transfer matrices when the potential strength constant is involved into the regularization process, resulting in an extension of resonance sets for the transmission across a δ′-barrier.