bluuebunny/crossref_metadata_2025 huggingface dataset:
Trees to treehoppers: genetic variation in host plants contributes to variation in the mating signals of a plant‐feeding insect
Authors: Rebar Darren , Rodríguez Rafael L.
Published: December 2013

Community genetics research has demonstrated ‘bottom‐up’ effects of genetic variation within a plant species in shaping the larger community with which it interacts, such as compositions of arthropod faunas. We demonstrate that such cross‐trophic interactions also influence sexually selected traits. We used a member of the Enchenopa binotata species complex of treehoppers (Hemiptera: Membracidae) to ask whether male mating signals are influenced by host plant genetic variation. We reared a random sample of the treehoppers on potted replicates of a sample of host plant clone lines. We found that treehopper male signals varied according to the clone line on which they developed, showing that genetic variation in host plants affects male treehoppers' behavioural phenotypes. This is the first demonstration of cross‐trophic indirect genetic effects on a sexually selected trait. We discuss how such effects may play an important role in the maintenance of variation and within‐population phenotypic differentiation, thereby promoting evolutionary divergence.
Antagonistic interaction networks are structured independently of latitude and host guild
Authors: Morris Rebecca J. , Gripenberg Sofia , Lewis Owen T. , Roslin Tomas
Published: December 2013

An increase in species richness with decreasing latitude is a prominent pattern in nature. However, it remains unclear whether there are corresponding latitudinal gradients in the properties of ecological interaction networks. We investigated the structure of 216 quantitative antagonistic networks comprising insect hosts and their parasitoids, drawn from 28 studies from the High Arctic to the tropics. Key metrics of network structure were strongly affected by the size of the interaction matrix (i.e. the total number of interactions documented between individuals) and by the taxonomic diversity of the host taxa involved. After controlling for these sampling effects, quantitative networks showed no consistent structural patterns across latitude and host guilds, suggesting that there may be basic rules for how sets of antagonists interact with resource species. Furthermore, the strong association between network size and structure implies that many apparent spatial and temporal variations in network structure may prove to be artefacts.
Outcome of fulminant bacterial meningitis in adult patients
Authors: Muralidharan R. , Mateen F. J. , Rabinstein A. A.
Published: December 2013

Background and purpose

The objective of our study was to identify neurological factors associated with poor outcome in adult patients with fulminant bacterial meningitis.

Methods

This was a retrospective review of consecutive adult patients with fulminant bacterial meningitis, defined as meningitis causing coma within 24–48 h of hospitalization, at Mayo Clinic Rochester between January 2000 and November 2010. Functional status was assessed at discharge and upon last follow‐up using the modified Rankin scale (mRS). The primary end‐point was death or new major disability (increase of >2 on the mRS) at last follow‐up.

Results

Thirty‐nine patients were identified. Encephalopathy (44%), coma (28%), focal seizures (3%) or a combination of these (26%) were present on admission. The most common pathogen was Streptococcus pneumoniae (57%). All patients were treated with broad spectrum antibiotics and 51% received steroids. Serious systemic complications were seen in 23 patients. Sixteen patients (41%) died during hospitalization. Median mRS at hospital discharge for surviving patients was 3; four patients had new major disability with a mean follow‐up of 11 months. Predictors of death or new major disability included lower Glasgow Coma Scale score at nadir [P = 0.002; age‐ and sex‐adjusted odds ratio (OR) 0.46, 95% confidence interval (CI) 0.28–0.48], longer duration of symptoms before hospitalization (P = 0.045; adjusted OR 2.34, 95% CI 1.02–5.37), abnormal head imaging at presentation (P = 0.008; adjusted OR 9.40, 95% CI 1.78−49.6) and use of intracranial pressure monitoring (P = 0.010, adjusted OR 51.0, 95% CI 2.51−1036).

Conclusion

Many adult patients who survive hospitalization are able to regain their pre‐morbid level of function. Aggressive management of bacterial meningitis is justified even in comatose adult patients.
The effects of a mineral trioxide aggregate‐based sealer on the production of reactive oxygen species, nitrogen species and cytokines by two macrophage subtypes
Authors: Braga J. M. , Oliveira R. R. , Martins R. C. , Ribeiro Sobrinho A. P.
Published: December 2013

Aim

To test the effects of a mineral trioxide aggregate‐based sealer (MTA Fillapex®) and MTA (MTA‐Ângelus®) on viability and on the production of cytokines, reactive oxygen species (ROS) and nitrogen species (NO) by M1 and M2 inflammatory macrophages.

Methodology

M1 (from C57BL/6 mice) and M2 (from BALB/c mice) peritoneal inflammatory macrophages were obtained and cultured in vitro in the presence of original and diluted extracts of MTA and MTA Fillapex (FLPX). The cell viability, ROS release and the release of tumour necrosis factor‐a, interleukin (IL)‐12, IL‐10 and NO in response to stimulation with interferon‐γ and Fusobacterium nucleatum or Peptostreptococcus anaerobius were evaluated. The data were analysed using the Mann–Whitney test and Student's t‐test.

Results

Fillapex was cytotoxic at the highest concentrations (1 : 1;1 : 2) and decreased the viability (P < 0.05) of both macrophage types (<20%). MTA did not interfere with cellular viability. FLPX inhibited the release of ROS and decreased NO release in F. nucleatum and P. anaerobius ‐stimulated M1 and M2 macrophages (≤25 μ mol L–1). F. nucleatum–stimulated M2 macrophage cultures released lower levels of TNF‐α when FLPX was added (≤1 ng mL−1). M2 macrophages released higher (>5 ng mL−1) levels of IL‐10 than M1 macrophages. Only M1 macrophage cultures produced IL‐12p70.

Conclusions

Fillapex impaired effector immune responses during inflammation (M1 macrophages), as well as during healing (M2 macrophages) responses.
Clinical accuracy of two electronic apex locators in teeth with large periapical lesions
Authors: Çalışkan M. K. , Kaval M. E. , Tekin U.
Published: December 2013

Aim

To evaluate in vivo the accuracy of two electronic apex locators (EALs) in determining the position of the apical foramen of teeth with large periapical lesions and persistent intracanal exudate.

Methodology

Thirty‐three maxillary anterior teeth assigned for periapical surgery were selected. Following the preparation of standard endodontic access cavities, electronic working lengths were determined using the ProPex and Apex Pointer apex locators. During endodontic surgery, the actual root canal length of each tooth was measured by positioning a K‐file at the most coronal border of the major foramen. Root canal treatments combined with apical surgery were then completed. Data were analysed with paired t‐tests.

Results

ProPex and Apex Pointer were accurate (within ± 0.5 mm) 97% and 94% of the time. No significant differences were detected between the apex locators (P = 0.325).

Conclusions

Despite the presence of exudate in the root canals, the position of the major foramen in teeth with large periapical lesions can be determined with high level of precision either by ProPex or Apex Pointer. Both EALs can be used safely in working length determination of teeth with large periapical lesions, which have persistent intracanal exudate.
Estimating the Annual Number of Strokes and the Issue of Imperfect Data: An Example from Australia
Authors: Cadilhac Dominique A. , Vos Theo , Thrift Amanda G.
Published: December 2013

Background

Estimates of strokes in Australia are typically obtained using 1996–1997 age-specific attack rates from the pilot North East Melbourne Stroke Incidence (NEMESIS) Study (eight postcode regions). Declining hospitalizations for stroke indicate the potential to overestimate cases.

Aims

To illustrate how current methods may potentially overestimate the number of strokes in Australia.

Methods

Hospital separations data (primary discharge ICD10 codes I60 to I64) and three stroke projection models were compared. Each model had age- and gender-specific attack rates from the NEMESIS study applied to the 2003 population. One model used the 2003 Burden of Disease approach where the ratio of the 1996–1997 NEMESIS study incidence to hospital separation rate in the same year was adjusted by the 2002/2003 hospital separation rate within the same geographic region using relevant ICD-primary diagnosis codes. Hospital separations data were inflated by 12.1% to account for nonhospitalized stroke, while the Burden of Disease model was inflated by 27.6% to account for recurrent stroke events in that year. The third model used 1997–1999 attack rates from the larger 22-postcode NEMESIS study region.

Results

In 2003, Australian hospitalizations for stroke (I60 to I64) were 33 022, and extrapolation to all stroke (hospitalized and nonhospitalized) was 37 568. Applying NEMESIS study attack rates to the 2003 Australian population, 50 731 strokes were projected. Fewer cases for 2003 were estimated with the Burden of Disease model (28 364) and 22-postcode NEMESIS study rates (41 332).

Conclusions

Estimating the number of strokes in a country can be highly variable depending on the recency of data, the type of data available, and the methods used.
Critical stoichiometric ratio of CD4+ CD25+ FoxP3+ regulatory T cells and CD4+ CD25− responder T cells influence immunosuppression in patients with B‐cell acute lymphoblastic leukaemia
Authors: Bhattacharya Kaushik , Chandra Sarmila , Mandal Chitra
Published: December 2013

Regulatory T (Treg) cells act to suppress activation of the immune system and thereby maintain immunological homeostasis and tolerance to self‐antigens. The frequency and suppressing activity of Treg cells in general are high in different malignancies. We wanted to identify the role and regulation of CD4+ CD25+ FoxP3+ Treg cells in B‐cell acute lymphoblastic leukaemia (B‐ALL). We have included patients at diagnosis (n = 54), patients in clinical remission (n = 32) and normal healthy individuals (n = 35). These diagnosed patients demonstrated a lower number of CD4+ CD25+ cells co‐expressing a higher level of FoxP3, interleukin‐10, transforming growth factor‐β and CD152/CTLA‐4 than the normal population. Treg cells from patients showed a higher suppressive capability on CD4+ CD25− responder T (Tresp) cells than normal. The frequency and immunosuppressive potential of CD4+ CD25+ FoxP3+ Treg cells became high with the progression of malignancy in B‐ALL. Relative distribution of Tresp and Treg cells was only ~5 : 1 in B‐ALL but ~35 : 1 in normal healthy individuals, further confirming the elevated immunosuppression in patients. A co‐culture study at these definite ex vivo ratios, indicated that Treg cells from B‐ALL patients exhibited higher immunosuppression than Treg cells from normal healthy individuals. After chemotherapy using the MCP841 protocol, the frequency of CD4+ CD25+ cells was gradually enhanced with the reduction of FoxP3, interleukin‐10 positivity corresponded with disease presentation, indicating reduced immunosuppression. Taken together, our study indicated that the CD4+ CD25+ FoxP3+ Treg cells played an important role in immunosuppression, resulting in a positive disease‐correlation in these patients. To the best of our knowledge, this is the first detailed report on the frequency, regulation and functionality of Treg cells in B‐ALL.
Artificial incubation of Maleo Macrocephalon maleo eggs at the Bronx Zoo/Wildlife Conservation Society, New York
Authors: Cornejo J. , Iorizzo M. , Clum N.
Published: December 2013

Megapodes are characterized by using means other than body heat to incubate their eggs. The Maleo Macrocephalon maleo is endemic to Sulawesi where it is Endangered, and lays its eggs in pits excavated in soil heated by geothermal sources. A novel method used to incubate Maleo eggs at the Bronx Zoo/Wildlife Conservation Society, NY, USA, is reported here. Using a forced‐air hatcher, the eggs rest on a bed of plastic beads inside a plastic container. Incubation parameters were 32·5°C and 89–90% relative humidity, with an 83% hatch success after an incubation period of c. 70 days. A strong correlation was found between higher incubation temperature and shorter incubation period. The eggs lost an average of 21% of their initial weight between evaporation through the shell during incubation and the liquid discharged from the egg at hatching. The rate of weight loss changed during incubation, starting very slowly and increasing dramatically at the end of the period. Further studies should investigate the effects of humidity on hatchability and survival of chicks, the effect of temperature on the sex ratio of hatchings, as well as the effect of the orientation of the egg during incubation on hatchability.
Suffrage Extensions and Voting Patterns in Latin America: Is Mobilization a Source of Decay?
Authors: Kellam Marisa
Published: December 2013

This article examines whether changes in electoral participation contributed to electoral volatility in Latin America between 1945 and 2000. As a result of literacy voting requirements and authoritarian interludes that disenfranchised large portions of the population, new voters in Latin America probably had different political interests from the previous electorate and were not socialized to electoral politics. The article considers the hypothesis that the inclusion of new voters with different interests produces an immediate, short-term change in aggregate voting patterns, and a lack of socialization of new voters generates lingering instability in electoral behavior. Accounting for confounding factors, the analysis of legislative elections in 12 countries indicates that the expansion of the electorate temporarily disrupted voting patterns in Latin America but did not lead to long-run party system decay.
Conformidad selectiva con la ley y crecimiento autorrestringido de las pequeñas empresas en Sudáfrica
Authors: BISCHOFF Christine , WOOD Geoffrey
Published: December 2013

Sobre la base de entrevistas en profundidad, se examina por qué muchas pequeñas empresas sudafricanas cumplen solo parcialmente la legislación laboral: suelen respetar la normativa general, pero no la dimanante de los consejos de negociación sectoriales previstos en la ley. La antipatía hacia los sindicatos en la era post‐apartheid podría explicarlo. Además, el control de estos consejos sobre las empresas se intensifica cuanto mayor sea el número de trabajadores, por lo que las más pequeñas prefieren subcontratar para aumentar su producción o no declarar todos sus efectivos. Se bascula pues entre el ámbito formal y el informal «jugando» con la dimensión de la empresa.
Subcontratación y evitación de la relación de trabajo en la industria francesa entre 1984 y 2003
Authors: PERRAUDIN Corinne , THÈVENOT Nadine , VALENTIN Julie
Published: December 2013

A partir de una base de datos exhaustiva de las empresas de veinte asalariados o más de la industria francesa de 1984 a 2003, las autoras cuantifican el recurso a la subcontratación y ponen de manifiesto su generalización a partir de mediados de los años ochenta, así como la sustitución del trabajo interno por trabajo externo que de ello se deriva. El análisis empírico de las motivaciones conduce a pensar en comportamientos de evitación de los efectos de la relación de trabajo y de las obligaciones del empleador en virtud del derecho laboral.
Directional biases in phylogenetic structure quantification: a Mediterranean case study
Authors: Molina‐Venegas Rafael , Roquet Cristina
Published: December 2013

Recent years have seen an increasing effort to incorporate phylogenetic hypotheses to the study of community assembly processes. The incorporation of such evolutionary information has been eased by the emergence of specialized software for the automatic estimation of partially resolved supertrees based on published phylogenies. Despite this growing interest in the use of phylogenies in ecological research, very few studies have attempted to quantify the potential biases related to the use of partially resolved phylogenies and to branch length accuracy, and no work has examined how tree shape may affect inference of community phylogenetic metrics. In this study, we tested the influence of phylogenetic resolution and branch length information on the quantification of phylogenetic structure, and also explored the impact of tree shape (stemminess) on the loss of accuracy in phylogenetic structure quantification due to phylogenetic resolution. For this purpose, we used 9 sets of phylogenetic hypotheses of varying resolution and branch lengths to calculate three indices of phylogenetic structure: the mean phylogenetic distance (NRI), the mean nearest taxon distance (NTI) and phylogenetic diversity (stdPD) metrics. The NRI metric was the less sensitive to phylogenetic resolution, stdPD showed an intermediate sensitivity, and NTI was the most sensitive one; NRI was also less sensitive to branch length accuracy than NTI and stdPD, the degree of sensitivity being strongly dependent on the dating method and the sample size. Directional biases were generally towards type II errors. Interestingly, we detected that tree shape influenced the accuracy loss derived from the lack of phylogenetic resolution, particularly for NRI and stdPD. We conclude that well‐resolved molecular phylogenies with accurate branch length information are needed to identify the underlying phylogenetic structure of communities, and also that sensitivity of phylogenetic structure measures to low phylogenetic resolution can strongly vary depending on phylogenetic tree shape.
Primulina minor sp. nov. (Gesneriaceae) from a limestone cave in Hunan, China
Authors: Wen Fang , Hong Xin , Zhao Zhi‐Guo , Wei Yi‐Gang
Published: December 2013

Primulina minor from the Daoxian county, Hunan province in China is described. This new species is similar to Primulina jingxiensis (Yan Liu, W. B. Xu & H. S. Gao) W. B. Xu & K. F. Chung and P. longzhouensis (B. Pan & W. H. Wu) W. B. Xu & K. F. Chung, but differs by its number of leaves (4–6), broadly ovate, orbicular‐ovate or orbicular leaf blade, 2–4 cymes, short peduncle (1.8–2.0 cm long), white (or white with light purple tinge) corolla, small corolla (8–10 mm long), 3 staminoides of which the lateral ones are short (0.75–0.90 mm long) and adnate to 1.6–1.7 mm above the corolla base.
Verrucous carcinoma of the head and neck – not a human papillomavirus‐related tumour?
Authors: Odar Katarina , Kocjan Boštjan J. , Hošnjak Lea , Gale Nina , Poljak Mario , Zidar Nina
Published: December 2013

Association between verrucous carcinoma (VC) of the head and neck and human papillomaviruses (HPV) is highly controversial. Previous prevalence studies focused mostly on α‐PV, while little is known about other PV genera. Our aim was to investigate the prevalence of a broad spectrum of HPV in VC of the head and neck using sensitive and specific molecular assays. Formalin‐fixed, paraffin‐embedded samples of 30 VC and 30 location‐matched normal tissue samples were analysed, by using six different polymerase chain reaction‐based methods targeting DNA of at least 87 HPV types from α‐PV, β‐PV, γ‐PV and μ‐PV genera, and immunohistochemistry against p16 protein. α‐PV, γ‐PV and μ‐PV were not detected. β‐PV DNA was detected in 5/30 VC (16.7%) and in 18/30 normal tissue samples (60.0%): HPV‐19, ‐24 and ‐36 were identified in VC, and HPV‐5, ‐9, ‐12, ‐23, ‐24, ‐38, ‐47, ‐49 and ‐96 in normal tissue, whereas HPV type was not determined in 2/5 cases of VC and in 6/18 normal tissue samples. p16 expression was detected in a subset of samples and was higher in VC than in normal tissue. However, the reaction was predominantly cytoplasmic and only occasionally nuclear, and the extent of staining did not exceed 75%. Our results indicate that α‐PV, γ‐PV and μ‐PV are not associated with aetiopathogenesis of VC of the head and neck. β‐PV DNA in a subset of VC and normal tissue might reflect incidental colonization, but its potential biological significance needs further investigation.
Clinical factors associated with accuracy of EUS‐FNA for pancreatic or peripancreatic solid mass without on‐site cytopathologists
Authors: Kim Jaihwan , Ryu Ji Kon , Park Jin Myung , Paik Woo Hyun , Song Byeong Jun , Kim Yong‐Tae , Yoon Yong Bum
Published: December 2013

Background and Aims

Endoscopic ultrasound‐guided fine needle aspiration (EUS‐FNA) is a safe and effective technique for tissue diagnosis in patients with pancreatic or peripancreatic solid masses. However, the procedure is difficult to accomplish without an on‐site cytopathologist. The aims of this study were to examine the outcomes of EUS‐FNA for pancreatic or peripancreatic solid masses without an on‐site cytopathologist and to determine the factors associated with diagnostic accuracy.

Methods

From December 2005 to November 2011, 230 patients with pancreatic or peripancreatic solid masses had 240 EUS‐FNAs performed without an on‐site cytopathologist. The medical records of the 230 patients from a single tertiary center were retrospectively reviewed.

Results

Among the 230 patients who underwent EUS‐FNA, 201 patients (88%) had malignancy, which included 171 adenocarcinomas (74%). Assuming that the cytopathological malignancy was positive or suspicious for malignant cells with cytology, the accuracy without an on‐site cytopathologist was 67.9%. However, the accuracy increased from 40.0% for the first 30 cases (from 2006 to 2008) to 83.3% for the last 30 cases (in 2011) and was constantly over 80.0% starting from the sixth octile onwards for every 30 cases (in 2011). From the analysis of factors associated with the accuracy of the diagnosis using logistic regression analysis, the number of needle passes and the experience of endosonographer were statistically associated with the diagnostic accuracy.

Conclusions

In the case of performing EUS‐FNA for pancreatic or peripancreatic solid masses without an on‐site cytopathologist, the experience of the endosonographer, and the number of needle passes were associated with the diagnostic accuracy.
Adverse events appear to unblind clinical trials in irritable bowel syndrome
Authors: Shah E. , Triantafyllou K. , Hana A. A. , Pimentel M.
Published: December 2013

Background

Clinical trial design is challenging in irritable bowel syndrome (IBS) due in part to a high placebo effect. We postulated that the mere presence of an adverse event (AE) may unmask patients in clinical trials who are assigned to the active agent, and this may lead to higher reported efficacy.

Methods

We evaluated therapies receiving at least a Grade 1B from the American College of Gastroenterology Task Force for IBS or which passed recent phase III clinical trials. Therapies with AE data derived from less than 50 patients in each study arm were excluded. Statistically significant excess AE were identified, risk difference was calculated for each AE, and incidence of AE in the treatment arm was reported. We examined the relationship of attributable drug benefit, defined as the reciprocal of number‐needed‐to‐treat found in literature, with various measures of AE incidence.

Key Results

Attributable drug benefit correlated significantly with average AE risk difference, calculated as treatment arm AE incidence minus placebo arm AE incidence (R2 = 0.70, p = 0.039), and also with highest treatment arm AE incidence (R2 = 0.70, p = 0.038) for each therapy. There were also trends toward correlation with average treatment arm AE incidence (R2 = 0.54, p = 0.096) and highest AE risk difference (R2 = 0.63, p = 0.059) for each therapy.

Conclusions & Inferences

Our study suggests that higher AE incidence on active therapy is associated with more beneficial patient‐reported outcomes in IBS clinical trials. This raises the issue of spontaneous unblinding.
Changes in peak fat oxidation in response to different doses of endurance training
Authors: Rosenkilde M. , Reichkendler M. H. , Auerbach P. , Bonne T. C. , Sjödin A. , Ploug T. , Stallknecht B. M.
Published: December 2013

The effect of different doses of endurance training on the capacity to oxidize fat during exercise in sedentary, overweight men and assessment of variables associated with changes in peak fat oxidation (PFO) were evaluated. Young, sedentary, overweight men were randomized to either the high‐dose (HIGH, 600 kcal/day, n = 17) or moderate‐dose (MOD, 300 kcal/day, n = 18) endurance training groups or controls (CON, n = 15). PFO and peak oxygen uptake (VO2 peak) were measured using indirect calorimetry, body composition using dual‐energy x‐ray absorptiometry, and protein levels of mitochondrial enzymes determined by Western blotting. PFO increased in both MOD [1.2 mg/kg fat‐free mass (FFM)/min, 95% confidence interval (CI): 0.08:2.3, P = 0.03] and HIGH (1.8 mg/kg FFM/min, CI: 0.6:2.9, P < 0.001) compared with CON. Skeletal muscle expression of citrate synthase, β‐hydroxyacyl‐CoA dehydrogenase, and mitochondrial oxphos complexes II‐V increased similarly in MOD and HIGH. Stepwise multiple linear regression analysis with backward elimination of individual variables correlated with changes in PFO revealed increases in cycling efficiency, FFM, and VO2 peak as the remaining associated variables. In conclusion, PFO during exercise increased with both moderate‐ and high‐dose endurance training. Increases in PFO were mainly predicted by changes in VO2 peak, FFM, and cycling efficiency, and less with skeletal muscle mitochondrial enzymes.
Next‐generation sequencing can reveal in vitro‐generated PCR crossover products: some artifactual sequences correspond to HLA alleles in the IMGT/HLA database
Authors: Holcomb C. L. , Rastrou M. , Williams T. C. , Goodridge D. , Lazaro A. M. , Tilanus M. , Erlich H. A.
Published: December 2013

The high‐resolution human leukocyte antigen (HLA) genotyping assay that we developed using 454 sequencing and Conexio software uses generic polymerase chain reaction (PCR) primers for DRB exon 2. Occasionally, we observed low abundance DRB amplicon sequences that resulted from in vitro PCR ‘crossing over’ between DRB1 and DRB3/4/5. These hybrid sequences, revealed by the clonal sequencing property of the 454 system, were generally observed at a read depth of 5%–10% of the true alleles. They usually contained at least one mismatch with the IMGT/HLA database, and consequently, were easily recognizable and did not cause a problem for HLA genotyping. Sometimes, however, these artifactual sequences matched a rare allele and the automatic genotype assignment was incorrect. These observations raised two issues: (1) could PCR conditions be modified to reduce such artifacts? and (2) could some of the rare alleles listed in the IMGT/HLA database be artifacts rather than true alleles? Because PCR crossing over occurs during late cycles of PCR, we compared DRB genotypes resulting from 28 and (our standard) 35 cycles of PCR. For all 21 cell line DNAs amplified for 35 cycles, crossover products were detected. In 33% of the cases, these hybrid sequences corresponded to named alleles. With amplification for only 28 cycles, these artifactual sequences were not detectable. To investigate whether some rare alleles in the IMGT/HLA database might be due to PCR artifacts, we analyzed four samples obtained from the investigators who submitted the sequences. In three cases, the sequences were generated from true alleles. In one case, our 454 sequencing revealed an error in the previously submitted sequence.
Dynamic Force on an Elbow Caused by a Traveling Liquid Slug
Authors: Hou Darcy Q. , Tijsseling Arris S. , Bozkus Zafer
Published: December 2013

The impact force on an elbow induced by traveling isolated liquid slugs in a horizontal pipeline is studied. A literature review reveals that the force on the elbow is mainly due to momentum transfer in changing the fluid flow direction around the elbow. Therefore, to accurately calculate the magnitude and duration of the impact force, the slug arrival velocity at the elbow needs to be well predicted. The hydrodynamic behavior of the slug passing through the elbow needs to be properly modeled too. A combination of 1D and 2D models is used in this paper to analyze this problem. The 1D model is used to predict the slug motion in the horizontal pipeline. With the obtained slug arrival velocity, slug length, and driving air pressure as initial conditions, the 2D Euler equations are solved by the smoothed particle hydrodynamics (SPH) method to analyze the slug dynamics at the elbow. The 2D SPH solution matches experimental data and clearly demonstrates the occurrence of flow separation at the elbow, which is a typical effect of high Reynolds flows. Using the obtained flow contraction coefficient, an improved 1D model with nonlinear elbow resistance is proposed and solved by SPH. The 1D SPH results show the best fit with experimental data obtained so far.
Modulation of the work function of fullerenes C60 and C70 by alkaline earth metal adsorption: A theoretical study
Authors: Sun Yue-Qiang , Xu Shun-Fu , Liu Wei-Hui , Li Zeng-Sheng , Zheng Xin-Qing , Sang Chun-E , Zhu Xiu-Mei , Zhang Xiao-Chun , Li Chun , Yuan Guang , Mimura Hitenori
Published: December 2013

The significant influence of alkaline earth metal (Be/Mg/Ca/Sr/Ba/Ra) adsorption on work functions of fullerenes C60 and C70 was investigated by first-principles calculations. The work functions of fullerenes C60 and C70 with Ca/Sr/Ba/Ra adatoms decrease linearly with the electronegativities of the alkaline earth metals. The work functions are also affected considerably by adsorption positions. The variations of the work functions depend on the changes of Fermi level (which is attributed to charge transfer) and the changes of vacuum levels (which is attributed to induced dipole moments). Moreover, the alkaline earth metal adsorption can also improve the electric conductivity of a fullerene mixture.
DNA Barcoding from NYC to Belize
Authors: Harris Stephen E. , Bellino Marissa
Published: December 2013

The Student DNA Barcoding Project, an IBI prize–winning module, develops student-generated research to study local biodiversity using molecular biology skills.
Money Woes Cloud Future of Workhorse U.S. Telescopes
Authors: Bhattacharjee Yudhijit
Published: December 2013

Five federally funded optical and radio telescopes in the United States could be forced to shut down over the next 3 years because of budget cuts by the National Science Foundation.
The Seventh Pandemic Vibrio cholerae O1 El Tor Isolate in China Has Undergone Genetic Shifts
Authors: Zhang Ping , Li Fengjuan , Liang Weili , Li Jie , Kan Biao , Wang Duochun
Published: December 2013

A total of 330 clinical
Vibrio cholerae
O1 serogroups from China dating between 1961 and 2010 were investigated. By phenotypic biotyping and genetic analysis, during the seventh pandemic of
V. cholerae
O1 in China, the isolates of hybrid biotype (mixed classical phenotypes) were present during the entire1961-2010 period, while El Tor genetic shifts appeared in 1992 and replaced the prototype El Tor from 2002 to 2010.
Interaction of Foot-and-Mouth Disease Virus Nonstructural Protein 3A with Host Protein DCTN3 Is Important for Viral Virulence in Cattle
Authors: Gladue D. P. , O'Donnell V. , Baker-Bransetter R. , Pacheco J. M. , Holinka L. G. , Arzt J. , Pauszek S. , Fernandez-Sainz I. , Fletcher P. , Brocchi E. , Lu Z. , Rodriguez L. L. , Borca M. V.
Published: December 2013

Nonstructural protein 3A of foot-and-mouth disease virus (FMDV) is a partially conserved protein of 153 amino acids in most FMDVs examined to date. The role of 3A in virus growth and virulence within the natural host is not well understood. Using a yeast two-hybrid approach, we identified cellular protein DCTN3 as a specific host binding partner for 3A. DCTN3 is a subunit of the dynactin complex, a cofactor for dynein, a motor protein. The dynactin-dynein duplex has been implicated in several subcellular functions involving intracellular organelle transport. The 3A-DCTN3 interaction identified by the yeast two-hybrid approach was further confirmed in mammalian cells. Overexpression of DCTN3 or proteins known to disrupt dynein, p150/Glued and 50/dynamitin, resulted in decreased FMDV replication in infected cells. We mapped the critical amino acid residues in the 3A protein that mediate the protein interaction with DCTN3 by mutational analysis and, based on that information, we developed a mutant harboring the same mutations in O1 Campos FMDV (O1C3A-PLDGv). Although O1C3A-PLDGv FMDV and its parental virus (O1Cv) grew equally well in LFBK-αvβ6, O1C3A-PLDGv virus exhibited a decreased ability to replicate in primary bovine cell cultures. Importantly, O1C3A-PLDGv virus exhibited a delayed disease in cattle compared to the virulent parental O1Campus (O1Cv). Virus isolated from lesions of animals inoculated with O1C3A-PLDGv virus contained amino acid substitutions in the area of 3A mediating binding to DCTN3. Importantly, 3A protein harboring similar amino acid substitutions regained interaction with DCTN3, supporting the hypothesis that DCTN3 interaction likely contributes to virulence in cattle.

IMPORTANCE
The objective of this study was to understand the possible role of a FMD virus protein 3A, in causing disease in cattle. We have found that the cellular protein, DCTN3, is a specific binding partner for 3A. It was shown that manipulation of DCTN3 has a profound effect in virus replication. We developed a FMDV mutant virus that could not bind DCTN3. This mutant virus exhibited a delayed disease in cattle compared to the parental strain highlighting the role of the 3A-DCTN3 interaction in virulence in cattle. Interestingly, virus isolated from lesions of animals inoculated with mutant virus contained mutations in the area of 3A that allowed binding to DCTN3. This highlights the importance of the 3A-DCTN3 interaction in FMD virus virulence and provides possible mechanisms of virus attenuation for the development of improved FMD vaccines.
Mechanism of Neutralization of Herpes Simplex Virus by Antibodies Directed at the Fusion Domain of Glycoprotein B
Authors: Cairns Tina M. , Fontana Juan , Huang Zhen-Yu , Whitbeck J. Charles , Atanasiu Doina , Rao Samhita , Shelly Spencer S. , Lou Huan , Ponce de Leon Manuel , Steven Alasdair C. , Eisenberg Roselyn J. , Cohen Gary H.
Published: December 2013

Glycoprotein B (gB), the fusogen of herpes simplex virus (HSV), is a class III fusion protein with a trimeric ectodomain of known structure for the postfusion state. Seen by negative-staining electron microscopy, it presents as a rod with three lobes (base, middle, and crown). gB has four functional regions (FR), defined by the physical location of epitopes recognized by anti-gB neutralizing monoclonal antibodies (MAbs). Located in the base, FR1 contains two internal fusion loops (FLs) and is the site of gB-lipid interaction (the fusion domain). Many of the MAbs to FR1 are neutralizing, block cell-cell fusion, and prevent the association of gB with lipid, suggesting that these MAbs affect FL function. Here we characterize FR1 epitopes by using electron microscopy to visualize purified Fab-gB ectodomain complexes, thus confirming the locations of several epitopes and localizing those of MAbs DL16 and SS63. We also generated MAb-resistant viruses in order to localize the SS55 epitope precisely. Because none of the epitopes of our anti-FR1 MAbs mapped to the FLs, we hyperimmunized rabbits with FL1 or FL2 peptides to generate polyclonal antibodies (PAbs). While the anti-FL1 PAb failed to bind gB, the anti-FL2 PAb had neutralizing activity, implying that the FLs become exposed during virus entry. Unexpectedly, the anti-FL2 PAb (and the anti-FR1 MAbs) bound to liposome-associated gB, suggesting that their epitopes are accessible even when the FLs engage lipid. These studies provide possible mechanisms of action for HSV neutralization and insight into how gB FR1 contributes to viral fusion.

IMPORTANCEFor herpesviruses, such as HSV, entry into a target cell involves transfer of the capsid-encased genome of the virus to the target cell after fusion of the lipid envelope of the virus with a lipid membrane of the host. Virus-encoded glycoproteins in the envelope are responsible for fusion. Antibodies to these glycoproteins are important biological tools, providing a way of examining how fusion works. Here we used electron microscopy and other techniques to study a panel of anti-gB antibodies. Some, with virus-neutralizing activity, impair gB-lipid association. We also generated a peptide antibody against one of the gB fusion loops; its properties provide insight into the way the fusion loops function as gB transits from its prefusion form to an active fusogen.
Epigenetic Regulation of HIV-1 Latency in Astrocytes
Authors: Narasipura Srinivas D. , Kim Stephanie , Al-Harthi Lena
Published: December 2013

HIV infiltrates the brain at early times postinfection and remains latent within astrocytes and macrophages. Because astrocytes are the most abundant cell type in the brain, we evaluated epigenetic regulation of HIV latency in astrocytes. We have shown that class I histone deacetylases (HDACs) and a lysine-specific histone methyltransferase, SU(VAR)3-9, play a significant role in silencing of HIV transcription in astrocytes. Our studies add to a growing body of evidence demonstrating that astrocytes are a reservoir for HIV.
Analysis of T Cell Responses during Active Varicella-Zoster Virus Reactivation in Human Ganglia
Authors: Steain Megan , Sutherland Jeremy P. , Rodriguez Michael , Cunningham Anthony L. , Slobedman Barry , Abendroth Allison
Published: December 2013

Varicella-zoster virus (VZV) is responsible for both varicella (chickenpox) and herpes zoster (shingles). During varicella, the virus establishes latency within the sensory ganglia and can reactivate to cause herpes zoster, but the immune responses that occur in ganglia during herpes zoster have not previously been defined. We examined ganglia obtained from individuals who, at the time of death, had active herpes zoster. Ganglia innervating the site of the cutaneous herpes zoster rash showed evidence of necrosis, secondary to vasculitis, or localized hemorrhage. Despite this, there was limited evidence of VZV antigen expression, although a large inflammatory infiltrate was observed. Characterization of the infiltrating T cells showed a large number of infiltrating CD4
+
T cells and cytolytic CD8
+
T cells. Many of the infiltrating T cells were closely associated with neurons within the reactivated ganglia, yet there was little evidence of T cell-induced neuronal apoptosis. Notably, an upregulation in the expression of major histocompatibility complex class I (MHC-I) and MHC-II molecules was observed on satellite glial cells, implying these cells play an active role in directing the immune response during herpes zoster. This is the first detailed characterization of the interaction between T cells and neuronal cells within ganglia obtained from patients suffering herpes zoster at the time of death and provides evidence that CD4
+
and cytolytic CD8
+
T cell responses play an important role in controlling VZV replication in ganglia during active herpes zoster.

IMPORTANCE
VZV is responsible for both varicella (chickenpox) and herpes zoster (shingles). During varicella, the virus establishes a life-long dormant infection within the sensory ganglia and can reawaken to cause herpes zoster, but the immune responses that occur in ganglia during herpes zoster have not previously been defined. We examined ganglia obtained from individuals who, at the time of death, had active herpes zoster. We found that specific T cell subsets are likely to play an important role in controlling VZV replication in ganglia during active herpes zoster.
Poor adherence of randomised trials in surgery to CONSORT guidelines for non-pharmacological treatments (NPT): a cross-sectional study
Authors: Nagendran Myura , Harding Daniel , Teo Wendy , Camm Christian , Maruthappu Mahiben , McCulloch Peter , Hopewell Sally
Published: December 2013

Objective

To systematically assess adherence of randomised trials in surgery to Consolidated Standards of Reporting Trials (CONSORT) guidelines for non-pharmacological treatments (NPT). Surgical trials are considered more difficult to design and execute than pharmacological trials. Furthermore, the original CONSORT statement does not address some aspects that are vital to the transparent reporting of surgical trials. The CONSORT-NPT extension was designed to address these issues but adherence in medical and surgical journals has not been assessed.

Design

Cross-sectional study.

Sample

We identified eight general medical and eight surgical journals, indexed in PubMed and published in 2011, with the highest impact factors in their respective categories.

Main outcomes

Adherence to CONSORT statement and CONSORT-NPT extension items.

Results

We identified 54 surgical trials (22 published in medical journals and 32 in surgical journals). There were eight items for which there was less than 30% overall compliance (seven were specific to the CONSORT-NPT extension). These seven items are related to: a full description of the care providers, centres and blinding status in the abstract (n=7/54, 13%), eligibility criteria for centres performing the interventions (n=13/54, 24%), how adherence of care providers with the protocol was assessed or enhanced (n=7/54, 13%), how clustering by care providers or centres was addressed as it relates to sample size (n=3/54, 6%), how care providers were allocated to each group (n=9/54, 17%), how clustering by care providers or centres was addressed as it relates to statistical methods (n=2/54, 4%), a description of care providers (case volume, qualification, expertise, etc) and centres (volume) in each group (n=0/54, 0%).

Conclusions

Adherence of surgical trials to CONSORT-NPT extension items is much poorer than to the standard CONSORT statement. Adherence also appears to be superior in general medical journals compared with surgical journals. Raising awareness and conducting qualitative research to identify areas for specific intervention will be important going forward.
Rationale and design of the PRognostic Importance of MIcrovascular Dysfunction in asymptomatic patients with Aortic Stenosis (PRIMID-AS): a multicentre observational study with blinded investigations
Authors: Singh Anvesha , Ford Ian , Greenwood John P , Khan Jamal N , Uddin Akhlaque , Berry Colin , Neubauer Stefan , Prendergast Bernard , Jerosch-Herold Michael , Williams Bryan , Samani Nilesh J , McCann Gerry P
Published: December 2013

Introduction

Aortic stenosis (AS) is the commonest valve disorder in the developed world requiring surgery. Surgery in patients with severe asymptomatic AS remains controversial. Exercise testing can identify asymptomatic patients at increased risk of death and symptom development, but with limited specificity, especially in older adults. Cardiac MRI (CMR), including myocardial perfusion reserve (MPR) may be a novel imaging biomarker in AS.

Aims

(1) To improve risk stratification in asymptomatic patients with AS and (2) to determine whether MPR is a better predictor of outcome than exercise testing and brain natriuretic peptide (BNP).

Method/design

Multicentre, prospective observational study in the UK, comparing MPR with exercise testing and BNP (with blinded CMR analysis) for predicting outcome.

Population

170 asymptomatic patients with moderate-to-severe AS, who would be considered for aortic valve replacement (AVR).

Primary outcome

Composite of: typical symptoms necessitating referral for AVR and major adverse cardiovascular events. Follow-up: 12–30 months (minimum 12 months).

Primary hypothesis

MPR will be a better predictor of outcome than exercise testing and BNP.

Ethics/dissemination

The study has full ethical approval and is actively recruiting patients. Data collection will be completed in November 2014 and the study results will be submitted for publication within 6 months of completion.

ClinicalTrials.gov identifier

NCT01658345.
Correlation of AOL recanalization, TIMI reperfusion and TICI reperfusion with infarct growth and clinical outcome
Authors: Marks Michael P , Lansberg Maarten G , Mlynash Michael , Kemp Stephanie , McTaggart Ryan , Zaharchuk Greg , Bammer Roland , Albers Gregory W
Published: December 2013

Objective

To understand how three commonly used measures of endovascular therapy correlate with clinical outcome and infarct growth.

Methods

Prospectively enrolled patients underwent baseline MRI and started endovascular therapy within 12 h of stroke onset. The final angiogram was given a primary arterial occlusive lesion (AOL) recanalization score (0–3), a Thrombolysis in Myocardial Infarction (TIMI) score (0–3) and a Thrombolysis in Cerebral Infarction (TICI) score (0–3). The scores were dichotomized into poor revascularization (AOL 0–2, TIMI 0–1 and TICI 0–2a) versus good revascularization (AOL 3, TIMI 2–3, TICI 2b–3). Patients were classified according to whether or not they had target mismatch (TMM). Good outcome was defined as a 90-day modified Rankin Scale score of 0–2.

Results

Endovascular treatment was attempted in 100. A good outcome was achieved in 57% of patients with a TICI score of 2b–3 and in 24% of patients with a TICI score of 0–2a (p=0.001). Patients with TIMI scores of 2–3 and an AOL score of 3 had lower rates of good outcome (44% and 47%, respectively), which were not significantly better than those with TIMI scores of 0–1 or AOL scores of 0–2. In patients with TMM, these rates of good outcome improved with all the scoring systems and were significantly better for TIMI and TICI scores. Patients with a TICI score of 2a had rates of good functional outcome and lesion growth which were not different from those with TICI scores of 0–1 but were significantly worse than those with TICI scores of 2b–3.

Conclusions

TIMI 2–3 and TICI 2b–3 reperfusion scores demonstrated improved outcome in patients with tissue mismatch with a small infarct core and a larger hypoperfused region but AOL scores did not. Patients with a TICI score of 2a had a poorer outcome and more lesion growth than those with TICI scores of 2b–3.
Recombinant globular adiponectin inhibits lipid deposition by p38 MAPK/ATF-2 and TOR/p70 S6 kinase pathways in chicken adipocytes
Authors: Jun Yan , Xiao Tan , Guoyong Yan , Min Feng , Haili Yang , Chao Sun
Published: December 2013

Adiponectin plays a fundamental role in lipid and carbohydrate metabolism. However, its role in adipocyte differentiation remains controversial. To investigate the effect of gAd on lipid deposition in chicken adipocytes and its related signaling pathways, 200 μg/mL recombinant globular adiponectin, isoproterenol, SB253580, leucine, and rapamycin were used to treat chicken adipocytes. Results demonstrated that gAd increased the expression of endogenous adiponectin and AdipoR1 (P < 0.01); gAd inhibited triglyceride (TG) accumulation in chicken adipocyte and increased the release of free fatty acids (FFA) in medium; gAd decreased the expression of adipogenic marker genes CCAAT/enhancer binding protein alpha (C/EBPα) and fatty acid synthase (FAS), while activating the expression of lipolytic marker gene adipose triglyceride lipase (ATGL) (P < 0.01). Meanwhile, gAd activated the phosphorylation levels of p38 mitogen-activated protein kinase (p38 MAPK) and activating transcription factor 2 (ATF-2), and suppressed the phosphorylation levels of rapamycin (TOR) and p70 S6 Kinase (P < 0.01). In conclusion, the results demonstrate that gAd has an ability to inhibit lipids deposition in chicken adipocyte, which depends on the p38 MAPK/ATF–2 and TOR/p70 S6 Kinase pathways.