bluuebunny/crossref_metadata_2025 huggingface dataset:
Do not disturb the family: roles of colony size and human disturbance in the genetic structure of lesser kestrel
Authors: Di Maggio R. , Mengoni C. , Mucci N. , Campobello D. , Randi E. , Sarà M.
Published: November 2014

Dispersal and philopatry are fundamental processes influencing the genetic structure and persistence of populations, and might be affected by isolation and habitat perturbation. Habitat degradation induced by human activities could have detrimental consequences on the genetic structure of populations. Therefore, it is crucial to understand the role of human impact in promoting or disrupting the genetic structure. Here, we conducted a genetic analysis using 12 polymorphic microsatellite markers of 70 lesser kestrelsFalco naumannifrom 10 breeding colonies of two subpopulations inSicily (southernItaly). Genetic differentiation between the two subpopulations was negligible, and linear distances played no role in the level of genetic relatedness recorded in the two sites. Linear distances between nests also resulted in no effects on the relatedness recorded within and between colonies in the largest subpopulation. Clusters of more‐versus less‐related individuals resulted when the two‐dimensional positions of colonies (i.e., latitude and longitude) were tested as predictors of genetic proximity instead of linear distances. Specifically, analyses of colony features showed colony size and human disturbance as factors negatively affecting the relatedness among chicks from different nests. Regardless of colony size, less‐related individuals were born in colonies located in the core of the agricultural plain, where we quantified a higher level of human disturbance. In contrast, more related individuals were in colonies located in the marginal, less disturbed, agricultural area. Given the high philopatry of this species, our results are consistent with disruption of colony fidelity related to intensification of agricultural practices. We discuss the possible implications of long‐term effects of genetic variability in small and disturbed colonies on fitness and population viability.
Intrafollicular classical Hodgkin lymphoma mimicking nodular lymphocyte predominant Hodgkin lymphoma: A report of two cases
Authors: Tatsuno Mai , Maeshima Akiko Miyagi , Kim Sung‐Won , Maruyama Dai , Taniguchi Hirokazu , Miyamoto Ken‐ichi , Fukuhara Suguru , Kobayashi Yukio , Tobinai Kensei , Kushima Ryoji
Published: November 2014

We here report on two rare cases of intrafollicular classical Hodgkin lymphoma (CHL). Case 1 was a 34‐year‐old man who underwent left supraclavicular lymph node biopsy. Case 2 was a 28‐year‐old woman who underwent surgical resection of an anterior mediastinal mass. The histology and microenvironment of both specimens resembled those of nodular lymphocyte predominant Hodgkin lymphoma. Nodular architecture was observed, which comprised normal‐appearing small lymphocytes and scattered lymphocyte predominant (LP)‐like cells. CD23+ follicular dendritic cell meshworks were present in the nodules, surrounded by a mantle zone containing IgD+ B cells. The LP‐like cells were ringed by CD3+ and PD‐1+ T cells, and numerous CD20+ B cells were present in the background. However, the immunophenotypes of the LP‐like cells resembled those of Hodgkin/Reed‐Sternberg cells of CHL; they were positive for CD15, CD30, and PAX5, and negative for CD20, Bcl6, Oct2, and Bob1. These histopathological findings indicate that CHL can be derived from the germinal center.
Functional characterization of CCR in birch (Betula platyphylla × Betula pendula) through overexpression and suppression analysis
Authors: Zhang Wenbo , Wei Rui , Chen Su , Jiang Jing , Li Huiyu , Huang Haijiao , Yang Guang , Wang Shuo , Wei Hairong , Liu Guifeng
Published: November 2014

We cloned a Cinnamoyl‐CoA Reductase gene (BpCCR1) from an apical meristem and first internode of Betula platyphylla and characterized its functions in lignin biosynthesis, wood formation and tree growth through transgenic approaches. We generated overexpression and suppression transgenic lines and analyzed them in comparison with the wild‐type in terms of lignin content, anatomical characteristics, height and biomass. We found that BpCCR1 overexpression could increase lignin content up to 14.6%, and its underexpression decreased lignin content by 6.3%. Surprisingly, modification of BpCCR1 expression led to conspicuous changes in wood characteristics, including xylem vessel number and arrangement, and secondary wall thickness. The growth of transgenic trees in terms of height was also significantly influenced by the modification of BpCCR1 genes. We discuss the functions of BpCCR1 in the context of a phylogenetic tree built with CCR genes from multiple species.
Pope Paul V's global design: the fresco cycle in the Quirinal Palace
Authors: Fujikawa Mayu
Published: November 2014

Commissioned by Paul V, the monumental fresco in the Sala Regia of the Quirinal Palace, Rome, represents Kongolese, Ethiopian, Persian, and Japanese ambassadors, in addition to what can be regarded as Chinese figures. The present article investigates how the fresco emphasizes the pope's evangelical successes, and his desire to increase conversions and unite other Christian Churches under the supreme leadership of the papacy despite Portugal and Spain's claim for padroado. The fresco also reflects papal ambition to establish a pan‐continental military and commercial network in order to counter the Ottomans and Protestants. The pope's intertwined foreign policies towards the nations represented in the fresco are examined to clarify these points. The fresco appropriates the presumptive power of the non‐European potentates and manipulates imagery of their envoys (both actual and imagined) to promote the pope's authority. In particular, the individualized representation of the East Asians contributes to the display of the papacy's global knowledge and its power. Apart from the images of the foreign dignitaries, other understudied figures in the fresco are analysed. The surrounding urban environment is related to the mood of levity in the fresco, which stresses eternal bliss for the pope's devotees and divine punishment for the disobedient.
Regulation of Vesicular Traffic at the T Cell Immune Synapse: Lessons from the Primary Cilium
Authors: Finetti Francesca , Onnis Anna , Baldari Cosima T.
Published: November 2014

The signals that orchestrate the process of T cell activation are coordinated at the specialized interface that forms upon contact with an antigen presenting cell displaying a specific MHC‐associated peptide ligand, known as the immune synapse. The central role of vesicular traffic in the assembly of the immune synapse has emerged only in recent years with the finding that sustained T‐cell receptor (TCR) signaling involves delivery of TCR/CD3 complexes from an intracellular pool associated with recycling endosomes. A number of receptors as well as membrane‐associated signaling mediators have since been demonstrated to exploit this process to localize to the immune synapse. Here, we will review our current understanding of the mechanisms responsible for TCR recycling, with a focus on the intraflagellar transport system, a multimolecular complex that is responsible for the assembly and function of the primary cilium which we have recently implicated in polarized endosome recycling to the immune synapse.
A Genetic Algorithm Based Multi-Objective Shape Optimization Scheme for Cementless Femoral Implant
Authors: Chanda Souptick , Gupta Sanjay , Kumar Pratihar Dilip
Published: November 2014

The shape and geometry of femoral implant influence implant-induced periprosthetic bone resorption and implant-bone interface stresses, which are potential causes of aseptic loosening in cementless total hip arthroplasty (THA). Development of a shape optimization scheme is necessary to achieve a trade-off between these two conflicting objectives. The objective of this study was to develop a novel multi-objective custom-based shape optimization scheme for cementless femoral implant by integrating finite element (FE) analysis and a multi-objective genetic algorithm (GA). The FE model of a proximal femur was based on a subject-specific CT-scan dataset. Eighteen parameters describing the nature of four key sections of the implant were identified as design variables. Two objective functions, one based on implant-bone interface failure criterion, and the other based on resorbed proximal bone mass fraction (BMF), were formulated. The results predicted by the two objective functions were found to be contradictory; a reduction in the proximal bone resorption was accompanied by a greater chance of interface failure. The resorbed proximal BMF was found to be between 23% and 27% for the trade-off geometries as compared to ∼39% for a generic implant. Moreover, the overall chances of interface failure have been minimized for the optimal designs, compared to the generic implant. The adaptive bone remodeling was also found to be minimal for the optimally designed implants and, further with remodeling, the chances of interface debonding increased only marginally.
Low-Cycle Fatigue and Ratcheting Responses of Elbow Piping Components
Authors: Hassan T. , Rahman M. , Bari S.
Published: November 2014

The objective of this study was to investigate low-cycle fatigue and ratcheting responses of elbows through experimental and analytical studies. Low-cycle fatigue and ratcheting damage accumulation in piping components may occur under repeated reversals of loading induced by earthquake and/or thermomechanical operation. Ratcheting and fatigue damage accumulation can cause failure of piping systems through fatigue cracks or plastic buckling. However, the ratcheting damage induced failures are yet to be understood clearly; consequently, ASME Code design provisions against ratcheting failure continue to be a controversial issue over the last two decades. A systematic set of piping component experimental responses involving ratcheting and a computational tool to simulate these responses will be essential to rationally address the issue. Development of a constitutive model for simulating component ratcheting responses remains to be a challenging problem. In order to develop an experimentally validated constitutive model, a set of elbow experiments was conducted. The loading prescribed in the experiments involved displacement-controlled or force-controlled in-plane cyclic bending with or without internal pressure. Force, displacement, internal pressure, elbow diameter change, and strains at four locations of the elbow specimens were recorded. This article presents and discusses the results from the experimental study. A sister article evaluates seven different constitutive models against simulating these elbow ratcheting and fatigue responses.
Ambient Temperature Operation of a Platinum-Free Direct Formate Fuel Cell
Authors: Nguyen Tien Q. , Minami Daniel , Hua Chau , Miller Austin , Tran Kevin , Haan John L.
Published: November 2014

Several reports have been made recently of the direct formate fuel cell (DFFC) operating at high-temperature and using Pt cathode catalyst. In the present work, we demonstrate a Pt-free DFFC employing ACTA HypermecTM 4020 Fe–Co second-generation cathode catalyst operating at low-temperature. We report a maximum power density (PD) of 45 mW cm−2 at ambient temperature (20 °C), when the fuel stream was 1 M HCOOK and 2 M KOH with oxygen used at the cathode. When air was used at the cathode, the maximum PD was 35 mW cm−2. When hydroxide was removed from the fuel stream and oxygen used at the cathode, the maximum PD at 20 °C was 18 mW cm−2. This low-temperature, KOH-free operation is important to development of a practical DFFC.
Conservation Properties of the Trapezoidal Rule in Linear Time Domain Analysis of Acoustics and Structures
Authors: Jog C. S. , Nandy Arup
Published: November 2014

The trapezoidal rule, which is a special case of the Newmark family of algorithms, is one of the most widely used methods for transient hyperbolic problems. In this work, we show that this rule conserves linear and angular momenta and energy in the case of undamped linear elastodynamics problems, and an “energy-like measure” in the case of undamped acoustic problems. These conservation properties, thus, provide a rational basis for using this algorithm. In linear elastodynamics problems, variants of the trapezoidal rule that incorporate “high-frequency” dissipation are often used, since the higher frequencies, which are not approximated properly by the standard displacement-based approach, often result in unphysical behavior. Instead of modifying the trapezoidal algorithm, we propose using a hybrid finite element framework for constructing the stiffness matrix. Hybrid finite elements, which are based on a two-field variational formulation involving displacement and stresses, are known to approximate the eigenvalues much more accurately than the standard displacement-based approach, thereby either bypassing or reducing the need for high-frequency dissipation. We show this by means of several examples, where we compare the numerical solutions obtained using the displacement-based and hybrid approaches against analytical solutions.
An in‐vivo investigation of the therapeutic effect of pulsed focused ultrasound on tumor growth
Authors: Ma C.‐M. , Chen Xiaoming , Cvetkovic Dusica , Chen Lili
Published: November 2014

Purpose:

High‐intensity focused ultrasound (HIFU) has been investigated for ablative therapy and drug enhancement for gene therapy and chemotherapy. The aim of this work is to explore the feasibility of pulsed focused ultrasound (pFUS) for cancer therapy using an in vivo animal model.

Methods:

A clinical HIFU system (InSightec ExAblate 2000) integrated with a 1.5 T GE MR scanner was used in this study. Suitable ultrasound parameters were investigated to perform nonthermal sonications, keeping the temperature elevation below 4 °C as measured in real time by MR thermometry. LNCaP cells (106) were injected into the prostates of male mice (n = 20). When tumors reached a diameter of about 5 mm in 3D as measured on magnetic resonance imaging (MRI), the tumor‐bearing mice (n = 8) were treated with pFUS (1 MHz frequency; 25 W acoustic power; 0.1 duty cycle; 60 s duration). A total of 4–6 sonications were used to cover the entire tumor volume under MR image guidance. The animals were allowed to survive for 4 weeks after the treatment. The tumor growth was monitored on high‐resolution (0.2 mm) MRI weekly post treatment and was compared with that of the control group (n = 12).

Results:

Significant tumor growth delay was observed in the tumor‐bearing mice treated with pFUS. The mean tumor volume for the pFUS treated mice remained the same 1 week after the treatment while the mean tumor volume of the control mice grew 42% over the same time. Two weeks after the pFUS treatment, the control group had a mean tumor volume 40% greater than that of the treated group. There was a greater variation in tumor volume at 4 weeks post treatment for both treated and control mice and a slightly faster tumor growth for the pFUS treated mice.

Conclusions:

The authors’ results demonstrated that pFUS may have a great potential for cancer therapy. Further experiments are warranted to understand the predominantly nonthermal cell killing mechanisms of pFUS and to derive optimal ultrasound parameters and fractionation schemes to maximize the therapeutic effect of pFUS.
Seasonal Training-Load Quantification in Elite English Premier League Soccer Players
Authors: Malone James J. , Di Michele Rocco , Morgans Ryland , Burgess Darren , Morton James P. , Drust Barry
Published: November 2014

Purpose:

To quantify the seasonal training load completed by professional soccer players of the English Premier League.

Methods:

Thirty players were sampled (using GPS, heart rate, and rating of perceived exertion [RPE]) during the daily training sessions of the 2011–12 preseason and in-season period. Preseason data were analyzed across 6 × 1-wk microcycles. In-season data were analyzed across 6 × 6-wk mesocycle blocks and 3 × 1-wk microcycles at start, midpoint, and end-time points. Data were also analyzed with respect to number of days before a match.

Results:

Typical daily training load (ie, total distance, high-speed distance, percent maximal heart rate [%HRmax], RPE load) did not differ during each week of the preseason phase. However, daily total distance covered was 1304 (95% CI 434–2174) m greater in the 1st mesocycle than in the 6th. %HRmax values were also greater (3.3%, 1.3−5.4%) in the 3rd mesocycle than in the first. Furthermore, training load was lower on the day before match (MD-1) than 2 (MD-2) to 5 (MD-5) d before a match, although no difference was apparent between these latter time points.

Conclusions:

The authors provide the 1st report of seasonal training load in elite soccer players and observed that periodization of training load was typically confined to MD-1 (regardless of mesocycle), whereas no differences were apparent during MD-2 to MD-5. Future studies should evaluate whether this loading and periodization are facilitative of optimal training adaptations and match-day performance.
Adolescents’ Physical Activity and Sedentary Behavior: A Pathway in Reducing Overweight and Obesity: The PRALIMAP 2-Year Cluster Randomized Controlled Trial
Authors: Omorou Abdou Y. , Langlois Johanne , Lecomte Edith , Vuillemin Anne , Briançon Serge , _ _
Published: November 2014

Background:

explaining why and how overweight prevention programs were effective was a real need; especially the potential role of physical activity (PA) and sedentary behavior (SB) should be highlighted. This study aimed to evaluate the 2-year effectiveness of a screening and care strategy in adolescents’ weight reduction with regards to PA and SB change.

Methods:

1745 adolescents aged 15.1 years from PRALIMAP trial was included (n = 840 for screening and care group and n = 905 for control group). PA and SB time (international physical activity questionnaire: IPAQ), body mass index (BMI), and BMI z-score were assessed at inclusion and after 2-year intervention. Hierarchical mixed models were applied.

Results:

Compared with the control group, screening and care strategy was associated with an increase in global PA (58 min/week), a moderate PA (43 min/week), the adherence to the French PA guidelines (OR = 1.3), and a decrease in SB (−198 min/week). The 2-year weight change decreased when adjusted for PA and SB suggesting that the effect of screening and care strategy was partly mediated by PA and SB.

Conclusion:

Screening and care intervention seemed to be effective in increasing PA and decreasing SB. The induced PA and SB modifications contributed to the observed weight change.
Using the Transtheoretical Model to Examine the Effects of Exergaming on Physical Activity Among Children
Authors: Pope Zachary C. , Lewis Beth A. , Gao Zan
Published: November 2014

Background:

The Transtheoretical Model (TTM) has been widely used to understand individuals’ physical activity (PA) correlates and behavior. However, the theory’s application among children in exergaming remains unknown.

Purpose:

Investigate the effects of an exergaming program on children’s TTM-based PA correlates and PA levels.

Methods:

At pretest and posttest, 212 upper elementary children (mean age = 11.17 years) from the greater Mountain West Region were administered measures regarding stages of change (SOC) for PA behavior, decisional balance for PA behaviors, PA self-efficacy, and self-reported PA levels. Following the pretest, a weekly 30-minute, 18-week Dance Dance Revolution (DDR) program was implemented. Children were classified into 3 SOC groups: progressive children (ie, progressed to a higher SOC stage); stable children (ie, remained at the same SOC stage); and regressive children (ie, regressed to a lower SOC stage).

Results:

Progressive children had greater increased PA levels than regressive children (P < .01) from pretest to posttest. Similarly, progressive children had greater increased self-efficacy (P < .05) and decision balance (P < .05) than regressive children.

Conclusions:

The findings indicate that progressive children had more improvements on self-efficacy, decisional balance, and PA levels than regressive children over time. Implications of findings are discussed.
Recombination initiation maps of individual human genomes
Authors: Pratto Florencia , Brick Kevin , Khil Pavel , Smagulova Fatima , Petukhova Galina V. , Camerini-Otero R. Daniel
Published: November 2014

DNA double-strand breaks (DSBs) are introduced in meiosis to initiate recombination and generate crossovers, the reciprocal exchanges of genetic material between parental chromosomes. Here, we present high-resolution maps of meiotic DSBs in individual human genomes. Comparing DSB maps between individuals shows that along with DNA binding by PRDM9, additional factors may dictate the efficiency of DSB formation. We find evidence for both GC-biased gene conversion and mutagenesis around meiotic DSB hotspots, while frequent colocalization of DSB hotspots with chromosome rearrangement breakpoints implicates the aberrant repair of meiotic DSBs in genomic disorders. Furthermore, our data indicate that DSB frequency is a major determinant of crossover rate. These maps provide new insights into the regulation of meiotic recombination and the impact of meiotic recombination on genome function.
The evolution of infanticide by males in mammalian societies
Authors: Lukas Dieter , Huchard Elise
Published: November 2014

Male mammals often kill conspecific offspring. The benefits of such infanticide to males, and its costs to females, probably vary across mammalian social and mating systems. We used comparative analyses to show that infanticide primarily evolves in social mammals in which reproduction is monopolized by a minority of males. It has not promoted social counterstrategies such as female gregariousness, pair living, or changes in group size and sex ratio, but is successfully prevented by female sexual promiscuity, a paternity dilution strategy. These findings indicate that infanticide is a consequence, rather than a cause, of contrasts in mammalian social systems affecting the intensity of sexual conflict.
The hydrological legacy of deforestation on global wetlands
Authors: Woodward C. , Shulmeister J. , Larsen J. , Jacobsen G. E. , Zawadzki A.
Published: November 2014

Increased catchment erosion and nutrient loading are commonly recognized impacts of deforestation on global wetlands. In contrast, an increase in water availability in deforested catchments is well known in modern studies but is rarely considered when evaluating past human impacts. We used a Budyko water balance approach, a meta-analysis of global wetland response to deforestation, and paleoecological studies from Australasia to explore this issue. After complete deforestation, we demonstrated that water available to wetlands increases by up to 15% of annual precipitation. This can convert ephemeral swamps to permanent lakes or even create new wetlands. This effect is globally significant, with 9 to 12% of wetlands affected, including 20 to 40% of Ramsar wetlands, but is widely unrecognized because human impact studies rarely test for it.
Improving planet-finding spectrometers
Authors: Crepp Justin R.
Published: November 2014

Adaptive optics will enhance the precision of exoplanet surveys
Will pork be back on the menu?
Authors: Mervis Jeffrey
Published: November 2014

Congress may reinstate earmarks as a way to pass legislation.
Mesenchymal progenitor panoply
Authors: Lee Joo-Hyeon , Kim Carla F.
Published: November 2014

Distinct pools of progenitor cells develop stromal tissues of the lung

[Also see Research Article by

Kumar
et al.

]
Dynamic genome engineering in living cells
Authors: Ausländer Simon , Fussenegger Martin
Published: November 2014

Engineered gene expression systems provide cells with a molecular memory of their past

[Also see Research Article by
Farzadfard and Lu
]
Out of sight, out of mind
Authors: Woolley Mary , Leshner Alan I.
Published: November 2014

The 2014 mid-term elections are over, and at least 62 new members of the U.S. Congress will be taking office on 3 January 2015. Many will be accompanied by new staff, not all of them familiar with science and science policy. Compounding the ambiguity that always comes with new legislators is that the leadership of the Senate has changed from Democratic to Republican. It is as yet unknown where the new leaders and committee chairs will stand on science policy issues, but so far, science has not been declared among the priorities put forward by either party. All of this is taking place just as many of science's long-time legislative champions are retiring. Overall research and development spending has already fallen 16% in inflation-adjusted dollars from fiscal year (FY) 2010 to the FY 2015 budget request. The federal government's investment in science and technology now stands at roughly 0.78% of the economy, the lowest point in 50 years. This is the right time for scientists to introduce themselves to their new legislators, congratulate them on their election, offer their services if needed on policy matters that would benefit from science input, and emphasize the importance of science to the country.
Characterization of Alpha-Toxin
hla
Gene Variants, Alpha-Toxin Expression Levels, and Levels of Antibody to Alpha-Toxin in Hemodialysis and Postsurgical Patients with Staphylococcus aureus Bacteremia
Authors: Sharma-Kuinkel Batu K. , Wu Yuling , Tabor David E. , Mok Hoyin , Sellman Bret R. , Jenkins Amy , Yu Li , Jafri Hasan S. , Rude Thomas H. , Ruffin Felicia , Schell Wiley A. , Park Lawrence P. , Yan Qin , Thaden Joshua T. , Messina Julia A. , Fowler Vance G. , Esser Mark T.
Published: November 2014

Alpha-toxin is a major
Staphylococcus aureus
virulence factor. This study evaluated potential relationships between
in vitro
alpha-toxin expression of
S. aureus
bloodstream isolates, anti-alpha-toxin antibody in serum of patients with
S. aureus
bacteremia (SAB), and clinical outcomes in 100 hemodialysis and 100 postsurgical SAB patients. Isolates underwent
spa
typing and
hla
sequencing. Serum anti-alpha-toxin IgG and neutralizing antibody levels were measured by using an enzyme-linked immunosorbent assay and a red blood cell (RBC)-based hemolysis neutralization assay. Neutralization of alpha-toxin by an anti-alpha-toxin monoclonal antibody (MAb MEDI4893) was tested in an RBC-based lysis assay. Most isolates encoded
hla
(197/200; 98.5%) and expressed alpha-toxin (173/200; 86.5%).
In vitro
alpha-toxin levels were inversely associated with survival (cure, 2.19 μg/ml, versus failure, 1.09 μg/ml;
P
< 0.01). Both neutralizing (hemodialysis, 1.26 IU/ml, versus postsurgical, 0.95;
P
< 0.05) and IgG (hemodialysis, 1.94 IU/ml, versus postsurgical, 1.27;
P
< 0.05) antibody levels were higher in the hemodialysis population. Antibody levels were also significantly higher in patients infected with alpha-toxin-expressing
S. aureus
isolates (
P
< 0.05). Levels of both neutralizing antibodies and IgG were similar among patients who were cured and those not cured (failures). Sequence analysis of
hla
revealed 12 distinct
hla
genotypes, and all genotypic variants were susceptible to a neutralizing monoclonal antibody in clinical development (MEDI4893). These data demonstrate that alpha-toxin is highly conserved in clinical
S. aureus
isolates. Higher
in vitro
alpha-toxin levels were associated with a positive clinical outcome. Although patients infected with alpha-toxin-producing
S. aureus
exhibited higher anti-alpha-toxin antibody levels, these levels were not associated with a better clinical outcome in this study.
Evaluation of the Aspergillus Western Blot IgG Kit for Diagnosis of Chronic Aspergillosis
Authors: Oliva A. , Flori P. , Hennequin C. , Dubus J.-C. , Reynaud-Gaubert M. , Charpin D. , Vergnon J. M. , Gay P. , Colly A. , Piarroux R. , Pelloux H. , Ranque S.
Published: November 2014

Immunoprecipitin detection (IPD) is the current reference confirmatory technique for anti-
Aspergillus
antibody detection; however, the lack of standardization is a critical drawback of this assay. In this study, we evaluated the performance of the
Aspergillus
Western blot (
Asp
-WB) IgG kit (LDBio Diagnostics, Lyon, France), a recently commercialized immunoblot assay for the diagnosis of various clinical presentations of chronic aspergillosis. Three hundred eight serum samples from 158 patients with aspergillosis
sensu lato
(s.l.) were analyzed. More specifically, 267 serum samples were derived from patients with
Aspergillus
disease, including 89 cases of chronic pulmonary aspergillosis, 10 of aspergilloma, and 32 of allergic bronchopulmonary aspergillosis, while 41 samples were from patients with
Aspergillus
colonization, including 15 cystic fibrosis (CF) and 12 non-CF patients. For blood donor controls, the
Asp
-WB specificity was 94%, while the kit displayed a sensitivity for the aspergillosis s.l. diagnosis of 88.6%, with a diagnostic odds ratio (DOR) of 119 (95% confidence interval [CI], 57 to 251). The DOR values were 185.22 (95% CI,78.79 to 435.45) and 43.74 (95% CI, 15.65 to 122.20) for the diagnosis of
Aspergillus
disease and
Aspergillus
colonization, respectively. Among the patients, the sensitivities of the
Asp
-WB in the diagnosis of
Aspergillus
colonization were 100% and 41.7% in CF and non-CF patients, respectively. The
Asp
-WB yielded fewer false-negative results than did IPD. In conclusion, the
Asp
-WB kit performed well for the diagnosis of various clinical presentations of aspergillosis in nonimmunocompromised patients, with an enhanced standardization and a higher sensitivity than with IPD, which is the current reference method.
Comparative Evaluation of a New Commercial Colorimetric Microdilution Assay (SensiQuattro Candida EU) with MIC Test Strip and EUCAST Broth Microdilution Methods for Susceptibility Testing of Invasive Candida Isolates
Authors: Koehling Hedda Luise , Willinger Birgit , Buer Jan , Rath Peter-Michael , Steinmann Joerg
Published: November 2014

Candidemia is an important cause of morbidity and mortality in immunosuppressed patients.
Candida
isolates must be cultivated, identified, and tested for susceptibility. We compared the performance of a new colorimetric broth microdilution panel (SensiQuattro
Candida
EU) for antifungal susceptibility testing to that of Liofilchem's MIC test strip and the EUCAST reference broth microdilution protocol. We tested 187 blood culture isolates of 5
Candida
spp. (120
C. albicans
, 38
C. glabrata
, 10
C. parapsilosis
, 12
C. tropicalis
, and 7
C. krusei
) against seven antifungal agents (amphotericin B, fluconazole, voriconazole, posaconazole, caspofungin, anidulafungin, and micafungin) and interpreted the MICs according to the EUCAST recommendations. If applicable, the overall essential agreement (EA) of the SensiQuattro panel with the reference broth microdilution was slightly higher for
C. albicans
(87%) than for other species (85.8%). We found that SensiQuattro performed best in testing amphotericin B (EA, 100%), voriconazole (EA, 93.7%), and posaconazole (EA, 94.8%) against
C. albicans
, but its error rate for this species was high (29.6%) because of mainly major errors (26.7%) in testing anidulafungin and micafungin. Compared to the SensiQuattro panel, the MIC test strip exhibited a higher level of agreement for most isolates. SensiQuattro assays are easy to perform, but they are currently not suitable for testing echinocandins against
Candida
spp.
Eilat Virus Host Range Restriction Is Present at Multiple Levels of the Virus Life Cycle
Authors: Nasar Farooq , Gorchakov Rodion V. , Tesh Robert B. , Weaver Scott C.
Published: November 2014

Most alphaviruses are mosquito-borne and exhibit a broad host range, infecting many different vertebrates, including birds, rodents, equids, humans, and nonhuman primates. This ability of most alphaviruses to infect arthropods and vertebrates is essential for their maintenance in nature. Recently, a new alphavirus, Eilat virus (EILV), was described, and in contrast to all other mosquito-borne viruses, it is unable to replicate in vertebrate cell lines. Investigations into the nature of its host range restriction showed the inability of genomic EILV RNA to replicate in vertebrate cells. Here, we investigated whether the EILV host range restriction is present at the entry level and further explored the viral factors responsible for the lack of genomic RNA replication. Utilizing Sindbis virus (SINV) and EILV chimeras, we show that the EILV vertebrate host range restriction is also manifested at the entry level. Furthermore, the EILV RNA replication restriction is independent of the 3′ untranslated genome region (UTR). Complementation experiments with SINV suggested that RNA replication is restricted by the inability of the EILV nonstructural proteins to form functional replicative complexes. These data demonstrate that the EILV host range restriction is multigenic, involving at least one gene from both nonstructural protein (nsP) and structural protein (sP) open reading frames (ORFs). As EILV groups phylogenetically within the mosquito-borne virus clade of pathogenic alphaviruses, our findings have important evolutionary implications for arboviruses.

IMPORTANCE
Our work explores the nature of host range restriction of the first “mosquito-only alphavirus,” EILV. EILV is related to pathogenic mosquito-borne viruses (Eastern equine encephalitis virus [EEEV], Western equine encephalitis virus [WEEV], Venezuelan equine encephalitis virus [VEEV], and Chikungunya virus [CHIKV]) that cause severe disease in humans. Our data demonstrate that EILV is restricted both at entry and genomic RNA replication levels in vertebrate cells. These findings have important implications for arbovirus evolution and will help elucidate the viral factors responsible for the broad host range of pathogenic mosquito-borne alphaviruses, facilitate vaccine development, and inform potential strategies to reduce/prevent alphavirus transmission.
Wongabel Rhabdovirus Accessory Protein U3 Targets the SWI/SNF Chromatin Remodeling Complex
Authors: Joubert D. Albert , Rodriguez-Andres Julio , Monaghan Paul , Cummins Michelle , McKinstry William J. , Paradkar Prasad N. , Moseley Gregory W. , Walker Peter J.
Published: November 2014

Wongabel virus (WONV) is an arthropod-borne rhabdovirus that infects birds. It is one of the growing array of rhabdoviruses with complex genomes that encode multiple accessory proteins of unknown function. In addition to the five canonical rhabdovirus structural protein genes (N, P, M, G, and L), the 13.2-kb negative-sense single-stranded RNA (ssRNA) WONV genome contains five uncharacterized accessory genes, one overlapping the N gene (Nx or U4), three located between the P and M genes (U1 to U3), and a fifth one overlapping the G gene (Gx or U5). Here we show that WONV U3 is expressed during infection in insect and mammalian cells and is required for efficient viral replication. A yeast two-hybrid screen against a mosquito cell cDNA library identified that WONV U3 interacts with the 83-amino-acid (aa) C-terminal domain of SNF5, a component of the SWI/SNF chromatin remodeling complex. The interaction was confirmed by affinity chromatography, and nuclear colocalization was established by confocal microscopy. Gene expression studies showed that SNF5 transcripts are upregulated during infection of mosquito cells with WONV, as well as West Nile virus (Flaviviridae) and bovine ephemeral fever virus (Rhabdoviridae), and that SNF5 knockdown results in increased WONV replication. WONV U3 also inhibits SNF5-regulated expression of the cytokine geneCSF1. The data suggest that WONV U3 targets the SWI/SNF complex to block the host response to infection.

IMPORTANCEThe rhabdoviruses comprise a large family of RNA viruses infecting plants, vertebrates, and invertebrates. In addition to the major structural proteins (N, P, M, G, and L), many rhabdoviruses encode a diverse array of accessory proteins of largely unknown function. Understanding the role of these proteins may reveal much about host-pathogen interactions in infected cells. Here we examine accessory protein U3 of Wongabel virus, an arthropod-borne rhabdovirus that infects birds. We show that U3 enters the nucleus and interacts with SNF5, a component of the chromatin remodeling complex that is upregulated in response to infection and restricts viral replication. We also show that U3 inhibits SNF5-regulated expression of the cytokine colony-stimulating factor 1 (CSF1), suggesting that it targets the chromatin remodeling complex to block the host response to infection. This study appears to provide the first evidence of a virus targeting SNF5 to inhibit host gene expression.
Cyclic Avian Mass Mortality in the Northeastern United States Is Associated with a Novel Orthomyxovirus
Authors: Allison Andrew B. , Ballard Jennifer R. , Tesh Robert B. , Brown Justin D. , Ruder Mark G. , Keel M. Kevin , Munk Brandon A. , Mickley Randall M. , Gibbs Samantha E. J. , Travassos da Rosa Amelia P. A. , Ellis Julie C. , Ip Hon S. , Shearn-Bochsler Valerie I. , Rogers Matthew B. , Ghedin Elodie , Holmes Edward C. , Parrish Colin R. , Dwyer Chris
Published: November 2014

Since 1998, cyclic mortality events in common eiders (
Somateria mollissima
), numbering in the hundreds to thousands of dead birds, have been documented along the coast of Cape Cod, MA, USA. Although longitudinal disease investigations have uncovered potential contributing factors responsible for these outbreaks, detecting a primary etiological agent has proven enigmatic. Here, we identify a novel orthomyxovirus, tentatively named Wellfleet Bay virus (WFBV), as a potential causative agent of these outbreaks. Genomic analysis of WFBV revealed that it is most closely related to members of the
Quaranjavirus
genus within the family
Orthomyxoviridae
. Similar to other members of the genus, WFBV contains an alphabaculovirus gp64-like glycoprotein that was demonstrated to have fusion activity; this also tentatively suggests that ticks (and/or insects) may vector the virus in nature. However, in addition to the six RNA segments encoding the prototypical structural proteins identified in other quaranjaviruses, a previously unknown RNA segment (segment 7) encoding a novel protein designated VP7 was discovered in WFBV. Although WFBV shows low to moderate levels of sequence similarity to
Quaranfil virus
and
Johnston Atoll
virus
, the original members of the
Quaranjavirus
genus, additional antigenic and genetic analyses demonstrated that it is closely related to the recently identified Cygnet River virus (CyRV) from South Australia, suggesting that WFBV and CyRV may be geographic variants of the same virus. Although the identification of WFBV in part may resolve the enigma of these mass mortality events, the details of the ecology and epidemiology of the virus remain to be determined.

IMPORTANCE
The emergence or reemergence of viral pathogens resulting in large-scale outbreaks of disease in humans and/or animals is one of the most important challenges facing biomedicine. For example, understanding how orthomyxoviruses such as novel influenza A virus reassortants and/or mutants emerge to cause epidemic or pandemic disease is at the forefront of current global health concerns. Here, we describe the emergence of a novel orthomyxovirus, Wellfleet Bay virus (WFBV), which has been associated with cyclic large-scale bird die-offs in the northeastern United States. This initial characterization study provides a foundation for further research into the evolution, epidemiology, and ecology of newly emerging orthomyxoviruses, such as WFBV, and their potential impacts on animal and/or human health.
Attenuated West Nile Virus Mutant NS1
130-132QQA/175A/207A
Exhibits Virus-Induced Ultrastructural Changes and Accumulation of Protein in the Endoplasmic Reticulum
Authors: Whiteman Melissa C. , Popov Vsevolod , Sherman Michael B. , Wen Julie , Barrett Alan D. T.
Published: November 2014

We have previously shown that ablation of the three N-linked glycosylation sites in the West Nile virus NS1 protein completely attenuates mouse neuroinvasiveness (≥1,000,000 PFU). Here, we compared the replication of the NS1
130-132QQA/175A/207A
mutant to that of the parental NY99 strain in monkey kidney Vero cells. The results suggest that the mechanism of attenuation is a lack of NS1 glycosylation, which blocks efficient replication, maturation, and NS1 secretion from the endoplasmic reticulum and results in changes to the virus-induced ultrastructure.
The ORF012 Gene of Marek's Disease Virus Type 1 Produces a Spliced Transcript and Encodes a Novel Nuclear Phosphoprotein Essential for Virus Growth
Authors: Schippers Timo , Jarosinski Keith , Osterrieder Nikolaus
Published: November 2014

Marek's disease virus (MDV), an alphaherpesvirus, is the causative agent of a lethal disease in chickens characterized by generalized nerve inflammation and rapid lymphoma development. The extensive colinearity of the MDV genome with those of related herpesviruses has eased functional characterization of many MDV genes. However, MDV carries a number of unique open reading frames (ORFs) that have not yet been investigated regarding their coding potentials and the functions of their products. Among these unique ORFs are two putative ORFs, ORF011 and ORF012, which are found at the extreme left end of the MDV unique long region. Using reverse transcriptase PCR, we showed that ORF011 and ORF012 are not individual genes but form a single gene through mRNA splicing of a small intron, resulting in the novel ORF012. We generated an ORF012-null virus using an infectious clone of MDV strain RB-1B. The deletion virus had a marked growth defect
in vitro
and could not be passaged in cultured cells, suggesting an essential role for the ORF012 product in virus replication. Further studies revealed that protein 012 (p012) localized to the nucleus in transfected and infected cells, and we identified by site-directed mutagenesis and green fluorescent protein (GFP) reporter fusion assays a nuclear localization signal (NLS) that was mapped to a 23-amino-acid sequence at the protein's C terminus. Nuclear export was blocked using leptomycin B, suggesting a potential role for p012 as a nuclear/cytoplasmic shuttling protein. Finally, p012 is phosphorylated at multiple residues, a modification that could possibly regulate its subcellular distribution.

IMPORTANCE
Marek's disease virus (MDV) causes a devastating oncogenic disease in chickens with high morbidity and mortality. The costs for disease prevention reach several billion dollars annually. The functional investigation of MDV genes is necessary to understand its complex replication cycle, which eventually could help us to interfere with MDV and herpesviral pathogenesis. We have identified a previously unidentified phosphoprotein encoded by MDV ORF012. We were able to show experimentally that predicted splicing of the gene based on bioinformatics data does indeed occur during replication. The newly identified p012 is essential for MDV replication and localizes to the nucleus due to the presence of a transferable nuclear localization signal at its C terminus. Our results also imply that p012 could constitute a nucleocytoplasmic shuttle protein, a feature that could prove interesting and important.
A case of ureteric injury postappendectomy presenting as ureterocutaneous fistula
Authors: Kumar Santosh , Parmar Kalpesh Mahesh , Singh Shivanshu , Jayant Kumar
Published: November 2014

Ureteric injuries, although uncommon, are a potential complication in pelvic and gynaecological surgeries and can have serious implications. The risk is mainly related to the complexity of the surgical procedure and the presence of eventual periureteric pathology. Ureteric injury during appendectomy is rare. The ureter may be damaged by laceration, being crushed, or thermal or ischaemic injury. The retrocaecal appendix, due to its proximity to the ureter, may also get accidentally injured. The most effective measure to prevent iatrogenic injury is to have a sound knowledge of abdominal and pelvic anatomy, meticulous surgical technique and an identification of factors that increase the likelihood of developing such complications.
RESPOND: a patient-centred programme to prevent secondary falls in older people presenting to the emergency department with a fall—protocol for a mixed methods programme evaluation
Authors: Morris R L , Brand C A , Hill K D , Ayton D R , Redfern J , Nyman S R , Lowthian J A , Hill A M , Etherton-Beer C D , Flicker L , Hunter P C , Barker A L
Published: November 2014

Background

Programme evaluations conducted alongside randomised controlled trials (RCTs) have potential to enhance understanding of trial outcomes. This paper describes a multi-level programme evaluation to be conducted alongside an RCT of a falls prevention programme (RESPOND).

Objectives

(1) To conduct a process evaluation in order to identify the degree of implementation fidelity and associated barriers and facilitators. (2) To evaluate the primary intended impact of the programme: participation in fall prevention strategies and the factors influencing participation. (3) To identify the factors influencing RESPOND RCT outcomes: falls, fall injuries and emergency department (ED) re-presentations.

Methods/design

528 community-dwelling adults aged 60–90 years presenting to two EDs with a fall will be recruited and randomly assigned to the intervention or standard care group. All RESPOND participants and RESPOND clinicians will be included in the evaluation. A mixed methods design will be used and a programme logic model will frame the evaluation. Data will be sourced from interviews, focus groups, questionnaires, clinician case notes, recruitment records, participant-completed calendars, hospital administrative datasets and audio-recordings of intervention contacts. Quantitative data will be analysed via descriptive and inferential statistics and qualitative data will be interpreted using thematic analysis.

Discussion

The RESPOND programme evaluation will provide information about contextual and influencing factors related to the RESPOND RCT outcomes. The results will assist researchers, clinicians and policy makers regarding decisions about future falls prevention interventions. Insights gained may be applicable to a range of chronic conditions where similar preventive intervention approaches are indicated.

Trial registration number

This programme evaluation is linked to the RESPOND RCT which is registered with the Australian New Zealand Clinical Trials Registry (ACTRN12614000336684).
An extension to flat band ferromagnetism
Authors: Gulacsi M. , Kovacs G. , Gulacsi Z.
Published: November 2014

From flat band ferromagnetism, we learned that the lowest energy half-filled flat band gives always ferromagnetism if the localized Wannier states on the flat band satisfy the connectivity condition. If the connectivity conditions are not satisfied, ferromagnetism does not appear. We show that this is not always the case namely, we show that ferromagnetism due to flat bands can appear even if the connectivity condition does not hold due to a peculiar behavior of the band situated just above the flat band.
Molecular vibrational dynamics in PMMA studied by femtosecond CARS
Authors: Zhao Yang , Zhang Sheng , Zhou Boyang , Fan Rongwei , Chen Deying , Zhang Zhonghua , Xia Yuanqin
Published: November 2014

The ultrafast molecular vibrational dynamics in PMMA sheets is studied by femtosecond time-resolved coherent anti-Stokes Raman spectroscopy at room temperature. The C – H stretch modes at 2870 cm-1 and 3008 cm-1 in PMMA sheets are excited and detected. The coherence relaxation times and beat wavenumbers of the Raman modes are obtained.