bluuebunny/crossref_metadata_2025 huggingface dataset:
Draft Genome Sequence of Broad-Spectrum Antifungal Bacterium Burkholderia gladioli Strain NGJ1, Isolated from Healthy Rice Seeds
Authors: Jha Gopaljee , Tyagi Isha , Kumar Rajeev , Ghosh Srayan
Published: July 2015

We report here the draft genome sequence of
Burkholderia gladioli
strain NGJ1. The strain was isolated from healthy rice seeds and exhibits broad-spectrum antifungal activity against several agriculturally important pathogens, including
Rhizoctonia solani
,
Magnaporthe oryzae
,
Venturia inaequalis
, and
Fusarium oxysporum
.
Complete Genome Sequence of an
Edwardsiella piscicida
-Like Species Isolated from Diseased Grouper in Israel
Authors: Reichley Stephen R. , Waldbieser Geoffrey C. , Ucko Michal , Colorni Angelo , Dubytska Lidiya , Thune Ronald L. , Lawrence Mark L. , Griffin Matt J.
Published: July 2015

The
Edwardsiella piscicida
-like sp. is a Gram-negative facultative anaerobe that causes disease in some fish species. We report here the complete genome sequence of a virulent isolate from a diseased white grouper (
Epinephelus aeneus
) raised on the Red Sea in Israel, which contains a chromosome of 3,934,167 bp and no plasmids.
A Single Nucleotide Polymorphism at the TaqMan Probe-Binding Site Impedes Real-Time Reverse Transcription-PCR-Based Detection of Norovirus GII.4 Sydney
Authors: Zhuo Ran , Hasing Maria Eloisa ,   Team of Molecular Diagnostics, Pang Xiaoli
Published: July 2015

A single nucleotide polymorphism (SNP) in the TaqMan probe-binding site resulted in decreased sensitivity of real-time reverse transcription-PCR (RT-rtPCR) for detection of norovirus genogroup II genotype 4 (GII.4) Sydney. A new degenerate probe was designed that improved the sensitivity of the detection while not interfering with the detection of other GII and GI strains.
Systematic Evaluation of Different Nucleic Acid Amplification Assays for Cytomegalovirus Detection: Feasibility of Blood Donor Screening
Authors: Vollmer T. , Knabbe C. , Dreier J.
Published: July 2015

Acute primary cytomegalovirus (CMV) infections, which commonly occur asymptomatically among blood donors, represent a significant risk for serious morbidity in immunocompromised patients (a major group of transfusion recipients). We implemented a routine CMV pool screening procedure for plasma for the identification of CMV DNA-positive donors, and we evaluated the sensitivities and performance of different CMV DNA amplification systems. Minipools (MPs) of samples from 18,405 individual donors (54,451 donations) were screened for CMV DNA using the RealStar CMV PCR assay (Altona Diagnostic Technologies), with a minimum detection limit of 11.14 IU/ml. DNA was extracted with a high-volume protocol (4.8 ml, Chemagic Viral 5K kit; PerkinElmer) for blood donor pool screening (MP-nucleic acid testing [NAT]) and with the Nuclisens easyMAG system (0.5 ml; bioMérieux) for individual donation (ID)-NAT. In total, six CMV DNA-positive donors (0.03%) were identified by routine CMV screening, with DNA concentrations ranging from 4.35 × 102to 4.30 × 103IU/ml. Five donors already showed seroconversion and detectable IgA, IgM, and/or IgG antibody titers (IgA+/IgM+/IgG−or IgA+/IgM+/IgG+), and one donor showed no CMV-specific antibodies. Comparison of three commercial assays, i.e., the RealStar CMV PCR kit, the Sentosa SA CMV quantitative PCR kit (Vela Diagnostics), and the CMV R-gene PCR kit (bioMérieux), for MP-NAT and ID-NAT showed comparably good analytical sensitivities, ranging from 10.23 to 11.14 IU/ml (MP-NAT) or from 37.66 to 57.94 IU/ml (ID-NAT). The clinical relevance of transfusion-associated CMV infections requires further investigation, and the evaluated methods present powerful basic tools providing sensitive possibilities for viral testing. The application of CMV MP-NAT facilitated the identification of one donor with a window-phase donation during acute primary CMV infection.
Development of a Multilocus Sequence Typing Scheme for Molecular Typing of Mycoplasma pneumoniae
Authors: Brown Rebecca J. , Holden Matthew T. G. , Spiller O. Brad , Chalker Victoria J.
Published: July 2015

Mycoplasma pneumoniaeis a major human respiratory pathogen causing both upper and lower respiratory disease in humans of all ages, and it can also result in other serious extrapulmonary sequelae. A multilocus sequence typing (MLST) scheme forM. pneumoniaewas developed based on the sequences of eight housekeeping genes (ppa,pgm,gyrB,gmk,glyA,atpA,arcC, andadk) and applied to 55M. pneumoniaeclinical isolates and the two type strains M129 and FH. A total of 12 sequence types (STs) resulted for 57M. pneumoniaeisolates tested, with a discriminatory index of 0.21 STs per isolate. The MLST loci used in this scheme were shown to be stable in 10 strains following 10 sequential subculture passages. Phylogenetic analysis of concatenated sequences of the eight loci indicated two distinct genetic clusters that were directly linked to multilocus variable-number tandem repeat analysis (MLVA) type. Genetic MLST clustering was confirmed by genomic sequence analysis, indicating that the MLST scheme developed in this study is representative of the genome. Furthermore, this MLST scheme was shown to be more discriminatory than both MLVA and P1 typing for theM. pneumoniaeisolates examined, providing a method for further and more detailed analysis of observed epidemic peaks ofM. pneumoniaeinfection. This scheme is supported by a public Web-based database (http://pubmlst.org/mpneumoniae).
Limited Variation in BK Virus T-Cell Epitopes Revealed by Next-Generation Sequencing
Authors: Sahoo Malaya K. , Tan Susanna K. , Chen Sharon F. , Kapusinszky Beatrix , Concepcion Katherine R. , Kjelson Lynn , Mallempati Kalyan , Farina Heidi M. , Fernández-Viña Marcelo , Tyan Dolly , Grimm Paul C. , Anderson Matthew W. , Concepcion Waldo , Pinsky Benjamin A.
Published: July 2015

BK virus (BKV) infection causing end-organ disease remains a formidable challenge to the hematopoietic cell transplant (HCT) and kidney transplant fields. As BKV-specific treatments are limited, immunologic-based therapies may be a promising and novel therapeutic option for transplant recipients with persistent BKV infection. Here, we describe a whole-genome, deep-sequencing methodology and bioinformatics pipeline that identify BKV variants across the genome and at BKV-specific HLA-A2-, HLA-B0702-, and HLA-B08-restricted CD8 T-cell epitopes. BKV whole genomes were amplified using long-range PCR with four inverse primer sets, and fragmentation libraries were sequenced on the Ion Torrent Personal Genome Machine (PGM). An error model and variant-calling algorithm were developed to accurately identify rare variants. A total of 65 samples from 18 pediatric HCT and kidney recipients with quantifiable BKV DNAemia underwent whole-genome sequencing. Limited genetic variation was observed. The median number of amino acid variants identified per sample was 8 (range, 2 to 37; interquartile range, 10), with the majority of variants (77%) detected at a frequency of <5%. When normalized for length, there was no statistical difference in the median number of variants across all genes. Similarly, the predominant virus population within samples harbored T-cell epitopes similar to the reference BKV strain that was matched for the BKV genotype. Despite the conservation of epitopes, low-level variants in T-cell epitopes were detected in 77.7% (14/18) of patients. Understanding epitope variation across the whole genome provides insight into the virus-immune interface and may help guide the development of protocols for novel immunologic-based therapies.
Redundant Function of Plasmacytoid and Conventional Dendritic Cells Is Required To Survive a Natural Virus Infection
Authors: Kaminsky Lauren W. , Sei Janet J. , Parekh Nikhil J. , Davies Michael L. , Reider Irene E. , Krouse Tracy E. , Norbury Christopher C.
Published: July 2015

Viruses that spread systemically from a peripheral site of infection cause morbidity and mortality in the human population. Innate myeloid cells, including monocytes, macrophages, monocyte-derived dendritic cells (mo-DC), and dendritic cells (DC), respond early during viral infection to control viral replication, reducing virus spread from the peripheral site. Ectromelia virus (ECTV), an orthopoxvirus that naturally infects the mouse, spreads systemically from the peripheral site of infection and results in death of susceptible mice. While phagocytic cells have a requisite role in the response to ECTV, the requirement for individual myeloid cell populations during acute immune responses to peripheral viral infection is unclear. In this study, a variety of myeloid-specific depletion methods were used to dissect the roles of individual myeloid cell subsets in the survival of ECTV infection. We showed that DC are the primary producers of type I interferons (T1-IFN), requisite cytokines for survival, following ECTV infection. DC, but not macrophages, monocytes, or granulocytes, were required for control of the virus and survival of mice following ECTV infection. Depletion of either plasmacytoid DC (pDC) alone or the lymphoid-resident DC subset (CD8α+DC) alone did not confer lethal susceptibility to ECTV. However, the function of at least one of the pDC or CD8α+DC subsets is required for survival of ECTV infection, as mice depleted of both populations were susceptible to ECTV challenge. The presence of at least one of these DC subsets is sufficient for cytokine production that reduces ECTV replication and virus spread, facilitating survival following infection.

IMPORTANCEPrior to the eradication of variola virus, the orthopoxvirus that causes smallpox, one-third of infected people succumbed to the disease. Following successful eradication of smallpox, vaccination rates with the smallpox vaccine have significantly dropped. There is now an increasing incidence of zoonotic orthopoxvirus infections for which there are no effective treatments. Moreover, the safety of the smallpox vaccine is of great concern, as complications may arise, resulting in morbidity. Like many viruses that cause significant human diseases, orthopoxviruses spread from a peripheral site of infection to become systemic. This study elucidates the early requirement for innate immune cells in controlling a peripheral infection with ECTV, the causative agent of mousepox. We report that there is redundancy in the function of two innate immune cell subsets in controlling virus spread early during infection. The viral control mediated by these cell subsets presents a potential target for therapies and rational vaccine design.
Transcriptional Profiling of the Immune Response to Marburg Virus Infection
Authors: Connor John H. , Yen Judy , Caballero Ignacio S. , Garamszegi Sara , Malhotra Shikha , Lin Kenny , Hensley Lisa , Goff Arthur J.
Published: July 2015

Marburg virus is a genetically simple RNA virus that causes a severe hemorrhagic fever in humans and nonhuman primates. The mechanism of pathogenesis of the infection is not well understood, but it is well accepted that pathogenesis is appreciably driven by a hyperactive immune response. To better understand the overall response to Marburg virus challenge, we undertook a transcriptomic analysis of immune cells circulating in the blood following aerosol exposure of rhesus macaques to a lethal dose of Marburg virus. Using two-color microarrays, we analyzed the transcriptomes of peripheral blood mononuclear cells that were collected throughout the course of infection from 1 to 9 days postexposure, representing the full course of the infection. The response followed a 3-stage induction (early infection, 1 to 3 days postexposure; midinfection, 5 days postexposure; late infection, 7 to 9 days postexposure) that was led by a robust innate immune response. The host response to aerosolized Marburg virus was evident at 1 day postexposure. Analysis of cytokine transcripts that were overexpressed during infection indicated that previously unanalyzed cytokines are likely induced in response to exposure to Marburg virus and further suggested that the early immune response is skewed toward a Th2 response that would hamper the development of an effective antiviral immune response early in disease. Late infection events included the upregulation of coagulation-associated factors. These findings demonstrate very early host responses to Marburg virus infection and provide a rich data set for identification of factors expressed throughout the course of infection that can be investigated as markers of infection and targets for therapy.

IMPORTANCE
Marburg virus causes a severe infection that is associated with high mortality and hemorrhage. The disease is associated with an immune response that contributes to the lethality of the disease. In this study, we investigated how the immune cells circulating in the blood of infected primates respond following exposure to Marburg virus. Our results show that there are three discernible stages of response to infection that correlate with presymptomatic, early, and late symptomatic stages of infection, a response format similar to that seen following challenge with other hemorrhagic fever viruses. In contrast to the ability of the virus to block innate immune signaling
in vitro
, the earliest and most sustained response is an interferon-like response. Our analysis also identifies a number of cytokines that are transcriptionally upregulated during late stages of infection and suggest that there is a Th2-skewed response to infection. When correlated with companion data describing the animal model from which our samples were collected, our results suggest that the innate immune response may contribute to overall pathogenesis.
Temporal Characterization of Marburg Virus Angola Infection following Aerosol Challenge in Rhesus Macaques
Authors: Lin Kenny L. , Twenhafel Nancy A. , Connor John H. , Cashman Kathleen A. , Shamblin Joshua D. , Donnelly Ginger C. , Esham Heather L. , Wlazlowski Carly B. , Johnson Joshua C. , Honko Anna N. , Botto Miriam A. , Yen Judy , Hensley Lisa E. , Goff Arthur J.
Published: July 2015

Marburg virus (MARV) infection is a lethal hemorrhagic fever for which no licensed vaccines or therapeutics are available. Development of appropriate medical countermeasures requires a thorough understanding of the interaction between the host and the pathogen and the resulting disease course. In this study, 15 rhesus macaques were sequentially sacrificed following aerosol exposure to the MARV variant Angola, with longitudinal changes in physiology, immunology, and histopathology used to assess disease progression. Immunohistochemical evidence of infection and resulting histopathological changes were identified as early as day 3 postexposure (p.e.). The appearance of fever in infected animals coincided with the detection of serum viremia and plasma viral genomes on day 4 p.e. High (>10
7
PFU/ml) viral loads were detected in all major organs (lung, liver, spleen, kidney, brain, etc.) beginning day 6 p.e. Clinical pathology findings included coagulopathy, leukocytosis, and profound liver destruction as indicated by elevated liver transaminases, azotemia, and hypoalbuminemia. Altered cytokine expression in response to infection included early increases in Th2 cytokines such as interleukin 10 (IL-10) and IL-5 and late-stage increases in Th1 cytokines such as IL-2, IL-15, and granulocyte-macrophage colony-stimulating factor (GM-CSF). This study provides a longitudinal examination of clinical disease of aerosol MARV Angola infection in the rhesus macaque model.

IMPORTANCE
In this study, we carefully analyzed the timeline of Marburg virus infection in nonhuman primates in order to provide a well-characterized model of disease progression following aerosol exposure.
Protection from Severe Influenza Virus Infections in Mice Carrying theMx1Influenza Virus Resistance Gene Strongly Depends on Genetic Background
Authors: Shin Dai-Lun , Hatesuer Bastian , Bergmann Silke , Nedelko Tatiana , Schughart Klaus
Published: July 2015

Influenza virus infections represent a serious threat to human health. Both extrinsic and intrinsic factors determine the severity of influenza. The MX dynamin-like GTPase 1 (Mx1) gene has been shown to confer strong resistance to influenza A virus infections in mice. Most laboratory mouse strains, including C57BL/6J, carry nonsense or deletion mutations inMx1and thus a nonfunctional allele, whereas wild-derived mouse strains carry a wild-typeMx1allele. Congenic C57BL/6J (B6-Mx1r/r) mice expressing a wild-type allele from the A2G mouse strain are highly resistant to influenza A virus infections, to both mono- and polybasic subtypes. Furthermore, in genetic mapping studies,Mx1was identified as the major locus of resistance to influenza virus infections. Here, we investigated whether theMx1protective function is influenced by the genetic background. For this, we generated a congenic mouse strain carrying the A2G wild-typeMx1resistance allele on a DBA/2J background (D2-Mx1r/r). Most remarkably, congenic D2-Mx1r/rmice expressing a functionalMx1wild-type allele are still highly susceptible to H1N1 virus. However, pretreatment of D2-Mx1r/rmice with alpha interferon protected them from lethal infections. Our results showed, for the first time, that the presence of anMx1wild-type allele from A2G as such does not fully protect mice from lethal influenza A virus infections. These observations are also highly relevant for susceptibility to influenza virus infections in humans.

IMPORTANCEInfluenza A virus represents a major health threat to humans. Seasonal influenza epidemics cause high economic loss, morbidity, and deaths each year. Genetic factors of the host strongly influence susceptibility and resistance to virus infections. TheMx1(MX dynamin-like GTPase 1) gene has been described as a major resistance gene in mice and humans. Most inbred laboratory mouse strains are deficient inMx1, but congenic B6-Mx1r/rmice that carry the wild-typeMx1gene from the A2G mouse strain are highly resistant. Here, we show that, very unexpectedly, congenic D2-Mx1r/rmice carrying the wild-typeMx1gene from the A2G strain are not fully protected against lethal influenza virus infections. These observations demonstrate that the genetic background is very important for the protective function of theMx1resistance gene. Our results are also highly relevant for understanding genetic susceptibility to influenza virus infections in humans.
The Cellular Factor NXP2/MORC3 Is a Positive Regulator of Influenza Virus Multiplication
Authors: Ver Lorena S. , Marcos-Villar Laura , Landeras-Bueno Sara , Nieto Amelia , Ortín Juan
Published: July 2015

Transcription and replication of influenza A virus are carried out in the nuclei of infected cells in the context of viral ribonucleoproteins (RNPs). The viral polymerase responsible for these processes is a protein complex composed of the PB1, PB2, and PA proteins. We previously identified a set of polymerase-associated cellular proteins by proteomic analysis of polymerase-containing intracellular complexes expressed and purified from human cells. Here we characterize the role of NXP2/MORC3 in the infection cycle. NXP2/MORC3 is a member of the Microrchidia (MORC) family that is associated with the nuclear matrix and has RNA-binding activity. Influenza virus infection led to a slight increase in NXP2/MORC3 expression and its partial relocalization to the cytoplasm. Coimmunoprecipitation and immunofluorescence experiments indicated an association of NXP2/MORC3 with the viral polymerase and RNPs during infection. Downregulation of NXP2/MORC3 by use of two independent short hairpin RNAs (shRNAs) reduced virus titers in low-multiplicity infections. Consistent with these findings, analysis of virus-specific RNA in high-multiplicity infections indicated a reduction of viral RNA (vRNA) and mRNA after NXP2/MORC3 downregulation. Silencing of NXP2/MORC3 in a recombinant minireplicon system in which virus transcription and replication are uncoupled showed reductions in
cat
mRNA and chloramphenicol acetyltransferase (CAT) protein accumulation but no alterations in
cat
vRNA levels, suggesting that NXP2/MORC3 is important for influenza virus transcription.

IMPORTANCE
Influenza virus infections appear as yearly epidemics and occasional pandemics of respiratory disease, with high morbidity and occasional mortality. Influenza viruses are intracellular parasites that replicate and transcribe their genomic ribonucleoproteins in the nuclei of infected cells, in a complex interplay with host cell factors. Here we characterized the role of the human NXP2/MORC3 protein, a member of the Microrchidia family that is associated with the nuclear matrix, during virus infection. NXP2/MORC3 associates with the viral ribonucleoproteins in infected cells. Downregulation of NXP2/MORC3 reduced virus titers and accumulations of viral genomic RNA and mRNAs. Silencing of NXP2/MORC3 in an influenza virus CAT minireplicon system diminished CAT protein and
cat
mRNA levels but not genomic RNA levels. We propose that NXP2/MORC3 plays a role in influenza virus transcription.
Determinants of Human CD134 Essential for Entry of Human Herpesvirus 6B
Authors: Tang Huamin , Mori Yasuko
Published: July 2015

We identified two key amino acid residues within human CD134 (hCD134) that are required for its interaction with human herpesvirus 6B (HHV-6B) and for HHV-6B entry into cells. One of the residues (K79) allows access of the HHV-6B ligand to hCD134. Murine CD134 (mCD134) functioned as an HHV-6B receptor when these two amino acid residues were replaced with homologous human residues. This study identifies both the HHV-6B receptor-ligand interaction and the species-specific determinants of hCD134 essential for HHV-6B entry.
Emphysematous cystitis-gas in bladder: a rare urological emergency
Authors: Sharma Rakesh , Mitra Subrata K , Choudhary Arpan , Majee Prasenjit
Published: July 2015

Emphysematous cystitis is an unusual inflammatory condition characterised by the presence of air within the bladder wall and lumen. It is usually seen in patients with diabetes, and in those with long-term catheterisation or of immunocompromised status. Its presentation varies from asymptomatic to frank urosepsis. It is diagnosed after radiological studies. Treatment requires establishment of prompt urinary drainage, antibiotic coverage and correction of offending factors, if any. We report a case of 41-year-old, non-diabetic, otherwise healthy woman presenting with lower urinary tract symptoms with pneumaturia, which was managed conservatively. A review of the recent literature is also presented.
Spontaneous multisystem deep venous thrombosis as an unusual presentation of Behçet's disease in a young Afro-Caribbean patient
Authors: Mitra Anuja
Published: July 2015

Behçet's disease is an autoimmune mediated multisystem vasculitis. It is most prevalent in Middle Eastern and Mediterranean patients and considered rare in Afro-Caribbean populations. The disease phenotype in Afro-Caribbean patients is more severe with systemic involvement, in particular lesions affecting the vascular system known as angio-Behçet's. The archetypal triad of disease in Behçet's includes oral stomatitis, genital ulceration and ocular lesions, however, the variety of symptoms patients experience is recognised by the revised International Criteria for Behçet's disease and is reflected in the clinical scoring criteria. The authors report an unusual case of Behçet's disease in a young Afro-Caribbean patient presenting with spontaneous bilateral renal, cerebral and pulmonary venous thrombosis as first presentation. Physicians should be aware of the aggressive and atypical manner in which Behçet's can present in Afro-Caribbean patients in order to avoid diagnostic delay and remain vigilant for thromboembolic lesions in this population.
Clinical characteristics, complications, comorbidities and treatment patterns among patients with type 2 diabetes mellitus in a large integrated health system
Authors: Pantalone Kevin M , Hobbs Todd M , Wells Brian J , Kong Sheldon X , Kattan Michael W , Bouchard Jonathan , Yu Changhong , Sakurada Brian , Milinovich Alex , Weng Wayne , Bauman Janine M , Zimmerman Robert S
Published: July 2015

Purpose

To compare the prevalence of diabetes-related complications and comorbidities, clinical characteristics, glycemic control, and treatment patterns in patients with type 2 diabetes (T2D) within a large integrated healthcare system in 2008 vs 2013.

Methods

An electronic health record system was used to create a cross-sectional summary of all patients with T2D as on 1 July 2008 and 1 July 2013. Differences between the two data sets were assessed after adjusting for age, gender, race, and household income.

Results

In 2008 and 2013, 24 493 and 41 582 patients with T2D were identified, respectively, of which the majority were male (52.3% and 50.1%) and Caucasian (79% and 75.2%). The mean ages (years) were 64.8 and 64.3. The percentages of patients across the defined A1C categories were 64.3 and 66.7 for <7%, 21.1 and 18.8 for 7–7.9%, 7.8 and 7.5 for 8–8.9%, and 6.8 and 7.0 for ≥9% in 2008 and 2013, respectively. The most prevalent T2D-related comorbidities were hypertension (82.5% and 87.2%) and cardiovascular disease (26.9% and 22.3%) in 2008 and 2013, respectively. Thiazolidinedione and sulfonylurea use decreased, whereas metformin and dipeptidyl peptidase-4 inhibitor use increased in the 5-year period.

Conclusions

Patients with T2D are characterized by a high number of comorbidities. Over 85% of the patients had an A1C<8% within our integrated health delivery system in 2008 and 2013. In 2008 and 2013, metformin therapy was the most commonly utilized antidiabetic agent, and sulfonylureas were the most commonly utilized oral antidiabetic agent in combination with metformin. As integrated health systems assume greater shared financial risk in newer payment models, achieving glycemic targets (A1C) and the management of comorbidities will become ever-more important, for preventing diabetes-related complications, as well as to ensure reimbursement for the medical care that is rendered to patients with diabetes.
Farm environment during infancy and lung function at the age of 31: a prospective birth cohort study in Finland
Authors: Lampi Jussi , Koskela Heikki , Hartikainen Anna-Liisa , Ramasamy Adaikalavan , Couto Alves Alexessander , Järvelin Marjo-Riitta , Pekkanen Juha
Published: July 2015

Objectives

Farming as an occupation is considered a risk factor for asthma and reduced lung function. By contrast, living on a farm during infancy has been reported to be associated with lower risk of asthma in adulthood. However, little is known about the association between farming environment during infancy and lung function in adulthood. We aimed to study the prospective longitudinal association between farming environment during infancy and lung function in adulthood.

Design

A prospective birth cohort study.

Setting

Northern Finland.

Participants

5666 participants born in 1966 were followed up at the age of 31 years.

Primary outcome measures

Spirometry at the age of 31 years.

Results

To be born into a farmer’s family was associated with higher forced expiratory volume in 1 s (FEV1) (36 mL; 95% CI 6 to 67 mL) and forced vital capacity (FVC) (40 mL; 95% CI 5 to 75 mL) at the age of 31 years. Contact with farm animals during infancy was associated with higher FEV1. No associations were seen with FEV1/FVC (FEV1/FVC ratio). Having dogs in childhood revealed similar associations. There was a suggestive dose-dependent association with the number of animal species during childhood and higher FEV1 and FVC at adulthood, especially among women.

Conclusions

Farming environment in early life may have a positive impact on lung function in adulthood.
‘You are just left to get on with it’: qualitative study of patient and carer experiences of the transition to secondary progressive multiple sclerosis
Authors: Davies F , Edwards A , Brain K , Edwards M , Jones R , Wallbank R , Robertson N P , Wood F
Published: July 2015

Objectives

Although the transition to secondary progressive multiple sclerosis (SPMS) is known to be a period of uncertainty for clinicians, who may find progressive disease challenging to objectively identify, little research has explored the experiences of patients and carers specifically during this transition period. Our objective was to explore what patients and their carers understand about their disease stage and describe their experiences and perspectives on the transition to SPMS.

Design

Semistructured qualitative interviews and subsequent validation focus groups were analysed using inductive thematic analysis.

Setting

South East Wales, UK.

Participants

20 patients with MS and 13 carers were interviewed. Eight patients and two carers participated in focus groups.

Results

Four main themes around disease progression were identified. ‘Realisation’ describes how patients came to understand they had SPMS while ‘reaction’ describes their response to this realisation. The ‘realities’ of living with SPMS, including dealing with the healthcare system during this period, were described along with ‘future challenges’ envisaged by patients and carers.

Conclusions

Awareness that the transition to SPMS has occurred, and subsequent emotional reactions and coping strategies, varied widely between patients and their carers. The process of diagnosing the transition was often not transparent and some individuals wanted information to help them understand what the transition to SPMS meant for them.
Exploring the impact of consultants’ experience on hospital mortality by day of the week: a retrospective analysis of hospital episode statistics
Authors: Ruiz Milagros , Bottle Alex , Aylin Paul P
Published: July 2015

Objective

To examine the association of consultants’ experience with mortality by day of the week when elective surgery was performed.

Design

Retrospective observational study using English hospital administrative data.

Setting

All acute and specialist English National Health Service (NHS) hospitals carrying out elective surgery between financial years 2008–2009 and 2010–2011.

Participants

Patients undergoing elective surgical procedures.

Main outcome measures

Death in or out of hospital within 30 days of the surgical procedure taking place.

Results

We examined 3 922 091 (26 409 deaths) elective procedures with valid consultant information between 2008–2009 and 2010–2011 in English hospitals; there were 21 196 consultants in charge of these procedures, which took place in 163 NHS hospitals. Consultant seniority had no significant impact in predicting mortality (p=0.345). Patients undergoing elective surgery underjuniorconsultants had slightly lower odds of 30-day death when compared with patients under more experienced consultants (OR 0.95, 95% CI 0.91 to 0.99). We found significant mortality variation among consultants in charge of elective procedures within hospitals, with only moderate variation between hospitals. The adjusted odds of death remained higher for Friday (OR 1.48, 95% CI 1.42 to 1.54), Saturday (OR 1.97, 95% CI 1.83 to 2.12) and Sunday (OR 1.67, 95% CI 1.50 to 1.85) after adjusting for consultant seniority and patient characteristics. Consultant experience is significantly lower (p<0.0001) on a Friday (median (SD) was 7.9 years (4.4)) than the Monday to Thursday average (median (SD) was 8.5 years (4.3)).

Conclusions

Our cohort of patients shows that consultant seniority is not a significant factor in predicting 30-day mortality following elective surgery by day of the week. The end-of-the-week effect remains significant after adjusting for patient, consultant and hospital effects, suggesting that other unobserved factors may be driving the higher mortality towards the end of the week. Consultant's years of experience are lowest on a Friday; however, we do not believe that this small variation has any impact on patient outcomes.
Increasingly exotic…
Authors: Cracknell Jonathan
Published: July 2015

Continuing Veterinary Record's series of articles discussing the state of different sectors of the veterinary profession, Jonathan Cracknell considers the role of the exotics vet and how this sector has evolved over time.
Woodland mouse and vole response to increased structural diversity following midrotation commercial thinning in spruce plantations
Authors: Dracup Evan C. , Keppie Daniel M. , Forbes Graham J.
Published: July 2015

We assessed whether commercially thinning (CT) spruce (Picea spp.) plantations (40% basal area removal) can cause structural changes in fine woody debris (FWD) and understory vegetation to improve habitat quality for small rodents in northwestern New Brunswick, Canada. We created three contrasting environments (FWD rich – understory vegetation rich, FWD poor – understory vegetation rich, and FWD poor – understory vegetation poor) by establishing CT with debris retention (merchantable trunk removal), CT with all debris removed (full tree removal), and non-CT (plantation without CT) in six midrotation white spruce (Picea glauca (Moench) Voss) plantations. We live-trapped small mammals in each plantation during spring and summer of 2011 and 2012 and estimated animal density and survival with capture–recapture models. Southern red-backed vole (Myodes gapperi (Vigors, 1830)) density was two to three times greater in CT with debris retention than in either non-CT or CT with debris removal, and their survival rate was twice that in CT with debris removal. Woodland jumping mouse (Napaeozapus insignis (Miller, 1891)) density was two to five times greater in non-CT than in either CT treatment. Deer mice (Peromyscus maniculatus (Wagner, 1845)) did not show any treatment effect. Productivity and demographics were not affected by CT treatment for any species. We found evidence that midrotation spruce plantations are used differently by small mammal species based on stand condition and recommend that managers maintain plantations in CT and non-CT states.
Comparison of gut fill in sheep (Ovis aries) measured by intake, digestibility, and digesta retention compared with measurements at harvest
Authors: Munn Adam , Stewart Mathew , Price Elizabeth , Peilon Alice , Savage Tom , Van Ekris Irene , Clauss Marcus
Published: July 2015

Gut capacity is an important factor in digestive physiology and is often measured as dry matter fill (DMF) following dissection, which prevents repeated measures in the same animal. It was proposed to calculate DMF from food intake, digestibility, and gut mean retention time (MRT), but empirical tests of this are few. We calculated DMF from intake, digestibility, and the MRT of small-particle (1 mm) and large-particle (20 mm) markers in 20 sheep (Ovis aries L., 1758) fed at different intake levels and compared results with DMF at dissection at the end of the feeding trial. MRT for smaller particles was significantly shorter than for larger particles (34.4 ± 6.1 vs. 42.5 ± 7.6 h, respectively). Correspondingly, DMF calculated from smaller particles (0.98 ± 0.27 kg) was significantly lower than DMF calculated from larger particles (1.20 ± 0.30 kg). The latter was not significantly different from DMF measured at dissection (1.18 ± 0.34 kg). These results suggest that DMF can be estimated from measures of digestive physiology. The choice of particle marker to determine MRT is crucial for the accuracy of the proxy. In ruminants, where small particles are consistently eliminated faster than larger particles, considerations of marker particle size are particularly important.
Banach function norms via Cauchy polynomials and applications
Authors: Anatriello Giuseppina , Fiorenza Alberto , Vincenzi Giovanni
Published: July 2015

Let X1,…,Xk be quasinormed spaces with quasinorms | ⋅ |j, j = 1,…,k, respectively. For any f = (f1,⋯,fk) ∈ X1 ×⋯× Xk let ρ(f) be the unique non-negative root of the Cauchy polynomial [Formula: see text]. We prove that ρ(⋅) (which in general cannot be expressed by radicals when k ≥ 5) is a quasinorm on X1 ×⋯× Xk, which we call root quasinorm, and we find a characterization of this quasinorm as limit of ratios of consecutive terms of a linear recurrence relation. If X1,…,Xk are normed, Banach or Banach function spaces, then the same construction gives respectively a normed, Banach or a Banach function space. Norms obtained as roots of polynomials are already known in the framework of the variable Lebesgue spaces, in the case of the exponent simple function with values 1,…,k. We investigate the properties of the root quasinorm and we establish a number of inequalities, which come from a rich literature of the past century.
The indium oxide micro and nanopyramids: Morphology materializing and H2S sensing properties
Authors: Shariati Mohsen
Published: July 2015

Indium oxide ( In 2 O 3) pyramidal nano and microstructures were prepared by a thermal evaporation and condensation method. The preannealing step affected the nanostructures morphologies and their sensing capability. The nanosize structures have been fabricated in nucleated preorganized situation. By changing from prepared sites to undesired sites, the morphology was deteriorated. The synthesized In 2 O 3 structures were characterized by field emission scanning electron microscopy (FESEM) and the X-ray diffraction (XRD) measurements. The FESEM images showed that nanostructures with 100–250 nm in size were fabricated. The XRD patterns indicated that most of the samples are crystalline. Then, the fabricated structures were investigated for H 2 S gas sensing. The nanocrystal pyramids were found to be sensitive to as low as 100 ppb of H 2 S gas at room temperature and microcrystal ones to 300 ppb. The nanopyramids demonstrated that they were very sensitive to gas presence and their response and recovery time were in a few seconds.
The AJ-Conjecture and cabled knots over torus knots
Authors: Ruppe Dennis , Zhang Xingru
Published: July 2015

We show that most cabled knots over torus knots in S3 satisfy the AJ-conjecture, namely each (r, s)-cabled knot over each (p, q)-torus knot satisfies the AJ-conjecture if r is not a number between 0 and pqs.
ELECTRONIC AND MAGNETIC PROPERTIES OF MONOLAYER WS2 DOPED WITH MnXm (m = 0, 3, 6; = N, O, F)
Authors: YUAN JIAREN , YAN XIAOHONG , DAI CHANGJIE , XIAO YANG , GUO YANDONG
Published: July 2015

The structural, electronic and magnetic properties of monolayer WS 2 doped with single Mn atom, MnX 3 and MnX 6 clusters ( X = N , O and F ) are investigated using first principles approach. Monolayer WS 2 doped with single Mn atom displays a spin gapless semiconducting character. WS 2 embedded with MnX 3 and MnX 6 presents rich electronic and magnetic properties. For example, monolayer WS 2 incorporated with MnF 3 exhibits a half-metallic nature. The substitutions of impurities introduce magnetism except MnN 3. The calculation results demonstrate that monolayer WS 2 is a promising material for spintronic device when doped with MnX m.
Distant Speaker Recognition: An Overview
Authors: Nematollahi Mohammad Ali , Al-Haddad S. A. R.
Published: July 2015

Distant speaker recognition (DSR) system assumes the microphones are far away from the speaker’s mouth. Also, the position of microphones can vary. Furthermore, various challenges and limitation in terms of coloration, ambient noise and reverberation can bring some difficulties for recognition of the speaker. Although, applying speech enhancement techniques can attenuate speech distortion components, it may remove speaker-specific information and increase the processing time in real-time application. Currently, many efforts have been investigated to develop DSR for commercial viable systems. In this paper, state-of-the-art techniques in DSR such as robust feature extraction, feature normalization, robust speaker modeling, model compensation, dereverberation and score normalization are discussed to overcome the speech degradation components i.e., reverberation and ambient noise. Performance results on DSR show that whenever speaker to microphone distant increases, recognition rates decreases and equal error rate (EER) increases. Finally, the paper concludes that applying robust feature and robust speaker model varying lesser with distant, can improve the DSR performance.
TECHNOLOGICAL SPILLOVERS THROUGH A PATENT CITATION ANALYSIS
Authors: ALDIERI LUIGI , VINCI CONCETTO PAOLO
Published: July 2015

The aim of this paper is to analyse the pattern of knowledge flows as evidenced by the patent citations in three economic areas: USA, Japan and Europe. In each economic area, we exploit information from two international patent offices data, the United States Patent and Trademarks Office (USPTO) data and the European Patent Office (EPO) data. In this way, we can investigate the link between the technological proximity and knowledge spillovers for 240 international firms. In particular, the contribution to the existing literature is twofold: First, we use an international sample so that we can compare the empirical results among different economic markets; second, we explore the robustness of results with respect to patent system features. In order to compute the technological proximity, we consider both the symmetrical measure and asymmetrical one. The empirical results indicate that there is a statistically significant correlation between technological proximity and knowledge spillovers measured by patent citations and that these results are robust with respect to patent office data used in the analysis.
Transport of Cu–H2O nanofluid through a channel with wavy walls under velocity slip and connective boundary conditions
Authors: Abbasi F. M. , Hayat T. , Alsaedi A.
Published: July 2015

Present study examines the mixed convective peristaltic transport of Cu–H2O nanofluid with velocity slip and convective boundary conditions. Analysis is performed using the two-phase model of the nanofluid. Viscous dissipation and heat generation/absorption effects are also taken into account. Problem is formulated using the long wavelength and low Reynolds number approach. Numerical solutions for the pressure rise per wavelength, pressure gradient, axial velocity, temperature and heat transfer rate at the boundary are obtained and studied through graphs. Results show that the area of peristaltic pumping decreases with an increase in the nanoparticles volume fraction. Increase in the velocity slip parameter shows an increase of the pressure gradient in the occluded part of the channel. Further, addition of copper nanoparticles reduces both the axial velocity and temperature of the base fluid. Temperature of the nanofluid also decreases sufficiently for an increase in the value of Biot number.
On singular values distribution of a matrix large auto-covariance in the ultra-dimensional regime
Authors: Wang Qinwen , Yao Jianfeng
Published: July 2015

Let [Formula: see text] be a sequence of independent real random vectors of [Formula: see text]-dimension and let [Formula: see text] be the lag-[Formula: see text] ([Formula: see text] is a fixed positive integer) auto-covariance matrix of [Formula: see text]. This paper investigates the limiting behavior of the singular values of [Formula: see text] under the so-called ultra-dimensional regime where [Formula: see text] and [Formula: see text] in a related way such that [Formula: see text]. First, we show that the singular value distribution of [Formula: see text], after a suitable normalization, converges to a non-random limit [Formula: see text] (quarter law) under the fourth-moment condition. Second, we establish the convergence of its largest singular value to the right edge of the support of [Formula: see text]. Both results are derived using the moment method.
Rhesus rotavirus VP4 sequence-specific activation of mononuclear cells is associated with cholangiopathy in murine biliary atresia
Authors: Walther Ashley , Mohanty Sujit K. , Donnelly Bryan , Coots Abigail , Lages Celine S. , Lobeck Inna , Dupree Phylicia , Meller Jaroslaw , McNeal Monica , Sestak Karol , Tiao Greg
Published: July 2015

Biliary atresia (BA), a neonatal obstructive cholangiopathy, remains the most common indication for pediatric liver transplantation in the United States. In the murine model of BA, Rhesus rotavirus (RRV) VP4 surface protein determines biliary duct tropism. In this study, we investigated how VP4 governs induction of murine BA. Newborn mice were injected with 16 strains of rotavirus and observed for clinical symptoms of BA and mortality. Cholangiograms were performed to confirm bile duct obstruction. Livers and bile ducts were harvested 7 days postinfection for virus titers and histology. Flow cytometry assessed mononuclear cell activation in harvested cell populations from the liver. Cytotoxic NK cell activity was determined by the ability of NK cells to kill noninfected cholangiocytes. Of the 16 strains investigated, the 6 with the highest homology to the RRV VP4 (>87%) were capable of infecting bile ducts in vivo. Although the strain Ro1845 replicated to a titer similar to RRV in vivo, it caused no symptoms or mortality. A Ro1845 reassortant containing the RRV VP4 induced all BA symptoms, with a mortality rate of 89%. Flow cytometry revealed that NK cell activation was significantly increased in the disease-inducing strains and these NK cells demonstrated a significantly higher percentage of cytotoxicity against noninfected cholangiocytes. Rotavirus strains with >87% homology to RRV's VP4 were capable of infecting murine bile ducts in vivo. Development of murine BA was mediated by RRV VP4-specific activation of mononuclear cells, independent of viral titers.
Blood flow-restricted strength training displays high functional and biological efficacy in women: a within-subject comparison with high-load strength training
Authors: Ellefsen Stian , Hammarström Daniel , Strand Tor A. , Zacharoff Erika , Whist Jon E. , Rauk Irene , Nygaard Håvard , Vegge Geir , Hanestadhaugen Marita , Wernbom Mathias , Cumming Kristoffer T. , Rønning Roar , Raastad Truls , Rønnestad Bent R.
Published: July 2015

Limited data exist on the efficacy of low-load blood flow-restricted strength training (BFR), as compared directly to heavy-load strength training (HST). Here, we show that 12 wk of twice-a-week unilateral BFR [30% of one repetition maximum (1RM) to exhaustion] and HST (6-10RM) of knee extensors provide similar increases in 1RM knee extension and cross-sectional area of distal parts of musculus quadriceps femoris in nine untrained women (age 22 ± 1 yr). The two protocols resulted in similar acute increases in serum levels of human growth hormone. On the cellular level, 12 wk of BFR and HST resulted in similar shifts in muscle fiber composition in musculus vastus lateralis, evident as increased MyHC2A proportions and decreased MyHC2X proportions. They also resulted in similar changes of the expression of 29 genes involved in skeletal muscle function, measured both in a rested state following 12 wk of training and subsequent to singular training sessions. Training had no effect on myonuclei proportions. Of particular interest, 1) gross adaptations to BFR and HST were greater in individuals with higher proportions of type 2 fibers, 2) both BFR and HST resulted in approximately four-fold increases in the expression of the novel exercise-responsive gene Syndecan-4, and 3) BFR provided lesser hypertrophy than HST in the proximal half of musculus quadriceps femoris and also in CSApeak, potentially being a consequence of pressure from the tourniquet utilized to achieve blood flow restriction. In conclusion, BFR and HST of knee extensors resulted in similar adaptations in functional, physiological, and cell biological parameters in untrained women.