bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Muc5b promoter polymorphism on disease predisposition and survival in idiopathic interstitial pneumonias
Authors: van der Vis Joanne J. , Snetselaar Reinier , Kazemier Karin M. , ten Klooster Liesbeth , Grutters Jan C. , van Moorsel Coline H.M. 
Published: December 2015

AbstractBackground and objectiveA common polymorphism in the MUC5B gene (rs35705950) is associated with susceptibility to idiopathic pulmonary fibrosis (IPF) and familial interstitial pneumonia (FIP). We investigated predisposition of the MUC5B polymorphism to fibrotic interstitial pneumonias in Dutch Caucasian patient cohorts. Furthermore, we investigated the correlation between MUC5B genotype and survival in these cohorts.MethodsSporadic IPF (spIPF, n = 115), FIP (n = 55), idiopathic non‐specific interstitial pneumonia (iNSIP, n = 43), connective tissue disease associated interstitial pneumonia (CTD_IP, n = 35) and a control cohort (n = 249) were genotyped for rs35705950.ResultsRs35705950 minor allele frequency (MAF) in controls was 0.09. Case‐control analysis showed significant allelic association with spIPF (MAF = 0.27; P = 5.0 × 10−10), FIP (MAF = 0.30; P = 2.7 × 10−9) and iNSIP (MAF = 0.22; P = 3.4 × 10−4). No association was observed in CTD_IP (MAF = 0.07). FIP subgroup analysis revealed an association between MUC5B and telomerase mutated FIP (P = 0.003), and between MUC5B and FIP with unknown genetic cause (P = 1.2 × 10−8). In spIPF carriership of MUC5B minor allele did not influence survival. In FIP MUC5B minor allele carriers had better survival (non‐carriers 37 vs carriers 53 months, P = 0.01). In iNSIP survival analysis showed an opposite effect. Worse survival was found in iNSIP patients that carried the MUC5B minor allele (non‐carriers 118 vs carriers 46 months, P = 0.027)Conclusion This study showed that MUC5B minor allele predisposes to spIPF, FIP and iNSIP. In spIPF, survival is not influenced by MUC5B alleles. In FIP, MUC5B minor allele predicts better survival, pointing towards a subgroup of FIP patients with a milder, MUC5B‐driven form of pulmonary fibrosis.
The initiation of pull‐apart basins and transform continental margins: results from numerical experiments of kinematic partitioning in divergent settings
Authors: Basile Christophe , Braun Jean 
Published: December 2015

AbstractWe present a set of numerical models to investigate how transform faults initiate in pull‐apart basins or transform continental margins. The model represents an elastic plate with three aligned weak spots. Applying strain on the edge of the model firstly propagates extensional cracks from the pre‐existing damaged spots. The subsequent evolution depends on the angle (obliquity) between the applied strain and the alignment of the damaged spots. For obliquity <50°, transform faults form to connect en‐échelon divergent cracks; for obliquity >60°, transtensional transfer zones connect the divergent cracks and no transform fault forms. These experiments suggest that pull‐apart basins do not form as previously assumed by connection of overlapping transform faults, but that transform faults form as connections of extensional areas.
Can gossip change nutrition behaviour? Results of a mass media and community‐based intervention trial in East Java, Indonesia
Authors: White Sian , Schmidt Wolf , Sahanggamu Daniel , Fatmaningrum Dewi , van Liere Marti , Curtis Val 
Published: December 2015

AbstractObjectiveIt is unclear how best to go about improving child feeding practices. We studied the effect of a novel behaviour change intervention, Gerakan Rumpi Sehat (the Healthy Gossip Movement), on infant and young child feeding practices in peri‐urban Indonesia.MethodsThe pilot intervention was designed based on the principles of a new behaviour change theory, Behaviour Centred Design (BCD). It avoided educational messaging in favour of employing emotional drivers of behaviour change, such as affiliation, nurture and disgust and used television commercials, community activations and house‐to‐house visits as delivery channels. The evaluation took the form of a 2‐arm cluster randomised trial with a non‐randomised control arm. One intervention arm received TV only, while the other received TV plus community activations. The intervention components were delivered over a 3‐month period in 12 villages in each arm, each containing an average of 1300 households. There were two primary outcomes: dietary diversity of complementary food and the provision of unhealthy snacks to children aged 6–24 months.ResultsDietary diversity scores increased by 0.8 points in the arm exposed to TV adverts only (95% CI: 0.4–1.2) and a further 0.2 points in the arm that received both intervention components (95% CI: 0.6–1.4). In both intervention arms, there were increases in the frequency of vegetable and fruit intake. We found inconsistent evidence of an effect on unhealthy snacking.ConclusionThe study suggests that novel theory‐driven approaches which employ emotional motivators are capable of having an effect on improving dietary diversity and the regularity of vegetable and fruit intake among children aged 6–24 months. Mass media can have a measurable effect on nutrition‐related behaviour, but these effects are likely to be enhanced through complementary community activations. Changing several behaviours at once remains a challenge.
Transforming growth factor beta (TGF‐β) isoforms in wound healing and fibrosis
Authors: Lichtman Michael K. , Otero‐Vinas Marta , Falanga Vincent 
Published: December 2015

AbstractScar formation, with persistent alteration of the normal tissue structure, is an undesirable and significant result of both wound healing and fibrosing disorders. There are few strategies to prevent or to treat scarring. The transforming growth factor beta (TGF‐β) superfamily is an important mediator of tissue repair. Each TGF‐β isoform may exert a different effect on wound healing, which may be context‐dependent. In particular, TGF‐β1 may mediate fibrosis in adults’ wounds, while TGF‐β3 may promote scarless healing in the fetus and reduced scarring in adults. Thus, TGF‐β3 may offer a scar‐reducing therapy for acute and chronic wounds and fibrosing disorders.
Ventral hippocampus modulates bradycardic response to peripheral chemoreflex activation in awake rats
Authors: Kuntze Luciana Bärg , Ferreira‐Junior Nilson Carlos , Lagatta Davi Campos , Resstel Leonardo Barbosa Moraes 
Published: December 2015

New Findings

What is the central question of this study?
Does reversible synaptic inactivation by CoCl2 in the dorsal (DH) or ventral (VH) portions of the hippocampus have a modulatory effect on cardiovascular and respiratory responses evoked by chemoreflex activation in awake rats?

What is the main finding and its importance?
Using i.v. infusion of KCN to activate the peripheral chemoreflex before and after microinjection of CoCl2 into VH, we showed that the bradycardic response was increased, but not the pressor and tachypnoeic responses even if the tidal volume had been increased. Thus, VH but not DH may be involved in the modulation of the parasympathoexcitatory component of the peripheral chemoreflex.

In rats, peripheral chemoreflex activation evokes pressor and bradycardic responses as well as a tachypnoeic response. Studies have shown that limbic structures, such as the hippocampus, can modulate autonomic reflexes. Evidence suggests that the dorsal (DH) and the ventral (VH) portions of the hippocampus are structurally and functionally distinct; therefore, in the present study we tested the hypothesis that local neurotransmission of the DH and VH are involved in the neural pathways of the cardiovascular and ventilatory responses to chemoreflex activation. Thus, the goal of the present study was to compare the chemoreflex responses elicited by i.v. injection of KCN (40 μg per rat) in awake rats before and after DH and VH synaptic transmission was temporarily inhibited by bilateral microinjections of 500 nl of the unspecific synapse blocker, CoCl2 (1 mm). Bilateral inhibition of VH, but not DH, 10 min before KCN infusion was able to enhance the bradycardic response (P < 0.05), with no changes in the typical pressor and tachypnoeic responses evoked by chemoreflex activation (P > 0.05). Furthermore, the tidal volume was significantly increased (P < 0.05) even though no other respiratory parameter had been significantly changed (P > 0.05), suggesting that VH can exert a tonic modulatory action on tidal volume. Therefore, the present study reports, for the first time, that DH neurotransmission did not exert an influence on chemoreflex responses, whereas VH mediates, at least in part, the parasympathoexcitatory component of the peripheral chemoreflex.
Complete Genome Sequence of a Hepatitis D Virus Genotype 1 Strain Isolated in Guangdong, China
Authors: Liao Baolin , Chen Weilie , Ping Qu , Shi Haiyan , He Haolan , Liu Huiyuan , Tan Yizhou , Lei Chunliang , Cai Weiping 
Published: December 2015

ABSTRACT
Here, we report the first complete genome sequence of a hepatitis D virus genotype 1 strain, GZ37, isolated in Guangzhou, Guangdong Province, China, in 2014. The sequence information provided here will help us understand the molecular epidemiology of hepatitis D virus and contribute to disease control in mainland China.
Draft Genome Sequence of “
Candidatus
Liberibacter asiaticus” from a Citrus Tree in San Gabriel, California
Authors: Wu F. , Kumagai L. , Liang G. , Deng X. , Zheng Z. , Keremane M. , Chen J. 
Published: December 2015

ABSTRACT

The draft genome sequence of “
Candidatus
Liberibacter asiaticus” strain SGCA5 from an orange citrus tree in San Gabriel, California, is reported here. SGCA5 has a genome size of 1,201,445 bp, a G+C content of 36.4%, 1,152 predicted open reading frames (ORFs), and 42 RNA genes.
Complete Genome Sequence of Bovine Viral Diarrhea Virus-1 Strain Egy/Ismailia/2014, Subtype 1b
Authors: Soltan Mohamed A. , Wilkes Rebecca P. , Elsheery Mohamed N. , Elhaig Mahmoud M. , Riley Matthew C. , Kennedy Melissa A. 
Published: December 2015

ABSTRACT
Here, we report the complete genome sequence of bovine viral diarrhea virus-1b (BVDV-1b), strain Egy/Ismailia/2014. The virus genome is composed of 12,217 nucleotides organized as one open reading frame encoding 3,898 amino acids. This report will assist efforts in diagnostics, studying molecular epidemiology, and control of BVDV in Egypt.
A Pan-HIV Strategy for Complete Genome Sequencing
Authors: Berg Michael G. , Yamaguchi Julie , Alessandri-Gradt Elodie , Tell Robert W. , Plantier Jean-Christophe , Brennan Catherine A. 
Published: December 2015

ABSTRACT

Molecular surveillance is essential to monitor HIV diversity and track emerging strains. We have developed a universal library preparation method (HIV-SMART [i.e.,
s
witching
m
echanism
a
t 5′ end of
R
NA
t
ranscript]) for next-generation sequencing that harnesses the specificity of HIV-directed priming to enable full genome characterization of all HIV-1 groups (M, N, O, and P) and HIV-2. Broad application of the HIV-SMART approach was demonstrated using a panel of diverse cell-cultured virus isolates. HIV-1 non-subtype B-infected clinical specimens from Cameroon were then used to optimize the protocol to sequence directly from plasma. When multiplexing 8 or more libraries per MiSeq run, full genome coverage at a median ∼2,000× depth was routinely obtained for either sample type. The method reproducibly generated the same consensus sequence, consistently identified viral sequence heterogeneity present in specimens, and at viral loads of ≤4.5 log copies/ml yielded sufficient coverage to permit strain classification. HIV-SMART provides an unparalleled opportunity to identify diverse HIV strains in patient specimens and to determine phylogenetic classification based on the entire viral genome. Easily adapted to sequence any RNA virus, this technology illustrates the utility of next-generation sequencing (NGS) for viral characterization and surveillance.
Structure-Based Mutagenesis of Sulfolobus Turreted Icosahedral Virus B204 Reveals Essential Residues in the Virion-Associated DNA-Packaging ATPase
Authors: Dellas Nikki , Snyder Jamie C. , Dills Michael , Nicolay Sheena J. , Kerchner Keshia M. , Brumfield Susan K. , Lawrence C. Martin , Young Mark J. 
Published: December 2015

ABSTRACT

Sulfolobus
turreted icosahedral virus (STIV), an archaeal virus that infects the hyperthermoacidophile
Sulfolobus solfataricus
, is one of the most well-studied viruses of the domain
Archaea
. STIV shares structural, morphological, and sequence similarities with viruses from other domains of life, all of which are thought to belong to the same viral lineage. Several of these common features include a conserved coat protein fold, an internal lipid membrane, and a DNA-packaging ATPase. B204 is the ATPase encoded by STIV and is thought to drive packaging of viral DNA during the replication process. Here, we report the crystal structure of B204 along with the biochemical analysis of B204 mutants chosen based on structural information and sequence conservation patterns observed among members of the same viral lineage and the larger FtsK/HerA superfamily to which B204 belongs. Both
in vitro
ATPase activity assays and transfection assays with mutant forms of B204 confirmed the essentiality of conserved and nonconserved positions. We also have identified two distinct particle morphologies during an STIV infection that differ in the presence or absence of the B204 protein. The biochemical and structural data presented here are not only informative for the STIV replication process but also can be useful in deciphering DNA-packaging mechanisms for other viruses belonging to this lineage.

IMPORTANCE
STIV is a virus that infects a host from the domain
Archaea
that replicates in high-temperature, acidic environments. While STIV has many unique features, there exist several striking similarities between this virus and others that replicate in different environments and infect a broad range of hosts from
Bacteria
and
Eukarya
. Aside from structural features shared by viruses from this lineage, there exists a significant level of sequence similarity between the ATPase genes carried by these different viruses; this gene encodes an enzyme thought to provide energy that drives DNA packaging into the virion during infection. The experiments described here highlight the elements of this enzyme that are essential for proper function and also provide supporting evidence that B204 is present in the mature STIV virion.
Homologous Recombination Repair Factors Rad51 and BRCA1 Are Necessary for Productive Replication of Human Papillomavirus 31
Authors: Chappell William H. , Gautam Dipendra , Ok Suzan T. , Johnson Bryan A. , Anacker Daniel C. , Moody Cary A. 
Published: December 2015

ABSTRACT
High-risk human papillomavirus 31 (HPV31)-positive cells exhibit constitutive activation of the ATM-dependent DNA damage response (DDR), which is necessary for productive viral replication. In response to DNA double-strand breaks (DSBs), ATM activation leads to DNA repair through homologous recombination (HR), which requires the principal recombinase protein Rad51, as well as BRCA1. Previous studies from our lab demonstrated that Rad51 and BRCA1 are expressed at high levels in HPV31-positive cells and localize to sites of viral replication. These results suggest that HPV may utilize ATM activity to increase HR activity as a means to facilitate viral replication. In this study, we demonstrate that high-risk HPV E7 expression alone is sufficient for the increase in Rad51 and BRCA1 protein levels. We have found that this increase occurs, at least in part, at the level of transcription. Studies analyzing protein stability indicate that HPV may also protect Rad51 and BRCA1 from turnover, contributing to the overall increase in cellular levels. We also demonstrate that Rad51 is bound to HPV31 genomes, with binding increasing per viral genome upon productive replication. We have found that depletion of Rad51 and BRCA1, as well as inhibition of Rad51's recombinase activity, abrogates productive viral replication upon differentiation. Overall, these results indicate that Rad51 and BRCA1 are required for the process of HPV31 genome amplification and suggest that productive replication occurs in a manner dependent upon recombination.

IMPORTANCE
Productive replication of HPV31 requires activation of an ATM-dependent DNA damage response, though how ATM activity contributes to replication is unclear. Rad51 and BRCA1 play essential roles in repair of double-strand breaks, as well as the restart of stalled replication forks through homologous recombination (HR). Given that ATM activity is required to initiate HR repair, coupled with the requirement of Rad51 and BRCA1 for productive viral replication, our findings suggest that HPV may utilize ATM activity to ensure localization of recombination factors to productively replicating viral genomes. The finding that E7 increases the levels of Rad51 and BRCA1 suggests that E7 contributes to productive replication by providing DNA repair factors required for viral DNA synthesis. Our studies not only imply a role for recombination in the regulation of productive HPV replication but provide further insight into how HPV manipulates the DDR to facilitate the productive phase of the viral life cycle.
Microbial Surface Colonization and Biofilm Development in Marine Environments
Authors: Dang Hongyue , Lovell Charles R. 
Published: December 2015

SUMMARYBiotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration.
Paediatric abdominal tuberculosis in developed countries: case series and literature review
Authors: Delisle Megan , Seguin Jade , Zeilinski David , Moore Dorothy L 
Published: December 2015

ObjectiveTo provide an insight into the presentation, diagnosis and management of paediatric abdominal tuberculosis (TB) in developed countries.MethodsThe records of all children at the Montreal Children's Hospital (MCH) admitted with abdominal TB between 1990 and 2014 were reviewed. An automated and manual literature search from 1946 to 2014 was performed.Results(1) Case series: six cases were identified at the MCH. All were male between 5 and 17 years of age. All were from populations known to have high rates of TB (aboriginal, immigrant). Three underwent major surgical interventions and three underwent ultrasound (US) or CT aspiration or biopsy for diagnosis. (2) Literature review: 29 male (64%) and 16 female subjects (36%) aged between 14 months and 18 years were identified, including the MCH patients. All patients except one were from populations with a high incidence of TB. Most presented with a positive tuberculin skin test (90%), abdominal pain (76%), fever (71%) and weight loss (68%). On imaging, 22 (49%) were classified with gastrointestinal TB with colonic wall irregularity (41%) and 19 (42%) with peritoneal TB with ascites (68%). A positive culture was obtained in 33 (73%) patients. Three cases used CT- or US-guided aspiration or biopsy to obtain tissue samples. A surgical intervention was performed in 34 (76%) children; 13 (38%) of these were for diagnosis.ConclusionsDiagnosis based on clinical features (abdominal pain, fever and weight loss) and CT- or US-guided aspiration or biopsy may encourage physicians to adopt a more conservative approach to abdominal TB.
Families’ priorities in life-limiting illness: improving quality with online empowerment
Authors: Harris Nicola , Beringer Antonia , Fletcher Margaret 
Published: December 2015

ObjectiveImproving quality of life (QOL) is the central focus of palliative care support for children with life-limiting illness (LLI), but achieving this can be challenging.InterventionMyQuality is an online tool that enables families to choose and monitor parameters they identify as having an impact on their QOL, which aims to improve patient–professional communications and also to enhance patient empowerment within healthcare dialogues.DesignA longitudinal, multisite mixed-method evaluation of MyQuality. Families were invited to use MyQuality and completed semi-structured interviews and a Family Empowerment Scale (FES) at T=0 and T+3 months.Patients and settingThirty-two families of children with LLIs, attending three children's hospices in one UK region.Outcome measuresWebsite access, usage patterns and parameter choice, FES scores and qualitative evaluation of interviews.Results23/32 families chose to use the website. Mean duration of use was 106 days (range 2–301), with families choosing two or three parameters (range 1–15), most commonly seizures (24/32), constipation (9/32), pain (6/32) and sleep problems (6/32). Mean FES scores increased over time (3.45–3.85). Interview feedback confirmed the acceptability and ease of use of the website, and the value of a graphic record of change over time to support ongoing management and collaborative review of medical, nursing or social interventions.ConclusionsThe identification and monitoring of patient-generated priorities via the MyQuality website empowers families and supports collaboration between parents and professionals to ensure that palliative care is truly patient and family centred.