bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Review of Simulation Modelling Approaches Used for the Spread of Zoonotic Influenza Viruses in Animal and Human Populations
Authors: Dorjee S. , Poljak Z. , Revie C. W. , Bridgland J. , McNab B. , Leger E. , Sanchez J. 
Published: September 2012

SummaryIncreasing incidences of emerging and re‐emerging diseases that are mostly zoonotic (e.g. severe acute respiratory syndrome, avian influenza H5N1, pandemic influenza) has led to the need for a multidisciplinary approach to tackling these threats to public and animal health. Accordingly, a global movement of ‘One‐Health/One‐Medicine’ has been launched to foster collaborative efforts amongst animal and human health officials and researchers to address these problems. Historical evidence points to the fact that pandemics caused by influenza A viruses remain a major zoonotic threat to mankind. Recently, a range of mathematical and computer simulation modelling methods and tools have increasingly been applied to improve our understanding of disease transmission dynamics, contingency planning and to support policy decisions on disease outbreak management. This review provides an overview of methods, approaches and software used for modelling the spread of zoonotic influenza viruses in animals and humans, particularly those related to the animal‐human interface. Modelling parameters used in these studies are summarized to provide references for future work. This review highlights the limited application of modelling research to influenza in animals and at the animal‐human interface, in marked contrast to the large volume of its research in human populations. Although swine are widely recognized as a potential host for generating novel influenza viruses, and that some of these viruses, including pandemic influenza A/H1N1 2009, have been shown to be readily transmissible between humans and swine, only one study was found related to the modelling of influenza spread at the swine‐human interface. Significant gaps in the knowledge of frequency of novel viral strains evolution in pigs, farm‐level natural history of influenza infection, incidences of influenza transmission between farms and between swine and humans are clearly evident. Therefore, there is a need to direct additional research to the study of influenza transmission dynamics in animals and at the animal‐human interface.
Performances of a large mass ZnMoO4 scintillating bolometer for a next generation 0νDBD experiment
Authors: Beeman J. W. , Bellini F. , Brofferio C. , Cardani L. , Casali N. , Cremonesi O. , Dafinei I. , Di Domizio S. , Ferroni F. , Gorello E. , Galashov E. N. , Gironi L. , Nagorny S. S. , Orio F. , Pavan M. , Pattavina L. , Pessina G. , Piperno G. , Pirro S. , Previtali E. , Rusconi C. , Shlegel V. N. , Tomei C. , Vignati M. 
Published: September 2012

AbstractWe present the performances of a 330 g zinc molybdate (ZnMoO4) crystal working as scintillating bolometer as a possible candidate for a next generation experiment to search for neutrinoless double beta decay of 100Mo. The energy resolution, evaluated at the 2615 keV γ-line of 208Tl, is 6.3 keV FWHM. The internal radioactive contaminations of the ZnMoO4 were evaluated as <6 μBq/kg (228Th) and 27±6 μBq/kg (226Ra). We also present the results of the α vs β/γ discrimination, obtained through the scintillation light as well as through the study of the shape of the thermal signal alone.
TSUNAMI FORCE ON BUILDINGS WITH OPENINGS AND PROTECTION
Authors: TRIATMADJA RADIANTA , NURHASANAH ANY 
Published: September 2012

The force from a tsunami will damage buildings, such as houses, bridges, and many other coastal infrastructures. The impact and drag force of a tsunami depend on the scale and the characteristics of the tsunami as well as the infrastructures' characteristics. This study was conducted using physical modeling to determine the effect of openings and protection on buildings to reduce the effects of a tsunami attack. The openings were symmetrical about the front and rear walls and were oriented in the direction of the tsunami. Barriers with dimensions that were the same width and three times higher than the building and of various lengths were used to simulate protection against a tsunami. The results indicated that the force on the buildings depends on but is not linearly correlated to the opening. The barrier upstream of the building significantly reduced the force depending on its distance to the building and the surge Froude number; however, the openings still play an important role in reducing the force on a protected building. Simple equations for practical use are proposed to calculate the tsunami force on a building with openings with or without protection.
A low resting heart rate at diagnosis predicts favourable long-term outcome in pulmonary arterial and chronic thromboembolic pulmonary hypertension. A prospective observational study
Authors: Hildenbrand Florian F , Fauchère Ivan , Huber Lars C , Keusch Stephan , Speich Rudolf , Ulrich Silvia 
Published: September 2012

Abstract

Background
A low resting heart rate (HR) is prognostically favourable in healthy individuals and in patients with left heart disease. In this study we investigated the impact of HR at diagnosis on long-term outcome in patients with differently classified precapillary pulmonary hypertension (pPH).

Methods
pPH patients diagnosed as pulmonary arterial (PAH) or inoperable chronic thromboembolic pulmonary hypertension (CTEPH) were registered and regularly followed at our centre Baseline characteristics and events defined as either death or lung transplantation were noted. The prognostic value of HR was analysed using Kaplan Meier estimates, live tables and Cox regression.

Results
206 patients with PAH (148) and inoperable CTEPH (58) were included. The median HR was 82 bpm. pPH with a HR below 82 bpm had a significantly longer overall event-free survival (2409 vs.1332 days, p = .000). This advantage was similarly found if PAH and CTEPH were analysed separately. Although a lower HR was associated with a better hemodynamic and functional class, HR was a strong and independent prognostic marker for transplant free survival even if corrected for age, sex, hemodynamics and functional status.

Conclusion
We show that resting HR at diagnosis is a strong and independent long-term prognostic marker in PAH and CTEPH. Whether reducing HR by pharmacological agents would improve outcome in pPH has to be assessed by future trials with high attention to safety.
TFinDit: transcription factor-DNA interaction data depository
Authors: Turner Daniel , Kim RyangGuk , Guo Jun-tao 
Published: September 2012

Abstract

Background
One of the crucial steps in regulation of gene expression is the binding of transcription factor(s) to specific DNA sequences. Knowledge of the binding affinity and specificity at a structural level between transcription factors and their target sites has important implications in our understanding of the mechanism of gene regulation. Due to their unique functions and binding specificity, there is a need for a transcription factor-specific, structure-based database and corresponding web service to facilitate structural bioinformatics studies of transcription factor-DNA interactions, such as development of knowledge-based interaction potential, transcription factor-DNA docking, binding induced conformational changes, and the thermodynamics of protein-DNA interactions.

Description
TFinDit is a relational database and a web search tool for studying transcription factor-DNA interactions. The database contains annotated transcription factor-DNA complex structures and related data, such as unbound protein structures, thermodynamic data, and binding sequences for the corresponding transcription factors in the complex structures. TFinDit also provides a user-friendly interface and allows users to either query individual entries or generate datasets through culling the database based on one or more search criteria.

Conclusions
TFinDit is a specialized structural database with annotated transcription factor-DNA complex structures and other preprocessed data. We believe that this database/web service can facilitate the development and testing of TF-DNA interaction potentials and TF-DNA docking algorithms, and the study of protein-DNA recognition mechanisms.
Genetic module and miRNome trait analyses reflect the distinct biological features of endothelial progenitor cells from different anatomic locations
Authors: Cheng Cheng-Chung , Lo Hung-Hao , Huang Tse-Shun , Cheng Yi-Chieh , Chang Shi-Ting , Chang Shing-Jyh , Wang Hsei-Wei 
Published: September 2012

Abstract

Background
Endothelial progenitor cells (EPCs) play a fundamental role in post-natal vascular repair, yet EPCs from different anatomic locations possess unique biological properties. The underlying mechanisms are unclear.

Results
EPCs from CB expressed abundant genes involved in cell cycle, hypoxia signalling and blood vessel development, correlating with the phenotypes that CB-EPCs proliferated more rapidly, migrated faster, and formed tubule structure more efficiently. smRNA-seq further deciphered miRNome patterns in EPCs isolated from CB or PB: 54 miRNAs were enriched in CB-EPCs, while another 50 in PB-EPCs. Specifically, CB-EPCs expressed more angiogenic miRNAs such as miR-31, while PB-EPCs possessed more tumor suppressive miRNAs including miR-10a. Knocking down miR-31 levels in CB-EPCs suppressed cell migration and microtubule formation, while overexpressing miR-31 in PB-EPCs helped to recapitulate some of CB-EPC functions.

Conclusions
Our results show the foundation for a more detailed understanding of EPCs from different anatomic sources. Stimulating the expression of angiogenic microRNAs or genes in EPCs of low activity (such as those from patients with cardiovascular diseases) might allow the development of novel therapeutic strategies.
Constructing episodes of inpatient care: data infrastructure for population-based research
Authors: Fransoo Randy , Yogendran Marina , Olafson Kendiss , Ramsey Clare , McGowan Kari-Lynne , Garland Allan 
Published: September 2012

Abstract

Background
Databases used to study the care of patients in hospitals and Intensive Care Units (ICUs) typically contain a separate entry for each segment of hospital or ICU care. However, it is not uncommon for patients to be transferred between hospitals and/or ICUs, and when transfers occur it is necessary to combine individual entries to accurately reconstruct the complete episodes of hospital and ICU care. Failure to do so can lead to erroneous lengths-of-stay, and rates of admissions, readmissions, and death.

Methods
This study used a clinical ICU database and administrative hospital abstracts for the adult population of Manitoba, Canada from 2000–2008. We compared five methods for identifying patient transfers and constructing hospital episodes, and the ICU episodes contained within them. Method 1 ignored transfers. Methods 2–5 considered the time gap between successive entries (≤1 day vs. ≤2 days), with or without use of data fields indicating inter-hospital transfer. For the five methods we compared the resulting number and lengths of hospital and ICU episodes.

Results
During the study period, 48,551 hospital abstracts contained 53,246 ICU records. For Method 1 these were also the number of hospital and ICU episodes, respectively. Methods 2–5 gave remarkably similar results, with transfers included in approximately 25% of ICU-containing hospital episodes, and 10% of ICU episodes. Comparison with Method 1 showed that failure to account for such transfers resulted in overestimating the number of episodes by 7-10%, and underestimating mean or median lengths-of-stay by 9-30%.

Conclusions
In Manitoba is it not uncommon for critically ill patients to be transferred between hospitals and between ICUs. Failure to account for transfers resulted in inaccurate assessment of parameters relevant to researchers, clinicians, and policy-makers. The details of the method used to identify transfers, at least among the variations tested, made relatively little difference. In addition, we showed that these methods for constructing episodes of hospital and ICU care can be implemented in a large, complex dataset.
Bacterial brain abscess in patients with nasopharyngeal carcinoma following radiotherapy: microbiology, clinical features and therapeutic outcomes
Authors: Fang Peng-Hsiang , Lin Wei-Che , Tsai Nai-Wen , Chang Wen-Neng , Huang Chi-Ren , Chang Hsueh-Wen , Huang Tai-Lin , Lin Hsin-Ching , Lin Yu-Jun , Cheng Ben-Chung , Su Ben Yu-Jih , Kung Chia-Te , Wang Hung-Chen , Lu Cheng-Hsien 
Published: September 2012

Abstract

Background
This study aimed to analyze the clinical features, causative pathogens, neuro-imaging findings, and therapeutic outcomes of bacterial brain abscess in patients with nasopharyngeal carcinoma (NPC) following radiotherapy.

Methods
NPC patients with bacterial brain abscess were evaluated. Their clinical data were collected over a 22-year period. For comparison, the clinical features, causative pathogens, neuro-imaging findings, and therapeutic outcomes between NPC and non-NPC patients were analyzed.

Results
NPC accounted for 5.7% (12/210) of the predisposing factors, with Viridans streptococci and Staphylococcus aureus as the two most common causative pathogens. Significant statistical analysis between the two groups (NPC and non-NPC patients) included chronic otitis media (COM) as the underlying disease, post-radiation necrosis by neuro-imaging, and the temporal lobe as the most common site of brain abscesses. The fatality rate in patients with and without NPC was 16.7% and 20.7%, respectively.

Conclusions
NPC patients with bacterial brain abscess frequently have COM as the underlying disease. Neuro-imaging often reveals both post-radiation necrosis and the temporal lobe as the most common site of brain abscesses, the diagnosis of which is not always a straightforward process. Radiation necrosis can mimic brain abscess on neuro-imaging and pose significant diagnostic challenges. Early diagnosis and treatment is essential for survival.
Protocol for a drugs exposure pregnancy registry for implementation in resource-limited settings
Authors: Mehta Ushma , Clerk Christine , Allen Elizabeth , Yore Mackensie , Sevene Esperança , Singlovic Jan , Petzold Max , Mangiaterra Viviana , Elefant Elizabeth , Sullivan Frank M , Holmes Lewis B , Gomes Melba 
Published: September 2012

Abstract

Background
The absence of robust evidence of safety of medicines in pregnancy, particularly those for major diseases provided by public health programmes in developing countries, has resulted in cautious recommendations on their use. We describe a protocol for a Pregnancy Registry adapted to resource-limited settings aimed at providing evidence on the safety of medicines in pregnancy.

Methods/Design
Sentinel health facilities are chosen where women come for prenatal care and are likely to come for delivery. Staff capacity is improved to provide better care during the pregnancy, to identify visible birth defects at delivery and refer infants with major anomalies for surgical or clinical evaluation and treatment. Consenting women are enrolled at their first antenatal visit and careful medical, obstetric and drug-exposure histories taken; medical record linkage is encouraged. Enrolled women are followed up prospectively and their histories are updated at each subsequent visit. The enrolled woman is encouraged to deliver at the facility, where she and her baby can be assessed.

Discussion
In addition to data pooling into a common WHO database, the WHO Pregnancy Registry has three important features: First is the inclusion of pregnant women coming for antenatal care, enabling comparison of birth outcomes of women who have been exposed to a medicine with those who have not. Second is its applicability to resource-poor settings regardless of drug or disease. Third is improvement of reproductive health care during pregnancies and at delivery. Facility delivery enables better health outcomes, timely evaluation and management of the newborn, and the collection of reliable clinical data. The Registry aims to improve maternal and neonatal care and also provide much needed information on the safety of medicines in pregnancy.
Severe conjunctivochalasis in association with classic type Ehlers-Danlos syndrome
Authors: Whitaker John K , Alexander Philip , Chau David YS , Tint Naing L 
Published: September 2012

Abstract

Background
Inferior conjunctivochalasis is common, but is rarely severe enough to require conjunctival excision. This report describes a patient with severe conjunctivochalasis who was subsequently diagnosed with Ehlers Danlos Syndrome, Classic Type.

Case presentation
A patient suffering from foreign body sensation, frequent blinking and bilateral inferior conjunctivochalasis was referred and treated by topical ocular lubrication. However, no improvement was observed prompting potential excision of conjunctivochalasis. Following patient consultation and clinical diagnosis including hypermobile joints and skin elasticity, poor wound healing and wide scar morphology, Ehlers-Danlos syndrome was confirmed in the patient.

Conclusion
This case highlights the need for direct patient questioning and provides the first reported association between conjunctiovochalasis and Ehlers-Danlos syndrome.
A dual tag system for facilitated detection of surface expressed proteins in Escherichia coli
Authors: Jarmander Johan , Gustavsson Martin , Do Thi-Huyen , Samuelson Patrik , Larsson Gen 
Published: September 2012

Abstract

Background
The discovery of the autotransporter family has provided a mechanism for surface expression of proteins in laboratory strains of Escherichia coli. We have previously reported the use of the AIDA-I autotransport system to express the Salmonella enterica serovar Enteritidis proteins SefA and H:gm. The SefA protein was successfully exposed to the medium, but the orientation of H:gm in the outer membrane could not be determined due to proteolytic cleavage of the N-terminal detection-tag. The goal of the present work was therefore to construct a vector containing elements that facilitates analysis of surface expression, especially for proteins that are sensitive to proteolysis or otherwise difficult to express.

Results
The surface expression system pAIDA1 was created with two detection tags flanking the passenger protein. Successful expression of SefA and H:gm on the surface of E. coli was confirmed with fluorescently labeled antibodies specific for the N-terminal His6-tag and the C-terminal Myc-tag. While both tags were detected during SefA expression, only the Myc-tag could be detected for H:gm. The negative signal indicates a proteolytic cleavage of this protein that removes the His6-tag facing the medium.

Conclusions
Expression levels from pAIDA1 were comparable to or higher than those achieved with the formerly used vector. The presence of the Myc- but not of the His6-tag on the cell surface during H:gm expression allowed us to confirm the hypothesis that this fusion protein was present on the surface and oriented towards the cell exterior. Western blot analysis revealed degradation products of the same molecular weight for SefA and H:gm. The size of these fragments suggests that both fusion proteins have been cleaved at a specific site close to the C-terminal end of the passenger. This proteolysis was concluded to take place either in the outer membrane or in the periplasm. Since H:gm was cleaved to a much greater extent then the three times smaller SefA, it is proposed that the longer translocation time for the larger H:gm makes it more susceptible to proteolysis.
Analysis of the trap gene provides evidence for the role of elevation and vector abundance in the genetic diversity of Plasmodium relictum in Hawaii
Authors: Farias Margaret E M , Atkinson Carter T , LaPointe Dennis A , Jarvi Susan I 
Published: September 2012

Abstract

Background
The avian disease system in Hawaii offers an ideal opportunity to investigate host-pathogen interactions in a natural setting. Previous studies have recognized only a single mitochondrial lineage of avian malaria (Plasmodium relictum) in the Hawaiian Islands, but cloning and sequencing of nuclear genes suggest a higher degree of genetic diversity.

Methods
In order to evaluate genetic diversity of P. relictum at the population level and further understand host-parasite interactions, a modified single-base extension (SBE) method was used to explore spatial and temporal distribution patterns of single nucleotide polymorphisms (SNPs) in the thrombospondin-related anonymous protein (trap) gene of P. relictum infections from 121 hatch-year amakihi (Hemignathus virens) on the east side of Hawaii Island.

Results
Rare alleles and mixed infections were documented at three of eight SNP loci; this is the first documentation of genetically diverse infections of P. relictum at the population level in Hawaii. Logistic regression revealed that the likelihood of infection with a rare allele increased at low-elevation, but decreased as mosquito capture rates increased. The inverse relationship between vector capture rates and probability of infection with a rare allele is unexpected given current theories of epidemiology developed in human malarias.

Conclusions
The results of this study suggest that pathogen diversity in Hawaii may be driven by a complex interaction of factors including transmission rates, host immune pressures, and parasite-parasite competition.
Pulmonary sclerosing hemangioma: report of two cases
Authors: He Chuang , Fang Hongyang , Liu Yun , Huang Xuequan , Zhen Wei , Ren Li 
Published: September 2012

Abstract
Pulmonary sclerosing hemangioma (PSH) is a rare benign tumor of the lungs. These tumors are composed of cuboidal surface cells and polygonal stromal cells and show four histological manifestations: hemorrhagic, papillary, solid, and sclerotic. PSH predominantly affects asymptomatic middle-aged women. The tumor often occurs at the intralobar site, and less commonly in the bronchus and mediastinum. PSH is easy to be misdiagnosed preoperatively. In this study, we present in detail the treatment procedures followed for two atypical cases of PSH. Case 1 was a 62-year-old woman bearing a tumor for 15 years. The tumor lesion was found to be located in the oblique fissure of the left lung. PSH was confirmed by surgical resection and postoperative pathological diagnosis. There was no sign of recurrence and metastasis 1.5 years after surgery. Case 2 was a 54-year-old woman diagnosed with bilateral multiple nodules by physical examination. This patient was diagnosed with definite PSH through computed tomography-guided percutaneous lung biopsy. Surgical resection was not performed. The patient also showed no sign of enlarged tumor and metastasis after 2 years of follow-up. Although PSH can be cured by surgical resection, the findings in our cases indicate that surgical resection need not be considered the preferred course of treatment. If PSH is diagnosed before surgery, the patients may survive while bearing the tumor.