bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic sequence of temperate phage Smp131 of Stenotrophomonas maltophilia that has similar prophages in xanthomonads
Authors: Lee Chia-Ni , Tseng Tsai-Tien , Chang Hsiao-Chuan , Lin Juey-Wen , Weng Shu-Fen 
Published: January 2014

Abstract

Background

Stenotrophomonas maltophilia is a ubiquitous Gram-negative bacterium previously named as Xanthomonas maltophilia. This organism is an important nosocomial pathogen associated with infections in immunocompromised patients. Clinical isolates of S. maltophilia are mostly resistant to multiple antibiotics and treatment of its infections is becoming problematic. Several virulent bacteriophages, but not temperate phage, of S. maltophilia have been characterized.

Results
In this study, a temperate myophage of S. maltophilia (Smp131) was isolated and characterized. Sequence analysis showed that its genome is 33,525-bp long with 47 open reading frames (ORFs). Its similarity to P2-like phages and prophages in S. maltophilia and several Xanthomonas pathovars includes genomic organization, arrangement of several operons, and possession of a slippery sequence T7G for translational frameshifting in tail assembly genes. Smp131 encodes a tyrosine family integrase that shares low degrees of similarity with those of other phages and a lysin belonging to family 19 chitinase that is observed in plants and some bacteria, although not in phages. tRNA are the preferred sites for host integration of Smp131 and the related phages: tRNA-Thr for Smp131 and prophage of S. maltophilia K279a; tRNA-Lys for prophages of X. campestris pv. campestris ATCC33913, X. oryzae pv. oryzae strains MAFF311018, and KACC10331; and tRNA-Asn for prophage of X. oryzae pv. oryzae PXO99A and remnant of X. axonopodis pv. citri 306. Regions flanking the prophages are varied highly in nucleotide sequence and rich in transposase genes, suggesting that frequent insertion/excision had occurred.

Conclusions
Prevalence of closely related prophages in Stenotrophomonas and Xanthomonads may have contributed to the diversity of these closely related species owing to possible horizontal gene transfer mediated by the phages.
Bronchial isomerism in a Kabuki syndrome patient with a novel mutation in MLL2gene
Authors: Cappuccio Gerarda , Rossi Alessandro , Fontana Paolo , Acampora Emma , Avolio Valeria , Merla Giuseppe , Zelante Leopoldo , Secinaro Aurelio , Andria Generoso , Melis Daniela 
Published: January 2014

Abstract

Background
Kabuki syndrome (KS) is a rare, multiple congenital anomalies/intellectual disability syndrome caused by mutations of MLL2 gene, which codifies for a histone methyltrasferase that regulates the embryogenesis and the tissue development. Left-bronchial isomerism is a rare congenital abnormality that can be defined as the absence of the normal lateralizing features which distinguish right and left-sides in the lungs. To date, this is the first report of left-bronchial isomerism in association with KS.

Case presentation
A one-month-old Caucasian male patient underwent our attention for microcephaly, dysmorphic features (long palpebral fissures, eyebrows with sparse lateral third, everted lower eyelids, blue sclerae, large dysplastic ears, lower lip pits), persistent fetal fingertip pads, short stature, heart defects (interventricular defect and aortic coarctation), unilateral cryptorchidism, hypotonia and delay in gross motor skills. These features suggested a diagnosis of KS and a molecular analysis confirmed a novel frame-shift mutation in the exon 11 of MLL2 gene. Subsequently, given recurrent respiratory infections with a normal immunological status, he underwent a chest CT scan that showed a left bronchial isomerism.

Conclusion
We report a patient affected by KS, with a novel MLL2 mutation and an atypical phenotype characterized by left-side bronchial isomerism. Interestingly, genes involved in the heterotaxia/isomerism such as ROCK2 and SHROOM3 are known to interact with MLL2 gene. In order to achieve a correct diagnosis and an appropriate therapy, the presence of pulmonary anatomical variations should be investigated in KS patients with respiratory signs not associated to immunological deficiency. Finally, our findings support the hypothesis that the mutations leading to a complete loss of function of MLL2 gene is often associated with complex visceral malformations.
Effect on the tensile strength of human acellular dermis (Epiflex®) of in-vitro incubation simulating an open abdomen setting
Authors: Vitacolonna Mario , Mularczyk Michael , Herrle Florian , Schulze Torsten J , Haupt Hans , Oechsner Matthias , Pilz Lothar R , Hohenberger Peter , Rössner Eric Dominic 
Published: January 2014

Abstract

Background
The use of human acellular dermis (hAD) to close open abdomen in the treatment process of severe peritonitis might be an alternative to standard care. This paper describes an investigation of the effects of fluids simulating an open abdomen environment on the biomechanical properties of Epiflex® a cell-free human dermis transplant.

Methods
hAD was incubated in Ringers solution, blood, urine, upper gastrointestinal (upper GI) secretion and a peritonitis-like bacterial solution in-vitro for 3 weeks. At day 0, 7, 14 and 21 breaking strength was measured, tensile strength was calculated and standard fluorescence microscopy was performed.

Results
hAD incubated in all five of the five fluids showed a decrease in mean breaking strength at day 21 when compared to day 0. However, upper GI secretion was the only incubation fluid that significantly reduced the mechanical strength of Epiflex after 21days of incubation when compared to incubation in Ringer’s solution.

Conclusion
hAD may be a suitable material for closure of the open abdomen in the absence of upper GI leakage and pancreatic fistulae.
First-principles study on transition metal-doped anatase TiO2
Authors: Wang Yaqin , Zhang Ruirui , Li Jianbao , Li Liangliang , Lin Shiwei 
Published: January 2014

Abstract
The electronic structures, formation energies, and band edge positions of anatase TiO2 doped with transition metals have been analyzed by ab initio band calculations based on the density functional theory with the planewave ultrasoft pseudopotential method. The model structures of transition metal-doped TiO2 were constructed by using the 24-atom 2 × 1 × 1 supercell of anatase TiO2 with one Ti atom replaced by a transition metal atom. The results indicate that most transition metal doping can narrow the band gap of TiO2, lead to the improvement in the photoreactivity of TiO2, and simultaneously maintain strong redox potential. Under O-rich growth condition, the preparation of Co-, Cr-, and Ni-doped TiO2 becomes relatively easy in the experiment due to their negative impurity formation energies, which suggests that these doping systems are easy to obtain and with good stability. The theoretical calculations could provide meaningful guides to develop more active photocatalysts with visible light response.
Trans-activation, post-transcriptional maturation, and induction of antibodies to HERV-K (HML-2) envelope transmembrane protein in HIV-1 infection
Authors: Michaud Henri-Alexandre , de Mulder Miguel , SenGupta Devi , Deeks Steven G , Martin Jeffrey N , Pilcher Christopher D , Hecht Frederick M , Sacha Jonah B , Nixon Douglas F 
Published: January 2014

Abstract

Background
Human Endogenous Retroviruses (HERVs) comprise about 8% of the human genome and have lost their ability to replicate or to produce infectious particles after having accumulated mutations over time. We assessed the kinetics of expression of HERV-K (HML-2) Envelope mRNA transcript and surface unit (SU) and transmembrane (TM) subunit proteins during HIV-1 infection. We also mapped the specificity of the humoral response to HERV-K (HML-2) Envelope protein in HIV-1 infected subjects at different stages of disease, and correlated the response with plasma viral load.

Results
We found that HIV-1 modified HERV-K (HML-2) Env mRNA expression, resulting in the expression of a fully N-glycosylated HERV-K (HML-2) envelope protein on the cell surface. Serological mapping of HERV-K (HML-2) envelope protein linear epitopes revealed two major immunogenic domains, one on SU and another on the ectodomain of TM. The titers of HERV-K (HML-2) TM antibodies were dramatically increased in HIV-1 infected subjects (p < 0.0001). HIV-1 infected adults who control HIV-1 in the absence of therapy (“elite” controllers) had a higher titer response against TM compared to antiretroviral-treated adults (p < 0.0001) and uninfected adults (p < 0.0001).

Conclusions
These data collectively suggest that HIV-1 infection induces fully glycosylated HERV-K (HML-2) envelope TM protein to which antibodies are induced. These anti-HERV-K (HML-2) TM antibodies are a potential marker of HIV-1 infection, and are at higher titer in elite controllers. HERV-K (HML-2) envelope TM protein may be a new therapeutic target in HIV-1 infection.
A Comparison of RNA-Seq and Exon Arrays for Whole Genome Transcription Profiling of the L5 Spinal Nerve Transection Model of Neuropathic Pain in the Rat
Authors: Perkins James R , Antunes-Martins Ana , Calvo Margarita , Grist John , Rust Werner , Schmid Ramona , Hildebrandt Tobias , Kohl Matthias , Orengo Christine , McMahon Stephen B , Bennett David LH 
Published: January 2014

Background: The past decade has seen an abundance of transcriptional profiling studies of preclinical models of persistent pain, predominantly employing microarray technology. In this study we directly compare exon microarrays to RNA-seq and investigate the ability of both platforms to detect differentially expressed genes following nerve injury using the L5 spinal nerve transection model of neuropathic pain. We also investigate the effects of increasing RNA-seq sequencing depth. Finally we take advantage of the “agnostic” approach of RNA-seq to discover areas of expression outside of annotated exons that show marked changes in expression following nerve injury. Results: RNA-seq and microarrays largely agree in terms of the genes called as differentially expressed. However, RNA-seq is able to interrogate a much larger proportion of the genome. It can also detect a greater number of differentially expressed genes than microarrays, across a wider range of fold changes and is able to assign a larger range of expression values to the genes it measures. The number of differentially expressed genes detected increases with sequencing depth. RNA-seq also allows the discovery of a number of genes displaying unusual and interesting patterns of non-exonic expression following nerve injury, an effect that cannot be detected using microarrays. Conclusion: We recommend the use of RNA-seq for future high-throughput transcriptomic experiments in pain studies. RNA-seq allowed the identification of a larger number of putative candidate pain genes than microarrays and can also detect a wider range of expression values in a neuropathic pain model. In addition, RNA-seq can interrogate the whole genome regardless of prior annotations, being able to detect transcription from areas of the genome not currently annotated as exons. Some of these areas are differentially expressed following nerve injury, and may represent novel genes or isoforms. We also recommend the use of a high sequencing depth in order to detect differential expression for genes with low levels of expression.
Anopheles sinensis mosquito insecticide resistance: comparison of three mosquito sample collection and preparation methods and mosquito age in resistance measurements
Authors: Xu Tielong , Zhong Daibin , Tang Linhua , Chang Xuelian , Fu Fengyang , Yan Guiyun , Zheng Bin 
Published: January 2014

Abstract

Background
Insecticide resistance monitoring in malaria mosquitoes is essential for guiding the rational use of insecticides in vector control programs. Resistance bioassay is the first step for insecticide monitoring and it lays an important foundation for molecular examination of resistance mechanisms. In the literature, various mosquito sample collection and preparation methods have been used, but how mosquito sample collection and preparation methods affect insecticide susceptibility bioassay results is largely unknown. The objectives of this study were to determine whether mosquito sample collection and preparation methods affected bioassay results, which may cause incorrect classification of mosquito resistance status.

Methods
The study was conducted in Anopheles sinensis mosquitoes in two study sites in central China. Three mosquito sample collection and preparation methods were compared for insecticide susceptibility, kdr frequencies and metabolic enzyme activities: 1) adult mosquitoes collected from the field; 2) F1 adults from field collected, blood-fed mosquitoes; and 3) adult mosquitoes reared from field collected larvae.

Results
Mosquito sample collection and preparation methods significantly affected mortality rates in the standard WHO tube resistance bioassay. Mortality rate of field-collected female adults was 10-15% higher than in mosquitoes reared from field-collected larvae and F1 adults from field collected blood-fed females. This pattern was consistent in mosquitoes from the two study sites. High kdr mutation frequency (85-95%) with L1014F allele as the predominant mutation was found in our study populations. Field-collected female adults consistently exhibited the highest monooxygenase and GST activities. The higher mortality rate observed in the field-collected female mosquitoes may have been caused by a mixture of mosquitoes of different ages, as older mosquitoes were more susceptible to deltamethrin than younger mosquitoes.

Conclusions
Female adults reared from field-collected larvae in resistance bioassays are recommended to minimize the effect of confounding factors such as mosquito age and blood feeding status so that more reliable and reproducible mortality may be obtained.
The Queensland high risk foot form (QHRFF) – is it a reliable and valid clinical research tool for foot disease?
Authors: Lazzarini Peter A , Ng Vanessa , Kinnear Ewan M , Kamp Maarten C , Kuys Suzanne S , Hurst Cameron , Reed Lloyd F 
Published: January 2014

AbstractBackgroundFoot disease complications, such as foot ulcers and infection, contribute to considerable morbidity and mortality. These complications are typically precipitated by “high‐risk factors”, such as peripheral neuropathy and peripheral arterial disease. High‐risk factors are more prevalent in specific “at risk” populations such as diabetes, kidney disease and cardiovascular disease. To the best of the authors' knowledge a tool capturing multiple high‐risk factors and foot disease complications in multiple at risk populations has yet to be tested. This study aimed to develop and test the validity and reliability of a Queensland High Risk Foot Form (QHRFF) tool.MethodsThe study was conducted in two phases. Phase one developed a QHRFF using an existing diabetes foot disease tool, literature searches, stakeholder groups and expert panel. Phase two tested the QHRFF for validity and reliability. Four clinicians, representing different levels of expertise, were recruited to test validity and reliability. Three cohorts of patients were recruited; one tested criterion measure reliability (n = 32), another tested criterion validity and inter‐rater reliability (n = 43), and another tested intra‐rater reliability (n = 19). Validity was determined using sensitivity, specificity and positive predictive values (PPV). Reliability was determined using Kappa, weighted Kappa and intra‐class correlation (ICC) statistics.ResultsA QHRFF tool containing 46 items across seven domains was developed. Criterion measure reliability of at least moderate categories of agreement (Kappa > 0.4; ICC > 0.75) was seen in 91% (29 of 32) tested items. Criterion validity of at least moderate categories (PPV > 0.7) was seen in 83% (60 of 72) tested items. Inter‐ and intra‐rater reliability of at least moderate categories (Kappa > 0.4; ICC > 0.75) was seen in 88% (84 of 96) and 87% (20 of 23) tested items respectively.ConclusionsThe QHRFF had acceptable validity and reliability across the majority of items; particularly items identifying relevant co‐morbidities, high‐risk factors and foot disease complications. Recommendations have been made to improve or remove identified weaker items for future QHRFF versions. Overall, the QHRFF possesses suitable practicality, validity and reliability to assess and capture relevant foot disease items across multiple at risk populations.
Role of LET and chromatin structure on chromosomal inversion in CHO10B2 cells
Authors: Cartwright Ian M , Genet Matthew D , Fujimori Akira , Kato Takamitsu A 
Published: January 2014

Background
In this study we evaluated the effect of linear energy transfer (LET) and chromatin structure on the induction of chromosomal inversion. High LET radiation causes more complex DNA damage than low LET radiation; this “dirty” damage is more difficult to repair and may result in an increase in inversion formation. CHO10B2 cells synchronized in either G1 or M phase were exposed 0, 1, or 2 Gy of 5 mm Al and Cu filters at 200 kVp and 20 mA X-rays or 500 MeV/nucleon of initial energy and 200 keV/μ m Fe ion radiation. In order to increase the sensitivity of prior techniques used to study inversions, we modified the more traditional Giemsa plus fluorescence technique so that cells were only allowed to incorporate BrdU for a single cycle verses 2 cycles. The BrdU incorporated DNA strand was labeled using a BrdU antibody and an Alexa Fluor 488 probe. This modified technique allowed us to observe inversions smaller than 0.6 megabases (Mb).

Results
In this study we have shown that high LET radiation induces significantly more inversions in G1 cells than in M phase cells. Additionally, we have shown that the sizes of the induced inversions not only differ between Fe ion and X-rays, but also between G1 and M phase cells exposed to Fe ions.

Conclusion
We have effectively shown that both radiation quality and chromosome structure interact to alter not only the number of inversions induced, but also the size of the inversions.
Clinical Impact of Delaying Initiation of Adjuvant Chemotherapy in Patients With Breast Cancer
Authors: Gagliato Debora de Melo , Gonzalez-Angulo Ana M. , Lei Xiudong , Theriault Richard L. , Giordano Sharon H. , Valero Vicente , Hortobagyi Gabriel N. , Chavez-MacGregor Mariana 
Published: January 2014

Purpose For patients with breast cancer (BC), the optimal time to initiation of adjuvant chemotherapy (TTC) after definitive surgery is unknown. We evaluated the association between TTC and survival according to breast cancer subtype and stage at diagnosis. Patients and Methods Women diagnosed with BC stages I to III between 1997 and 2011 who received adjuvant chemotherapy at our institution were included. Patients were categorized into three groups according to TTC: ≤ 30, 31 to 60, and ≥ 61 days. Survival outcomes were estimated and compared according to TTC and by BC subtype. Results Among the 6,827 patients included, the 5-year overall survival (OS), relapse-free survival (RFS), and distant RFS (DRFS) estimates were similar for the different TTC categories. Initiation of chemotherapy ≥ 61 days after surgery was associated with adverse outcomes among patients with stage II (DRFS: hazard ratio [HR], 1.20; 95% CI, 1.02 to 1.43) and stage III (OS: HR, 1.76; 95% CI, 1.26 to 2.46; RFS: HR, 1.34; 95% CI, 1.01 to 1.76; and DRFS: HR, 1.36; 95% CI, 1.02 to 1.80) BC. Patients with triple-negative BC (TNBC) tumors and those with human epidermal growth factor receptor 2 (HER2) –positive tumors treated with trastuzumab who started chemotherapy ≥ 61 days after surgery had worse survival (HR, 1.54; 95% CI, 1.09 to 2.18 and HR, 3.09; 95% CI, 1.49 to 6.39, respectively) compared with those who initiated treatment in the first 30 days after surgery. Conclusion TTC influenced survival outcomes in the overall study cohort. This finding was particularly meaningful for patients with stage III BC, TNBC, and trastuzumab-treated HER2-positive tumors who experienced worse outcomes when chemotherapy was delayed. Our findings suggest that early initiation of chemotherapy should be granted for patients in these high-risk groups.
Underlying issues in the emergence of China and Brazil as major global players in the new South–South trade and investment axis
Authors: Wilkinson John , Wesz Junior Valdemar João 
Published: January 2014

Abstract
This article compares the evolution of the Brazilian and Chinese economies and focuses on the way asymmetrical trading and investment relations have become consolidated. The agro-industrial and agro-food sectors are analysed in this light, with particular attention to trade in soy which is by far the most important product. The article details the way in which the shift in soy trade from South–North to South–South has been accompanied by changes in composition and investment strategies. The article concludes by situating these trends within broader changes affecting overall trade and investment between the two countries.
Heat conduction at micro and nanoscales: A review through the prism
of Extended Irreversible Thermodynamics
Authors: Lebon Georgy 
Published: January 2014

Abstract.
This review paper is dedicated to a description of heat transport at micro
and nanoscales from the viewpoint of Extended Irreversible Thermodynamics.
After a short survey of the classical heat conduction laws, like those of
Fourier, Cattaneo, and Guyer–Krumhansl, we briefly overview the hypotheses
and objectives of Extended Irreversible Thermodynamics, which is
particularly well suited to cope with processes at short length and time
scales. A selection of some important items typical of nanomaterials and
technology are reviewed. Particular attention is brought to the notion of
effective thermal conductivity: its expression in terms of size and
frequency dependence is formulated, its significant increase in nanofluids
formed by a matrix and nanoparticles is discussed, the problem of pore-size
dependence and its incidence on thermal rectifiers is also investigated.
Transient heat conduction through thin one-dimensional films receives
special treatment. The results obtained from a generalized Fourier law are
compared with those provided by a more sophisticated ballistic-diffusion
model. Our survey ends with general considerations on boundary conditions
whose role is of fundamental importance in nanomaterials.
Finite-time thermodynamics: The maximal productivity of binary distillation and selection of optimal separation sequence for an ideal ternary mixture
Authors: Tsirlin Anatoly M. , Sukin Ivan A. 
Published: January 2014

Abstract.
The paper shows that an attainability region of a binary fractionating column depends on two parameters. These parameters are expressed through kinetic coefficients and mixture properties. The paper also considers a problem of finding the maximal productivity of the ternary distillation. Selection conditions for an optimal separation order and expressions for the maximal productivity of this process were obtained.