bluuebunny/crossref_metadata_2025_split huggingface dataset:
A reduced dose of fluconazole as primary antifungal prophylaxis is not associated with increased risk of invasive fungal infections after allogeneic stem cell transplantation from a HLA identical sibling
Authors: Sarina Barbara , Mariotti Jacopo , Bramanti Stefania , Morabito Lucio , Crocchiolo Roberto , Rimondo Andrea , Tordato Federica , Pocaterra Daria , Casari Erminia , De Philippis Chiara , Carlo‐Stella Carmelo , Santoro Armando , Castagna Luca 
Published: April 2018

AbstractBackgroundInvasive fungal infections (IFI) represent a common side effect of allogeneic hematopoietic stem cell transplant (allo‐SCT), resulting in increased non relapse mortality (NRM) and reduced overall survival (OS) rates. Seventy‐five days of Fluconazole 400 mg/d represents the standard primary antifungal prophylaxis (PAP) after allo‐SCT, especially for low‐risk transplants. However, the ideal dosage of fluconazole has never been tested.MethodsHere, we report the experience of our institution on 113 consecutive patients receiving an allo‐SCT from a HLA identical sibling between 1999 and 2015, where PAP consisted of fluconazole 100 mg/d only during the pre‐engraftment phase. At the time of transplant, all patients were considered at low‐risk for mold infection according to ECIL‐5 guidelines.ResultsCumulative incidence of possible‐probable‐proven IFI was 11.7%, while proven‐probable (PP‐IFI) occurred in 5.5% of patients by day 100 post transplant. Of note, only 1 patient developed invasive Candidiasis due to a non‐albicans strain and stool‐screening tests were negative for colonization by Candida albicans species. The incidence of 1‐year acute and 2‐year chronic graft‐versus‐host‐disease (GVHD) was 30% and 45%, respectively. Three‐year OS and 1‐year NRM were 53% and 11.3%, respectively.ConclusionIn summary, fungal prophylaxis with fluconazole 100 mg/d results in very low incidence of PP‐IFI, GVHD and NRM in low‐risk allo‐SCT.
Apple S‐RNase interacts with an actin‐binding protein, MdMVG, to reduce pollen tube growth by inhibiting its actin‐severing activity at the early stage of self‐pollination induction
Authors: Yang Qing , Meng Dong , Gu Zhaoyu , Li Wei , Chen Qiuju , Li Yang , Yuan Hui , Yu Jie , Liu Chunsheng , Li Tianzhong 
Published: April 2018

SummaryIn S‐RNase‐mediated self‐incompatibility, S‐RNase secreted from the style destroys the actin cytoskeleton of the self‐pollen tubes, eventually halting their growth, but the mechanism of this process remains unclear. In vitro biochemical assays revealed that S‐RNase does not bind or sever filamentous actin (F‐actin). In apple (Malus domestica), we identified an actin‐binding protein containing myosin, villin and GRAM (MdMVG), that physically interacts with S‐RNase and directly binds and severs F‐actin. Immunofluorescence assays and total internal reflection fluorescence microscopy indicated that S‐RNase inhibits the F‐actin‐severing activity of MdMVG in vitro. In vivo, the addition of S‐RNase to self‐pollen tubes increased the fluorescence intensity of actin microfilaments and reduced the severing frequency of microfilaments and the rate of pollen tube growth in self‐pollination induction in the presence of MdMVG overexpression. By generating 25 single‐, double‐ and triple‐point mutations in the amino acid motif E‐E‐K‐E‐K of MdMVG via mutagenesis and testing the resulting mutants with immunofluorescence, we identified a triple‐point mutant, MdMVG(E167A/E171A/K185A), that no longer has F‐actin‐severing activity or interacts with any of the four S‐haplotype S‐RNases, indicating that all three amino acids (E167, E171 and K185) are essential for the severing activity of MdMVG and its interaction with S‐RNases. We conclude that apple S‐RNase interacts with MdMVG to reduce self‐pollen tube growth by inhibiting its F‐actin‐severing activity.
A molecular network for functional versatility of HECATE transcription factors
Authors: Gaillochet Christophe , Jamge Suraj , van der Wal Froukje , Angenent Gerco , Immink Richard , Lohmann Jan U. 
Published: April 2018

SummaryDuring the plant life cycle, diverse signaling inputs are continuously integrated and engage specific genetic programs depending on the cellular or developmental context. Consistent with an important role in this process, HECATE (HEC) basic helix–loop–helix transcription factors display diverse functions, from photomorphogenesis to the control of shoot meristem dynamics and gynoecium patterning. However, the molecular mechanisms underlying their functional versatility and the deployment of specific HEC subprograms remain elusive. To address this issue, we systematically identified proteins with the capacity to interact with HEC1, the best‐characterized member of the family, and integrated this information with our data set of direct HEC1 target genes. The resulting core genetic modules were consistent with specific developmental functions of HEC1, including its described activities in light signaling, gynoecium development and auxin homeostasis. Importantly, we found that HEC genes also play a role in the modulation of flowering time, and uncovered that their role in gynoecium development may involve the direct transcriptional regulation of NGATHA1 (NGA1) and NGA2 genes. NGA factors were previously shown to contribute to fruit development, but our data now show that they also modulate stem cell homeostasis in the shoot apical meristem. Taken together, our results delineate a molecular network underlying the functional versatility of HEC transcription factors. Our analyses have not only allowed us to identify relevant target genes controlling shoot stem cell activity and a so far undescribed biological function of HEC1, but also provide a rich resource for the mechanistic elucidation of further context‐dependent HEC activities.
Unpacking research and practice in world Englishes and Second Language Acquisition
Authors: Kubota Ryuko 
Published: April 2018

AbstractResearch on world Englishes and Second Language Acquisition has conceptualized language, language users, and language learning as diverse and dynamic, broadening conventional knowledge. Yet, research outputs have not influenced language education policies in Expanding Circle countries, which favor Inner Circle standardized English, promote teaching English to young learners, and require monolingual teaching of English, as seen in the case of Japanese primary and secondary education. These activities are perpetuated by macro‐level language ideology and broader political, historical, and economic forces including neoliberalism that exist at a super macro level. Examining the roots of these practices directs our attention to both macro and super‐macro issues as well as to complicities between research/researchers and broader ideological and structural issues. Recommendations are offered to invite researchers to begin exploring how research can make impacts on real‐world issues.
Coda 1 World Englishes and Second Language Acquisition: Working towards a common goal
Authors: Gass Susan 
Published: April 2018

AbstractAlthough some have argued that world Englishes and Second Language Acquisition are in a relationship of conflict, my own view is that this is not necessarily the case. Indeed, it is possible to argue that the relationship between the two paradigms is better characterized as ‘benign neglect’ rather than that of conflict. Both fields, I would suggest, might benefit from truly collaborative research and scholarship, but such collaboration does not necessarily come easily, as researchers typically have expertise in one field rather than another, and this can frequently lead to miscommunication and misunderstanding, however well‐intentioned potential collaborators might be. From the point of view of SLA, one might also question the heavy emphasis on ‘Englishes’ in this context, and I end this coda with a discussion of the writing of Lahiri (2016), whose written account of the learning of Italian illustrates the interconnection of both cognitive and social factors in second language development.
Coda 2 A bridge half‐built: Toward a holistic theory of Second Language Acquisition and world Englishes
Authors: Sridhar S.N. , Sridhar Kamal K. 
Published: April 2018

AbstractIn the concluding contribution to this special issue, we return to the key issue that motivated our 1986 article on world Englishes (WE) and Second Language Acquisition (SLA). This coda begins by considering the impact of WE on SLA at a number of levels, with reference to the pluricentricity of English, conceptions of the ‘native speaker’, formalist ontology, functional perspectives, multilingualism, and other dynamic approaches to SLA. We then proceed to consider recent critiques of the WE paradigm, before moving to a discussion of the current synergy between world Englishes and Second Language Acquisition studies, noting that in many contemporary approaches to SLA, ‘the monolingual bias has given way to a multilingual turn.’ Nevertheless, even if there is a far greater appreciation of world Englishes than three decades ago, it is still evidently the case that textbooks in Second Language Acquisition continue to be focused on cognitive and structural dimensions of language acquisition, and often fail to incorporate social, functional and multilingual perspectives.
Comparative study between four ultrasound Shear Waves Elastographic methods for liver fibrosis assessment
Authors: Sporea Ioan , Mare Ruxandra , Lupusoru Raluca , Popescu Alina , Danila Mirela , Bende Felix , Sirli Roxana 
Published: April 2018

Aims: Non-invasive methods to assess the severity of chronic liver diseases have become more and more popular. The aim of our study was to evaluate the correlation of four Shear Waves Elastographic methods in a cohort of patients with chronic liver diseases of mixed etiologies and to compare their performances for liver fibrosis evaluation.Material and methods: A prospective study was conducted on 127 consecutive patients with chronic liver diseases of mixed etiologies. LS measurements were performed in all subjects, in one session, during the same day, by means of 4 elastographic methods: Transient Elastography (TE), Virtual Touch Quantification (VTQ), ElastPQ and 2D-SWE.SSI. The diagnosis accuracies of VTQ, ElastPQ, 2D-SWE.SSI were then compared using TE as reference method.Results: Valid LS measurements by all four shear waves ultrasound elastographic methods were obtained in 116/127 subjects with VTQ, in 108/127 subjects with 2D-SWE.SSI, in 111/127 with TE and in 109/127 with ElastPQ, so the final analysis included 82/127 subjects (64.5%). A good and significant correlation was found between all 4 elastographic methods. The diagnostic accuracy of VTQ, 2D-SWE.SSI and ElastPQ for the diagnosis of significant and severe fibrosis (F2/F3), and liver cirrhosis were similar for all elastographic techniques: VTQ vs 2D-SWE.SSI vs ElastPQ: 84.1% vs 85.3% vs. 84% (p>0.05); 93.9% vs 94% vs 94% (p>0.05).Conclusion: considering TE as the reference method for liver fibrosis evaluation, VTQ, ElastPQ, and 2D-SWE.SSI obtained similar accuracies for diagnosing at least significant fibrosis (F≥2) and liver cirrhosis.
Complete and Draft Genome Sequences of Nine Lactobacillus sakei Strains Selected from the Three Known Phylogenetic Lineages and Their Main Clonal Complexes
Authors: Loux Valentin , Coeuret Gwendoline , Zagorec Monique , Champomier Vergès Marie-Christine , Chaillou Stéphane 
Published: April 2018

ABSTRACT

We present here the complete and draft genome sequences of nine
Lactobacillus sakei
strains, selected from the entire range of clonal complexes from the three known lineages of the species. The strains were chosen to provide a wide view of pangenomic and plasmidic diversity for this important foodborne species.
Complete Genome Sequence of the Poly-γ-Glutamate-Synthesizing Bacterium Bacillus subtilis Bs-115
Authors: Wang Fengqing , Gong Lijuan , Zhou Lihong , Liang Jinzhong 
Published: April 2018

ABSTRACT

Bacillus subtilis
Bs-115 was isolated from the soil of a corn field in Yutai County, Jinan City, Shandong Province, People’s Republic of China, and is characterized by the efficient synthesis of poly-γ-glutamate (γ-PGA), with corn saccharification liquid as the sole energy and carbon source during the process of γ-PGA formation. Here, we report the complete genome sequence of
Bacillus subtilis
Bs-115 and the genes associated with poly-γ-glutamate synthesis.
Draft Genome Sequences of 116 Campylobacter jejuni Strains Isolated from Humans, Animals, Food, and the Environment in Brazil
Authors: Frazão Miliane Rodrigues , Cao Guojie , Medeiros Marta Inês Cazentini , Duque Sheila da Silva , Leon Maria Sanchez , Allard Marc William , Falcão Juliana Pfrimer 
Published: April 2018

ABSTRACT

Campylobacter jejuni
is a major zoonotic pathogen that causes foodborne gastroenteritis worldwide. However, clinical cases of campylobacteriosis have been underreported and underdiagnosed in Brazil. Herein, we describe the draft genome sequences of 116
C. jejuni
strains isolated from diverse sources in Brazil.
Draft Genome Sequences of Six Multidrug-Resistant Clinical Strains of Acinetobacter baumannii, Isolated at Two Major Hospitals in Kuwait
Authors: Nasser Kother , Mustafa Abu Salim , Khan Mohd Wasif , Purohit Prashant , Al-Obaid Inaam , Dhar Rita , Al-Fouzan Wadha 
Published: April 2018

ABSTRACT

Acinetobacter baumannii
is an important opportunistic pathogen in global health care settings. Its dissemination and multidrug resistance pose an issue with treatment and outbreak control. Here, we present draft genome assemblies of six multidrug-resistant clinical strains of
A. baumannii
isolated from patients admitted to one of two major hospitals in Kuwait.
Draft Genome Sequences of Pseudomonas sp. Strain 382 and Pantoea coffeiphila 342, Endophytic Bacteria Isolated from Brazilian Guarana [Paullinia cupana (Mart.) Ducke]
Authors: de Siqueira Kátia Aparecida , Liotti Rhavena Graziela , Mendes Tiago Antônio de Oliveira , Soares Marcos Antônio 
Published: April 2018

ABSTRACT

Pseudomonas
sp. strain 382 and
Pantoea coffeiphila
342 are two endophytic bacterial strains isolated from
Paullinia cupana
(guarana) seeds. Their draft genome sizes were 5.96 and 6.38 Mbp, with 315 and 266 scaffolds and 52% and 62% GC content, respectively.
Complete Genome Sequence of Spiroplasma floricola 23-6
T
(ATCC 29989), a Bacterium Isolated from a Tulip Tree (Liriodendron tulipifera L.)
Authors: Tsai Yi-Ming , Wu Pei-Shan , Lo Wen-Sui , Kuo Chih-Horng 
Published: April 2018

ABSTRACT

Spiroplasma floricola
23-6
T
(ATCC 29989) was isolated from the flower surface of a tulip tree (
Liriodendron tulipifera
L.). Here, we report the complete genome sequence of this bacterium to facilitate the investigation of its biology and the comparative genomics among
Spiroplasma
species.
Draft Genome Sequences of Interpatient and Intrapatient Epidemiologically Linked Neisseria gonorrhoeae Isolates
Authors: Hirk Sonja , Lepuschitz Sarah , Cabal Rosel Adriana , Huhulescu Steliana , Blaschitz Marion , Stöger Anna , Stadlbauer Silke , Hasenberger Petra , Indra Alexander , Schmid Daniela , Ruppitsch Werner , Allerberger Franz 
Published: April 2018

ABSTRACT

Neisseria gonorrhoeae
is the causative agent of gonorrhea and was identified by the World Health Organization as an urgent public health threat due to emerging antibiotic resistance. Here, we report 13 draft genome sequences of
N. gonorrhoeae
isolates derived from two epidemiologically linked cases from Austria.
Characterization of Three Novel Linear Neutralizing B-Cell Epitopes in the Capsid Protein of Swine Hepatitis E Virus
Authors: Chen Yiyang , Liu Baoyuan , Sun Yani , Li Huixia , Du Taofeng , Nan Yuchen , Hiscox Julian A. , Zhou En-Min , Zhao Qin 
Published: April 2018

ABSTRACT

Hepatitis E virus (HEV) causes liver disease in humans and is thought to be a zoonotic infection, with domestic animals, including swine and rabbits, being a reservoir. One of the proteins encoded by the virus is the capsid protein. This is likely the major immune-dominant protein and a target for vaccination. Four monoclonal antibodies (MAbs), three novel, 1E4, 2C7, and 2G9, and one previously characterized, 1B5, were evaluated for binding to the capsid protein from genotype 4 swine HEV. The results indicated that
625
DFCP
628
,
458
PSRPF
462
, and
407
EPTV
410
peptides on the capsid protein comprised minimal amino acid sequence motifs recognized by 1E4, 2C7, and 2G9, respectively. The data suggested that 2C7 and 2G9 epitopes were partially exposed on the surface of the capsid protein. Truncated genotype 4 swine HEV capsid protein (sp239, amino acids 368 to 606) can exist in multimeric forms. Preincubation of swine HEV with 2C7, 2G9, or 1B5 before addition to HepG2 cells partially blocked sp239 cell binding and inhibited swine HEV infection. The study indicated that 2C7, 2G9, and 1B5 partially blocked swine HEV infection of rabbits better than 1E4 or normal mouse IgG. The cross-reactivity of antibodies suggested that capsid epitopes recognized by 2C7 and 2G9 are common to HEV strains infecting most host species. Collectively, MAbs 2C7, 2G9, and 1B5 were shown to recognize three novel linear neutralizing B-cell epitopes of genotype 4 HEV capsid protein. These results enhance understanding of HEV capsid protein structure to guide vaccine and antiviral design.

IMPORTANCE
Genotype 3 and 4 HEVs are zoonotic viruses. Here, genotype 4 HEV was studied due to its prevalence in human populations and pig herds in China. To improve HEV disease diagnosis and prevention, a better understanding of the antigenic structure and neutralizing epitopes of HEV capsid protein are needed. In this study, the locations of three novel linear B-cell recognition epitopes within genotype 4 swine HEV capsid protein were characterized. Moreover, the neutralizing abilities of three MAbs specific for this protein, 2C7, 2G9, and 1B5, were studied
in vitro
and
in vivo
. Collectively, these findings reveal structural details of genotype 4 HEV capsid protein and should facilitate development of applications for the design of vaccines and antiviral drugs for broader prevention, detection, and treatment of HEV infection of diverse human and animal hosts.
CD4 T Cell Epitope Specificity and Cytokine Potential Are Preserved as Cells Transition from the Lung Vasculature to Lung Tissue following Influenza Virus Infection
Authors: DiPiazza Anthony , Laniewski Nathan , Rattan Ajitanuj , Topham David J. , Miller Jim , Sant Andrea J. 
Published: April 2018

ABSTRACTPulmonary CD4 T cells are critical in respiratory virus control, both by delivering direct effector function and through coordinating responses of other immune cells. Recent studies have shown that following influenza virus infection, virus-specific CD4 T cells are partitioned between pulmonary vasculature and lung tissue. However, very little is known about the peptide specificity or functional differences of CD4 T cells within these two compartments. Using a mouse model of influenza virus infection in conjunction with intravascular labelingin vivo, the cell surface phenotype, epitope specificity, and functional potential of the endogenous polyclonal CD4 T cell response was examined by tracking nine independent CD4 T cell epitope specificities. These studies revealed that tissue-localized CD4 cells were globally distinct from vascular cells in expression of markers associated with transendothelial migration, residency, and micropositioning. Despite these differences, there was little evidence for remodeling of the viral epitope specificity or cytokine potential as cells transition from vasculature to the highly inflamed lung tissue. Our studies also distinguished cells in the pulmonary vasculature from peripheral circulating CD4 T cells, providing support for the concept that the pulmonary vasculature does not simply reflect circulating cells that are trapped within the narrow confines of capillary vessels but rather is enriched in transitional cells primed in the draining lymph node that have specialized potential to enter the lung tissue.IMPORTANCECD4 T cells convey a multitude of functions in immunity to influenza, including those delivered in the lymph node and others conveyed by CD4 T cells that leave the lymph node, enter the blood, and extravasate into the lung tissue. Here, we show that the transition of recently primed CD4 cells detected in the lung vasculature undergo profound changes in expression of markers associated with tissue localization as they establish residence in the lung. However, this transition does not edit CD4 T cell epitope specificity or the cytokine potential of the CD4 T cells. Thus, CD4 T cells that enter the infected lung can convey diverse functions and have a sufficiently broad viral antigen specificity to detect the complex array of infected cells within the infected tissue, offering the potential for more effective protective function.
Reproduction of the UV-vis spectra of boron subphthalocyanine chloride in different solvents using time-dependent generalized Kohn–Sham density functionals with first solvation shell
Authors: Chen Xue , Chen Wenlan , Zheng Shaohui 
Published: April 2018

Because of the unique physical, chemical and optical characteristics of boron subphthalocyanine chloride, it has been widely applied in different research fields and attracted global researchers. Deep insight into its UV-vis spectrum is required to understand the mechanism of the photon absorption of boron subphthalocyanine chloride in its condensed phase. In the present work, we utilize generalized Kohn–Sham density functionals with a non-equilibrium solvation model to simulate the UV-vis spectra of boron subphthalocyanine chloride in different solvents. Without considering the first solvation shell, we find that the slopes of lines drawn with [Formula: see text]B97XD and CAM-B3LYP results vs. experimental absorption wavelengths are close to 1.0 and root–mean–square deviations are less than 40 nm. We also find that the inclusion of the first solvation shell surrounding boron subphthalocyanine chloride monomers generally makes the calculated results worse. Finally, we discover that the simulated results overestimate oscillator strength of electronic absorption spectra in the ultraviolet region with respect to experimental spectra. These results imply that it may be important to consider the aggregation of solute molecules in order to understand the electronic absorption spectra of subPC in solution
Analyzing Node-Weighted Oblivious Matching Problem via Continuous LP with Jump Discontinuity
Authors: Chan T.-H. Hubert , Chen Fei , Wu Xiaowei 
Published: April 2018

We prove the first non-trivial performance ratio strictly above 0.5 for the weighted Ranking algorithm on the oblivious matching problem where nodes in a general graph can have arbitrary weights.
We have discovered a new structural property of the ranking algorithm: if a node has two unmatched neighbors, then it will still be matched even when its rank is demoted to the bottom. This property allows us to form LP constraints for both the weighted and the unweighted versions of the problem.
Using a new class of continuous linear programming (LP), we prove that the ratio for the weighted case is at least 0.501512, and we improve the ratio for the unweighted case to 0.526823 (from the previous best 0.523166 in SODA 2014). Unlike previous continuous LP, in which the primal solution must be continuous everywhere, our new continuous LP framework allows the monotone component of the primal function to have jump discontinuities, and the other primal components to take non-conventional forms, such as the Dirac δ function.