bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of the Cold Core Eddy on Tropical Cyclone Intensity and Structure under Idealized Air–Sea Interaction Conditions
Authors: Ma Zhanhong , Fei Jianfang , Liu Lei , Huang Xiaogang , Cheng Xiaoping 
Published: September 2012

Abstract
The impacts of ocean feedback on tropical cyclones (TCs) are investigated using a coupled atmosphere–ocean model under idealized TC and cold core eddy (CCE) conditions. Results reveal negative impacts of the ocean coupling on TC development. The cold wake induced by a TC not only weakens the TC intensity but also limits the expansion of the storm circulation. The presence of CCE has boosted the TC-induced sea surface temperature cooling, which conversely inhibits the TC development. The TC appears to be weakened as it encounters the CCE edge. The intensity reduction attains a maximum shortly after the TC passes over the CCE center, and simultaneously the CCE-induced asymmetry of the storm structure is most significant as well. The TC undergoes a period of recovery after departure from the CCE, lasting about 36–48 h. During this time the residual asymmetry caused by the CCE is smoothed gradually by storm axisymmetrization. The CCE has induced smaller TC size throughout the simulation even after the TC intensity has completely recovered, an indication of longer recovery time for the TC size. Notably cooler and moister eye air in the lower troposphere, just under the warm-core height, is found in the experiment with CCE. The water vapor mixing ratio budget analysis indicates that it is primarily attributed to changes in vertical advection that occurred in the eye, that is, the undermined eye subsidence associated with the suppressed eyewall convection. The horizontal patterns of vertical motion in the boundary layer are also distinctly changed by the CCE.
Perceived Family Support and Depression among People Living with HIV/AIDS in the Kathmandu Valley, Nepal
Authors: Shrestha Sadhana , Poudel Krishna C. , Poudel-Tandukar Kalpana , Kobayashi Jun , Pandey Basu Dev , Yasuoka Junko , Otsuka Keiko , Jimba Masamine 
Published: September 2012

Background: Depression is emerging as a highly prevalent psychiatric condition among people living with HIV/AIDS (PLWHA). Perceived family support (PFS) buffers depression among chronic disease patients. However, a similar relationship among PLWHA is unexplored. Objective: To examine the relationship between PFS and depression among PLWHA in the Kathmandu Valley, Nepal. Methods: In this cross-sectional study, depression was measured by Beck Depression Inventory Ia. Perceived family support was measured by Nepali Family Support and Difficulties Scale. The status of depression was compared between 208 PLWHA and 208 HIV-negative participants. The relationship between PFS and depression was examined only among PLWHA. Results: Among each of the 208 participants, the number of depressed PLWHA (n = 61,29.3%) was higher than that of HIV-negative participants (n = 13,6.2%; P < .001). Perceived family support had a negative association with depression in PLWHA (adjusted odds ratio [AOR] = 0.20, 95% confidence interval [CI] = 0.08-0.53). Conclusion: In Nepal, PLWHA display a higher level of depression than HIV-negative people, and a lower level of PFS is associated with depression among PLWHA. Improved family support might be helpful in reducing depression among Nepalese PLWHA.
Water-based exercise in COPD with physical comorbidities: a randomised controlled trial
Authors: McNamara Renae J. , McKeough Zoe J. , McKenzie David K. , Alison Jennifer A. 
Published: September 2012

Land-based exercise is often difficult for people with chronic obstructive pulmonary disease (COPD) who have coexisting obesity or musculoskeletal or neurological conditions. This randomised controlled trial aimed to determine the effectiveness of water-based exercise training in improving exercise capacity and quality of life compared to land-based exercise training and control (no exercise) in people with COPD and physical comorbidities.Participants referred to pulmonary rehabilitation were randomly allocated to a water-based exercise, land-based exercise or the control group. The two exercise groups trained for 8 weeks, completing three sessions per week.45 out of 53 participants (mean±sdage 72±9 years; forced expiratory volume in 1 s 59±15% predicted) completed the study. Compared to controls, water-based exercise training significantly increased 6-min walking distance, incremental and endurance shuttle walk distances, and improved Chronic Respiratory Disease Questionnaire (CRDQ) dyspnoea and fatigue. Compared to land-based exercise training, water-based exercise training significantly increased incremental shuttle walk distance (mean difference 39 m, 95% CI 5–72 m), endurance shuttle walk distance (mean difference 228 m, 95% CI 19–438 m) and improved CRDQ fatigue.Water-based exercise training was significantly more effective than land-based exercise training and control in increasing peak and endurance exercise capacity and improving aspects of quality of life in people with COPD and physical comorbidities.
Efficacy and safety of meropenem–clavulanate added to linezolid-containing regimens in the treatment of MDR-/XDR-TB
Authors: De Lorenzo Saverio , Alffenaar Jan Wilem , Sotgiu Giovanni , Centis Rosella , D'Ambrosio Lia , Tiberi Simon , Bolhuis Mathieu S. , van Altena Richard , Viggiani Piero , Piana Andrea , Spanevello Antonio , Migliori Giovanni Battista 
Published: September 2012

Clinical experience on meropenem–clavulanate to treat tuberculosis (TB) is anecdotal (according to case reports on 10 patients). The aim of our case–control study was to evaluate the contribution of meropenem–clavulanate when added to linezolid-containing regimens in terms of efficacy and safety/tolerability in treating multidrug-resistant (MDR) and extensively drug-resistant (XDR) TB cases after 3 months of second-line treatment.37 cases with MDR-/XDR-TB were prescribed meropenem–clavulanate (3 g daily dose) in addition to a linezolid-containing regimen (dosage range 300–1200 mg·day−1), designed according to international guidelines, which was prescribed to 61 controls.The clinical severity of cases was worse than that of controls (drug susceptibility profile, proportion of sputum-smear positive and of re-treatment cases). The group of cases yielded a higher proportion of sputum-smear converters (28 (87.5%) out of 32versusnine (56.3%) out of 16; p=0.02) and culture converters (31 (83.8%) out of 37versus15 (62.5%) out of 24; p=0.06). Excluding XDR-TB patients (11 (11.2%) out of 98), cases scored a significantly higher proportion of culture converters than controls (p=0.03). One case had to withdraw from meropenem–clavulanate due to increased transaminase levels.The results of our study provide: 1) preliminary evidence on effectiveness and safety/tolerability of meropenem–clavulanate; 2) reference to design further trials; and 3) a guide to clinicians for its rationale use within salvage/compassionate regimens.
Pulmonary arteriole gene expression signature in idiopathic pulmonary fibrosis
Authors: Patel Nina M. , Kawut Steven M. , Jelic Sanja , Arcasoy Selim M. , Lederer David J. , Borczuk Alain C. 
Published: September 2012

A third of patients with idiopathic pulmonary fibrosis (IPF) develop pulmonary hypertension (PH-IPF), which is associated with increased mortality. Whether an altered gene expression profile in the pulmonary vasculature precedes the clinical onset of PH-IPF is unknown. We compared gene expression in the pulmonary vasculature of IPF patients with and without PH with controls.Pulmonary arterioles were isolated using laser capture microdissection from 16 IPF patients: eight with PH (PH-IPF) and eight with no PH (NPH-IPF), and seven controls. Probe was prepared from extracted RNA, and hybridised to Affymetrix Hu133 2.0 Plus genechips. Biometric Research Branch array tools and Ingenuity Pathway Analysis software were used for analysis of the microarray data.Univariate analysis revealed 255 genes that distinguished IPF arterioles from controls (p<0.001). Mediators of vascular smooth muscle and endothelial cell proliferation, Wnt signalling and apoptosis were differentially expressed in IPF arterioles. Unsupervised and supervised clustering analyses revealed similar gene expression in PH-IPF and NPH-IPF arterioles.The pulmonary arteriolar gene expression profile is similar in IPF patients with and without coexistent PH. Pathways involved in vascular proliferation and aberrant apoptosis, which may contribute to pulmonary vascular remodelling, are activated in IPF patients.
Analysis of TIR- and non-TIR-NBS-LRR disease resistance gene analogous in pepper: characterization, genetic variation, functional divergence and expression patterns
Authors: Wan Hongjian , Yuan Wei , Ye Qingjing , Wang Rongqing , Ruan Meiying , Li Zhimiao , Zhou Guozhi , Yao Zhuping , Zhao Jing , Liu Shujun , Yang Yuejian 
Published: September 2012

Abstract

Background
Pepper (Capsicum annuum L.) is one of the most important vegetable crops worldwide. However, its yield and fruit quality can be severely threatened by several pathogens. The plant nucleotide-binding site (NBS)-leucine-rich repeat (LRR) gene family is the largest class of known disease resistance genes (R genes) effective against such pathogens. Therefore, the isolation and identification of such R gene homologues from pepper will provide a critical foundation for improving disease resistance breeding programs.

Results
A total of 78 R gene analogues (CaRGAs) were identified in pepper by degenerate PCR amplification and database mining. Phylogenetic tree analysis of the deduced amino acid sequences for 51 of these CaRGAs with typically conserved motifs ( P-loop, kinase-2 and GLPL) along with some known R genes from Arabidopsis and tomato grouped these CaRGAs into the non-Toll interleukin-1 receptor (TIR)-NBS-LRR (CaRGAs I to IV) and TIR-NBS-LRR (CaRGAs V to VII) subfamilies. The presence of consensus motifs (i.e. P-loop, kinase-2 and hydrophobic domain) is typical of the non-TIR- and TIR-NBS-LRR gene subfamilies. This finding further supports the view that both subfamilies are widely distributed in dicot species. Functional divergence analysis provided strong statistical evidence of altered selective constraints during protein evolution between the two subfamilies. Thirteen critical amino acid sites involved in this divergence were also identified using DIVERGE version 2 software. Analyses of non-synonymous and synonymous substitutions per site showed that purifying selection can play a critical role in the evolutionary processes of non-TIR- and TIR-NBS-LRR RGAs in pepper. In addition, four specificity-determining positions were predicted to be responsible for functional specificity. qRT-PCR analysis showed that both salicylic and abscisic acids induce the expression of CaRGA genes, suggesting that they may primarily be involved in defence responses by activating signaling pathways.

Conclusion
The identified CaRGAs are a valuable resource for discovering R genes and developing RGA molecular markers for genetic map construction. They will also be useful for improving disease resistance in pepper. The findings of this study provide a better understanding of the evolutionary mechanisms that drive the functional diversification of non-TIR- and TIR-NBS-LRR R genes in pepper.
Proteomic analysis of Clostridium thermocellum core metabolism: relative protein expression profiles and growth phase-dependent changes in protein expression
Authors: Rydzak Thomas , McQueen Peter D , Krokhin Oleg V , Spicer Vic , Ezzati Peyman , Dwivedi Ravi C , Shamshurin Dmitry , Levin David B , Wilkins John A , Sparling Richard 
Published: September 2012

Abstract

Background

Clostridium thermocellum produces H2 and ethanol, as well as CO2, acetate, formate, and lactate, directly from cellulosic biomass. It is therefore an attractive model for biofuel production via consolidated bioprocessing. Optimization of end-product yields and titres is crucial for making biofuel production economically feasible. Relative protein expression profiles may provide targets for metabolic engineering, while understanding changes in protein expression and metabolism in response to carbon limitation, pH, and growth phase may aid in reactor optimization. We performed shotgun 2D-HPLC-MS/MS on closed-batch cellobiose-grown exponential phase C. thermocellum cell-free extracts to determine relative protein expression profiles of core metabolic proteins involved carbohydrate utilization, energy conservation, and end-product synthesis. iTRAQ (isobaric tag for relative and absolute quantitation) based protein quantitation was used to determine changes in core metabolic proteins in response to growth phase.

Results
Relative abundance profiles revealed differential levels of putative enzymes capable of catalyzing parallel pathways. The majority of proteins involved in pyruvate catabolism and end-product synthesis were detected with high abundance, with the exception of aldehyde dehydrogenase, ferredoxin-dependent Ech-type [NiFe]-hydrogenase, and RNF-type NADH:ferredoxin oxidoreductase. Using 4-plex 2D-HPLC-MS/MS, 24% of the 144 core metabolism proteins detected demonstrated moderate changes in expression during transition from exponential to stationary phase. Notably, proteins involved in pyruvate synthesis decreased in stationary phase, whereas proteins involved in glycogen metabolism, pyruvate catabolism, and end-product synthesis increased in stationary phase. Several proteins that may directly dictate end-product synthesis patterns, including pyruvate:ferredoxin oxidoreductases, alcohol dehydrogenases, and a putative bifurcating hydrogenase, demonstrated differential expression during transition from exponential to stationary phase.

Conclusions
Relative expression profiles demonstrate which proteins are likely utilized in carbohydrate utilization and end-product synthesis and suggest that H2 synthesis occurs via bifurcating hydrogenases while ethanol synthesis is predominantly catalyzed by a bifunctional aldehyde/alcohol dehydrogenase. Differences in expression profiles of core metabolic proteins in response to growth phase may dictate carbon and electron flux towards energy storage compounds and end-products. Combined knowledge of relative protein expression levels and their changes in response to physiological conditions may aid in targeted metabolic engineering strategies and optimization of fermentation conditions for improvement of biofuels production.
Molecular epidemiology, antimicrobial susceptibilities and resistance mechanisms of Streptococcus pyogenes isolates resistant to erythromycin and tetracycline in Spain (1994–2006)
Authors: Rubio-López Virginia , Valdezate Sylvia , Álvarez David , Villalón Pilar , Medina María José , Salcedo Celia , Sáez-Nieto Juan-Antonio 
Published: September 2012

Abstract

Background
Group A Streptococcus (GAS) causes human diseases ranging in severity from uncomplicated pharyngitis to life-threatening necrotizing fasciitis and shows high rates of macrolide resistance in several countries. Our goal is to identify antimicrobial resistance in Spanish GAS isolates collected between 1994 and 2006 and to determine the molecular epidemiology (emm/T typing and PFGE) and resistance mechanisms of those resistant to erythromycin and tetracycline.

Results
Two hundred ninety-five out of 898 isolates (32.8%) were erythromycin resistant, with the predominance of emm 4T4, emm 75T25, and emm 28T28, accounting the 67.1% of the 21 emm/T types. Spread of emm 4T4, emm 75T25 and emm 28T28 resistant clones caused high rates of macrolide resistance. The distribution of the phenotypes was M (76.9%), cMLSB (20.3%), iMLSB (2.7%) with the involvement of the erythromycin resistance genes mef(A) (89.5%), msr(D) (81.7%), erm(B) (37.3%) and erm(A) (35.9%).
Sixty-one isolates were tetracycline resistant, with the main representation of the emm 77T28 among 20 emm/T types. To note, the combination of tet(M) and tet(O) tetracycline resistance genes were similar to tet(M) alone reaching values close to 40%. Resistance to both antibiotics was detected in 19 isolates of 7 emm/T types, being emm 11T11 and the cMLSB phenotype the most frequent ones. erm(B) and tet(M) were present in almost all the strains, while erm(A), mef(A), msr(D) and tet(O) appeared in less than half of them.

Conclusions
Spanish GAS were highly resistant to macrolides meanwhile showed minor resistance rate to tetracycline. A remarkable correlation between antimicrobial resistance and emm/T type was noticed. Clonal spread of emm 4T4, emm 75T25 and emm 28T28 was the main responsable for macrolide resistance where as that emm 77T28 clones were it to tetraclycline resistance. A wide variety of macrolide resistance genes were responsible for three macrolide resistance phenotypes.
Excessive proinflammatory cytokine and chemokine responses of human monocyte-derived macrophages to enterovirus 71 infection
Authors: Gong Xun , Zhou Jianfang , Zhu Wenfei , Liu Na , Li Jinsong , Li Lili , Jin Yu , Duan Zhaojun 
Published: September 2012

Abstract

Background
The levels of proinflammatory cytokine or chemokine in blood and cerebrospinal fluid are thought to be one of predictors for clinical severity of enterovirus 71 (EV71) infection, yet the cellular sources or signalling mechanism remain undefined. Here, we focused on the response of human primary monocyte-derived macrophages (MDMs) to EV71 virus and its possible mechanisms.

Methods
Human primary MDMs were infected by EV71 virus in vitro. Infectivity and viral replication were assayed, and cytokine responses were determined by Cytometric Bead Array(CBA) analysis. The relative changes of Toll-like receptors, retinoic acid-inducible gene I (RIG-I) and melamoma differentiation associated gene 5 (MDA5) mRNA expression were detected by real-time RT-PCR.

Results
Effective infection and viral replication were detected in EV71-infected MDMs. The titters of progeny virus released from EV71-infected MDMs gradually increased from 6-h to 48-h point of infection (POI.). Proinflammatory cytokines: IL-1, IL-6, TNF-α but not IFN-α and γ were induced in MDMs by EV71. EV71 infection significantly increased the release of IL-8, IP-10 and RANTES at 12-h or 24-h POI. Upregulation of TLR2, TLR7 and TLR8 mRNA expression rather than TLR3, TLR4, TLR6, TLR9, TLR10, RIG-I, MDA5 were found at different time points in EV71-infected MDMs.

Conclusions
Our findings suggested that macrophages are not only the important target cells but also the effectors during EV71 infection, and they may play an important role in the pathogenesis of EV71 infection. And the proinflammatory cytokine and chemokine responses in EV71-infected MDMs may be mediated by the activation of differential pattern of TLRs.
The changes of Th17 cells and the related cytokines in the progression of human colorectal cancers
Authors: Wang Jiansheng , Xu Kaiyu , Wu Jing , Luo Chenghua , Li Yuchen , Wu Xuebin , Gao Hong , Feng Guosheng , Yuan Bao-Zhu 
Published: September 2012

Abstract

Background
The role of Th17 cells in colorectal tumorigenesis and development still remains unclear, despite the fact that it has been established in the pathogenesis of autoimmune diseases.

Methods
We first analyzed Th17 cells and Treg cells using flow cytometry in the circulation of colorectal adenoma (CRA) and colorectal carcinoma (CRC) patients and healthy controls, and the frequency of Th17 cells in peripheral blood mononuclear cells (PBMCs) stimulated by anti-CD3 plus anti-CD28 and treated by IL-1β, IL-6, and TGF-β in different concentrations. We then detected cytokines IL-1β, IL-6, IL-17A, IL-21, IL-23 or TGF-β by ELISA in sera and supernatants from both normal and tumor tissues cultured ex vivo.

Results
It was found that the percentage of Th17 and Treg cells increased in the circulation of both CRA and CRC patients; the increase of Th17 cells in the circulation occurred in early stages, whereas the increase of Treg cells in the circulation and the increase of Th17 cells in tumor tissues occurred in advanced stages. The subsequent cytokine profiling showed that, along CRC progression, IL-1β, IL-17A and IL-23 underwent a similar change, while IL-6 in CRC exhibited an opposite change, with Th17 cells. In addition, high levels of TGF-β and IL-17A were detected in tumor tissues rather than in normal mucosa. The in vitro experiment further demonstrated that IL-1β, IL-6 or TGF-β modulated Th17 cell expansion in PBMC.

Conclusions
Our study reveals a unique change of Th17 cells, which is regulated possibly by IL-1β, IL-6 and TGF-β in the progression of CRC.
Short-chain fluorescent tryptophan tags for on-line detection of functional recombinant proteins
Authors: Siepert Eva-Maria , Gartz Esther , Tur Mehmet Kemal , Delbrück Heinrich , Barth Stefan , Büchs Jochen 
Published: September 2012

Abstract

Background
Conventional fluorescent proteins, such as GFP, its derivatives and flavin mononucleotide based fluorescent proteins (FbFPs) are often used as fusion tags for detecting recombinant proteins during cultivation. These reporter tags are state-of-the-art; however, they have some drawbacks, which can make on-line monitoring challenging. It is discussed in the literature that the large molecular size of proteins of the GFP family may stress the host cell metabolism during production. In addition, fluorophore formation of GFP derivatives is oxygen-dependent resulting in a lag-time between expression and fluorescence detection and the maturation of the protein is suppressed under oxygen-limited conditions. On the contrary, FbFPs are also applicable in an oxygen-limited or even anaerobic environment but are still quite large (58% of the size of GFP).

Results
As an alternative to common fluorescent tags we developed five novel tags based on clustered tryptophan residues, called W-tags. They are only 5-11% of the size of GFP. Based on the property of tryptophan to fluoresce in absence of oxygen it is reasonable to assume that the functionality of our W-tags is also given under anaerobic conditions. We fused these W-tags to a recombinant protein model, the anti-CD30 receptor single-chain fragment variable antibody (scFv) Ki-4(scFv) and the anti-MucI single-chain fragment variable M12(scFv). During cultivation in Microtiter plates, the overall tryptophan fluorescence intensity of all cultures was measured on-line for monitoring product formation via the different W-tags. After correlation of the scattered light signal representing biomass concentration and tryptophan fluorescence for the uninduced cultures, the fluorescence originating from the biomass was subtracted from the overall tryptophan signal. The resulting signal, thus, represents the product fluorescence of the tagged and untagged antibody fragments. The product fluorescence signal was increased. Antibodies with W-tags generated stronger signals than the untagged construct.

Conclusions
Our low-molecular-weight W-tags can be used to monitor the production of antibody fragments on-line. The binding specificity of the recombinant fusion protein is not affected, even though the binding activity decreases slightly with increasing number of tryptophan residues in the W-tags. Thus, the newly designed W-tags offer a versatile and generally applicable alternative to current fluorescent fusion tags.