bluuebunny/crossref_metadata_2025_split huggingface dataset:
The alr-groEL1 operon in Mycobacterium tuberculosis: an interplay of multiple regulatory elements
Authors: Bhat Aadil H. , Pathak Deepika , Rao Alka 
Published: March 2017

AbstractThreonylcarbamoyladenosine is a universally conserved essential modification of tRNA that ensures translational fidelity in cellular milieu. TsaD, TsaB and TsaE are identified as tRNA-A37-threonylcarbamoyl (t6A)-transferase enzymes that have been reconstituted in vitro, in few bacteria recently. However, transcriptional organization and regulation of these genes are not known in any of these organisms. This study describes the intricate architecture of a complex multicistronic alr-groEL1 operon, harboring essential genes, namely tsaD, tsaB, tsaE, groES, groEL1, and alr (required for cell wall synthesis), and rimI encoding an N-α- acetyltransferase in Mycobacterium tuberculosis. Using northern blotting, RT-PCR and in vivo fluorescence assays, genes alr to groEL1 were found to constitute an ~6.3 kb heptacistronic operon with multiple internal promoters and an I-shaped intrinsic hairpin-like cis-regulatory element. A strong promoter PtsaD within the coding sequence of rimI gene is identified in M. tuberculosis, in addition. The study further proposes an amendment in the known bicistronic groESL1 operon annotation by providing evidence that groESL1 is co-transcribed as sub-operon of alr-groEL1 operon. The architecture of alr-groEL1 operon, conservation of the genetic context and a mosaic transcriptional profile displayed under various stress conditions convincingly suggest the involvement of this operon in stress adaptation in M. tuberculosis.
Empty-nest-related psychological distress is associated with progression of brain white matter lesions and cognitive impairment in the elderly
Authors: Duan Dandan , Dong Yuanli , Zhang Hua , Zhao Yingxin , Diao Yutao , Cui Yi , Wang Juan , Chai Qiang , Liu Zhendong 
Published: March 2017

AbstractThis study evaluated the association between empty-nest-related psychological distress and the progression of white matter lesions (WMLs) and cognitive impairment in 219 elderly subjects aged 60 years or over. Psychological distress was assessed using the University of California at Los Angeles Loneliness Scale (UCLA-LS) and Geriatric Depression Scale (GDS) Short-Form. Cognitive function was evaluated using the MMSE and MoCA. White matter hyperintensities (WMH) were assessed using magnetic resonance imaging. After 5.2-year follow-up, the reductions in MMSE and MoCA scores and the increases in periventricular (P)WMH, deep (D)WMH, and total WMH volumes in the empty-nest elderly were greater than those in the non-empty-nest elderly (P < 0.05). The reduced MMSE and MoCA scores and increased volumes of PWMH and total WMH in the empty-nest elderly living alone were greater than those in the empty-nest elderly living with a spouse (P < 0.05). UCLA-LS and GDS scores were significantly and independently associated with reduced MMSE and MoCA scores and the increased volumes of PWMH, DWMH, and total WMH. The results indicate that empty-nest-related psychological distress is associated with progression of WMLs and cognitive impairment in the elderly.
Prognosis and Progression of ESCC Patients with Perineural Invasion
Authors: Xu Guanghui , Feng Fan , Liu Zhen , Liu Shushang , Zheng Gaozan , Xiao Shuao , Cai Lei , Yang Xuewen , Li Guocai , Lian Xiao , Guo Man , Sun Li , Yang Jianjun , Fan Daiming , Lu Qun , Zhang Hongwei 
Published: March 2017

AbstractPerineural invasion (PNI) has been recognized as a poor prognostic factor in several malignancies, but the definition and pathogenesis of PNI in esophageal squamous cell carcinoma (ESCC) remains to be defined. PNI was evaluated by H&E staining and S100 immunohistochemistry. The predictive value of PNI in the prognosis of ESCC patients was analyzed. PNI was evaluated in vitro and in vivo. A total of 54 specimens (17.88%) were defined as PNI-a and 99 specimens (32.78%) as PNI-b. S100 staining was superior to H&E staining for PNI detection (50.66% vs 27.15%, P < 0.001, κ = 0.506). Tumor depth (P = 0.001), tumor stage (P = 0.010), and vascular invasion (P < 0.001) were significantly associated with PNI. PIN-a and PNI-b had significant lower disease free survival (DFS) and disease specific survival (DSS) than PNI-0 patients, and the prognosis of PNI-b patients was significantly worse than PNI-a patients for DFS (P = 0.009). PNI was an independent predictor for DFS and DSS in ESCC as evaluated by univariate and multivariate analyses. ESCC cells could metastasize along the nerve in vitro and in vivo, and PNI was a dynamic process. S100 staining significantly improved the accuracy of PNI detection. PNI was associated with local recurrence and poor prognosis of ESCC patients.
CD61 promotes the differentiation of canine ADMSCs into PGC-like cells through modulation of TGF-β signaling
Authors: Fang Jia , Wei Yudong , Lv Changrong , Peng Sha , Zhao Shanting , Hua Jinlian 
Published: March 2017

AbstractPrevious studies have shown that CD61 (integrin-β3) promotes the differentiation of human umbilical cord mesenchymal stem cells (hUC-MSCs) into germ-like cells. However, the mechanism remains unclear. In this study, we showed that overexpression of CD61 in canine adipose-derived mesenchymal stem cells (cADMSCs) promotes their differentiation into primordial germ cell (PGC)-like cells. Quantitative real-time PCR, immunocytochemistry and western blot detected higher levels of PGC-specific markers in CD61-overexpressed cADMSCs compared with those in control cells. Moreover, phosphorylation of Smad2, a downstream mediator of transforming growth factor beta (TGF-β), was increased in CD61-overexpressed cADMSCs than that in control cells. However, the expression of PGC-specific markers was downregulated in cADMSCs treated with a TGF-β inhibitor. These results suggested that CD61 could induce cADMSCs to differentiate into PGC-like cells by relying on the activation of TGF-β pathway. ADMSCs possess a considerable potential in treating the infertility of rare animal species.
Proline dehydrogenase from Thermus thermophilus does not discriminate between FAD and FMN as cofactor
Authors: Huijbers Mieke M. E. , Martínez-Júlvez Marta , Westphal Adrie H. , Delgado-Arciniega Estela , Medina Milagros , van Berkel Willem J. H. 
Published: March 2017

AbstractFlavoenzymes are versatile biocatalysts containing either FAD or FMN as cofactor. FAD often binds to a Rossmann fold, while FMN prefers a TIM-barrel or flavodoxin-like fold. Proline dehydrogenase is denoted as an exception: it possesses a TIM barrel-like fold while binding FAD. Using a riboflavin auxotrophic Escherichia coli strain and maltose-binding protein as solubility tag, we produced the apoprotein of Thermus thermophilus ProDH (MBP-TtProDH). Remarkably, reconstitution with FAD or FMN revealed that MBP-TtProDH has no preference for either of the two prosthetic groups. Kinetic parameters of both holo forms are similar, as are the dissociation constants for FAD and FMN release. Furthermore, we show that the holo form of MBP-TtProDH, as produced in E. coli TOP10 cells, contains about three times more FMN than FAD. In line with this flavin content, the crystal structure of TtProDH variant ΔABC, which lacks helices αA, αB and αC, shows no electron density for an AMP moiety of the cofactor. To the best of our knowledge, this is the first example of a flavoenzyme that does not discriminate between FAD and FMN as cofactor. Therefore, classification of TtProDH as an FAD-binding enzyme should be reconsidered.
Shrubland primary production and soil respiration diverge along European climate gradient
Authors: Reinsch Sabine , Koller Eva , Sowerby Alwyn , de Dato Giovanbattista , Estiarte Marc , Guidolotti Gabriele , Kovács-Láng Edit , Kröel-Dulay György , Lellei-Kovács Eszter , Larsen Klaus S. , Liberati Dario , Peñuelas Josep , Ransijn Johannes , Robinson David A. , Schmidt Inger K. , Smith Andrew R. , Tietema Albert , Dukes Jeffrey S. , Beier Claus , Emmett Bridget A. 
Published: March 2017

AbstractAbove- and belowground carbon (C) stores of terrestrial ecosystems are vulnerable to environmental change. Ecosystem C balances in response to environmental changes have been quantified at individual sites, but the magnitudes and directions of these responses along environmental gradients remain uncertain. Here we show the responses of ecosystem C to 8–12 years of experimental drought and night-time warming across an aridity gradient spanning seven European shrublands using indices of C assimilation (aboveground net primary production: aNPP) and soil C efflux (soil respiration: Rs). The changes of aNPP and Rs in response to drought indicated that wet systems had an overall risk of increased loss of C but drier systems did not. Warming had no consistent effect on aNPP across the climate gradient, but suppressed Rs more at the drier sites. Our findings suggest that above- and belowground C fluxes can decouple, and provide no evidence of acclimation to environmental change at a decadal timescale. aNPP and Rs especially differed in their sensitivity to drought and warming, with belowground processes being more sensitive to environmental change.
Volatile metabolomic signature of human breast cancer cell lines
Authors: Silva Catarina L. , Perestrelo Rosa , Silva Pedro , Tomás Helena , Câmara José S. 
Published: March 2017

AbstractBreast cancer (BC) remains the most prevalent oncologic pathology in women, causing huge psychological, economic and social impacts on our society. Currently, the available diagnostic tools have limited sensitivity and specificity. Metabolome analysis has emerged as a powerful tool for obtaining information about the biological processes that occur in organisms, and is a useful platform for discovering new biomarkers or make disease diagnosis using different biofluids. Volatile organic compounds (VOCs) from the headspace of cultured BC cells and normal human mammary epithelial cells, were collected by headspace solid-phase microextraction (HS-SPME) and analyzed by gas chromatography combined with mass spectrometry (GC–MS), thus defining a volatile metabolomic signature. 2-Pentanone, 2-heptanone, 3-methyl-3-buten-1-ol, ethyl acetate, ethyl propanoate and 2-methyl butanoate were detected only in cultured BC cell lines. Multivariate statistical methods were used to verify the volatomic differences between BC cell lines and normal cells in order to find a set of specific VOCs that could be associated with BC, providing comprehensive insight into VOCs as potential cancer biomarkers. The establishment of the volatile fingerprint of BC cell lines presents a powerful approach to find endogenous VOCs that could be used to improve the BC diagnostic tools and explore the associated metabolomic pathways.
Comparing the Effects of Speech-Generating Device Display Organization on Symbol Comprehension and Use by Three Children With Developmental Delays
Authors: Barton-Hulsey Andrea , Wegner Jane , Brady Nancy C. , Bunce Betty H. , Sevcik Rose A. 
Published: March 2017

Purpose
Three children ages 3;6 to 5;3 with developmental and language delays were provided experience with a traditional grid-based display and a contextually organized visual scene display on a speech-generating device to illustrate considerations for practice and future research in augmentative and alternative communication assessment and intervention.

Method
Twelve symbols were taught in a grid display and visual scene display using aided input during dramatic play routines. Teaching sessions were 30 minutes a day, 5 days a week for 3 weeks. Symbol comprehension and use was assessed pre and post 3 weeks of experience.

Results
Comprehension of symbol vocabulary on both displays increased after 3 weeks of experience. Participants 1 and 2 used both displays largely for initiation. Participant 3 had limited expressive use of either display.

Conclusions
The methods used in this study demonstrate one way to inform individual differences in learning and preference for speech-generating device displays when making clinical decisions regarding augmentative and alternative communication supports for a child and their family. Future research should systematically examine the role of extant comprehension, symbol experience, functional communication needs, and the role of vocabulary type in the learning and use of grid displays versus visual scene displays.
Increased Response to Altered Auditory Feedback in Dyslexia: A Weaker Sensorimotor Magnet Implied in the Phonological Deficit
Authors: van den Bunt Mark R. , Groen Margriet A. , Ito Takayuki , Francisco Ana A. , Gracco Vincent L. , Pugh Ken R. , Verhoeven Ludo 
Published: March 2017

Purpose
The purpose of this study was to examine whether developmental dyslexia (DD) is characterized by deficiencies in speech sensory and motor feedforward and feedback mechanisms, which are involved in the modulation of phonological representations.

Method
A total of 42 adult native speakers of Dutch (22 adults with DD; 20 participants who were typically reading controls) were asked to produce /bep/ while the first formant (F1) of the /e/ was not altered (baseline), increased (ramp), held at maximal perturbation (hold), and not altered again (after-effect). The F1 of the produced utterance was measured for each trial and used for statistical analyses. The measured F1s produced during each phase were entered in a linear mixed-effects model.

Results
Participants with DD adapted more strongly during the ramp phase and returned to baseline to a lesser extent when feedback was back to normal (after-effect phase) when compared with the typically reading group. In this study, a faster deviation from baseline during the ramp phase, a stronger adaptation response during the hold phase, and a slower return to baseline during the after-effect phase were associated with poorer reading and phonological abilities.

Conclusion
The data of the current study are consistent with the notion that the phonological deficit in DD is associated with a weaker sensorimotor magnet for phonological representations.
Stepwise inference of likely dynamic flux distributions from metabolic time series data
Authors: Faraji Mojdeh , Voit Eberhard O 
Published: March 2017

Abstract

Motivation
Most metabolic pathways contain more reactions than metabolites and therefore have a wide stoichiometric matrix that corresponds to infinitely many possible flux distributions that are perfectly compatible with the dynamics of the metabolites in a given dataset. This under-determinedness poses a challenge for the quantitative characterization of flux distributions from time series data and thus for the design of adequate, predictive models. Here we propose a method that reduces the degrees of freedom in a stepwise manner and leads to a dynamic flux distribution that is, in a statistical sense, likely to be close to the true distribution.

Results
We applied the proposed method to the lignin biosynthesis pathway in switchgrass. The system consists of 16 metabolites and 23 enzymatic reactions. It has seven degrees of freedom and therefore admits a large space of dynamic flux distributions that all fit a set of metabolic time series data equally well. The proposed method reduces this space in a systematic and biologically reasonable manner and converges to a likely dynamic flux distribution in just a few iterations. The estimated solution and the true flux distribution, which is known in this case, show excellent agreement and thereby lend support to the method.

Availability and Implementation
The computational model was implemented in MATLAB (version R2014a, The MathWorks, Natick, MA). The source code is available at https://github.gatech.edu/VoitLab/Stepwise-Inference-of-Likely-Dynamic-Flux-Distributions and www.bst.bme.gatech.edu/research.php.

Supplementary information
Supplementary data are available at Bioinformatics online.
Current Practice Trends for Use of Early Venous Thromboembolism Prophylaxis After Intracerebral Hemorrhage
Authors: Cherian Laurel J , Smith Eric E , Schwamm Lee H , Fonarow Gregg C , Schulte Phillip J , Xian Ying , Wu Jingjing , Prabhakaran Shyam K 
Published: March 2017

Abstract

BACKGROUND
Venous thromboembolism (VTE) is common after intracerebral hemorrhage (ICH). Guidelines recommend early VTE prophylaxis.

OBJECTIVE
To determine characteristics associated with early chemoprophylaxis (CP) after ICH in the Get With The Guidelines-Stroke registry.

METHODS
In this observational cohort study, we identified patients with ICH between January 1, 2009 and September 30, 2013, who (1) were non-ambulatory and/or not comfort care measures by hospital day 2; (2) were not transferred to another acute care facility; and (3) had known VTE prophylaxis status at end of hospital day 2. Categories for VTE prophylaxis were as follows: (1) mechanical non-CP or (2) CP with or without mechanical prophylaxis. Early prophylaxis was defined as occurring by hospital day 2. Using multivariable logistic regression, we assessed patient, hospital, and geographic factors independently associated with early CP use.

RESULTS
Among 74 283 patients with ICH from 1358 hospitals, 5929 (7.9%) received early CP, 66 444 (89.4%) received early mechanical/non-CP, and 1910 (2.6%) had no prophylaxis, mechanical or CP, within the first 2 days. There was no increase in early CP use over the study period; 60% of hospitals provided early CP to <9% of patients. In multivariable analysis, female sex, atrial fibrillation, diabetes, coronary, carotid, and peripheral artery disease, prior ischemic stroke or transient ischemic attack, hospital size >500 beds, and geographic region were independently associated with early vs no early CP use.

CONCLUSION
Nationwide, the large majority of ICH patients receive early mechanical VTE prophylaxis only, without CP. Patient comorbidities and hospital characteristics such as geographic location are determinants of higher use of early CP.
Demystifying Nursing Theory
Authors: Schaffer Marjorie A. , Sandau Kristin , Missal Bernita 
Published: March 2017

ABSTRACT:
How does nursing theory apply to nursing practice? Nursing theory can explain the why and how of nursing practice, guide nursing interventions, and provide a framework for measuring outcomes. This article briefly explains nursing theory, provides examples for applying theory to nursing practice, and proposes questions for examining the consistency of nursing theories with Christian perspectives. A helpful table illustrating grand, middle-range, and situation-specific theories and their application to nursing practice and research, along with references, is provided online as supplemental digital content. Three caring theories are analyzed from biblical beliefs.
Phase II Study of Adjuvant Chemoradiotherapy Using Docetaxel/Cisplatin/5-Fluorouracil Before and After Intensity-modulated Radiotherapy With Concurrent Docetaxel in Patients With Completely (R0) Resected Gastric Carcinoma
Authors: Liu Yong , Zhao Guoqi , Xu Yi , Zhang Tiening , Chen Zhixiao , Yan Ge , Tu Wenzhi , Hu Ye , Chen Ying , He Xia , Li Xiaodong , Chen Hui , Yao Shengyu , Hu Zhekai , Chen Xuming , Chen Tingfeng 
Published: March 2017

Objectives:
The Intergroup 0116 study has demonstrated a significant survival benefit for completely resected (R0) gastric cancer patients treated with a fluorouracil/leucovorin chemoradiotherapy regimen. However, this regimen is also toxic and less effective in terms of distant disease control. Therefore, a more efficacious and safer regimen is urgently needed.

Methods:
Patients with R0 resected gastric carcinoma received up to two 21-day cycles of postoperative adjuvant preradiation and postradiation DCF chemotherapy (docetaxel 37.5 mg/m2 on days 1 and 8, cisplatin 25 mg/m2 on days 1 to 3, and a continuous infusion of fluorouracil 750 mg/m2 on days 1 to 5), respectively. Chemoradiotherapy between preradiation and postradiation chemotherapy was initiated on day 43 and consisted of intensity-modulated radiotherapy (45 Gy) plus concurrent docetaxel 20 mg/m2 weekly for 5 weeks.

Results:
A total of 55 patients were evaluated and 76% (42) of patients completed the prescribed therapy. With a median follow-up of 61 months, the 3- and 5-year progression-free survival rates were 67% (95% confidence interval [CI], 54%-80%) and 59% (95% CI, 46%-72%), respectively; and the 3- and 5-year overall survival rates were 72% (95% CI, 60%-84%) and 61% (95% CI, 48%-74%), respectively. The most common grade 3 or greater toxicity, during the chemotherapy phase, was neutropenia (24%). Common grade 3/4 toxicities during concurrent chemoradiotherapy were nausea (32%), vomiting (26%), fatigue (15%), and anorexia (19%).

Conclusions:
These results demonstrate that this adjuvant regimen is active with an acceptable toxicity profile. A randomized phase 3 trial comparing the Intergroup 0116 chemoradiotherapy regimen with this regimen is underway.
The Role of Radiotherapy in Early-stage Primary Diffuse Large B-Cell Lymphoma of the Waldeyer Ring
Authors: Lee Shing Fung , Ng Ting Ying , Wong Frank Chi Sing , Tung Stewart Yuk 
Published: March 2017

Objectives:
The role of radiotherapy (RT) in improving survival of patients with diffuse large B-cell lymphoma (DLBCL) of the Waldeyer ring (WR) remains controversial. Therefore, this retrospective cohort study aimed to determine the role of RT in the treatment of DLBCL of the WR as well as the effects of associated covariates.

Materials and Methods:
Patients (n=35) with stage I to II DLBCL of the WR who underwent treatment at our center between 1994 and 2010 were retrospectively investigated. All patients had histologic diagnosis and staging workup completed. Overall survival (OS), event-free survival (EFS), and disease-free survival (DFS) were analyzed. Variables with a P-value of <0.1 were subjected to multivariate Cox proportional hazards model analyses.

Results:
The median OS was 8.1 years. The 5-year OS, DFS, and EFS rates were 59.4%, 53.8%, and 70.7%, respectively; the corresponding 10-year rates were 34.9%, 29.5%, and 51.0%, respectively. The 5-year OS rate was significantly higher in the RT group than in the non-RT group (65.4% vs. 36.4%, respectively; P=0.008). On multivariate analysis, RT was associated with improved OS (hazard ratio=0.15; 95% confidence interval [CI], 0.04-0.50; P=0.002) and EFS (hazard ratio=0.29; 95% CI, 0.095-0.86; P=0.026). An Eastern Cooperative Oncology Group performance status >1 and age above 60 years were also found to negatively influence OS and EFS.

Conclusions:
RT was associated with improved OS and EFS in stage I to II DLBCL of the WR. Future prospective studies are required to confirm these findings.