bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cyclic diguanosine monophosphate represses bacterial flagella synthesis by interacting with the Walker A motif of the enhancer-binding protein FleQ
Authors: Baraquet Claudine , Harwood Caroline S. 
Published: October 2013

SignificanceMany bacteria respond to environmental cues by producing cyclic diguanosine monophosphate (c-di-GMP), which binds to proteins to modulate transitions between sessile and motile lifestyles important for chronic and acute infections, respectively. The breadth of protein targets and mechanisms of action of c-di-GMP remain unknown. In the opportunistic pathogenPseudomonas aeruginosa, c-di-GMP binds to FleQ, a transcription factor that is the master regulator of flagella synthesis and a member of the large family of AAA+ ATPase proteins. We found that c-di-GMP competitively inhibits FleQ ATPase activity and interacts with the ATP-binding site on FleQ. We suggest that AAA+ ATPases from other bacteria may respond to c-di-GMP, and that interference with ATPase activity is one mechanism of c-di-GMP action.
AllergenFP: allergenicity prediction by descriptor fingerprints
Authors: Dimitrov Ivan , Naneva Lyudmila , Doytchinova Irini , Bangov Ivan 
Published: October 2013

AbstractMotivation: Allergenicity, like antigenicity and immunogenicity, is a property encoded linearly and non-linearly, and therefore the alignment-based approaches are not able to identify this property unambiguously. A novel alignment-free descriptor-based fingerprint approach is presented here and applied to identify allergens and non-allergens. The approach was implemented into a four step algorithm. Initially, the protein sequences are described by amino acid principal properties as hydrophobicity, size, relative abundance, helix and β-strand forming propensities. Then, the generated strings of different length are converted into vectors with equal length by auto- and cross-covariance (ACC). The vectors were transformed into binary fingerprints and compared in terms of Tanimoto coefficient.Results: The approach was applied to a set of 2427 known allergens and 2427 non-allergens and identified correctly 88% of them with Matthews correlation coefficient of 0.759. The descriptor fingerprint approach presented here is universal. It could be applied for any classification problem in computational biology. The set of E-descriptors is able to capture the main structural and physicochemical properties of amino acids building the proteins. The ACC transformation overcomes the main problem in the alignment-based comparative studies arising from the different length of the aligned protein sequences. The conversion of protein ACC values into binary descriptor fingerprints allows similarity search and classification.Availability and implementation: The algorithm described in the present study was implemented in a specially designed Web site, named AllergenFP (FP stands for FingerPrint). AllergenFP is written in Python, with GIU in HTML. It is freely accessible at http://ddg-pharmfac.net/Allergen FP.Contact: idoytchinova@pharmfac.net or ivanbangov@shu-bg.net
Activity‐Guided Fractionation to Identify Blue Wheat (UC66049 Triticum aestivum L.) Constituents Capable of Inhibiting In Vitro Starch Digestion
Authors: Tyl Catrin E. , Bunzel Mirko 
Published: October 2013

ABSTRACTThe inhibition or delay of starch digestion by dietary compounds could help manage postprandial blood glucose levels. The objective of this study was to identify constituents from whole grain blue wheat capable of decreasing α‐amylase‐catalyzed starch digestion. An activity‐guided fractionation approach based on liquid chromatography was used to identify solvent‐ and alkaline‐extractable blue wheat constituents reducing α‐amylase‐mediated starch digestion in vitro. Fatty acids, potentially released from cell wall polymers by alkaline hydrolysis, inhibited the digestion of amylose, probably through the formation of amylose‐lipid complexes. However, the degradation of amylopectin was not affected by fatty acids. In addition, 1‐(3,5‐dihydroxyphenyl)heneicosan‐2‐one, a 5‐(2′‐oxoalkyl)resorcinol, was found to reduce starch digestion. However, because the digestion of both amylopectin and amylose was reduced, the inhibition mechanism was different from that of fatty acids. Further research is needed to evaluate whether this component also reduces starch digestion in vivo. Other phenolic compounds of blue wheat such as anthocyanins or hydroxycinnamates were not identified as major starch digestion inhibitors by using the activity‐guided fractionation approach.
Comparative genomics of the marine bacterial genus Glaciecola reveals the high degree of genomic diversity and genomic characteristic for cold adaptation
Authors: Qin Qi‐Long , Xie Bin‐Bin , Yu Yong , Shu Yan‐Li , Rong Jin‐Cheng , Zhang Yan‐Jiao , Zhao Dian‐Li , Chen Xiu‐Lan , Zhang Xi‐Ying , Chen Bo , Zhou Bai‐Cheng , Zhang Yu‐Zhong 
Published: October 2013

SummaryTo what extent the genomes of different species belonging to one genus can be diverse and the relationship between genomic differentiation and environmental factor remain unclear for oceanic bacteria. With many new bacterial genera and species being isolated from marine environments, this question warrants attention. In this study, we sequenced all the type strains of the published species of Glaciecola, a recently defined cold‐adapted genus with species from diverse marine locations, to study the genomic diversity and cold‐adaptation strategy in this genus. The genome size diverged widely from 3.08 to 5.96 Mb, which can be explained by massive gene gain and loss events. Horizontal gene transfer and new gene emergence contributed substantially to the genome size expansion. The genus Glaciecola had an open pan‐genome. Comparative genomic research indicated that species of the genus Glaciecola had high diversity in genome size, gene content and genetic relatedness. This may be prevalent in marine bacterial genera considering the dynamic and complex environments of the ocean. Species of Glaciecola had some common genomic features related to cold adaptation, which enable them to thrive and play a role in biogeochemical cycle in the cold marine environments.
Management of placenta percreta: a review of published cases
Authors: Clausen Caroline , Lönn Lars , Langhoff‐Roos Jens 
Published: October 2013

AbstractPublications on abnormally invasive placenta in general report what can be considered a mixture of the conditions true accreta, increta and percreta varieties. The aim of this review was to identify all published cases of the most severe condition, placenta percreta in order to describe complications associated with the three commonly used surgical strategies: local resection, hysterectomy or leaving the placenta in situ, and to describe the outcome, with respect to blood loss and transfusion requirements, with the different endovascular interventions that may be used as adjuncts in the management of the conditions. A PubMed search was performed in April 2013 and the final review included 119 published placenta percreta cases. Conservative management, where the placenta is left in situ for resorption, seems to be associated with severe long‐term complications of hemorrhage and infections, including a 58% risk that a hysterectomy will eventually be needed up till nine months after the delivery. Local resection seems to be associated with fewer complications within 24 h postoperatively compared with hysterectomy or leaving the placenta in situ. A selection bias in the direction of less severe cases for the local resection technique might in part explain the lower complication rates with that approach. Future prospective data collection activities should include intended as well as actual management, and long‐term follow‐up of all cases is of vital importance.
Temporal Leukocyte Numbers and Granulocyte Activation in Pulsatile and Rotary Ventricular Assist Device Patients
Authors: Woolley Joshua R. , Teuteberg Jeffrey J. , Bermudez Christian A. , Bhama Jay K. , Lockard Kathleen L. , Kormos Robert L. , Wagner William R. 
Published: October 2013

AbstractIndividual ventricular assist device (VAD) design may affect leukocytes and impact immunity. Few studies have presented leukocyte and infection profiles in VAD patients over the course of the implant period. CD11b (MAC‐1) expression on granulocytes is an indicator of activation during inflammation, mediating extravasation and the release of reactive oxygen species in tissue. No reported studies have presented MAC‐1 expression on circulating granulocytes in VAD patients. Fifty‐six patients implanted at a single center with a HeartMate II (HMII; n = 32), HeartWare (HW; n = 12), or Thoratec pneumatic VAD (PVAD; n = 12) between 1999 and 2011 were followed for 120 days of support. The leukocyte profiles and infectious events of all patients were evaluated; additionally, a subset had MAC‐1 expression on circulating granulocytes was measured (HMII n = 9; HW n = 7; PVAD n = 4). All groups exhibited a significant peak in leukocyte numbers at postoperative day (POD) 14 while simultaneously experiencing a significant decrease in hematocrit. HMII patients exhibited a 3.2‐fold increase in granulocyte MAC‐1 expression at POD 14, and the temporal trend over the implant period differed from that experienced by HW patients. Further, HW patients experienced significantly fewer infection events. Alterations in leukocyte profiles and granulocyte activation experienced by VAD patients appear to be device‐specific. Elevations in leukocyte activation may be related to an increased risk for infection, although the specific relationship between these phenomena in this patient group is not known.
Association of pretreatment neutrophil‐to‐lymphocyte ratio (NLR) and overall survival (OS) in patients with metastatic castration‐resistant prostate cancer (mCRPC) treated with first‐line docetaxel
Authors: Nuhn Philipp , Vaghasia Ajay M. , Goyal Jatinder , Zhou Xian C. , Carducci Michael A. , Eisenberger Mario A. , Antonarakis Emmanuel S. 
Published: October 2013

Objective
To determine whether the pretreatment neutrophil‐to‐lymphocyte ratio (NLR), a measure of systemic inflammatory response, is associated with overall survival (OS) in men receiving chemotherapy with docetaxel for metastatic castration‐resistant prostate cancer (mCRPC).
Patients and Methods
Records from 238 consecutive patients who were treated with first‐line docetaxel‐containing chemotherapy for mCRPC at a single high‐volume centre from 1998 to 2010 (and who had adequate information to enable calculation of NLR) were reviewed.
Univariable and multivariable Cox regression models were used to predict OS after chemotherapy initiation.
Results
In univariable analyses, the NLR as a discrete variable (optimal threshold 3.0) was significantly associated with OS (P = 0.001).
In multivariable analyses, a lower NLR (≤3.0) was associated with lower risk of all‐cause mortality (P = 0.002).
In Kaplan–Meier analysis, the median OS was higher (18.3 vs 14.4 months) in patients that did not have an elevated NLR than in those with an elevated NLR (log‐rank; P < 0.001).
Conclusions
Men who were treated with first‐line docetaxel for mCRPC who had a low pretreatment NLR (≤3.0) had significantly longer OS.
NLR may be a potentially useful clinical marker of systemic inflammatory response in predicting OS in men with mCRPC who receive docetaxel and may be helpful to stratify patients for clinical trials.
These findings derived from a retrospective analysis need to be validated in larger populations in prospective studies, and in the context of different therapies.
Nuclear expression of CDK4 correlates with disease progression and poor prognosis in human nasopharyngeal carcinoma
Authors: Jiang Qingping , Mai Chunping , Yang Huiling , Wu Qiangyun , Hua Shengni , Yan Chen , Long Yufei , Zhang Yajie , Long Xiaobin , Fang Weiyi , Liu Zhen 
Published: October 2013

AimsThe purpose of this study was to examine the correlation between nuclear expression of cyclin‐dependent kinase 4 (CDK4) and clinicopathological data in nasopharyngeal carcinoma (NPC), including patient survival.Methods and resultsUsing real‐time PCR and immunohistochemistry, the expression of CDK4 was examined in NPC and nasopharyngeal (NP) tissues. We observed that mRNA expression of CDK4 was elevated significantly in NPC tissues compared to NP tissues. Further, we found that CDK4 protein was expressed in both the nucleus and cytoplasm. Nuclear expression of CDK4 was correlated positively with clinical stage (P = 0.048), but not associated with other clinical features. Patients with tumours showing nuclear expression of CDK4 had poorer overall survival rates than those without nuclear tumour expression of CDK4. Nuclear expression of CDK4 was associated inversely with survival time for NPC patients in stages T1–2, stages N2–3 and clinical stages III–IV, and after treatment with radiotherapy or chemotherapy. Nuclear expression of CDK4 was an independent and unfavourable prognostic factor for patients with NPC.ConclusionsOur findings suggest that nuclear expression of CDK4 is a potential marker for the progression and poor prognosis of NPC.
Alcohol consumption, dating relationships, and preliminary sexual outcomes in collegiate natural drinking groups
Authors: Devos‐Comby Loraine , Daniel Jason , Lange James E. 
Published: October 2013

AbstractThis study tested the effects of committed relationships and presence of dates on alcohol consumption and preliminary sexual outcomes in natural drinking groups (NDGs). Undergraduate drinkers (N = 302) answered an online questionnaire on their most recent participation in a NDG. The interaction between relationship commitment and presence of a date on alcohol consumption was significant. Among students not in committed relationships, those dating within their NDG reported heavier drinking than those not dating. Students in committed relationships drank less than those who were not committed only when their partners were present. The positive correlation between drinking and sexual contact was significant only for those who were not in committed relationships. Implications for future research and interventions are discussed.
Parallel invasions produce heterogenous patterns of life history adaptation: rapid divergence in an invasive insect
Authors: Seiter S. , Ohsaki N. , Kingsolver J. 
Published: October 2013

AbstractBiotic invasions provide a natural experiment in evolution: when invasive species colonize new ranges, they may evolve new clines in traits in response to environmental gradients. Yet it is not clear how rapidly such patterns can evolve and whether they are consistent between regions. We compare four populations of the invasive cabbage white butterfly (Pieris rapae) from North America and Japan, independently colonized by P. rapae 150 years ago and 300 years ago, respectively. On each continent, we employed a northern and southern population to compare the effects of latitude on body mass, development rate and immune function. For each population, we used a split‐sibling family design in which siblings were reared at either warm (26.7 °C) or cool (20 °C) temperatures to determine reaction norms for each trait. Latitudinal patterns in development time were similar between the two continents. In contrast, there were strong geographical differences in reaction norms for body size, but no consistent effects of latitude; there were no detectable effects of latitude or continent on immune function. These results imply that some life history traits respond consistently to selection along climatic gradients, whereas other traits may respond to local environmental factors, or not at all.
Two Hydroxypyruvate Reductases Encoded by OsHPR1 and OsHPR2 are Involved in Photorespiratory Metabolism in Rice
Authors: Ye Nenghui , Yang Guozhen , Chen Yan , Zhang Chan , Zhang Jianhua , Peng Xinxiang 
Published: October 2013

AbstractMutations in the photorespiration pathway display a lethal phenotype in atmospheric air, which can be fully recovered by elevated CO2. An exception is that mutants of peroxisomal hydroxypyruvate reductase (HPR1) do not have this phenotype, indicating the presence of cytosolic bypass in the photorespiration pathway. In this study, we constructed overexpression of the OsHPR1 gene and RNA interference plants of OsHPR1 and OsHPR2 genes in rice (Oryza sativa L. cv. Zhonghua 11). Results from reverse transcription‐polymerase chain reaction (RT‐PCR), Western blot, and enzyme assays showed that HPR1 activity changed significantly in corresponding transgenic lines without any effect on HPR2 activity, which is the same for HPR2. However, metabolite analysis and the serine glyoxylate aminotransferase (SGAT) activity assay showed that the metabolite flux of photorespiration was disturbed in RNAi lines of both HPR genes. Furthermore, HPR1 and HPR2 proteins were located to the peroxisome and cytosol, respectively, by transient expression experiment. Double mutant hpr1 × hpr2 was generated by crossing individual mutant of hpr1 and hpr2. The phenotypes of all transgenic lines were determined in ambient air and CO2‐elevated air. The phenotype typical of photorespiration mutants was observed only where activity of both HPR1 and HPR2 were downregulated in the same line. These findings demonstrate that two hydroxypyruvate reductases encoded by OsHPR1 and OsHPR2 are involved in photorespiratory metabolism in rice.
Roles of the N domain of the AAA+ Lon protease in substrate recognition, allosteric regulation and chaperone activity
Authors: Wohlever Matthew L. , Baker Tania A. , Sauer Robert T. 
Published: October 2013

SummaryDegron binding regulates the activities of the AAA+ Lon protease in addition to targeting proteins for degradation. The sul20 degron from the cell‐division inhibitor SulA is shown here to bind to the N domain of Escherichia coli Lon, and the recognition site is identified by cross‐linking and scanning for mutations that prevent sul20‐peptide binding. These N‐domain mutations limit the rates of proteolysis of model sul20‐tagged substrates and ATP hydrolysis by an allosteric mechanism. Lon inactivation of SulA in vivo requires binding to the N domain and robust ATP hydrolysis but does not require degradation or translocation into the proteolytic chamber. Lon‐mediated relief of proteotoxic stress and protein aggregation in vivo can also occur without degradation but is not dependent on robust ATP hydrolysis. In combination, these results demonstrate that Lon can function as a protease or a chaperone and reveal that some of its ATP‐dependent biological activities do not require translocation.
Nitric oxide: an effective weapon of the plant or the pathogen?
Authors: Arasimowicz‐Jelonek Magdalena , Floryszak‐Wieczorek Jolanta 
Published: October 2013

SummaryAn explosion of research in plant nitric oxide (NO) biology during the last two decades has revealed that NO is a key signal involved in plant development, abiotic stress responses and plant immunity. During the course of evolutionary changes, microorganisms parasitizing plants have developed highly effective offensive strategies, in which NO also seems to be implicated. NO production has been demonstrated in several plant pathogens, including fungi, but the origin of NO seems to be as puzzling as in plants. So far, published studies have been spread over multiple species of pathogenic microorganisms in various developmental stages; however, the data clearly indicate that pathogen‐derived NO is an important regulatory molecule involved not only in developmental processes, but also in pathogen virulence and its survival in the host. This review also focuses on the search for potential mechanisms by which pathogens convert NO messages into a physiological response or detoxify both endo‐ and exogenous NO. Finally, taking into account the data available from model bacteria and yeast, a basic draft for the mode of NO action in phytopathogenic microorganisms is proposed.
An Evaluation of the Determinants and Implications of Panel Attrition in the National Income Dynamics Survey (2008‐2010)
Authors: Baigrie Nic , Eyal Katherine 
Published: October 2013

AbstractPanel surveys offer a valuable tool for researchers to explore the dynamics underlying individual and household behaviours. The Achilles heel of panel data is attrition. This paper examines the determinants and implications of attrition in the first two waves of South Africa's National Income Dynamics Survey. Multivariate tests in labour market and health specifications show that there is some moderate evidence of attrition bias in estimated coefficients based on the non‐attriting sample. This bias can be seen in labour market specifications, in particular for men, and for Africans, and to a much lesser degree in health specifications, in particular for small samples of Whites. Researchers should take care when using the panel data set to generalise to the overall population.
Early‐onset thrombocytopenia in near‐term and term infants with perinatal asphyxia
Authors: Boutaybi N. , Steggerda S. J. , Smits‐Wintjens V. E. H. J. , van Zwet E. W. , Walther F. J. , Lopriore E. 
Published: October 2013

BackgroundNeonates after perinatal asphyxia are at increased risk of thrombocytopenia. The correlation between perinatal asphyxia and the risk and severity of early‐onset thrombocytopenia is not well known.ObjectiveTo estimate the incidence, severity and risk factors for early‐onset thrombocytopenia in neonates after perinatal asphyxia.MethodsWe included all newborns (gestational age ≥ 36 weeks) admitted to our neonatal nursery due to perinatal asphyxia in this retrospective study. We collected platelet counts that were obtained within the first 48 h of life to estimate the incidence and severity of early‐onset thrombocytopenia.ResultsA total number of 171 neonates with perinatal asphyxia were included in the study. The incidence of early‐onset thrombocytopenia (platelet count < 150 × 109/l) was 51% (87/171). Several factors were associated with increased risk of early‐onset thrombocytopenia, including prolonged prothrombin time (PT) [odds ratio (OR) 1·18, 95% confidence interval (CI) 1·08–1·30, P < 0·01], prolonged activated partial thromboplastin time (APTT) (OR 1·07, 95% CI 1·03–1·11, P < 0·01), low Apgar score at 10 min (OR 1·25, 95% CI 1·08–1·45, P < 0·01) and high serum lactate (OR 1·12, 95% CI 1·06–1·19, P < 0·01). After multiple logistic regression analysis, we found an independent association between early‐onset thrombocytopenia and prolonged PT (OR 1·15, 95% CI 1·00–1·33, P = 0·045) and higher lactate level (OR 1·15, 95% CI 1·03–1·28, P = 0·01).ConclusionsEarly‐onset thrombocytopenia occurs frequently in neonates after perinatal asphyxia and is independently associated with PT and lactate level.