bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene Network Analysis and Functional Studies of Senescence‐associated Genes Reveal Novel Regulators of Arabidopsis Leaf SenescenceF
Authors: Li Zhonghai , Peng Jinying , Wen Xing , Guo Hongwei 
Published: June 2012

AbstractPlant leaf senescence has been recognized as the last phase of plant development, a highly ordered process regulated by genes known as senescence associated genes (SAGs). However, the function of most of SAGs in regulating leaf senescence as well as regulators of those functionally known SAGs are still unclear. We have previously developed a curated database of genes potentially associated with leaf senescence, the Leaf Senescence Database (LSD). In this study, we built gene networks to identify common regulators of leaf senescence in Arabidopsis thaliana using promoting or delaying senescence genes in LSD. Our results demonstrated that plant hormones cytokinin, auxin, nitric oxide as well as small molecules, such as Ca2+, delay leaf senescence. By contrast, ethylene, ABA, SA and JA as well as small molecules, such as oxygen, promote leaf senescence, altogether supporting the idea that phytohormones play a critical role in regulating leaf senescence. Functional analysis of candidate SAGs in LSD revealed that a WRKY transcription factor WRKY75 and a Cys2/His2–type transcription factor AZF2 are positive regulators of leaf senescence and loss‐of‐function of WRKY75 or AZF2 delayed leaf senescence. We also found that silencing of a protein phosphatase, AtMKP2, promoted early senescence. Collectively, LSD can serve as a comprehensive resource for systematic study of the molecular mechanism of leaf senescence as well as offer candidate genes for functional analyses.
EVALUATION OF FPA‐FTIR SPECTROSCOPY AS A TOOL IN THE DIFFERENTIATION OFCAMPYLOBACTER JEJUNIFROMCAMPYLOBACTER COLIISOLATED FROM RETAIL CHICKEN SAMPLES
Authors: CARRANZA L.C. , ALVAREZ P.A. , GHETLER A. , IUGOVAZ I. , SEDMAN J. , CARRILLO C.D. , ISMAIL A.A. 
Published: June 2012

ABSTRACTA method for differentiation ofCampylobacter jejuniandCampylobacter colibased on focal‐plane‐array Fourier transform infrared (FPA‐FTIR) spectroscopy was evaluated as an alternative to the current cumbersome methodology. Two types of reference data banks were constructed, one containing FTIR spectra ofC. jejuniandC. colistrains, and the other containing FTIR spectra of 11Campylobacterspecies. The FPA–FTIR method was tested by identifying 40C. jejuniand 16C. coliisolates from poultry, previously identified biochemically and by a multiplex polymerase chain reaction, through comparison of their spectra against the data banks. Employing theC. jejuniandC. colidata bank produced high sensitivity towardC. jejuni(95%) andC. coli(94%) and high overall specificity (95%). With theCampylobacterspp. data bank, the corresponding values were 82, 88 and 84%, respectively. We conclude that FPA‐FTIR spectroscopy is a valuable tool for the differentiation ofC. jejuniandC. coli,particularly whenC. jejuniandC. colidata banks are used.PRACTICAL APPLICATIONSFoodborneCampylobacterinfections are highly prevalent, and therefore proper detection and identification ofCampylobacterstrains are of paramount importance. Accurate and fast methods for the identification ofCampylobacter jejuniandCampylobacter coliare pressing needs. This study presents a rapid, accurate method for differentiation betweenC. jejuniandC. colibased on Fourier transform infrared (FTIR) spectroscopy. By employing FTIR imaging instrumentation equipped with an infrared microscope and a focal‐plane‐array detector, thousands of spectra are recorded from each isolate in the amount of time a traditional FTIR spectrometer records a single spectrum. In turn, rich biochemical characterizations of bacterial strains, often termed “whole‐organism fingerprints,” are rapidly produced. Comparison of the FTIR spectra of unknown microorganisms against spectral databases of reference strains through the use of principal component analysis allows quick and accurate identification ofC. jejuniandC. colistrains, offering an invaluable tool for food safety assurance and surveillance.
Intra‐articular morphine, bupivacaine or no treatment for postoperative analgesia following unilateral elbow joint arthroscopy
Authors: Gurney M. A. , Rysnik M. , Comerford E. J. , Cripps P. J. , Iff I. 
Published: June 2012

ObjectivesTo compare intra‐articular morphine or bupivacaine against no treatment following unilateral elbow joint arthroscopy using force plate analysis and pain scoring.MethodsThirty‐one dogs were randomly allocated to receive 0·1 mg/kg intra‐articular morphine, 0·5 mg/kg bupivacaine or no treatment following elbow arthroscopy. Force plate analysis, pain scoring and kinematic evaluation were performed before anaesthesia, 4 and 24 hours after surgery. Peak vertical force index, symmetry index, rate of loading, rate of unloading, stance time and range of motion were obtained from gait analysis. Pain scoring was performed every 4 hours and interventional analgesia (0·3 mg/kg methadone) was administered if necessary.ResultsOf 29 dogs analysed, peak vertical force index (P<0·001), symmetry index (P=0·01) and rate of unloading (P=0·01) decreased significantly over time in each group; however, this was not affected by treatment. No significant differences were observed in stance time or rate of loading over time. Kinematic (range of motion) evaluation was not complete for all dogs. Pain scores increased significantly at both time points postoperatively in the no treatment group (P=0·007) and in morphine‐treated dogs at 4 hours compared to baseline (P=0·03). For intra‐articular bupivacaine significant increases in pain scores were not detected (P=0·28).Clinical SignificanceNo benefit to intra‐articular bupivacaine or morphine was detected using peak vertical force index from force plate analysis. Bupivacaine prevented increases in pain scores at both time points as did morphine at the 24‐hour evaluation, compared to no treatment.
Influence of exercise intensity on skeletal muscle blood flow, O2 extraction and O2 uptake on‐kinetics
Authors: Jones Andrew M. , Krustrup Peter , Wilkerson Daryl P. , Berger Nicolas J. , Calbet José A. , Bangsbo Jens 
Published: June 2012

Key points
Following the start of low‐intensity exercise in healthy humans, it has been established that the kinetics of muscle O2 delivery is faster than, and does not limit, the kinetics of muscle O2 uptake.
Direct data are lacking, however, on the question of whether O2 delivery might limit O2 uptake kinetics during high‐intensity exercise.
In this study, we made frequent measurements of muscle blood flow, arterial‐to‐venous O2 difference (a–difference) and O2 uptake following the onset of multiple transitions of both low‐intensity and high‐intensity knee‐extension exercise in the same subjects.
We show that although blood flow kinetics is slower for high‐intensity compared with low‐intensity exercise, this does not result in slower O2 uptake kinetics.
These results indicate that muscle O2 delivery does not limit O2 uptake during knee‐extension exercise in healthy humans.
Abstract  Following the start of low‐intensity exercise in healthy humans, it has been established that the kinetics of skeletal muscle O2 delivery is faster than, and does not limit, the kinetics of muscle O2 uptake (). Direct data are lacking, however, on the question of whether O2 delivery might limit kinetics during high‐intensity exercise. Using multiple exercise transitions to enhance confidence in parameter estimation, we therefore investigated the kinetics of, and inter‐relationships between, muscle blood flow (), a– difference and following the onset of low‐intensity (LI) and high‐intensity (HI) exercise. Seven healthy males completed four 6 min bouts of LI and four 6 min bouts of HI single‐legged knee‐extension exercise. Blood was frequently drawn from the femoral artery and vein during exercise and , a– difference and were calculated and subsequently modelled using non‐linear regression techniques. For LI, the fundamental component mean response time (MRTp) for kinetics was significantly shorter than kinetics (mean ± SEM, 18 ± 4 vs. 30 ± 4 s; P < 0.05), whereas for HI, the MRTp for and was not significantly different (27 ± 5 vs. 29 ± 4 s, respectively). There was no difference in the MRTp for either or between the two exercise intensities; however, the MRTp for a– difference was significantly shorter for HI compared with LI (17 ± 3 vs. 28 ± 4 s; P < 0.05). Excess O2, i.e. oxygen not taken up (×), was significantly elevated within the first 5 s of exercise and remained unaltered thereafter, with no differences between LI and HI. These results indicate that bulk O2 delivery does not limit kinetics following the onset of LI or HI knee‐extension exercise.
Analysis of
Helicobacter pylori cagA
Promoter Elements Required for Salt-Induced Upregulation of CagA Expression
Authors: Loh John T. , Friedman David B. , Piazuelo M. Blanca , Bravo Luis E. , Wilson Keith T. , Peek Richard M. , Correa Pelayo , Cover Timothy L. 
Published: June 2012

ABSTRACT

Helicobacter pylori
infection and consumption of a high-salt diet are each associated with an increased risk for the development of gastric cancer. To investigate potential synergism between these factors, we used a global proteomic approach to analyze
H. pylori
strains cultured in media containing varying salt concentrations. Among the differentially expressed proteins identified, CagA exhibited the greatest increase in expression in response to high salt concentrations. Analysis of 36
H. pylori
strains isolated from patients in two regions of Colombia with differing incidences of gastric cancer revealed marked differences among strains in salt-responsive CagA expression. Sequence analysis of the
cagA
promoter region in these strains revealed a DNA motif (TAATGA) that was present in either one or two copies. Salt-induced upregulation of CagA expression was detected more commonly in strains containing two copies of the TAATGA motif than in strains containing one copy. Mutagenesis experiments confirmed that two copies of the TAATGA motif are required for salt-induced upregulation of CagA expression. In summary, there is considerable heterogeneity among
H. pylori
strains in salt-regulated CagA expression, and these differences are attributable to variation in a specific DNA motif upstream of the
cagA
transcriptional start site.
BUILDING SEMANTIC NETWORKS FROM PLAIN TEXT AND WIKIPEDIA WITH APPLICATION TO SEMANTIC RELATEDNESS AND NOUN COMPOUND PARAPHRASING
Authors: WOJTINNEK PIA-RAMONA , PULMAN STEPHEN , VÖLKER JOHANNA 
Published: June 2012

The construction of suitable and scalable representations of semantic knowledge is a core challenge in Semantic Computing. Manually created resources such as WordNet have been shown to be useful for many AI and NLP tasks, but they are inherently restricted in their coverage and scalability. In addition, they have been challenged by simple distributional models on very large corpora, questioning the advantage of structured knowledge representations. We present a framework for building large-scale semantic networks automatically from plain text and Wikipedia articles using only linguistic analysis tools. Our constructed resources cover up to 2 million concepts and were built in less than 6 days. Using the task of measuring semantic relatedness, we show that we achieve results comparable to the best WordNet based methods as well as the best distributional methods while using a corpus of a size several magnitudes smaller. In addition, we show that we can outperform both types of methods by combining the results of our two network variants. Initial experiments on noun compound paraphrasing show similar results, underlining the quality as well as the flexibility of our constructed resources.
The Quest for Self-Identity: Not All Cancer Stem Cells Are the Same
Authors: Hjelmeland Anita B. , Rich Jeremy N. 
Published: June 2012

Abstract
A central critique of the cancer stem cell (CSC) hypothesis involves the robustness of CSC markers. Zorniak and colleagues suggest that different progenitor marker profiles can classify CSCs, and improved modeling of cellular hierarchies can be achieved by incorporating inter- and intratumoral diversity. Clin Cancer Res; 18(13); 3495–8. ©2012 AACR.
Depressive Symptom Clusters and 5-Year Incidence of Coronary Artery Calcification
Authors: Stewart Jesse C. , Zielke Desiree J. , Hawkins Misty A.W. , Williams David R. , Carnethon Mercedes R. , Knox Sarah S. , Matthews Karen A. 
Published: June 2012

Background—
Because depression is a multidimensional construct and few studies have compared the relative importance of its facets in predicting cardiovascular risk, we evaluated the utility of depressive symptom clusters in predicting the 5-year incidence of coronary artery calcification (CAC).

Methods and Results—

Participants were 2171 middle-aged adults (58% female; 43% black) from the Coronary Artery Risk Development in Young Adults (CARDIA) study who were free of cardiovascular disease. Depressive symptom clusters (
z
scores) were measured by questionnaires in 2000 to 2001, and CAC was measured by electron beam computed tomography in 2000 to 2001 and 2005 to 2006. There were 243 cases (11%) of incident CAC, defined as the absence of CAC at baseline and the presence of CAC at follow-up. Total depressive symptoms (odds ratio, 1.16; 95% confidence interval, 1.02–1.33;
P
=0.03) and the depressed affect cluster (odds ratio, 1.17; 95% confidence interval, 1.03–1.33;
P
=0.02) predicted incident CAC; however, the somatic, interpersonal distress, low positive affect, and pessimism clusters did not. The depressed affect–incident CAC relationship was independent of age, sex, race, education, and antidepressant use; was similar across sex and racial groups; and was partially accounted for by tobacco use and mean arterial pressure.

Conclusions—
In contrast to recent results indicating that the somatic cluster is the most predictive of cardiovascular outcomes, we found that the prospective association between depressive symptoms and incident CAC was driven by the depressed affect cluster. Our findings raise the possibility that there may not be 1 facet of depression that is the most cardiotoxic across all contexts.
Mitochondrial modulators for bipolar disorder: A pathophysiologically informed paradigm for new drug development
Authors: Nierenberg Andrew A , Kansky Christine , Brennan Brian P , Shelton Richard C , Perlis Roy , Iosifescu Dan V 
Published: June 2012

Objectives: Bipolar patients frequently relapse within 12 months of their previous mood episode, even in the context of adequate treatment, suggesting that better continuation and maintenance treatments are needed. Based on recent research of the pathophysiology of bipolar disorder, we review the evidence for mitochondrial dysregulation and selected mitochondrial modulators (MM) as potential treatments. Methods: We reviewed the literature about mitochondrial dysfunction and potential MMs worthy of study that could improve the course of bipolar disorder, reduce subsyndromal symptoms, and prevent subsequent mood episodes. Results: MM treatment targets mitochondrial dysfunction, oxidative stress, altered brain energy metabolism and the dysregulation of multiple mitochondrial genes in patients with bipolar disorder. Several tolerable and readily available candidates include N-acetyl-cysteine (NAC), acetyl-L-carnitine (ALCAR), S-adenosylmethionine (SAMe), coenzyme Q10 (CoQ10), alpha-lipoic acid (ALA), creatine monohydrate (CM), and melatonin. The specific metabolic pathways by which these MMs may improve the symptoms of bipolar disorder are discussed and combinations of selected MMs could be of interest as well. Conclusions: Convergent data implicate mitochondrial dysfunction as an important component of the pathophysiology of bipolar disorder. Clinical trials of individual MMs as well as combinations are warranted.
The Economic Cost of Substance Abuse Treatment in the State of Florida
Authors: Alexandre Pierre K. , Beulaygue Isabelle C. , French Michael T. , McCollister Kathryn E. , Popovici Ioana , Sayed Bisma A. 
Published: June 2012

Objective: Public and private stakeholders of substance abuse treatment services require economic cost data to guide program evaluations and funding decisions. Background: Rigorous cost assessments have been conducted for several treatment programs across the United States, but a systematic and comprehensive evaluation of programs in a particular state has never been attempted. Research Design: The present study recruited all publicly funded treatment programs in the State of Florida and administered the Brief Drug Abuse Treatment Cost Analysis Program. Subjects: A total of 175 programs participated in the study, representing a 71% response rate. Measures: Annual, weekly, and episode costs are estimated by modality. Conclusion: The study procedures and empirical findings from this research can be used by program evaluators and government officials in Florida and other states as they develop service reimbursement algorithms and initiate more extensive evaluations of publicly funded substance abuse treatment programs.
Efficacy and tolerability of rizatriptan in pediatric migraineurs: Results from a randomized, double-blind, placebo-controlled trial using a novel adaptive enrichment design
Authors: Ho Tony W , Pearlman Eric , Lewis Donald , Hämäläinen Mirja , Connor Kathryn , Michelson David , Zhang Ying , Assaid Christopher , Mozley Lyn Harper , Strickler Nancy , Bachman Robert , Mahoney Erin , Lines Christopher , Hewitt David J ,   for the Rizatriptan Protocol 082 Pediatric Migraine Study Group
Published: June 2012

Background Treatment options for children and adolescents with migraine are limited. This study evaluated rizatriptan for the acute treatment of migraine in children and adolescents. Methods Randomized, double-blind, placebo-controlled, parallel-group trial in migraineurs 6–17 years old with unsatisfactory response to nonsteroidal anti-inflammatory drugs or acetaminophen/paracetamol. The trial included a double-blind run-in with weight-based rizatriptan dosing (5 mg for <40 kg, 10 mg for ≥40 kg). In the Stage 1 run-in, patients were randomized in a ratio of 20:1 placebo:rizatriptan and were instructed to treat within 30 minutes of a moderate/severe migraine. Patients with mild/no pain after 15 minutes of treatment (responders) took no further study medication, whereas patients with moderate/severe pain (non-responders) proceeded to take study medication in Stage 2. Non-responders who received placebo in Stage 1 were randomized 1:1 to rizatriptan:placebo, whereas non-responders who received rizatriptan in Stage 1 were allocated to placebo in Stage 2. The primary efficacy endpoint was pain freedom at 2 hours after Stage 2 dose in 12–17-year-olds. Results A higher proportion of 12–17-year-olds on rizatriptan had pain freedom at 2 hours compared with those on placebo: 87/284 (30.6%) versus 63/286 (22.0%), odds ratio = 1.55 [95% CI: 1.06 to 2.26], p = 0.025. Adverse events within 14 days of dose in 12–17-year-olds were similar for rizatriptan and placebo. The pattern of findings was similar in 6–17-year-olds. Conclusion Rizatriptan demonstrated a statistically significant improvement over placebo in eliminating pain and was generally well tolerated in migraineurs aged 12–17 and 6–17 years. Trial Registration ClinicalTrials.gov NCT01001234
Migraine and vascular diseases: A review of the evidence and potential implications for management
Authors: Sacco Simona , Ricci Silvia , Carolei Antonio 
Published: June 2012

Introduction The higher-than-expected incidence of vascular diseases reported in migraineurs suggests that migraine may, in some cases, be a dangerous condition rather than just a distressing but harmless disorder. We provide a systematic review of data linking migraine to vascular diseases. Migraine and vascular diseases Available data indicate an increased risk of ischemic stroke in subjects suffering from migraine with aura. In addition, evidence suggests an association between migraine with aura and cardiac disease, intracerebral hemorrhage, retinal vasculopathy and mortality that needs to be further corroborated; consequently, for those conditions, migraine with aura can be only considered among the less-well-documented risk factors. As the absolute risk of ischemic stroke in the overall migraineur population is low, subjects suffering from migraine with aura should be made aware of the possible link but not unduly alarmed. It is a common notion that the vascular risk of migraineurs may be further increased by the presence of easily treatable vascular risk factors such as arterial hypertension, cigarette smoking and oral contraceptive use. Conclusions Forthcoming guidelines should appropriately recommend supporting migraineurs not only with measures aimed at decreasing headache frequency, thus improving quality of life, but also with general measures and preventive strategies aimed to reduce the overall vascular risk. In fact, headache specialists should take care not only of relieving pain but also of assessing and treating concurrent vascular risk factors, while gynecologists, in particular, should routinely consider the presence and type of migraine before prescribing oral contraceptives.
Molecular mechanisms of the glucocorticoid receptor in steroid therapy – lessons from transgenic mice
Authors: Hübner Sabine , Tuckermann Jan 
Published: June 2012

AbstractGlucocorticoids (GCs) are potent anti-inflammatory agents that are used to treat chronic inflammatory diseases, allergic conditions, and some cancers. However, their therapeutic effects are hampered by severe side effects, such as muscle weakness, insulin resistance, fat redistribution, and osteoporosis. GCs act on many cell types that express the GC receptor (GR) via several modes of action. One of them includes GR homodimers recognizing binding sequences in the DNA of gene promoters. Another mode involves the modulation of other DNA-bound transcription factors via dimer-independent mechanisms. To what extent these mechanisms contribute to GC-mediated effects is currently being elucidated from analyses of mice with conditional and function-selective mutations of the GR and is summarized in this review. Whether GR homodimerization or its monomer activity is decisive in the therapeutic effectiveness and associated side effects of GCs for the treatment of inflammatory conditions depends on the type of the pathological condition. Thus, the classic criterion for selective GR modulators, discrimination between GR dimer- and GR monomer-dependent protein-protein interaction, will not help in any condition to avoid side effects and maintain anti-inflammatory activity. Rather, novel criteria for selective GR modulators have to be defined that take into consideration the tissue-specific mechanisms of the GR to achieve optimized anti-inflammatory therapies with reduced side effects. In the case of avoiding osteoporosis as a side effect, a first example of such optimized compounds can be provided.
The intracellular phospholipase A1 protein family
Authors: Tani Katsuko , Kogure Takeshi , Inoue Hiroki 
Published: June 2012

AbstractPhospholipase A1 is an enzyme that hydrolyzes phospholipids, producing 2-acyl-lysophospholipids and fatty acids. The intracellular phospholipase A1 (iPLA1) protein family is a relatively recently discovered lipid-metabolizing enzyme family. Lower eukaryotes, such as yeasts and nematodes, and plants have only one iPLA1 protein, whereas mammals have three iPLA1 family proteins (PA-PLA1/DDHD1/iPLA1α, p125/Sec23IP/iPLA1β and KIAA0725p/DDHD2/iPLA1γ). Mammalian iPLA1 proteins are localized in different cellular compartments, and two of them, p125 and KIAA0725p, have been implicated in membrane trafficking events. Recent gene targeting studies on several organisms showed that iPLA1 family proteins are involved in various physiological functions, including plant shoot gravitropism, epithelial stem cell differentiation and spermiogenesis. In this review, we describe the features of iPLA1 family proteins and recent progress regarding our understanding of their physiological functions.