bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recent nonhybrid origin of sunflower ecotypes in a novel habitat
Authors: Andrew Rose L. , Kane Nolan C. , Baute Greg J. , Grassa Christopher J. , Rieseberg Loren H. 
Published: October 2012

AbstractThe genomics of local adaptation is an increasingly active field, providing insights into the forces driving ecological speciation and the repeatability of evolution. Demography and gene flow play an important role in determining the paths by which parallel evolution occurs and the genomic signatures of adaptation. In the annual sunflowers, hybridization between species has repeatedly led to the colonization of extreme habitats, such as sand dunes. In a new case of adaptation to sand dunes that occurs in populations of H. petiolaris growing at Great Sand Dunes National Park and Preserve (Colorado), we wished to determine the age and long‐term migration patterns of the system, as well as its ancestry. We addressed these questions with restriction‐associated DNA (RAD) sequence data, aligned to a reference transcriptome. In an isolation with migration model using RAD sequences, coalescent analysis showed that the dune ecotype originated since the last ice age, which is very recent compared with the hybrid dune species, H. anomalus. Large effective population sizes and substantial numbers of gene migrants per generation between dune and nondune ecotypes explained the highly heterogeneous divergence observed among loci. Analysis of RAD‐derived SNPs identified heterogeneous divergence between the dune and nondune ecotypes, as well as identifying its nearest relative. Our results did not support the hypothesis that the dune ecotype has hybrid ancestry, suggesting that adaptation of sunflowers to dunes has occurred by multiple mechanisms. The ancestry and long‐term history of gene flow between incipient sunflower species provides valuable context for our understanding of ecological speciation and parallel adaptation.
A role for topoisomeraseIIIinEscherichia colichromosome segregation
Authors: Perez‐Cheeks Brenda A. , Lee Chong , Hayama Ryo , Marians Kenneth J. 
Published: October 2012

SummaryThe cellular function ofEscherichia colitopoisomeraseIIIremains elusive. We show that rescue of temperature‐sensitive mutants inparEandparC(encoding the subunits of the chromosomal decatenase topoisomeraseIV) at restrictive temperatures by high‐copy suppressors is strictly dependent ontopB(encoding topoisomeraseIII). Double mutants ofparEΔtopBandparCΔtopBwere barely viable, grew slowly, and were defective in chromosome segregation at permissive temperatures. ThetopBmutant phenotype did not result from accumulation of toxic recombination intermediates, because it was not relieved by mutations in eitherrecQorrecA. In addition, in an otherwise wild‐type genetic background,ΔtopBcells treated with the typeIItopoisomerase inhibitor novobiocin displayed aberrant chromosome segregation. This novobiocin sensitivity was attributable to an increased demand for topoisomeraseIVand is unlikely to define a new role for topoisomeraseIII; therefore, these results suggest that topoisomeraseIIIparticipates in orderly and efficient chromosome segregation inE. coli.
Sonographic demonstration of human small intestinal migrating motor complex phase III
Authors: Liu C. J. , Huang S. C. , Huang Y. C. , Liu C. Y. , Chen H. I. 
Published: October 2012

AbstractBackground  Migrating motor complex phase III (MMC phase III) of intestine is an important physiological mechanism traditionally recognized by myoelectric recordings or pressure tracings. Direct imaging is difficult and sonographic visualization in human has not been reported.Methods  We have demonstrated this unique phenomenon in three patients who underwent abdominal sonographic examinations. Characteristic images were recorded by videotape and both spatial and temporal features were analyzed.Key Results  Occurrences of multiple equally spaced, rhythmic intestinal contractions were observed. Parameters including wave frequency, propagation velocity, and duration of the events agreed with those of the well‐known phase III. The presence of distinct cyclic patterns observed in two and abolition by meal in the other patient further support our conclusion.Conclusions & Inferences  We conclude that the migrating waves observed in our study represent the human MMC phase III. This unique finding in human subjects merits further investigation.
Eliminating the purple acid phosphatase AtPAP26 in Arabidopsis thaliana delays leaf senescence and impairs phosphorus remobilization
Authors: Robinson Whitney D. , Carson Ira , Ying Sheng , Ellis Kaya , Plaxton William C. 
Published: October 2012

Summary

Limitation of crop productivity by suboptimal phosphorus (P) nutrition is a widespread concern. Enhanced crop P‐use efficiency could be achieved by improving P remobilization from senescing leaves to developing tissues and seeds. Transcriptomic studies indicate that hundreds of Arabidopsis thaliana genes are up‐regulated during leaf senescence, including that encoding the purple acid phosphatase (PAP) AtPAP26 (At5g34850).

In this study, biochemical and functional genomic tools were integrated to test the hypothesis that AtPAP26 participates in P remobilization during leaf senescence.

An eightfold increase in acid phosphatase activity of senescing leaves was correlated with the accumulation of AtPAP26 transcripts and immunoreactive AtPAP26 polypeptides. Senescing leaves of an atpap26 T‐DNA insertion mutant displayed a > 90% decrease in acid phosphatase activity, markedly impaired P remobilization efficiency and delayed senescence. This was paralleled by reduced seed total P concentrations and germination rates.

These results demonstrate that AtPAP26 loss of function causes dramatic effects that cannot be compensated for by any other PAP isozyme, even though Arabidopsis contains 29 different PAP genes. Our current and earlier studies establish that AtPAP26 not only helps to scavenge P from organic P sources when Arabidopsis is cultivated in inorganic orthophosphate (Pi)‐deficient soils, but also has an important P remobilization function during leaf senescence.
Pretransplant six‐minute walk test predicts peri‐ and post‐operative outcomes after pediatric lung transplantation
Authors: Yimlamai Dean , Freiberger Dawn A. , Gould Anne , Zhou Jing , Boyer Debra 
Published: October 2012

AbstractThe purpose of the pretransplant assessment in lung transplantation is to determine a patient's need for transplant as well as their potential survival post‐procedure. In 2005, the UNOS introduced the LAS, a calculation based on multiple physiologic measures to determine need and likelihood for survival. Measures include NYHA class and the 6‐MWT. Some adult studies indicate a positive correlation with 6‐MWT and waiting list survival. In pediatric/adolescent patients, there are minimal data regarding the predictive value of physiologic markers in either wait list survival or post‐transplant outcome. A retrospective cohort study of 60 consecutive lung transplantations from 1990 to 2008 was performed at a pediatric tertiary care facility. Functional pretransplant assessments were abstracted from the medical record and compared with outcomes after transplantation. Results: a 6‐MWT of >1000 ft (305 m) prior to transplantation correlated with a shorter ICU stay (7 vs. 11 days, p = 0.046) and fewer days of mechanical ventilation (2 vs. 4, p = 0.04). A pretransplant 6‐MWT greater than 750 ft (229 m) correlated with shorter overall hospitalization (37 vs. 20 days, p = 0.03). Measuring pretransplant 6‐MWT tests for pediatric patients is valuable in predicting peri‐operative outcomes after lung transplantation.
Quantitative Evaluation of Reference Genes for Real‐Time PCR During In Vitro Maturation of Ovine Oocytes
Authors: O'Connor T , Wilmut I , Taylor J 
Published: October 2012

ContentsQuantitative reverse transcription PCR (RT‐qPCR) is a powerful molecular technique that enables gene expression studies to be performed on extremely small samples such as oocytes and pre‐implantation embryos. However, the high sensitivity of this technique requires that to prevent bias in expression data interpretation, the reference genes used for normalization are fully validated before use. Difficulties in choosing a reference gene are further compounded by the variable RNA content of the maturing oocyte. In the present study, we evaluated eight commonly used reference genes such as ACTB, GAPDH, H2AFZ, HPRT1, PPIA, SDHA, TUBB and YWHAZ and for sheep oocyte RT‐qPCR before and after in vitro maturation. We have also compared different cDNA priming strategies using random hexamers or oligo‐dT. GeNorm analysis of the results identified the most reliable genes for normalization to be SDHA, TUBB and PPIA when oocyte cDNA was made with random hexamers, and YWHAZ, TUBB and SDHA when oligo‐dT primers were used (H2AFZ and HPRT1 were excluded from the geNorm analysis). Interestingly, the analysis revealed that the least stable genes were ACTB and GAPDH, which are the conventional ‘housekeeping’ genes used in many studies. We recommend the use of three reference genes to calculate a normalization factor to accurately quantify transcript abundance in sheep oocytes and these vary with the cDNA priming strategy employed.
From Basic Biology to Randomized Clinical Trial: The Beta Radiation for ArterioVenous Graft Outflow Stenosis (BRAVO II)
Authors: Roy‐Chaudhury Prabir , Arnold Perry , Seigel Jeff , Misra Sanjay 
Published: October 2012

AbstractThe BRAVO‐II study was a randomized controlled study of endovascular radiation therapy as compared to sham radiation therapy, following angioplasty of a thrombosed PRFE graft. The results did not show a benefit of endovascular radiation therapy, albeit in the context of an early termination of the study at less than 50% enrollment due to business reasons. Emphasis is laid on the fact that there may still be a role for radiation therapy in specific clinical settings associated with dialysis vascular access dysfunction.
Diagnosis and Treatment of Peripheral Arterial Disease in CKD Patients
Authors: Yevzlin Alexander S. , Gimelli Giorgio 
Published: October 2012

AbstractPeripheral arterial disease (PAD) is a cardiovascular disease risk equivalent and is a common problem in chronic kidney disease patients. Unlike in the general population, PAD in CKD occurs due to medial calcification as opposed to intimal atherosclerotic process. PAD intervention should be performed in select symptomatic patients, as described by the guidelines, and CVD risk factor modification should occur in all CKD patient, regardless of the presence of PAD. As a discipline, Interventional Nephrology has emerged out of a desire to create better outcomes for our patients and to “fix a problem.” The core values of our discipline have evolved out of this fundamental desire to meet an unmet clinical need, to provide insight into a disease state specific to our patients, and to offer clinical/academic excellence in doing so. We must endeavor to follow a similar path in our approach to PAD. The purpose of this review is to educate interventional nephrologists in the diagnosis and treatment of PAD in their CKD patients.
Cholinergic control of the cerebral vasculature in humans
Authors: Hamner J. W. , Tan Can Ozan , Tzeng Yu‐Chieh , Taylor J. Andrew 
Published: October 2012

Key pointsCerebral autoregulation maintains cerebral perfusion relatively constant in the face of slow changes in arterial pressure, but is less effective against more rapid changes (i.e. functions as a ‘high‐pass’ filter).While thought to be maintained mainly through myogenic adjustments to changes in transmural pressure, recent work has highlighted a possibility of active autonomic involvement in cerebral autoregulation.In this study we examined the cerebrovascular effects of cholinergic blockade on nine healthy volunteers during the application of oscillatory lower body pressure at six frequencies from 0.03 to 0.08 Hz.Cholinergic blockade impaired autoregulation at frequencies above 0.04 Hz, suggesting a role for active cholinergic vasodilatation in the maintenance of cerebral perfusion.Abstract Despite growing evidence of autonomic nervous system involvement in the regulation of cerebral blood flow, the specific contribution of cholinergic vasodilatation to cerebral autoregulation remains unknown. We examined cerebral and forearm blood flow responses to augmented arterial pressure oscillations with and without cholinergic blockade. Oscillatory lower body negative pressure was applied at six frequencies from 0.03 to 0.08 Hz in nine healthy subjects with and without cholinergic blockade via glycopyrrolate. Cholinergic blockade increased cross‐spectral coherence between arterial pressure and cerebral flow at all frequencies except 0.03 Hz and increased the transfer function gain at frequencies above 0.05 Hz. In contrast, gain between pressure and forearm flow increased only at frequencies below 0.06 Hz. These data demonstrate that the cholinergic system plays an active and unique role in cerebral autoregulation. The frequency region and magnitude of effect is very similar to what has been seen with sympathetic blockade, indicating a possible balance between the two reflexes to most effectively respond to rising and falling pressure. These findings might have implications for the role of dysfunction in autonomic control of the vasculature in cerebrovascular disease states.
Stability of Colistimethate Sodium in Aqueous Solution
Authors: Healan A. M. , Gray W. , Fuchs E. J. , Griffiss J. M. , Salata R. A. , Blumer J. 
Published: October 2012

ABSTRACT
Colistimethate sodium, increasingly used to treat multidrug-resistant Gram-negative infections, spontaneously hydrolyzes to form colistin A (polymyxin E1) and B (polymyxin E2/B) when mixed with water. High levels of these active breakdown products at the time of administration have been associated with nephrotoxicity and even death. In this study, reconstituted colistimethate sodium was shown to be stable (<1.0% colistin A/B formation) for up to 24 h when stored at 21, 0, −20, and −70°C.
In Vitro
Activities of Antibiotics and Antimicrobial Cationic Peptides Alone and in Combination against Methicillin-Resistant Staphylococcus aureus Biofilms
Authors: Mataraci Emel , Dosler Sibel 
Published: October 2012

ABSTRACT

Methicillin-resistant
Staphylococcus aureus
(MRSA) strains are most often found as hospital- and community-acquired infections. The danger of MRSA infections results from not only the emergence of multidrug resistance but also the occurrence of bacteria that form strong biofilms. We investigated the
in vitro
activities of antibiotics (daptomycin, linezolid, teichoplanine, azithromycin, and ciprofloxacin) and antimicrobial cationic peptides {AMPs; indolicidin, CAMA [cecropin (1-7)–melittin A (2-9) amide], and nisin} alone or in combination against MRSA ATCC 43300 biofilms. The MICs and minimum biofilm eradication concentrations (MBECs) were determined by the broth microdilution technique. Antibiotic and AMP combinations were assessed using the checkerboard technique. For MRSA planktonic cells, MICs of antibiotics and AMPs ranged between 0.125 and 512 and 8 and 16 mg/liter, respectively, and the MBEC values were between 512 and 5,120 and 640 mg/liter, respectively. With a fractional inhibitory concentration of ≤0.5 as the borderline, synergistic interactions against MRSA biofilms were frequent with almost all antibiotic-antibiotic and antibiotic-AMP combinations. Against planktonic cells, they generally had an additive effect. No antagonism was observed. All of the antibiotics, AMPs, and their combinations were able to inhibit the attachment of bacteria at 1/10 MIC and biofilm formation at 1× MIC. Biofilm-associated MRSA was not affected by therapeutically achievable concentrations of antimicrobial agents. Use of a combination of antimicrobial agents can provide a synergistic effect, which rapidly enhances antibiofilm activity and may help prevent or delay the emergence of resistance. AMPs seem to be good candidates for further investigations in the treatment of MRSA biofilms, alone or in combination with antibiotics.
Comparative Sequence Analysis of a Multidrug-Resistant Plasmid from Aeromonas hydrophila
Authors: del Castillo Carmelo S. , Hikima Jun-ichi , Jang Ho-Bin , Nho Seong-Won , Jung Tae-Sung , Wongtavatchai Janenuj , Kondo Hidehiro , Hirono Ikuo , Takeyama Haruko , Aoki Takashi 
Published: October 2012

ABSTRACT

Aeromonas hydrophila
is a pathogenic bacterium that has been implicated in fish, animal, and human disease. Recently, a multidrug resistance (MDR) plasmid, pR148, was isolated from
A. hydrophila
obtained from a tilapia (
Oreochromis niloticus
) farm in Thailand. pR148 is a 165,906-bp circular plasmid containing 147 coding regions showing highest similarity to pNDM-1_Dok1, an MDR plasmid isolated from a human pathogen. pR148 was also very similar to other IncA/C plasmids isolated from humans, animals, food, and fish. pR148 contains a mercuric resistance operon and encodes the complete set of genes for the type 4 secretion system. pR148 encodes a Tn
21
type transposon. This transposon contains the drug resistance genes
qacH
,
bla
OXA-10
,
aadA1
, and
sul1
in a class 1 integron;
tetA
and
tetR
in transposon Tn
1721
; and
catA2
and a duplicate
sul1
in a locus showing 100% similarity to IncU plasmids isolated from fish. The
bla
OXA-10
and
aadA1
genes showed 100% similarity to those from the
Acinetobacter baumannii
AYE genome. The similarity of pR148 to a human pathogen-derived plasmid indicates that the plasmids were either transferred between different genera or that they are derived from a common origin. Previous studies have shown that IncA/C plasmids retain a conserved backbone, while the accessory region points to lateral gene transfer. These observations point out the dangers of indiscriminate use of antibiotics in humans and in animals and the necessity of understanding how drug resistance determinants are disseminated and transferred.
Chelator-Based Catheter Lock Solutions in Eradicating Organisms in Biofilm
Authors: Raad I. , Rosenblatt J. , Reitzel R. , Jiang Y. , Dvorak T. , Hachem R. 
Published: October 2012

ABSTRACT
Two different chelator-based antimicrobial catheter lock solutions, methylene blue-citrate-parabens (MB-CIT) and minocycline-EDTA-25% ethanol (M-EDTA-25% ETOH), were compared in 2-h biofilm eradication experiments. Eradication of both mature and immature Gram-positive, Gram-negative, and fungal biofilms was assessed. M-EDTA-25% ETOH was able to fully eradicate all biofilms within 2 h. MB-CIT was only effective against immature biofilms but was unable to fully eradicate most of the mature biofilms tested.
Real-Time Sequencing To Decipher the Molecular Mechanism of Resistance of a Clinical Pan-Drug-Resistant Acinetobacter baumannii Isolate from Marseille, France
Authors: Rolain Jean-Marc , Diene Seydina M. , Kempf Marie , Gimenez Gregory , Robert Catherine , Raoult Didier 
Published: October 2012

ABSTRACT

We compare the whole-genome sequences of two multidrug-resistant clinical
Acinetobacter baumannii
isolates recovered in the same patient before (ABIsac_ColiS susceptible to colistin and rifampin only) and after (ABIsac_ColiR resistant to colistin and rifampin) treatment with colistin and rifampin. We decipher all the molecular mechanisms of antibiotic resistance, and we found mutations in the
rpoB
gene and in the PmrAB two-component system explaining resistance to rifampin and colistin in ABIsac_ColiR, respectively.
A Mutation of the RNA Polymerase β′ Subunit (
rpoC
) Confers Cephalosporin Resistance in Bacillus subtilis
Authors: Lee Yong Heon , Nam Ki Hyun , Helmann John D. 
Published: October 2012

ABSTRACT

In bacteria, mutations affecting the major catalytic subunits of RNA polymerase (encoded by
rpoB
and
rpoC
) emerge in response to a variety of selective pressures. Here we isolated a
Bacillus subtilis
strain with high-level resistance to cefuroxime (CEF). Whole-genome resequencing revealed only one missense mutation affecting an invariant residue in close proximity to the C-terminal DNA-binding domain of RpoC (G1122D). Genetic reconstruction experiments demonstrate that this substitution is sufficient to confer CEF resistance. The G1122D mutation leads to elevated expression of stress-responsive regulons, including those of extracytoplasmic function (ECF) σ factors (σ
M
, σ
W
, and σ
X
) and the general stress σ factor (σ
B
). The increased CEF resistance of the
rpoC
G1122D
strain is lost in the
sigM rpoC
G1122D
double mutant, consistent with a major role for σ
M
in CEF resistance. However, a
sigM
mutant is very sensitive to CEF, and this sensitivity is still reduced by the G1122D mutation, suggesting that other regulatory effects are also important. Indeed, the ability of the G1122D mutation to increase CEF resistance is further reduced in a triple mutant strain lacking three ECF σ factors (σ
M
, σ
W
, and σ
X
), which are known from prior studies to control overlapping sets of genes. Collectively, our findings highlight the ability of mutations in RNA polymerase to confer antibiotic resistance by affecting the activity of alternative σ factors that control cell envelope stress-responsive regulons.
Short-Term Monotherapy with IDX184, a Liver-Targeted Nucleotide Polymerase Inhibitor, in Patients with Chronic Hepatitis C Virus Infection
Authors: Lalezari Jacob , Asmuth David , Casiró Arnaldo , Vargas Hugo , Lawrence Shannon , Dubuc-Patrick Gloria , Chen Jie , McCarville Joseph , Pietropaolo Keith , Zhou Xiao-Jian , Sullivan-Bólyai John , Mayers Douglas 
Published: October 2012

ABSTRACT

IDX184 is a liver-targeted prodrug of 2′-methylguanosine (2′-MeG) monophosphate. This study investigated the safety, tolerability, antiviral activity, and pharmacokinetics of IDX184 as a single agent in treatment-naïve patients with genotype-1 chronic hepatitis C virus (HCV) infection. Forty-one patients with baseline HCV RNA ≥ 5 log
10
IU/ml, alanine aminotransferase (ALT) ≤ 2.5× the upper limit of normal, and compensated liver disease were dosed. Sequential cohorts of 10 patients, randomized 8:2 (active:placebo), received 25, 50, 75, and 100 mg of IDX184 once daily for 3 days, with a 14-day follow-up. There were no safety-related treatment discontinuations or serious adverse events. The adverse events and laboratory abnormalities observed for IDX184- and placebo-treated patients were similar. At the end of the 3-day treatment period, changes from baseline in HCV RNA levels (means ± standard deviations) were −0.5 ± 0.6, −0.7 ± 0.2, −0.6 ± 0.3, and −0.7 ± 0.5 log
10
for the 25-, 50-, 75-, and 100-mg doses, respectively, while viral load remained unchanged for the pooled placebo patients (−0.05 ± 0.3 log
10
). Patients with genotype-1a and patients with genotype-1b responded similarly. Serum ALT levels decreased, especially at daily doses ≥ 75 mg. During the posttreatment period, plasma viremia and serum aminotransferase levels returned to near pretreatment levels. No resistance mutations associated with IDX184 were detected. Plasma exposure of IDX184 and its nucleoside metabolite 2′-MeG was dose related and low. Changes in plasma viral load correlated with plasma exposure of 2′-MeG. In conclusion, the results from this proof-of-concept study show that small doses of the liver-targeted prodrug IDX184 were able to deliver significant antiviral activity and support further clinical evaluation of the drug candidate.