bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparing sleep measures of infants derived from parental reports in sleep diaries and acceleration sensors
Authors: Asaka Yoko , Takada Satoshi 
Published: February 2011

AbstractAim:  Comparing sleep measures of infants derived from two data collection methods, acceleration sensors and sleep diaries, and identify the clinical application for each data collection method.Methods:  The participants were 52 pairs of infants and mothers. Infant sleep measures were obtained through the actigraphs (Micro‐mini RC, Ambulatory Monitoring Inc., Ardsley, NY, USA) and sleep diaries for over a period of 7 days.Results:  The results showed that the concordance in sleep measures derived from two methods showed decreases in the following order: sleep offset time [r = 0.91 (p = 0.00)], sleep onset time r = 0.89 (p = 0.00), nocturnal sleep duration [r = 0.75 (p = 0.00)], the number of night wakings [r = 0.46 (p < 0.01)] and WASO [r = 0.34 (p < 0.05)]. It was revealed that the accuracy of sleep diary records was affected by the sleeping place and varied throughout the study period.Conclusion:  It was confirmed that the sleep measures indicating sleep schedule reported from the sleep diaries had high concordances compared with the data from the actigraphs. Using the sleep diary was recommended to understand behaviours when focusing on infant’s daily rhythms. In terms of accuracy and stability of recording throughout the study period, understanding sleep quality and independence of sleeping places, the choice of actigraph was recommended.
High prevalence of BCR‐ABL fusion transcripts with poor prognostic impact among adult ALL patients: report from Pakistan
Authors: FAIZ Mariam , IQBAL Qazi Javed , QURESHI Asif 
Published: February 2011

AbstractAim:  Philadelphia (Ph) chromosome positive acute lymphoblastic leukemia (ALL) is a common cytogenetic abnormality associated with poor outcome in adults. This preliminary study, in the absence of substantial evidence, reported the prevalence of the BCR‐ABL gene fusion in ALL patients by RT‐PCR in Pakistan. Moreover, the prognostic significance of BCR‐ABL fusion along with other characteristics was also ascertained.Methods:  One hundred forty six newly diagnosed ALL patients treated at our center between 2005 and 2008 comprised the study group. The patients were treated with a Children and Leukemia Group B induction regimen.Results:  Among these patients, BCR‐ABL fusion oncogene was present in 43 of 78 patients (55%). A statistically significant difference in BCR‐ABL‐positivity within three age groups (<20 years, 20–50 years, >50 years) was observed (P= 0.001). The median age was significantly higher in the BCR‐ABL+ group (30 vs 19 years; P= 0.001). BCR‐ABL+ patients were also characterized by higher median WBC counts (96 000/µL vs 23 000//µL, P= 0.002). Complete remission was achieved in 74% BCR‐ABL− patients and 35% BCR‐ABL+ patients (P= 0.001). Only 10% of BCR‐ABL− patients achieved continued complete remission (CR). None of the BCR‐ABL+ patients maintained a CR further to induction therapy. With the available therapeutic protocol, the presence of a BCR‐ABL fusion predicted a lower survival (P= 0.001).Conclusion:  A high prevalence of BCR‐ABL gene fusion was observed that appeared as a poor prognostic factor. Identification of this genetic entity at diagnosis is crucial for understanding the nature of adult ALL and for deciding optimal treatment.
Calibrating emission lines as quasar bolometers
Authors: Punsly Brian , Zhang Shaohua 
Published: February 2011

Abstract
Historically, emission lines have been considered a valuable tool for estimating the bolometric thermal luminosity of the accretion flow in active galactic nucleus, Lbol. We study the reliability of this method by comparing line strengths to the optical/ultraviolet continuum luminosity of Sloan Digital Sky Survey (SDSS) Data Release 7 (DR7) radio-quiet quasars with 0.4 &lt; z &lt; 0.8. We find formulae for Lbol as a function of single line strengths for the broad components of Hβ and Mg ii, as well as the narrow lines of [O iii] and [O ii]. We determine the standard errors of the formulae that are fitted to the data. Our new estimators are shown to be more accurate than archival line strength estimations in the literature. It is demonstrated that broad lines are superior estimators of the continuum luminosity (and Lbol) with Hβ being the most reliable. The fidelity of each of the estimators is determined in the context of the SDSS DR7 radio-loud quasars as an illustrative application of our results. In general, individual researchers can use our results as a tool to decide if a particular line strength provides an adequate estimate of Lbol for their purposes. Finally, it is shown that considering all four line strengths, simultaneously, can yield information on both Lbol and the radio jet power.
Competition, cooperation, and corporate culture
Authors: Kosfeld Michael , von Siemens Ferdinand A. 
Published: February 2011

Cooperation between workers can be of substantial value to a firm, yet its level often varies substantially between firms. We show that these differences can unfold in a competitive labor market if workers have heterogeneous social preferences and preferences are private information. In our model, workers differ in their willingness to cooperate voluntarily. We show that there always exists a separating equilibrium in which workers self‐select into firms that differ in their monetary incentives as well as their level of worker cooperation. Our model highlights the role of sorting and worker heterogeneity in the emergence of heterogeneous corporate cultures. It also provides a new explanation for the coexistence of nonprofit and for‐profit firms.
“Here you don’t communicate. And sometimes you end up not knowing things. … Everyone says we need effective communication. But it’s a low priority in action. … The hardest thing at the gates when flights are delayed is to get information.”Customer service supervisor, American Airlines
“There is constant communication between service and the ramp. When planes have to be switched and bags must be moved, customer service will advise the ramp directly or through operations. If there’s an aircraft swap operations keeps everyone informed. … It happens smoothly.”Customer service supervisor, Southwest Airlines1
Discovering bipartite substructure in directed networks
Authors: Taylor Alan , Vass J. Keith , Higham Desmond J. 
Published: February 2011

AbstractBipartivity is an important network concept that can be applied to nodes, edges and communities. Here we focus on directed networks and look for subnetworks made up of two distinct groups of nodes, connected by ‘one-way’ links. We show that a spectral approach can be used to find hidden substructures of this form. Theoretical support is given for the idealized case where there is limited overlap between subnetworks. Numerical experiments show that the approach is robust to spurious and missing edges. A key application of this work is in the analysis of high-throughput gene expression data, and we give an example where a biologically meaningful directed bipartite subnetwork is found from a cancer microarray dataset.
Exploring Platelet Chemokine Antimicrobial Activity: Nuclear Magnetic Resonance Backbone Dynamics of NAP-2 and TC-1
Authors: Nguyen Leonard T. , Kwakman Paulus H. S. , Chan David I. , Liu Zhihong , de Boer Leonie , Zaat Sebastian A. J. , Vogel Hans J. 
Published: February 2011

ABSTRACTThe platelet chemokines neutrophil-activating peptide-2 (NAP-2) and thrombocidin-1 (TC-1) differ by only two amino acids at their carboxy-terminal ends. Nevertheless, they display a significant difference in their direct antimicrobial activities, with the longer NAP-2 being inactive and TC-1 being active. In an attempt to rationalize this difference in activity, we studied the structure and the dynamics of both proteins by nuclear magnetic resonance (NMR) spectroscopy. Using15N isotope-labeled protein, we confirmed that the two monomeric proteins essentially have the same overall structure in aqueous solution. However, NMR relaxation measurements provided evidence that the negatively charged carboxy-terminal residues of NAP-2 experience a restricted motion, whereas the carboxy-terminal end of TC-1 moves in an unrestricted manner. The same behavior was also seen in molecular dynamic simulations of both proteins. Detailed analysis of the protein motions through model-free analysis, as well as a determination of their overall correlation times, provided evidence for the existence of a monomer-dimer equilibrium in solution, which seemed to be more prevalent for TC-1. This finding was supported by diffusion NMR experiments. Dimerization generates a larger cationic surface area that would increase the antimicrobial activities of these chemokines. Moreover, these data also show that the negatively charged carboxy-terminal end of NAP-2 (which is absent in TC-1) folds back over part of the positively charged helical region of the protein and, in doing so, interferes with the direct antimicrobial activity.
Rationale-Based,
De Novo
Design of Dehydrophenylalanine-Containing Antibiotic Peptides and Systematic Modification in Sequence for Enhanced Potency
Authors: Pathak Sarika , Chauhan Virander Singh 
Published: February 2011

ABSTRACT

Increased microbial drug resistance has generated a global requirement for new anti-infective agents. As part of an effort to develop new, low-molecular-mass peptide antibiotics, we used a rationale-based minimalist approach to design short, nonhemolytic, potent, and broad-spectrum antibiotic peptides with increased serum stability. These peptides were designed to attain an amphipathic structure in helical conformations. VS1 was used as the lead compound, and its properties were compared with three series of derivates obtained by (i) N-terminal amino acid addition, (ii) systematic Trp substitution, and (iii) peptide dendrimerization. The Trp substitution approach underlined the optimized sequence of VS2 in terms of potency, faster membrane permeation, and cost-effectiveness. VS2 (a variant of VS1 with two Trp substitutions) was found to exhibit good antimicrobial activity against both the Gram-negative
Escherichia coli
and the Gram-positive bacterium
Staphylococcus aureus
. It was also found to have noncytolytic activity and the ability to permeate and depolarize the bacterial membrane. Lysis of the bacterial cell wall and inner membrane by the peptide was confirmed by transmission electron microscopy. A combination of small size, the presence of unnatural amino acids, high antimicrobial activity, insignificant hemolysis, and proteolytic resistance provides fundamental information for the
de novo
design of an antimicrobial peptide useful for the management of infectious disease.
Activity of and Development of Resistance to Corallopyronin A, an Inhibitor of RNA Polymerase
Authors: Mariner Katherine , McPhillie Martin , Trowbridge Rachel , Smith Catriona , O'Neill Alex J. , Fishwick Colin W. G. , Chopra Ian 
Published: February 2011

ABSTRACT

We explored the properties of corallopyronin A (CorA), a poorly characterized inhibitor of bacterial RNA polymerase (RNAP). It displayed a 50% inhibitory concentration of 0.73 μM against RNAP, compared with 11.5 nM for rifampin. The antibacterial activity of CorA was also inferior to rifampin, and resistant mutants of
Staphylococcus aureus
were easily selected. The mutations conferring resistance resided in the
rpoB
and
rpoC
subunits of RNAP. We conclude that CorA is not a promising antibacterial drug candidate.
Cellulose- and Xylan-Degrading Thermophilic Anaerobic Bacteria from Biocompost
Authors: Sizova M. V. , Izquierdo J. A. , Panikov N. S. , Lynd L. R. 
Published: February 2011

ABSTRACT

Nine thermophilic cellulolytic clostridial isolates and four other noncellulolytic bacterial isolates were isolated from self-heated biocompost via preliminary enrichment culture on microcrystalline cellulose. All cellulolytic isolates grew vigorously on cellulose, with the formation of either ethanol and acetate or acetate and formate as principal fermentation products as well as lactate and glycerol as minor products. In addition, two out of nine cellulolytic strains were able to utilize xylan and pretreated wood with roughly the same efficiency as for cellulose. The major products of xylan fermentation were acetate and formate, with minor contributions of lactate and ethanol. Phylogenetic analyses of 16S rRNA and glycosyl hydrolase family 48 (GH48) gene sequences revealed that two xylan-utilizing isolates were related to a
Clostridium clariflavum
strain and represent a distinct novel branch within the GH48 family. Both isolates possessed high cellulase and xylanase activity induced independently by either cellulose or xylan. Enzymatic activity decayed after growth cessation, with more-rapid disappearance of cellulase activity than of xylanase activity. A mixture of xylan and cellulose was utilized simultaneously, with a significant synergistic effect observed as a reduction of lag phase in cellulose degradation.
The Probiotic
Escherichia coli
Nissle 1917 Reduces Pathogen Invasion and Modulates Cytokine Expression in Caco-2 Cells Infected with Crohn's Disease-Associated
E. coli
LF82
Authors: Huebner Claudia , Ding Yaoyao , Petermann Ivonne , Knapp Christoph , Ferguson Lynnette R. 
Published: February 2011

ABSTRACT

Increased numbers of adherent invasive
Escherichia coli
(AIEC) have been found in Crohn's disease (CD) patients. In this report, we investigate the potential of the probiotic
Escherichia coli
Nissle 1917 (EcN) to reduce features associated with AIEC pathogenicity in an already established infection with AIEC reference strain LF82.
Genetic Diversity of O-Antigen Biosynthesis Regions in
Vibrio cholerae
Authors: Aydanian Antonina , Tang Li , Morris J. Glenn , Johnson Judith A. , Stine O. Colin 
Published: February 2011

ABSTRACT

O-antigen biosynthetic (
wbf
) regions for
Vibrio cholerae
serogroups O5, O8, and O108 were isolated and sequenced. Sequences were compared to those of other published
V. cholerae
O-antigen regions. These
wbf
regions showed a high degree of heterogeneity both in gene content and in gene order. Genes identified frequently showed greater similarities to polysaccharide biosynthesis genes from species other than
V. cholerae
. Our results demonstrate the plasticity of O-antigen genes in
V. cholerae
, the diversity of the genetic pool from which they are drawn, and the likelihood that new pandemic serogroups will emerge.
Marker Removal System for
Thermoanaerobacterium saccharolyticum
and Development of a Markerless Ethanologen
Authors: Shaw A. Joe , Covalla Sean F. , Hogsett David A. , Herring Christopher D. 
Published: February 2011

ABSTRACT

Marker removal strategies were developed for
Thermoanaerobacterium saccharolyticum
to select against the
pyrF
gene and the
pta
and
ack
genes. The
pta
- and
ack
-based haloacetate selective strategy was subsequently used to create strain M0355, a markerless Δ
ldh
Δ
pta
Δ
ack
strain that produces ethanol at a high yield.
Temperature Adaptation Markedly Determines Evolution within the GenusSaccharomyces
Authors: Salvadó Z. , Arroyo-López F. N. , Guillamón J. M. , Salazar G. , Querol A. , Barrio E. 
Published: February 2011

ABSTRACTThe present study uses a mathematical-empirical approach to estimate the cardinal growth temperature parameters (Tmin, the temperature below which growth is no longer observed;Topt, the temperature at which the μmaxequals its optimal value; μopt, the optimal value of μmax; andTmax, the temperature above which no growth occurs) of 27 yeast strains belonging to differentSaccharomycesand non-Saccharomycesspecies.S. cerevisiaewas the yeast best adapted to grow at high temperatures within theSaccharomycesgenus, with the highest optimum (32.3°C) and maximum (45.4°C) growth temperatures. On the other hand,S. kudriavzeviiandS. bayanusvar.uvarumshowed the lowest optimum (23.6 and 26.2°C) and maximum (36.8 and 38.4°C) growth temperatures, respectively, confirming that both species are more psychrophilic thanS. cerevisiae. The remainingSaccharomycesspecies (S. paradoxus,S. mikatae,S. arboricolus, andS. cariocanus) showed intermediate responses. With respect to the minimum temperature which supported growth, this parameter ranged from 1.3 (S. cariocanus) to 4.3°C (S. kudriavzevii). We also tested whether these physiological traits were correlated with the phylogeny, which was accomplished by means of a statistical orthogram method. The analysis suggested that the most important shift in the adaptation to grow at higher temperatures occurred in theSaccharomycesgenus after the divergence of theS. arboricolus,S. mikatae,S. cariocanus,S. paradoxus, andS. cerevisiaelineages from theS. kudriavzeviiandS. bayanusvar.uvarumlineages. Finally, our mathematical models suggest that temperature may also play an important role in the imposition ofS. cerevisiaeversus non-Saccharomycesspecies during wine fermentation.
Determination of Adhesin Gene Sequences in, and Biofilm Formation by, O157 and Non-O157 Shiga Toxin-ProducingEscherichia coliStrains Isolated from Different Sources
Authors: Biscola Franciele Tafarello , Abe Cecilia Mari , Guth Beatriz Ernestina Cabilio 
Published: February 2011

ABSTRACTBiofilm formation by Shiga toxin-producingEscherichia coli(STEC) has been associated with the expression of different adhesins (type 1 fimbria, curli, Ag43, Cah, and EhaA). In this study, biofilm formation and the presence of adhesin-related gene sequences were determined by PCR in 18 O157 strains and 33 non-O157 strains isolated from different sources (human, animal, food, and water). The expression of different adhesins was also assessed by reverse transcription-PCR (RT-PCR), Congo red agar plates, and mannose-sensitive hemagglutination (MSHA) assay. Biofilm formation occurred in 5/18 (28%) O157 STEC strains and 17/33 (51%) non-O157 STEC strains from different serotypes and sources, when the assays were performed at 28°C for 48 h. Among the non-O157 biofilm-producing isolates, 12/17 (71%) expressed type 1 fimbriae and 11/17 (65%) expressed curli and produced cellulose, while 8/17 (47%) were considered to be Ag43+by RT-PCR. Among O157 strains, a close correlation was observed between biofilm formation and expression of curli and cellulose. In non-O157 strains, it seems that, in addition to the presence of curli, the ability to form biofilm is associated with the presence of other factors such as type 1 fimbriae and autotransporter proteins, which may contribute to the persistence of these organisms in the environment.
Spatial Genetic Structure of a Vector-Borne Generalist Pathogen
Authors: Coletta-Filho Helvécio D. , Bittleston Leonora S. , Almeida Rodrigo P. P. 
Published: February 2011

ABSTRACTVector-borne generalist pathogens colonize several reservoir species and are usually dependent on polyphagous arthropods for dispersal; however, their spatial genetic structure is generally poorly understood. Using fast-evolving genetic markers (20 simple sequence repeat loci, resulting in a total of 119 alleles), we studied the genetic structure of the vector-borne plant-pathogenic bacteriumXylella fastidiosain Napa Valley, CA, where it causes Pierce's disease when it is transmitted to grapevines from reservoir plants in adjacent riparian vegetation. Eighty-three differentX. fastidiosamultilocus microsatellite genotypes were found in 93 isolates obtained from five vineyards, resulting in an index of clonal fraction closer to 0 and a Simpson's genotypic diversity index (D) closer to a maximum value of 1. Moderate values of Nei's gene diversity (HNei; averageHNei= 0.41) were observed for most of theX. fastidiosapopulations. The low Wright's index of genetic diversity among populations calculated by the FSTAT software (Wright'sFSTindex) among population pairs (0.0096 to 0.1080) indicated a weak or absent genetic structure among the five populations; a panmictic population was inferred by Bayesian analyses (with the STRUCTURE and BAPS programs). Furthermore, a Mantel test showed no significant genetic isolation by distance when both Nei (r= −0.3459,P= 0.268) and linearized θ (r= −0.3106,P= 0.269) indices were used. These results suggest that the riparian vegetation from which vectors acquire the pathogen prior to inoculation of grapevines supports a diverse population ofX. fastidiosa.
Activity and Distribution of Thermophilic Prokaryotes in Hydrothermal Fluid, Sulfidic Structures, and Sheaths of Alvinellids (East Pacific Rise, 13°N)
Authors: Bonch-Osmolovskaya Elizaveta A. , Perevalova Anna A. , Kolganova Tatiana V. , Rusanov Igor I. , Jeanthon Christian , Pimenov Nikolay V. 
Published: February 2011

ABSTRACT

Processes of inorganic carbon assimilation, methanogenesis, sulfate reduction, and acetate oxidation to CO
2
occurring in samples from the East Pacific Rise at 13°N were traced, using radioisotopically labeled substrates, at temperatures ranging from 65 to 100°C. Molecular hydrogen stimulated lithotrophic methanogenesis and sulfate reduction but inhibited inorganic carbon assimilation. Active mineralization of acetate was observed in an organic-rich
Alvinella
-associated system at 80°C. Members of the
Thermococcales
were the most numerous hyperthermophilic archaea in these samples, their density achieving 10
8
cells per cm
3
, while the numbers of cultured hydrogen-utilizing thermophilic lithotrophs were several orders of magnitude lower.
Construction of a Bacterial Assay for Estrogen Detection Based on an Estrogen-Sensitive Intein
Authors: Liang Rubing , Zhou Jing , Liu Jianhua 
Published: February 2011

ABSTRACTEscherichia colistrain DIER was constructed for estrogen detection by inserting an estrogen-sensitive intein (VMAERintein) into the specific site of the constitutively expressed chromosomallacZgene. This VMAERintein was generated by replacing the endonuclease region of theSaccharomyces cerevisiaeVMA intein with the estrogen binding region of the human estrogen receptor α (hERα). When there were estrogens or analogs, the splicing of the VMAERintein was induced to produce the mature LacZ protein, which was detected through a β-galactosidase colorimetric assay. Eight typical chemicals (17-β-estradiol, bisphenol A, chrysene, 6-OH-chrysene, benz[a]anthracene, pyrene, progesterone, and testosterone) were detected using this DIER strain, and the whole detection procedure was accomplished in 2 h. Their 50% effective concentrations (EC50), relative estrogenic activities, and estradiol equivalency factors were calculated and were quite consistent with those detected with the yeast estrogen screening (YES) system. Furthermore, the estrogenic activities of the synthetic musk samples extracted from the wastewater and waste sludge of a sewage treatment plant of Shanghai (China) were detected, and their results were comparable to those obtained from the YES system and gas chromatography-mass spectrometry (GC-MS). In conclusion, the DIER bioassay could fill a niche for the efficient, rapid, high-throughput screening of estrogenic compounds and has potential for the remote, near-real-time monitoring of environmental estrogens.