bluuebunny/crossref_metadata_2025_split huggingface dataset:
Safety and Efficacy of One‐Week Triple Therapy for Eradicating Helicobacter pylori in Children
Authors: Kato Seiichi , Ritsuno Hideyo , Ohnuma Kenji , Iinuma Kazuie , Sugiyama Toshiro , Asaka Masahiro 
Published: November 2010

Background.Proton pump inhibitor‐based eradication therapy of Helicobacter pylori has been widely studied in adults, but there have been only a few reports about this therapy in children. The purpose of this study was to investigate the safety and efficacy of 1‐week triple therapy for eradication of H. pylori and ulcer healing in children.Patients and Methods.We prospectively studied 15 patients aged 2–17 years (5 with gastric ulcers, 8 with duodenal ulcers, and 2 with nodular gastritis alone). Three patients had H2 blocker‐resistant duodenal ulcers. Patients received 0.75 mg/kg of lansoprazole b.i.d., 25 mg/kg of amoxicillin b.i.d., and 10 mg/kg of clarithromycin b.i.d. for 7 days. No additional therapy (including antisecretory drugs) was administered to any patients following eradication therapy. Patients underwent endoscopy to obtain antral biopsies (culture, urease test and histology) and to evaluate the mucosal status, and underwent a 13C‐urea breath test before and 4–8 weeks after the completion of a 1‐week course of therapy.Results.All patients received the full drug regimen. Endoscopy showed complete healing of ulcers in 12 of 13 patients with peptic ulcer disease (92%). H. pylori was eradicated in 13 of 15 patients (87%). Diarrhea and/or an altered taste sensation occurred in 5 patients (33%). There were no hematological or biochemical abnormalities related to therapy.Conclusion.The 1‐week triple therapy was safe and effective for eradicating H. pylori. The present study showed that ulcer healing in juveniles is closely associated with eradication of H. pylori, and that no additional therapy is required when H. pylori is eradicated. A shorter course of eradication therapy than 2 weeks may be suitable for children with H. pylori infection.
Sequence-specific assembly of FtsK hexamers establishes directional translocation on DNA
Authors: Graham James E. , Sherratt David J. , Szczelkun Mark D. 
Published: November 2010

FtsK is a homohexameric, RecA-like dsDNA translocase that plays a key role in bacterial chromosome segregation. The FtsK regulatory γ-subdomain determines directionality of translocation through its interaction with specific 8 base pair chromosomal sequences [(KOPS); FtsK Orienting / Polarizing Sequence(s)] that are cooriented with the direction of replication in the chromosome. We use millisecond-resolution ensemble translocation and ATPase assays to analyze the assembly, initiation, and translocation of FtsK. We show that KOPS are used to initiate new translocation events rather than reorient existing ones. By determining kinetic parameters, we show sigmoidal dependences of translocation and ATPase rates on ATP concentration that indicate sequential cooperative coupling of ATP hydrolysis to DNA motion. We also estimate the ATP coupling efficiency of translocation to be 1.63–2.11 bp of dsDNA translocated/ATP hydrolyzed. The data were used to derive a model for the assembly, initiation, and translocation of FtsK hexamers.
pH-(low)-insertion-peptide (pHLIP) translocation of membrane impermeable phalloidin toxin inhibits cancer cell proliferation
Authors: An Ming , Wijesinghe Dayanjali , Andreev Oleg A. , Reshetnyak Yana K. , Engelman Donald M. 
Published: November 2010

We find that pH-(low)-insertion-peptide (pHLIP)-facilitated translocation of phalloidin, a cell-impermeable polar toxin, inhibits the proliferation of cancer cells in a pH-dependent fashion. The monomeric pHLIP inserts its C terminus across a membrane under slightly acidic conditions (pH 6–6.5), forming a transmembrane helix. The delivery construct carries phalloidin linked to its inserting C terminus via a disulfide bond that is cleaved inside cells, releasing the toxin. To facilitate delivery of the polar agent, a lipophilic rhodamine moiety is also attached to the inserting end of pHLIP. After a 3 h incubation at pH 6.1–6.2 with 2–4
μ
M concentrations of the construct, proliferation in cultures of HeLa, JC, and M4A4 cancer cells is severely disrupted (> 90% inhibition of cell growth). Treated cells also show signs of cytoskeletal immobilization and multinucleation, consistent with the expected binding of phalloidin to F actin, stabilizing the filaments against depolymerization. The antiproliferative effect was not observed without the hydrophobic facilitator (rhodamine). The biologically active delivery construct inserts into 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine lipid bilayers with an apparent pK
a
of ∼6.15, similar to that of the parent pHLIP peptide. Sedimentation velocity experiments show that the delivery construct is predominantly monomeric (> 90%) in solution under the conditions employed to treat cells (pH 6.2, 4 μM). These results provide a lead for antitumor agents that would selectively destroy cells in acidic tumors. Such a targeted approach may reduce both the doses needed for cancer chemotherapy and the side effects in tissues with a normal pH.
Characterizing the regularity of tetrahedral packing motifs in protein tertiary structure
Authors: Day Ryan , Lennox Kristin P. , Dahl David B. , Vannucci Marina , Tsai Jerry W. 
Published: November 2010

Abstract
Motivation: While protein secondary structure is well understood, representing the repetitive nature of tertiary packing in proteins remains difficult. We have developed a construct called the relative packing group (RPG) that applies the clique concept from graph theory as a natural basis for defining the packing motifs in proteins. An RPG is defined as a clique of residues, where every member contacts all others as determined by the Delaunay tessellation. Geometrically similar RPGs define a regular element of tertiary structure or tertiary motif (TerMo). This intuitive construct provides a simple approach to characterize general repetitive elements of tertiary structure.
Results: A dataset of over 4 million tetrahedral RPGs was clustered using different criteria to characterize the various aspects of regular tertiary structure in TerMos. Grouping this data within the SCOP classification levels of Family, Superfamily, Fold, Class and PDB showed that similar packing is shared across different folds. Classification of RPGs based on residue sequence locality reveals topological preferences according to protein sizes and secondary structure. We find that larger proteins favor RPGs with three local residues packed against a non-local residue. Classifying by secondary structure, helices prefer mostly local residues, sheets favor at least two local residues, while turns and coil populate with more local residues. To depict these TerMos, we have developed 2 complementary and intuitive representations: (i) Dirichlet process mixture density estimation of the torsion angle distributions and (ii) kernel density estimation of the Cartesian coordinate distribution. The TerMo library and representations software are available upon request.
Contact: jtsai@pacific.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
The heterozygous abp1/ABP1 insertional mutant has defects in functions requiring polar auxin transport and in regulation of early auxin‐regulated genes
Authors: Effendi Yunus , Rietz Steffen , Fischer Urs , Scherer Günther F. E. 
Published: November 2010

SummaryAUXIN‐BINDING PROTEIN 1 (ABP1) is not easily accessible for molecular studies because the homozygous T‐DNA insertion mutant is embryo‐lethal. We found that the heterozygous abp1/ABP1 insertion mutant has defects in auxin physiology‐related responses: higher root slanting angles, longer hypocotyls, agravitropic roots and hypocotyls, aphototropic hypocotyls, and decreased apical dominance. Heterozygous plants flowered earlier than wild‐type plants under short‐day conditions. The length of the main root, the lateral root density and the hypocotyl length were little altered in the mutant in response to auxin. Compared to wild‐type plants, transcription of early auxin‐regulated genes (IAA2, IAA11, IAA13, IAA14, IAA19, IAA20, SAUR9, SAUR15, SAUR23, GH3.5 and ABP1) was less strongly up‐regulated in the mutant by 0.1, 1 and 10 μm IAA. Surprisingly, ABP1 was itself an early auxin‐up‐regulated gene. IAA uptake into the mutant seedlings during auxin treatments was indistinguishable from wild‐type. Basipetal auxin transport in young roots was slower in the mutant, indicating a PIN2/EIR1 defect, while acropetal transport was indistinguishable from wild‐type. In the eir1 background, three of the early auxin‐regulated genes tested (IAA2, IAA13 and ABP1) were more strongly induced by 1 μm IAA in comparison to wild‐type, but eight of them were less up‐regulated in comparison to wild‐type. Similar but not identical disturbances in regulation of early auxin‐regulated genes indicate tight functional linkage of ABP1 and auxin transport regulation. We hypothesize that ABP1 is involved in the regulation of polar auxin transport, and thus affects local auxin concentration and early auxin gene regulation. In turn, ABP1 itself is under the transcriptional control of auxin.
Differential response to salinity and water deficit stress in Polypogon monspeliensis (L.) Desf. provenances during germination
Authors: Atia A. , Smaoui A. , Barhoumi Z. , Abdelly C. , Debez A. 
Published: November 2010

AbstractThe effects of provenance, salinity (0, 100, 200, 300 and 400 mm NaCl) and water deficit (0, −0.6, −1.1, −1.6 and −2.1 MPa mannitol solutions) on germination success of Polypogon monspeliensis were investigated. Eight Tunisian provenances from different bioclimatic origins were considered. Seed mass varied significantly between populations. Germination percentage was significantly affected by provenance, salinity and their interaction. Even at 300 mm NaCl, germination percentage of Tabarka, Kelbia and Kebili ranged from ca. 60% to ca. 85%, whereas Monastir, Gabes and El Haouaria succeeded in germinating in 200 mm NaCl. The 300 mm NaCl treatment highly reduced germination of Monastir and El Haouaria, and inhibited that of Gabes. Soliman and El Jem were the least salt‐tolerant provenances. The severity of water deficit impact on seed germination was also provenance‐dependent, especially at osmotic potentials of −1.1 to −1.6 MPa. At −1.6 MPa, germination percentage of Tabarka, Monastir and Kebili was close to 80%, while that of Gabes, El Jem and Kelbia was 0%, 5% and 20%, respectively. Regardless of provenance, germination was strongly impaired at −2.1 MPa. The variability of stress tolerance in P. monspeliensis could be of practical significance in programmes aimed at restoring arid and salt‐affected lands since it allows use of provenances that germinate and establish successfully under unfavourable conditions prevailing in such zones.
The language of nitric oxide signalling
Authors: Baudouin E. 
Published: November 2010

AbstractNitric oxide (NO) has recently joined the select circle of the ubiquitous molecules of plant signalling networks. Indeed, the last decade has produced a tremendous amount of data that evidence the diversity of physiological situations in which NO is involved in plants and the complexity of NO biology. These data also underline our difficulties in providing simple answers to the cardinal questions of where NO comes from and how the NO message is converted into a physiological response. The identification of NO primary targets and NO‐regulated genes provides new opportunities to connect NO biochemistry and NO biology. This review summarises our current understanding of NO signalling, from the generation of the NO message to its execution into a cellular response. The review particularly considers whether and how NO may be responsible for specific signalling in different physiological processes.
Expression analyses of AtAGP17 and AtAGP19, two lysine‐rich arabinogalactan proteins, in Arabidopsis
Authors: Yang J. , Zhang Y. , Liang Y. , Showalter A. M. 
Published: November 2010

AbstractAtAGP17 and AtAGP19 are members of the lysine‐rich arabinogalactan protein (AGP) subfamily in Arabidopsis. Detailed anatomical analysis of promoter activity of the AtAGP19 gene was carried out using transgenic Arabidopsis plants expressing a PAtAGP19:GUS fusion. AtAGP19 promoter activity was tissue‐specific and associated with vascular bundles, particularly differentiating xylem elements. Peptide‐specific antibodies were raised against the Lys‐rich regions of AtAGP17 and AtAGP19 and used to study the organ‐specific expression patterns of these two AGPs. AtAGP17 and AtAGP19 were most abundant in roots and flowers, moderately abundant in stems, seedlings and siliques and virtually absent in leaves. Antibodies specific for AtAGP17 and AtAGP19, as reported here, represent valuable tools for understanding the biology of these two AGPs.
The Orientational Consequences of Flocking Behaviour in Homing Pigeons, Columba livia
Authors: Perera Theresa Burt de , Guilford Tim 
Published: November 2010

AbstractTwo experiments are described which investigate the orientational consequences of flocking in homing pigeons Columba livia. Previous experiments have shown that homing pigeons placed inside a clear‐sided release box for 5 min before release from a familiar site have enhanced ground homing speed compared with those placed in an opaque‐sided box. It is assumed that previewing the surrounding landscape allows for faster homing since a bird denied this information must accumulate the knowledge on release. In experiment 1, using the same technique developed in these experiments but releasing the birds in pairs we showed that within familiar areas, homing pigeons can exploit a partner that has acquired more information, allowing them to home more quickly. In experiment 2 we attempted to test three potential strategies which may occur during homing flights. The results do not conclusively distinguish between these three mechanisms but suggest that orientation of the pairs of birds is most likely to have resulted from a compromise of individual tendencies, or from following the best homer, but not from following a ‘governing leader’. The consequence of these mechanisms is discussed.
Talorchestia tricornuta Shoemaker (Amphipoda, Talitridae) from Sandy Shores of Gabon: Compass Mechanisms of Orientation
Authors: Ugolini Alberto , Vignali Barbara , Posso Paul 
Published: November 2010

AbstractWe studied the capacity for zonal recovery in an equatorial sandhopper, Talorchestia tricornuta, inhabiting the sandy beaches of equatorial West Africa. These beaches are often narrow and backed by an evident landscape. The sky usually has heavy cloud cover. The experiments were performed both in a confined environment and in the field, in full sun or an overcast sky, with the magnetic field natural, deviated or absent T. tricornuta was able to assume the correct direction using the sun and magnetic field as orienting factors. Moreover, the releases in the field with the natural landscape visible indicate that the landscape may constitute a further important orienting factor in zonal recovery.
Correlation between Serum and Plasma Antibody Titers to Mycobacterial Antigens
Authors: Siev Michael , Yu Xian , Prados-Rosales Rafael , Martiniuk Frank T. , Casadevall Arturo , Achkar Jacqueline M. 
Published: November 2010

ABSTRACT

The ability to utilize serum or plasma samples interchangeably is useful for tuberculosis (TB) serology. We demonstrate a strong correlation between antibody titers to several mycobacterial antigens in serum versus plasma from HIV-infected and non-HIV-infected TB and non-TB patients (
r
= 0.99 to 0.89;
P
< 0.0001). Plasma and serum can be used interchangeably in the same antibody detection assays.
Evaluation of Cobas TaqMan MTB PCR for Detection of
Mycobacterium tuberculosis
Authors: Kim Jeong Hyun , Kim Young Jae , Ki Chang-Seok , Kim Ji-Youn , Lee Nam Yong 
Published: November 2010

ABSTRACT

Nucleic acid-based amplification tests allow the rapid detection of
Mycobacterium tuberculosis
. Recently, a real-time PCR assay for
M. tuberculosis
complex, the Cobas TaqMan MTB test (Roche Diagnostics, Basel, Switzerland), was introduced. We performed a prospective study to evaluate the diagnostic performance of the Cobas TaqMan MTB test system. A total of 406 specimens collected from 247 patients were simultaneously tested by conventional culture, Cobas Amplicor MTB PCR, and TaqMan MTB PCR. The cross-reactivity with other
Mycobacterium
species and the detection limit were also evaluated. Among 406 specimens, a total of 24 specimens (5.9%) were culture positive: 14 specimens were positive by both TaqMan and Amplicor MTB PCRs, while 5 specimens were positive by only TaqMan PCR. The remaining five specimens were negative by both PCR methods. Seven specimens with negative culture results were positive by TaqMan PCR, but five of these were negative by Amplicor MTB PCR. The sensitivity, specificity, and positive (PPV) and negative (NPV) predictive values were 79.1%, 98.2%, 73.1%, and 98.7% for TaqMan and 58.3%, 99.5%, 87.5%, and 97.4% for the Amplicor MTB PCR test, respectively. There was no cross-reactivity with
M. tuberculosis
and nontuberculous mycobacterial species. The detection limit for the Cobas TaqMan MTB PCR test was 4.0 copies/μl. The Cobas TaqMan MTB PCR test showed higher sensitivity for detection of the
M. tuberculosis
complex without disturbing the specificity and NPV than the Amplicor MTB PCR test.
Hepatitis B Virus (HBV) Infection and Recombination between HBV Genotypes D and E in Asymptomatic Blood Donors from Khartoum, Sudan
Authors: Mahgoub Shaza , Candotti Daniel , El Ekiaby Magdy , Allain Jean-Pierre 
Published: November 2010

ABSTRACT

Sudan is a highly endemic area for hepatitis B virus (HBV), and >5% of blood donors are chronically infected. To examine potential strategies to improve HBV blood safety, 404 replacement donor samples previously screened for HBV surface antigen (HBsAg) were tested for antibody to HBV core (anti-HBc), anti-surface antigen (anti-HBs), and HBV DNA. Of 145 anti-HBc-containing samples (36%) identified, 16 retested were HBsAg positive (11%). Anti-HBs was detected in 43/77 (56%) anti-HBc-reactive samples. Six samples were HBsAg
−
/anti-HBc
+
/anti-HBs
+
and contained HBV DNA, meeting the definition of occult HBV infection (OBI). OBIs had low HBV DNA loads (<10 IU/ml) and were genotype B (
n
= 1) or genotype D (
n
= 5). Pre-S/S and/or whole genome sequences were obtained from 47 randomly selected HBsAg-positive donors added to the previous 16. Genotype E was identified in 27 strains (57.5%), genotype D in 19 strains (40.5%), and genotype A2 in 1 strain (2%). Two outlier strains within genotype D ultimately were identified as recombinants of genotypes D and E with identical recombination points, suggesting circulating, infectious, recombinant strains. Anti-HBc screening does not appear to be a sustainable blood safety strategy because of the cost and the negative impact on the Sudanese blood supply, even when reduced by anti-HBs testing. Being at the junction between two main African HBV genotypes, genetic recombination occurred and became part of the molecular epidemiology of HBV in Sudan.
Multiple-Genome Comparison Reveals New Loci for
Mycobacterium
Species Identification
Authors: Dai Jianli , Chen Yuansha , Dean Susan , Morris J. Glenn , Salfinger Max , Johnson Judith A. 
Published: November 2010

ABSTRACT

To identify loci useful for species identification and to enhance our understanding of the population structure and genetic variability of the genus
Mycobacterium
, we conducted a multiple-genome comparison of a total of 27 sequenced genomes in the suborder of
Corynebacterineae
(18 from the
Mycobacterium
genus, 7 from the
Corynebacterium
genus, 1 each from the
Nocardia
and
Rhodococcus
genera). Our study revealed 26 informative loci for species identification in
Mycobacterium
. The sequences from these loci were used in a phylogenetic analysis to infer the evolutionary relations of the 18 mycobacterial genomes. Among the loci that we identified,
rpoBC
,
dnaK
, and
hsp65
were amplified from 29 ATCC reference strains and 17 clinical isolates and sequenced. The phylogenetic trees generated from these loci show similar topologies. The newly identified
dnaK
locus is more discriminatory and more robust than the widely used
hsp65
locus. The length-variable
rpoBC
locus is the first intergenic locus between two protein-encoding genes being used for mycobacterial species identification. A multilocus sequence analysis system including the
rpoBC
,
dnaK
, and
hsp65
loci is a robust tool for accurate identification of
Mycobacterium
species.
Isolation of
Robinsoniella peoriensis
from Four Human Specimens
Authors: Gomez Eric , Gustafson Daniel R. , Colgrove Robin , Ly Tam , Santana Rafael , Rosenblatt Jon E. , Patel Robin 
Published: November 2010

ABSTRACT

Robinsoniella peoriensis
is a recently described anaerobic, spore-forming, Gram-positive bacillus originally recovered from swine manure. We report four human cases in which
R. peoriensis
was isolated from clinical samples.
Age-Stratified Bayesian Analysis To Estimate Sensitivity and Specificity of Four Diagnostic Tests for Detection of
Cryptosporidium
Oocysts in Neonatal Calves
Authors: De Waele Valerie , Berzano Marco , Berkvens Dirk , Speybroeck Niko , Lowery Colm , Mulcahy Grace M. , Murphy Thomas M. 
Published: November 2010

ABSTRACT

There is no gold standard diagnostic test for the detection of bovine cryptosporidiosis. Infection is usually highest in 2-week-old calves, and these calves also excrete high numbers of oocysts. These factors may give rise to variations in the sensitivity and specificity of the various diagnostic tests used to detect infection in calves of various ages. An age-stratified Bayesian analysis was carried out to determine the optimum diagnostic test to identify asymptomatic and clinical
Cryptosporidium
sp. infection in neonatal calves. Fecal samples collected from 82 calves at 1 week, 2 weeks, 3 weeks, and 4 weeks of age were subjected to the following tests: microscopic examination of smears stained with either phenol-auramine O or fluorescein isothiocyanate (FITC)-conjugated anti-
Cryptosporidium
monoclonal antibody, nested-PCR, and quantitative real-time PCR. The results confirmed a high prevalence of
Cryptosporidium
sp. infection, as well as a high level of oocyst excretion, in 2-week-old calves. The sensitivities of all the tests varied with the age of the calves. Quantitative real-time PCR proved to be the most sensitive and specific test for detecting infection irrespective of the age of the calf. The microscopic techniques were the least sensitive and exhibited only moderate efficiency with 2-week-old calves excreting large numbers of oocysts, the majority of which were diarrheic. It was concluded that, when interpreting the results of routine tests for bovine cryptosporidiosis, cognizance should be taken of the sensitivity of the tests in relation to the age of the calves and stage of infection.
The Kaposi's Sarcoma-Associated Herpesvirus G Protein-Coupled Receptor Contains an Immunoreceptor Tyrosine-Based Inhibitory Motif That Activates Shp2
Authors: Philpott Nicola , Bakken Thomas , Pennell Christopher , Chen Liwei , Wu Jie , Cannon Mark 
Published: November 2010

ABSTRACTThe Kaposi's sarcoma-associated herpesvirus (KSHV) G protein-coupled receptor (vGPCR) is a constitutively active, highly angiogenic homologue of the interleukin-8 (IL-8) receptors that signals in part via the cytoplasmic protein tyrosine phosphatase Shp2. We show that vGPCR contains a bona fide immunoreceptor tyrosine-based inhibitory motif (ITIM) that binds and constitutively activates Shp2.