bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hypervariations of a Protease-Encoding Gene, PD0218 (
pspB
), in
Xylella fastidiosa
Strains Causing Almond Leaf Scorch and Pierce's Disease in California
Authors: Chen J. , Civerolo E. , Tubajika K. , Livingston S. , Higbee B. 
Published: May 2008

ABSTRACT

Xylella fastidiosa
is a gram-negative plant pathogenic bacterium that causes almond leaf scorch disease (ALSD) and Pierce's disease (PD) of grape in many regions of North America and Mexico. Of the two 16S rRNA gene genotypes described in California, A genotype strains cause ALSD only and G genotype strains cause both PD and ALSD. While G genotype strains cause two different diseases, little is known about their genetic variation. In this study, we identified a putative protease locus, PD0218 (
pspB
), in the genome of
X. fastidiosa
and evaluated the variation at this locus in
X. fastidiosa
populations. PD0218 contains tandem repeats of ACDCCA, translated to threonine and proline (TP), upstream of the putative protease conserved domain. Among 116
X. fastidiosa
ALSD and PD strains isolated from seven locations in California, tandem repeat numbers (TRNs) varied from 9 to 47, with a total of 30 TRN genotypes, indicating that
X. fastidiosa
possesses an active mechanism for contracting and expanding tandem repeats at this locus. Significant TRN variation was found among PD strains (mean = 29.9), which could be further divided into two TRN groups: PD-G
small
(mean = 17.3) and PD-G
large
(mean = 44.3). Less variation was found in ALSD strains (mean = 21.7). The variation was even smaller after ALSD strains were subdivided into the A and G genotypes (mean = 13.3, for the G genotype; mean = 27.1, for the A genotype). Genetic variation at the PD0218 locus is potentially useful for sensitive discrimination of
X. fastidiosa
strains. However, TRN stability, variation range, and correlation to phenotypes should be evaluated in epidemiological applications such as pathotype identification and delineation of pathogen origin.
Effect of Growth Temperature on Crl-Dependent Regulation of σ
S
Activity in
Salmonella enterica
Serovar Typhimurium
Authors: Robbe-Saule Véronique , Carreira Ingrid , Kolb Annie , Norel Françoise 
Published: May 2008

ABSTRACT

The small regulatory protein Crl favors association of the stationary-phase sigma factor σ
S
(RpoS) with the core enzyme polymerase and thereby increases σ
S
activity. Crl has a major physiological impact at low levels of σ
S
. Here, we report that the Crl effects on σ
S
-dependent gene expression, the H
2
O
2
resistance of
Salmonella enterica
serovar Typhimurium, and the resistance of this organism to acidic pH are greater at 28°C than at 37°C. Immunoblot experiments revealed a negative correlation between σ
S
and Crl levels; the production of Crl was slightly greater at 28°C than at 37°C, whereas the σ
S
levels were about twofold lower at 28°C than at 37°C. At both temperatures, Crl was present in excess of σ
S
, and increasing the Crl level further did not increase the H
2
O
2
resistance level of
Salmonella
and the expression of the σ
S
-dependent gene
katE
encoding the stationary-phase catalase. In contrast, increasing the σ
S
level rendered
Salmonella
more resistant to H
2
O
2
at 28°C, increased the expression of
katE
, and reduced the magnitude of Crl activation. In addition, the effect of Crl on
katE
transcription in vitro was not dependent on temperature. These results suggest that the effect of temperature on Crl-dependent regulation of the
katE
gene and H
2
O
2
resistance are mediated mainly via an effect on σ
S
levels. In addition, our results revealed that σ
S
exerts a negative effect on the production of Crl in stationary phase when the cells contain high levels of σ
S
.
Extracytoplasmic Processes Impaired by Inactivation of
trxA
(Thioredoxin Gene) in
Bacillus subtilis
Authors: Möller Mirja Carlsson , Hederstedt Lars 
Published: May 2008

ABSTRACT

The
trxA
gene is regarded as essential in
Bacillus subtilis
, but the roles of the TrxA protein in this gram-positive bacterium are largely unknown. Inactivation of
trxA
results in deoxyribonucleoside and cysteine or methionine auxotrophy. This phenotype is expected if the TrxA protein is important for the activity of the class Ib ribonucleotide reductase and adenosine-5′-phosphosulfate/3′-phosphoadenosine-5′-phosphosulfate reductase. We demonstrate here that a TrxA deficiency in addition causes defects in endospore and cytochrome
c
synthesis. These effects were suppressed by BdbD deficiency, indicating that TrxA in the cytoplasm is the primary electron donor to several different thiol-disulfide oxidoreductases active on the outer side of the
B. subtilis
cytoplasmic membrane.
Estimation of total settlement of embankments by field measurements
Authors: Matyas Elmer L , Rothenburg Leo 
Published: May 2008

In the absence of compressibility data from laboratory tests, the total primary consolidation settlement of a structure founded on clay can be estimated from settlement measurements taken over a period of time. In this note, the hyperbolic and Asaoka methods are applied to a case history where an embankment fill was placed on a clay exhibiting secondary compression. It is shown that significant inaccuracies in timesettlement predictions can result if an appropriate time factor versus degree of consolidation relationship is not taken into account. Key words: primary and secondary compressibility, coefficient of consolidation, field measurements, hyperbolic method, Asaoka method.
The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates
Authors: McCoy Skip R , Kuehl Jennifer V , Boore Jeffrey L , Raubeson Linda A 
Published: May 2008

Abstract

Background

Welwitschia mirabilis is the only extant member of the family Welwitschiaceae, one of three lineages of gnetophytes, an enigmatic group of gymnosperms variously allied with flowering plants or conifers. Limited sequence data and rapid divergence rates have precluded consensus on the evolutionary placement of gnetophytes based on molecular characters. Here we report on the first complete gnetophyte chloroplast genome sequence, from Welwitschia mirabilis, as well as analyses on divergence rates of protein-coding genes, comparisons of gene content and order, and phylogenetic implications.

Results
The chloroplast genome of Welwitschia mirabilis [GenBank: EU342371] is comprised of 119,726 base pairs and exhibits large and small single copy regions and two copies of the large inverted repeat (IR). Only 101 unique gene species are encoded. The Welwitschia plastome is the most compact photosynthetic land plant plastome sequenced to date; 66% of the sequence codes for product. The genome also exhibits a slightly expanded IR, a minimum of 9 inversions that modify gene order, and 19 genes that are lost or present as pseudogenes. Phylogenetic analyses, including one representative of each extant seed plant lineage and based on 57 concatenated protein-coding sequences, place Welwitschia at the base of all seed plants (distance, maximum parsimony) or as the sister to Pinus (the only conifer representative) in a monophyletic gymnosperm clade (maximum likelihood, bayesian). Relative rate tests on these gene sequences show the Welwitschia sequences to be evolving at faster rates than other seed plants. For these genes individually, a comparison of average pairwise distances indicates that relative divergence in Welwitschia ranges from amounts about equal to other seed plants to amounts almost three times greater than the average for non-gnetophyte seed plants.

Conclusion
Although the basic organization of the Welwitschia plastome is typical, its compactness, gene content and high nucleotide divergence rates are atypical. The current lack of additional conifer plastome sequences precludes any discrimination between the gnetifer and gnepine hypotheses of seed plant relationships. However, both phylogenetic analyses and shared genome features identified here are consistent with either of the hypotheses that link gnetophytes with conifers, but are inconsistent with the anthophyte hypothesis.
The effect of walnut intake on factors related to prostate and vascular health in older men
Authors: Spaccarotella Kim J , Kris-Etherton Penny M , Stone William L , Bagshaw Deborah M , Fishell Valerie K , West Sheila G , Lawrence Frank R , Hartman Terryl J 
Published: May 2008

Abstract

Background
Tocopherols may protect against prostate cancer and cardiovascular disease (CVD).

Methods
We assessed the effect of walnuts, which are rich in tocopherols, on markers of prostate and vascular health in men at risk for prostate cancer. We conducted an 8-week walnut supplement study to examine effects of walnuts on serum tocopherols and prostate specific antigen (PSA). Subjects (n = 21) consumed (in random order) their usual diet +/- a walnut supplement (75 g/d) that was isocalorically incorporated in their habitual diets. Prior to the supplement study, 5 fasted subjects participated in an acute timecourse experiment and had blood taken at baseline and 1, 2, 4, and 8 h after consuming walnuts (75 g).

Results
During the timecourse experiment, triglycerides peaked at 4 h, and gamma-tocopherol (γ-T) increased from 4 to 8 h. Triglyceride – normalized γ-T was two-fold higher (P = 0.01) after 8 versus 4 h. In the supplement study, change from baseline was +0.83 ± 0.52 μmol/L for γ-T, -2.65 ± 1.30 μmol/L for alpha-tocopherol (α-T) and -3.49 ± 1.99 for the tocopherol ratio (α-T: γ-T). A linear mixed model showed that, although PSA did not change, the ratio of free PSA:total PSA increased and approached significance (P = 0.07). The α-T: γ-T ratio decreased significantly (P = 0.01), partly reflecting an increase in serum γ-T, which approached significance (P = 0.08).

Conclusion
The significant decrease in the α-T: γ-T ratio with an increase in serum γ-T and a trend towards an increase in the ratio of free PSA:total PSA following the 8-week supplement study suggest that walnuts may improve biomarkers of prostate and vascular status.
Facilities for mentally impaired patients: three years experience of a semi-secure unit
Authors: Mayor Janet , Bhate Milan , Firth Hugh , Graham Anne , Knox Pam , Tyrer Stephen 
Published: May 2008

The Working Party on Security in NHS Hospitals (The Glancy Report, DHSS, 1974a) and the interim report of The Butler Committee (DHSS, 1974b) both recommended that secure provision should be made available for the treatment of mentally disordered patients who required greater security than could be provided in a standard hospital setting. They recommended that patients with mild or borderline mental handicap should be treated together with the mentally ill but that “severely subnormal patients” should be treated separately. Later the Royal College of Psychiatrists (1981) largely endorsed this advice proposing that:
(a) individuals with borderline and mild mental handicap could be adequately treated in the secure units for mentally ill individuals(b) individuals with moderate mental handicap needed a special secure facility(c) individuals with severe mental handicap did not need high security, and should be managed in high-staffed wards in mental handicap hospitals.
Carbamazepine monitoring
Authors: Paton Carol , Procter Andrew W. 
Published: May 2008

Background of the studyRationale for monitoring carbamazepine levelsCarbamazepine fulfils some of the criteria required in order to render a drug suitable for serum level monitoring in that there is poor inter-individual reproducibility of the serum levels achieved with fixed dosage regimes, interbrand differences in bioavailability are known to occur and serum levels can be raised significantly by several commonly prescribed drugs; dextropropoxyphene (a constituent of coprozamol), erythromycin, isoniazid and cimetidine.
4. On artificial intelligence (Al): is there a ghost in the machine?
Authors: Johnson Bankole Akindeinde 
Published: May 2008

“I am superior in many ways but would gladly give it up to be human.”Lieutenant-Commander Data – on android and serving officer on the Starship Enterprise Circa the 25th century atEncounter Farpoint.(See Fig. 1).Striking advances in artificial intelligence (AI) have brought to life philosophical debates about the concept of the mind, and of consciousness. Strong advocates of AI suggest the symbiosis of man and computers is the next step in our evolution, and to control this process, we need to address the “Big Question”: what is the meaning of life, and specifically, what are we? Understanding what we are is of great interest to us all; for psychiatrists, philosophers, and psychologists it is their life's work. In this paper, I shall introduce some of the main ideas about AI under the following headings. Can computers have a mind, improve our understanding of, or be integrated with our mental processes?
Thunniform swimming: muscle dynamics and mechanical power production of aerobic fibres in yellowfin tuna (Thunnus albacares)
Authors: Shadwick Robert E. , Syme Douglas A. 
Published: May 2008

SUMMARYWe studied the mechanical properties of deep red aerobic muscle of yellowfin tuna (Thunnus albacares), using both in vivo and in vitro methods. In fish swimming in a water tunnel at 1–3 L s–1 (where L is fork length), muscle length changes were recorded by sonomicrometry, and activation timing was quantified by electromyography. In some fish a tendon buckle was also implanted on the caudal tendon to measure instantaneous muscle forces transmitted to the tail. Between measurement sites at 0.45 to 0.65 L, the wave of muscle shortening progressed along the body at a relatively high velocity of 1.7 L per tail beat period, and a significant phase shift(31±4°) occurred between muscle shortening and local midline curvature, both suggesting red muscle power is directed posteriorly, rather than causing local body bending, which is a hallmark of thunniform swimming. Muscle activation at 0.53 L was initiated at about 50° of the tail beat period and ceased at about 160°, where 90° is peak muscle length and 180° is minimum length. Strain amplitude in the deep red fibres at 0.5 L was ±5.4%, double that predicted from midline curvature analysis. Work and power production were measured in isolated bundles of red fibres from 0.5 L by the work loop technique. Power was maximal at 3–4 Hz and fell to less than 50% of maximum after 6 Hz. Based on the timing of activation, muscle strain, tail beat frequencies and forces in the caudal tendon while swimming, we conclude that yellowfin tuna,like skipjack, use their red muscles under conditions that produce near-maximal power output while swimming. Interestingly, the red muscles of yellowfin tuna are slower than those of skipjack, which corresponds with the slower tail beat frequencies and cruising speeds in yellowfin.
Cutaneous water loss and sphingolipids covalently bound to corneocytes in the stratum corneum of house sparrowsPasser domesticus
Authors: Gu Yu , Muñoz-Garcia Agustí , Brown Johnie C. , Ro Jennifer , Williams Joseph B. 
Published: May 2008

SUMMARYThe barrier to water loss from the skin of birds and mammals is localized in the stratum corneum (SC), the outer layer of the epidermis. The SC consists of corneocytes, each surrounded by a protein envelope, and a lipid compartment, formed by an extracellular matrix of lipids and by lipids covalently bound to the protein envelope. In mammals, covalently bound lipids in the SC consist of ω-hydroxyceramides attached to the outer surface of corneocytes. Evidence suggests that covalently bound lipids in the SC might be crucial for the establishment of a competent permeability barrier. In this study we assessed the composition of covalently bound lipids of the avian SC and their relationship to cutaneous water loss (CWL) in two populations of house sparrows, one living in the deserts of Saudi Arabia and the other in mesic Ohio. Previously, we showed that CWL of adult desert sparrows was 25%lower than that of mesic birds. In the present study we characterize covalently bound lipids of the SC using thin layer chromatography and high performance liquid chromatography coupled with atmospheric pressure Photospray® ionization mass spectrometry. Our study is the first to demonstrate the existence of sphingolipids covalently bound to corneocytes in the SC of birds. Although ω-hydroxyceramides occurred in the lipid envelope surrounding corneocytes, the major constituent of the covalently bound lipid envelope in house sparrows was ω-hydroxycerebrosides,ceramides with a hexose molecule attached. Sparrows from Saudi Arabia had more covalently bound cerebrosides, fewer covalently bound ceramides and a lower ceramide to cerebroside ratio than sparrows living in Ohio; these differences were associated with CWL.
Reviews
Authors: Townsley Michael , Fleming Jenny , Antonopoulos Georgios A. , Biles David 
Published: May 2008

Law and Order:An Honest Citizen's Guide to Crime and Control; Robert Reiner; (2007) Cambridge,Polity, 168 pages, ISBNs:978-0-7456-2997-1, 978-0-7456-2996-4 Policing the Rural Crisis; Russell Hogg and Kerry Carrington; (2006) Leichhardt, The Federation Press, 246 pp, ISBN 9781862875814 Policing the Rural Crisis; Russell Hogg and Kerry Carrington; (2006) Leichhardt, The Federation Press, 246 pp, ISBN 9781862875814 Imagining the Victim of Crime; S. Walklate; (2007) Maidenhead: Open University Press/McGraw-Hill Education, pp. 189, ISBN-10:0335 21727 3 Outsmarting the Terrorists; Ronald V. Clarke and Graeme R. Newman; 2006. Westport, Connecticut: Praeger, 316 pp., ISBN 0-275-99230-6
High-sensitivity C-reactive protein is a good marker of cardiovascular risk in obese children and adolescents.
Authors: Soriano-Guillén Leandro , Hernández-García Bárbara , Pita Jimena , Domínguez-Garrido Nieves , Del Río-Camacho Genoveva , Rovira Adela 
Published: May 2008

ObjectiveWe intend to assess the utility of the high-sensitivity C-reactive protein (hs-CRP) as a marker of cardiovascular risk in obese children and adolescents.MethodsThe study included children and adolescents between 6 and 18 years of age with a body mass index (BMI) higher than 2 SDS. All the patients had their blood pressure taken and hs-CRP, hepatic function, lipid profile and uric acid were determined after 12 h of fasting. Likewise, an oral glucose tolerance test was performed, determining basal glucose and insulin levels, and after stimulus. We considered the presence of metabolic syndrome when the obese children and teenagers showed at least two of the following conditions: decreased high density lipoprotein (HDL)-cholesterol, hypertriglyceridemia, hypertension or alteration in glucose metabolism.ResultsOut of the 115 obese children studied, 24% showed signs of metabolic syndrome. Those with metabolic syndrome presented higher levels of hs-CRP (mean: 3.8 mg/l; 95% CI: 2.8–4.8) in comparison with the obese patients who did not show signs of metabolic syndrome (mean: 2 mg/l; 95% CI: 1.5–2.5). After a multivariate analysis, the variables that appear to influence the changes in hs-CRP were BMI, triglycerides and HDL-cholesterol levels.ConclusionThe hs-CRP is a useful tool for early diagnosis of cardiovascular risk in obese children and teenagers.
Paraxial Mesodermal Progenitors Derived from Mouse Embryonic Stem Cells Contribute to Muscle Regeneration via Differentiation into Muscle Satellite Cells
Authors: Sakurai Hidetoshi , Okawa Yayoi , Inami Yuta , Nishio Naomi , Isobe Ken-ichi 
Published: May 2008

Abstract
Pluripotent embryonic stem (ES) cells hold great potential for cell-based therapies. Although several recent studies have reported the potential of ES cell-derived progenitors for skeletal muscle regeneration, how the cells contribute to reconstitution of the damaged myofibers has remained elusive. Here, we demonstrated the process of injured muscle regeneration by the engraftment of ES cell-derived mesodermal progenitors. Mesodermal progenitor cells were induced by a conventional differentiation system and isolated by flow cytometer of platelet-derived growth factor receptor-α (PDGFR-α), a marker of paraxial mesoderm, and vascular endothelial growth factor receptor-2 (VEGFR-2), a marker of lateral mesoderm. The PDGFR-α+ population that represented the paraxial mesodermal character demonstrated significant engraftment when transplanted into the injured muscle of immunodeficient mouse. Moreover, the PDGFR-α+ population could differentiate into the muscle satellite cells that were the stem cells of adult muscle and characterized by the expression of Pax7 and CD34. These ES cell-derived satellite cells could form functional mature myofibers in vitro and generate myofibers fused with the damaged host myofibers in vivo. On the other hand, the PDGFR-α−VEGFR-2+ population that showed lateral mesodermal character exhibited restricted potential to differentiate into the satellite cells in injured muscle. Our results show the potential of ES cell-derived paraxial mesodermal progenitor cells to generate functional muscle stem cells in vivo without inducing or suppressing gene manipulation. This knowledge could be used to form the foundation of the development of stem cell therapies to repair diseased and damaged muscles.
Disclosure of potential conflicts of interest is found at the end of this article.
Baseflow Nitrate in Relation to Stream Order and Agricultural Land Use
Authors: Kang Shujiang , Lin Henry , Gburek William J. , Folmar Gordon J. , Lowery Birl 
Published: May 2008

AbstractManagement of agricultural nonpoint‐source pollution continues to be a challenge because of spatial and temporal variability. Using stream order as an index, we explored the distribution of nitrate concentration and load along the stream network of a large agricultural watershed in Pennsylvania—the East Mahantango Creek Watershed and two of its sub‐watersheds. To understand nitrate concentration variation in the stream water contributed from ground water, this study focused on baseflow. Impacts of agricultural land use area on baseflow nitrate in the stream network were investigated. Nitrate concentration showed a general decreasing trend with increasing stream order based on stream order averaged values; however, considerable spatial and temporal variability existed within each snapshot sampling. Nitrate loads increased with stream order in a power function because of the dominant effect of stream flow rate over the nitrate concentration. Within delineated sub‐watersheds based on stream orders, positive linear functions were found between agricultural land use area percentage and the baseflow nitrate concentration and between agricultural drainage area and the nitrate load. The slope of the positive linear regression between the baseflow nitrate concentration and percent agricultural land area seems to be a valuable indicator of a watershed's water quality as influenced by agricultural practices, watershed size, and specific physiographic setting. Stream order seems to integrate, to a certain degree, the source and transport aspects of nonpoint‐source pollution on a yearly averaged basis and thus might provide a quick estimate of the overall trend in baseflow nitrate concentration and load distribution along complex stream networks in agricultural watersheds.