bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and molecular characterization of numerous Histomonas meleagridis proteins using a cDNA library
Authors: BILIC I. , LEBERL M. , HESS M. 
Published: January 2009

SUMMARYHistomonas meleagridis is a protozoan parasite of various galliform birds causing a type of enterohepatitis termed histomonosis or ‘blackhead disease’. Due to the ban of chemotherapeutic substances and an increase in free-range poultry production, histomonosis is currently a re-emerging disease. So far limited molecular knowledge is available. In the present work, mRNAs coding for antigenic proteins of H. meleagridis were identified. For this purpose, a cDNA expression library was constructed from a mono-eukaryotic culture of H. meleagridis. The library was screened with polyclonal rabbit serum raised against purified H. meleagridis trophozoites. Polyclonal rabbit serum specifically recognized the same major H. meleagridis antigens as chicken and turkey sera originating from animal trials, but displayed a significantly lower bacteria-dependent background signal. After 2 rounds of screening, a total of 95 positive clones were sequenced. Bioinformatics analyses were performed on nucleotide and deduced amino acid sequences, identifying 37 unique clones. Based on the homology to other protozoan parasites, mostly Trichomonas vaginalis, the clones were grouped according to functional aspects: structural proteins, possible surface proteins, oxygen reducing proteins, ribosomal proteins, protein kinases and various other intracellular proteins.
Sensitivity of pooled serum testing for screening antibody of schistosomiasis japonica by IHA in a mountainous area of Yunnan, China
Authors: JIA X. M. , SRIPLUNG H. , CHONGSUVIVATWONG V. , GEATER A. 
Published: January 2009

SUMMARYPooled sample testing (PST) as a strategy for avoiding testing the majority of individual negative samples has been proposed for screening of diseases in low prevalence areas. There has been no standard guideline for PST in screening ofSchistosoma japonicuminfection of Yunnan, China. To document the optimum pool size with acceptable sensitivity of PST for screening ofSchistosoma japonicuminfection in this setting, an experimental pooling of each of 31 positive sera by IHA with various numbers of 24 negative sera was done. The results were used to create a statistical model which was subsequently used for simulation to predict sensitivity of the pooled serum tests in the population with varying prevalence and pool size. We found that to keep the sensitivity of PST above 90%, 1:05 should be the maximum dilution, that is, the optimum pool size should not be greater than 6. Antigen will have rather little interference if the prevalence of infection is low e.g. 1% or the antigen:antibody ratio is 1:100 or below. Pooled serum testing by IHA is an acceptable sensitive method for detecting antibody forSchistosoma japonicuminfection in this area.
Impaired inhibitory control is associated with higher-order repetitive behaviors in autism spectrum disorders
Authors: Mosconi M. W. , Kay M. , D'Cruz A.-M. , Seidenfeld A. , Guter S. , Stanford L. D. , Sweeney J. A. 
Published: January 2009

BackgroundImpairments in executive cognitive control, including a reduced ability to inhibit prepotent responses, have been reported in autism spectrum disorders (ASD). These deficits may underlie patterns of repetitive behaviors associated with the disorder.MethodEighteen individuals with ASD and 15 age- and IQ-matched healthy individuals performed an antisaccade task and a visually guided saccade control task, each with gap and overlap conditions. Measures of repetitive behaviors were obtained using the Autism Diagnostic Inventory – Revised (ADI-R) and examined in relation to neurocognitive task performance.ResultsIndividuals with an ASD showed increased rates of prosaccade errors (failures to inhibit prepotent responses) on the antisaccade task regardless of task condition (gap/overlap). Prosaccade error rates were associated with the level of higher-order (e.g. compulsions, preoccupations) but not sensorimotor repetitive behaviors in ASD.ConclusionsNeurocognitive disturbances in voluntary behavioral control suggest that alterations in frontostriatal systems contribute to higher-order repetitive behaviors in ASD.
Linear Partial Differential Equations with Constant Coefficients: an Elementary Proof of an Existence Theorem
Authors: Parsons D. H. 
Published: January 2009

We consider a linear partial differential equation with constant coefficients in one dependent and m independent variables, the right-hand side being zero,P being a symbolic polynomial in D1, …, Dm. If P can be decomposed into two factors, so that the equation can be writtenit is evident that the sum of any solution ofand any solution ofis also a solution of (1).
Structural analysis of outer membrane beta-stranded porins using B-factor
Authors: Kumar Abhishek , Krishnaswamy S 
Published: January 2009

AbstractComputational and statistical analysis has formed a large component of the biophysical efforts put forth to understand protein structure and function, due to the diversity and complexity of their structure. Outer membrane proteins form a diverse and complex set of proteins. Of these, porins that allow passage of molecules across the membrane interface have been analyzed here from a biophysical and structural perspective. The objective of this study is to analyze the structural organization of porins using atomic temperature factor as a parameter. Generally atomic temperature factors of molecules from crystal structures indicate the degree of mobility or disorder seen in the crystal structure. As good crystal structures have lesser possibilities of errors so there is lesser chance that errors are playing roles in temperature factors. Structures of six porins (four 16-stranded beta barrel porins and two 8-stranded beta barrel porins) were taken from the PDB for the analysis based on resolution and R-factor. Programs and scripts were written for extracting the temperature factors for the beta strands, loops and turns so that the analysis could be done for different atom-types and residue-types. The residue distribution and mobility distribution was found to be characteristic of each of the porins. The mobility and residue distribution amongst the secondary structural elements were found to follow the level of homology at the sequence and structural level. The loops that had defined functional roles in structural terms were found to have lower temperature factors than the other loops. The turn regions that are thought to face the periplasmic region in the cell, showed higher temperature factors. For both the 16 stranded and the 8-stranded barrels it was found one part of the barrel (the lower wall or 'inner' wall comprising the trimer interface in the case of the 16-stranded barrels) was more rigid and the other half of the barrel (the higher or 'outer' wall) showed more mobility as seen from the temperature factors. This seems to be an intrinsic structural component of the beta barrels.
Expansion of radiofrequency ablation volume by saturated NaCL saline injection in the area of vaporization
Authors: Shimizu A. , Ishizaka H. , Awata S. , Shiraishi A. , Hirasawa S. , Tatezawa T. , Kano M. , Shimodaira K. , Taketomi-Takahashi A. , Tsushima Y. , Endo K. 
Published: January 2009

Background: Vaporization around the radiofrequency (RF) electrode after RF application (RFA) limits the RF ablation area. Purpose: To determine whether saturated saline injected into the area of vaporization after initial RFA extends ablation area after further RFA. Material and Methods: RFA was performed in 18 ex vivo porcine livers and four in vivo rabbit erector spinae muscles. An RF electrode was used to ablate an area with 40W of parallel current for 15 min. The ablation margin was determined using a thermocouple, and the radius of the ablated area was measured. After RF electrode removal, saturated saline was infused through a percutaneous ethanol injection needle into the site of the original RFA in 11 liver samples and two erector spinae muscles. Three minutes later, RFA was resumed for 15 min. The remaining seven control liver samples and two spinae muscles received RFA without saline injection. The radius of the final ablated area was then measured. Results: In the ex vivo study, injection of saturated saline significantly decreased tissue impedance (87.7±9.4 to 51.1±9.7Ω, P<0.0001), and increased the mean radius of the ablated area (15.9±3.0 to 25.0±3.6 mm, P<0.0001). These significant changes were not observed without injection of saturated saline. Similar trends were found in the in vivo study. Conclusion: Injection of saturated saline into the area of vaporization around the RF electrode, followed by additional RFA, caused concentric expansion of the final ablation area, facilitating more efficient tumor ablation.
BEYOND HIERARCHICAL REPRESENTATIONS OF THE FORMAL/INFORMAL EMPLOYMENT DUALISM
Authors: Williams Colin C. , Round John 
Published: January 2009

ABSTRACT
This paper evaluates critically the conventional hierarchical representation of the formal/informal employment dualism, which depicts formal employment as extensive and positively contributing to economic development and social cohesion, and the separate realm of informal employment as weaker, inhabiting the margins and impairing progress and development. Although the discourses of informal employment as weak, marginal and separate from formal employment have been previously put under the spotlight, there has been little questioning of whether informal employment is a negative phenomenon. Through a study of Ukraine, however, this paper finds evidence that informal employment positively contributes to not only economic development as a seedbed for enterprise and entrepreneurship but also social cohesion as a primary vehicle for delivering community self-help. The outcome is a call for a finer-grained understanding of informal (and ultimately also formal) employment that recognises its plurality of forms and their varying consequences for economic development and social cohesion.
CONCENTRATION OF WORKING-AGE MALE MORTALITY AMONG MANUAL WORKERS IN URBAN LATVIA AND RUSSIA, 1970–1989
Authors: Andreev Evgueni , Hoffmann Rasmus , Carlson Elwood , Shkolnikov Vladimir , Kharkova Tatiana L. 
Published: January 2009

ABSTRACT
Until recently data on mortality by socioeconomic status were not available for the initial period of mortality increase in the former Soviet Union from 1965 to 1979. Newly discovered data from the Russian State Archive of Economics allow us to close this gap and to compare mortality trends in urban Latvia and several urban areas of Russia with the concentration of rising male mortality among manual workers already found in several eastern European countries. A similar trend appears in these data for rising mortality to concentrate among manual workers over time. Unfavorable trends in the life expectancy of the total population were largely driven by mortality increase among manual workers. Possible determinants of the pattern include a special type of economic growth in the USSR in the 1970s and 1980s associated with dominance of heavy industries and military sector, and low consumer goods’ production, high prevalence of hard manual labor, massive rural–urban migrations and poor living conditions of new coming industrial workers, growing psychosocial stress and high prevalence of adverse health behaviors. These characteristics are discussed in the framework of an incomplete modernization and distinct health life styles in state socialist countries.
An upper bound on the characteristic polynomial of a nonnegative matrix leading to a proof of the Boyle-Handelman conjecture
Authors: Goldberger Assaf , Neumann Michael 
Published: January 2009

In their celebrated 1991 paper on the inverse eigenvalue problem for nonnegative matrices, Boyle and Handelman conjectured that if

A
A

is an

(
n
+
1
)
×
(
n
+
1
)

(n+1)\times (n+1)

nonnegative matrix whose nonzero eigenvalues are:

λ
0

≥

|

λ
i

|

\lambda _0 \geq |\lambda _i|

,

i
=
1
,
…
,
r

i=1,\ldots ,r

,

r
≤

n

r \leq \ n

, then for all

x
≥

λ
0

x \geq \lambda _0

,

(
∗
)

∏

i
=
0

r

(
x
−

λ
i

)
≤

x

r
+
1

−

λ
0

r
+
1

.

\begin{equation} \prod _{i=0}^{r} (x-\lambda _i) \leq x^{r+1}-\lambda _0^{r+1}.\tag *{$(\ast )$} \end{equation}

To date the status of this conjecture is that Ambikkumar and Drury (1997) showed that the conjecture is true when

2
(
r
+
1
)
≥
(
n
+
1
)

2(r+1)\geq (n+1)

, while Koltracht, Neumann, and Xiao (1993) showed that the conjecture is true when

n
≤
4

n\leq 4

and when the spectrum of

A
A

is real. They also showed that the conjecture is asymptotically true with the dimension.

Here we prove a slightly stronger inequality than in

(
∗
)

(\ast )

, from which it follows that the Boyle–Handelman conjecture is true. Actually, we do not start from the assumption that the

λ
i

\lambda _i

’s are eigenvalues of a nonnegative matrix, but that

λ
1

,
…
,

λ

r
+
1

\lambda _1,\ldots , \lambda _{r+1}

satisfy

λ
0

≥

|

λ
i

|

\lambda _0\geq |\lambda _i|

,

i
=
1
,
…
,
r

i=1,\ldots , r

, and the trace conditions:

(
∗
∗
)

∑

i
=
0

r

λ
i
k

≥
0
,

for all

k
≥
1.

\begin{equation} \sum _{i=0}^{r} \lambda _i^k \geq 0, \ \mbox {for all} k \geq 1.\tag *{$(\ast \ast )$} \end{equation}

A strong form of the Boyle–Handelman conjecture, conjectured in 2002 by the present authors, says that (

∗
*

) continues to hold if the trace inequalities in (

∗
∗

**

) hold only for

k
=
1
,
…
,
r

k=1,\ldots ,r

. We further improve here on earlier results of the authors concerning this stronger form of the Boyle–Handelman conjecture.
Repression of Seed Maturation Genes by a Trihelix Transcriptional Repressor inArabidopsisSeedlings
Authors: Gao Ming-Jun , Lydiate Derek J. , Li Xiang , Lui Helen , Gjetvaj Branimir , Hegedus Dwayne D. , Rozwadowski Kevin 
Published: January 2009

AbstractThe seed maturation program is repressed during germination and seedling development so that embryonic genes are not expressed in vegetative organs. Here, we describe a regulator that represses the expression of embryonic seed maturation genes in vegetative tissues. ASIL1 (for Arabidopsis 6b-interacting protein 1-like 1) was isolated by its interaction with the Arabidopsis thaliana 2S3 promoter. ASIL1 possesses domains conserved in the plant-specific trihelix family of DNA binding proteins and belongs to a subfamily of 6b-interacting protein 1-like factors. The seedlings of asil1 mutants exhibited a global shift in gene expression to a profile resembling late embryogenesis. LEAFY COTYLEDON1 and 2 were markedly derepressed during early germination, as was a large subset of seed maturation genes, such as those encoding seed storage proteins and oleosins, in seedlings of asil1 mutants. Consistent with this, asil1 seedlings accumulated 2S albumin and oil with a fatty acid composition similar to that of seed-derived lipid. Moreover, ASIL1 specifically recognized a GT element that overlaps the G-box and is in close proximity to the RY repeats of the 2S promoters. We suggest that ASIL1 targets GT-box–containing embryonic genes by competing with the binding of transcriptional activators to this promoter region.
Bias and conflict in phylogenetic inference of myco‐heterotrophic plants: a case study in Thismiaceae
Authors: Merckx Vincent , Bakker Freek T. , Huysmans Suzy , Smets Erik 
Published: January 2009

AbstractDue to morphological reduction and absence of amplifiable plastid genes, the identification of photosynthetic relatives of heterotrophic plants is problematic. Although nuclear and mitochondrial gene sequences may offer a welcome alternative source of phylogenetic markers, the presence of rate heterogeneity in these genes may introduce bias/systematic error in phylogenetic analyses. We examine the phylogenetic position of Thismiaceae based on nuclear 18S rDNA and mitochondrial atpA DNA sequence data, as well as using parsimony, likelihood and Bayesian inference methods. Significant differences in evolutionary rates of these genes between closely related taxa lead to conflicting results: while parsimony analyses of 18S rDNA and combined data strongly support the monophyly of Thismiaceae, Bayesian inference, with and without a relaxed molecular clock, as well as the Swofford–Olsen–Waddell–Hillis (SOWH) test confidently reject this hypothesis. We show that rate heterogeneity in our data leads to long‐branch attraction artifacts in parsimony analysis. However, using model‐based inference methods the question of whether Thismiaceae are monophyletic remains elusive. On the one hand maximum likelihood nonparametric bootstrapping and parametric hypothesis tests fail to support a paraphyletic Thismiaceae, on the other hand Bayesian inference methods (both without and with a relaxed clock) significantly reject a monophyletic Thismiaceae. These results show that an adequate sampling, the use of rate homogeneous data, and the application of different inference methods are important factors for developing phylogenetic hypotheses of myco‐heterotrophic plants. © The Willi Hennig Society 2009.
Secondary chemistry and ribosomal DNA data congruencies in Arnica (Asteraceae)
Authors: Ekenäs Catarina , Rosén Josefin , Wagner Steffen , Merfort Irmgard , Backlund Anders , Andreasen Katarina 
Published: January 2009

AbstractTo investigate possible congruencies between DNA sequence data and secondary chemistry, we compared nuclear ribosomal DNA (nrDNA) sequence data, sesquiterpene lactone (STL) contents, and cytometric data from 35 accessions of 16 Arnica (Asteraceae) species and two outgroup taxa (Layia hieracioides and Madia sativa), using phylogenetic inference and principal component analysis (PCA). Several groups supporting multiple accessions of the same species (of A. montana, A. longifolia, A. gracilis, and A. chamissonis) are congruent between the phylogenetic trees based on nrDNA and STL data. Sesquiterpene lactone profiles were found to be highly consistent within multiple samples of A. montana and A. longifolia respectively. Moreover, sesquiterpene lactone data support subspecies classifications of A. chamissonis and A. parryi, with additional support from DNA sequence data and cytometric data. Morphology, STL data (PCA), cytometric data and DNA sequence data suggest a hybrid origin of one accession (A. gracilis × longifolia). In A. gracilis, A. latifolia, and Layia hieracioides, previously not investigated for STLs, we found large amounts of xanthalongin derivatives. This is the first time STLs have been reported from subtribe Madiinae.© The Willi Hennig Society 2009.
Immunolocalization and serum antibody responses to Brugia malayi pepsin inhibitor homolog (Bm‐33)
Authors: Krushna Nagampalli S. A. , Shiny Chandanpurath , Dharanya Srinivasan , Sindhu Arivazhagan , Aishwarya Sridharan , Narayanan Rangarajan B. 
Published: January 2009

ABSTRACTcDNA coding for Brugia malayi pepsin inhibitor homolog (Bm‐33) from the human filarial parasite was cloned in pRSET for large‐scale expression and functional characterization. The pRSET‐B cloned gene did not yield recombinant protein expression and the reason was attributed to the presence of an N‐terminal signal peptide. The gene was subcloned in pRSET‐A without a signal peptide and the 33 kDa histidine‐tagged recombinant protein was purified by IMAC. All individuals from an endemic area generated IgG responses against Bm‐33 in the order MF>CP>EN. Isotype analysis indicated an elevated IgG4 reactivity in the order MF>EN>CP. Bm‐33‐specific IgE levels were elevated in MF, CP and EN compared to non‐endemic normals with no significant differences among the groups. Paraffin‐embedded sections of Setaria digitata (cattle filarial parasite) stained with mouse anti‐Bm‐33 antibodies exhibited the hypodermal nature of Bm‐33. These findings suggest that Bm‐33 is an immunodominant antigen and contributes to filarial pathogenesis.
Prevalence and characteristics of cytolethal distending toxin‐producing Escherichia coli from children with diarrhea in Japan
Authors: Hinenoya Atsushi , Naigita Akira , Ninomiya Keiko , Asakura Masahiro , Shima Kensuke , Seto Kazuko , Tsukamoto Teizo , Ramamurthy T. , Faruque Shah M. , Yamasaki Shinji 
Published: January 2009

ABSTRACTIn the present study, we examined the prevalence and characteristics of CTEC among diarrheal children in Japan during a year‐long surveillance study. A PCR‐RFLP assay for the detection and differentiation of five types of E. coli cdtB gene (types I through V) was developed, and 362 stool specimens collected from patients reporting to pediatric departments in two hospitals were analyzed. Of the 35 samples (9.7%) that were positive for the cdtB gene, 21 were positive for cdt‐I, three for cdt‐II, four for cdt‐III, three for cdt‐IV and four samples were positive for cdt‐V, as determined by different molecular techniques. The recovery of CTEC having cdt alleles was a little less, which included 19 with cdt‐I, one cdt‐II, three cdt‐III, three cdt‐IV and four with cdt‐V. Among 30 CTEC strains isolated, the majority of them (43%) belonged to serogroup O2. The other virulence genes such as astA, cnf1, eaeA, cnf2 and bfpA genes were detected in 14 (47%), 11 (37%), four (13%), three (10%) and one (3.3%) strains of CTEC, respectively. However, the other common virulence‐associated genes specific for DEC were not detected in these strains. Interestingly, an untypable cdt gene was detected by PCR‐RFLP in Providencia alcalifaciens. Our data indicate that CTEC may be associated with diarrheal children in Japan and most of them do not belong to a conventional enteropathogenic pathovar and thus differ from strains isolated in developing countries.
Clinical trial: a randomized, study comparing meperidine (pethidine) and fentanyl in adult gastrointestinal endoscopy
Authors: ROBERTSON D. J. , JACOBS D. P. , MACKENZIE T. A. , ORINGER J. A. , ROTHSTEIN R. I. 
Published: January 2009

SummaryBackground  There is little evidence to guide choice between meperidine (pethidine) and fentanyl for sedation for gastrointestinal endoscopy.Aim  To compare meperidine with fentanyl in terms of procedure time and analgesia.Methods  Single centre randomized controlled trial. Patients received narcotic doses and midazolam at the discretion of the attending endoscopist who was unaware of narcotic assignment. Endoscopy and recovery times were then recorded. The main outcome was total procedure time, defined as endoscopy time plus recovery time. Patient discomfort was assessed prior to discharge via visual analogue scale (VAS).Results  In total, 55 patients were randomized to meperidine [44 colonoscopy and 11 esophagogastroduodenoscopy (EGD)] and 56 to fentanyl (45 colonoscopy and 11 EGD). Total procedure time was shorter for those receiving fentanyl (mean = 87.7 min) than for those receiving meperidine (mean = 102.9 min) (P = 0.05). The difference between the groups was explained by a shorter mean recovery time in the fentanyl group (63.0 min) than in the meperidine group (76.2 min) (P = 0.07). Based on post procedure pain scores, examinations with meperidine (mean = 1.99) were less painful when compared with those receiving fentanyl (mean = 2.86, P = 0.03).Conclusions  Fentanyl shortened total procedure time by reducing recovery time. A simple change in narcotic choice could increase endoscopy unit efficiency.