bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution and phylogeny of the mud shrimps (Crustacea: Decapoda) revealed from complete mitochondrial genomes
Authors: Lin Feng-Jiau , Liu Yuan , Sha Zhongli , Tsang Ling Ming , Chu Ka Hou , Chan Tin-Yam , Liu Ruiyu , Cui Zhaoxia 
Published: November 2012

AbstractBackgroundThe evolutionary history and relationships of the mud shrimps (Crustacea: Decapoda: Gebiidea and Axiidea) are contentious, with previous attempts revealing mixed results. The mud shrimps were once classified in the infraorder Thalassinidea. Recent molecular phylogenetic analyses, however, suggest separation of the group into two individual infraorders, Gebiidea and Axiidea. Mitochondrial (mt) genome sequence and structure can be especially powerful in resolving higher systematic relationships that may offer new insights into the phylogeny of the mud shrimps and the other decapod infraorders, and test the hypothesis of dividing the mud shrimps into two infraorders.ResultsWe present the complete mitochondrial genome sequences of five mud shrimps,Austinogebia edulis,Upogebia major,Thalassina kelanang(Gebiidea),Nihonotrypaea thermophilusandNeaxius glyptocercus(Axiidea). All five genomes encode a standard set of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a putative control region. Except forT.kelanang, mud shrimp mitochondrial genomes exhibited rearrangements and novel patterns compared to the pancrustacean ground pattern. Each of the two Gebiidea species (A.edulisandU.major) and two Axiidea species (N.glyptocercusandN.thermophiles) share unique gene order specific to their infraorders and analyses further suggest these two derived gene orders have evolved independently. Phylogenetic analyses based on the concatenated nucleotide and amino acid sequences of 13 protein-coding genes indicate the possible polyphyly of mud shrimps, supporting the division of the group into two infraorders. However, the infraordinal relationships among the Gebiidea and Axiidea, and other reptants are poorly resolved. The inclusion of mt genome from more taxa, in particular the reptant infraorders Polychelida and Glypheidea is required in further analysis.ConclusionsPhylogenetic analyses on the mt genome sequences and the distinct gene orders provide further evidences for the divergence between the two mud shrimp infraorders, Gebiidea and Axiidea, corroborating previous molecular phylogeny and justifying their infraordinal status. Mitochondrial genome sequences appear to be promising markers for resolving phylogenetic issues concerning decapod crustaceans that warrant further investigations and our present study has also provided further information concerning the mt genome evolution of the Decapoda.
Construction of a highly flexible and comprehensive gene collection representing the ORFeome of the human pathogen Chlamydia pneumoniae
Authors: Maier Christina J , Maier Richard H , Virok Dezso Peter , Maass Matthias , Hintner Helmut , Bauer Johann W , Önder Kamil 
Published: November 2012

Abstract

Background
The Gram-negative bacterium Chlamydia pneumoniae (Cpn) is the leading intracellular human pathogen responsible for respiratory infections such as pneumonia and bronchitis. Basic and applied research in pathogen biology, especially the elaboration of new mechanism-based anti-pathogen strategies, target discovery and drug development, rely heavily on the availability of the entire set of pathogen open reading frames, the ORFeome. The ORFeome of Cpn will enable genome- and proteome-wide systematic analysis of Cpn, which will improve our understanding of the molecular networks and mechanisms underlying and governing its pathogenesis.

Results
Here we report the construction of a comprehensive gene collection covering 98.5% of the 1052 predicted and verified ORFs of Cpn (Chlamydia pneumoniae strain CWL029) in Gateway® ‘entry’ vectors. Based on genomic DNA isolated from the vascular chlamydial strain CV-6, we constructed an ORFeome library that contains 869 unique Gateway® entry clones (83% coverage) and an additional 168 PCR-verified ‘pooled’ entry clones, reaching an overall coverage of ~98.5% of the predicted CWL029 ORFs. The high quality of the ORFeome library was verified by PCR-gel electrophoresis and DNA sequencing, and its functionality was demonstrated by expressing panels of recombinant proteins in Escherichia coli and by genome-wide protein interaction analysis for a test set of three Cpn virulence factors in a yeast 2-hybrid system. The ORFeome is available in different configurations of resource stocks, PCR-products, purified plasmid DNA, and living cultures of E. coli harboring the desired entry clone or pooled entry clones. All resources are available in 96-well microtiterplates.

Conclusion
This first ORFeome library for Cpn provides an essential new tool for this important pathogen. The high coverage of entry clones will enable a systems biology approach for Cpn or host–pathogen analysis. The high yield of recombinant proteins and the promising interactors for Cpn virulence factors described here demonstrate the possibilities for proteome-wide studies.
High viremia and low level of transmitted drug resistance in anti-retroviral therapy-naïve perinatally-infected children and adolescents with HIV-1 subtype C infection
Authors: Neogi Ujjwal , Sahoo Pravat Nalini , De Costa Ayesha , Shet Anita 
Published: November 2012

Abstract

Background
High plasma viremia in HIV-1 infection is associated with rapid CD4 cell decline and faster disease progression. Children with HIV infection have high viral loads, particularly in early childhood. In this study we sought to understand the relationship between duration of HIV-1 infection and viral dynamics among perinatally-infected children and adolescents in India along with transmitted drug resistance in this population.

Methods
During 2007–2011, cross-sectional samples were collected from ART-naïve children (n = 105) with perinatally-acquired HIV infection, aged 2–16 years from Bangalore, India. CD4 counts, viral load and in-house genotyping were performed and transmitted drug resistance mutations were identified using the World Health Organization recommendations for Surveillance of Drug Resistance Mutations (SDRM_2009) list.

Results
Among 105 children studied, 73.3% (77/105) were asymptomatic, but had a median viral load of 5.24 log copies/mL (IQR 4.62-5.66). In the adolescent age group, 54% (21/39) had high levels of viremia (median 5.14 log copies/mL) but were asymptomatic. HIV-1 subtyping identified 98% strains (103/105) as subtype C; one A1 and one unique recombinant form (URF). Transmitted NRTI resistance was 1.9% (2/105); NNRTI resistance was 4.8% (5/105) and overall prevalence of transmitted drug resistance was 5.7% (6/105).

Conclusions
The high burden of plasma viremia found among untreated asymptomatic adolescents needs to be addressed both from an individual angle to halt disease progression, and from a public health perspective to arrest horizontal transmission. The low level of transmitted drug resistance among perinatally-infected children is reassuring; however with improving ART access globally, regular genotyping surveillance is indicated.
Influence of contact with schizophrenia on implicit attitudes towards schizophrenia patients held by clinical residents
Authors: Omori Ataru , Tateno Amane , Ideno Takashi , Takahashi Hidehiko , Kawashima Yoshitaka , Takemura Kazuhisa , Okubo Yoshiro 
Published: November 2012

Abstract

Background
Patients with schizophrenia and their families have suffered greatly from stigmatizing effects. Although many efforts have been made to eradicate both prejudice and stigma, they still prevail even among medical professionals, and little is known about how contact with schizophrenia patients affects their attitudes towards schizophrenia.

Methods
We assessed the impact of the renaming of the Japanese term for schizophrenia on clinical residents and also evaluated the influence of contact with schizophrenia patients on attitudes toward schizophrenia by comparing the attitudes toward schizophrenia before and after a one-month clinical training period in psychiatry. Fifty-one clinical residents participated. Their attitudes toward schizophrenia were assessed twice, before and one month after clinical training in psychiatry using the Implicit Association Test (IAT) as well as Link’s devaluation-discrimination scale.

Results
The old term for schizophrenia, “Seishin-Bunretsu-Byo”, was more congruent with criminal than the new term for schizophrenia, “Togo-Shitcho-Sho”, before clinical training. However, quite opposite to our expectation, after clinical training the new term had become even more congruent with criminal than the old term. There was no significant correlation between Link's scale and IAT effect.

Conclusions
Renaming the Japanese term for schizophrenia still reduced the negative images of schizophrenia among clinical residents. However, contact with schizophrenia patients unexpectedly changed clinical residents’ attitudes towards schizophrenia negatively. Our results might contribute to an understanding of the formation of negative attitudes about schizophrenia and assist in developing appropriate clinical training in psychiatry that could reduce prejudice and stigma concerning schizophrenia.
A dedicated surveillance network for congenital toxoplasmosis in Greece, 2006-2009: assessment of the results
Authors: Aptouramani Maria , Theodoridou Maria , Syrogiannopoulos George , Mentis Andreas , Papaevangelou Vasiliki , Gaitana Katerina , Daponte Alexandros , Hadjichristodoulou Christos ,   the Toxoplasmosis Study Group of the Greece-Cyprus Pediatric Surveillance Unit
Published: November 2012

Abstract

Background
Toxoplasmosis is caused by infection with the protozoan parasite Toxoplasma gondii. Acute infections in pregnant women may be transmitted to the fetus and cause severe illness. The purpose of this study was to establish a dedicated surveillance network (DSN) for congenital toxoplasmosis (CT) in Greece, in order to assess the birth prevalence of CT.

Methods
A DSN of thirty clinicians was established for reporting CT cases from hospitals throughout Greece. The clinicians were selected on the basis that there was a high possibility the suspected cases would be referred to them from district hospitals or private clinics. Suspected cases of CT were reported on a monthly basis with a zero reporting card during a surveillance period from April 2006 to December 2009. A questionnaire was sent for any suspected case to record information including demographic parameters, clinical signs and symptoms and laboratory results. Serological and molecular confirmation of cases was performed by the Pasteur Hellenic Institute. All newborns suspected of CT received treatment and were serologically and clinically followed up for one year.

Results
The monthly response rate reached 100%, although only after reminders sent to 65% of the participant physicians. Sixty-three suspected CT cases were recorded by the DSN during the study period including fourteen confirmed and seven probable cases. Ten cases (47.6%) presented with symptoms at birth. Chorioretinitis was the most prominent manifestation, occurring in five symptomatic CT cases (50%). No other symptoms appeared by the end of the one year clinical follow up. No case was recorded by the existing surveillance system of the Hellenic Center of Disease Control and Prevention (HCDCP) during the same time period. Birth prevalence was estimated at 0.45, 0.51 and 0.51 per 10,000 births for 2007, 2008 and 2009 respectively. The incidence rate of symptomatic CT at birth was estimated at 0.10 cases per 10,000 births per year in Greece (for the period 2007–2009).

Conclusion
The DSN for CT proved to be more sensitive than the classical notification system, easy in application and very efficient in reporting rare diseases such as CT. Similar DSNs could be used to provide useful information on other rare diseases.
Coadministration of tacrolimus with corticosteroid accelerates recovery in refractory patients with polymyositis/ dermatomyositis: a retrospective study
Authors: Shimojima Yasuhiro , Ishii Wataru , Matsuda Masayuki , Tazawa Ko-ichi , Ikeda Shu-ichi 
Published: November 2012

Abstract

Background
To investigate whether or not coadministration of tacrolimus (TAC) with prednisolone (PSL) can produce a beneficial effect in the treatment of polymyositis/ dermatomyositis (PM/DM).

Methods
We reviewed medical records of 32 PM/DM patients who had been admitted to our hospital, and abstracted those who had received TAC in addition to oral PSL for treatment. The clinical usefulness of TAC in PM/DM was objectively evaluated focusing upon the manual muscle strength test (MMT) score, serum creatine kinase (CK) and tapering of PSL.

Results
Nine patients with PM and 6 with DM were enrolled in this study. TAC was added because of difficulty in reduction of PSL in 12 patients and recurrence with corticosteroid-induced complications in the remaining 3. Both PM and DM patients showed significant increases in the MMT score and significant decreases in serum CK 1 to 3 months after starting TAC compared with before. Skin symptoms in a clinically amyopathic DM patient also improved 1 month after starting TAC. The daily dosage of PSL could be significantly reduced in both PM and DM after starting TAC compared with before. No serious adverse events ascribable to TAC occurred in any patients.

Conclusion
Additional use of TAC with PSL may safely promote improvement of PM/DM and also accelerate tapering of the latter.
The effects of rear-wheel camber on the kinematics of upper extremity during wheelchair propulsion
Authors: Tsai Chung-Ying , Lin Chien-Ju , Huang Yueh-Chu , Lin Po-Chou , Su Fong-Chin 
Published: November 2012

Abstract

Background
The rear-wheel camber, defined as the inclination of the rear wheels, is usually used in wheelchair sports, but it is becoming increasingly employed in daily propulsion. Although the rear-wheel camber can increase stability, it alters physiological performance during propulsion. The purpose of the study is to investigate the effects of rear-wheel cambers on temporal-spatial parameters, joint angles, and propulsion patterns.

Methods
Twelve inexperienced subjects (22.3±1.6 yr) participated in the study. None had musculoskeletal disorders in their upper extremities. An eight-camera motion capture system was used to collect the three-dimensional trajectory data of markers attached to the wheelchair-user system during propulsion. All participants propelled the same wheelchair, which had an instrumented wheel with cambers of 0°, 9°, and 15°, respectively, at an average velocity of 1 m/s.

Results
The results show that the rear-wheel camber significantly affects the average acceleration, maximum end angle, trunk movement, elbow joint movement, wrist joint movement, and propulsion pattern. The effects are especially significant between 0° and 15°. For a 15° camber, the average acceleration and joint peak angles significantly increased (p < 0.01). A single loop pattern (SLOP) was adopted by most of the subjects.

Conclusions
The rear-wheel camber affects propulsion patterns and joint range of motion. When choosing a wheelchair with camber adjustment, the increase of joint movements and the base of support should be taken into consideration.
Comparative studies of Al-doped ZnO and Ga-doped ZnO transparent conducting oxide thin films
Authors: Jun Min-Chul , Park Sang-Uk , Koh Jung-Hyuk 
Published: November 2012

Abstract
We have investigated the influences of aluminum and gallium dopants (0 to 2.0 mol%) on zinc oxide (ZnO) thin films regarding crystallization and electrical and optical properties for application in transparent conducting oxide devices. Al- and Ga-doped ZnO thin films were deposited on glass substrates (corning 1737) by sol–gel spin-coating process. As a starting material, AlCl3⋅6H2O, Ga(NO3)2, and Zn(CH3COO)2⋅2H2O were used. A lowest sheet resistance of 3.3 × 103 Ω/□ was obtained for the GZO thin film doped with 1.5 mol% of Ga after post-annealing at 650°C for 60 min in air. All the films showed more than 85% transparency in the visible region. We have studied the structural and microstructural properties as a function of Al and Ga concentrations through X-ray diffraction and scanning electron microscopy analysis. In addition, the optical bandgap and photoluminescence were estimated.
Replication of somatic micronuclei in bovine enucleated oocytes
Authors: Canel Natalia , Bevacqua Romina , Hiriart María Inés , Salamone Daniel 
Published: November 2012

Abstract

Background
Microcell-mediated chromosome transfer (MMCT) was developed to introduce a low number of chromosomes into a host cell. We have designed a novel technique combining part of MMCT with somatic cell nuclear transfer, which consists of injecting a somatic micronucleus into an enucleated oocyte, and inducing its cellular machinery to replicate such micronucleus. It would allow the isolation and manipulation of a single or a low number of somatic chromosomes.

Methods
Micronuclei from adult bovine fibroblasts were produced by incubation in 0.05 μg/ml demecolcine for 46 h followed by 2 mg/ml mitomycin for 2 h. Cells were finally treated with 10 μg/ml cytochalasin B for 1 h. In vitro matured bovine oocytes were mechanically enucleated and intracytoplasmatically injected with one somatic micronucleus, which had been previously exposed [Micronucleus- injected (+)] or not [Micronucleus- injected (−)] to a transgene (50 ng/μl pCX-EGFP) during 5 min. Enucleated oocytes [Enucleated (+)] and parthenogenetic [Parthenogenetic (+)] controls were injected into the cytoplasm with less than 10 pl of PVP containing 50 ng/μl pCX-EGFP. A non-injected parthenogenetic control [Parthenogenetic (−)] was also included. Two hours after injection, oocytes and reconstituted embryos were activated by incubation in 5 μM ionomycin for 4 min + 1.9 mM 6-DMAP for 3 h. Cleavage stage and egfp expression were evaluated. DNA replication was confirmed by DAPI staining. On day 2, Micronucleus- injected (−), Parthenogenetic (−) and in vitro fertilized (IVF) embryos were karyotyped. Differences among treatments were determined by Fisher′s exact test (p≤0.05).

Results
All the experimental groups underwent the first cell divisions. Interestingly, a low number of Micronucleus-injected embryos showed egfp expression. DAPI staining confirmed replication of micronuclei in most of the evaluated embryos. Karyotype analysis revealed that all Micronucleus-injected embryos had fewer than 15 chromosomes per blastomere (from 1 to 13), while none of the IVF and Parthenogenetic controls showed less than 30 chromosomes per spread.

Conclusions
We have developed a new method to replicate somatic micronuclei, by using the replication machinery of the oocyte. This could be a useful tool for making chromosome transfer, which could be previously targeted for transgenesis.
The isotropic fractionator provides evidence for differential loss of hippocampal neurons in two mouse models of Alzheimer's disease
Authors: Brautigam Hannah , Steele John W , Westaway David , Fraser Paul E , George-Hyslop Peter H St , Gandy Sam , Hof Patrick R , Dickstein Dara L 
Published: November 2012

AbstractBackgroundThe accumulation of amyloid beta (Aβ) oligomers or fibrils is thought to be one of the main causes of synaptic and neuron loss, believed to underlie cognitive dysfunction in Alzheimer’s disease (AD). Neuron loss has rarely been documented in amyloid precursor protein (APP) transgenic mouse models. We investigated whether two APP mouse models characterized by different folding states of amyloid showed different neuronal densities using an accurate method of cell counting.FindingsWe examined total cell and neuronal populations in Swedish/Indiana APP mutant mice (TgCRND8) with severe Aβ pathology that includes fibrils, plaques, and oligomers, and Dutch APP mutant mice with only Aβ oligomer pathology. Using the isotropic fractionator, we found no differences from control mice in regional total cell populations in either TgCRND8 or Dutch mice. However, there were 31.8% fewer hippocampal neurons in TgCRND8 compared to controls, while no such changes were observed in Dutch mice.ConclusionsWe show that the isotropic fractionator is a convenient method for estimating neuronal content in milligram quantities of brain tissue and represents a useful tool to assess cell loss efficiently in transgenic models with different types of neuropathology. Our data support the hypothesis that TgCRND8 mice with a spectrum of Aβ plaque, fibril, and oligomer pathology exhibit neuronal loss whereas Dutch mice with only oligomers, showed no evidence for neuronal loss. This suggests that the combination of plaques, fibrils, and oligomers causes more damage to mouse hippocampal neurons than Aβ oligomers alone.
Sequence based analysis of U-2973, a cell line established from a double-hit B-cell lymphoma with concurrent MYC and BCL2 rearrangements
Authors: Hooper Sean D , Jiao Xiang , Sundström Elisabeth , Rehman Farah L , Tellgren-Roth Christian , Sjöblom Tobias , Cavelier Lucia 
Published: November 2012

Abstract

Background
Double-hit lymphoma is a complex and highly aggressive sub-type of B-cell lymphoma, which has recently been classified and is an area of active research interest due to the poor prognosis for patients with this disease. It is characterized by the presence of both an activating MYC chromosomal translocation and a simultaneous additional oncogenic translocation, often of the BCL2 gene. Recently, a cell line was established from a patient with this complex lymphoma and analyzed using conventional tools revealing it contains both MYC and BCL2 translocation events.

Findings
In this work, we reanalyzed the genome of the cell line using next generation whole genome sequencing technology in order to catalogue translocations, insertions and deletions which may contribute to the pathology of this lymphoma type.

Conclusions
We describe the cell line in much greater detail, and pinpoint the exact locations of the chromosomal breakpoints. We also find several rearrangements within cancer-associated genes, which were not found using conventional tools, suggesting that high throughput sequencing may reveal novel targets for therapy, which could be used concurrently with existing treatments.