bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pathogen-origin horizontally transferred genes contribute to the evolution of Lepidopteran insects
Authors: Li Zi-Wen , Shen Yi-Hong , Xiang Zhong-Huai , Zhang Ze 
Published: December 2011

Abstract

Background
Horizontal gene transfer (HGT), a source of genetic variation, is generally considered to facilitate hosts' adaptability to environments. However, convincing evidence supporting the significant contribution of the transferred genes to the evolution of metazoan recipients is rare.

Results
In this study, based on sequence data accumulated to date, we used a unified method consisting of similarity search and phylogenetic analysis to detect horizontally transferred genes (HTGs) between prokaryotes and five insect species including Drosophila melanogaster, Anopheles gambiae, Bombyx mori, Tribolium castaneum and Apis mellifera. Unexpectedly, the candidate HTGs were not detected in D. melanogaster, An. gambiae and T. castaneum, and 79 genes in Ap. mellifera sieved by the same method were considered as contamination based on other information. Consequently, 14 types of 22 HTGs were detected only in the silkworm. Additionally, 13 types of the detected silkworm HTGs share homologous sequences in species of other Lepidopteran superfamilies, suggesting that the majority of these HTGs were derived from ancient transfer events before the radiation of Ditrysia clade. On the basis of phylogenetic topologies and BLAST search results, donor bacteria of these genes were inferred, respectively. At least half of the predicted donor organisms may be entomopathogenic bacteria. The predicted biochemical functions of these genes include four categories: glycosyl hydrolase family, oxidoreductase family, amino acid metabolism, and others.

Conclusions
The products of HTGs detected in this study may take part in comprehensive physiological metabolism. These genes potentially contributed to functional innovation and adaptability of Lepidopteran hosts in their ancient lineages associated with the diversification of angiosperms. Importantly, our results imply that pathogens may be advantageous to the subsistence and prosperity of hosts through effective HGT events at a large evolutionary scale.
Mining the Gene Wiki for functional genomic knowledge
Authors: Good Benjamin M , Howe Douglas G , Lin Simon M , Kibbe Warren A , Su Andrew I 
Published: December 2011

Abstract

Background
Ontology-based gene annotations are important tools for organizing and analyzing genome-scale biological data. Collecting these annotations is a valuable but costly endeavor. The Gene Wiki makes use of Wikipedia as a low-cost, mass-collaborative platform for assembling text-based gene annotations. The Gene Wiki is comprised of more than 10,000 review articles, each describing one human gene. The goal of this study is to define and assess a computational strategy for translating the text of Gene Wiki articles into ontology-based gene annotations. We specifically explore the generation of structured annotations using the Gene Ontology and the Human Disease Ontology.

Results
Our system produced 2,983 candidate gene annotations using the Disease Ontology and 11,022 candidate annotations using the Gene Ontology from the text of the Gene Wiki. Based on manual evaluations and comparisons to reference annotation sets, we estimate a precision of 90-93% for the Disease Ontology annotations and 48-64% for the Gene Ontology annotations. We further demonstrate that this data set can systematically improve the results from gene set enrichment analyses.

Conclusions
The Gene Wiki is a rapidly growing corpus of text focused on human gene function. Here, we demonstrate that the Gene Wiki can be a powerful resource for generating ontology-based gene annotations. These annotations can be used immediately to improve workflows for building curated gene annotation databases and knowledge-based statistical analyses.
Molecular detection and speciation of pathogenic Leptospiraspp. in blood from patients with culture-negative leptospirosis
Authors: Boonsilp Siriphan , Thaipadungpanit Janjira , Amornchai Premjit , Wuthiekanun Vanaporn , Chierakul Wirongrong , Limmathurotsakul Direk , Day Nicholas P , Peacock Sharon J 
Published: December 2011

Abstract

Background
Pathogenic Leptospira spp. present in the blood of patients with leptospirosis during the first week of symptoms can be detected using culture or PCR. A proportion of patients who are positive by PCR are negative by culture. Leptospira spp. are fastidious bacteria, and we hypothesized that a false-negative culture result may represent infection with a distinct bacterial subset that fail to grow in standard culture medium.

Methods
We evaluated our hypothesis during a prospective study of 418 consecutive patients presenting to a hospital in northeast Thailand with an acute febrile illness. Admission blood samples were taken for Leptospira culture and PCR. A single tube nested PCR that amplified a region of the rrs gene was developed and applied, amplicons sequenced and a phylogenetic tree reconstructed.

Results
39/418 (9%) patients were culture-positive for Leptospira spp., and 81/418 (19%) patients were culture-negative but rrs PCR-positive. The species associated with culture-positive leptospirosis (37 L. interrogans and 2 L. borgpetersenii) were comparable to those associated with culture-negative, PCR-positive leptospirosis (76 L. interrogans, 4 L. borgpetersenii, 1 unidentified, possibly new species).

Conclusion
Molecular speciation failed to identify a unique bacterial subset in patients with culture-negative, PCR-positive leptospirosis. The rate of false-negative culture was high, and we speculate that antibiotic pre-treatment is the most likely explanation for this.
Circulating levels of insulin-like growth factor-I (IGF-I) correlate with disease status in leprosy
Authors: Rodrigues Luciana Silva , Hacker Mariana Andrea , Illarramendi Ximena , Castelar Pinheiro Maria Fernanda Miguens , da Costa Nery José Augusto , Sarno Euzenir Nunes , Vidal Pessolani Maria Cristina 
Published: December 2011

AbstractBackgroundCaused byMycobacterium leprae(ML), leprosy presents a strong immune-inflammatory component, whose status dictates both the clinical form of the disease and the occurrence of reactional episodes. Evidence has shown that, during the immune-inflammatory response to infection, the growth hormone/insulin-like growth factor-I (GH/IGF-I) plays a prominent regulatory role. However, in leprosy, little, if anything, is known about the interaction between the immune and neuroendocrine systems.MethodsIn the present retrospective study, we measured the serum levels of IGF-I and IGBP-3, its major binding protein. These measurements were taken at diagnosis in nonreactional borderline tuberculoid (NR BT), borderline lepromatous (NR BL), and lepromatous (NR LL) leprosy patients in addition to healthy controls (HC). LL and BL patients who developed reaction during the course of the disease were also included in the study. The serum levels of IGF-I, IGFBP-3 and tumor necrosis factor-alpha (TNF-α) were evaluated at diagnosis and during development of reversal (RR) or erythema nodosum leprosum (ENL) reaction by the solid phase, enzyme-labeled, chemiluminescent-immunometric method.ResultsThe circulating IGF-I/IGFBP-3 levels showed significant differences according to disease status and occurrence of reactional episodes. At the time of leprosy diagnosis, significantly lower levels of circulating IGF-I/IGFBP-3 were found in NR BL and NR LL patients in contrast to NR BT patients and HCs. However, after treatment, serum IGF-I levels in BL/LL patients returned to normal. Notably, the levels of circulating IGF-I at diagnosis were low in 75% of patients who did not undergo ENL during treatment (NR LL patients) in opposition to the normal levels observed in those who suffered ENL during treatment (R LL patients). Nonetheless, during ENL episodes, the levels observed in RLL sera tended to decrease, attaining similar levels to those found in NR LL patients. Interestingly, IGF-I behaved contrary to what was observed during RR episodes in R BL patients.ConclusionsOur data revealed important alterations in the IGF system in relation to the status of the host immune-inflammatory response to ML while at the same time pointing to the circulating IGF-I/IGFBP-3 levels as possible predictive biomarkers for ENL in LL patients at diagnosis.
Combining M-FISH and Quantum Dot technology for fast chromosomal assignment of transgenic insertions
Authors: Yusuf Mohammed , Bauer David LV , Lipinski Daniel M , MacLaren Robert E , Wade-Martins Richard , Mir Kalim U , Volpi Emanuela V 
Published: December 2011

Abstract

Background
Physical mapping of transgenic insertions by Fluorescence in situ Hybridization (FISH) is a reliable and cost-effective technique. Chromosomal assignment is commonly achieved either by concurrent G-banding or by a multi-color FISH approach consisting of iteratively co-hybridizing the transgenic sequence of interest with one or more chromosome-specific probes at a time, until the location of the transgenic insertion is identified.

Results
Here we report a technical development for fast chromosomal assignment of transgenic insertions at the single cell level in mouse and rat models. This comprises a simplified 'single denaturation mixed hybridization' procedure that combines multi-color karyotyping by Multiplex FISH (M-FISH), for simultaneous and unambiguous identification of all chromosomes at once, and the use of a Quantum Dot (QD) conjugate for the transgene detection.

Conclusions
Although the exploitation of the unique optical properties of QD nanocrystals, such as photo-stability and brightness, to improve FISH performance generally has been previously investigated, to our knowledge this is the first report of a purpose-designed molecular cytogenetic protocol in which the combined use of QDs and standard organic fluorophores is specifically tailored to assist gene transfer technology.
Prescription practices and availability of artemisinin monotherapy in India: where do we stand?
Authors: Mishra Neelima , Anvikar Anupkumar R , Shah Naman K , Kamal Vineet Kumar , Sharma Surya Kant , Srivastava Harish Chandra , Das Manoj Kumar , Pradhan Khageswar , Kumar Hemant , Gupta Yogendra K , Gupta Pooja , Dash Aditya Prasad , Valecha Neena 
Published: December 2011

Abstract

Background
The World Health Organization has urged all member states to deploy artemisinin-based combination therapy and progressively withdraw oral artemisinin monotherapies from the market due to their high recrudescence rates and to reduce the risk of drug resistance. Prescription practices by physicians and the availability of oral artemisinin monotherapies with pharmacists directly affect the pattern of their use. Thus, treatment practices for malaria, with special reference to artemisinin monotherapy prescription, in selected states of India were evaluated.

Methods
Structured, tested questionnaires were used to conduct convenience surveys of physicians and pharmacists in eleven purposively selected districts across six states in 2008. In addition, exit interviews of patients with a diagnosis of uncomplicated malaria or a prescription for an anti-malarial drug were also performed. Logistic regression was used to determine patient clinical care, and institutional factors associated with artemisinin monotherapy prescription.

Results
Five hundred and eleven physicians from 196 health facilities, 530 pharmacists, and 1, 832 patients were interviewed. Artemisinin monotherapy was available in 72.6% of pharmacies and was prescribed by physicians for uncomplicated malaria in all study states. Exit interviews among patients confirmed the high rate of use of artemisinin monotherapy with 14.8% receiving such a prescription. Case management, i.e. method of diagnosis and overall treatment, varied by state and public or private sector. Treatment in the private sector (OR 8.0, 95%CI: 3.8, 17) was the strongest predictor of artemisinin monotherapy prescription when accounting for other factors. Use of the combination therapy recommended by the national drug policy, artesunate + sulphadoxine-pyrimethamine, was minimal (4.9%), with the exception of one state.

Conclusions
Artemisinin monotherapy use was widespread across India in 2008. The accessible sale of oral artemisinin monotherapy in retail market and an inadequate supply of recommended drugs in the public sector health facilities promoted its prescription. This study resulted in notifications to all state drug controllers in India to withdraw the oral artemisinin formulations from the market. In 2010, artesunate + sulphadoxine-pyrimethamine became the universal first-line treatment for confirmed Plasmodium falciparum malaria and was deployed at full scale.
Assessing healthcare providers' knowledge and practices relating to insecticide-treated nets and the prevention of malaria in Ghana, Laos, Senegal and Tanzania
Authors: Hoffman Steven J , Guindon G Emmanuel , Lavis John N , Ndossi Godwin D , Osei Eric JA , Sidibe Mintou Fall , Boupha Boungnong ,   the Research to Policy & Practice Study Team
Published: December 2011

Abstract

Background
Research evidence is not always being disseminated to healthcare providers who need it to inform their clinical practice. This can result in the provision of ineffective services and an inefficient use of resources, the implications of which might be felt particularly acutely in low- and middle-income countries. Malaria prevention is a particularly compelling domain to study evidence/practice gaps given the proven efficacy, cost-effectiveness and disappointing utilization of insecticide-treated nets (ITNs).

Methods
This study compares what is known about ITNs to the related knowledge and practices of healthcare providers in four low- and middle-income countries. A new questionnaire was developed, pilot tested, translated and administered to 497 healthcare providers in Ghana (140), Laos (136), Senegal (100) and Tanzania (121). Ten questions tested participants' knowledge and clinical practice related to malaria prevention. Additional questions addressed their individual characteristics, working context and research-related activities. Ordinal logistic regressions with knowledge and practices as the dependent variable were conducted in addition to descriptive statistics.

Results
The survey achieved a 75% response rate (372/497) across Ghana (107/140), Laos (136/136), Senegal (51/100) and Tanzania (78/121). Few participating healthcare providers correctly answered all five knowledge questions about ITNs (13%) or self-reported performing all five clinical practices according to established evidence (2%). Statistically significant factors associated with higher knowledge within each country included: 1) training in acquiring systematic reviews through the Cochrane Library (OR 2.48, 95% CI 1.30-4.73); and 2) ability to read and write English well or very well (OR 1.69, 95% CI 1.05-2.70). Statistically significant factors associated with better clinical practices within each country include: 1) reading scientific journals from their own country (OR 1.67, 95% CI 1.10-2.54); 2) working with researchers to improve their clinical practice or quality of working life (OR 1.44, 95% CI 1.04-1.98); 3) training on malaria prevention since their last degree (OR 1.68, 95% CI 1.17-2.39); and 4) easy access to the internet (OR 1.52, 95% CI 1.08-2.14).

Conclusions
Improving healthcare providers' knowledge and practices is an untapped opportunity for expanding ITN utilization and preventing malaria. This study points to several strategies that may help bridge the gap between what is known from research evidence and the knowledge and practices of healthcare providers. Training on acquiring systematic reviews and facilitating internet access may be particularly helpful.
Expression of circadian clock gene human Period2 (hPer2) in human colorectal carcinoma
Authors: Wang Yaping , Hua Luchun , Lu Chao , Chen Zongyou 
Published: December 2011

Abstract

Background
Recent studies have shown that disruption of circadian rhythms is one of the tumor promoting factors which contribute to mammalian cancer development and progression, but very little is known about the molecular changes of circadian genes in colorectal carcinoma (CRC). Thus, in this study, changes in the expression of human Period2 (hPer2), one of the key circadian clock regulators, in CRC and its correlation with prognosis were investigated.

Methods
Immunohistochemical (IHC) staining and real-time PCR for hPer2 were performed for 38 CRC cases.

Results
IHC analysis detected positive staining for hPer2 in 81.6% (31/38) of CRC tissues and 97.4% (37/38) of surrounding non-cancerous tissues (P < 0.05). Most colorectal cells in non-cancerous tissues were homogeneously stained. In contrast, in the paired cancerous tissues, a heterogeneous pattern was found with a significant portion of cancer cells displaying negative or weak hPer2 staining. In over 60% cases (24/38), the staining for hPer2 was much stronger in non-cancerous cells than in the paired cancerous cells. Well-differentiated cancer cells are more likely to maintain hPer2 expression than poorly-differentiated ones. Furthermore, associations of decreased hPer2 levels with patients' age, histological grade, TNM stage and expression of nucleus proliferation related antigen: Ki67 were also detected (P < 0.05). Expression of hPer2 did not correlate with that of either p53 or C-erB-2. Similar to hPer2 protein expression, quantitative RT-PCR for hPer2 also showed decreased mRNA expression in CRC.

Conclusion
These results suggest a role for hPer2 in normal colorectal cell function and the potential deregulation of hPer2 expression in the development, invasion, and metastasis of CRC.
Structural evolution of GeMn/Ge superlattices grown by molecular beam epitaxy under different growth conditions
Authors: Wang Ya , Liao Zhiming , Xu Hongyi , Xiu Faxian , Kou Xufeng , Wang Yong , Wang Kang L , Drennan John , Zou Jin 
Published: December 2011

AbstractGeMn/Ge epitaxial 'superlattices' grown by molecular beam epitaxy with different growth conditions have been systematically investigated by transmission electron microscopy. It is revealed that periodic arrays of GeMn nanodots can be formed on Ge and GaAs substrates at low temperature (approximately 70°C) due to the matched lattice constants of Ge (5.656 Å) and GaAs (5.653 Å), while a periodic Ge/GeMn superlattice grown on Si showed disordered GeMn nanodots with a large amount of stacking faults, which can be explained by the fact that Ge and Si have a large lattice mismatch. Moreover, by varying growth conditions, the GeMn/Ge superlattices can be manipulated from having disordered GeMn nanodots to ordered coherent nanodots and then to ordered nanocolumns.PACS: 75.50.Pp; 61.72.-y; 66.30.Pa; 68.37.L.
Selection of recombinant MVA by rescue of the essential D4R gene
Authors: Ricci Patricia S , Schäfer Birgit , Kreil Thomas R , Falkner Falko G , Holzer Georg W 
Published: December 2011

Abstract
Modified vaccinia virus Ankara (MVA) has become a promising vaccine vector due to its immunogenicity and its proven safety in humans. As a general approach for stringent and rapid selection of recombinant MVA, we assessed marker rescue of the essential viral D4R gene in an engineered deletion mutant that is fully replication defective in wild-type cells. Recombinant, replicating virus was obtained by re-introduction of the deleted viral gene as a dominant selection marker into the deletion mutant.
Construction and characterization of an infectious clone of coxsackievirus A16
Authors: Liu Fei , Liu Qingwei , Cai Yicun , Leng Qibin , Huang Zhong 
Published: December 2011

AbstractBackgroundCoxsackievirus A16 (CVA16) is a member of theEnterovirusgenus of thePicornaviridaefamily and it is a major etiological agent of hand, foot, and mouth disease (HFMD), which is a common illness affecting children. CVA16 possesses a single-stranded positive-sense RNA genome containing approximately 7410 bases. Current understanding of the replication, structure and virulence determinants of CVA16 is very limited, partly due to difficulties in directly manipulating its RNA genome.ResultsTwo overlapping cDNA fragments were amplified by RT-PCR from the genome of the shzh05-1 strain of CVA16, encompassing the nucleotide regions 1-4392 and 4381-7410, respectively. These two fragments were then joinedviaa nativeXbaI site to yield a full-length cDNA. A T7 promoter and poly(A) tail were added to the 5' and 3' ends, respectively, forming a full CVA16 cDNA clone. Transfection of RD cellsin vitrowith RNA transcribed directly from the cDNA clone allowed the recovery of infectious virus in culture. The CVA16 virus recovered from these cultures was functionally and genetically identical to its parent strain.ConclusionsWe report the first construction and characterization of an infectious cDNA clone of CVA16. The availability of this infectious clone will greatly enhance future virological investigations and vaccine development for CVA16.
Efficacy of vinblastine in central nervous system Langerhans cell histiocytosis: a nationwide retrospective study
Authors: Ng Wing Tin Sophie , Martin-Duverneuil Nadine , Idbaih Ahmed , Garel Catherine , Ribeiro Maria , Parker Judith Landman , Defachelles Anne-Sophie , Lambilliotte Anne , Barkaoui Mohamed , Munzer Martine , Gardembas Martine , Sibilia Jean , Lutz Patrick , Fior Renato , Polak Michel , Robert Alain , Aumaitre Olivier , Plantaz Dominique , Armari-Alla Corinne , Genereau Thierry , Berard Perrine Marec , Talom Ghislain Nokam , Pennaforte Jean-Loup , Le Pointe Hubert Ducou , Barthez Marie-Anne , Couillault Gérard , Haroche Julien , Mokhtari Karima , Donadieu Jean , Hoang-Xuan Khê ,   the French LCH study group
Published: December 2011

Abstract

Background
Vinblastine (VBL) is the standard treatment for systemic Langerhans cell histiocytosis (LCH), but little is known about its efficacy in central nervous system (CNS) mass lesions.

Methods
A retrospective chart review was conducted. Twenty patients from the French LCH Study Group register met the inclusion criteria. In brief, they had CNS mass lesions, had been treated with VBL, and were evaluable for radiologic response.

Results
The median age at diagnosis of LCH was 11.5 years (range: 1-50). Intravenous VBL 6 mg/m2 was given in a 6-week induction treatment, followed by a maintenance treatment. The median total duration was 12 months (range: 3-30). Eleven patients received steroids concomitantly. Fifteen patients achieved an objective response; five had a complete response (CR: 25%), ten had a partial response (PR: 50%), four had stable disease (SD: 20%) and one patient progressed (PD: 5%). Of interest, four out of the six patients who received VBL without concomitant steroids achieved an objective response. With a median follow-up of 6.8 years, the 5-year event-free and overall survival was 61% and 84%, respectively. VBL was well-tolerated and there were no patient withdrawals due to adverse events.

Conclusion
VBL, with or without steroids, could potentially be a useful therapeutic option in LCH with CNS mass lesions, especially for those with inoperable lesions or multiple lesions. Prospective clinical trials are warranted for the evaluation of VBL in this indication.