bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct evidence of the importance of vitronectin and its interaction with the urokinase receptor in tumor growth
Authors: Pirazzoli Valentina , Ferraris Gian Maria Sarra , Sidenius Nicolai 
Published: January 2013

Key PointsWe demonstrate that vitronectin plays an important role in tumor growth. We show that the urokinase receptor can promote tumor growth through its interaction with vitronectin.
The Rac GTPase effector p21-activated kinase is essential for hematopoietic stem/progenitor cell migration and engraftment
Authors: Dorrance Adrienne M. , De Vita Serena , Radu Maria , Reddy Pavankumar N. G. , McGuinness Meaghan K. , Harris Chad E. , Mathieu Ronald , Lane Steven W. , Kosoff Rachelle , Milsom Michael D. , Chernoff Jonathan , Williams David A. 
Published: January 2013

Key Points
The Rac effector p21-activated kinase (Pak) regulates hematopoietic engraftment. Pak integrates cytoskeletal changes and proliferation pathways.
Identification of Dirofilaria immitis miRNA using illumina deep sequencing
Authors: Fu Yan , Lan Jingchao , Wu Xuhang , Yang Deying , Zhang Zhihe , Nie Huaming , Hou Rong , Zhang Runhui , Zheng Wanpeng , Xie Yue , Yan Ning , Yang Zhi , Wang Chengdong , Luo Li , Liu Li , Gu Xiaobin , Wang Shuxian , Peng Xuerong , Yang Guangyou 
Published: January 2013

AbstractThe heartwormDirofilaria immitisis the causative agent of cardiopulmonary dirofilariosis in dogs and cats, which also infects a wide range of wild mammals and humans. The complex life cycle ofD. immitiswith several developmental stages in its invertebrate mosquito vectors and its vertebrate hosts indicates the importance of miRNA in growth and development, and their ability to regulate infection of mammalian hosts. This study identified the miRNA profiles ofD. immitisof zoonotic significance by deep sequencing. A total of 1063 conserved miRNA candidates, including 68 anti-sense miRNA (miRNA*) sequences, were predicted by computational methods and could be grouped into 808 miRNA families. A significant bias towards family members, family abundance and sequence nucleotides was observed. Thirteen novel miRNA candidates were predicted by alignment with theBrugia malayigenome. Eleven out of 13 predicted miRNA candidates were verified by using a PCR-based method. Target genes of the novel miRNA candidates were predicted by using the heartworm transcriptome dataset. To our knowledge, this is the first report of miRNA profiles inD. immitis, which will contribute to a better understanding of the complex biology of this zoonotic filarial nematode and the molecular regulation roles of miRNA involved. Our findings may also become a useful resource for small RNA studies in other filarial parasitic nematodes.
Development and validation of microsatellite markers for Brachiaria ruziziensisobtained by partial genome assembly of Illumina single-end reads
Authors: Silva Pedro IT , Martins Alexandre M , Gouvea Ediene G , Pessoa-Filho Marco , Ferreira Márcio E 
Published: January 2013

Abstract

Background

Brachiaria ruziziensis is one of the most important forage species planted in the tropics. The application of genomic tools to aid the selection of superior genotypes can provide support to B. ruziziensis breeding programs. However, there is a complete lack of information about the B. ruziziensis genome. Also, the availability of genomic tools, such as molecular markers, to support B. ruziziensis breeding programs is rather limited. Recently, next-generation sequencing technologies have been applied to generate sequence data for the identification of microsatellite regions and primer design. In this study, we present a first validated set of SSR markers for Brachiaria ruziziensis, selected from a de novo partial genome assembly of single-end Illumina reads.

Results
A total of 85,567 perfect microsatellite loci were detected in contigs with a minimum 10X coverage. We selected a set of 500 microsatellite loci identified in contigs with minimum 100X coverage for primer design and synthesis, and tested a subset of 269 primer pairs, 198 of which were polymorphic on 11 representative B. ruziziensis accessions. Descriptive statistics for these primer pairs are presented, as well as estimates of marker transferability to other relevant brachiaria species. Finally, a set of 11 multiplex panels containing the 30 most informative markers was validated and proposed for B. ruziziensis genetic analysis.

Conclusions
We show that the detection and development of microsatellite markers from genome assembled Illumina single-end DNA sequences is highly efficient. The developed markers are readily suitable for genetic analysis and marker assisted selection of Brachiaria ruziziensis. The use of this approach for microsatellite marker development is promising for species with limited genomic information, whose breeding programs would benefit from the use of genomic tools. To our knowledge, this is the first set of microsatellite markers developed for this important species.
Identification and profiling of conserved and novel microRNAs from Chinese Qinchuan bovine longissimus thoracis
Authors: Sun Jiajie , Li Mijie , Li Zhuanjian , Xue Jing , Lan Xianyong , Zhang Chunlei , Lei Chuzhao , Chen Hong 
Published: January 2013

Abstract

Background
MicroRNAs (miRNAs) are a family of ~22 nucleotide small RNA molecules that regulate gene expression by fully or partially binding to their complementary sequences. Recently, a large number of miRNAs and their expression patterns have been identified in various species. However, to date no miRNAs have been reported to modulate muscle development in beef cattle.

Results
Total RNAs from the Chinese Qinchuan bovine longissimus thoracis at fetal and adult stages were used to construct small RNA libraries for Solexa SBS technology sequencing. A total of 15,454,182 clean reads were obtained from the fetal bovine library and 13,558,164 clean reads from the adult bovine library. In total, 521 miRNAs including 104 novel miRNA candidates were identified. Furthermore, the nucleotide bias, base edit and family of the known miRNAs were also analyzed. Based on stem-loop qPCR, 25 high-read miRNAs were detected, and the results showed that bta-miRNA-206, miRNA-1, miRNA-133, miRNAn12, and miRNAn17 were highly expressed in muscle-related tissue or organs, suggesting that these miRNAs may play a role in the development of bovine muscle tissues.

Conclusions
This study confirmed the authenticity of 417 known miRNAs, discovered 104 novel miRNAs in bos taurus, and identified five muscle-specific miRNAs. The identification of novel miRNAs significantly expanded the repertoire of bovine miRNAs and could contribute to further studies on the muscle development of cattle.
A qualitative exploration of Malaysian cancer patients’ perceptions of cancer screening
Authors: Farooqui Maryam , Hassali Mohamed Azmi , Knight Aishah , Shafie Asrul Akmal , Farooqui Muhammad Aslam , Saleem Fahad , Haq Noman-ul , Aljadhey Hisham 
Published: January 2013

Abstract

Background
Despite the existence of different screening methods, the response to cancer screening is poor among Malaysians. The current study aims to examine cancer patients’ perceptions of cancer screening and early diagnosis.

Methods
A qualitative methodology was used to collect in-depth information from cancer patients. After obtaining institutional ethical approval, patients with different types and stages of cancer from the three major ethnic groups (Malay, Chinese and Indian) were approached. Twenty semi-structured interviews were conducted. All interviews were audiotaped, transcribed verbatim, and translated into English for thematic content analysis.

Results
Thematic content analysis yielded four major themes: awareness of cancer screening, perceived benefits of cancer screening, perceived barriers to cancer screening, and cues to action. The majority of respondents had never heard of cancer screening before their diagnosis. Some participants reported hearing about mammogram and Pap smear tests but did not undergo screening due to a lack of belief in personal susceptibility. Those who had negative results from screening prior to diagnosis perceived such tests as untrustworthy. Lack of knowledge and financial constraints were reported as barriers to cancer screening. Finally, numerous suggestions were given to improve screening behaviour among healthy individuals, including the role of mass media in disseminating the message ‘prevention is better than cure’.

Conclusions
Patients’ narratives revealed some significant issues that were in line with the Health Belief Model which could explain negative health behaviour. The description of the personal experiences of people with cancer could provide many cues to action for those who have never encountered this potentially deadly disease, if incorporated into health promotion activities.
Prevalence and risk factors of hepatitis B and C virus infections among the general population and blood donors in Morocco
Authors: Baha Warda , Foullous Abderrahim , Dersi Noureddine , They-they Thierry Paluku , alaoui Khadija El , Nourichafi Nadia , Oukkache Bouchra , Lazar Fatiha , Benjelloun Soumaya , Ennaji My Mustapha , Elmalki Abdelouhad , Mifdal Hassan , Bennani Abdelouaheb 
Published: January 2013

AbstractBackgroundViral hepatitis is a serious public health problem affecting billions of people globally. Limited information is available on this issue in Morocco. This cross-sectional study was undertaken with the aim of determining the seroprevalence and risk factors of hepatitis B virus (HBV) and hepatitis C virus (HCV) among the general population and among blood donors.MethodsBlood samples from volunteers, have been screened with ELISA tests for detecting the hepatitis-B surface antigen (HBsAg) and anti-HCV. Within the seroreactive patients for HCV in the general population, RT-PCR was performed by the Cobas Ampliprep/Cobas Amplicor.ResultsHCV and HBV-seropositivity was documented in 1.58% and 1.81% out of 41269 and 23578 participants respectively from the general population. Two patients were found to be co-infected. HCV-RNA was detected by PCR in 70.9% of the 195 anti-HCV positive subjects. The anti-HCV prevalence was not different among males and females (P = 0.3). It increased with age; the highest prevalence was observed among subjects with >50 years old (3.12%). Various risk factors for acquiring HCV infection were identified; age, dental treatment, use of glass syringes and surgical history. In addition to these factors, gender and sexual risk behaviors were found to be associated with higher prevalence of hepatitis B. The HBV positivity was significantly higher among males than females participants in all age groups (P < 0.01). The peak was noticed among males aged 30–49 years (2.4%). None of the 152 persons younger than 20 years had HBsAg or anti-HCV. The prevalence of anti-HCV and HBsAg among 169605 blood donors was 0.62% and 0.96% respectively.ConclusionsOur study provided much important information concerning hepatitis B and C prevalence and risk factors; it confirmed the intermediate endemicity for HCV infection and pointed to a decreasing trend of HBV incidence, which might reclassify Morocco in low HBV endemicity area. This could be attributed primarily to the universal HBV vaccination among infants and healthcare workers over the past 13 years. HCV and HBV infections in the present survey were mainly associated with nosocomial exposures. Prevention and control of HBV infection are needed to reduce HBV transmission between adults.
Illness perceptions in patients receiving rheumatology rehabilitation: association with health and outcomes at 12 months
Authors: Løchting Ida , Fjerstad Elin , Garratt Andrew M 
Published: January 2013

Abstract

Background
Illness perceptions have been found to change over time and following health care. Hence, addressing illness perceptions alongside existing health care interventions may be important for the sustainment of health gains following rehabilitation. The aim of this study was to measure the illness perceptions of patients receiving inpatient rheumatology rehabilitation and assess the association with aspects of health and outcomes at baseline, discharge and 12 months.

Methods
Patients with a rehabilitation stay of one week or more at three institutions in Norway in 2009 were invited to participate in the study. At baseline, discharge and 12 months, patients completed The Rheumatic Disease Illness Perception Questionnaire (RD-IPQ) which includes aspects of illness perceptions important to patients with rheumatic diseases. Stepwise regression analysis was used to assess associations between RD-IPQ scores and different aspects of health at baseline and follow-up after controlling for other aspects of health and sociodemographic variables.

Results
For the 134 patients included in the study, baseline RD-IPQ scores had a mean of 58.2 (SD 14.9) on a 0–100 scale, where 100 is the worst possible. Scores showed improvement after the rehabilitation stay which were maintained at 12 months. RD-IPQ scores were positively associated with health and outcomes. At baseline RD-IPQ scores were statistically significant in explaining variation in pain, physical function and SF-36 mental health scores. Baseline RD-IPQ scores were significant in explaining fatigue, pain, SF-36 role limitations and social function scores following rehabilitation and at 12 months.

Conclusion
Illness perceptions as measured by the RD-IPQ were associated with health and outcomes as measured by rheumatology-specific and generic instruments. The consideration of illness perceptions as a component of rehabilitation may be important in achieving desired outcomes.
POU1F1 is a novel fusion partner of NUP98 in acute myeloid leukemia with t(3;11)(p11;p15)
Authors: Lisboa Susana , Cerveira Nuno , Bizarro Susana , Correia Cecília , Vieira Joana , Torres Lurdes , Mariz José M , Teixeira Manuel R 
Published: January 2013

Abstract

Background

NUP98 gene rearrangements have been reported in acute myeloid leukemia, giving rise to fusion proteins that seem to function as aberrant transcription factors, and are thought to be associated with poor prognosis.

Findings
A patient with treatment-related acute myeloid leukemia presented a t(3;11)(p11;p15) as the only cytogenetic abnormality. FISH and molecular genetic analyses identified a class 1 homeobox gene, POU1F1, located on chromosome 3p11, as the fusion partner of NUP98. In addition, we have found that the patient harbored an FLT3-ITD mutation, which most likely collaborated with the NUP98-POU1F1 fusion gene in malignant transformation.

Conclusions
We have identified POU1F1 as the NUP98 fusion partner in therapy-related AML with a t(3;11)(p11;p15). This is the first POU family member identified as a fusion partner in human cancer.
Deep transcriptome-sequencing and proteome analysis of the hydrothermal vent annelid Alvinella pompejana identifies the CvP-bias as a robust measure of eukaryotic thermostability
Authors: Holder Thomas , Basquin Claire , Ebert Judith , Randel Nadine , Jollivet Didier , Conti Elena , Jékely Gáspár , Bono Fulvia 
Published: January 2013

Abstract

Background

Alvinella pompejana is an annelid worm that inhabits deep-sea hydrothermal vent sites in the Pacific Ocean. Living at a depth of approximately 2500 meters, these worms experience extreme environmental conditions, including high temperature and pressure as well as high levels of sulfide and heavy metals. A. pompejana is one of the most thermotolerant metazoans, making this animal a subject of great interest for studies of eukaryotic thermoadaptation.

Results
In order to complement existing EST resources we performed deep sequencing of the A. pompejana transcriptome. We identified several thousand novel protein-coding transcripts, nearly doubling the sequence data for this annelid. We then performed an extensive survey of previously established prokaryotic thermoadaptation measures to search for global signals of thermoadaptation in A. pompejana in comparison with mesophilic eukaryotes. In an orthologous set of 457 proteins, we found that the best indicator of thermoadaptation was the difference in frequency of charged versus polar residues (CvP-bias), which was highest in A. pompejana. CvP-bias robustly distinguished prokaryotic thermophiles from prokaryotic mesophiles, as well as the thermophilic fungus Chaetomium thermophilum from mesophilic eukaryotes. Experimental values for thermophilic proteins supported higher CvP-bias as a measure of thermal stability when compared to their mesophilic orthologs. Proteome-wide mean CvP-bias also correlated with the body temperatures of homeothermic birds and mammals.

Conclusions
Our work extends the transcriptome resources for A. pompejana and identifies the CvP-bias as a robust and widely applicable measure of eukaryotic thermoadaptation.

Reviewer
This article was reviewed by Sándor Pongor, L. Aravind and Anthony M. Poole.
C-reactive protein, haptoglobin, serum amyloid A and pig major acute phase protein response in pigs simultaneously infected with H1N1 swine influenza virus and Pasteurella multocida
Authors: Pomorska-Mól Małgorzata , Markowska-Daniel Iwona , Kwit Krzysztof , Stępniewska Katarzyna , Pejsak Zygmunt 
Published: January 2013

Abstract

Background
Swine influenza (SI) is an acute respiratory disease caused by swine influenza virus (SIV). Swine influenza is generally characterized by acute onset of fever and respiratory symptoms. The most frequent complications of influenza are secondary bacterial pneumonia. The objective of this work was to study the acute phase proteins (APP) responses after coinfection of piglets with H1N1 swine influenza virus (SwH1N1) and Pasteurella multocida (Pm) in order to identify whether the individual APP response correlate with disease severity and whether APP could be used as markers of the health status of coinfected pigs.

Results
In all coinfected pigs clinical sings, including fever, coughing and dyspnea, were seen. Viral shedding was observed from 2 to 7 dpi. The mean level of antibodies against Pm dermonecrotoxin in infected piglets increase significantly from 7 dpi. Anti-SwH1N1 antibodies in the serum were detected from 7 dpi. The concentration of C-reactive protein (CRP) increased significantly at 1 dpi as compared to control pigs, and remained significantly higher to 3 dpi. Level of serum amyloid A (SAA) was significantly higher from 2 to 3 dpi. Haptoglobin (Hp) was significantly elevated from 3 dpi to the end of study, while pig major acute phase protein (Pig-MAP) from 3 to 7 dpi. The concentrations of CRP, Hp and SAA significantly increased before specific antibodies were detected. Positive correlations were found between serum concentration of Hp and SAA and lung scores, and between clinical score and concentrations of Pig-MAP and SAA.

Conclusions
The results of current study confirmed that monitoring of APP may revealed ongoing infection, and in this way may be useful in selecting clinically healthy pigs (i.e. before integration into an uninfected herd). Present results corroborated our previous findings that SAA could be a potentially useful indicator in experimental infection studies (e.g. vaccine efficiency investigations) or as a marker for disease severity, because of correlation observed between its concentration in serum and disease severity (lung scores, clinical scores).
SignaLink 2 – a signaling pathway resource with multi-layered regulatory networks
Authors: Fazekas Dávid , Koltai Mihály , Türei Dénes , Módos Dezső , Pálfy Máté , Dúl Zoltán , Zsákai Lilian , Szalay-Bekő Máté , Lenti Katalin , Farkas Illés J , Vellai Tibor , Csermely Péter , Korcsmáros Tamás 
Published: January 2013

Abstract

Background
Signaling networks in eukaryotes are made up of upstream and downstream subnetworks. The upstream subnetwork contains the intertwined network of signaling pathways, while the downstream regulatory part contains transcription factors and their binding sites on the DNA as well as microRNAs and their mRNA targets. Currently, most signaling and regulatory databases contain only a subsection of this network, making comprehensive analyses highly time-consuming and dependent on specific data handling expertise. The need for detailed mapping of signaling systems is also supported by the fact that several drug development failures were caused by undiscovered cross-talk or regulatory effects of drug targets. We previously created a uniformly curated signaling pathway resource, SignaLink, to facilitate the analysis of pathway cross-talks. Here, we present SignaLink 2, which significantly extends the coverage and applications of its predecessor.

Description
We developed a novel concept to integrate and utilize different subsections (i.e., layers) of the signaling network. The multi-layered (onion-like) database structure is made up of signaling pathways, their pathway regulators (e.g., scaffold and endocytotic proteins) and modifier enzymes (e.g., phosphatases, ubiquitin ligases), as well as transcriptional and post-transcriptional regulators of all of these components. The user-friendly website allows the interactive exploration of how each signaling protein is regulated. The customizable download page enables the analysis of any user-specified part of the signaling network. Compared to other signaling resources, distinctive features of SignaLink 2 are the following: 1) it involves experimental data not only from humans but from two invertebrate model organisms, C. elegans and D. melanogaster; 2) combines manual curation with large-scale datasets; 3) provides confidence scores for each interaction; 4) operates a customizable download page with multiple file formats (e.g., BioPAX, Cytoscape, SBML). Non-profit users can access SignaLink 2 free of charge at http://SignaLink.org.

Conclusions
With SignaLink 2 as a single resource, users can effectively analyze signaling pathways, scaffold proteins, modifier enzymes, transcription factors and miRNAs that are important in the regulation of signaling processes. This integrated resource allows the systems-level examination of how cross-talks and signaling flow are regulated, as well as provide data for cross-species comparisons and drug discovery analyses.
Topical tacrolimus 0.1% ointment for treatment of cutaneous Crohn’s Disease
Authors: Rice Shantini A , Woo Pick N , El-Omar Emad , Keenan Ronald A , Ormerod Anthony D 
Published: January 2013

Abstract

Background
Cutaneous Crohn’s Disease is a notoriously difficult condition to treat and causes significant morbidity, impacting heavily on quality of life. This is the first study in adults examining the effect of topical tacrolimus on the different cutaneous manifestations of Crohn’s Disease.

Methods
This open label observational study of 20 patients with heterogeneous forms of cutaneous Crohn’s disease used topical tacrolimus 0.1% ointment once daily to affected areas for 12 weeks with a maximal total dose of 90g. Therapy was stopped at 12 weeks to assess whether the condition relapsed. Thereafter relapsing patients optionally continued an open label extension of topical tacrolimus therapy and were observed for a total of 12 months.

Results
Of seventeen patients completing the twelve-week study, fifteen improved using a specifically designed physicians’ global severity scale. One patient cleared, four showed a pronounced improvement (51-75%) and ten demonstrated a mild (1-25%) or moderate improvement (25-50%) in twelve weeks. Over twelve months eleven patients remained in the study, nine of which improved, one cleared and one showed no change. Perineal disease responded better with two out of twelve clearing, four showing pronounced benefit and four mild to moderate improvement. Long-term application of 0.1% tacrolimus applied to broken skin and mucosa was safe and serum levels of tacrolimus were undetectable in all subjects throughout the study.

Conclusion
0.1% tacrolimus ointment was safe and effective in treating cutaneous manifestations of Crohn’s disease, particularly perineal disease and pyoderma gangrenosum, yet it seldom cleared the condition.

Clinical trial registration
ClinicalTrials.gov Protocol Registration System ID: 33000332