bluuebunny/crossref_metadata_2025_split huggingface dataset:
Au-delà des « groupes vulnérables »: contextes et dynamique de la vulnérabilité
Authors: Zarowsky Christina , Haddad Slim , Nguyen Vinh-Kim 
Published: April 2013

Résumé Cet article examine des approches de la vulnérabilité en santé publique et introduit une série de 10 articles qui abordent la vulnérabilité en santé en Afrique. Nous comprenons la vulnérabilité comme étant simultanément un état et un processus. Les inégalités sociales sont évidentes dans la vulnérabilité et en accentuent trois dimensions essentielles : le niveau initial de bien-être, le degré d’exposition au risque et la capacité à gérer le risque de façon efficace. Nous mettons un accent particulier sur les interactions dynamiques qui relient le manque matériel et social, la pauvreté, l’impuissance et la mauvaise santé : les risques, ou les chocs, et leurs impacts sur la santé sont intimement connectés entre eux et se renforcent l’un l’autre dans un cycle qui, en l’absence d’interventions efficaces, accroît la vulnérabilité. Un processus inductif qui ne commence pas par une définition ou une mesure a priori de la « vulnérabilité » et qui ne présume pas de l’existence de « groupes vulnérables » définis nous a permis à la fois de réaffirmer les aspects essentiels des cadres de référence conceptuels existants, et de nous engager dans de nouvelles voies avec une littérature abordant spécifiquement la vulnérabilité et la résilience au niveau de la population, de même qu’avec une littérature – par exemple en écologie, ainsi que sur le concept de fragilité dans la recherche sur le vieillissement – à laquelle les chercheurs du domaine de la santé et de la pauvreté en Afrique ne sont peut-être pas habitués. Nous encourageons le travail conceptuel et empirique sur la vulnérabilité dans des cadres systémiques complexes. Ces perspectives privilégient les contextes et la causalité non linéaire, soutenant ainsi les analyses sur la vulnérabilité et la résilience comme étant toutes deux des marqueurs et des propriétés émergentes d’interactions dynamiques. Nous acceptons une définition fonctionnelle de la vulnérabilité et nous reconnaissons que certains groupes définissables de personnes sont plus susceptibles que d’autres de subir des dommages du fait de leur exposition à des risques en matière de santé. Mais nous suggérons que le vrai travail – tant au niveau intellectuel qu’au niveau politique – réside dans la compréhension et la réponse apportée à la dynamique, à la signification et aux relations de pouvoir qui sous-tendent les cas et les processus réels de vulnérabilité et de dommages.
Agreement in Arthroscopic and Arthrotomy Assessment of Full-Thickness Articular Cartilage Lesions of the Knee in a Clinical Setting in 33 Consecutive Patients
Authors: Årøen Asbjørn , Røtterud Jan Harald , Sivertsen Einar Andreas 
Published: April 2013

Objective To evaluate the accuracy of arthroscopic measurement of full-thickness (International Cartilage Repair Society grades 3-4) cartilage lesions of the knee. Design In 33 consecutive arthroscopically evaluated cartilage lesion knees the lesion size was routinely estimated. At the final treatment, a knee arthrotomy was performed, and the lesion was reestimated. The 2 estimates were then compared by paired t test and the area estimated by knee arthrotomy was used as the gold standard. Results. The mean area of the cartilage lesion estimated by arthroscopic surgery was 3.5 cm2 (standard deviation [SD] = 1.7) whereas in the open surgery the mean area was 3.2 cm2 (SD = 1.5). The mean difference was 0.3 cm2, indicating a tendency toward overestimation by the arthroscopic evaluation, but the difference was not significant ( P = 0.09). Additional MRI assessment of the area demonstrated a mean area of 2.3 cm2 (SD = 1.6). This underestimated the size of the lesion by 1.2 cm2 (SD = 0.8; P = 0.015). Conclusion Knee arthroscopic examination estimated a cartilage full-thickness lesion with an error of less than 25 % in the majority of the patients.
The shortest isoform of C/EBPβ, liver inhibitory protein (LIP), collaborates with Evi1 to induce AML in a mouse BMT model
Authors: Watanabe-Okochi Naoko , Yoshimi Akihide , Sato Tomohiko , Ikeda Toshiyuki , Kumano Keiki , Taoka Kazuki , Satoh Yumiko , Shinohara Akihito , Tsuruta Takako , Masuda Akiko , Yokota Hiromitsu , Yatomi Yutaka , Takahashi Koki , Kitaura Jiro , Kitamura Toshio , Kurokawa Mineo 
Published: April 2013

Key PointsThe shortest isoform of C/EBPβ, liver inhibitory protein (LIP), collaborates with Evi1 in leukemogenesis.
C/EBPα is required for development of dendritic cell progenitors
Authors: Welner Robert S. , Bararia Deepak , Amabile Giovanni , Czibere Akos , Benoukraf Touati , Bach Christian , Wansa K. Disnika Senali Abayratna , Ye Min , Zhang Hong , Iino Tadafumi , Hetherington Christopher J. , Akashi Koichi , Tenen Daniel G. 
Published: April 2013

Key PointsC/EBPα is needed for transition from stem/progenitor cells to common dendritic cell progenitors. C/EBPα is dispensable in later stages of dendritic cell maturation.
CD44 regulates the apoptotic response and promotes disease development in chronic lymphocytic leukemia
Authors: Fedorchenko Oleg , Stiefelhagen Marius , Peer-Zada Abdul A. , Barthel Romy , Mayer Petra , Eckei Laura , Breuer Alexandra , Crispatzu Giuliano , Rosen Natascha , Landwehr Thomas , Lilienthal Nils , Möllmann Michael , Montesinos-Rongen Manuel , Heukamp Lukas , Dürig Jan , Hallek Michael , Fingerle-Rowson Günter , Herling Marco 
Published: April 2013

Key PointsCD44 expression in CLL is micromilieu instructed and promotes leukemic cell survival, which can be antagonized by CD44 antibodies. As a surface coreceptor, CD44 supports leukemogenesis by modulating stimuli of MCL1 expression (eg, B-cell receptor signals).
Species and condition specific adaptation of the transcriptional landscapes in Candida albicans and Candida dubliniensis
Authors: Grumaz Christian , Lorenz Stefan , Stevens Philip , Lindemann Elena , Schöck Ulrike , Retey Julia , Rupp Steffen , Sohn Kai 
Published: April 2013

Abstract

Background
Although Candida albicans and Candida dubliniensis are most closely related, both species behave significantly different with respect to morphogenesis and virulence. In order to gain further insight into the divergent routes for morphogenetic adaptation in both species, we investigated qualitative along with quantitative differences in the transcriptomes of both organisms by cDNA deep sequencing.

Results
Following genome-associated assembly of sequence reads we were able to generate experimentally verified databases containing 6016 and 5972 genes for C. albicans and C. dubliniensis, respectively. About 95% of the transcriptionally active regions (TARs) contain open reading frames while the remaining TARs most likely represent non-coding RNAs. Comparison of our annotations with publically available gene models for C. albicans and C. dubliniensis confirmed approximately 95% of already predicted genes, but also revealed so far unknown novel TARs in both species. Qualitative cross-species analysis of these databases revealed in addition to 5802 orthologs also 399 and 49 species-specific protein coding genes for C. albicans and C. dubliniensis, respectively. Furthermore, quantitative transcriptional profiling using RNA-Seq revealed significant differences in the expression of orthologs across both species. We defined a core subset of 84 hyphal-specific genes required for both species, as well as a set of 42 genes that seem to be specifically induced during hyphal morphogenesis in C. albicans.

Conclusions
Species-specific adaptation in C. albicans and C. dubliniensis is governed by individual genetic repertoires but also by altered regulation of conserved orthologs on the transcriptional level.
Identification of molecular processes needed for vascular formation through transcriptome analysis of different vascular systems
Authors: Xu Peng , Kong Yimeng , Li Xuan , Li Laigeng 
Published: April 2013

Abstract

Background
Vascular system formation has been studied through molecular and genetic approaches in Arabidopsis, a herbaceous dicot that is used as a model system. Different vascular systems have developed in other plants such as crops and trees. Uncovering shared mechanisms underlying vascular development by transcriptome analysis of different vascular systems may help to transfer knowledge acquired from Arabidopsis to other economically important species.

Results
Conserved vascular genes and biological processes fundamental to vascular development were explored across various plants. Through comparative transcriptome analysis, 226 genes from Arabidopsis, 217 genes from poplar and 281 genes from rice were identified as constituting 107 conserved vascular gene groups. These gene groups are expressed mainly in vascular tissues and form a complex coexpression network with multiple functional connections. To date, only half of the groups have been experimentally investigated. The conserved vascular gene groups were classified into 9 essential processes for vascular development. 18 groups (17%) lack of annotations were classified as having unknown functions.

Conclusion
The study provides a map of fundamental biological processes conserved across different vascular systems. It identifies gaps in the experimental investigation of pathways active in vascular formation, which if explored, could lead to a more complete understanding of vascular development.
Energy status of ripening and postharvest senescent fruit of litchi (Litchi chinensis Sonn.)
Authors: Wang Hui , Qian Zhengjiang , Ma Sanmei , Zhou Yuchuan , Patrick John W , Duan Xuewu , Jiang Yueming , Qu Hongxia 
Published: April 2013

Abstract

Background
Recent studies have demonstrated that cellular energy is a key factor switching on ripening and senescence of fruit. However, the factors that influence fruit energy status remain largely unknown.

Results
HPLC profiling showed that ATP abundance increased significantly in developing preharvest litchi fruit and was strongly correlated with fruit fresh weight. In contrast, ATP levels declined significantly during postharvest fruit senescence and were correlated with the decrease in the proportion of edible fruit. The five gene transcripts isolated from the litchi fruit pericarp were highly expressed in vegetative tissues and peaked at 70 days after flowering (DAF) consistent with fruit ADP concentrations, except for uncoupling mitochondrial protein 1 (UCP1), which was predominantly expressed in the root, and ATP synthase beta subunit (AtpB), which was up-regulated significantly before harvest and peaked 2 days after storage. These results indicated that the color-breaker stage at 70 DAF and 2 days after storage may be key turning points in fruit energy metabolism. Transcript abundance of alternative oxidase 1 (AOX1) increased after 2 days of storage to significantly higher levels than those of LcAtpB, and was down-regulated significantly by exogenous ATP. ATP supplementation had no significant effect on transcript abundance of ADP/ATP carrier 1 (AAC1) and slowed the changes in sucrose non-fermenting-1-related kinase 2 (SnRK2) expression, but maintained ATP and energy charge levels, which were correlated with delayed senescence.

Conclusions
Our results suggest that senescence of litchi fruit is closely related with energy. A surge of LcAtpB expression marked the beginning of fruit senescence. The findings may provide a new strategy to extend fruit shelf life by regulating its energy level.
Hemodialysis and hemodiafiltration differently modulate left ventricular diastolic function
Authors: Czifra Árpád , Páll Alida , Kulcsár Julianna , Barta Kitti , Kertész Attila , Paragh György , Lőrincz István , Jenei Zoltán , Agarwal Anupam , Zarjou Abolfazl , Balla József , Szabó Zoltán 
Published: April 2013

Abstract

Background
Renal replacement therapy may have a favorable effect on diastolic left ventricular function, but it is not clear whether hemodiafiltration is superior to hemodialysis in this field. Nitric oxide (NO) and asymmetric dimethylarginine (ADMA) may play a role in the changes of intracardiac hemodynamics, but it is not clear whether the different renal replacement methods have disparate influence on the metabolism of these materials.

Methods
Thirty patients on renal replacement therapy were investigated. First, data was analyzed while patients received hemodiafiltration over a period of three months. Then, the same patients were evaluated during treatment with hemodialysis for at least another three months. Echocardiography was performed before and after renal replacement therapy.

Results
No significant difference was found in the volume removals between hemodialysis and hemodiafiltration. The left atrial diameter and transmitral flow velocities (E/A) decreased significantly only during hemodiafiltration. A positive correlation was observed between the left atrial diameter and E/Ea representing the left ventricular pressure load during hemodiafiltration. Significant correlations between NO and A and E/A were observed only in the case of hemodiafiltration.

Conclusion
Hemodiafiltration has a beneficial effect on echocardiographic markers representing left ventricular diastolic function. This could be attributed to the differences between the dynamics of volume removal and its distribution among liquid compartments.
The Wnt signalling pathway is upregulated in an in vitro model of acquired tamoxifen resistant breast cancer
Authors: Loh Yan Ni , Hedditch Ellen L , Baker Laura A , Jary Eve , Ward Robyn L , Ford Caroline E 
Published: April 2013

Abstract

Background
Acquired resistance to Tamoxifen remains a critical problem in breast cancer patient treatment, yet the underlying causes of resistance have not been fully elucidated. Abberations in the Wnt signalling pathway have been linked to many human cancers, including breast cancer, and appear to be associated with more metastatic and aggressive types of cancer. Here, our aim was to investigate if this key pathway was involved in acquired Tamoxifen resistance, and could be targeted therapeutically.

Methods
An in vitro model of acquired Tamoxifen resistance (named TamR) was generated by growing the estrogen receptor alpha (ER) positive MCF7 breast cancer cell line in increasing concentrations of Tamoxifen (up to 5 uM). Alterations in the Wnt signalling pathway and epithelial to mesenchymal transition (EMT) in response to Tamoxifen and treatment with the Wnt inhibitor, IWP-2 were measured via quantitative RT-PCR (qPCR) and TOP/FOP Wnt reporter assays. Resistance to Tamoxifen, and effects of IWP-2 treatment were determined by MTT proliferation assays.

Results
TamR cells exhibited increased Wnt signalling as measured via the TOP/FOP Wnt luciferase reporter assays. Genes associated with both the β-catenin dependent (AXIN2, MYC, CSNK1A1) and independent arms (ROR2, JUN), as well as general Wnt secretion (PORCN) of the Wnt signalling pathway were upregulated in the TamR cells compared to the parental MCF7 cell line. Treatment of the TamR cell line with human recombinant Wnt3a (rWnt3a) further increased the resistance of both MCF7 and TamR cells to the anti-proliferative effects of Tamoxifen treatment. TamR cells demonstrated increased expression of EMT markers (VIM, TWIST1, SNAI2) and decreased CDH1, which may contribute to their resistance to Tamoxifen. Treatment with the Wnt inhibitor, IWP-2 inhibited cell proliferation and markers of EMT.

Conclusions
These data support the role of the Wnt signalling pathway in acquired resistance to Tamoxifen. Further research into the mechanism by which activated Wnt signalling inhibits the effects of Tamoxifen should be undertaken. As a number of small molecules targeting the Wnt pathway are currently in pre-clinical development, combinatorial treatment with endocrine agents and Wnt pathway inhibitors may be a useful therapeutic option in the future for a subset of breast cancer patients.
Plasmatic higher levels of homocysteine in Non-alcoholic fatty liver disease (NAFLD)
Authors: de Carvalho Sylene Coutinho Rampche , Muniz Maria Tereza Cartaxo , Siqueira Maria Deozete Vieira , Siqueira Erika Rabelo Forte , Gomes Adriana Vieira , Silva Karina Alves , Bezerra Laís Carvalho Luma , D’Almeida Vânia , de Oliveira Claudia Pinto Marques Souza , Pereira Leila Maria M Beltrão 
Published: April 2013

Abstract

Background
Non-alcoholic fatty liver disease (NAFLD) is a chronic liver disease, which includes a spectrum of hepatic pathology such as simple steatosis, steatohepatitis, fibrosis and cirrhosis. The increased serum levels of homocysteine (Hcy) may be associated with hepatic fat accumulation. Genetic mutations in the folate route may only mildly impair Hcy metabolism. The aim of this study was to investigate the relation between liver steatosis with plasma homocysteine level and MTHFR C677T and A1298C polymorphisms in Brazilian patients with NAFLD.

Methods
Thirty-five patients diagnosed with NAFLD by liver biopsy and forty-five healthy controls neither age nor sex matched were genotyped for C677T and A1298C MTHFR polymorphisms using PCR-RFLP and PCR-ASA, respectively, and Hcy was determined by HPLC. All patients were negative for markers of Wilson’s, hemochromatosis and autoimmune diseases. Their daily alcohol intake was less than 100 g/week. A set of metabolic and serum lipid markers were also measured at the time of liver biopsies.

Results
The plasma Hcy level was higher in NAFLD patients compared to the control group (p = 0.0341). No statistical difference for genotypes 677C/T (p = 0.110) and 1298A/C (p = 0.343) in patients with NAFLD and control subjects was observed. The genotypes distribution was in Hardy-Weinberg equilibrium (677C/T p = 0.694 and 1298 A/C p = 0.188). The group of patients and controls showed a statistically significant difference (p < 0.001) for BMI and HOMA_IR, similarly to HDL cholesterol levels (p < 0,006), AST, ALT, γGT, AP and triglycerides levels (p < 0.001). A negative correlation was observed between levels of vitamin B12 and Hcy concentration (p = 0.005).

Conclusion
Our results indicate that plasma Hcy was higher in NAFLD than controls. The MTHFR C677T and A1298C polymorphisms did not differ significantly between groups, despite the 677TT homozygous frequency was higher in patients (17.14%) than in controls (677TT = 4.44%) (p > 0.05). The suggested genetic susceptibility to the MTHFR C677T and A1298C should be confirmed in large population based studies.
Implementation of the CDC translational informatics platform - from genetic variants to the national Swedish Rheumatology Quality Register
Authors: Abugessaisa Imad , Gomez-Cabrero David , Snir Omri , Lindblad Staffan , Klareskog Lars , Malmström Vivianne , Tegnér Jesper 
Published: April 2013

Abstract

Background
Sequencing of the human genome and the subsequent analyses have produced immense volumes of data. The technological advances have opened new windows into genomics beyond the DNA sequence. In parallel, clinical practice generate large amounts of data. This represents an underused data source that has much greater potential in translational research than is currently realized. This research aims at implementing a translational medicine informatics platform to integrate clinical data (disease diagnosis, diseases activity and treatment) of Rheumatoid Arthritis (RA) patients from Karolinska University Hospital and their research database (biobanks, genotype variants and serology) at the Center for Molecular Medicine, Karolinska Institutet.

Methods
Requirements engineering methods were utilized to identify user requirements. Unified Modeling Language and data modeling methods were used to model the universe of discourse and data sources. Oracle11g were used as the database management system, and the clinical development center (CDC) was used as the application interface. Patient data were anonymized, and we employed authorization and security methods to protect the system.

Results
We developed a user requirement matrix, which provided a framework for evaluating three translation informatics systems. The implementation of the CDC successfully integrated biological research database (15172 DNA, serum and synovial samples, 1436 cell samples and 65 SNPs per patient) and clinical database (5652 clinical visit) for the cohort of 379 patients presents three profiles. Basic functionalities provided by the translational medicine platform are research data management, development of bioinformatics workflow and analysis, sub-cohort selection, and re-use of clinical data in research settings. Finally, the system allowed researchers to extract subsets of attributes from cohorts according to specific biological, clinical, or statistical features.

Conclusions
Research and clinical database integration is a real challenge and a road-block in translational research. Through this research we addressed the challenges and demonstrated the usefulness of CDC. We adhered to ethical regulations pertaining to patient data, and we determined that the existing software solutions cannot meet the translational research needs at hand. We used RA as a test case since we have ample data on active and longitudinal cohort.
Presence of alternative lengthening of telomeres associated circular extrachromosome telomere repeats in primary leukemia cells of chronic myeloid leukemia
Authors: Samassekou Oumar , Malina Abba , Hébert Josée , Yan Ju 
Published: April 2013

Abstract

Background
The predominant mechanism by which human tumors maintain telomere length is via telomerase. In ~10% of tumor samples, however, telomere length is conserved, despite no detectable telomerase activity, in part through activation of the alternative lengthening of telomeres (ALT) pathway.

Methods
We studied the circular extra-chromosomal telomeric repeat (ECTR), an ALT hallmark, and telomerase activity in 24 chronic myeloid leukemia (CML) patients in chronic phase (CP).

Results
We identified the presence of ECTR in primary leukemia cells from some of these samples, which indicates the possible involvement of an ALT mechanism. Moreover, we found that some samples exhibited both circular ECTR and telomerase activities, suggesting that both mechanisms can contribute to the onset of CML.

Conclusion
We propose that ALT or the combined activities of ALT and telomerase might be required for the early stages of leukemogenesis. These findings shed new light into the oncogenic pathways responsible for the maintenance of telomere length in leukemia, which will ultimately determine the effectiveness of anti-telomerase-based treatment protocols.