bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sudden death possibly related to lenalidomide given for cardiac and muscle AL amyloidosis secondary to light chain deposition disease
Authors: Finsterer Josef , Höftberger Romana , Stöllberger Claudia , Wöhrer Adelheid , Regele Heinz 
Published: April 2012

Objectives: Restrictive cardiomyopathy due to AL amyloidosis has not been reported as the cause of sudden death. The risk of sudden death in AL amyloidosis may be further increased by potentially cardiotoxic medication, as in the following case. Case report: In a 69-year-old female, AL amyloidosis from light-chain deposition disease manifested as gastrointestinal pseudo-obstruction, restrictive cardiomyopathy, and secondary myopathy. AL amyloidosis was histologically confirmed by endomyocardial biopsy and muscle biopsy. One month after initiation of steroids and lenalidomide the patient suddenly died during sleep. It is speculated that sudden death was due to restrictive cardiomyopathy, cardiotoxicity of lenalidomide, pulmonary embolism, sudden unexplained death in epilepsy syndrome or stroke. The possible causes of sudden death are discussed. Conclusions: This case shows that AL amyloidosis from light-chain deposition disease may predominantly affect the intestines, myocardium and the skeletal muscle and that lenalidomide may have a beneficial effect on the amyloidosis but should be given with caution for its potential arrhythmogenic and thrombogenic side-effects.
A qualitative exploration into young children’s perspectives and understandings of emotional difficulties in other children
Authors: Dixon Clare , Murray Craig , Daiches Anna 
Published: April 2012

Research into children’s perspectives and understandings of emotional difficulties is limited and methodologically varied. In this paper we explore young children’s perspectives and understandings of emotional difficulties in their peers. We conducted five focus groups involving a total of 25 children. The children, aged eight and nine, were presented with vignettes representing peers experiencing emotional difficulties, and invited to discuss their perspectives on possible causes. We also explored their emotional and behavioural reactions to the vignette characters. Using interpretative phenomenological analysis we identified three themes: Searching for an Explanation; Empathy versus Blame; and Consequences and Solutions. The children drew on their own emotional experiences in their sense-making, and the extent to which they held the character responsible for their behaviour was particularly important in influencing their responses towards the characters.
Control of murine Ly6Chigh monocyte traffic and immunosuppressive activities by atypical chemokine receptor D6
Authors: Savino Benedetta , Castor Marina G. , Caronni Nicoletta , Sarukhan Adelaida , Anselmo Achille , Buracchi Chiara , Benvenuti Federica , Pinho Vanessa , Teixeira Mauro M. , Mantovani Alberto , Locati Massimo , Bonecchi Raffaella 
Published: April 2012

Abstract
The atypical chemokine receptor D6 is a decoy and scavenger receptor for most inflammatory CC chemokines and prevents the development of exacerbated inflammatory reactions. Here we report that mice lacking D6 expression in the nonhematopoietic compartment have a selective increase in the number of Ly6Chigh monocytes in the circulation and in secondary lymphoid tissues. Under inflammatory conditions, Ly6Chigh monocytes accumulate in increased number in secondary lymphoid organs of D6−/− mice in a CCR2-dependent manner. Ly6Chigh monocytes derived from D6−/− mice have enhanced immunosuppressive activity, inhibit the development of adaptive immune responses, and partially protect mice from the development of GVHD. Thus, control of CCR2 ligands by D6 regulates the traffic of Ly6Chigh monocytes and controls their immunosuppressive potential.
A context-based approach to identify the most likely mapping for RNA-seq experiments
Authors: Bonfert Thomas , Csaba Gergely , Zimmer Ralf , Friedel Caroline C 
Published: April 2012

Abstract

Background
Sequencing of mRNA (RNA-seq) by next generation sequencing technologies is widely used for analyzing the transcriptomic state of a cell. Here, one of the main challenges is the mapping of a sequenced read to its transcriptomic origin. As a simple alignment to the genome will fail to identify reads crossing splice junctions and a transcriptome alignment will miss novel splice sites, several approaches have been developed for this purpose. Most of these approaches have two drawbacks. First, each read is assigned to a location independent on whether the corresponding gene is expressed or not, i.e. information from other reads is not taken into account. Second, in case of multiple possible mappings, the mapping with the fewest mismatches is usually chosen which may lead to wrong assignments due to sequencing errors.

Results
To address these problems, we developed ContextMap which efficiently uses information on the context of a read, i.e. reads mapping to the same expressed region. The context information is used to resolve possible ambiguities and, thus, a much larger degree of ambiguities can be allowed in the initial stage in order to detect all possible candidate positions. Although ContextMap can be used as a stand-alone version using either a genome or transcriptome as input, the version presented in this article is focused on refining initial mappings provided by other mapping algorithms. Evaluation results on simulated sequencing reads showed that the application of ContextMap to either TopHat or MapSplice mappings improved the mapping accuracy of both initial mappings considerably.

Conclusions
In this article, we show that the context of reads mapping to nearby locations provides valuable information for identifying the best unique mapping for a read. Using our method, mappings provided by other state-of-the-art methods can be refined and alignment accuracy can be further improved.

Availability

http://www.bio.ifi.lmu.de/ContextMap.
High glucose concentrations induce TNF-α production through the down-regulation of CD33 in primary human monocytes
Authors: Gonzalez Yolanda , Herrera M Teresa , Soldevila Gloria , Garcia-Garcia Lourdes , Fabián Guadalupe , Pérez-Armendariz E Martha , Bobadilla Karen , Guzmán-Beltrán Silvia , Sada Eduardo , Torres Martha 
Published: April 2012

Abstract

Background
CD33 is a membrane receptor containing a lectin domain and a cytoplasmic immunoreceptor tyrosine-based inhibitory motif (ITIM) that is able to inhibit cytokine production. CD33 is expressed by monocytes, and reduced expression of CD33 correlates with augmented production of inflammatory cytokines, such as IL-1β, TNF-α, and IL-8. However, the role of CD33 in the inflammation associated with hyperglycemia and diabetes is unknown. Therefore, we studied CD33 expression and inflammatory cytokine secretion in freshly isolated monocytes from patients with type 2 diabetes. To evaluate the effects of hyperglycemia, monocytes from healthy donors were cultured with different glucose concentrations (15-50 mmol/l D-glucose), and CD33 expression and inflammatory cytokine production were assessed. The expression of suppressor of cytokine signaling protein-3 (SOCS-3) and the generation of reactive oxygen species (ROS) were also evaluated to address the cellular mechanisms involved in the down-regulation of CD33.

Results
CD33 expression was significantly decreased in monocytes from patients with type 2 diabetes, and higher levels of TNF-α, IL-8 and IL-12p70 were detected in the plasma of patients compared to healthy donors. Under high glucose conditions, CD33 protein and mRNA expression was significantly decreased, whereas spontaneous TNF-α secretion and SOCS-3 mRNA expression were increased in monocytes from healthy donors. Furthermore, the down-regulation of CD33 and increase in TNF-α production were prevented when monocytes were treated with the antioxidant α-tocopherol and cultured under high glucose conditions.

Conclusion
Our results suggest that hyperglycemia down-regulates CD33 expression and triggers the spontaneous secretion of TNF-α by peripheral monocytes. This phenomenon involves the generation of ROS and the up-regulation of SOCS-3. These observations support the importance of blood glucose control for maintaining innate immune function and suggest the participation of CD33 in the inflammatory profile associated with type 2 diabetes.
Hepatitis B surface antigen variants in voluntary blood donors in Nanjing, China
Authors: Yong-lin Yang , Qiang Fu , Ming-shun Zhang , Jie Cai , Gui-ming Ma , Zu-hu Huang , Xu-bing Cai 
Published: April 2012

AbstractBackgroundHepatitis B virus (HBV) is still one of the serious infectious risks for the blood transfusion safety in China. One plausible reason is the emergence of the variants in the major antigenic alpha determinant within the major hydrophilic region (MHR) of hepatitis B surface antigen (HBsAg), which have been assumed to evade the immune surveillance and pose a challenge to the disease diagnosis. It is well documented that some commercial ELISA kits could detect the wild-type but not the mutant viruses. The high prevalence of HBV in China also impaired the application of nucleic acid testing (NAT) in the improvement of blood security. Molecular epidemiological study of HBsAg variations in China is still limited. This study was designed to identify the prevalence of mutations in the HBsAg in voluntary blood donors in Nanjing, China.MethodsA total of 20,326 blood units were enrolled in this study, 39 donors were positive for HBV S gene in the nested-PCR. Mutations in the major hydrophilic region (MHR; aa 99-169) were identified by direct sequencing of S region.ResultsAmong of 20,326 blood units in the Red Cross Transfusion Center of Nanjing from October 2008 to April 2009, 296 samples (1.46%, 296/20,326) were HBsAg positive in the 2 successive rounds of the ELISA test. In these HBsAg positive units, HBV S gene could be successfully amplified from 39 donors (13.18%, 39/296) in the nested-PCR. Sequence analysis revealed that 32 strains (82.1%, 32/39) belong to genotype B, 7 strains (17.9%, 7/39) to genotype C. Besides well known G145R, widely dispersed variations in the MHR of S region, were observed in 20 samples of all the strains sequenced.ConclusionsHBV/B and HBV/C are dominant in Nanjing, China. The mutations in the MHR of HBsAg associated with disease diagnosis are common.
Properties and Power of the Drosophila Synthetic Population Resource for the Routine Dissection of Complex Traits
Authors: King Elizabeth G , Macdonald Stuart J , Long Anthony D 
Published: April 2012

AbstractThe Drosophila Synthetic Population Resource (DSPR) is a newly developed multifounder advanced intercross panel consisting of &gt;1600 recombinant inbred lines (RILs) designed for the genetic dissection of complex traits. Here, we describe the inference of the underlying mosaic founder structure for the full set of RILs from a dense set of semicodominant restriction-site–associated DNA (RAD) markers and use simulations to explore how variation in marker density and sequencing coverage affects inference. For a given sequencing effort, marker density is more important than sequence coverage per marker in terms of the amount of genetic information we can infer. We also assessed the power of the DSPR by assigning genotypes at a hidden QTL to each RIL on the basis of the inferred founder state and simulating phenotypes for different experimental designs, different genetic architectures, different sample sizes, and QTL of varying effect sizes. We found the DSPR has both high power (e.g., 84% power to detect a 5% QTL) and high mapping resolution (e.g., ∼1.5 cM for a 5% QTL).
Chaperoning the Chaperone: A Role for the Co-chaperone Cpr7 in Modulating Hsp90 Function in Saccharomyces cerevisiae
Authors: Zuehlke Abbey D , Johnson Jill L 
Published: April 2012

Abstract
Heat-shock protein 90 (Hsp90) of Saccharomyces cerevisiae is an abundant essential eukaryotic molecular chaperone involved in the activation and stabilization of client proteins, including several transcription factors and oncogenic kinases. Hsp90 undergoes a complex series of conformational changes and interacts with partner co-chaperones such as Sba1, Cpr6, Cpr7, and Cns1 as it binds and hydrolyzes ATP. In the absence of nucleotide, Hsp90 is dimerized only at the carboxy-terminus. In the presence of ATP, Hsp90 also dimerizes at the amino-terminus, creating a binding site for Sba1. Truncation of a charged linker region of yeast Hsp90 (Hsp82Δlinker) was known to disrupt the ability of Hsp82 to undergo amino-terminal dimerization and bind Sba1. We found that yeast expressing Hsp82Δlinker constructs exhibited a specific synthetic lethal phenotype in cells lacking CPR7. The isolated tetratricopeptide repeat domain of Cpr7 was both necessary and sufficient for growth in those strains. Cpr6 and Cpr7 stably bound the carboxy-terminus of wild-type Hsp82 only in the presence of nonhydrolyzable ATP and formed an Hsp82–Cpr6–Cpr7 ternary complex. However, in cells expressing Hsp82Δlinker or lacking CPR7, Cpr6 was able to bind Hsp82 in the presence or absence of nucleotide. Overexpression of CNS1, but not of other co-chaperones, in cpr7 cells restored nucleotide-dependent Hsp82–Cpr6 interaction. Together, our results suggest that the in vivo functions of Cpr7 include modulating Hsp90 conformational changes, mediating proper signaling of the nucleotide-bound state to the carboxy-terminus of Hsp82, or regulating Hsp82–Cpr6 interaction.
Ribosomal DNA Organization Before and After Magnification in Drosophila melanogaster
Authors: Bianciardi Alessio , Boschi Manuela , Swanson Ellen E , Belloni Massimo , Robbins Leonard G 
Published: April 2012

Abstract
In all eukaryotes, the ribosomal RNA genes are stably inherited redundant elements. In Drosophila melanogaster, the presence of a Ybb− chromosome in males, or the maternal presence of the Ribosomal exchange (Rex) element, induces magnification: a heritable increase of rDNA copy number. To date, several alternative classes of mechanisms have been proposed for magnification: in situ replication or extra-chromosomal replication, either of which might act on short or extended strings of rDNA units, or unequal sister chromatid exchange. To eliminate some of these hypotheses, none of which has been clearly proven, we examined molecular-variant composition and compared genetic maps of the rDNA in the bb2 mutant and in some magnified bb+ alleles. The genetic markers used are molecular-length variants of IGS sequences and of R1 and R2 mobile elements present in many 28S sequences. Direct comparison of PCR products does not reveal any particularly intensified electrophoretic bands in magnified alleles compared to the nonmagnified bb2 allele. Hence, the increase of rDNA copy number is diluted among multiple variants. We can therefore reject mechanisms of magnification based on multiple rounds of replication of short strings. Moreover, we find no changes of marker order when pre- and postmagnification maps are compared. Thus, we can further restrict the possible mechanisms to two: replication in situ of an extended string of rDNA units or unequal exchange between sister chromatids.
Effects of Ad-atom Diffusivity Throughout Sb-Mediated Formation of Ge/Si Nanoislands
Authors: Tonkikh Alexander A. , Zakharov Nikolay D. , Suvorova Alexandra A. , Werner Peter 
Published: April 2012

ABSTRACTThe effect of Sb on the formation of Ge nano islands in Si by means of molecular beam epitaxy is reported. We observe in the Ge/Si(100) system a non-monotonic dependence of the Stranski-Krastanov critical thickness of Ge islands formation on the adsorbed Sb amount. Dome- and hut-shaped Ge islands are replaced with the pyramids, when Ge is deposited on the Sb-covered Si(100) surface. The Sb-mediated conservation of the shape of Ge islands during embedding them in Si is shown. We assume that the decrease of the surface diffusion of Si and Ge ad-atoms causes these effects.
The Global Dimensions of Public Health Preparedness and Implications for US Action
Authors: Moore Melinda 
Published: April 2012

The globalization of public health is both real and relevant throughout the United States and to Americans traveling or residing abroad. US public policy responses are evolving, but a crisper and more comprehensive global perspective is needed. I suggest four timely US actions to address today’s competing realities of globalization and economic austerity: raise awareness among clinicians and local health departments; capture and share exemplary disaster management practices across countries; ensure that US global health investments are effective, efficient, and sustainable; and think globally while acting locally to enhance US health security. The reauthorization of the Pandemic and All-Hazards Preparedness Act of 2006 provides an opportunity to more clearly address the global dimensions of domestic preparedness.
A Dynamic Model of US Adolescents’ Smoking and Friendship Networks
Authors: Schaefer David R. , Haas Steven A. , Bishop Nicholas J. 
Published: April 2012

Objectives. We investigated the associations between smoking and friend selection in the social networks of US adolescents. Methods. We used a stochastic actor-based model to simultaneously test the effects of friendship networks on smoking and several ways that smoking can affect the friend selection process. Data are from 509 US high school students in the National Longitudinal Study of Adolescent Health, 1994–1996 (46.6% female, mean age at outset = 15.4 years). Results. Over time, adolescents’ smoking became more similar to their friends. Smoking also affected who adolescents selected as friends; adolescents were more likely to select friends whose smoking level was similar to their own, and smoking enhanced popularity such that smokers were more likely to be named as friends than were nonsmokers, after controlling for other friend selection processes. Conclusions. Both friend selection and peer influence are associated with smoking frequency. Interventions to reduce adolescent smoking would benefit by focusing on selection and influence mechanisms.
Recent Progress and Effects Analysis of ASP Flooding Field Tests
Authors: Zhu Youyi , Hou Qingfeng , Liu Weidong , Ma Desheng , Liao Guangzhi 
Published: April 2012

Abstract
Alkali-surfactant-polymer combination flooding (ASP flooding) is one of the main chemical EOR techniques for the significant increase of crude oil recovery in PetroChina. In this paper, the progress in field tests of ASP flooding, effects analysis and related problems in application are introduced and discussed. The development trend of ASP flooding is suggested.
Field tests of ASP flooding in PetroChina have been performed since 1994, including six pilot tests in both sandstone and conglomerate reservoirs and three industrial tests, and the incremental oil recoveries of such tests were more than 19–20%.
It is found that three factors are responsible for successful ASP flooding field tests : (1) Good performance of oil displacement agents. (2) Good profile control and oil displacement ability. (3) Reasonable well pattern and well spacing.
Side effects encountered in field tests are as follows: (1) scaling and corrosion damaged the lifting system and shorten the average pump-checking cycle accordingly. (2) Strong emulsification resulted in many liquid treatment problems such as the excess of solid particle content over the standard of water circulation and high cost of water treatment. (3)The liquid production decreased greatly.
The development trends in chemical combination flooding technique are proposed based on results of ASP flooding field tests. The strong alkali ASP flooding should be replaced by weak alkali ASP flooding or even alkali-free SP combination flooding. The application reservoir will cover from sandstone to conglomerate and carbonate, from low salinity and low temperature reservoirs to high salinity and high temperature ones, etc. The corresponding key techniques such as development of new chemical agents and advanced produced liquid treatment system should be considered in future tests and application of chemical combination flooding.
Three-Phase Relative Permeability and Hystresis Model for Simulation of Water Alternating Gas (WAG) Injection
Authors: Shahverdi H. , Sohrabi M. 
Published: April 2012

Abstract
Water- Alternating- Gas (WAG) injection in waterflooded reservoirs can increase oil recovery and extend the life of these reservoirs. Reliable reservoir simulations are needed to predict the performance of WAG injection before field implementation. This requires accurate sets of relative permeability (kr) and capillary pressure (Pc) functions for each fluid phase, in a three-phase flow regime. The WAG process also involves another major complication, hysteresis, which is caused by flow reversal happening during WAG injection. Hysteresis is one of the most phenomena manipulating the performance of WAG injection and hence, it has to be carefully accounted for.
In this study we have benefited from the results of a series of coreflood experiments that we have been running since 1997 as a part of the Characterization of Three-Phase Flow and WAG Injection JIP (joint industry project) at Heriot-Watt University. In particular we focus on a WAG experiment carried out on a water wet core to obtain three-phase relative permeability values for oil, water and gas. The relative permeabilities exhibit significant and irreversible hysteresis for, oil, water and gas. The observed hysteresis, which is due to the cyclic injection of water and gas during the experiment, is not predicted by the existing hysteresis models.
We present a new three-phase relative permeability model coupled with hysteresis effect for modelling of the observed cycle- dependent relative permeabilities taking place during WAG injection. The approach was successfully tested and verified using the measured three-phase relative permeability values obtained from WAG experiment. In line with our laboratory observations, the new model predicts the reduction of the gas mobility during consecutive water and gas injection cycles as well as the increase in oil relative permeability happening in consecutive water injection cycles.