bluuebunny/crossref_metadata_2025_split huggingface dataset:
Arthroscopic-Assisted Reduction and Percutaneous Cannulated Screw Fixation for Ideberg Type III Glenoid Fractures
Authors: Yang Hai-bo , Wang Dong , He Xi-jing 
Published: June 2011

Background: Traditionally, open reduction and internal fixation is an acceptable choice for treating displaced glenoid articular fracture. Considering some major complications associated with open surgery, however, surgeons have explored a less invasive way to achieve fixation. Purpose: This investigation was undertaken to evaluate the clinical results of arthroscopic-assisted reduction and percutaneous cannulated screw fixation for the treatment of Ideberg type III glenoid fractures. Study Design: Case series; Level of evidence, 4. Methods: Twenty-three consecutive patients with Ideberg type III glenoid fractures underwent arthroscopic-assisted reduction and percutaneous cannulated screw fixation. Eighteen patients (78.3%) were available for the final follow-up, at a mean of 37.6 months (range, 24-61 months). There were 12 men and 6 women, with an average age of 41.2 years (range, 22-62 years). Dominant sides were involved in 10 patients. The mean time from injury to surgery was 5.9 ± 2.7 days. Results: The average ranges of motion of the affected shoulders at the final follow-up were 162.8° ± 8.3° in forward elevation, 67.2° ± 4.6° in external rotation at the side, and T8 ± 2 in internal rotation. The average visual analog scale pain score was 0.7 ± 0.9 (range, 0-3), the average American Shoulder and Elbow Surgeons score was 96.0 ± 5.4 (range, 80-100), the average Constant-Murley score was 96.8 ± 2.9 (range, 90-100), and the average University of California, Los Angeles, score was 34.3 ± 0.9 (range, 33-35). No hardware failure or redisplacement of the fracture occurred, and all fractures healed without any major complication associated with the surgery. Conclusion: Arthroscopic-assisted reduction and percutaneous cannulated screw fixation is a safe and effective method for the treatment of Ideberg type III glenoid fractures.
Incorporation of an interferon-β neutralizing antibody assay into routine clinical practice
Authors: Farrell RA , Espasandin M , Lakdawala N , Creeke PI , Worthington V , Giovannoni G 
Published: June 2011

Background: Incorporation of routine clinical testing for neutralizing antibodies (NAbs) to interferon (IFN)-β has remained problematic. With increasing treatment choice for patients, routine NAb testing should be incorporated to aid therapeutic decisions. Objective: We sought to improve interpretation of NAb results by combining the luciferase NAb assay (luciferase gene expression assay under control of interferon-stimulated response element) and in-vivo biomarker (myxovirus A protein, MxA) induction in patients with MS. Methods: Blood samples (serum and PAXGene® for RNA) were obtained pre-injection and 12 hours post-injection of IFN-β from 144 subjects. Sera were tested for NAbs using the luciferase assay. MxA expression was quantified by real-time polymerase chain reaction (PCR). Results: 26% of samples were NAb positive (titre > 20 NU). There was no difference in NAb titres in the pre- or post-dose sera ( p = 0.643). MxA expression was inhibited in a dose-dependent fashion in NAb positive samples. Mean MxA level post-IFN-β: NAb negative 2330 (95% CI 1940–2719), NAb 20–99 NU 1533 (95% CI 741–2324), NAb 100–600 NU 832 (186–1478) and NAb > 600 NU 101 (95% CI 0–224). NAb titre and MxA level correlated strongly: MxA pre- (Spearman r = −0.72, p < 0.0001), MxA post- (Spearman r = −0.79, p < 0.0001) and MxA induction (Spearman r = −0.67, p = 0.0004). Conclusion: A single, 12-hour post-injection sample should be used to test for NAbs using the luciferase assay and IFN-β bioactivity (MxA) in the clinical setting.
Tumor suppressor genes FHIT and WWOX are deleted in primary effusion lymphoma (PEL) cell lines
Authors: Roy Debasmita , Sin Sang-Hoon , Damania Blossom , Dittmer Dirk P. 
Published: June 2011

AbstractPrimary effusion lymphoma (PEL) is a diffuse-large B-cell lymphoma with poor prognosis. One hundred percent of PELs carry the genome of Kaposi sarcoma–associated herpesvirus and a majority are coinfected with Epstein-Barr virus (EBV). We profiled genomic aberrations in PEL cells using the Affymetrix 6.0 SNP array. This identified for the first time individual genes that are altered in PEL cells. Eleven of 13 samples (85%) were deleted for the fragile site tumor suppressors WWOX and FHIT. Alterations were also observed in the DERL1, ETV1, RASA4, TPK1, TRIM56, and VPS41 genes, which are yet to be characterized for their roles in cancer. Coinfection with EBV was associated with significantly fewer gross genomic aberrations, and PEL could be segregated into EBV-positive and EBV-negative clusters on the basis of host chromosome alterations. This suggests a model in which both host genetic aberrations and the 2 viruses contribute to the PEL phenotype.
Plasmodium falciparum uses a key functional site in complement receptor type-1 for invasion of human erythrocytes
Authors: Tham Wai-Hong , Schmidt Christoph Q. , Hauhart Richard E. , Guariento Mara , Tetteh-Quarcoo Patience B. , Lopaticki Sash , Atkinson John P. , Barlow Paul N. , Cowman Alan F. 
Published: June 2011

AbstractThe Plasmodium falciparum adhesin PfRh4 binds to complement receptor type-1 (CR1) on human erythrocytes and mediates a glycophorin-independent invasion pathway. CR1 is a complement regulator and immune-adherence receptor on erythrocytes required for shuttling of C3b/C4b-opsonized particles to liver and spleen for phagocytosis. Using recombinant CR1 constructs, we mapped the recognition site for PfRh4 to complement control protein modules 1 to 3 (CCP1-3) at the membrane-distal amino terminus of CR1. This region of CR1 binds to C4b and C3b and accelerates decay of both classic pathway and alternative pathway C3 and C5 convertases. CCP1-3 competed for PfRh4 binding to erythroid CR1 and inhibited the PfRh4-CR1 invasion pathways across a wide range of P falciparum strains. PfRh4 did not bind significantly to other CR1 constructs, including CCP15-17, which is 85% identical to CCP1-3. PfRh4 binding to CR1 did not affect its C3b/C4b binding capability, and we show evidence for a ternary complex between CCP1-3, C4b, and PfRh4. PfRh4 binding specifically inhibited CR1's convertase decay-accelerating activity, whereas there was no effect on factor H-mediated decay-accelerating activity. These results increase our understanding of the functional implications of CR1 engagement with PfRh4 and highlight the interplay between complement regulation and infection.
Increase of nitrosative stress in patients with eosinophilic pneumonia
Authors: Furukawa Kanako , Sugiura Hisatoshi , Matsunaga Kazuto , Ichikawa Tomohiro , Koarai Akira , Hirano Tsunahiko , Yanagisawa Satoru , Minakata Yoshiaki , Akamatsu Keiichiro , Kanda Masae , Nishigai Manabu , Ichinose Masakazu 
Published: June 2011

Abstract

Background
Exhaled nitric oxide (NO) production is increased in asthma and reflects the degree of airway inflammation. The alveolar NO concentration (Calv) in interstitial pneumonia is reported to be increased. However, it remains unknown whether NO production is increased and nitrosative stress occurs in eosinophilic pneumonia (EP). We hypothesized that nitrosative stress markers including Calv, inducible type of NO synthase (iNOS), and 3-nitrotyrosine (3-NT), are upregulated in EP.

Methods
Exhaled NO including fractional exhaled NO (FENO) and Calv was measured in ten healthy subjects, 13 patients with idiopathic pulmonary fibrosis (IPF), and 13 patients with EP. iNOS expression and 3-NT formation were assessed by immunocytochemistory in BALf cells. The exhaled NO, lung function, and systemic inflammatory markers of the EP patients were investigated after corticosteroid treatment for 4 weeks.

Results
The Calv levels in the EP group (14.4 ± 2.0 ppb) were significantly higher than those in the healthy subjects (5.1 ± 0.6 ppb, p < 0.01) and the IPF groups (6.3 ± 0.6 ppb, p < 0.01) as well as the FENO and the corrected Calv levels (all p < 0.01). More iNOS and 3-NT positive cells were observed in the EP group compared to the healthy subject and IPF patient. The Calv levels had significant positive correlations with both iNOS (r = 0.858, p < 0.05) and 3-NT positive cells (r = 0.924, p < 0.01). Corticosteroid treatment significantly reduced both the FENO (p < 0.05) and the Calv levels (p < 0.01). The magnitude of reduction in the Calv levels had a significant positive correlation with the peripheral blood eosinophil counts (r = 0.802, p < 0.05).

Conclusions
These results suggested that excessive nitrosative stress occurred in EP and that Calv could be a marker of the disease activity.
Querying large read collections in main memory: a versatile data structure
Authors: Philippe Nicolas , Salson Mikaël , Lecroq Thierry , Léonard Martine , Commes Thérèse , Rivals Eric 
Published: June 2011

Abstract

Background
High Throughput Sequencing (HTS) is now heavily exploited for genome (re-) sequencing, metagenomics, epigenomics, and transcriptomics and requires different, but computer intensive bioinformatic analyses. When a reference genome is available, mapping reads on it is the first step of this analysis. Read mapping programs owe their efficiency to the use of involved genome indexing data structures, like the Burrows-Wheeler transform. Recent solutions index both the genome, and the k-mers of the reads using hash-tables to further increase efficiency and accuracy. In various contexts (e.g. assembly or transcriptome analysis), read processing requires to determine the sub-collection of reads that are related to a given sequence, which is done by searching for some k-mers in the reads. Currently, many developments have focused on genome indexing structures for read mapping, but the question of read indexing remains broadly unexplored. However, the increase in sequence throughput urges for new algorithmic solutions to query large read collections efficiently.

Results
Here, we present a solution, named Gk arrays, to index large collections of reads, an algorithm to build the structure, and procedures to query it. Once constructed, the index structure is kept in main memory and is repeatedly accessed to answer queries like "given a k-mer, get the reads containing this k-mer (once/at least once)". We compared our structure to other solutions that adapt uncompressed indexing structures designed for long texts and show that it processes queries fast, while requiring much less memory. Our structure can thus handle larger read collections. We provide examples where such queries are adapted to different types of read analysis (SNP detection, assembly, RNA-Seq).

Conclusions

Gk arrays constitute a versatile data structure that enables fast and more accurate read analysis in various contexts. The Gk arrays provide a flexible brick to design innovative programs that mine efficiently genomics, epigenomics, metagenomics, or transcriptomics reads. The Gk arrays library is available under Cecill (GPL compliant) license from http://www.atgc-montpellier.fr/ngs/.
Histone deacetylase activity is necessary for left-right patterning during vertebrate development
Authors: Carneiro Katia , Donnet Claudia , Rejtar Tomas , Karger Barry L , Barisone Gustavo A , Díaz Elva , Kortagere Sandhya , Lemire Joan M , Levin Michael 
Published: June 2011

Abstract

Background
Consistent asymmetry of the left-right (LR) axis is a crucial aspect of vertebrate embryogenesis. Asymmetric gene expression of the TGFβ superfamily member Nodal related 1 (Nr1) in the left lateral mesoderm plate is a highly conserved step regulating the situs of the heart and viscera. In Xenopus, movement of maternal serotonin (5HT) through gap-junctional paths at cleavage stages dictates asymmetry upstream of Nr1. However, the mechanisms linking earlier biophysical asymmetries with this transcriptional control point are not known.

Results
To understand how an early physiological gradient is transduced into a late, stable pattern of Nr1 expression we investigated epigenetic regulation during LR patterning. Embryos injected with mRNA encoding a dominant-negative of Histone Deacetylase (HDAC) lacked Nr1 expression and exhibited randomized sidedness of the heart and viscera (heterotaxia) at stage 45. Timing analysis using pharmacological blockade of HDACs implicated cleavage stages as the active period. Inhibition during these early stages was correlated with an absence of Nr1 expression at stage 21, high levels of heterotaxia at stage 45, and the deposition of the epigenetic marker H3K4me2 on the Nr1 gene. To link the epigenetic machinery to the 5HT signaling pathway, we performed a high-throughput proteomic screen for novel cytoplasmic 5HT partners associated with the epigenetic machinery. The data identified the known HDAC partner protein Mad3 as a 5HT-binding regulator. While Mad3 overexpression led to an absence of Nr1 transcription and randomized the LR axis, a mutant form of Mad3 lacking 5HT binding sites was not able to induce heterotaxia, showing that Mad3's biological activity is dependent on 5HT binding.

Conclusion
HDAC activity is a new LR determinant controlling the epigenetic state of Nr1 from early developmental stages. The HDAC binding partner Mad3 may be a new serotonin-dependent regulator of asymmetry linking early physiological asymmetries to stable changes in gene expression during organogenesis.
Balancing selection is common in the extended MHC region but most alleles with opposite risk profile for autoimmune diseases are neutrally evolving
Authors: Cagliani Rachele , Riva Stefania , Pozzoli Uberto , Fumagalli Matteo , Comi Giacomo P , Bresolin Nereo , Clerici Mario , Sironi Manuela 
Published: June 2011

Abstract

Background
Several susceptibility genetic variants for autoimmune diseases have been identified. A subset of these polymorphisms displays an opposite risk profile in different autoimmune conditions. This observation open interesting questions on the evolutionary forces shaping the frequency of these alleles in human populations.
We aimed at testing the hypothesis whereby balancing selection has shaped the frequency of opposite risk alleles.

Results
Since balancing selection signatures are expected to extend over short genomic portions, we focused our analyses on 11 regions carrying putative functional polymorphisms that may represent the disease variants (and the selection targets). No exceptional nucleotide diversity was observed for ZSCAN23, HLA-DMB, VARS2, PTPN22, BAT3, C6orf47, and IL10; summary statistics were consistent with evolutionary neutrality for these gene regions. Conversely, CDSN/PSORS1C1, TRIM10/TRIM40, BTNL2, and TAP2 showed extremely high nucleotide diversity and most tests rejected neutrality, suggesting the action of balancing selection. For TAP2 and BTNL2 these signatures are not secondary to linkage disequilibrium with HLA class II genes. Nonetheless, with the exception of variants in TRIM40 and CDSN, our data suggest that opposite risk SNPs are not selection targets but rather have accumulated as neutral variants.

Conclusion
Data herein indicate that balancing selection is common within the extended MHC region and involves several non-HLA loci. Yet, the evolutionary history of most SNPs with an opposite effect for autoimmune diseases is consistent with evolutionary neutrality. We suggest that variants with an opposite effect on autoimmune diseases should not be considered a distinct class of disease alleles from the evolutionary perspective and, in a few cases, the opposite effect on distinct diseases may derive from complex haplotype structures in regions with high genetic diversity.
Implication of next-generation sequencing on association studies
Authors: Siu Hoicheong , Zhu Yun , Jin Li , Xiong Momiao 
Published: June 2011

Abstract

Background
Next-generation sequencing technologies can effectively detect the entire spectrum of genomic variation and provide a powerful tool for systematic exploration of the universe of common, low frequency and rare variants in the entire genome. However, the current paradigm for genome-wide association studies (GWAS) is to catalogue and genotype common variants (5% < MAF). The methods and study design for testing the association of low frequency (0.5% < MAF ≤ 5%) and rare variation (MAF ≤ 0.5%) have not been thoroughly investigated. The 1000 Genomes Project represents one such endeavour to characterize the human genetic variation pattern at the MAF = 1% level as a foundation for association studies. In this report, we explore different strategies and study designs for the near future GWAS in the post-era, based on both low coverage pilot data and exon pilot data in 1000 Genomes Project.

Results
We investigated the linkage disequilibrium (LD) pattern among common and low frequency SNPs and its implication for association studies. We found that the LD between low frequency alleles and low frequency alleles, and low frequency alleles and common alleles are much weaker than the LD between common and common alleles. We examined various tagging designs with and without statistical imputation approaches and compare their power against de novo resequencing in mapping causal variants under various disease models. We used the low coverage pilot data which contain ~14 M SNPs as a hypothetical genotype-array platform (Pilot 14 M) to interrogate its impact on the selection of tag SNPs, mapping coverage and power of association tests. We found that even after imputation we still observed 45.4% of low frequency SNPs which were untaggable and only 67.7% of the low frequency variation was covered by the Pilot 14 M array.

Conclusions
This suggested GWAS based on SNP arrays would be ill-suited for association studies of low frequency variation.
Functional characterization of an alkaline exonuclease and single strand annealing protein from the SXT genetic element of Vibrio cholerae
Authors: Chen Wen-yang , Ho John WS , Huang Jian-dong , Watt Rory M 
Published: June 2011

Abstract
Background
SXT is an integrating conjugative element (ICE) originally isolated from Vibrio cholerae, the bacterial pathogen that causes cholera. It houses multiple antibiotic and heavy metal resistance genes on its ca. 100 kb circular double stranded DNA (dsDNA) genome, and functions as an effective vehicle for the horizontal transfer of resistance genes within susceptible bacterial populations. Here, we characterize the activities of an alkaline exonuclease (S066, SXT-Exo) and single strand annealing protein (S065, SXT-Bet) encoded on the SXT genetic element, which share significant sequence homology with Exo and Bet from bacteriophage lambda, respectively.

Results
SXT-Exo has the ability to degrade both linear dsDNA and single stranded DNA (ssDNA) molecules, but has no detectable endonuclease or nicking activities. Adopting a stable trimeric arrangement in solution, the exonuclease activities of SXT-Exo are optimal at pH 8.2 and essentially require Mn2+ or Mg2+ ions. Similar to lambda-Exo, SXT-Exo hydrolyzes dsDNA with 5'- to 3'-polarity in a highly processive manner, and digests DNA substrates with 5'-phosphorylated termini significantly more effectively than those lacking 5'-phosphate groups. Notably, the dsDNA exonuclease activities of both SXT-Exo and lambda-Exo are stimulated by the addition of lambda-Bet, SXT-Bet or a single strand DNA binding protein encoded on the SXT genetic element (S064, SXT-Ssb). When co-expressed in E. coli cells, SXT-Bet and SXT-Exo mediate homologous recombination between a PCR-generated dsDNA fragment and the chromosome, analogous to RecET and lambda-Bet/Exo.

Conclusions
The activities of the SXT-Exo protein are consistent with it having the ability to resect the ends of linearized dsDNA molecules, forming partially ssDNA substrates for the partnering SXT-Bet single strand annealing protein. As such, SXT-Exo and SXT-Bet may function together to repair or process SXT genetic elements within infected V. cholerae cells, through facilitating homologous DNA recombination events. The results presented here significantly extend our general understanding of the properties and activities of alkaline exonuclease and single strand annealing proteins of viral/bacteriophage origin, and will assist the rational development of bacterial recombineering systems.
Infection control in delivery care units, Gujarat state, India: A needs assessment
Authors: Mehta Rajesh , Mavalankar Dileep V , Ramani KV , Sharma Sheetal , Hussein Julia 
Published: June 2011

Abstract

Background
Increasingly, women in India attend health facilities for childbirth, partly due to incentives paid under government programs. Increased use of health facilities can alleviate the risks of infections contracted in unhygienic home deliveries, but poor infection control practices in labour and delivery units also cause puerperal sepsis and other infections of childbirth. A needs assessment was conducted to provide information on procedures and practices related to infection control in labour and delivery units in Gujarat state, India.

Methods
Twenty health care facilities, including private and public primary health centres and referral hospitals, were sampled from two districts in Gujarat state, India. Three pre-tested tools for interviewing and for observation were used. Data collection was based on existing infection control guidelines for clean practices, clean equipment, clean environment and availability of diagnostics and treatment. The study was carried out from April to May 2009.

Results
Seventy percent of respondents said that standard infection control procedures were followed, but a written procedure was only available in 5% of facilities. Alcohol rubs were not used for hand cleaning and surgical gloves were reused in over 70% of facilities, especially for vaginal examinations in the labour room. Most types of equipment and supplies were available but a third of facilities did not have wash basins with "hands-free" taps. Only 15% of facilities reported that wiping of surfaces was done immediately after each delivery in labour rooms. Blood culture services were available in 25% of facilities and antibiotics are widely given to women after normal delivery. A few facilities had data on infections and reported rates of 3% to 5%.

Conclusions
This study of current infection control procedures and practices during labour and delivery in health facilities in Gujarat revealed a need for improved information systems, protocols and procedures, and for training and research. Simply incentivizing the behaviour of women to use health facilities for childbirth via government schemes may not guarantee safe delivery.