bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enlarging a training set for genomic selection by imputation of un-genotyped animals in populations of varying genetic architecture
Authors: Pimentel Eduardo CG , Wensch-Dorendorf Monika , König Sven , Swalve Hermann H 
Published: April 2013

Abstract

Background
The most common application of imputation is to infer genotypes of a high-density panel of markers on animals that are genotyped for a low-density panel. However, the increase in accuracy of genomic predictions resulting from an increase in the number of markers tends to reach a plateau beyond a certain density. Another application of imputation is to increase the size of the training set with un-genotyped animals. This strategy can be particularly successful when a set of closely related individuals are genotyped.

Methods
Imputation on completely un-genotyped dams was performed using known genotypes from the sire of each dam, one offspring and the offspring’s sire. Two methods were applied based on either allele or haplotype frequencies to infer genotypes at ambiguous loci. Results of these methods and of two available software packages were compared. Quality of imputation under different population structures was assessed. The impact of using imputed dams to enlarge training sets on the accuracy of genomic predictions was evaluated for different populations, heritabilities and sizes of training sets.

Results
Imputation accuracy ranged from 0.52 to 0.93 depending on the population structure and the method used. The method that used allele frequencies performed better than the method based on haplotype frequencies. Accuracy of imputation was higher for populations with higher levels of linkage disequilibrium and with larger proportions of markers with more extreme allele frequencies. Inclusion of imputed dams in the training set increased the accuracy of genomic predictions. Gains in accuracy ranged from close to zero to 37.14%, depending on the simulated scenario. Generally, the larger the accuracy already obtained with the genotyped training set, the lower the increase in accuracy achieved by adding imputed dams.

Conclusions
Whenever a reference population resembling the family configuration considered here is available, imputation can be used to achieve an extra increase in accuracy of genomic predictions by enlarging the training set with completely un-genotyped dams. This strategy was shown to be particularly useful for populations with lower levels of linkage disequilibrium, for genomic selection on traits with low heritability, and for species or breeds for which the size of the reference population is limited.
Different healing process of esophageal large mucosal defects by endoscopic mucosal dissection between with and without steroid injection in an animal model
Authors: Nonaka Kouichi , Miyazawa Mitsuo , Ban Shinichi , Aikawa Masayasu , Akimoto Naoe , Koyama Isamu , Kita Hiroto 
Published: April 2013

Abstract

Background
Stricture formation is one of the major complications after endoscopic removal of large superficial squamous cell neoplasms of the esophagus, and local steroid injections have been adopted to prevent it. However, fundamental pathological alterations related to them have not been well analyzed so far. The aim of this study was to analyze the time course of the healing process of esophageal large mucosal defects resulting in stricture formation and its modification by local steroid injection, using an animal model.

Methods
Esophageal circumferential mucosal defects were created by endoscopic mucosal dissection (ESD) for four pigs. One pig was sacrificed five minutes after the ESD, and other two pigs were followed-up on endoscopy and sacrificed at the time of one week and three weeks after the ESD, respectively. The remaining one pig was followed-up on endoscopy with five times of local steroid injection and sacrificed at the time of eight weeks after the ESD. The esophageal tissues of all pigs were subjected to pathological analyses.

Results
For the pigs without steroid injection, the esophageal stricture was completed around three weeks after the ESD on both endoscopy and esophagography. Histopathological examination of the esophageal tissues revealed that spindle-shaped α-smooth muscle actin (SMA)-positive myofibroblasts arranged in a parallel fashion and extending horizontally were identified at the ulcer bed one week after the ESD, and increased contributing to formation of the stenotic luminal ridge covered with the regenerated epithelium three weeks after the ESD. The proper muscle layer of the stricture site was thinned with some myocytes which seemingly showed transition to the myofibroblast layer. By contrast, for the pig with steroid injection, esophageal stricture formation was not evident with limited appearance of the spindle-shaped myofibroblasts, instead, appearance of stellate or polygocal SMA-positive stromal cells arranged haphazardly in the persistent granulation tissue of the ulcer site.

Conclusions
Proliferation of spindle-shaped myofibroblasts arranged in a parallel fashion is likely to play an important role in stricture formation after circumferential mucosal defects by esophageal ESD, which may be related to the thinning of the proper muscle layer in the healing course of the defects. Local steroid injection seems to be effective to prevent the stricture through the modification of this process.
Analysis of EIF4G1 in ethnic Chinese
Authors: Li Kai , Tang Bei-sha , Guo Ji-feng , Lou Ming-xing , Lv Zhan-yun , Liu Zhen-hua , Tian Yun , Song Cheng-yuan , Xia Kun , Yan Xin-xiang 
Published: April 2013

Abstract

Background
Eukaryotic translation initiation factor 4-gamma 1 (EIF4G1) gene mutations have recently been reported in autosomal dominant, late-onset Parkinson’s disease (LOPD). We carried out genetic analysis to determine the prevalence of EIF4G1 variants in an ethnic Chinese population and to better understand the association between EIF4G1 and PD.

Methods
We conducted a comprehensive genetic analysis of EIF4G1 in a cohort of 29 probands of autosomal dominant, LOPD families. Polymerase chain reaction (PCR) analysis and sequencing was carried out of the entire EIF4G1 exonic regions and exon-intron boundaries. Specific mutation and exonic variants were chosen for further sequencing in a case–control study including 503 sporadic PD and 508 healthy controls. Statistical significance was analyzed by the Chi-square test.

Results
Our analysis revealed three exonic variants (rs2230571, rs13319149 and rs2178403) and eight intronic variants across the entire EIF4G1 gene. No reported mutations were detected in EIF4G1 exonic regions. The synonymous coding variant rs2230571 in exon 27 and the eight intronic variants were not used for further sequencing, but the specific mutation c.3614G > A (p.R1205H) and the two nonsynonymous variants (rs13319149 and rs2178403) were chosen for further analysis in a case–control study. None of the 503 sporadic PD or 508 healthy controls carried p.R1205H, and there was no statistical significance in rs2178403 genotype or allele frequencies in EIF4G1 between the PD cases and the healthy controls (p = 0.184 and p = 0.774, respectively; Chi-square test). The rs13319149 genotype in all PD cases and healthy controls was GG.

Conclusions
Our data indicate that in an ethnic Chinese population, the pathogenic mutation p.R1205H in EIF4G1 is not common and that EIF4G1 exonic variants rs2178403 and rs13319149 are not associated with PD. EIF4G1 does not appear to be a frequent cause of PD in this ethnic Chinese population.
A pilot study: sequential gemcitabine/cisplatin and icotinib as induction therapy for stage IIB to IIIA non-small-cell lung adenocarcinoma
Authors: Lv Chao , Ma Yuanyuan , Feng Qin , Fang Fang , Bai Hua , Zhao Bingtian , Yan Shi , Wu Nan , Zheng Qingfeng , Li Shaolei , Chen Jinfeng , Wang Jia , Feng Yuan , Wang Yuzhao , Pei Yuquan , Fang Jian , Yang Yue 
Published: April 2013

Abstract

Background
A phase II clinical trial previously evaluated the sequential administration of erlotinib after chemotherapy for advanced non-small-cell lung cancer (NSCLC). This current pilot study assessed the feasibility of sequential induction therapy in patients with stage IIB to IIIA NSCLC adenocarcinoma.

Methods
Patients received gemcitabine 1,250 mg/m2 on days 1 and 8 and cisplatin 75 mg/m2 on day 1, followed by oral icotinib (125 mg, three times a day) on days 15 to 28. A repeatcomputed tomography(CT) scan evaluated the response to the induction treatment after two 4-week cycles and eligible patients underwent surgical resection. The primary objective was to assess the objective response rate (ORR), while EGFR and KRAS mutations and mRNA and protein expression levels of ERCC1 and RRM1 were analyzed in tumor tissues and blood samples.

Results
Eleven patients, most with stage IIIA disease, completed preoperative treatment. Five patients achieved partial response according to the Response Evaluation Criteria in Solid Tumors (RECIST) criteria (ORR=45%) and six patients underwent resection. Common toxicities included neutropenia, alanine transaminase (ALT) elevation, fatigue, dry skin, rash, nausea, alopecia and anorexia. No serious complications were recorded perioperatively. Three patients had exon 19 deletions and those with EGFR mutations were more likely to achieve a clinical response (P= 0.083). Furthermore, most cases who achieved a clinical response had low levels of ERCC1 expression and high levels of RRM1.

Conclusions
Two cycles of sequentially administered gemcitabine/cisplatin with icotinib as an induction treatment is a feasible and efficacious approach for stage IIB to IIIA NSCLC adenocarcinoma, which provides evidence for the further investigation of these chemotherapeutic and molecularly targeted therapies.
Improved seam carving for stereo image resizing
Authors: Yue Bin , Hou Chun-ping , Zhou Yuan 
Published: April 2013

Abstract
When stereo images are shown in three-dimensional (3D) display devices of different aspect ratios, the resizing algorithm for single image could lead to shape and depth distortion of the stereo image’s main content. This paper aims to propose a novel method for retargeting stereo image pairs without distorting important objects in the scene while still maintaining the consistency between the left and right images. We extended seam carving algorithm to stereo images. The novelty of our method is that important objects are determined by jointly considering the intensities of gradients and visual fusion area. The retargeted stereo pair has a feasible 3D interpretation that is similar to the original one. Our method protected the important content and reduced the visual distortion in each of the images as well as the depth distortion. Experimental results are presented to demonstrate that the proposed method effectively guaranteed the geometric consistency of resized stereo images.
Existence of solutions and nonnegative solutions for a class of "Equation missing" -Laplacian differential systems with multipoint and integral boundary value conditions
Authors: Zhi Guizhen , Guo Yunrui , Wang Yan , Zhang Qihu 
Published: April 2013

Abstract
This paper explores the existence of solutions for a class of

p
(
t
)

-Laplacian differential systems with multipoint and integral boundary value conditions via Leray-Schauder’s degree. Moreover, the existence of nonnegative solutions is discussed.

MSC:34B10.
Fast CAVLD of H.264/AVC on bitstream decoding processor
Authors: Seo Jung-Han , Jo Hyun-Ho , Sim Dong-Gyu , Kim Doo-Hyun , Song Joon-Ho 
Published: April 2013

Abstract
This paper presents a fast context-based adaptive variable-length decoding (CAVLD) method of H.264/AVC with a very long instruction word-based bitstream processing unit (BsPU) designed for entropy decoding of multiple video formats. A new table mapping algorithm for the coeff_token, level, and run_before syntax elements of the quantized transform coefficients is proposed, and many branch operations are removed by utilizing several designated instructions in the BsPU. By applying designated instructions and the proposed table mapping algorithm to CAVLD, we found that the proposed fast CAVLD method achieves an increase of approximately 47% in the decoding speed and a reduction of approximately 59% in memory requirements for the table mapping.
Secure relay selection based on learning with negative externality in wireless networks
Authors: Zhao Caidan , Xiao Liang , Kang Shan , Chen Guiquan , Li Yunzhou , Huang Lianfen 
Published: April 2013

Abstract
In this paper, we formulate relay selection into a Chinese restaurant game. A secure relay selection strategy is proposed for a wireless network, where multiple source nodes send messages to their destination nodes via several relay nodes, which have different processing and transmission capabilities as well as security properties. The relay selection utilizes a learning-based algorithm for the source nodes to reach their best responses in the Chinese restaurant game. In particular, the relay selection takes into account the negative externality of relay sharing among the source nodes, which learn the capabilities and security properties of relay nodes according to the current signals and the signal history. Simulation results show that this strategy improves the user utility and the overall security performance in wireless networks. In addition, the relay strategy is robust against the signal errors and deviations of some user from the desired actions.
Group I p21-activated kinases facilitate Tax-mediated transcriptional activation of the human T-cell leukemia virus type 1 long terminal repeats
Authors: Chan Ching-Ping , Siu Yeung-Tung , Kok Kin-Hang , Ching Yick-Pang , Tang Hei-Man Vincent , Jin Dong-Yan 
Published: April 2013

Abstract

Background
Human T-cell leukemia virus type 1 (HTLV-1) is the causative agent of adult T-cell leukemia and tropical spastic paraparesis. HTLV-1 encodes transactivator protein Tax that interacts with various cellular factors to modulate transcription and other biological functions. Additional cellular mediators of Tax-mediated transcriptional activation of HTLV-1 long terminal repeats (LTR) remain to be identified and characterized.

Results
In this study, we investigated the regulatory role of group I p21-activated kinases (Paks) in Tax-induced LTR activation. Both wild-type and kinase-dead mutants of Pak3 were capable of potentiating the activity of Tax to activate LTR transcription. The effect of Paks on the LTR was attributed to the N-terminal regulatory domain and required the action of CREB, CREB-regulating transcriptional coactivators (CRTCs) and p300/CREB-binding protein. Paks physically associated with Tax and CRTCs. Paks were recruited to the LTR in the presence of Tax. siRNAs against either Pak1 or Pak3 prevented the interaction of Tax with CRTC1 and the recruitment of Tax to the LTR. These siRNAs also inhibited LTR-dependent transcription in HTLV-1-transformed MT4 cells and in cells transfected with an infectious clone of HTLV-1.

Conclusion
Group I Paks augment Tax-mediated transcriptional activation of HTLV-1 LTR in a kinase-independent manner.
Intellectual disability associated with a homozygous missense mutation in THOC6
Authors: Beaulieu Chandree L , Huang Lijia , Innes A Micheil , Akimenko Marie-Andree , Puffenberger Erik G , Schwartz Charles , Jerry Paul , Ober Carole , Hegele Robert A , McLeod D Ross , Schwartzentruber Jeremy ,   FORGE Canada Consortium, Majewski Jacek , Bulman Dennis E , Parboosingh Jillian S , Boycott Kym M 
Published: April 2013

AbstractBackgroundWe recently described a novel autosomal recessive neurodevelopmental disorder with intellectual disability in four patients from two related Hutterite families. Identity-by-descent mapping localized the gene to a 5.1 Mb region at chromosome 16p13.3 containing more than 170 known or predicted genes. The objective of this study was to identify the causative gene for this rare disorder.Methods and resultsCandidate gene sequencing followed by exome sequencing identified a homozygous missense mutation p.Gly46Arg, inTHOC6. No other potentially causative coding variants were present within the critical region on chromosome 16. THOC6 is a member of the THO/TREX complex which is involved in coordinating mRNA processing with mRNA export from the nucleus.In situhybridization showed thatthoc6is highly expressed in the midbrain and eyes. Cellular localization studies demonstrated that wild-type THOC6 is present within the nucleus as is the case for other THO complex proteins. However, mutant THOC6 was predominantly localized to the cytoplasm, suggesting that the mutant protein is unable to carry out its normal function. siRNA knockdown ofTHOC6revealed increased apoptosis in cultured cells.ConclusionOur findings associate a missense mutation inTHOC6with intellectual disability, suggesting the THO/TREX complex plays an important role in neurodevelopment.
Characterization of the biology and infectivity of Leishmania infantum viscerotropic and dermotropic strains isolated from HIV+ and HIV- patients in the murine model of visceral leishmaniasis
Authors: Cunha Joana , Carrillo Eugenia , Sánchez Carmen , Cruz Israel , Moreno Javier , Cordeiro-da-Silva Anabela 
Published: April 2013

AbstractBackgroundLeishmaniasis is a group of diseases with a variety of clinical manifestations. The form of the disease is highly dependent on the infectiveLeishmaniaspecies and the immunological status of the host. The infectivity of the parasite strain also plays an important role in the progression of the infection. The aim of this work is to understand the influence of the natural infectivity ofLeishmaniastrains in the outcome of visceral leishmaniasis.MethodsIn this study we have characterized four strains ofL. infantumin terms of molecular typing,in vitrocultivation and differentiation. Two strains were isolated from HIV+ patients with visceral leishmaniasis (Bibiano and E390M), one strain was isolated from a cutaneous lesion in an immunocompetent patient (HL) and another internal reference strain causative of visceral leishmaniasis (ST) also from an immunocompetent patient was used for comparison. For this objective, we have compared their virulence byin vitroandin vivoinfectivity in a murine model of visceral leishmaniasis.ResultsMolecular typing unraveled a newk26sequence attributed to MON-284 zymodeme and allowed the generation of a molecular signature for the identification of each strain.In vitrocultivation enabled the production of promastigotes with comparable growth curves and metacyclogenesis development. The HL strain was the most infective, showing the highest parasite loadsin vitrothat were corroborated with thein vivoassays, 6 weeks post-infection in BALB/c mice. The two strains isolated from HIV+ patients, both belonging to two different zymodemes, revealed different kinetics of infection.ConclusionDifferences ininvitro andin vivoinfectivity found in the murine model were then attributed to intrinsic characteristics of each strain. This work is supported by other studies that present the parasite’s inherent features as factors for the multiplicity of clinical manifestations and severity of leishmaniasis.
Ammonia-oxidizing archaea and bacteria are structured by geography in biological soil crusts across North American arid lands
Authors: Marusenko Yevgeniy , Bates Scott T , Anderson Ian , Johnson Shannon L , Soule Tanya , Garcia-Pichel Ferran 
Published: April 2013

Abstract

Introduction
Biological soil crusts (BSCs) can dominate surface cover in dry lands worldwide, playing an integral role in arid land biogeochemistry, particularly in N fertilization through fixation and cycling. Nitrification is a characteristic and universal N transformation in BSCs that becomes important for the export of N beyond the microscopic bounds of the crust itself. The contribution of ammonia-oxidizing bacteria (AOB) in BSCs has been shown, but the role and extent of the recently discovered ammonia-oxidizing archaea (AOA) have not.

Methods
We sampled various types of crusts in four desert regions across the western United States and characterized the composition and size of ammonia-oxidizing communities using clone libraries and quantitative PCR targeting the amoA gene, which codes for the ammonia monooxygenase enzyme, universally present in ammonia-oxidizing microbes.

Results
All archaeal amoA sequences retrieved from BSCs belonged to the Thaumarchaeota (Nitrososphaera associated Group I.1b). Sequences from the Sonoran Desert, Colorado Plateau, and Great Basin were indistinguishable from each other but distinct from those of the Chihuahuan Desert. Based on amoA gene abundances, archaeal and bacterial ammonia oxidizers were ubiquitous in our survey, but the ratios of archaeal to bacterial ammonia oxidizers shifted from bacterially dominated in northern, cooler deserts to archaeally dominated in southern, warmer deserts.

Conclusions
Archaea are shown to be potentially important biogeochemical agents of biological soil crust N cycling. Conditions associated with different types of BSCs and biogeographical factors reveal a niche differentiation between AOA and AOB, possibly driven by temperature.
Effects of illness duration and treatment resistance on grey matter abnormalities in majordepression
Authors: Serra-Blasco Maria , Portella Maria J. , Gómez-Ansón Beatriz , de Diego-Adeliño Javier , Vives-Gilabert Yolanda , Puigdemont Dolors , Granell Ester , Santos Alicia , Álvarez Enric , Pérez Víctor 
Published: April 2013

BackgroundFindings of brain structural changes in major depressive disorder are still inconsistent, partly because some crucial clinical variables have not been taken into account.AimsTo investigate the effect of major depressive disorder on grey matter volumes.MethodVoxel-based morphometry was used to compare 66 patients with depression at different illness stages (22 each with first-episode, remitted-recurrent and treatment resistant/chronic depression) with 32 healthy controls. Brain volumes were correlated with clinical variables.ResultsVoxel-based morphometry showed a significant group effect in right superior frontal gyrus, left medial frontal gyrus and left cingulate gyrus (P<0.05, family wise error-corrected). Patients whose condition was treatment resistant/chronic exhibited the smallest volumes in frontotemporal areas. Longer illness duration was negatively correlated with decreases in right medial frontal cortex and left insula.ConclusionsFrontotemporolimbic areas are smaller in the patients with severe depression and are associated with duration of illness, but not with medication patterns, suggesting negative effects of long-lasting major depressive disorder on grey matter.
Incidence and 12-Month Outcome of Non-Transient Childhood Conversion Disorder in the Uk and Ireland
Authors: Ani Cornelius , Reading Richard , Lynn Richard , Forlee Simone , Garralda Elena 
Published: April 2013

BackgroundLittle is known about conversion disorder in childhood.AimsTo document clinical incidence, features, management and 12-month outcome of non-transient conversion disorder in under 16-year-olds in the UK and Ireland.MethodSurveillance through the British Paediatric Surveillance Unit and Child and Adolescent Psychiatry Surveillance System.ResultsIn total, 204 cases (age range 7-15 years) were reported, giving a 12-month incidence of 1.30/100 000 (95% CI 1.11-1.52). The most common symptoms were motor weakness and abnormal movements. Presentation with multiple symptoms was the norm. Antecedent stressors were reported for 80.8%, most commonly bullying in school. Most children required in-patient admission with frequent medical investigations. Follow-up at 12 months was available for 147 children, when all conversion disorder symptoms were reported as improved. Most families (91%) accepted a nonmedical explanation of the symptoms either fully or partially.ConclusionsChildhood conversion disorder represents an infrequent but significant clinical burden in the UK and Ireland.