bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association analysis of frost tolerance in rye using candidate genes and phenotypic data from controlled, semi-controlled, and field phenotyping platforms
Authors: Li Yongle , Böck Andreas , Haseneyer Grit , Korzun Viktor , Wilde Peer , Schön Chris-Carolin , Ankerst Donna P , Bauer Eva 
Published: October 2011

Abstract

Background
Frost is an important abiotic stress that limits cereal production in the temperate zone. As the most frost tolerant small grain cereal, rye (Secale cereale L.) is an ideal cereal model for investigating the genetic basis of frost tolerance (FT), a complex trait with polygenic inheritance. Using 201 genotypes from five Eastern and Middle European winter rye populations, this study reports a multi-platform candidate gene-based association analysis in rye using 161 single nucleotide polymorphisms (SNPs) and nine insertion-deletion (Indel) polymorphisms previously identified from twelve candidate genes with a putative role in the frost responsive network.

Results
Phenotypic data analyses of FT in three different phenotyping platforms, controlled, semi-controlled and field, revealed significant genetic variations in the plant material under study. Statistically significant (P < 0.05) associations between FT and SNPs/haplotypes of candidate genes were identified. Two SNPs in ScCbf15 and one in ScCbf12, all leading to amino acid exchanges, were significantly associated with FT over all three phenotyping platforms. Distribution of SNP effect sizes expressed as percentage of the genetic variance explained by individual SNPs was highly skewed towards zero with a few SNPs obtaining large effects. Two-way epistasis was found between 14 pairs of candidate genes. Relatively low to medium empirical correlations of SNP-FT associations were observed across the three platforms underlining the need for multi-level experimentation for dissecting complex associations between genotypes and FT in rye.

Conclusions
Candidate gene based-association studies are a powerful tool for investigating the genetic basis of FT in rye. Results of this study support the findings of bi-parental linkage mapping and expression studies that the Cbf gene family plays an essential role in FT.
Decreasing incidence of severe malaria and community-acquired bacteraemia among hospitalized children in Muheza, north-eastern Tanzania, 2006-2010
Authors: Mtove George , Amos Ben , Nadjm Behzad , Hendriksen Ilse CE , Dondorp Arjen M , Mwambuli Abraham , Kim Deok Ryun , Ochiai R Leon , Clemens John D , von Seidlein Lorenz , Reyburn Hugh , Deen Jacqueline 
Published: October 2011

Abstract

Background
The annual incidence and temporal trend of severe malaria and community-acquired bacteraemia during a four-year period in Muheza, Tanzania was assessed.

Methods
Data on severely ill febrile children aged 2 months to 14 years from three prospective studies conducted at Muheza District Hospital from 2006 to 2010 was pooled and analysed. On admission, each enrolled child had a thin and thick blood film and at least one rapid diagnostic test for falciparum malaria, as well as a blood culture. The annual incidence of bacteraemia and severe malaria among children coming from Muheza was calculated and their temporal trend was assessed.

Results
Overall, 1, 898 severe falciparum malaria and 684 bacteraemia cases were included. Of these, 1, 356 (71%) and 482 (71%), respectively, were from the referral population of Muheza. The incidence of falciparum malaria and all-cause bacteraemia in Muheza decreased five-fold and three-fold, respectively, from the first to the fourth year of surveillance (p < 0.0001). During this period, the median ages of children from Muheza admitted with severe malaria increased from 1.7 to 2.5 years (p < 0.0001). The reduction in all-cause bacteraemia was mainly driven by the 11-fold decline in the incidence of non-typhoidal salmonellosis. The annual incidences of Haemophilus influenzae and pneumococcal invasive bacterial infections decreased as well but were much fewer in number.

Conclusions
These results add to the growing evidence of the decline in malaria associated with a decrease in non-typhoidal salmonellosis and possibly other bacteraemias. Malarial prevention and control strategies may provide a greater benefit than the mere reduction of malaria alone.
Performance evaluation of a motor-imagery-based EEG-Brain computer interface using a combined cue with heterogeneous training data in BCI-Naive subjects
Authors: Choi Donghag , Ryu Yeonsoo , Lee Youngbum , Lee Myoungho 
Published: October 2011

Abstract

Background
The subjects in EEG-Brain computer interface (BCI) system experience difficulties when attempting to obtain the consistent performance of the actual movement by motor imagery alone. It is necessary to find the optimal conditions and stimuli combinations that affect the performance factors of the EEG-BCI system to guarantee equipment safety and trust through the performance evaluation of using motor imagery characteristics that can be utilized in the EEG-BCI testing environment.

Methods
The experiment was carried out with 10 experienced subjects and 32 naive subjects on an EEG-BCI system. There were 3 experiments: The experienced homogeneous experiment, the naive homogeneous experiment and the naive heterogeneous experiment. Each experiment was compared in terms of the six audio-visual cue combinations and consisted of 50 trials. The EEG data was classified using the least square linear classifier in case of the naive subjects through the common spatial pattern filter. The accuracy was calculated using the training and test data set. The p-value of the accuracy was obtained through the statistical significance test.

Results
In the case in which a naive subject was trained by a heterogeneous combined cue and tested by a visual cue, the result was not only the highest accuracy (p < 0.05) but also stable performance in all experiments.

Conclusions
We propose the use of this measuring methodology of a heterogeneous combined cue for training data and a visual cue for test data by the typical EEG-BCI algorithm on the EEG-BCI system to achieve effectiveness in terms of consistence, stability, cost, time, and resources management without the need for a trial and error process.
Performance characterization of CSMA/CA adapted multi-user MIMO aware MAC in WLANs
Authors: Thapa Anup , Pudasaini Subodh , Shin Seokjoo 
Published: October 2011

Abstract
To realize the multi-user multiple input multiple output (MIMO) advantage over WLANs, it requires significant changes in the MAC protocol. Either the dominant MAC protocol carrier sense multiple access/collision avoidance (CSMA/CA) needs to be replaced by a novel multi-user MIMO aware MAC protocol or it should be upgraded into multi-user MIMO aware CSMA/CA. Nevertheless, the simplest approach would be upgrading the CSMA/CA. Simple modifications in the control packets format and/or the channel access mechanism can upgrade CSMA/CA into simple, yet practicable, multi-user MIMO aware MAC protocol. By utilizing convenient changes, several modification approaches can be provisioned for this purpose. Hence, it is important to understand their performance benefits and trade-offs. In this article, we discuss some of such modification approaches that best represent the possible modifications. We provide their detail performance analysis based on analytical modeling and derived expressions in terms of throughput and delay. We also derive expressions for achievable performance and present their performance limits too.
Increased HCMV seroprevalence in patients with hepatocellular carcinoma
Authors: Lepiller Quentin , Tripathy Manoj K , Di Martino Vincent , Kantelip Bernadette , Herbein Georges 
Published: October 2011

Abstract

Background
Hepatocellular carcinoma (HCC) is the most common primary liver cancer, usually arising after years of chronic liver inflammation that could result from viral infections such as hepatitis B virus (HBV) and hepatitic C virus (HCV) infections. Human cytomegalovirus (HCMV) infects primary human hepatocytes and remains an important cause of morbidity in immunocompromised persons where it may manifest as symptomatic end-organ disease including hepatitis. The goal of the present study was to determine a potential correlation between HCMV infection and the appearance of HCC.

Methods
First, we analyzed the seroprevalence of HCMV in a cohort of 11,318 patients hospitalized between 2003 and 2009 in different departments of a French University Hospital. Second, we studied HCMV seroprevalence in a cohort of 190 subjects who were stratified on the basis of age, gender, HCC, cirrhosis (Cir), and the exposition to hepatotropic viruses (HCV, HBV). We further determined whether HCMV DNA was present specifically in tumour area in liver biopsies from HCC-positive patients by using nested PCR.

Results
We found that the HCMV seroprevalence was high in the Hepatology department. The HCMV seroprevalence was significantly higher in patients infected with HCV and/or HBV than in patients who were not infected by those later viruses (76.2% versus 56.5%, p < 0.001). The HCMV seroprevalence was significantly higher in patients with HCC (74%) and lower in patients without HCC (54% for HCC-/Cir+ patients, 57% for HCC-/Cir- subjects). We observed a positive correlation between serum IL-6 levels and HCMV seroprevalence in cirrhotic patients, but not in HCC patients. Serum IL-6 levels correlated positively with C-reactive protein (CRP) levels. Preliminary histological studies from liver biopsies from HCC-positive patients highlighted that HCMV DNA can be detected in tumour area of some of the patients studied.

Conclusions
Our results indicate that HCMV seroprevalence in patients with HCC is significantly higher than in patients without HCC, is positively correlated with serum IL-6 levels in cirrhotic patients, and is positively associated with the presence of other hepatotropic viruses such as HCV and HBV.
Incidence and risk factors for malaria, pneumonia and diarrhea in children under 5 in UNHCR refugee camps: A retrospective study
Authors: Hershey Christine L , Doocy Shannon , Anderson Jamie , Haskew Christopher , Spiegel Paul , Moss William J 
Published: October 2011

Abstract

Background
United Nations High Commissioner for Refugees (UNHCR) refugee camps are located predominantly in rural areas of Africa and Asia in protracted or post-emergency contexts. Recognizing the importance of malaria, pneumonia and diarrheal diseases as major causes of child morbidity and mortality in refugee camps, we analyzed data from the UNHCR Health Information System (HIS) to estimate incidence and risk factors for these diseases in refugee children younger than five years of age.

Methods
Data from 90 UNHCR camps in 16 countries, including morbidity, mortality, health services and refugee health status, were obtained from the UNHCR HIS for the period January 2006 to February 2010. Monthly camp-level data were aggregated to yearly estimates for analysis and stratified by location in Africa (including Yemen) or Asia. Poisson regression models with random effects were constructed to identify factors associated with malaria, pneumonia and diarrheal diseases. Spatial patterns in the incidence of malaria, pneumonia and diarrheal diseases were mapped to identify regional heterogeneities.

Results
Malaria and pneumonia were the two most common causes of mortality, with confirmed malaria and pneumonia each accounting for 20% of child deaths. Suspected and confirmed malaria accounted for 23% of child morbidity and pneumonia accounted for 17% of child morbidity. Diarrheal diseases were the cause of 7% of deaths and 10% of morbidity in children under five. Mean under-five incidence rates across all refugee camps by region were: malaria [Africa 84.7 cases/1000 U5 population/month (95% CI 67.5-102.0), Asia 2.2/1000/month (95% CI 1.4-3.0)]; pneumonia [Africa 59.2/1000/month (95% CI 49.8-68.7), Asia 254.5/1000/month (95% CI 207.1-301.8)]; and diarrheal disease [Africa 35.5/1000/month (95% CI 28.7-42.4), Asia 69.2/1000/month (95% CI 61.0-77.5)]. Measles was infrequent and accounted for a small proportion of child morbidity (503 cases, < 1%) and mortality (6 deaths, < 1%).

Conclusions
As in stable settings, pneumonia and diarrhea are important causes of mortality among refugee children. Malaria remains a significant cause of child mortality in refugee camps in Africa and will need to be addressed as part of regional malaria control and elimination efforts. Little is known of neonatal morbidity and mortality in refugee settings, and neonatal deaths are likely to be under-reported. Global measles control efforts have reduced the incidence of measles among refugee children.
Quantitative copy number analysis by Multiplex Ligation-dependent Probe Amplification (MLPA) of BRCA1-associated breast cancer regions identifies BRCAness
Authors: Lips Esther H , Laddach Nadja , Savola Suvi P , Vollebergh Marieke A , Oonk Anne MM , Imholz Alex LT , Wessels Lodewyk FA , Wesseling Jelle , Nederlof Petra M , Rodenhuis Sjoerd 
Published: October 2011

Abstract
Introduction
Our group has previously employed array Comparative Genomic Hybridization (aCGH) to assess the genomic patterns of BRCA1-mutated breast cancers. We have shown that the so-called BRCA1-likeaCGH profile is also present in about half of all triple-negative sporadic breast cancers and is predictive for benefit from intensified alkylating chemotherapy. As aCGH is a rather complex method, we translated the BRCA1aCGH profile to a Multiplex Ligation-dependent Probe Amplification (MLPA) assay, to identify both BRCA1-mutated breast cancers and sporadic cases with a BRCA1-likeaCGH profile.

Methods
The most important genomic regions of the original aCGH based classifier (3q22-27, 5q12-14, 6p23-22, 12p13, 12q21-23, 13q31-34) were mapped to a set of 34 MLPA probes. The training set consisted of 39 BRCA1-likeaCGH breast cancers and 45 non-BRCA1-likeaCGH breast cancers, which had previously been analyzed by aCGH. The BRCA1-likeaCGH group consisted of germline BRCA1-mutated cases and sporadic tumours with low BRCA1 gene expression and/or BRCA1 promoter methylation. We trained a shrunken centroids classifier on the training set and validation was performed on an independent test set of 40 BRCA1-likeaCGH breast cancers and 32 non-BRCA1-likeaCGH breast cancer tumours. In addition, we validated the set prospectively on 69 new triple-negative tumours.

Results
BRCAness in the training set of 84 tumours could accurately be predicted by prediction analysis of microarrays (PAM) (accuracy 94%). Application of this classifier on the independent validation set correctly predicted BRCA-like status of 62 out of 72 breast tumours (86%). Sensitivity and specificity were 85% and 87%, respectively. When the MLPA-test was subsequently applied to 46 breast tumour samples from a randomized clinical trial, the same survival benefit for BRCA1-like tumours associated with intensified alkylating chemotherapy was shown as was previously reported using the aCGH assay.

Conclusions
Since the MLPA assay can identify BRCA1-deficient breast cancer patients, this method could be applied both for clinical genetic testing and as a predictor of treatment benefit. BRCA1-like tumours are highly sensitive to chemotherapy with DNA damaging agents, and most likely to poly ADP ribose polymerase (PARP)-inhibitors. The MLPA assay is rapid and robust, can easily be multiplexed, and works well with DNA derived from paraffin-embedded tissues.
Accurate calculation of the bound states of the quantum dipole problem in two dimensions
Authors: Amore Paolo 
Published: October 2011

Abstract
We present an accurate calculation of the energies of the bound states of the quantumdipole problemin two dimensions using a Rayleigh-Ritz approach. We obtain an upper bound for the energy of the ground state, which is by far the most precise in the literature for this problem. We also obtain an alternative estimate of the fundamental energy of the model performing an extrapolation of the results corresponding to different subspaces. Finally, our calculation of the energies of the first 500 states shows a perfect agreement with the expected asymptotic behavior.
Vegetation history reconstructed from anthracology and pollen analysis at the rescue excavation of the MO Motorway, Hungary
Authors: Náfrádi Katalin , Bodor Elvira , Törőcsik Tünde , Sümegi Pál 
Published: October 2011

AbstractThe significance of geoarchaeological investigations is indisputable in reconstructing the former environment and in studying the relationship between humans and their surroundings. Several disciplines have developed during the last few decades to give insight into earlier time periods and their climatic conditions (e.g. palynology, malacology, archaeobotany, phytology and animal osteology). Charcoal and pollen analytical studies from the rescue excavation of the MO motorway provide information about the vegetation changes of the past. These methods are used to reconstruct the environment of the former settlements and to detect the human impact and natural climatic changes. The sites examined span the periods of the Late-Copper Age, Late-Bronze Age, Middle-Iron Age, Late-Iron Age, Sarmatian period, Late Sarmatian period, Migration period, Late-Migration period and Middle Ages. The vegetation before the Copper Age is based only on pollen analytical data. Anthracological results show the overall dominance of Quercus and a great number of Ulmus, Fraxinus, Acer, Fagus, Alnus and Populus/Salix tree fossils, as well as the residues of fruit trees present in the charred wood assemblage.
Finite element analysis of endodontically treated tooth restored with different posts under thermal and mechanical loading
Authors: ADIGÜZEL Ozkan , YİĞİT ÖZER Senem , BAHŞİ Emrullah , YAVUZ İzzet 
Published: October 2011

Aim: This study compared the stress distributions of endodontically treated tooth restored with carbon and titanium post under thermal and mechanical loading conditions.
Methodology: A 3-dimensional finite element model was created to represent in a labiolingual cross-sectional view of an endodontically treated maxillary central incisor tooth with its supporting structures. It was modified according to two post systems with different physical properties consisting titanium, and carbon fiber. Stress distribution and stress values were then calculated by considering the three dimensional von Mises stress criteria.
Results: A 100-N static vertical occlusal load was applied on the node at the center of occlusal surface of the tooth. The von Mises stress values for carbon post model was on the coronal third and the cervical area of the root in the range of 436,16 and 3,59 MPa, for titanium post model was 590,55 and 3,05 MPa. Thermal stress values for carbon post model showed that maximum stress concentrations were noted on the coronal third and the top of the post area of the root in the range of 509,94 and 6,38 MPa. Titanium post model showed that maximum stress concentrations were noted on the coronal third and top of the post area of the root in the range of 1165,06 and 3,06 MPa.
Conclusion: This study shows that the titanium post yields larger stresses than the carbon post under thermal conditions.
How to cite this article: Adıgüzel Ö, Yiğit Özer S, Bahşi E, Yavuz İ. Finite element analysis of endodontically treated tooth restored with different posts under thermal and mechanical loading. Int Dent Res 2011;3:75-80.
Linguistic Revision: The English in this manuscript has been checked by at least two professional editors, both native speakers of English.
Gynecologic Cytology Proficiency Testing Failures: What Have We Learned?: Observations From the College of American Pathologists Gynecologic Cytology Proficiency Testing Program
Authors: Ducatman Barbara S. , Bentz Joel S. , Fatheree Lisa A. , Souers Rhona , Ostrowski Saula , Moriarty Ann T. , Henry Michael , Laucirica Rodolfo , Booth Christine N. , Wilbur David C. ,   for the Cytopathology Resource Committee, College of American Pathologists
Published: October 2011

Context.—In 2006, the first gynecologic cytology proficiency tests were offered by the College of American Pathologists. Four years of data are now available using field-validated slides, including conventional and liquid-based Papanicolaou tests.Objective.—To characterize the pattern of error types that resulted in initial proficiency-test failure for cytotechnologists, primary screening pathologists, and secondary pathologists (those whose slides are prescreened by cytotechnologists).Design.—The results of 37 029 initial College of American Pathologists Papanicolaou proficiency tests were reviewed from 4 slide-set modules: conventional, ThinPrep, SurePath, or a module containing all 3 slide types.Results.—During this 4-year period, cytotechnologists were least likely to fail the initial test (3.4%; 614 of 18 264), followed by secondary pathologists (ie, those reviewing slides already screened by a cytotechnologist) with a failure rate of 4.2% (728 of 17 346), and primary pathologists (ie, those screening their own slides) having the highest level of failure (13.7%; 194 of 1419). Failure rates have fallen for all 3 groups over time. Pathologists are graded more stringently on proficiency tests, and more primary pathologists would have passed if they had been graded as cytotechnologists. There were no significant differences among performances using different types of slide sets. False-positive errors were common for both primary (63.9%; 124 of 194 errors) and secondary (55.6%; 405 of 728 errors) pathologists, whereas automatic failures were most common for cytotechnologists (75.7%; 465 of 614 errors).Conclusions.—The failure rate is decreasing for all participants. The failures for primary pathologist screeners are due to false-positive responses. Primary screening cytotechnologists and secondary pathologists have automatic failures more often than do primary screening pathologists.
Voice Recognition Technology Implementation in Surgical Pathology: Advantages and Limitations
Authors: Singh Meenakshi , Pal Timothy R. 
Published: October 2011

Context.—Voice recognition technology (VRT) has been in use for medical transcription outside of laboratories for many years, and in recent years it has evolved to a level where it merits consideration by surgical pathologists.Objective.—To determine the feasibility and impact of making a transition from a transcriptionist-based service to VRT in surgical pathology.Design.—We have evaluated VRT in a phased manner for sign out of general and subspecialty surgical pathology cases after conducting a pilot study. We evaluated the effect on turnaround time, workflow, staffing, typographical error rates, and the overall ability of VRT to be adapted for use in surgical pathology.Results.—The stepwise implementation of VRT has resulted in real-time sign out of cases and improvement in average turnaround time from 4 to 3 days. The percentage of cases signed out in 1 day improved from 22% to 37%. Amendment rates for typographical errors have decreased. Use of templates and synoptic reports has been facilitated. The transcription staff has been reassigned to other duties and is successfully assisting in other areas. Resident involvement and exposure to complete case sign out has been achieved resulting in a positive impact on resident education.Conclusions.—Voice recognition technology allows for a seamless workflow in surgical pathology, with improvements in turnaround time and a positive impact on competency-based resident education. Individual practices may assess the value of VRT and decide to implement it, potentially with gains in many aspects of their practice.