bluuebunny/crossref_metadata_2025_split huggingface dataset:
How Do Agricultural Policy Restrictions on Global Trade and Welfare Differ Across Commodities?
Authors: Croser Johanna L. , Lloyd Peter J. , Anderson Kym 
Published: April 2010

AbstractFor decades the world's agricultural markets have been highly distorted by government policies, but differently for different commodities such that a ranking of weighted average nominal rates of assistance across countries can be misleading as an indicator of the trade or welfare effects of policies affecting global markets. This article develops two theory‐based indicators, drawing on the recent literature on trade restrictiveness indexes. It estimates those indicators for each of 28 key agricultural commodities from 1960 to 2004, based on a sample of 75 countries that together account for more than three‐quarters of the world's production of those agricultural commodities.
A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval
Authors: Swamidass S. Joshua , Azencott Chloé-Agathe , Daily Kenny , Baldi Pierre 
Published: April 2010

Abstract
Motivation: The performance of classifiers is often assessed using Receiver Operating Characteristic ROC [or (AC) accumulation curve or enrichment curve] curves and the corresponding areas under the curves (AUCs). However, in many fundamental problems ranging from information retrieval to drug discovery, only the very top of the ranked list of predictions is of any interest and ROCs and AUCs are not very useful. New metrics, visualizations and optimization tools are needed to address this ‘early retrieval’ problem.
Results: To address the early retrieval problem, we develop the general concentrated ROC (CROC) framework. In this framework, any relevant portion of the ROC (or AC) curve is magnified smoothly by an appropriate continuous transformation of the coordinates with a corresponding magnification factor. Appropriate families of magnification functions confined to the unit square are derived and their properties are analyzed together with the resulting CROC curves. The area under the CROC curve (AUC[CROC]) can be used to assess early retrieval. The general framework is demonstrated on a drug discovery problem and used to discriminate more accurately the early retrieval performance of five different predictors. From this framework, we propose a novel metric and visualization—the CROC(exp), an exponential transform of the ROC curve—as an alternative to other methods. The CROC(exp) provides a principled, flexible and effective way for measuring and visualizing early retrieval performance with excellent statistical power. Corresponding methods for optimizing early retrieval are also described in the Appendix.
Availability: Datasets are publicly available. Python code and command-line utilities implementing CROC curves and metrics are available at http://pypi.python.org/pypi/CROC/
Contact: pfbaldi@ics.uci.edu
Small RNAs in angiosperms: sequence characteristics, distribution and generation
Authors: Chen Dijun , Meng Yijun , Ma Xiaoxia , Mao Chuanzao , Bai Youhuang , Cao Junjie , Gu Haibin , Wu Ping , Chen Ming 
Published: April 2010

Abstract
High-throughput sequencing (HTS) has opened up a new era for small RNA (sRNA) exploration. Using HTS data for a global survey of sRNAs in 26 angiosperms, elevated GC contents were detected in the monocots, whereas the 5′-terminal compositions were quite uniform among the angiosperms. Chromosome-wide distribution patterns of sRNAs were investigated by using scrolling-window analysis. We performed de novo natural antisense transcript (NAT) prediction, and found that the overlapping regions of trans-NATs, but not cis-NATs, were hotspots for sRNA generation. One cis-NAT generates phased natural antisense short interfering RNAs (nat-siRNAs) specifically from flowers in Arabidopsis, while one in rice produces phased nat-siRNAs from grains, suggesting their organ-specific regulatory roles.
Contact: clspwu@zju.edu.cn; mchen@zju.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Correction of sequencing errors in a mixed set of reads
Authors: Salmela Leena 
Published: April 2010

Abstract
Motivation: High-throughput sequencing technologies produce large sets of short reads that may contain errors. These sequencing errors make de novo assembly challenging. Error correction aims to reduce the error rate prior assembly. Many de novo sequencing projects use reads from several sequencing technologies to get the benefits of all used technologies and to alleviate their shortcomings. However, combining such a mixed set of reads is problematic as many tools are specific to one sequencing platform. The SOLiD sequencing platform is especially problematic in this regard because of the two base color coding of the reads. Therefore, new tools for working with mixed read sets are needed.
Results: We present an error correction tool for correcting substitutions, insertions and deletions in a mixed set of reads produced by various sequencing platforms. We first develop a method for correcting reads from any sequencing technology producing base space reads such as the SOLEXA/Illumina and Roche/454 Life Sciences sequencing platforms. We then further refine the algorithm to correct the color space reads from the Applied Biosystems SOLiD sequencing platform together with normal base space reads. Our new tool is based on the SHREC program that is aimed at correcting SOLEXA/Illumina reads. Our experiments show that we can detect errors with 99% sensitivity and &gt;98% specificity if the combined sequencing coverage of the sets is at least 12. We also show that the error rate of the reads is greatly reduced.
Availability: The JAVA source code is freely available at http://www.cs.helsinki.fi/u/lmsalmel/hybrid-shrec/
Contact: leena.salmela@cs.helsinki.fi
Structural variation analysis with strobe reads
Authors: Ritz Anna , Bashir Ali , Raphael Benjamin J. 
Published: April 2010

AbstractMotivation: Structural variation including deletions, duplications and rearrangements of DNA sequence are an important contributor to genome variation in many organisms. In human, many structural variants are found in complex and highly repetitive regions of the genome making their identification difficult. A new sequencing technology called strobe sequencing generates strobe reads containing multiple subreads from a single contiguous fragment of DNA. Strobe reads thus generalize the concept of paired reads, or mate pairs, that have been routinely used for structural variant detection. Strobe sequencing holds promise for unraveling complex variants that have been difficult to characterize with current sequencing technologies.Results: We introduce an algorithm for identification of structural variants using strobe sequencing data. We consider strobe reads from a test genome that have multiple possible alignments to a reference genome due to sequencing errors and/or repetitive sequences in the reference. We formulate the combinatorial optimization problem of finding the minimum number of structural variants in the test genome that are consistent with these alignments. We solve this problem using an integer linear program. Using simulated strobe sequencing data, we show that our algorithm has better sensitivity and specificity than paired read approaches for structural variation identification.Contact: braphael@brown.edu
Nestin is expressed in HMB‐45 negative melanoma cells in dermal parts of nodular melanoma
Authors: KANOH Maho , AMOH Yasuyuki , TANABE Kenichi , MAEJIMA Hideki , TAKASU Hiroshi , KATSUOKA Kensei 
Published: April 2010

AbstractNestin, a marker of neural stem cells, is expressed in the stem cells of the mouse hair follicle. The nestin‐expressing hair follicle stem cells can differentiate into neurons, glia, keratocytes, smooth muscle cells and melanocytes in vitro. These pluripotent nestin‐expressing stem cells are keratin 15 (K15)‐negative, suggesting that they are in a relatively undifferentiated state. Recent studies suggest that the epithelial stem cells are important in tumorigenesis, and nestin expression is thought to be important in tumorigenesis. In the present study, we examined the expression of the hair follicle and neural stem cell marker nestin, as well as S‐100 and HMB‐45, in melanoma. Nestin immunoreactivity was observed in the HMB‐45‐negative melanoma cells in all five cases of amelanotic nodular melanomas. Moreover, nestin immunoreactivity was observed in the dermal parts in seven of 10 cases of melanotic nodular melanomas. Especially, nestin immunoreactivity was observed in the HMB‐45‐negative melanoma cells in the dermal parts of all 10 cases of HMB‐45‐negative amelanotic and melanotic nodular melanomas. On the other hand, nestin expression was negative in 10 of 12 cases of superficial spreading melanoma. These results suggest that nestin is an important marker of HMB‐45‐negative melanoma cells in the dermal parts of patients with nodular melanoma.
Positive treatment effects of ustekinumab in psoriasis: Analysis of lesional and systemic parameters
Authors: REDDY Manjula , TORRES Gisela , McCORMICK Thomas , MARANO Colleen , COOPER Kevin , YEILDING Newman , WANG Yuhua , PENDLEY Charles , PRABHAKAR Uma , WONG Jackson , DAVIS Cuc , XU Stephen , BRODMERKEL Carrie 
Published: April 2010

AbstractUstekinumab, a human anti‐interleukin (IL)‐12/IL‐23p40 monoclonal antibody has demonstrated significant efficacy in patients with moderate‐to‐severe psoriasis. Skin lesion biopsies, cell surface markers on peripheral blood lymphocytes, and ex vivo T‐helper (Th)1/Th2 cytokine responses from peripheral blood mononuclear cells (PBMC) from patients receiving ustekinumab 45 or 90 mg, or placebo were evaluated at baseline and week 12. Inflammatory serum protein levels were measured at baseline, week 2 and week 12. At week 12, median epidermal thickness decreased from 312.1 to 132.7 μm, and median levels of cellular proliferation (Ki67) and T‐cell infiltration (CD3) decreased by 84.3% and 70.7%, respectively, in the combined ustekinumab group (all P ≤ 0.002). Serum levels of tumor necrosis factor (TNF)‐α, C‐C motif ligand 27 (CCL27) and other inflammatory cytokines remained unchanged. Minimal variation in the percentage of T cells expressing cutaneous lymphocyte antigen (CLA) was observed following ustekinumab treatment, with no significant variation in the percentage of cells expressing CD45RA, CD45RO, CD25, human leukocyte antigen‐DR (HLA‐DR), and C‐X‐C motif receptor 3 (CXCR3). No apparent effect on the magnitude of Th1/Th2 responses to external stimuli in PBMC was observed following placebo or ustekinumab treatment. Ustekinumab improves histological psoriasis measures, with minimal impact on the systemic immune system.
Role of the subgroups of T, B, natural killer lymphocyte and serum levels of interleukin‐15, interleukin‐21 and immunoglobulin E in the pathogenesis of urticaria
Authors: HUILAN Zhu , RUNXIANG Li , BIHUA Liang , QING Guo 
Published: April 2010

AbstractThe immunological characterization in the pathogenesis of urticaria, mainly regarding cytokine profile, needs more investigation. In this study, subgroups of the T, B and natural killer (NK) lymphocyte from peripheral blood and serum levels of interleukin (IL)‐15, IL‐21 and immunoglobulin (Ig)E were examined in patients with acute urticaria (AU) and chronic urticaria (CU). Moreover, symptom scores and course of the patients were assessed. The percentage of NK cells and the ratio of CD4+/CD8+ increased, however, CD8+ decreased in CU compared to controls (P < 0.01). But no significant changes of T, B and NK lymphocyte were found in AU. IL‐15 and IL‐21 significantly decreased in AU and CU, but IgE increased. CU with a positive autologous serum skin test were more likely to be associated with longer course and higher CD3+, B cells and IL‐21, and lower IgE (P < 0.01). Weak negative correlations were demonstrated between CD3+, CD8+ and scores in CU (r = −0.23, −0.25, P < 0.05). Significant correlations were found between B cells and scores and course in CU (r = 0.49, 0.65, P < 0.01). Moreover, a significant correlation was found between IL‐21 and IgE (r = 0.42, P < 0.01) in CU. But no significant correlations were found in AU. Our findings supported the concept that both humoral immunity and cellular immunity dysregulation in the pathogenesis of urticaria – mainly related to the decrease of the serum levels of IL‐15 and IL‐21 – may induce the increasing expression of IgE produced by B cells.
Molecular typing ofTrichophyton mentagrophytesvar.interdigitaleisolated in a university hospital in Japan based on the non‐transcribed spacer region of the ribosomal RNA gene
Authors: WAKASA Asako , ANZAWA Kazushi , KAWASAKI Masako , MOCHIZUKI Takashi 
Published: April 2010

AbstractDetecting intraspecies polymorphisms in fungi causing dermatophytoses is important in elucidating routes of infection and determining whetherTinearecurrence is caused by exacerbation or re‐infection. In fungi, the non‐transcribed spacer region (NTS) of the ribosomal RNA gene shows the greatest accumulation of base sequence mutations. We therefore assessed NTS sequences in 64 clinical isolates ofTrichophyton mentagrophytesvar. interdigitale, the second most common species of dermatophytes in Japan. These isolates were among the clinical isolates of dermatophytes in the Department of Dermatology, Kanazawa Medical University Hospital in 2006 and were obtained by morphological and molecular biological identification methods. DNA was extracted from each isolate, as well as from one isolate maintained in our department, to detect length polymorphisms at each of three variable loci, TmiS0, TmiS1 and TmiS2, of the NTS for subtyping. We observed seven patterns for TmiS0, six patterns for TmiS1 and three patterns for TmiS2. The combinations of these patterns enabled us to classify the 65 isolates into 15 types. The most prevalent, constituted 46% (30/65) of all isolates. Eleven types were new combinations, whereas the other four were previously described. These results suggest that this method may be used to determine the molecular epidemiology ofT. mentagrophytesvar.interdigitalein Japan, because it generated results rapidly and in a sensitive manner.
Occupational injuries in children and adolescents in emergency services of Aracaju, Brazil
Authors: De Vasconcelos R. B. A. , Santos J. C. V. , Araujo R. F. , De Souza L. , Dantas R. A. A. , Gurgel R. Q. 
Published: April 2010

AbstractBackground  The incidence of occupational injuries among children and adolescents is not well known in Brazil. This study aims to identify occurrences and characteristics of occupational injuries in children and adolescents at the two major public emergency hospitals in Aracaju, Brazil.Methods  In a cross sectional study, all children and adolescents (5–17 years) attending the services because of accidents of external cause in October–November 2006 and May–June 2007 were evaluated. The patients and their responsibles were interviewed to obtain information about the injury, family and patient characteristics and relation to work in the last 7 days. Data were analysed in number and percentages using descriptive statistics and chi‐squared and Fisher's exact tests.Results  There were 917 patients with injuries of external cause in the period studied. Seventy‐one (8%) had worked in the last 7 days and in 40 (4%) the injury was related to work, with 2 (0.21%) deaths. Occupational injuries occurred more frequently in boys (95%); in the 14‐ to 17‐year‐old age group (77%); in agricultural (46%) and commercial activities (18%); to help with family budget (54%); without any safety training (73.5%) and not using personal protective equipment (94%). Main mechanisms of injuries were transportation incidents (42.5%) and contact with tools and equipment (27.5%). Injuries were mostly fractures (37.5%) and lacerations (22.5%). Upper extremities were injured in 49% of cases and the lower extremities in 26.5%. Comparison between the two groups (accident related or not related to labour) shows that there were significant differences for gender, age group, the main mechanism of injury and the part of the body injured, but not for the nature of injury.Conclusion  Working children and adolescents have been injured during their occupational activities and work‐related injuries represent 4% of injuries of external causes in the emergency departments of Aracaju with 5% lethality.
Use of the Griffiths Mental Development Scales in an agro‐industrial province in the Philippines
Authors: Reyes A. , Pacifico R. , Benitez B. , Villanueva‐Uy E. , Lam H. , Ostrea Jr E. M. 
Published: April 2010

AbstractBackground  There is a need to assess neurobehavioral performance of children in developing countries using standardized developmental tools.Methods  The Griffiths Mental Development Scales was evaluated in the Philippines by comparing the performance of 742 Filipino children longitudinally at 6, 12 and 24 months old to those of their British counterparts.Results  The mean general and subquotient scores of Filipino children were all within average for age. Comparison with British children showed that except for performance subscales, Filipino children had significantly higher developmental subquotients at 6 months old. As the Filipino infants grew older, their developmental subquotients in all subscales were significantly lower, except for personal and social skills at 24 months old. The genetic predisposition as evidenced by modest maternal scores on the Wechsler Intelligence Scales and lack of familiarity with test materials are factors that may influence the developmental patterns of Filipino children.Conclusion  Although the performance of the Filipino children in the Griffiths test were within average with age, their performance on developmental subquotients at later ages of 12 and 24 months were significantly lower than British children and may have been influenced by differences in ethnicity, cultural traditions and limited environmental resources.
Child sexual abuse in Lebanon during war and peace
Authors: Usta J. , Farver J. 
Published: April 2010

AbstractPurpose Child sexual abuse (CSA) is rarely addressed in the Arab world. This study examined the prevalence, risk factors and consequences associated with CSA in Lebanese children before, during and after the 2006 Hezbollah‐Israeli war.Method A total of 1028 Lebanese children (556 boys; 472 girls) were administered an interview questionnaire that included the International Child Abuse Screening Tool, the Trauma Symptom Checklist and the Family Functioning in Adolescence Questionnaire.Results In total, 249 (24%) children reported at least one incident of CSA; 110 (11%) occurred before the war, 90 (8%) took place in the 1‐year period after the war to the time of the data collection and 49 (5%) occurred during the 33‐day war. There were no gender differences in CSA reports before or after the war, but boys reported more incidents during the war than did girls. Girls who reported CSA had higher trauma‐related symptoms for sleep disturbance, somatization, Post Traumatic Stress Disorder (PTSD) and anxiety than did boys. There were geographic differences in the reports of abuse that may be associated with poverty and living standards. Logistic regression analyses correctly classified 89.9% of the cases and indicated that children's age, family size, fathers' education level and family functioning significantly predicted CSA during the period following the war.Conclusions The prevalence of CSA in the current study is within the reported international range. Given the increase in the incidents of CSA during the war and the significant findings for family‐related risk factors, there is an urgent need to provide multi‐component culturally appropriate interventions that target the child and the family system in times of peace and conflict.
Prevalence of overweight and obesity among preadolescent schoolchildren in Galicia, Spain
Authors: Vázquez F. L. , Díaz O. , Pomar C. 
Published: April 2010

AbstractBackground  Childhood obesity is rising rapidly in many countries. Preadolescents appear to be at particularly high risk. This study estimated the prevalence of overweight and obesity in preadolescent schoolchildren in Galicia, Spain.Methods  The heights and weights of a random sample of 2305 Galician schoolchildren aged 10–12 years were measured using calibrated standardized scales and measures. Overweight and obesity were identified using the criteria of the International Obesity Task Force.Results  The prevalences of obesity and overweight were respectively 9.2% and 31.0% among boys, 8.6% and 28.8% among girls and 8.9% and 29.9% overall. Taking boys and girls together, the combined prevalence of overweight and obesity fell significantly with increasing age. Overweight was more prevalent in rural than urban areas (30.7% vs. 28.4%), as also was obesity (9.8% vs. 7.2%).Conclusions  Our study evidences the emergence of the obesity epidemic among preadolescents in Galicia, especially in rural areas. Both overweight and obesity in this age group are more prevalent in Galicia than in other areas of Spain or most other Western nations.
The prevalence of carriage of meticillin‐resistant staphylococci by veterinary dermatology practice staff and their respective pets
Authors: Morris Daniel O. , Boston Raymond C. , O’Shea Kathleen , Rankin Shelley C. 
Published: April 2010

AbstractIt has been shown that people and pets can harbour identical strains of meticillin‐resistant (MR) staphylococci when they share an environment. Veterinary dermatology practitioners are a professional group with a high incidence of exposure to animals infected by Staphylococcus spp. The objective of this study was to assess the prevalence of carriage of MR Staphylococcus aureus (MRSA), MR S. pseudintermedius (MRSP) and MR S. schleiferi (MRSS) by veterinary dermatology practice staff and their personal pets. A swab technique and selective media were used to screen 171 veterinary dermatology practice staff and their respective pets (258 dogs and 160 cats). Samples were shipped by over‐night carrier. Human subjects completed a 22‐question survey of demographic and epidemiologic data relevant to staphylococcal transmission. The 171 human‐source samples yielded six MRSA (3.5%), nine MRSP (5.3%) and four MRSS (2.3%) isolates, while 418 animal‐source samples yielded eight MRSA (1.9%) 21 MRSP (5%), and two MRSS (0.5%) isolates. Concordant strains (genetically identical by pulsed‐field gel electrophoresis) were isolated from human subjects and their respective pets in four of 171 (2.9%) households: MRSA from one person/two pets and MRSP from three people/three pets. In seven additional households (4.1%), concordant strains were isolated from only the pets: MRSA in two households and MRSP in five households. There were no demographic or epidemiologic factors statistically associated with either human or animal carriage of MR staphylococci, or with concordant carriage by person–pet or pet–pet pairs. Lack of statistical associations may reflect an underpowered study.