2006 GEP-ISFG collaborative exercise on mtDNA: reflections about interpretation, artefacts, and DNA mixtures

We report the results of the seventh edition of the GEP-ISFG mitochondrial DNA (mtDNA) collaborative exercise. The samples submitted to the participant laboratories were blood stains from a maternity case and Simulated forensic samples, including a case of mixture. The success rate for the blood stains was moderate (similar to 77%); even though four inexperienced laboratories concentrated about one-third of the total errors. A similar success was obtained for the analysis of mixed samples (78.8% for a hair-saliva mixture and 69.2% for a saliva-saliva Mixture). Two laboratories also dissected the haplotypes contributing to the saliva-saliva mixture. Most of the errors were due to reading problems and misinterpretation of electropherograms, demonstrating once more that the lack of a solid devised experimental approach is the main cause of error in mtDNA testing. (C) 2007 Elsevier B.V. All rights reserved.

A GEP-ISFG collaborative study on the optimization of an X-STR decaplex: data on 15 Iberian and Latin American populations

In a collaborative work carried out by the Spanish and Portuguese ISFG Working Group (GEP-ISFG), a polymerase chain reaction multiplex was optimized in order to type ten X-chromosome short tandem repeats (STRs) in a single reaction, including: DXS8378, DXS9902, DXS7132, DXS9898, DXS6809, DXS6789, DXS7133, GATA172D05, GATA31E08, and DXS7423. Using this X-decaplex, each 17 of the participating laboratories typed a population sample of approximately 200 unrelated individuals (100 males and 100 females). In this work, we report the allele frequencies for the ten X-STRs in 15 samples from Argentina (Buenos Aires, CA(3)rdoba, Rio Negro, Entre Rios, and Misiones), Brazil (SA o pound Paulo, Rio de Janeiro, Parana, and Mato Grosso do Sul), Colombia (Antioquia), Costa Rica, Portugal (Northern and Central regions), and Spain (Galicia and Cantabria). Gene diversities were calculated for the ten markers in each population and all values were above 56%. The average diversity per locus varied between 66%, for DXS7133, and 82%, for DXS6809. For this set of STRs, a high discrimination power was obtained in all populations, both in males (a parts per thousand yen1 in 5 A- 10(5)) and females (a parts per thousand yen1 in 3 A- 10(9)), as well as high mean exclusion chance in father/daughter duos (a parts per thousand yen99.953%) and in father/mother/daughter trios (a parts per thousand yen99.999%). Genetic distance analysis showed no significant differences between northern and central Portugal or between the two Spanish samples from Galicia and Cantabria. Inside Brazil, significant differences were found between Rio de Janeiro and the other three populations, as well as between SA o pound Paulo and Parana. For the five Argentinean samples, significant distances were only observed when comparing Misiones with Entre Rios and with Rio Negro, the only two samples that do not differ significantly from Costa Rica. Antioquia differed from all other samples, except the one from Rio Negro.

Results of the GEP-ISFG collaborative study on an X-STR Decaplex

A collaborative work was carried out by the Spanish and Portuguese ISFG Working Group with a PCR multiplex for X chromosome STRs. Markers were selected among those described as polymorphic in humans and that have been used by some laboratories in forensics. Primers and various technical methods were investigated with the aim of optimizing a multiplex for the 10 selected X-STRs. Primer mix stock solutions were sent to the laboratories that were asked to analyse two female bloodstains, taking as reference the genetic profiles from 9947A, 9948 and NA3657 samples. In this work, we report the results obtained by 30 GEP-ISFG laboratories, using this Decaplex, as well as alternative technical conditions that also produced good results. © 2008 Elsevier B.V. All rights reserved.

GEP analysis validates high risk MDS and acute myeloid leukemia post MDS mice models and highlights novel dysregulated pathways

BACKGROUND: In spite of the recent discovery of genetic mutations in most myelodysplasic (MDS) patients, the pathophysiology of these disorders still remains poorly understood, and only few in vivo models are available to help unravel the disease.

METHODS: We performed global specific gene expression profiling and functional pathway analysis in purified Sca1+ cells of two MDS transgenic mouse models that mimic human high-risk MDS (HR-MDS) and acute myeloid leukemia (AML) post MDS, with NRASD12 and BCL2 transgenes under the control of different promoters MRP8NRASD12/tethBCL-2 or MRP8[NRASD12/hBCL-2], respectively.

RESULTS: Analysis of dysregulated genes that were unique to the diseased HR-MDS and AML post MDS mice and not their founder mice pointed first to pathways that had previously been reported in MDS patients, including DNA replication/damage/repair, cell cycle, apoptosis, immune responses, and canonical Wnt pathways, further validating these models at the gene expression level. Interestingly, pathways not previously reported in MDS were discovered. These included dysregulated genes of noncanonical Wnt pathways and energy and lipid metabolisms. These dysregulated genes were not only confirmed in a different independent set of BM and spleen Sca1+ cells from the MDS mice but also in MDS CD34+ BM patient samples.

CONCLUSIONS: These two MDS models may thus provide useful preclinical models to target pathways previously identified in MDS patients and to unravel novel pathways highlighted by this study.

EGHEP-ISFG collaborative exercise on mixture profiles of autosomal STRs (GHEP-MIX01, GHEP-MIX02 and GHEP-MIX03): Results and evaluation

One of the main objectives of the Spanish and Portuguese-Speaking Group of the International Society for Forensic Genetics (GHEP-ISFG) is to promote and contribute to the development and dissemination of scientific knowledge in the area of forensic genetics. Due to this fact, GHEP-ISFG holds different working commissions that are set up to develop activities in scientific aspects of general interest. One of them, the Mixture Commission of GHEP-ISFG, has organized annually, since 2009, a collaborative exercise on analysis and interpretation of autosomal short tandem repeat (STR) mixture profiles. Until now, three exercises have been organized (GHEP-MIX01, GHEP-MIX02 and GHEP-MIX03), with 32, 24 and 17 participant laboratories respectively. The exercise aims to give a general vision by addressing, through the proposal of mock cases, aspects related to the edition of mixture profiles and the statistical treatment. The main conclusions obtained from these exercises may be summarized as follows. Firstly, the data show an increased tendency of the laboratories toward validation of DNA mixture profiles analysis following international recommendations (ISO/IEC 17025: 2005). Secondly, the majority of discrepancies are mainly encountered in stutters positions (53.4%, 96.0% and 74.9%, respectively for the three editions). On the other hand, the results submitted reveal the importance of performing duplicate analysis by using different kits in order to reduce errors as much as possible. Regarding the statistical aspect (GHEP-MIX02 and 03), all participants employed the likelihood ratio (LR) parameter to evaluate the statistical compatibility and the formulas employed were quite similar. When the hypotheses to evaluate the LR value were locked by the coordinators (GHEP-MIX02) the results revealed a minor number of discrepancies that were mainly due to clerical reasons. However, the GHEP-MIX03 exercise allowed the participants to freely come up with their own hypotheses to calculate the LR value. In this situation the laboratories reported several options to explain the mock cases proposed and therefore significant differences between the final LR values were obtained. Complete information concerning the background of the criminal case is a critical aspect in order to select the adequate hypotheses to calculate the LR value. Although this should be a task for the judicial court to decide, it is important for the expert to account for the different possibilities and scenarios, and also offer this expertise to the judge. In addition, continuing education in the analysis and interpretation of mixture DNA profiles may also be a priority for the vast majority of forensic laboratories. (C) 2014 Elsevier Ireland Ltd. All rights reserved.

História clínica e alimentar de crianças atendidas em ambulatório de gastroenterologia pediátrica (GEP) com constipação intestinal crônica funcional (CICF) e suas possíveis complicações

In order to better understand the natural history of chronic functional constipation, a questionnaire was applied to 163 children and infants, before beginning standardized treatment. Median age (range) at start was 3 mo(0-108 mo) but age at arrival at the Pediatric Gastroenterology Unit was 53 mo(2-146 mo). In 62.4% of the cases symptoms began before or up to 3 mo after cow's milk introduction and rarely around (-/+ 6 mo) toilet training. Possible complications appeared progressively, often at preschool or school age or as the first noticeable manifestation: recurrent abdominal pain (61.1%), fecal soiling (45.4%), fecal blood (35%), enuresis (23.3%), vomiting (19%), urinary infection (17.9%), urinary retention (8.6%). Abdominal distension was rarely detected on physical examination and was usually discrete. In conclusion, children attended in Botucatu begin their constipation at an early age, frequently associated with weaning,and important complications may ensue along years. This evolution should be avoided by prevention and early treatment of constipation.

Peptide receptor expression in GEP-NET

Numerous peptide receptors have recently been reported to be expressed or overexpressed in various human cancers. For instance, somatostatin receptors are particularly frequently expressed in gastroenteropancreatic neuroendocrine tumors (GEP-NET), including both primaries and metastases. The density is often high, and the distribution is usually homogenous. While various somatostatin receptor subtypes can be expressed in these tumors, the sst(2) is clearly predominant. These receptors represent the molecular basis for a number of clinical applications, including symptomatic therapy with octreotide in hormone-secreting GEP-NET, in vivo diagnostic with radiolabeled diethylene triamine pentaacetic acid octreotide (Octreoscan) to evaluate the extend of the disease, and (90)Y- or (177)Lu-[(90)Y-DOTA]-D: -Phe(1)-Tyr(3) octreotide radiotherapy. GEP-NET can, however, express peptide receptors other than somatostatin receptor: Insulinomas have more glucagon-like peptide 1 receptors than somatostatin receptors; gastrinomas express very high levels of secretin receptors. GEP-NET may also express cholecystokinin 2, bombesin, neuropeptide Y, or vasoactive intestinal peptide receptors. Often, several of these peptide receptors are expressed simultaneously in GEP-NET, providing a molecular basis for in vivo multireceptor targeting of those tumors.

Bayesian methodology for genetics of complex diseases

Genetic research of complex diseases is a challenging, but exciting, area of research. The early development of the research was limited, however, until the completion of the Human Genome and HapMap projects, along with the reduction in the cost of genotyping, which paves the way for understanding the genetic composition of complex diseases. In this thesis, we focus on the statistical methods for two aspects of genetic research: phenotype definition for diseases with complex etiology and methods for identifying potentially associated Single Nucleotide Polymorphisms (SNPs) and SNP-SNP interactions. With regard to phenotype definition for diseases with complex etiology, we firstly investigated the effects of different statistical phenotyping approaches on the subsequent analysis. In light of the findings, and the difficulties in validating the estimated phenotype, we proposed two different methods for reconciling phenotypes of different models using Bayesian model averaging as a coherent mechanism for accounting for model uncertainty. In the second part of the thesis, the focus is turned to the methods for identifying associated SNPs and SNP interactions. We review the use of Bayesian logistic regression with variable selection for SNP identification and extended the model for detecting the interaction effects for population based case-control studies. In this part of study, we also develop a machine learning algorithm to cope with the large scale data analysis, namely modified Logic Regression with Genetic Program (MLR-GEP), which is then compared with the Bayesian model, Random Forests and other variants of logic regression.

Late Oligocene to middle Miocene rifting and syn-extensional magmatism in the southwestern Sierra Madre occidental, Mexico: the beginning of the Gulf of California rift

Although Basin and Range style extension affected several areas of western Mexico since the Late Eocene, extension in the Gulf of California region (the Gulf Extensional Province GEP) is thought to have started as subduction waned and ended at ~14 12.5 Ma. A general consensus also exists in considering the mid Miocene Comondú group as a suprasubduction volcanic arc. Our new integration of the geology of the south east Gulf region, backed by 43 new Ar Ar and U Pb mineral ages and geochemical studies, document a widespread phase of extension in the southern GEP between latest Oligocene and Early Miocene that subsequently focused in the region of the future Gulf in the Middle Miocene. Upper Oligocene to Lower Miocene rocks across the southern Sierra Madre Occidental (SMO)(northern Nayarit and southern Sinaloa) were affected by major ~N S to NNW striking normal faults prior to ~21 Ma. Then, between ~21 and 11 Ma, a system of NNW-SSE high angle extensional faults continued extending the southwestern side of the SMO. Rhyolitic domes, shallow intrusive bodies, and lesser basalts were emplaced along this extensional belt at 20-17 Ma. In northern Sinaloa, large grabens were floored by huge dome complexes at ~21-17 Ma and filled by continental sediments with interlayered basalts dated at 15-14 Ma, a setting and timing very similar to Sonora. Early to Middle Miocene volcanism, including the largely volcaniclastic Comondú strata in Baja California Sur, was thus emplaced in rift basins and was likely associated to decompression melting of upper mantle (inducing crustal partial melting) rather than to fluxing by fluids from the young subducting plate. Along the Nayarit and Sinaloa coast, flatlying basaltic lava flows dated at 11-10 Ma are exposed just above the present sea level. Here, crustal thickness is almost half that in the unextended core of the SMO, implying significant lithosphere stretching before ~11 Ma. Our study shows that rifting began much earlier than Late Miocene and provided a fundamental control on the style and composition of volcanism from at least 30 Ma. We envision a sustained period of lithospheric stretching and magmatism during which the pace and breadth of extension changed at ~20-18 Ma to be narrower and likely more rapid, and again at ~12.5 Ma, when the kinematics of rifting became more oblique.

Power System Stabilizers Design for Interconnected Power Systems

This paper proposes a method of designing fixed parameter decentralized power system stabilizers (PSS) for interconnected multi-machine power systems. Conventional design technique using a single machine infinite bus approximation involves the frequency response estimation called the GEP(s) between the AVR input and the resultant electrical torque. This requires the knowledge of equivalent external reactance and infinite bus voltage or their estimated values at each machine. Other design techniques using P-Vr characteristics or residues are based on complete system information. In the proposed method, information available at the high voltage bus of the step-up transformer is used to set up a modified Heffron-Phillip's model. With this model it is possible to decide the structure of the PSS compensator and tune its parameters at each machine in the multi-machine environment, using only those signals that are available at the generating station. The efficacy of the proposed design technique has been evaluated on three of the most widely used test systems. The simulation results have shown that the performance of the proposed stabilizer is comparable to that which could be obtained by conventional design but without the need for the estimation and computation of external system parameters.

Gene expression programming-fuzzy logic method for crop type classification

Crop type classification using remote sensing data plays a vital role in planning cultivation activities and for optimal usage of the available fertile land. Thus a reliable and precise classification of agricultural crops can help improve agricultural productivity. Hence in this paper a gene expression programming based fuzzy logic approach for multiclass crop classification using Multispectral satellite image is proposed. The purpose of this work is to utilize the optimization capabilities of GEP for tuning the fuzzy membership functions. The capabilities of GEP as a classifier is also studied. The proposed method is compared to Bayesian and Maximum likelihood classifier in terms of performance evaluation. From the results we can conclude that the proposed method is effective for classification.

克氏针茅草原的碳通量与碳收支

植被和大气之间CO2通量的长期观测有助于理解陆地生态系统的碳循环及其控制机理，评价生态系统碳循环及其对未来气候变化的响应。本研究以中国北方克氏针茅草原为研究对象，以涡度相关法为主要技术手段，利用克氏针茅草原观测站碳通量的长期连续观测数据，探讨了环境因子在不同时间尺度上对克氏针茅草原光合生产力(GEP)、系统呼吸(Re)和净CO2交换(NEE)的影响，分析了克氏针茅草原碳通量的季节变化和年际碳收支动态。主要得到以下结论： (1) 温度和土壤水分是调控克氏针茅草原光响应曲线的关键环境因子。10-20oC是克氏针茅草原瞬时GEP的最适温度，15-20oC是日GEP的最适温度。GEP日总值随土壤水分的增加呈二次曲线关系，当土壤含水量(SWC)超过0.2 m3m-3时，GEP日总值不再增加。 (2) 克氏针茅草原Re同时受温度和土壤水分的控制。降雨脉冲对短期系统呼吸有激发作用。Lloyd & Taylor方程对Re的拟合效果好于指数方程。 (3) 克氏针茅草原表现出白天净碳吸收和夜间净碳释放的日变化特征，并且往往出现上午碳吸收强、下午碳吸收弱的不对称现象。降雨的季节分布通过SWC的季节变异间接影响克氏针茅草原NEE的季节变化。在日尺度上，NEE主要受温度和土壤水分的控制，10-20oC的空气温度有助于克氏针茅草原吸收CO2。在月尺度上，NEE主要受土壤水分的控制。 (4) 生长季的长度是决定克氏针茅草原源汇变化的关键因子。 (5) 克氏针茅草原的GEP、Re和NEE都具有非常明显的季节变化。冬季或干旱胁迫下量级较低，温暖和湿润季节的量级较高。干旱胁迫同时抑制植被的GEP和Re，对GEP的抑制强度更大，随着土壤水分的下降，不同尺度的NEE累积值逐渐向正值转变，即生态系统由碳汇转变为碳源。 (6) 克氏针茅草原2005年降雨量只有174mm，当年GEP和Re也是三年中最低的，只有101和169gCm-2yr-1;2006年降雨量为215mm，GEP和Re是三年中最强的，分别为149 和187gCm-2yr-1;2004年降雨量为297mm，接近多年平均，但大部分降雨发生在8、9月份，GEP和Re分别为141和190gCm-2yr-1。 (7) 克氏针茅草原在2004、2005和2006年碳收支分别为：49、68和37 gCm-2yr-1。未来全球气候的变暖可能对克氏针茅草原的碳汇功能产生负面影响，降雨的季节不均匀分布可能加强这种影响。

浒苔多糖的化学组分及生物学活性的初步研究

浒苔（Enteromorpha）是青岛沿海常见的一种绿藻。2008年6月份，在我国黄海海域爆发了一场大面积浒苔“绿潮”。本文研究了青岛沿海产缘管浒苔(QE)和“绿潮”浒苔(GE)的化学组成，并对其多糖的化学组成、结构及生物学活性进行了初步研究，为进一步开发利用浒苔提供实验依据。 对两种浒苔主要化学组成进行了分析，QE除灰分含量明显高于GE的含量外，水分、碳水化合物、粗脂肪和粗蛋白含量均低于GE的。两种浒苔均含有丰富的氨基酸，其中含量最高的是天门冬氨酸和谷氨酸；必需氨基酸含量占总氨基酸含量的42.755%和44.989%。不饱和脂肪酸含量占总脂肪酸含量的34.156%和34.278%。结果表明浒苔是一种矿物质和蛋白含量高，脂肪含量低，必需氨基酸和必需脂肪酸含量高的优质食物资源。 以水提醇沉法制备浒苔多糖，QE和GE多糖分别命名为QEP和GEP，并利用琼脂糖凝胶离子交换色谱对所得多糖进行分级纯化。高效液相色谱测定单糖组成，两种多糖均为鼠李糖-木糖-葡萄糖醛酸聚合物，其中鼠李糖含量占中性糖的67.55%和65.56%，木糖占中性糖的24.61%和19.33%。离子交换色谱分级结果表明，QEP主要由两种组分，分别为鼠李糖-木糖-半乳糖-糖醛酸聚合物和鼠李糖-木糖-糖醛酸聚合物；GEP主要组分为鼠李糖-木糖-甘露糖-糖醛酸聚合物。利用红外光谱、甲基化分析和核磁共振分析多糖QEP的结构，并利用ChemNMR软件辅助分析NMR谱图，结果表明，多糖主要有(1→2,4)-和(1→4)-连接的鼠李糖残基，(1→4)-连接的木糖残基，硫酸根主要连接在鼠李糖基3位。 研究了QEP及其分级组分对超氧阴离子、羟自由基、1,1-二苯基苦基苯肼(DPPH)的清除作用和还原能力，结果表明各组分均具有一定的清除自由基能力，其中QEP各项清除能力均较强，且还原能力最强，具有良好的抗氧化活性。以透明质酸和甘油作为对照，研究了GEP和本实验室褐藻多糖硫酸酯(FPS)及其衍生物的保湿和吸湿能力，结果表明GEP、低分子量FPS，以及低分子量FPS的离子交换凝胶色谱分级产物均有较强的保湿和吸湿活性，且与天然活性保湿因子透明质酸的保湿和吸湿特征很相似。GEP相对透明质酸、低分子量FPS及其衍生物而言，样品制备简单，原材料来源丰富，是良好的保湿活性物质。

CO2 fluxes of alpine shrubland ecosystem on the north-eastern Tibetan plateau

We measured ecosystem CO2 fluxes for an alpine shrubland on the north-eastern Tibetan Plateau, Qinghai, China. The study is to understand (1) the seasonal variation of CO2 flux and (2) how environmental factors affect the seasonality of CO2 exchange in the alpine ecosystem. Daytime ecosystem respiration was extrapolated from the relationship between temperature and nighttime CO2 fluxes under high turbulent conditions.Seasonal patterns of gross ecosystem production, ecosystem respiration and net ecosystem CO2 exchange followed highly the seasonal change of aboveground biomass in the alpine shrubland. The net ecosystem CO2 exchange was mainly controlled by the variation of photosynthetic photon flux density, while the ecosystem respiration was closely correlated to the soil temperature at 5-cm depth. Integrated values of gross ecosystem production, ecosystem respiration and net ecosystem CO2 exchange for the period from November 1, 2002 to October 31 2003 were estimated to be 1418, 1155 and 222 g CO2 m(-2) yr(-1), respectively.