bluuebunny/crossref_metadata_2025_split huggingface dataset:
Organochlorine pesticide levels and risk of Alzheimer’s disease in north Indian population
Authors: Singh NK , Chhillar N , Banerjee BD , Bala K , Basu M , Mustafa Md 
Published: August 2012

Alzheimer’s disease (AD) could result from a multifactorial process involving both genetic predisposition and exposure to environmental factors like pesticides. A case control study of 70 patients of AD and 75 controls was done to examine the association between organochlorine pesticides (OCPs) and risk of AD. OCPs (hexachlorocyclohexane (HCH), aldrin, dieldrin, endosulfan, pp′-dichlorodiphenyldichloroethylene ( pp′-DDE), op′-DDE, pp′-dichlorodiphenyltrichloroethane ( pp′-DDT), op′-DDT, pp′-dichlorodiphenyldichloroethane ( pp′ -DDD) and op′-DDD) were extracted from blood and quantitatively estimated using gas chromatography. A Mann–Whitney U test revealed significant difference in β-HCH levels ( U = 1237.00, W = 4087.00, z = −6.296, p = 0.000, r = −0.71), dieldrin levels ( U = 1449.00, W = 4299.00, z = −5.809, p = 0.000, r = −0.68) and pp′-DDE levels ( U = 2062.00, W = 4912.00, z = −2.698, p = 0.007, r = −0.59) between AD patients and controls. In conclusion, this study supports epidemiological studies that associate exposure to pesticides with increased risk of AD, and we identified the specific pesticides β-HCH, dieldrin and pp′-DDE that are associated with the risk of AD in the north Indian population. However, further research is needed to establish the potential role of these OCPs as an etiologic agent for AD case.
High-speed micro particle image velocimetry studies of boundary-layer flows in a direct-injection engine
Authors: Jainski Christopher , Lu Louise , Dreizler Andreas , Sick Volker 
Published: August 2012

Mass and energy exchange processes near the in-cylinder walls have become increasingly important for internal combustion engine research and development. Heat-transfer and fuel-deposition processes are not well enough understood to fully predict their magnitude and temporal and spatial variation. To a large extent, improvements in modeling are limited because of a lack of experimental guidance on the dynamics of boundary-layer flows in engines. High-speed particle image velocimetry and micro particle image velocimetry were used to study the boundary-layer flow field at the cylinder head of a motored internal combustion engine for three different engine speeds (400, 800 and 1100 r/min). Velocity measurements were taken throughout the compression stroke and the beginning of the expansion stroke, and comparisons to the frequently used law-of-the-wall were made. The low-resolution particle image velocimetry images showed that the average bulk flow maintained a tumble flow throughout the compression and expansion strokes and velocities scaled with engine speed. Adequate spatial resolution of the boundary-layer flow required the use of high-resolution (micro particle image velocimetry) measurements which showed that the log-law does not accurately describe the experimental boundary-layer structure in the outer layer ([Formula: see text]). Using the log-law, the velocity for earlier crank angles (180–260 crank angle degrees) was over predicted while the velocity for later crank angles (300–330 crank angle degrees) was under predicted, as engine speed increased. However, the experimental velocity profiles near the wall ([Formula: see text]) matched the description of the viscous sublayer ([Formula: see text]). Furthermore, it was observed that the thickness of the viscous sublayer decreased as the engine speed increased. The viscous sublayer could not be adequately resolved at 1100 r/min because of the limitations in adequate seeding density near the surface and the resulting loss of data points closest to the wall. The capability of high-speed particle image velocimetry measurements is demonstrated by the ability to identify and track vortical structures that move through the outer and buffer layers. Future work must address the evolution of such flow structures, along with measurements of temperature, to enable development and validation of boundary-layer models that are not restricted by the assumptions necessary for the law-of-the-wall such as steady bulk flow conditions and properties.
The Consequences of Maltreatment on Children’s Lives
Authors: Fry Deborah , McCoy Amalee , Swales Diane 
Published: August 2012

This study explores the consequences of child maltreatment in East Asia and the Pacific region based on the results of a systematic review of 16 English and non-English databases for journal articles and “gray” literature published between January 2001 and November 2010. This review shows that children in the region experiencing maltreatment are at increased risk of experiencing mental health consequences, physical health sequelae, high-risk sexual behaviors, and increased exposure to future violence including intimate partner violence (IPV) as an adult. Children who suffer from child sexual abuse have a median twofold increased risk of experiencing mental health disorders than those who have never experienced child maltreatment. Similar findings were found for those who experience physical abuse. Children who have been maltreated in the region are also at an increased risk of suicide ideation and attempts than those that have experienced child sexual or physical abuse being at a median fourfold increased risk. Children who have experienced physical abuse or those who have witnessed parental domestic abuse as a child are at median twofold increased risk of experiencing IPV as an adult, while children who have been sexually abused have a median threefold increase in risk of IPV later in life. There are still gaps in our understanding of the consequences of child maltreatment, but we do know that the consequences are profound and far-reaching. The findings indicate that there is an urgent need for governments, civil society organizations, development agencies, and academia to advocate for, invest in, and collaborate across sectors for the strengthening of child protection systems in the East Asia and Pacific Region, with a focus on evidence-based child maltreatment prevention policies and programs.
Dysmegakaryopoiesis of FPD/AML pedigrees with constitutional RUNX1 mutations is linked to myosin II deregulated expression
Authors: Bluteau Dominique , Glembotsky Ana C. , Raimbault Anna , Balayn Nathalie , Gilles Laure , Rameau Philippe , Nurden Paquita , Alessi Marie Christine , Debili Najet , Vainchenker William , Heller Paula G. , Favier Remi , Raslova Hana 
Published: August 2012

AbstractFPD/AML is a familial platelet disorder characterized by platelet defects, predisposition to acute myelogenous leukemia (AML) and germ-line heterozygous RUNX1 alterations. Here we studied the in vitro megakaryopoiesis of 3 FPD/AML pedigrees. A 60% to 80% decrease in the output of megakaryocytes (MKs) from CD34+ was observed. MK ploidy level was low and mature MKs displayed a major defect in proplatelet formation. To explain these defects, we focused on myosin II expression as RUNX1 has been shown to regulate MYL9 and MYH10 in an inverse way. In FPD/AML MKs, expression of MYL9 and MYH9 was decreased, whereas MYH10 expression was increased and the MYH10 protein was still present in the cytoplasm of mature MKs. Myosin II activity inhibition by blebbistatin rescued the ploidy defect of FPD/AML MKs. Finally, we demonstrate that MYH9 is a direct target of RUNX1 by chromatin immunoprecipitation and luciferase assays and we identified new RUNX1 binding sites in the MYL9 promoter region. Together, these results demonstrate that the defects in megakaryopoiesis observed in FPD/AML are, in part, related to a deregulation of myosin IIA and IIB expression leading to both a defect in ploidization and proplatelet formation.
Targeting oncogenic Ras signaling in hematologic malignancies
Authors: Ward Ashley F. , Braun Benjamin S. , Shannon Kevin M. 
Published: August 2012

AbstractRas proteins are critical nodes in cellular signaling that integrate inputs from activated cell surface receptors and other stimuli to modulate cell fate through a complex network of effector pathways. Oncogenic RAS mutations are found in ∼ 25% of human cancers and are highly prevalent in hematopoietic malignancies. Because of their structural and biochemical properties, oncogenic Ras proteins are exceedingly difficult targets for rational drug discovery, and no mechanism-based therapies exist for cancers with RAS mutations. This article reviews the properties of normal and oncogenic Ras proteins, the prevalence and likely pathogenic role of NRAS, KRAS, and NF1 mutations in hematopoietic malignancies, relevant animal models of these cancers, and implications for drug discovery. Because hematologic malignancies are experimentally tractable, they are especially valuable platforms for addressing the fundamental question of how to reverse the adverse biochemical output of oncogenic Ras in cancer.
How we treat oral chronic graft-versus-host disease
Authors: Treister Nathaniel , Duncan Christine , Cutler Corey , Lehmann Leslie 
Published: August 2012

AbstractChronic graft-versus-host disease (cGVHD) is a major complication of allogeneic hematopoietic cell transplantation that is associated with a diminished quality of life. The oral cavity is frequently affected, with a wide variety of signs and symptoms that can result in significant short- and long-term complications ranging from mucosal sensitivity and limited oral intake to secondary malignancy and early death. This article provides a comprehensive approach to the diagnosis and clinical management of patients with oral cGVHD, with particular attention to differential diagnosis, control of symptoms, and prevention of and screening for secondary complications. The clinical considerations and recommendations presented are intended to be practical and relevant for all clinicians involved in the care of patients with oral cGVHD, with the ultimate goal of improving care and outcomes.
JAK2V617F homozygosity arises commonly and recurrently in PV and ET, but PV is characterized by expansion of a dominant homozygous subclone
Authors: Godfrey Anna L. , Chen Edwin , Pagano Francesca , Ortmann Christina A. , Silber Yvonne , Bellosillo Beatriz , Guglielmelli Paola , Harrison Claire N. , Reilly John T. , Stegelmann Frank , Bijou Fontanet , Lippert Eric , McMullin Mary F. , Boiron Jean-Michel , Döhner Konstanze , Vannucchi Alessandro M. , Besses Carlos , Campbell Peter J. , Green Anthony R. 
Published: August 2012

Abstract
Subclones homozygous for JAK2V617F are more common in polycythemia vera (PV) than essential thrombocythemia (ET), but their prevalence and significance remain unclear. The JAK2 mutation status of 6495 BFU-E, grown in low erythropoietin conditions, was determined in 77 patients with PV or ET. Homozygous-mutant colonies were common in patients with JAK2V617F-positive PV and were surprisingly prevalent in JAK2V617F-positive ET and JAK2 exon 12-mutated PV. Using microsatellite PCR to map loss-of-heterozygosity breakpoints within individual colonies, we demonstrate that recurrent acquisition of JAK2V617F homozygosity occurs frequently in both PV and ET. PV was distinguished from ET by expansion of a dominant homozygous subclone, the selective advantage of which is likely to reflect additional genetic or epigenetic lesions. Our results suggest a model in which development of a dominant JAK2V617F-homzygous subclone drives erythrocytosis in many PV patients, with alternative mechanisms operating in those with small or undetectable homozygous-mutant clones.
CaPSID: A bioinformatics platform for computational pathogen sequence identification in human genomes and transcriptomes
Authors: Borozan Ivan , Wilson Shane , Blanchette Paola , Laflamme Philippe , Watt Stuart N , Krzyzanowski Paul M , Sircoulomb Fabrice , Rottapel Robert , Branton Philip E , Ferretti Vincent 
Published: August 2012

Abstract

Background
It is now well established that nearly 20% of human cancers are caused by infectious agents, and the list of human oncogenic pathogens will grow in the future for a variety of cancer types. Whole tumor transcriptome and genome sequencing by next-generation sequencing technologies presents an unparalleled opportunity for pathogen detection and discovery in human tissues but requires development of new genome-wide bioinformatics tools.

Results
Here we present CaPSID (Computational Pathogen Sequence IDentification), a comprehensive bioinformatics platform for identifying, querying and visualizing both exogenous and endogenous pathogen nucleotide sequences in tumor genomes and transcriptomes. CaPSID includes a scalable, high performance database for data storage and a web application that integrates the genome browser JBrowse. CaPSID also provides useful metrics for sequence analysis of pre-aligned BAM files, such as gene and genome coverage, and is optimized to run efficiently on multiprocessor computers with low memory usage.

Conclusions
To demonstrate the usefulness and efficiency of CaPSID, we carried out a comprehensive analysis of both a simulated dataset and transcriptome samples from ovarian cancer. CaPSID correctly identified all of the human and pathogen sequences in the simulated dataset, while in the ovarian dataset CaPSID’s predictions were successfully validated in vitro.
Global changes in gene expression during compatible and incompatible interactions of cowpea (Vigna unguiculata L.) with the root parasitic angiosperm Striga gesnerioides
Authors: Huang Kan , Mellor Karolina E , Paul Shom N , Lawson Mark J , Mackey Aaron J , Timko Michael P 
Published: August 2012

Abstract

Background
Cowpea, Vigna unguiculata L. Walp., is one of the most important food and forage legumes in the semi-arid tropics. While most domesticated forms of cowpea are susceptible to the root parasitic weed Striga gesnerioides, several cultivars have been identified that show race-specific resistance. Cowpea cultivar B301 contains the RSG3-301 gene for resistance to S. gesnerioides race SG3, but is susceptible to race SG4z. When challenged by SG3, roots of cultivar B301 develop a strong resistance response characterized by a hypersensitive reaction and cell death at the site of parasite attachment. In contrast, no visible response occurs in B301 roots parasitized by SG4z.

Results
Gene expression in the roots of the cowpea cultivar B301 during compatible (susceptible) and incompatible (resistant) interactions with S. gesnerioides races SG4z and SG3, respectively, were investigated at the early (6 days post-inoculation (dpi)) and late (13 dpi) stages of the resistance response using a Nimblegen custom design cowpea microarray. A total of 111 genes were differentially expressed in B301 roots at 6 dpi; this number increased to 2102 genes at 13 dpi. At 13 dpi, a total of 1944 genes were differentially expressed during compatible (susceptible) interactions of B301 with SG4z. Genes and pathways involved in signal transduction, programmed cell death and apoptosis, and defense response to biotic and abiotic stress were differentially expressed in the early resistance response; at the later time point, enrichment was primarily for defense-related gene expression, and genes encoding components of lignifications and secondary wall formation. In compatible interactions (B301 – SG4z), multiple defense pathways were repressed, including those involved in lignin biosynthesis and secondary cell wall modifications, while cellular transport processes for nitrogen and sulfur were increased.

Conclusion
Distinct changes in global gene expression profiles occur in host roots following successful and unsuccessful attempted parasitism by Striga. Induction of specific defense related genes and pathways defines components of a unique resistance mechanism. Some genes and pathways up-regulated in the host resistance response to SG3 are repressed in the susceptible interactions, suggesting that the parasite is targeting specific components of the host’s defense. These results add to our understanding of plant-parasite interactions and the evolution of resistance to parasitic weeds.
Deciphering the complex leaf transcriptome of the allotetraploid species Nicotiana tabacum: a phylogenomic perspective
Authors: Bombarely Aureliano , Edwards Kieron D , Sanchez-Tamburrino Juan , Mueller Lukas A 
Published: August 2012

Abstract

Background
Polyploidization is an important mechanism in plant evolution. By analyzing the leaf transcriptomes taken from the allotetraploid Nicotiana tabacum (tobacco) and parental genome donors, N. sylvesteris (S-Genome) and N. tomentosiformis (T-Genome), a phylogenomic approach was taken to map the fate of homeologous gene pairs in this plant.

Results
A comparison between the genes present in the leaf transcriptomes of N. tabacum and modern day representatives of its progenitor species demonstrated that only 33% of assembled transcripts could be distinguished based on their sequences. A large majority of the genes (83.6% of the non parent distinguishable and 87.2% of the phylogenetic topology analyzed clusters) expressed above background level (more than 5 reads) showed similar overall expression levels. Homeologous sequences could be identified for 968 gene clusters, and 90% (6% of all genes) of the set maintained expression of only one of the tobacco homeologs. When both homeologs were expressed, only 15% (0.5% of the total) showed evidence of differential expression, providing limited evidence of subfunctionalization. Comparing the rate of synonymous nucleotide substitution (Ks) and non-synonymous nucleotide substitution (Kn) provided limited evidence for positive selection during the evolution of tobacco since the polyploidization event took place.

Conclusions
Polyploidization is a powerful mechanism for plant speciation that can occur during one generation; however millions of generations may be necessary for duplicate genes to acquire a new function. Analysis of the tobacco leaf transcriptome reveals that polyploidization, even in a young tetraploid such as tobacco, can lead to complex changes in gene expression. Gene loss and gene silencing, or subfunctionalization may explain why both homeologs are not expressed by the associated genes. With Whole Genome Duplication (WGD) events, polyploid genomes usually maintain a high percentage of gene duplicates. The data provided little evidence of preferential maintenance of gene expression from either the T- or S-genome. Additionally there was little evidence of neofunctionalization in Nicotiana tabacum suggesting it occurs at a low frequency in young polyploidy.
Direct cost associated with acquired brain injury in Ontario
Authors: Chen Amy , Bushmeneva Ksenia , Zagorski Brandon , Colantonio Angela , Parsons Daria , Wodchis Walter P 
Published: August 2012

Abstract

Background
Acquired Brain Injury (ABI) from traumatic and non traumatic causes is a leading cause of disability worldwide yet there is limited research summarizing the health system economic burden associated with ABI. The objective of this study was to determine the direct cost of publicly funded health care services from the initial hospitalization to three years post-injury for individuals with traumatic (TBI) and non-traumatic brain injury (nTBI) in Ontario Canada.

Methods
A population-based cohort of patients discharged from acute hospital with an ABI code in any diagnosis position in 2004 through 2007 in Ontario was identified from administrative data. Publicly funded health care utilization was obtained from several Ontario administrative healthcare databases. Patients were stratified according to traumatic and non-traumatic causes of brain injury and whether or not they were discharged to an inpatient rehabilitation center. Health system costs were calculated across a continuum of institutional and community settings for up to three years after initial discharge. The continuum of settings included acute care emergency departments inpatient rehabilitation (IR) complex continuing care home care services and physician visits. All costs were calculated retrospectively assuming the government payer’s perspective.

Results
Direct medical costs in an ABI population are substantial with mean cost in the first year post-injury per TBI and nTBI patient being $32132 and $38018 respectively. Among both TBI and nTBI patients those discharged to IR had significantly higher treatment costs than those not discharged to IR across all institutional and community settings. This tendency remained during the entire three-year follow-up period. Annual medical costs of patients hospitalized with a brain injury in Ontario in the first follow-up year were approximately $120.7 million for TBI and $368.7 million for nTBI. Acute care cost accounted for 46-65% of the total treatment cost in the first year overwhelming all other cost components.

Conclusions
The main finding of this study is that direct medical costs in ABI population are substantial and vary considerably by the injury cause. Although most expenses occur in the first follow-up year ABI patients continue to use variety of medical services in the second and third year with emphasis shifting over time from acute care and inpatient rehabilitation towards homecare physician services and long-term institutional care. More research is needed to capture economic costs for ABI patients not admitted to acute care.
Mental health of asylum seekers: a cross-sectional study of psychiatric disorders
Authors: Heeren Martina , Mueller Julia , Ehlert Ulrike , Schnyder Ulrich , Copiery Nadia , Maier Thomas 
Published: August 2012

Abstract

Background
Asylum procedures are known to be protracted, stretching to over ten years in many host countries. International research shows high levels of distress for asylum seekers. Little is known about actual psychiatric morbidity in this population, especially during the first few years postmigration.

Methods
The mental health status of two groups of asylum seekers was assessed: Group 1 (n = 43) had arrived in Switzerland 2.9 (SD 1.1) months prior to assessment, while Group 2 (n = 43) had arrived 15.5 (SD 3.2) months prior to assessment. Psychiatric disorders were diagnosed using the Mini International Neuropsychiatric Interview (MINI). Symptom severity of posttraumatic stress disorder (Posttraumatic Diagnostic Scale), anxiety (Hopkins Symptom Checklist), depression (Hopkins Symptom Checklist), and pain (Verbal Rating Scale) were assessed using self-report questionnaires. Postmigratory factors such as German language proficiency and social contacts were also assessed. Interviews were conducted with the assistance of trained interpreters.

Results
Four out of ten participants met diagnostic criteria for at least one DSM-IV disorder. Groups did not differ with respect to psychiatric morbidity or symptom levels. Major depression (31.4%) and PTSD (23.3%) were diagnosed most frequently. The number of experienced traumatic event types was highly correlated with psychiatric morbidity.

Conclusions
Psychiatric morbidity in asylum seekers in the first two years after arrival is high, with no indication of a decrease in mental distress over time. Traumatic experiences seem to play a major role in morbidity during this time. Considering the magnitude of clinically relevant distress, a short psychological screening upon arrival with a focus on traumatic experiences may be warranted.