bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Simple Model for Correcting Sodar and Lidar Errors in Complex Terrain
Authors: Bradley Stuart 
Published: October 2012

Abstract
Ground-based sensing of wind profiles by sodars and lidars is becoming the standard for wind energy and other applications. However, there remain difficulties in complex terrain since the instruments sense wind components in spatially separated volumes, and systematic spatial variations of the wind components can lead to systematic bias in wind estimation. The errors are typically less than 6%, so corrections do not need to be very sophisticated.
Analytic potential flow models are developed for the flow over a bell-shaped hill and over an escarpment. These models are then used to find the radial Doppler shift from sampling volumes in typical sodar and lidar beam geometries, thereby allowing spatial variation bias to be removed. Since the models are straightforward, bias removal is readily achieved, and also lends itself to an understanding of the significant parameters affecting wind errors.
The bell model is tested against field data from sodars and lidars in both moderately complex and in very complex terrain. It is found that corrected winds are to within approximately 1% of those measured by mast instruments. Much more complex models do not correct wind errors better than these simple models.
Upstream Orographic Enhancement of a Narrow Cold-Frontal Rainband Approaching the Andes
Authors: Viale Maximiliano , Houze Robert A. , Rasmussen Kristen L. 
Published: October 2012

Abstract
Upstream orographic enhancement of the rainfall from an extratropical cyclone approaching the Andes from the Pacific is investigated using the Weather Research and Forecasting (WRF) Model and the Tropical Rainfall Measuring Mission (TRMM) Precipitation Radar. The main precipitation from the cyclone over central and coastal Chile fell when a narrow cold-frontal rainband (NCFR) interacted with a midlevel layer cloud deck formed from the orographically induced ascent of the prefrontal “atmospheric river” upstream of the Andes. Model output indicates that low-level convergence enhanced the NCFR where it met low-level blocked flow near the mountains. The NCFR had stronger updrafts with decreasing distance from the mountains, and the NCFR produced larger rain accumulations over the land region upstream of the Andes than over the open ocean. A sensitivity simulation with a 50% reduction in the Andes topography, for comparison to various west coast mountain ranges of North America, demonstrates that the extreme height of the real mountain barrier strengthens frontogenesis and upstream blocking, which produces stronger frontal lifting and a slower progression of the frontal system. The model and the satellite data suggest that the larger precipitation rates upstream of the Andes resulted from a seeder–feeder effect connected with the orographically invigorated NCFR updrafts, when they penetrated the orographically enhanced midlevel stratiform clouds forming as a result of the upstream orographic ascent of the atmospheric river. The supercooled water of the NCFR updrafts formed a feeder zone for the snow particles in the midlevel stratiform cloud just upstream of the Andes.
Tissue-based Alzheimer gene expression markers–comparison of multiple machine learning approaches and investigation of redundancy in small biomarker sets
Authors: Scheubert Lena , Luštrek Mitja , Schmidt Rainer , Repsilber Dirk , Fuellen Georg 
Published: October 2012

AbstractBackgroundAlzheimer’s disease has been known for more than 100 years and the underlying molecular mechanisms are not yet completely understood. The identification of genes involved in the processes in Alzheimer affected brain is an important step towards such an understanding. Genes differentially expressed in diseased and healthy brains are promising candidates.ResultsBased on microarray data we identify potential biomarkers as well as biomarker combinations using three feature selection methods: information gain, mean decrease accuracy of random forest and a wrapper of genetic algorithm and support vector machine (GA/SVM). Information gain and random forest are two commonly used methods. We compare their output to the results obtained from GA/SVM. GA/SVM is rarely used for the analysis of microarray data, but it is able to identify genes capable of classifying tissues into different classes at least as well as the two reference methods.ConclusionCompared to the other methods, GA/SVM has the advantage of finding small, less redundant sets of genes that, in combination, show superior classification characteristics. The biological significance of the genes and gene pairs is discussed.
MetNet Online: a novel integrated resource for plant systems biology
Authors: Sucaet Yves , Wang Yi , Li Jie , Wurtele Eve Syrkin 
Published: October 2012

Abstract

Background
Plants are important as foods, pharmaceuticals, biorenewable chemicals, fuel resources, bioremediation tools and general tools for recombinant technology. The study of plant biological pathways is advanced by easy access to integrated data sources. Today, various plant data sources are scattered throughout the web, making it increasingly complicated to build comprehensive datasets.

Results
MetNet Online is a web-based portal that provides access to a regulatory and metabolic plant pathway database. The database and portal integrate Arabidopsis, soybean (Glycine max) and grapevine (Vitis vinifera) data. Pathways are enriched with known or predicted information on sub cellular location. MetNet Online enables pathways, interactions and entities to be browsed or searched by multiple categories such as sub cellular compartment, pathway ontology, and GO term. In addition to this, the “My MetNet” feature allows registered users to bookmark content and track, import and export customized lists of entities. Users can also construct custom networks using existing pathways and/or interactions as building blocks.

Conclusion
The site can be reached athttp://www.metnetonline.org. Extensive video tutorials on how to use the site are available throughhttp://www.metnetonline.org/tutorial/.
Neonatal intrahepatic cholestasis caused by citrin deficiency: prevalence and SLC25A13mutations among thai infants
Authors: Treepongkaruna Suporn , Jitraruch Suttiruk , Kodcharin Porawee , Charoenpipop Dussadee , Suwannarat Pim , Pienvichit Paneeya , Kobayashi Keiko , Wattanasirichaigoon Duangrurdee 
Published: October 2012

Abstract

Background
The most common causes of cholestatic jaundice are biliary atresia and idiopathic neonatal hepatitis (INH). Specific disorders underlying INH, such as various infectious and metabolic causes, including neonatal intrahepatic cholestasis caused by citrin deficiency (NICCD) especially, in East Asian populations are increasingly being identified. Since most NICCD infants recovered from liver disease by 1 year of age, they often are misdiagnosed with INH, leading to difficulty in determining the true prevalence of NICCD. Mutation(s) of human SLC25A13 gene encoding a mitochondrial aspartate/glutamate carrier isoform 2 (AGC2), can lead to AGC2 deficiency, resulting in NICCD and an adult-onset fatal disease namely citrullinemia type II (CTLN2). To study the prevalence of NICCD and SLC25A13 mutations in Thai infants, and to compare manifestations of NICCD and non-NICCD, infants with idiopathic cholestatic jaundice or INH were enrolled. Clinical and biochemical data were reviewed. Urine organic acid and plasma amino acids profiles were analyzed. PCR-sequencing of all 18 exons of SLC25A13 and gap PCR for the mutations IVS16ins3kb and Ex16+74_IVS17-32del516 were performed. mRNA were analyzed in selected cases with possible splicing error.

Results
Five out of 39 (12.8%) unrelated infants enrolled in the study were found to have NICCD, of which three had homozygous 851del4 (GTATdel) and two compound heterozygous 851del4/IVS16ins3kb and 851del4/1638ins23, respectively. Two missense mutations (p.M1? and p.R605Q) of unknown functional significance were identified. At the initial presentation, NICCD patients had higher levels of alkaline phosphatase (ALP) and alpha-fetoprotein (AFP) and lower level of alanine aminotransferase (ALT) than those in non-NICCD patients (p< 0.05). NICCD patients showed higher citrulline level and threonine/serine ratio than non-NICCD infants (p< 0.05). Fatty liver was found in 2 NICCD patients. Jaundice resolved in all NICCD and in 87.5% of non-NICCD infants at the median age of 9.5 and 4.0 months, respectively.

Conclusion
NICCD should be considered in infants with idiopathic cholestasis. The preliminary estimated prevalence of NICCD was calculated to be 1/48,228 with carrier rate of 1/110 among Thai infants. However, this number may be underestimated and required further analysis with mutation screening in larger control population to establish the true prevalence of NICCD and AGC2 deficiency.
Identification of key peptidoglycan hydrolases for morphogenesis, autolysis, and peptidoglycan composition of Lactobacillus plantarum WCFS1
Authors: Rolain Thomas , Bernard Elvis , Courtin Pascal , Bron Peter A , Kleerebezem Michiel , Chapot-Chartier Marie-Pierre , Hols Pascal 
Published: October 2012

Abstract

Background

Lactobacillus plantarum is commonly used in industrial fermentation processes. Selected strains are also marketed as probiotics for their health beneficial effects. Although the functional role of peptidoglycan-degrading enzymes is increasingly documented to be important for a range of bacterial processes and host-microbe interactions, little is known about their functional roles in lactobacilli. This knowledge holds important potential for developing more robust strains resistant to autolysis under stress conditions as well as peptidoglycan engineering for a better understanding of the contribution of released muramyl-peptides as probiotic immunomodulators.

Results
Here, we explored the functional role of the predicted peptidoglycan hydrolase (PGH) complement encoded in the genome of L. plantarum by systematic gene deletion. From twelve predicted PGH-encoding genes, nine could be individually inactivated and their corresponding mutant strains were characterized regarding their cell morphology, growth, and autolysis under various conditions. From this analysis, we identified two PGHs, the predicted N-acetylglucosaminidase Acm2 and NplC/P60 D,L-endopeptidase LytA, as key determinants in the morphology of L. plantarum. Acm2 was demonstrated to be required for the ultimate step of cell separation of daughter cells, whereas LytA appeared to be required for cell shape maintenance and cell-wall integrity. We also showed by autolysis experiments that both PGHs are involved in the global autolytic process with a dominant role for Acm2 in all tested conditions, identifying Acm2 as the major autolysin of L. plantarum WCFS1. In addition, Acm2 and the putative N-acetylmuramidase Lys2 were shown to play redundant roles in both cell separation and autolysis under stress conditions. Finally, the analysis of the peptidoglycan composition of Acm2- and LytA-deficient derivatives revealed their potential hydrolytic activities by the disappearance of specific cleavage products.

Conclusion
In this study, we showed that two PGHs of L. plantarum have a predominant physiological role in a range of growth conditions. We demonstrate that the N-acetylglucosaminidase Acm2 is the major autolysin whereas the D,L-endopeptidase LytA is a key morphogenic determinant. In addition, both PGHs have a direct impact on PG structure by generating a higher diversity of cleavage products that could be of importance for interaction with the innate immune system.
The differential expression pattern of the BMI-1, SALL4 and ABCA3 genes in myeloid leukemia
Authors: Shen Qi , Liu Sichu , Hu Junyan , Chen Shaohua , Yang Lijian , Li Bo , Wu Xiuli , Ma Yu , Yang Jianchang , Ma Yupo , Li Yangqiu 
Published: October 2012

Abstract

Background and methods
In order to characterize the expression pattern of SALL4, BMI-1 and ABCA3 genes in patients with myeloid leukemia and those who achieved complete remission (CR) after chemotherapy. Real-time PCR was used to determine the expression level of these genes in peripheral blood mononuclear cells from 24 patients with AML, eight patients with AML-CR, 13 patients with CML in the chronic phase (CML-CP), 12 patients with CML in blast crisis (CML-BC), 13 patients with CML-CR and 11 healthy individuals (HI).

Results
Overexpression of the BMI-1 gene was found in the AML, CML-CP and CML-BC groups as compared with HI group, while the BMI-1 expression level was lower in patients who achieved CR. In contrast, significantly increased SALL4 expression was only found in AML group, additionally, SALL4 expression was lower in the CML-CP and CML-CR groups compared with the HI group, while the SALL4 expression level in the CML-BC group was higher and significantly greater than that in the CML-CP and CML-CR groups. Moreover, a positive correlation between the expression of SALL4 and BMI-1 genes was found in samples from most groups. There was no significant difference of ABCA3 expression level in AML and CML-BC group in comparison with HI group. Interestingly, the ABCA3 expression level was significantly decreased in the CML-CP, AML-CR and CML-CR in comparison with the HI group. Moreover, the ABCA3 expression level in all of the CR groups was lower than that in their corresponding groups.

Conclusions
These results describe the altered SALL4, ABCA3 and BMI-1 expression pattern in different phases of myeloid leukemia, which may relate to the development and progression to different diseases. SALL4 expression was strongly correlated with BMI-1 in most of the myeloid leukemia patient groups, providing a potential link between SALL4 and BMI-1 in leukemogenesis.
The financial burden of cancer: Estimates from patients undergoing cancer care in a tertiary care hospital
Authors: Zaidi Adnan A , Ansari Tayyaba Z , Khan Aziz 
Published: October 2012

Abstract

Introduction
The emotional burden associated with the diagnosis of cancer is sometimes overshadowed by financial burden sustained by patient and the family. This is especially relevant for a developing country as there is limited state support for cancer treatment. We conducted this study to estimate the cost of cancer care for two major types of cancer and to assess the perception of patients and families regarding the burden of the cost for undergoing cancer treatment at a private tertiary care hospital.

Methods
This cross-sectional study was conducted at day care and radiotherapy unit of Aga Khan University, Hospital (AKUH) Karachi, Pakistan. All adult patients with breast and head & neck cancers diagnosed for 3 months or more were included. Data was collected using a structured questionnaire and analysed using SPSS.

Results
Sixty seven patients were interviewed during the study period. The mean and median monthly income of these patients was 996.4 USD and 562.5 USD respectively. Comparatively the mean and median monthly cost of cancer care was 1093.13 USD and 946.42 USD respectively. The cost of the treatment either fully or partially was borne by the family in most cases (94%). The financial burden of cancer was perceived as significant by 28 (42%) patients and unmanageable by 18 (27%) patients. This perceived level of burden was associated significantly with average monthly income (p = <0.001).

Conclusion
Our study indicates that the financial burden of cancer care is substantial and can be overwhelming. There is a desperate need for treatment support programs either by the government or other welfare organisations to support individuals and families who are already facing a difficult and challenging situation.
Caveolin-1 reduces HIV-1 infectivity by restoration of HIV Nef mediated impairment of cholesterol efflux by apoA-I
Authors: Lin Shanshan , Nadeau Peter E , Wang Xiaomei , Mergia Ayalew 
Published: October 2012

Abstract

Background
HIV infection results in inhibited cholesterol efflux by apolipoprotein A-I (apoA-I) in macrophages, and this impairment involves Nef mediated down-regulation and redistribution of ATP-binding cassette transporter A1 (ABCA-1). We investigated the effect of caveolin-1 (Cav-1) on the cholesterol efflux by apoA-I in HIV infected primary and THP-1 cell-differentiated macrophages as well as astrocyte derived glioblastoma U87 cells.

Results
Our results reveal that Cav-1 restores the Nef -mediated impairment of cholesterol efflux by apoA-I in both cell types. Co-immunoprecipitation studies indicate a physical association of Cav-1 and Nef. The level of ABCA-1 expression remains the same whether Cav-1 is over-expressed or not. In addition, we examined the cholesterol composition of HIV particles released from Cav-1 treated cells and identified that the cholesterol content is dramatically reduced. The infectivity level of these virus particles is also significantly decreased.

Conclusions
These observations suggest that the interplay of Cav-1 with Nef and cholesterol subsequently counters Nef induced impairment of cholesterol efflux by apoA-l. The findings provide a cellular mechanism by which Cav-1 has an ability to restore HIV mediated impairment of cholesterol efflux in macrophages. This subsequently influences the cholesterol content incorporated into virus particles thereby inhibiting HIV infectivity and contributing to HIV’s persistent infection of macrophages.
Ethyl Pyruvate Attenuates Formalin-Induced Inflammatory Nociception by Inhibiting Neuronal ERK Phosphorylation
Authors: Lee Min Jung , Jang Minhee , Jung Hyuk-Sang , Kim Sung-Hoon , Cho Ik-Hyun 
Published: October 2012

Background: Ethyl pyruvate (EP) possesses anti-inflammatory activity. However, the potential anti-nociceptive value of EP for the treatment of the inflammatory nociception is largely unknown. We investigated whether EP could have any anti-nociceptive effect on inflammatory pain, after systemic administration of EP (10, 50, and 100 mg/kg, i.p.), 1 hour before formalin (5%, 50 μl) injection into the plantar surface of the hind paws of rats. Results: EP significantly decreased formalin-induced nociceptive behavior during phase II, the magnitude of paw edema, and the activation of c-Fos in L4-L5 spinal dorsal horn. EP also attenuated the phosphorylation of extracellular signal-regulated kinase (ERK) in the neurons of L4-L5 spinal dorsal horn after formalin injection. Interestingly, the i.t. administration of PD98059, an ERK upstream kinase (MEK) inhibitor, completely blocked the formalin-induced inflammatory nociceptive responses. Conclusions: These results demonstrate that EP may effectively inhibit formalin-induced inflammatory nociception via the inhibition of neuronal ERK phosphorylation in the spinal dorsal horn, indicating its therapeutic potential in suppressing acute inflammatory pain.
Expression of concern: necrotizing fasciitis, literature review of contemporary strategies for diagnosing and management with three case reports: torso, abdominal wall, upper and lower limbs
Authors: Catena Fausto , Moore Frederick 
Published: October 2012

Abstract
The Editors-in-Chief would like to alert readers that the accuracy of details described in Case III (56 year old male) of this article [1] have been questioned by a reader. Unfortunately, for legal reasons, the authors’ institution has not been able to confirm or refute whether the events reported about the case are accurate. Consequently, readers are advised to interpret the details of Case III with caution.
Activation of the two microRNA clusters C19MC and miR-371-3 does not play prominent role in thyroid cancer
Authors: Rippe Volkhard , Flor Inga , Debler Johannes Wolfram , Drieschner Norbert , Rommel Birgit , Krause Daniel , Junker Klaus , Bullerdiek Jörn 
Published: October 2012

Abstract
Chromosomal rearrangements of band 19q13.4 are frequent cytogenetic alterations in benign thyroid adenomas. Apparently, these alterations lead to the upregulation of genes encoding microRNAs of two clusters mapping to the breakpoint region, i.e. miR-371-3 and C19MC. Since members of both clusters have been associated with neoplastic growth in other tumor entities the question arises whether or not their upregulation predisposes to malignant transformation of follicular cells of the thyroid. To address this question we have quantified the expression of miR-372 and miR-520c-3p in samples of 114 thyroid cancers including eight anaplastic thyroid carcinomas, 25 follicular thyroid carcinomas, 78 papillary thyroid carcinomas (including 13 follicular variants thereof), two medullary thyroid carcinomas and one oncocytic thyroid carcinoma. Additionally, we quantified miR-371a-3p and miR-519a-3p in selected samples. While in neither of the cases miR-520c-3p and miR-519a-3p were found to be upregulated, one papillary and one anaplastic thyroid carcinoma, respectively, showed upregulation of miR-372 and miR-371a-3p. However, in these cases fluorescence in situ hybridization did not reveal rearrangements of the common breakpoint region as affected in adenomas. Thus, these rearrangements do apparently not play a major role as first steps in malignant transformation of the thyroid epithelium. Moreover, there is no evidence that 19q13.4 rearrangements characterize a subgroup of thyroid adenomas associated with a higher risk to undergo malignant transformation. Vice versa, the mechanisms by which 19q13.4 rearrangements contribute to benign tumorigenesis in the thyroid remain to be elucidated.
The unfolded von Willebrand factor response in bloodstream: the self-association perspective
Authors: Yuan Hailong , Deng Ning , Zhang Songmei , Cao Yange , Wang Qiong , Liu Xin , Zhang Qing 
Published: October 2012

Abstract
von Willebrand factor (vWF) is a multimeric glycoprotein essential for hemostasis after vascular injury, which modulates platelet-surface and platelet–platelet interactions by linking platelet receptors to the extracellular matrix and to each other. The crucial role of vWF in platelet function is particularly apparent when hemodynamic conditions create blood flow with high shear stress. Through multiple functional domains, vWF mediates the attachment of platelets to exposed tissues, where immobilized vWF is able to support a homotypic and/or heterotypic self-association. The self-association of vWF is also supported by a rapidly expanding reservoir of novel evidences that the thiol/disulfide exchange regulates vWF multimer size in the blood circulation. Moreover, in addition to proteolysis and reduction of ADAMTS13 (a disintegrin and metalloproteinase with a thrombospondin type 1 motif, member 13), the regulation of vWF multimer size and self-association may depend on a disulfide bond reductase activity ascribed to thrombospondin-1 (TSP-1). Along with the classical signaling pathways in activated platelets, evidence is emerging that lipid rafts also play important roles in various phases of hemostasis and thrombosis and facilitate the interaction between the key signaling molecules. Developments in these areas will refine our understanding of the role played by vWF self-association in physiological hemostasis and pathological thrombosis.