bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reply to “Comments on ‘A Bias in the Midtropospheric Channel Warm Target Factor on the NOAA-9 Microwave Sounding Unit’”
Authors: Po-Chedley Stephen , Fu Qiang 
Published: January 2013

Abstract
The main finding by Po-Chedley and Fu was that the University of Alabama in Huntsville (UAH) microwave sounding unit (MSU) product has a bias in its NOAA-9 midtropospheric channel (TMT) warm target factor, which leads to a cold bias in the TMT trend. This reply demonstrates that the central arguments by Christy and Spencer to challenge Po-Chedley and Fu do not stand. This reply establishes that 1) Christy and Spencer found a similar, but insignificant, bias in the UAH target factor because their radiosonde data lack adequate sampling and measurement errors were considered twice; 2) the UAH individual satellite TMT difference between NOAA-9 and NOAA-6 reveals a bias of 0.082 ± 0.011 in the UAH NOAA-9 target factor; 3) comparing the periods before and after NOAA-9 is not an adequate method to draw conclusions about NOAA-9 because of the influence of other satellites; 4) using the Christy and Spencer trend sensitivity value, UAH TMT has a cold bias of 0.035 K decade−1 given a target factor bias of 0.082; 5) similar trends from UAH and Remote Sensing Systems (RSS) for the lower tropospheric temperature product (TLT) do not indicate that the UAH TMT and TLT NOAA-9 target factor is unbiased; and 6) the NOAA-9 warm target temperature signal in UAH TMT indicates a problem with the UAH empirical algorithm to derive the target factor.
Design and Sampling Characteristics of a New Airborne Aerosol Inlet for Aerosol Measurements in Clouds
Authors: Craig Lucas , Schanot Allen , Moharreri Arash , Rogers David C. , Dhaniyala Suresh 
Published: January 2013

Abstract
Design of a new submicron aerosol inlet (SMAI) for airborne sampling of aerosol particles is introduced and its performance characteristics under a range of sampling conditions are presented. Analysis of inlet performance in clear-air and cloud systems shows that submicron aerosols are sampled representatively by the inlet, and in comparison with other types of inlets the SMAI has a relatively minor or nonexistent problem of droplet shatter contamination. The SMAI has a flow-through cone, with a perpendicular subsampling tube inside it. The cone acts as a virtual blunt body and decelerates the velocity directed toward a subsampling tube within the cone, resulting in reduced droplet impaction velocities and negligible artifact particle generation. The use of a perpendicular subsampling tube helps eliminate large shattered droplets from entering the sample volume, though it also results in lowering the aerosol sampling cut size. The SMAI sampling characteristics are determined from computational fluid dynamics simulations, and its cut size is calculated to be ~3 μm. In warm clouds, the shatter artifacts in the SMAI measurements are significantly less than that in a diffuser-type inlet, and shatter artifacts are only observed to increase when concentrations of drops larger than ~100 μm increase. In cold-cloud systems, shatter artifacts are significantly reduced with SMAI and some dependence of the inlet’s performance on the shape of the ice particles is observed.
Documenting Storm Severity in the Mid-Atlantic Region Using Lightning and Radar Information
Authors: Rudlosky Scott D. , Fuelberg Henry E. 
Published: January 2013

Abstract
Storm severity in the mid-Atlantic region of the United States is examined using lightning, radar, and model-derived information. Automated Warning Decision Support System (WDSS) procedures are developed to create grids of lightning and radar parameters, cluster individual storm features, and data mine the lightning and radar attributes of 1252 severe and nonsevere storms. The study first examines the influence of serial correlation and uses autocorrelation functions to document the persistence of lightning and radar parameters. Decorrelation times are found to vary by parameter, storm severity, and mathematical operator, but the great majority are between three and six lags, suggesting that consecutive 2-min storm samples (following a storm) are effectively independent after only 6–12 min. The study next describes the distribution of lightning jumps in severe and nonsevere storms, differences between various types of severe storms (e.g., severe wind only), and relationships between lightning and radar parameters. The 2σ lightning jump algorithm (with a 10 flashes min−1 activation threshold) yields 0.92 jumps h−1 for nonsevere storms and 1.44 jumps h−1 in severe storms. Applying a 10-mm maximum expected size of hail (MESH) threshold to the 2σ lightning jump algorithm reduces the frequency of lightning jumps in nonsevere storms to 0.61 jumps h−1. Although radar-derived parameters are comparable between storms that produce severe wind plus hail and those that produce tornadoes, tornadic storms exhibit much greater intracloud (IC) and cloud-to-ground (CG) flash rates. Correlations further illustrate that lightning data provide complementary storm-scale information to radar-derived measures of storm intensity.
Surprisingly high number of Twintrons in vertebrates
Authors: Janice Jessin , Jąkalski Marcin , Makałowski Wojciech 
Published: January 2013

Abstract
Twintrons represent a special intronic arrangement in which introns of two different types occupy the same gene position. Consequently, alternative splicing of these introns requires two different spliceosomes competing for the same RNA molecule. So far, only two twintrons have been described in insects. Surprisingly, we discovered several such arrangements in vertebrate genomes, which are quite conserved throughout the lineages.

Reviewers

This article was reviewed by Fyodor Kondrashow and Eugene Koonin.
Dramatic early event in chronic allograft nephropathy: increased but not decreased expression of MMP-9 gene
Authors: Gu Dongfeng , Shi Yanling , Ding Yanan , Liu Xinyu , Zou Hequn 
Published: January 2013

Abstract

Objective
The infiltration of mononuclear cells and replication and migration of smooth muscle cells (SMCs) from media into the intima in the vascular wall are the cardinal pathological changes in the early stage of chronic allograft nephropathy (CAN). But the mechanism is unclear. Therefore we investigated the role of matrix metalloproteinase 9 (MMP-9) and its interaction with TGF-beta1, tubulointerstitial mononuclear cells infiltration and migration of SMCs in the early stage of CAN.

Methods
Kidneys of Fisher (F334) rats were orthotopically transplanted into bilaterally nephrectomized Lewis (LEW) recipients. To suppress an initial episode of acute rejection, rats were briefly treated with cyclosporine A (1.5 mg/kg/day) for the first 10 days. Animals were harvested at 12 weeks after transplantation for histological, immunohistochemistry and molecular biological analysis.

Results
The expression of MMP-9 was up-regulated in interstitium and vascular wall in the early stage of CAN, where there were interstitial mononuclear cells infiltration and SMCs migration and proliferation. Moreover the expression of MMP-9 were positively correlated with the degree of interstitial mononuclear cells infiltration, the quantity of SMCs in arteriolar wall, and also the increased TFG-beta1 expression in the tubulointerstitium and arteriolar wall.

Conclusions
MMP-9 may play an important role in the mechanism of pathological changes during the earlier period of CAN.

Virtual Slides
The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1582313332832700.
Plants used in artisanal fisheries on the Western Mediterranean coasts of Italy
Authors: Savo Valentina , La Rocca Arianna , Caneva Giulia , Rapallo Fabio , Cornara Laura 
Published: January 2013

Abstract
Background
Artisanal fisheries in the Mediterranean, especially in Italy, have been poorly investigated. There is a long history of fishing in this region, and it remains an important economic activity in many localities. Our research entails both a comprehensive review of the relevant literature and 58 field interviews with practitioners on plants used in fishing activities along the Western Mediterranean Italian coastal regions. The aims were to record traditional knowledge on plants used in fishery in these regions and to define selection criteria for plant species used in artisanal fisheries, considering ecology and intrinsic properties of plants, and to discuss the pattern of diffusion of shared uses in these areas.

Methods
Information was gathered both from a general review of ethnobotanical literature and from original data. A total of 58 semi-structured interviews were carried out in Liguria, Latium, Campania and Sicily (Italy). Information on plant uses related to fisheries were collected and analyzed through a chi-square residual analysis and the correspondence analysis in relation to habitat, life form and chorology.

Results
A total of 60 plants were discussed as being utilized in the fisheries of the Western Italian Mediterranean coastal regions, with 141 different uses mentioned. Of these 141 different uses, 32 are shared among different localities. A multivariate statistical analysis was performed on the entire dataset, resulting in details about specific selection criteria for the different usage categories (plants have different uses that can be classified into 11 main categories). In some uses, species are selected for their features (e.g., woody), or habitat (e.g., riverine), etc. The majority of uses were found to be obsolete (42%) and interviews show that traditional fishery knowledge is in decline. There are several reasons for this, such as climatic change, costs, reduction of fish stocks, etc.

Conclusions
Our research correlates functional characteristics of the plants used in artisanal fishery and habitats, and discusses the distribution of these uses. This research is the first comprehensive outline of plant role in artisanal fisheries and traditional fishery knowledge in the Mediterranean, specifically in Italy.
The ADAMTS18 gene is responsible for autosomal recessive early onset severe retinal dystrophy
Authors: Peluso Ivana , Conte Ivan , Testa Francesco , Dharmalingam Gopuraja , Pizzo Mariateresa , Collin Rob WJ , Meola Nicola , Barbato Sara , Mutarelli Margherita , Ziviello Carmela , Barbarulo Anna Maria , Nigro Vincenzo , Melone Mariarosa AB ,   the European Retinal Disease Consortium, Simonelli Francesca , Banfi Sandro 
Published: January 2013

Abstract

Background
Inherited retinal dystrophies, including Retinitis Pigmentosa and Leber Congenital Amaurosis among others, are a group of genetically heterogeneous disorders that lead to variable degrees of visual deficits. They can be caused by mutations in over 100 genes and there is evidence for the presence of as yet unidentified genes in a significant proportion of patients. We aimed at identifying a novel gene for an autosomal recessive form of early onset severe retinal dystrophy in a patient carrying no previously described mutations in known genes.

Methods
An integrated strategy including homozygosity mapping and whole exome sequencing was used to identify the responsible mutation. Functional tests were performed in the medaka fish (Oryzias latipes) model organism to gain further insight into the pathogenic role of the ADAMTS18 gene in eye and central nervous system (CNS) dysfunction.

Results
This study identified, in the analyzed patient, a homozygous missense mutation in the ADAMTS18 gene, which was recently linked to Knobloch syndrome, a rare developmental disorder that affects the eye and the occipital skull. In vivo gene knockdown performed in medaka fish confirmed both that the mutation has a pathogenic role and that the inactivation of this gene has a deleterious effect on photoreceptor cell function.

Conclusion
This study reveals that mutations in the ADAMTS18 gene can cause a broad phenotypic spectrum of eye disorders and contribute to shed further light on the complexity of retinal diseases.
7q36 deletion and 9p22 duplication: effects of a double imbalance
Authors: Pelegrino Karla de Oliveira , Sugayama Sofia , Catelani Ana Lúcia , Lezirovitz Karina , Kok Fernando , Chauffaille Maria de Lourdes 
Published: January 2013

AbstractThe etiology of mental retardation/developmental delay (MRDD) remains a challenge to geneticists and clinicians and can be correlated to environmental and genetic factors. Chromosomal aberrations are common causes of moderate to severe mental retardation and may represent 10% of these occurrences. Here we report the case of a boy with development delay, hypoplasia of corpus callosum, microcephaly, muscular hypotonia, and facial dysmorphisms. A deletion of 7q36.1 → 36.3 and duplication of 9p22.3 → 23 was detected as a result of an unbalanced translocation of paternal origin. Breakpoint delimitation was achieved with array comparative genomic hybridization assay. Additional multiplex ligation dependent probe amplification (MLPA) analyzes confirmed one copy loss of 7q36.3 region and one copy gain of 9p24.3 region. Patient resultant phenotype is consistent with the already described findings for both 7q deletion and 9p duplication syndromes.
Towards an effective control programme of soil-transmitted helminth infections among Orang Asli in rural Malaysia. Part 2: Knowledge, attitude, and practices
Authors: Nasr Nabil A , Al-Mekhlafi Hesham M , Ahmed Abdulhamid , Roslan Muhammad Aidil , Bulgiba Awang 
Published: January 2013

Abstract

Background
In the first part of this study, we investigated the prevalence and associated key factors of soil-transmitted helminth (STH) infections among Orang Asli children in rural Malaysia; an alarming high prevalence and five key factors significantly associated with infections were reported. Part 2 of this study aims to evaluate the knowledge, attitude and practices (KAP) on STH infections among Orang Asli in Peninsular Malaysia.

Methods
A cross-sectional study was carried out among 215 households from 13 villages in Lipis district, Pahang, Malaysia. Demographic and socioeconomic information of the participants and their KAP on STH were collected by using a pre-tested questionnaire.

Results
Overall, 61.4% of the participants had prior knowledge about intestinal helminths with a lack of knowledge on the transmission (28.8%), signs and symptoms (29.3%) as well as the prevention (16.3%). Half of the respondents considered STH as harmful, while their practices to prevent infections were still inadequate. Significant associations between the KAP and age, gender, educational and employment status, family size, and household monthly income were reported. Moreover, significantly lower prevalence of STH infections was reported among children of respondents who wear shoes/slippers when outside the house (72.8%; 95% CI= 62.6, 80.5 vs 87.0%; 95% CI= 81.4, 91.1), wash their hands before eating (32.4%; 95% CI= 24.3, 42.2 vs 51.4%; 95% CI= 44.7, 60.1), and wash their hands after defecation (47.8%; 95% CI= 35.7, 57.1 vs 69.2%; 95% CI= 63.7, 78.7) as compared to their counterparts. Multiple logistic regression analysis indicated that the educational level of the respondents was the most important factor significantly associated with the KAP on STH among this population.

Conclusion
This study reveals inadequate knowledge, attitude and practices on STH infections among Orang Asli in rural Malaysia. Hence, there is a great need for a proper health education programme and community mobilisation to enhance prevention and instil better knowledge on STH transmission and prevention. This is crucial for an effective and sustainable STH control programme to save the lives and future of the most vulnerable children in rural Malaysia.
A typical bilateral Toxoplasma retinochoroiditis in a bone marrow transplant patient with negative serum titers
Authors: Hazan Albert , Patel Rakesh M , Levinson David , Mian Umar , Gritz David C 
Published: January 2013

Abstract

Background

Toxoplasma retinochoroiditis can have an atypical presentation and be difficult to diagnose in immunocompromised patients. Accurate diagnosis and appropriate treatment is important since the disease can be aggressive in these patients. This paper is a case report with literature review, emphasizing on the diagnosis and treatment of Toxoplasma retinochoroiditis.

Findings
A 27-year-old male with chronic myelogenous leukemia with history of bone marrow transplantation presented with floaters in his right eye. Fundus exam showed bilateral, multifocal retinochoroiditis with subsequent development of a mild vitritis. Serum cytomegalovirus and toxoplasmosis antibody titers and syphilis screen were negative. Aqueous polymerase chain reaction (PCR) analysis revealed the presence of Toxoplasma gondii DNA OU. Clindamycin (1.0 mg/0.1 mL) was injected bilateral intravitreal OU twice at 4 days apart with subsequent resolution of retinochoroiditis.

Conclusions
When evaluating retinochoroiditis in an immunocompromised patient, one must keep a high index of suspicion for atypical presentations of well-known disease entities. Aqueous and vitreous samples for PCR can be useful in obtaining an accurate diagnosis and therefore provide appropriate management for the patient. Intravitreal clindamycin is an option for treatment in these patients.
The impact of microcarrier culture optimization on the glycosylation profile of a monoclonal antibody
Authors: Costa Ana Rita , Withers Joanne , Rodrigues Maria Elisa , McLoughlin Niaobh , Henriques Mariana , Oliveira Rosário , Rudd Pauline M , Azeredo Joana 
Published: January 2013

Abstract
Microcarriers are widely used for the large-scale culture of attachment-dependent cells with increased cell densities and, ultimately, higher product yield. In these processes, the specific culture conditions can affect the quality of the product, which is closely related to its glycosylation pattern. Furthermore, the lack of studies in the area reinforces the need to better understand the effects of microcarrier culture in product glycosylation. Consequently, in this work, the glycosylation profile of a monoclonal antibody (mAb) produced by adherent CHO-K1 cells grown in Cytodex 3 was evaluated under different conditions, and compared to that obtained of typical adherent cultures. It was found that microcarrier cultures result in a glycosylation profile with different characteristics from T-flask cultures, with a general increase in galactosylation and decrease in fucosylation levels, both with a potentially positive impact on mAb activity. Sialylation also varied but without a general tendency. This study then showed that the specific culture conditions used in microcarrier culture influence the mAb glycan profile, and each functional element (galactose, core fucose, sialic acid) is independently affected by these conditions. In particular, great reductions of fucosylation (from 79 to 55%) were obtained when using half volume at inoculation, and notable decreases in sialylation (from 23 to 2%) and glycoform heterogeneity (from 20 to 11 glycoforms) were observed for shake flask culture, potentially associated with the improved cell densities achieved in these culture vessels.
High prevalence of spondyloarthritis and ankylosing spondylitis among familial Mediterranean fever patients and their first-degree relatives: further evidence for the connection
Authors: Akar Servet , Soysal Ozgul , Balci Ali , Solmaz Dilek , Gerdan Vedat , Onen Fatos , Tunca Mehmet , Akkoc Nurullah 
Published: January 2013

Abstract
Introduction
Familial Mediterranean fever (FMF) is an auto-inflammatory disease characterized by recurrent attacks of fever and serositis. Limited data suggest that the prevalence of sacroiliitis is increased in patients with FMF. In our present study, we assessed the prevalence of spondyloarthritis (SpA), including ankylosing spondylitis (AS), among a cohort of FMF patients and their unaffected first-degree relatives (FDRs).

Methods
The current study cohort comprised a consecutive group of 201 unrelated patients with FMF and 319 FDRs (≥ 16 years old). These subjects were examined according to a standard protocol.

Results
A total of 157 FMF patients (78.1%) and 233 (73%) unaffected FDRs reported back pain. Fifteen FMF patients (7.5%) and nine unaffected FDRs fulfilled the modified New York (mNY) criteria for AS. One additional FDR with AS was identified after review of the medical records. None of the FMF patients with AS was HLA-B27 positive. The allele frequency of M694V among the FMF patients with radiographic sacroiliitis was significantly higher in comparison with those without sacroiliitis (OR 4.3). When compared with the general population, the risk ratios for SpA and AS among the FDRs of our FMF patients were 3.3 (95% CI; 2.0 to 5.5) and for AS 2.9 (95% CI; 1.3 to 6.4), respectively.

Conclusions
Our study suggests that a) factors other than HLA-B27 play a role in the association of FMF and SpA/AS; b) MEFV gene variations may be one of the geographic/region-specific potential pathogenetic links between these two disorders in the Turkish population.
Efficient Coding of the Minimum Image Convention
Authors: Deiters Ulrich K. 
Published: January 2013

Abstract
The computation of distances between interactions sites while observing the minimum image convention is one of the most frequently performed operations in computer simulations of fluids. In this work several ways of encoding the minimum image convention are discussed and their performances on different computers compared. It turns out that the optimal choice for the algorithm depends on the computer type as well as the optimization level of the compiler, and that a well adapted algorithm can achieve a significant reduction of the computation time.
Second Osmotic Virial Coefficients and Aggregation of Monoclonal Antibodies by Static Laser Light Scattering
Authors: Dieterle Michael , Blaschke Tim , Hasse Hans 
Published: January 2013

Abstract
The second osmotic virial coefficient and the apparent molar mass of two human and one mouse monoclonal antibodies were measured in different aequeous buffer solutions which also contained sodium chloride or ammonium sulfate, respectively, by static laser light scattering in batch mode. The apparent molar mass indicates aggregation. At a constant pH value of 6.5 the sodium chloride concentration was varied from 0 to 2 M and the ammonium sulfate concentration from 0 to 0.8 M, respectively. A 20 mM sodium-phosphate buffer was used for all experiments. Furthermore the pH value was varied without adding additional salt from 4.5 to 10. The results of the salt dependency are in line with the Hofmeister-series. The results of the pH dependency correspond to the net charge of the molecules.
The Local Structure of Antimony in High Dose Antimony Implants in Silicon by XAFS and SIMS.
Authors: Sahiner M. Alper , Novak Steven W. , Woicik Joe C. , Takamura Yayoi , Griffin Peter B. , Plummer James D. 
Published: January 2013

AbstractOne of the important challenges in semiconductor industry is to sustain high concentration of dopant atoms electrically active in very small areas. In investigating the optimum post implantation treatment methods that will help to attain these conditions, the local structural information around the dopant atom is crucial. In this study, we have used secondary ion mass spectroscopy (SIMS) and x-ray absorption fine structure spectroscopy (XAFS) to obtain the concentration depth profiles and the local structural information around the Sb atom in laser thermal annealed (LTA) Sb implants in Si wafers. The Sb implant doses used in this work are 6.4x1015/cm2 and 2.0x1016/cm2. The XAFS results for the 6.4x1015/cm2 Sb dose sample do not exhibit any rhombohedral-Sb precipitation as the Fourier Transformed (FT) data can be fit successfully using only substitutional-Sb in the Si lattice sites. However, a multi-shell analysis of the Fourier Transformed (FT) data for the 2.0x1016/cm2 Sb dose sample clearly indicates there is a substantial contribution from the Sb-Sb scattering, which is a signature of precipitated form of Sb.