bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Novel Class of Lipoprotein Lipase-Sensitive Molecules Mediates Toll-Like Receptor 2 Activation by Porphyromonas gingivalis
Authors: Jain Sumita , Coats Stephen R. , Chang Ana M. , Darveau Richard P. 
Published: February 2013

ABSTRACTInfection by the chronic periodontitis-associated pathogenPorphyromonas gingivalisactivates a Toll-like receptor 2 (TLR2) response that triggers inflammation in the host but also promotes bacterial persistence. Our aim was to define ligands on the surfaces of intactP. gingivaliscells that determine its ability to activate TLR2. Molecules previously reported as TLR2 agonists include lipopolysaccharide (LPS), fimbriae, the lipoprotein PG1828, and phosphoceramides. We demonstrate that these molecules do not comprise the major factors responsible for stimulating TLR2 by whole bacterial cells. First,P. gingivalismutants devoid of the reported protein agonists, PG1828 and fimbriae, activate TLR2 as strongly as the wild type. Second, two-phase extraction of whole bacteria resulted in a preponderance of TLR2 agonist activity partitioning to the hydrophilic phase, demonstrating that phosphoceramides are not a major TLR2 ligand. Third, analysis of LPS revealed that TLR2 activation is independent of lipid A structural variants. Instead, activation of TLR2 and TLR2/TLR1 by LPS is in large part due to copurifying molecules that are sensitive to the action of the enzyme lipoprotein lipase. Strikingly, intactP. gingivalisbacterial cells treated with lipoprotein lipase were attenuated in their ability to activate TLR2. We propose that a novel class of molecules comprised by lipoproteins constitutes the major determinants that confer toP. gingivalisthe ability to stimulate TLR2 signaling.
Concept location using formal concept analysis and information retrieval
Authors: Poshyvanyk Denys , Gethers Malcom , Marcus Andrian 
Published: February 2013

The article addresses the problem of concept location in source code by proposing an approach that combines Formal Concept Analysis and Information Retrieval. In the proposed approach, Latent Semantic Indexing, an advanced Information Retrieval approach, is used to map textual descriptions of software features or bug reports to relevant parts of the source code, presented as a ranked list of source code elements. Given the ranked list, the approach selects the most relevant attributes from the best ranked documents, clusters the results, and presents them as a concept lattice, generated using Formal Concept Analysis.
The approach is evaluated through a large case study on concept location in the source code on six open-source systems, using several hundred features and bugs. The empirical study focuses on the analysis of various configurations of the generated concept lattices and the results indicate that our approach is effective in organizing different concepts and their relationships present in the subset of the search results. In consequence, the proposed concept location method has been shown to outperform a standalone Information Retrieval based concept location technique by reducing the number of irrelevant search results across all the systems and lattice configurations evaluated, potentially reducing the programmers' effort during software maintenance tasks involving concept location.
mTOR Inhibitors Block Kaposi Sarcoma Growth by Inhibiting Essential Autocrine Growth Factors and Tumor Angiogenesis
Authors: Roy Debasmita , Sin Sang-Hoon , Lucas Amy , Venkataramanan Raman , Wang Ling , Eason Anthony , Chavakula Veenadhari , Hilton Isaac B. , Tamburro Kristen M. , Damania Blossom , Dittmer Dirk P. 
Published: February 2013

Abstract
Kaposi sarcoma originates from endothelial cells and it is one of the most overt angiogenic tumors. In Sub-Saharan Africa, where HIV and the Kaposi sarcoma–associated herpesvirus (KSHV) are endemic, Kaposi sarcoma is the most common cancer overall, but model systems for disease study are insufficient. Here, we report the development of a novel mouse model of Kaposi sarcoma, where KSHV is retained stably and tumors are elicited rapidly. Tumor growth was sensitive to specific allosteric inhibitors (rapamycin, CCI-779, and RAD001) of the pivotal cell growth regulator mTOR. Inhibition of tumor growth was durable up to 130 days and reversible. mTOR blockade reduced VEGF secretion and formation of tumor vasculature. Together, the results show that mTOR inhibitors exert a direct anti-Kaposi sarcoma effect by inhibiting angiogenesis and paracrine effectors, suggesting their application as a new treatment modality for Kaposi sarcoma and other cancers of endothelial origin. Cancer Res; 73(7); 2235–46. ©2012 AACR.
New Data Supporting Modified RECIST (mRECIST) for Hepatocellular Carcinoma
Authors: Lencioni Riccardo 
Published: February 2013

Abstract
The modified Response Evaluation Criteria in Solid Tumors (mRECIST) guideline has introduced specific amendments to standard RECIST to address the unique complexities involved in the evaluation of tumor response in hepatocellular carcinoma. A growing amount of data suggests that mRECIST, designed for response assessment in clinical trials, may translate into a tool for clinical practice. Clin Cancer Res; 19(6); 1312–4. ©2013 AACR.
Mini-invasive Mitchell-Kramer Method in the Operative Treatment of Hallux Valgus Deformity
Authors: Gądek Artur , Liszka Henryk 
Published: February 2013

Background: The mini-invasive Mitchell-Kramer procedure is a new method of operative correction of mild to moderate hallux valgus deformity. The aim of this study was to describe the technique and evaluate the results of the procedure. Methods: We evaluated 54 patients who underwent mini-invasive distal metatarsal osteotomy of the first metatarsal with preservation of the lateral cortex of the distal fragment. We did percutaneous 2-mm K-wire stabilization of the osteotomy and did not use cast immobilization with postoperative offloading of the forefoot. We used anteroposterior and lateral foot standing X-rays, visual analog scale (VAS), and American Orthopaedic Foot and Ankle Society (AOFAS) hallux-metatarsophalangeal-interphalangeal scale for the clinical assessment at 18 months’ follow-up. Results: Preoperatively, mean hallux valgus angle was 33.9 degrees; intermetatarsal angle, 14.8 degrees; VAS, 8.9; and AOFAS, 37.0. At follow-up period, hallux valgus angle was 14.2; intermetatarsal angle, 9.7; VAS, 2.6; and AOFAS, 90.7. The average first metatarsal shortening was 2.7 mm. No transfer metatarsalgia was noted at 18 months’ follow-up. We found 1 superficial infection, but all patients were satisfied. Conclusions: The mini-invasive Mitchell-Kramer method was indicated in mild to moderate hallux valgus deformity. Cast immobilization was unnecessary, and full weightbearing was allowed early. Using the minioscillating saw allowed for reduced surgical exposure. The technique of the osteotomy also allowed for rotational stability of the osteotomy. Level of Evidence: Level IV, retrospective case series.
Predictors of indoor absolute humidity and estimated effects on influenza virus survival in grade schools
Authors: Koep Tyler H , Enders Felicity T , Pierret Chris , Ekker Stephen C , Krageschmidt Dale , Neff Kevin L , Lipsitch Marc , Shaman Jeffrey , Huskins W Charles 
Published: February 2013

Abstract

Background
Low absolute humidity (AH) has been associated with increased influenza virus survival and transmissibility and the onset of seasonal influenza outbreaks. Humidification of indoor environments may mitigate viral transmission and may be an important control strategy, particularly in schools where viral transmission is common and contributes to the spread of influenza in communities. However, the variability and predictors of AH in the indoor school environment and the feasibility of classroom humidification to levels that could decrease viral survival have not been studied.

Methods
Automated sensors were used to measure temperature, humidity and CO2 levels in two Minnesota grade schools without central humidification during two successive winters. Outdoor AH measurements were derived from the North American Land Data Assimilation System. Variability in indoor AH within classrooms, between classrooms in the same school, and between schools was assessed using concordance correlation coefficients (CCC). Predictors of indoor AH were examined using time-series Auto-Regressive Conditional Heteroskedasticity models. Classroom humidifiers were used when school was not in session to assess the feasibility of increasing indoor AH to levels associated with decreased influenza virus survival, as projected from previously published animal experiments.

Results
AH varied little within classrooms (CCC >0.90) but was more variable between classrooms in the same school (CCC 0.81 for School 1, 0.88 for School 2) and between schools (CCC 0.81). Indoor AH varied widely during the winter (range 2.60 to 10.34 millibars [mb]) and was strongly associated with changes in outdoor AH (p < 0.001). Changes in indoor AH on school weekdays were strongly associated with CO2 levels (p < 0.001). Over 4 hours, classroom humidifiers increased indoor AH by 4 mb, an increase sufficient to decrease projected 1-hour virus survival by an absolute value of 30% during winter months.

Conclusions
During winter, indoor AH in non-humidified grade schools varies substantially and often to levels that are very low. Indoor results are predicted by outdoor AH over a season and CO2 levels (which likely reflects human activity) during individual school days. Classroom humidification may be a feasible approach to increase indoor AH to levels that may decrease influenza virus survival and transmission.
Cellulosic ethanol production using a yeast consortium displaying a minicellulosome and β-glucosidase
Authors: Kim Sujin , Baek Seung-Ho , Lee Kyusung , Hahn Ji-Sook 
Published: February 2013

Abstract

Background
Cellulosic biomass is considered as a promising alternative to fossil fuels, but its recalcitrant nature and high cost of cellulase are the major obstacles to utilize this material. Consolidated bioprocessing (CBP), combining cellulase production, saccharification, and fermentation into one step, has been proposed as the most efficient way to reduce the production cost of cellulosic bioethanol. In this study, we developed a cellulolytic yeast consortium for CBP, based on the surface display of cellulosome structure, mimicking the cellulolytic bacterium, Clostridium thermocellum.

Results
We designed a cellulolytic yeast consortium composed of four different yeast strains capable of either displaying a scaffoldin (mini CipA) containing three cohesin domains derived from C. thermocellum, or secreting one of the three types of cellulases, C. thermocellum CelA (endoglucanase) containing its own dockerin, Trichoderma reesei CBHII (exoglucanase) fused with an exogenous dockerin from C. thermocellum, or Aspergillus aculeatus BGLI (β-glucosidase). The secreted dockerin-containing enzymes, CelA and CBHI, were randomly assembled to the surface-displayed mini CipA via cohesin-dockerin interactions. On the other hand, BGLI was independently assembled to the cell surface since we newly found that it already has a cell adhesion characteristic. We optimized the cellulosome activity and ethanol production by controlling the combination ratio among the four yeast strains. A mixture of cells with the optimized mini CipA:CelA:CBHII:BGLI ratio of 2:3:3:0.53 produced 1.80 g/l ethanol after 94 h, indicating about 20% increase compared with a consortium composed of an equal amount of each cell type (1.48 g/l).

Conclusions
We produced cellulosic ethanol using a cellulolytic yeast consortium, which is composed of cells displaying mini cellulosomes generated via random assembly of CelA and CBHII to a mini CipA, and cells displaying BGLI independently. One of the advantages of this system is that ethanol production can be easily optimized by simply changing the combination ratio of the different populations. In addition, there is no limitation on the number of enzymes to be incorporated into this cellulosome structure. Not only cellulases used in this study, but also any other enzymes, including cellulases and hemicellulases, could be applied just by fusing dockerin domains to the enzymes.
Neoadjuvant chemoradiation therapy for borderline pancreatic adenocarcinoma: report of two cases
Authors: Galindo José , Gabrielli Mauricio , Guerra Juan Francisco , Cassina Juan Carlos , Garrido Marcelo , Jarufe Nicolás , Borghero Yerko , Madrid Jorge , Zoroquiain Pablo , Roa Juan Carlos , Martínez Jorge 
Published: February 2013

Abstract
Pancreatic cancer remains as one of the most aggressive human neoplasms, with overall poor survival rates. Radical surgery of the primary lesion is the best option for treatment. Borderline resectable pancreatic tumors (BRPT), defined as partial involvement of peripancreatic vasculature, may benefit from neoadjuvant therapy. We report on the first two BRPT cases treated with neoadjuvant chemoradiation at our institution. Preoperative CT and MRI demonstrated pancreatic tumors encasing the porto-mesenteric confluence suggestive of BRPT. Patients received neoadjuvant chemotherapy (gemcitabine/cisplatin), followed by radiochemotherapy. After treatment, follow-up images demonstrated tumor downsize, allowing for the tumors to be considered then as resectable. They underwent partial pancreatoduodenectomies (Whipple procedure). In case 1, histopathology revealed a complete, margin-free resection, whereas in case 2 there was a complete pathological response, with no evidence of residual tumor. According to the literature, our initial experience using neoadjuvant chemoradiotherapy on BRPT allowed us to downsize the tumor and, subsequently, to perform a curative surgery.
SMO expression level correlates with overall survival in patients with malignant pleural mesothelioma
Authors: Zhang Yi , He Jianxing , Zhang Fang , Li Hui , Yue Dongsheng , Wang Changli , Jablons David M , He Biao , Lui Natalie 
Published: February 2013

Abstract

Background
Malignant mesothelioma is an aggressive, treatment-resistant tumor arising from mesothelium of pleura, peritoneum and pericardium. Despite current combined regimen, its prognosis remains dismal, calling for more effective targeted therapies. We investigated whether aberrant Hh activation may play a role in mesothelioma.

Methods
SMO and SHH expression levels were analyzed in 46 mesothelioma tissue specimens with real-time RT-PCR, and correlation with survival was analyzed with univariate and multivariate Cox proportional hazards models, Kaplan-Meier survival curves, and the log-rank test. We also examined multiple mesothelioma cell lines for SMO expression and the effect of Hh inhibition by a specific SMO antagonist on cell proliferation by MTS assay.

Results
We observed strong correlation between higher SMO and SHH expression levels with poorer overall survival. Remarkably, Hh inhibition by a specific SMO inhibitor significantly suppressed cell proliferation in the mesothelioma cell lines examined.

Conclusion
Our data strongly support that Hh signaling deregulation plays critical roles in proliferation of mesothelioma, and consistently exerts significant impact on prognosis of the disease. Therefore our findings revealed the hitherto unappreciated role of Hh activation in mesothelioma, and pinpointed Hh signaling antagonist as a potential new therapy against this devastating disease.
Biomarkers for hepatocellular carcinoma: progression in early diagnosis, prognosis, and personalized therapy
Authors: Zhu Kai , Dai Zhi , Zhou Jian 
Published: February 2013

Abstract
Hepatocellular carcinoma (HCC) is one of the most common malignant tumors in the world. Currently, surgical resection, liver transplantation, and local ablation are considered curative therapeutic practices for HCC. The diagnosis of HCC without pathologic confirmation is achieved by analyzing serum alpha-fetoprotein (AFP) levels combined with imaging techniques, including ultrasonography, magnetic resonance imaging, and computerized tomography. Although progress has been made in the diagnosis and management of HCC, its prognosis remains dismal. Various new technologies have identified numerous novel biomarkers with potential diagnostic as well as prognostic value, including Dickkopf-1 and Golgi protein 73. These biomarkers not only help in the early diagnosis and prediction of prognosis, but also assist in identifying potential targets for therapeutic interventions. In this article, we provide an up-to-date review of the biomarkers that are used for early diagnosis, prognosis prediction, and personalized treatment of HCC.
De novo truncating mutations in ASXL3 are associated with a novel clinical phenotype with similarities to Bohring-Opitz syndrome
Authors: Bainbridge Matthew N , Hu Hao , Muzny Donna M , Musante Luciana , Lupski James R , Graham Brett H , Chen Wei , Gripp Karen W , Jenny Kim , Wienker Thomas F , Yang Yaping , Sutton V Reid , Gibbs Richard A , Ropers H Hilger 
Published: February 2013

Abstract
Background
Molecular diagnostics can resolve locus heterogeneity underlying clinical phenotypes that may otherwise be co-assigned as a specific syndrome based on shared clinical features, and can associate phenotypically diverse diseases to a single locus through allelic affinity. Here we describe an apparently novel syndrome, likely caused by de novo truncating mutations in ASXL3, which shares characteristics with Bohring-Opitz syndrome, a disease associated with de novo truncating mutations in ASXL1.

Methods
We used whole-genome and whole-exome sequencing to interrogate the genomes of four subjects with an undiagnosed syndrome.

Results
Using genome-wide sequencing, we identified heterozygous, de novo truncating mutations in ASXL3, a transcriptional repressor related to ASXL1, in four unrelated probands. We found that these probands shared similar phenotypes, including severe feeding difficulties, failure to thrive, and neurologic abnormalities with significant developmental delay. Further, they showed less phenotypic overlap with patients who had de novo truncating mutations in ASXL1.

Conclusion
We have identified truncating mutations in ASXL3 as the likely cause of a novel syndrome with phenotypic overlap with Bohring-Opitz syndrome.
The neutrophil in antineutrophil cytoplasmic autoantibody-associated vasculitis
Authors: Schreiber Adrian , Kettritz Ralph 
Published: February 2013

ABSTRACTNecrotizing, small-vessel vasculitis develops in patients with circulating ANCAs. Neutrophils and monocytes harbor the two major ANCA antigens, PR3 and MPO. A whole body of in vitro experiments implicated ANCA-activated neutrophil effector functions in the pathogenesis of vasculitis, whereas the role of monocytes is less well-characterized. Mouse models for anti-MPO-induced vasculitis were developed to study ANCA–neutrophil interactions in complex in vivo situations. We not only discuss the significance of ANCA–neutrophil interactions for disease induction but also how a detailed understanding of these interactions helps to identify novel treatment targets for ANCA vasculitis.
Almost harmonic Maass forms and Kac–Wakimoto
characters
Authors: Bringmann Kathrin , Folsom Amanda 
Published: February 2013

Abstract

We resolve a question of Kac and explain the automorphic properties of characters due to Kac–Wakimoto pertaining to

s
ℓ

(
m
|
n
)

∧

${s\ell (m|n)^{\wedge }}$

highest weight modules, for n ≥ 1. We prove that
the Kac–Wakimoto characters are essentially holomorphic parts of certain generalizations of harmonic weak Maass forms which we call “almost harmonic Maass forms”. Using a new approach, this generalizes prior work of the first author and Ono, and the authors, both of which treat only the case n = 1. We also provide an explicit asymptotic expansion for the characters.
Recollements induced from tilting modules over tame hereditary
algebras
Authors: Chen Hongxing , Xi Changchang 
Published: February 2013

Abstract
In this paper, we consider the endomorphism algebra
of an infinitely generated tilting module of the form R
𝒰 ⊕ R
𝒰/R over a tame hereditary k-algebra R
with k an arbitrary field, where R
𝒰 is the
universal localization of R at an arbitrary set 𝒰 of
simple regular R-modules. We show that the derived module category
of this endomorphism algebra is a recollement of the derived module
category 𝒟(R) of R and the derived module category 𝒟(𝔸𝒰) of the adèle ring 𝔸𝒰
associated with 𝒰. When k is an algebraically closed
field, the ring 𝔸𝒰 can be precisely
described in terms of Laurent power series ring k((x)) over k. Moreover, if 𝒰 is a union of finitely many cliques, we
give two different stratifications of the derived category of this
endomorphism algebra by derived categories of rings such that the
two stratifications are of different finite lengths.
The regulation, localization, and functions of oxygen-sensing prolyl hydroxylase PHD3
Authors: Jaakkola Panu M. , Rantanen Krista 
Published: February 2013

Abstract
The prolyl 4-hydroxylase domain protein 3 (PHD3) belongs to 2-oxoglutarate and iron-dependent dioxygenases. Together with the two closest paralogues, PHD1 and PHD2, these enzymes have been identified as cellular oxygen sensors that can mark the hypoxia-inducible factor α (HIF-α) for von Hippel-Lindau protein-mediated proteasomal destruction. Although having overlapping functions with PHD1 and PHD2, PHD3 markedly differs from the two isoforms. PHD3 shows a different expression pattern and subcellular localization as well as activity under low oxygen tension. Moreover, it has the widest range of non-HIF targets underlying its diverse functions. The functions of PHD3 differ depending on the cell type and also partially on the microenvironmental conditions it is expressed at. Under normoxia, PHD3 has been shown to be proapoptotic, but under hypoxia, it can have cell survival or proliferation-supporting functions. Here we discuss the regulation, targets, and functions of PHD3.
Study on Glass Defect Inspection Based on Projecting Grating Method
Authors: Jin Yong , Wang Zhaoba , Zhu Linquan , Yang Jiliang , Wei Bo 
Published: February 2013

Abstract
An inspection method based on transmission-mode projecting grating for glass defects has been proposed and verified by experiments. Sinusoidal fringe on the glass is collected using a linear CCD. The fringe curve can be corrected through the Fourier series fitting method to eliminate the constant non-uniformity of the light intensity of a light-emitting diode. The one-dimensional Fourier transform is applied to the corrected fringe curve; the Gaussian band-reject filter is designed to attenuate the first-order spectrum, and a Gaussian band-pass filter having the opposite characteristic attenuates other frequencies (except those in the first-order spectrum). In this way, the defect image and the phase map are obtained. A double threshold segmentation algorithm is applied to get a ternary-value image of the defects, with judgment of the defects’ size and position based on the connected region. Based on the phase map, a calculation method of diopters is proposed. A method for defect type judgment is raised. The results show that the resolution of the real-time testing can reach 0.1 mm × 0.1 mm.
Preparation of Small Silicon Carbide Quantum Dots by Wet Chemical Etching
Authors: Beke D. , Szekrényes Zs. , Balogh I. , Veres M. , Fazakas É , Varga L. K. , Czigány Zs. , Kamarás K. , Gali A. 
Published: February 2013

ABSTRACTLuminescence nanocrystals or quantum dots give grate potential for bio-analysis as well as optoelectronics. Here we report an effective and non-expensive fabrication method of silicon carbide nanocrystals, with diameter below 10 nm, based on electroless wet chemical etching. Our samples show strong violet-blue emission in the 410-450 nm region depending on the used solvents and particle size. Raman and infrared measurements suggest the varied nature of surfaces of silicon carbide nanocrystals which elucidate the behavior of the silicon carbide colloid solvents and also give opportunity to modify the surface easily for specific biological, medical or other application.