bluuebunny/crossref_metadata_2025_split huggingface dataset:
In Vitro
Resistance Profile of the Candidate HIV-1 Microbicide Drug Dapivirine
Authors: Schader Susan M. , Oliveira Maureen , Ibanescu Ruxandra-Ilinca , Moisi Daniela , Colby-Germinario Susan P. , Wainberg Mark A. 
Published: November 2011

ABSTRACT

Antiretroviral-based microbicides may offer a means to reduce the sexual transmission of HIV-1. Suboptimal use of a microbicide may, however, lead to the development of drug resistance in users that are already, or become, infected with HIV-1. In such cases, the efficacy of treatments may be compromised since the same (or similar) antiretrovirals used in treatments are being developed as microbicides. To help predict which drug resistance mutations may develop in the context of suboptimal use, HIV-1 primary isolates of different subtypes and different baseline resistance profiles were used to infect primary cells
in vitro
in the presence of increasing suboptimal concentrations of the two candidate microbicide antiretrovirals dapivirine (DAP) and tenofovir (TFV) alone or in combination. Infections were ongoing for 25 weeks, after which reverse transcriptase genotypes were determined and scrutinized for the presence of any clinically recognized reverse transcriptase drug resistance mutations. Results indicated that suboptimal concentrations of DAP alone facilitated the emergence of common nonnucleoside reverse transcriptase inhibitor resistance mutations, while suboptimal concentrations of DAP plus TFV gave rise to fewer mutations. Suboptimal concentrations of TFV alone did not frequently result in the development of resistance mutations. Sensitivity evaluations for stavudine (d4T), nevirapine (NVP), and lamivudine (3TC) revealed that the selection of resistance as a consequence of suboptimal concentrations of DAP may compromise the potential for NVP to be used in treatment, a finding of potential relevance in developing countries.
Reproductive phenology of the Caribbean cactus Harrisia portoricensis: rainfall and temperature associations
Authors: Rojas-Sandoval Julissa , Meléndez-Ackerman Elvia 
Published: November 2011

Phenological patterns often influence the extent of reproductive success of plants as well the interaction among species. In this study, we evaluated the association of local climatic factors and plant size with the reproductive phenology of the threatened cactus Harrisia portoricensis in the Caribbean dry forest of Mona Island. Analyses of phenological data gathered monthly in 572 plants over 2 years concluded that for this species, reproductive activity is continuous throughout the year and reproductive output is positively correlated with plant size. Bud production in H. portoricensis was positively associated with temporal changes in monthly mean and minimum temperatures, while flower production was positively associated with total monthly rainfall. When compared with other columnar cacti species, the combined phenological responses to temperature and rainfall in H. portoricensis represent a different strategy. We hypothesize that contrasting phenological responses among columnar cacti may stem from site-specific differences in the degree of intra-annual rainfall or temperature variability. If that is the case, then monitoring reproductive responses of cacti to expected changes in climate at a global scale would require gathering phenological data for this taxon across different geographic regions.
Surface morphology characteristics of rock discontinuities with particular reference to their genesis
Authors: Aydan Ömer , Shimizu Yasuhiro 
Published: November 2011

Abstract
A research program was undertaken to characterize the surface morphology of natural discontinuities with particular reference to their genesis. For this purpose a special profilometer, which could easily be transported and operated in the field, and was capable of measuring 480 mm long profiles, was designed. The recorded profiles were digitized and analysed to obtain surface morphology characteristics of the discontinuities in different rock types found in Central Japan. Natural discontinuities have an anisotropic surface topography which may be characterized by measuring profiles along their eigen directions. Consequently, surface morphology parameters are directional and differ depending upon the discontinuity type.
Observations on fractography with laboratory experiments for geologists
Authors: Kulander B. R. , Dean Stuart L. 
Published: November 2011

Abstract
Brittle fracture growth proceeds through unique stages, each marked by distinct fractographic features that can only develop during Mode I loading at the propagating crack tip. Fractographic features in any substance can be interpreted in terms of the location of the failure origin, as well as changes in propagation velocities, stress directions and stress magnitudes at the crack tip during failure. Joints in granular pervious rock, however, do not contain fractographic features, commonly formed in glass, that develop at unstable propagation rates under the influence of appreciable amounts of stored strain energy. Yet, features that develop at lower stable rates of propagation are present on fractures in glass and rock implying that the absence of certain fractographic features provides useful information.
Simple laboratory experiments, primarily on glass, are discussed to provide geologists an opportunity to recognize and qualitatively interpret fractographic features diagnostic of brittle failure. The exercises demonstrate the changing propagation dynamics that control the morphological evolution of artificially-induced fractures and natural joints in rock.
The expression of hydraulic fracturing in rocks and sediments
Authors: Cosgrove J. W. 
Published: November 2011

Abstract
The orientation and spatial organization of hydraulic fractures in rocks and sediments is determined by the magnitude of the differential stress, the orientation of the principal stress axes and the intrinsic properties of the rock, particularly its cohesive strength. Depending on the values of these various parameters the expression of hydraulic fracturing in a rock or sediment can be extremely varied ranging from conjugate shear fractures through parallel tension fractures to randomly oriented tension fractures and fluidized sediments.
The influence of a rock’s properties on its response to hydraulic fracturing is illustrated by considering the mechanics of formation of sedimentary dykes.
Compiler-Supported Thread Management for Multithreaded Network Processors
Authors: Zhuang Xiaotong , Pande Santosh 
Published: November 2011

Traditionally, runtime management involving CPU sharing, real-time scheduling, etc., is provided by the runtime environment (typically an operating system) using hardware support such as timers and interrupts. However, due to stringent performance requirements on network processors, neither OS nor hardware mechanisms are typically feasible/available. Mapping packet processing tasks on network processors involves complex trade-offs to maximize parallelism and pipelining. Due to an increase in the size of the code store and complexity of application requirements, network processors are being programmed with heterogeneous threads that may execute code belonging to different tasks on a given micro-engine. Also, most network applications are streaming applications that are typically processed in a pipelined fashion. Thus, the tasks on different micro-engines are pipelined in such a way as to maximize the throughput. Tasks themselves could have different runtime performance demands.
In this article, we focus on network processors on which hardware can only schedule threads in a round-robin fashion and no OS assistance is provided. We show that it is very difficult and inefficient for the programmer to meet the constraints of runtime management by coding them statically. Due to the infeasibility of hardware or OS solution (even in the near future), we undertake a compiler approach.
We propose a complete compiler solution to automatically insert explicit context switch (ctx) instructions provided on the network processor such that the execution of threads is better manipulated at runtime to meet their constraints. Two approaches are presented that can control programs’ runtime behavior with different applicability and overheads. We show that it is feasible and also opens new application domains that would need heterogeneous thread programming. Such approaches would in general become important for multicore processors.
Finally, our experiments show that the runtime constraints are enforced nearly ideally with minimal runtime degradation and small code growth.
Coherent parallel hashing
Authors: García Ismael , Lefebvre Sylvain , Hornus Samuel , Lasram Anass 
Published: November 2011

Recent spatial hashing schemes hash millions of keys in parallel, compacting sparse spatial data in small hash tables while still allowing for fast access from the GPU. Unfortunately, available schemes suffer from two drawbacks: Multiple runs of the construction process are often required before success, and the random nature of the hash functions decreases access performance.
We introduce a new parallel hashing scheme which reaches high load factor with a very low failure rate. In addition our scheme has the unique advantage to exploit coherence in the data and the access patterns for faster performance. Compared to existing approaches, it exhibits much greater locality of memory accesses and consistent execution paths within groups of threads. This is especially well suited to Computer Graphics applications, where spatial coherence is common. In absence of coherence our scheme performs similarly to previous methods, but does not suffer from construction failures.
Our scheme is based on the Robin Hood scheme modified to quickly abort queries of keys that are not in the table, and to preserve coherence. We demonstrate our scheme on a variety of data sets. We analyze construction and access performance, as well as cache and threads behavior.
Antifibrotic effects of curcumin are associated with overexpression of cathepsins K and L in bleomycin treated mice and human fibroblasts
Authors: Zhang Dongwei , Huang Chuangfang , Yang Changfu , Liu Renzuo J , Wang Jifeng , Niu Jianzhao , Brömme Dieter 
Published: November 2011

Abstract

Background
Lung fibrosis is characterized by fibroblast proliferation and the deposition of collagens. Curcumin, a polyphenol antioxidant from the spice tumeric, has been shown to effectively counteract fibroblast proliferation and reducing inflammation and fibrotic progression in animal models of bleomycin-induced lung injury. However, there is little mechanistic insight in the biological activity of curcumin. Here, we study the effects of curcumin on the expression and activity of cathepsins which have been implicated in the development of fibrotic lung diseases.

Methods
We investigated the effects of curcumin administration to bleomycin stimulated C57BL/6 mice and human fetal lung fibroblasts (HFL-1) on the expression of cathepsins K and L which have been implicated in matrix degradation, TGF-β1 modulation, and apoptosis. Lung tissues were evaluated for their contents of cathepsins K and L, collagen, and TGF-β1. HFL-1 cells were used to investigate the effects of curcumin and cathepsin inhibition on cell proliferation, migration, apoptosis, and the expression of cathepsins K and L and TGF-β1.

Results
Collagen deposition in lungs was decreased by 17-28% after curcumin treatment which was accompanied by increased expression levels of cathepsins L (25%-39%) and K (41%-76%) and a 30% decrease in TGF-β1 expression. Moreover, Tunel staining of lung tissue revealed a 33-41% increase in apoptotic cells after curcumin treatment. These in vivo data correlated well with data obtained from the human fibroblast line, HFL-1. Here, cathepsin K and L expression increased 190% and 240%, respectively, in the presence of curcumin and the expression of TGF-β1 decreased by 34%. Furthermore, curcumin significantly decreased cell proliferation and migration and increased the expression of surrogate markers of apoptosis. In contrast, these curcumin effects were partly reversed by a potent cathepsin inhibitor.

Conclusion
This study demonstrates that curcumin increases the expression of cathepsins K and L in lung which an effect on lung fibroblast cell behavior such as proliferation, migration and apoptosis rates and on the expression of TGF-β1 in mouse lung and HFL-1 cells. These results suggest that cathepsin-inducing drugs such as curcumin may be beneficial in the treatment of lung fibrosis.
Production of a reference transcriptome and transcriptomic database (PocilloporaBase) for the cauliflower coral, Pocillopora damicornis
Authors: Traylor-Knowles Nikki , Granger Brian R , Lubinski Tristan J , Parikh Jignesh R , Garamszegi Sara , Xia Yu , Marto Jarrod A , Kaufman Les , Finnerty John R 
Published: November 2011

Abstract

Background
Motivated by the precarious state of the world's coral reefs, there is currently a keen interest in coral transcriptomics. By identifying changes in coral gene expression that are triggered by particular environmental stressors, we can begin to characterize coral stress responses at the molecular level, which should lead to the development of more powerful diagnostic tools for evaluating the health of corals in the field. Furthermore, the identification of genetic variants that are more or less resilient in the face of particular stressors will help us to develop more reliable prognoses for particular coral populations. Toward this end, we performed deep mRNA sequencing of the cauliflower coral, Pocillopora damicornis, a geographically widespread Indo-Pacific species that exhibits a great diversity of colony forms and is able to thrive in habitats subject to a wide range of human impacts. Importantly, P. damicornis is particularly amenable to laboratory culture. We collected specimens from three geographically isolated Hawaiian populations subjected to qualitatively different levels of human impact. We isolated RNA from colony fragments ("nubbins") exposed to four environmental stressors (heat, desiccation, peroxide, and hypo-saline conditions) or control conditions. The RNA was pooled and sequenced using the 454 platform.

Description
Both the raw reads (n = 1, 116, 551) and the assembled contigs (n = 70, 786; mean length = 836 nucleotides) were deposited in a new publicly available relational database called PocilloporaBase http://www.PocilloporaBase.org. Using BLASTX, 47.2% of the contigs were found to match a sequence in the NCBI database at an E-value threshold of ≤.001; 93.6% of those contigs with matches in the NCBI database appear to be of metazoan origin and 2.3% bacterial origin, while most of the remaining 4.1% match to other eukaryotes, including algae and amoebae.

Conclusions

P. damicornis now joins the handful of coral species for which extensive transcriptomic data are publicly available. Through PocilloporaBase http://www.PocilloporaBase.org, one can obtain assembled contigs and raw reads and query the data according to a wide assortment of attributes including taxonomic origin, PFAM motif, KEGG pathway, and GO annotation.
Clinical characteristics and favorable long-term outcomes for patients with idiopathic inflammatory myopathies: a retrospective single center study in China
Authors: Shu Xiao Ming , Lu Xin , Xie Yao , Wang Guo Chun 
Published: November 2011

AbstractBackgroundLittle is known about the clinical features and true survival risk factors in Chinese Han population. We conducted the current study to investigate the clinical features, long-term outcome and true potential indicators associated with mortality of idiopathic inflammatory myopathies (IIM) in China.MethodsWe restrospectvely investigated 188 patients diagnosed with IIM at our hospital from January 1986 to April 2009. The primary outcome was determined with mortality. The secondary outcomes for survival patients were organ damage and disease activity, health status, and disability, which were assessed with Myositis Damage Index, Myositis Disease Activity Assessment Visual Analogue Scales, Health Assessment Questionnaire Disability Index, and the Modified Rankin Scale, respectively. Potential prognostic factors for mortality were analyzed with the multivariate Cox regression model.ResultsMean age at disease onset was 43.8 ± 15.8 years and male to female ratio was 1:2.1 in this cohort. The 1-, 5-, 10-, 15- and 20-year survival rates were 93.6%, 88.7%, 81%, 73.6% and 65.6%. The independent predicators for mortality were age at disease onset [hazard ratio (HR):1.05, 95% CI 1.02 - 1.08], presence of cancer (HR:3.68, 95%CI 1.39 - 9.74), and elevated IgA level at diagnosis (HR:2.80, 95% CI 1.16-6.74). At the end of the follow-up, 29 patients manifested drug withdrawal within an average 4.1 years (range 0.5-15.2 year), most patients (85.9%) had no disease activity and 130 patients (83.4%) had no disability.ConclusionsThe long-term outcomes of IIM patients in our cohort have improved dramatically. Those patients most likely to survive had a high chance of reaching stable disease status, and obtained long-term or possibly permanent remission to a large extent.
Cold-shock eliminates female nucleus in fertilized eggs to induce androgenesis in the loach (Misgurnus anguillicaudatus), a teleost fish
Authors: Morishima Kagayaki , Fujimoto Takafumi , Sato Mami , Kawae Ayako , Zhao Yan , Yamaha Etsuro , Arai Katsutoshi 
Published: November 2011

Abstract

Background
Androgenesis (all-male inheritance) is generally induced by means of irradiating the eggs to inactivate the maternal genome, followed by fertilization with normal sperm. In fish, the conventional technique for induced androgenesis has been applied for rapid fixation to traits, recovery of cryopreserved genotypes, sex-control, etc. A new method of androgenesis that eliminates the need to irradiate the egg was proposed using the loach, Misgurnus anguillicaudatus (a teleost fish).

Results
When the eggs of wild-type females were fertilized with sperm of albino or orange phenotype males and cold-shocked at 0 to 3°C for 60 min duration just after fertilization, generally more than 30% (with a peak of 100%) of the hatched progeny were androgenotes. While a few of them were the normal diploid, most of them turned out to be abnormal haploid. All-male inheritance was verified by the expression of the recessive color trait (albino or orange) and microsatellite genotypes comprising only paternally derived alleles. Nuclear behavior after the cold-shock treatment was traced by microscopic observation of DAPI (4'6-diamidino-2-phenylindole)-stained samples and hematoxylin-eosin stained histological sections, and the extrusion of egg (maternal) nucleus was observed in eggs treated in the optimum timing.

Conclusion
In this paper, we demonstrate that cold-shock treatment (at 0 and 3°C) of loach eggs for 60 min just after fertilization successfully induces androgenetic haploid development. The most likely mechanism of cold-shock induced androgenesis is an elimination of the egg nucleus together along with the second polar body and subsequent development of a decondensed sperm nucleus or male pronucleus.
A novel esterase gene cloned from a metagenomic library from neritic sediments of the South China Sea
Authors: Peng Qing , Zhang Xue , Shang Meng , Wang Xu , Wang Guili , Li Bingxue , Guan Guohua , Li Ying , Wang Youshao 
Published: November 2011

Abstract

Background
Marine microbes are a large and diverse group, which are exposed to a wide variety of pressure, temperature, salinity, nutrient availability and other environmental conditions. They provide a huge potential source of novel enzymes with unique properties that may be useful in industry and biotechnology. To explore the lipolytic genetic resources in the South China Sea, 23 sediment samples were collected in the depth < 100 m marine areas.

Results
A metagenomic library of South China Sea sediments assemblage in plasmid vector containing about 194 Mb of community DNA was prepared. Screening of a part of the unamplified library resulted in isolation of 15 unique lipolytic clones with the ability to hydrolyze tributyrin. A positive recombinant clone (pNLE1), containing a novel esterase (Est_p1), was successfully expressed in E. coli and purified. In a series of assays, Est_p1 displayed maximal activity at pH 8.57, 40°C, with ρ-Nitrophenyl butyrate (C4) as substrate. Compared to other metagenomic esterases, Est_p1 played a notable role in specificity for substrate C4 (k
cat/K
m value 11,500 S-1m M-1) and showed no inhibited by phenylmethylsulfonyl fluoride, suggested that the substrate binding pocket was suitable for substrate C4 and the serine active-site residue was buried at the bottom of substrate binding pocket which sheltered by a lid structure.

Conclusions
Esterase, which specificity towards short chain fatty acids, especially butanoic acid, is commercially available as potent flavoring tools. According the outstanding activity and specificity for substrate C4, Est_p1 has potential application in flavor industries requiring hydrolysis of short chain esters.
Gene-targeted embryonic stem cells: real-time PCR assay for estimation of the number of neomycin selection cassettes
Authors: Mancini Cecilia , Messana Erika , Turco Emilia , Brussino Alessandro , Brusco Alfredo 
Published: November 2011

Abstract
In the preparation of transgenic murine ES cells it is important to verify the construct has a single insertion, because an ectopic neomycin phosphortransferase positive selection cassette (NEO) may cause a position effect. During a recent work, where a knockin SCA28 mouse was prepared, we developed two assays based on Real-Time PCR using both SYBR Green and specific minor groove binder (MGB) probes to evaluate the copies of NEO using the comparative delta-delta Ct method versus the Rpp30 reference gene.
We compared the results from Southern blot, routinely used to quantify NEO copies, with the two Real-Time PCR assays. Twenty-two clones containing the single NEO copy showed values of 0.98 ± 0.24 (mean ± 2 S.D.), and were clearly distinguishable from clones with two or more NEO copies.
This method was found to be useful, easy, sensitive and fast and could substitute for the widely used, but laborious Southern blot method.