bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance‐driven instrumentation and mapping strategies using the LARA aspect‐oriented programming approach
Authors: Cardoso João M. P. , Coutinho José G. F. , Carvalho Tiago , Diniz Pedro C. , Petrov Zlatko , Luk Wayne , Gonçalves Fernando 
Published: December 2014

SummaryThe development of applications for high‐performance embedded systems is a long and error‐prone process because in addition to the required functionality, developers must consider various and often conflicting nonfunctional requirements such as performance and/or energy efficiency. The complexity of this process is further exacerbated by the multitude of target architectures and mapping tools. This article describes LARA, an aspect‐oriented programming language that allows programmers to convey domain‐specific knowledge and nonfunctional requirements to a toolchain composed of source‐to‐source transformers, compiler optimizers, and mapping/synthesis tools. LARA is sufficiently flexible to target different tools and host languages while also allowing the specification of compilation strategies to enable efficient generation of software code and hardware cores (using hardware description languages) for hybrid target architectures – a unique feature to the best of our knowledge not found in any other aspect‐oriented programming language. A key feature of LARA is its ability to deal with different models of join points, actions, and attributes. In this article, we describe the LARA approach and evaluate its impact on code instrumentation and analysis and on selecting critical code sections to be migrated to hardware accelerators for two embedded applications from industry. Copyright © 2014 John Wiley & Sons, Ltd.
Snai1 Promotes ESC Exit from the Pluripotency by Direct Repression of Self-Renewal Genes
Authors: Galvagni Federico , Lentucci Claudia , Neri Francesco , Dettori Daniela , De Clemente Caterina , Orlandini Maurizio , Anselmi Francesca , Rapelli Stefania , Grillo Michela , Borghi Sara , Oliviero Salvatore 
Published: December 2014

Abstract
Although much is known about the pluripotency self-renewal circuitry, the molecular events that lead embryonic stem cells (ESCs) exit from pluripotency and begin differentiation are largely unknown. We found that the zinc finger transcription factor Snai1, involved in gastrulation and epithelial-mesenchymal transition, is already expressed in the inner cell mass of the preimplantation blastocysts. In ESCs, Snai1 does not respond to TGFβ or BMP4 signaling but it is induced by retinoic acid treatment, which induces the binding, on the Snai1 promoter, of the retinoid receptors RARγ and RXRα, the dissociation of the Polycomb repressor complex 2 which results in the decrease of H3K27me3, and the increase of histone H3K4me3. Snai1 mediates the repression of pluripotency genes by binding directly to the promoters of Nanog, Nr5a2, Tcl1, c-Kit, and Tcfcp2l1. The transient activation of Snai1 in embryoid bodies induces the expression of the markers of all three germ layers. These results suggest that Snai1 is a key factor that triggers ESCs exit from the pluripotency state and initiate their differentiation processes. Stem Cells 2015;33:742–750
Phase I study of amatuximab, a novel monoclonal antibody to mesothelin, in Japanese patients with advanced solid tumors
Authors: Fujisaka Yasuhito , Kurata Takayasu , Tanaka Kaoru , Kudo Toshihiro , Okamoto Kunio , Tsurutani Junji , Kaneda Hiroyasu , Okamoto Isamu , Namiki Masayuki , Kitamura Chifumi , Nakagawa Kazuhiko 
Published: December 2014

SummaryAmatuximab is a chimeric monoclonal antibody that targets mesothelin, which is expressed in virtually all mesotheliomas and pancreatic adenocarcinomas. The objective of this study was to determine the dose-limiting toxicity and the maximum tolerated dose. Patients with mesothelioma, pancreatic adenocarcinoma or other mesothelin-positive solid tumors were eligible for this study. Amatuximab was administered weekly as an intravenous infusion in 4-week cycles at progressively increasing doses ranging from 50 to 200 mg/m2. Seventeen patients received amatuximab. Two dose-limiting toxicities were observed: one at 50 mg/m2 and one at 200 mg/m2; the maximum tolerated dose of this study was determined to be 200 mg/m2. Of the 17 patients, 13 patients (76.5 %) experienced treatment-related adverse events. The most common adverse events were grade 1 fatigue (29.4 %) and pyrexia (23.5 %). The maximum serum concentration and area under the concentration curve values increased in an almost dose-proportional manner. Three patients had stable disease. Amatuximab was generally well tolerated at doses up to 200 mg/m2. The pharmacokinetic profile of amatuximab in the Japanese population was similar to that seen in the United States population (Clinical Trials.gov Identifier: NCT01018784).
A Retrospective Comparison of the Management of Recalcitrant Lateral Elbow Tendinosis: Platelet-Rich Plasma Injections versus Surgery
Authors: Ford Ronald D. , Schmitt William P. , Lineberry Kyle , Luce Paul 
Published: December 2014

Background The aim of this study is to compare the outcomes of platelet-rich plasma (PRP) injections to surgical release and decortication for lateral elbow tendinosis within a similar patient population. Methods A retrospective chart review was performed on two groups of patients, receiving either PRP injections ( n=28) or surgery ( n=50). Patient demographics, clinical presentation, pain score, worker's compensation status, and previous steroid injections were recorded. Primary outcomes included pain and symptom improvement, range of motion, return to work, and postoperative complications. Results Demographics, duration of symptoms, and exam findings were similar between the PRP and surgical patients. There was no significant difference in pain and symptom improvement. Pain improvement was reported in 89.3 % of PRP patients and 84 % of surgical patients, with a reported percent reduction in pain of 61.1 and 55 %, respectively. Symptoms other than pain improved in 85.7 and 88 % of the PRP and surgical patients, respectively. Tenderness to palpation at the lateral epicondyle (64.3 % PRP, 44 % surgical), pain with resisted wrist extension (35.7 % PRP, 30 % surgical), or residual symptoms other than pain (14.3 % PRP, 10 % surgical) were not significantly different between groups at last follow-up. Eighty-two percent of patients in both the PRP and surgical groups returned to work. No complications were reported. Mean follow-up was 315 vs. 352 days for the PRP and surgical groups, respectively. Conclusions Similar outcomes in pain improvement and return to work may be achievable with either PRP injections or surgery in recalcitrant lateral elbow tendinosis. PRP injections may be a reasonable alternative for patients apprehensive to proceed with surgery or poor surgical candidates.
Identification of Differentially-Expressed Genes in Intestinal Gastric Cancer by Microarray Analysis
Authors: Zang Shizhu , Guo Ruifang , Xing Rui , Zhang Liang , Li Wenmei , Zhao Min , Fang Jingyuan , Hu Fulian , Kang Bin , Ren Yonghong , Zhuang Yonglong , Liu Siqi , Wang Rong , Li Xianghong , Yu Yingyan , Cheng Jing , Lu Youyong 
Published: December 2014

Abstract
Gastric cancer (GC) is one of the most frequent malignant tumors. In order to systematically characterize the cellular and molecular mechanisms of intestinal GC development, in this study, we used 22 K oligonucleotide microarrays and bioinformatics analysis to evaluate the gene expression profiles of GC in 45 tissue samples, including 20 intestinal GC tissue samples, 20 normal appearing tissues (NATs) adjacent to tumors and 5 noncancerous gastric mucosa tissue samples. These profiles allowed us to explore the transcriptional characteristics of GC and determine the change patterns in gene expression that may be of clinical significance. 1519 and 1255 differentially-expressed genes (DEGs) were identified in intestinal GC tissues and NATs, respectively, as determined by Bayesian analysis (P &lt; 0.001). These genes were associated with diverse functions such as mucosa secretion, metabolism, proliferation, signaling and development, which occur at different stages of GC development.
Heat flux enhancement by regular surface roughness in turbulent thermal convection
Authors: Wagner Sebastian , Shishkina Olga 
Published: December 2014

AbstractDirect numerical simulations (DNS) of turbulent thermal convection in a box-shaped domain with regular surface roughness at the heated bottom and cooled top surfaces are conducted for Prandtl number $\mathit{Pr}=0.786$ and Rayleigh numbers $\mathit{Ra}$ between $10^{6}$ and $10^{8}$. The surface roughness is introduced by four parallelepiped equidistantly distributed obstacles attached to the bottom plate, and four obstacles located symmetrically at the top plate. By varying $\mathit{Ra}$ and the height and width of the obstacles, we investigate the influence of the regular wall roughness on the turbulent heat transport, measured by the Nusselt number $\mathit{Nu}$. For fixed $\mathit{Ra}$, the change in the value of $\mathit{Nu}$ is determined not only by the covering area of the surface, i.e. the obstacle height, but also by the distance between the obstacles. The heat flux enhancement is found to be largest for wide cavities between the obstacles which can be ‘washed out’ by the flow. This is also manifested in an empirical relation, which is based on the DNS data. We further discuss theoretical limiting cases for very wide and very narrow obstacles and combine them into a simple model for the heat flux enhancement due to the wall roughness, without introducing any free parameters. This model predicts well the general trends and the order of magnitude of the heat flux enhancement obtained in the DNS. In the $\mathit{Nu}$ versus $\mathit{Ra}$ scaling, the obstacles work in two ways: for smaller $\mathit{Ra}$ an increase of the scaling exponent compared to the smooth case is found, which is connected to the heat flux entering the cavities from below. For larger $\mathit{Ra}$ the scaling exponent saturates to the one for smooth plates, which can be understood as a full washing-out of the cavities. The latter is also investigated by considering the strength of the mean secondary flow in the cavities and its relation to the wind (i.e. the large-scale circulation), that develops in the core part of the domain. Generally, an increase in the roughness height leads to stronger flows both in the cavities and in the bulk region, while an increase in the width of the obstacles strengthens only the large-scale circulation of the fluid and weakens the secondary flows. An increase of the Rayleigh number always leads to stronger flows, both in the cavities and in the bulk.
“You Have No Good Blood in Your Body”. Oral Communication in Sixteenth-Century Physicians’ Medical Practice
Authors: Stolberg Michael 
Published: December 2014

AbstractIn his personal notebooks, the little known Bohemian physician Georg Handsch (1529–c. 1578) recorded, among other things, hundreds of vernacular phrases and expressions he and other physicians used in their oral interaction with patients and families. Based primarily on this extraordinary source, this paper traces the terms, concepts and images to which sixteenth-century physicians resorted when they explained the nature of a patient’s disease and justified their treatment. At the bedside and in the consultation room, Handsch and his fellow physicians attributed most diseases to a local accumulation of impure, putrid or otherwise pathological humours. The latter were commonly said to result, in turn, from an insufficient concoction and assimilation of food and drink in the stomach and the liver or from an obstruction of the humoral flow inside the body and across its borders. By contrast, other notions and explanatory models, which had a prominent place in contemporary learned medical writing, hardly played a role at all in the physicians’ oral communication. Specific disease terms were rarely used, a mere imbalance of the four natural humours in the body was almost never inculpated, and the patient’s personal life-style and other non-naturals did not attract much attention either. These striking differences between the ways in which physicians explained the patients’ diseases in their daily practice and the explanatory models we find in contemporary textbooks, are attributed, above all, to the physicians’ precarious situation in the early modern medical marketplace. Since dissatisfied patients were quick to turn to another healer, physicians had to explain the disease and justify their treatment in a manner that was comprehensible to ordinary lay people and in line with their expectations and beliefs, which, at the time, revolved almost entirely around notions of impurity and evacuation.
Computational Complexity of Topological Invariants
Authors: Amann Manuel 
Published: December 2014

AbstractWe answer the following question posed by Lechuga: given a simply connected spaceXwith bothH*(X; ℚ) and π*(X) ⊗ ℚ being finite dimensional, what is the computational complexity of an algorithm computing the cup length and the rational Lusternik—Schnirelmann category ofX?Basically, by a reduction from the decision problem of whether a given graph isk-colourable fork≥ 3, we show that even stricter versions of the problems above are NP-hard.
Landscape influence on spatial patterns of meningeal worm and liver fluke infection in white-tailed deer
Authors: VANDERWAAL KIMBERLY L. , WINDELS STEVE K. , OLSON BRYCE T. , VANNATTA J. TREVOR , MOEN RON 
Published: December 2014

SUMMARYParasites that primarily infect white-tailed deer (Odocoileus virginianus), such as liver flukes (Fascioloides magna) and meningeal worm (Parelaphostrongylus tenuis), can cause morbidity and mortality when incidentally infecting moose (Alces alces). Ecological factors are expected to influence spatial variation in infection risk by affecting the survival of free-living life stages outside the host and the abundance of intermediate gastropod hosts. Here, we investigate how ecology influenced the fine-scale distribution of these parasites in deer in Voyageurs National Park, Minnesota. Deer pellet groups (N = 295) were sampled for the presence of P. tenuis larvae and F. magna eggs. We found that deer were significantly more likely to be infected with P. tenuis in habitats with less upland deciduous forest and more upland mixed conifer forest and shrub, a pattern that mirrored microhabitat differences in gastropod abundances. Deer were also more likely to be infected with F. magna in areas with more marshland, specifically rooted-floating aquatic marshes (RFAMs). The environment played a larger role than deer density in determining spatial patterns of infection for both parasites, highlighting the importance of considering ecological factors on all stages of a parasite's life cycle in order to understand its occurrence within the definitive host.
Cognitive performance and the course of depressive symptoms over 7 years of follow-up: the SMART-MR study
Authors: Kooistra M. , Zuithoff N. P. A. , Grool A. M. , Zinsmeester M. , Biessels G. J. , van der Graaf Y. , Geerlings M. I. 
Published: December 2014

BackgroundDepressive symptoms and cognitive impairment often co-occur, but their interactive relationship is complex and the direction of causation is still a topic of research. We examined the influence of cognitive performance on the course of depressive symptoms during 7 years of follow-up in patients with vascular disease.MethodWithin the SMART-MR study, 736 patients (mean age 62 ± 10 years) had neuropsychological assessment on four cognitive domains at baseline [memory (MEM), working memory (WMEM), executive functioning (EXEC), and information processing speed (SPEED)]. Depressive symptoms were assessed with the Patient Health Questionnaire-9 (PHQ-9) at baseline and every 6 months during 7 years of follow-up. Generalized Estimating Equation (GEE) models were used to assess the association between cognitive performance with depressive symptoms at multiple time points during follow-up. Interaction terms between the respective cognitive domains and time was included to examine if the course of depressive symptoms differed according to baseline cognitive performance.ResultsThe GEE analyses showed no significant interactions between the respective cognitive domains and time indicating no different course of depressive symptoms according to baseline cognitive performance. Lower MEM, EXEC or SPEED, but not WMEM performance, was significantly associated with more depressive symptoms during follow-up per z score decrease: MEM [B = 0.70, 95% confidence interval (CI) 0.35–1.05]; EXEC (B = 0.88, 95% CI 0.41–1.36), and SPEED (B = 0.57, 95% CI 0.21–0.92).ConclusionsPoorer cognitive performance on the domains MEM, EXEC and SPEED, but not WMEM, was associated with higher levels of depressive symptoms over 7 years of follow-up, but not with a different course of depressive symptoms over time.
Why Orientalism still matters: Reading ‘casual forgetting’ and ‘active remembering’ as neoliberal forms of contestation in international politics
Authors: el-MALIK SHIERA S. 
Published: December 2014

AbstractIn 2007, theBritish Journal of Politics and International Relations(BJPIR) devoted an issue to gendering International Relations. It opens with Cynthia Enloe addressing the ‘politics of casual forgetting’. I investigate this notion of casual forgetting using a framework informed by postcolonial and feminist scholarship. Working with ideas drawn from critiques of Orientalism and neoliberalism, I examine knowledge practices that centre binaries as forms of objectivity that disembed phenomena from context, and as forms of over-simplification that flatten the appearance of complexity. Together, these practices have a depoliticising effect; they obscure contestation, situate hierarchy as natural, and separate analysis from its embeddedness in historical and political conditions, even in work guided by critical agendas. I trace these depoliticising practices in a conversation in the 2007 Special Issue ofBJPIRand show that Enloe's comments present a push for critical analysis that was overlooked by the Special Issue's editors in their attempt to more clearly delineate the subdiscipline of Gender and International Relations (IR) as distinct from feminist IR. This article suggests that Enloe's plea is effectively one for ‘active remembering’ as a way to render visible the insidious forms of power that give a stable appearance to categories of social phenomena.
Breeding ecology and success of a reintroduced population of the endangered Crested Ibis Nipponia nippon
Authors: YU XIAOPING , LI XIA , HUO ZHIPING 
Published: December 2014

SummaryReintroduction projects usually attempt to re-establish a self-sustaining population of endangered species within their historical ranges through the release of captive-bred individuals into the wild. We studied the breeding biology and nesting success of a reintroduced population of Crested Ibis Nipponia nippon in Ningshan County on the south slope of the Qinling Mountains of Shaannxi Province, China. From May 2007 to October 2011, 56 captive-bred individuals, composed of 26 females and 30 males, were released into the area and monitored using radio-telemetry. The average age of individuals at release was 5.2 ± 2.5 years for females and 6.4 ± 2.9 years for males. Mean clutch size was 3.14±1.06 (range 1-5). Mean number of fledglings per active nest was 1.57 ± 1.03 and mean number of fledglings per successful nest was 2.00 ± 0.87. Most of the fledglings survived to complete their post-fledging dispersal. Mean annual survival rate was 0.552 ± 0.064 for all released birds, 0.815 ± 0.054 for breeders, and 0.515 ± 0.058 for first year fledglings. The average number of young produced/year/pair was 1.57 ± 1.03 and the growth rate (λ) of the reintroduced population was 1.2193. We confirmed that starvation and predation by King Rat Snake Elaphe carinata were the main causes of death of released individuals, nestlings and fledglings. This is the first attempt to reintroduce captive-bred Crested Ibis to former natural habitat. The ability of captive-bred ibis to survive and breed successfully bodes well for future releases of this and other endangered species.
Blocking autophagy enhanced cytotoxicity induced by recombinant human arginase in triple-negative breast cancer cells
Authors: Wang Z , Shi X , Li Y , Fan J , Zeng X , Xian Z , Wang Z , Sun Y , Wang S , Song P , Zhao S , Hu H , Ju D 
Published: December 2014

AbstractDepletion of arginine by recombinant human arginase (rhArg) has proven to be an effective cancer therapeutic approach for a variety of malignant tumors. Triple-negative breast cancers (TNBCs) lack of specific therapeutic targets, resulting in poor prognosis and limited therapeutic efficacy. To explore new therapeutic approaches for TNBC we studied the cytotoxicity of rhArg in five TNBC cells. We found that rhArg could inhibit cell growth in these five TNBC cells. Intriguingly, accumulation of autophagosomes and autophagic flux was observed in rhArg-treated MDA-MB-231 cells. Inhibition of autophagy by chloroquine (CQ), 3-methyladenine (3-MA) and siRNA targeting Beclin1 significantly enhanced rhArg-induced cytotoxic effect, indicating the cytoprotective role of autophagy in rhArg-induced cell death. In addition, N-acetyl-l-cysteine (NAC), a common antioxidant, blocked autophagy induced by rhArg, suggesting that reactive oxygen species (ROS) had an essential role in the cytotoxicity of rhArg. This study provides new insights into the molecular mechanism of autophagy involved in rhArg-induced cytotoxicity in TNBC cells. Meanwhile, our results revealed that rhArg, either alone or in combination with autophagic inhibitors, might be a potential novel therapy for the treatment of TNBC.
A loss of FUS/TLS function leads to impaired cellular proliferation
Authors: Ward C L , Boggio K J , Johnson B N , Boyd J B , Douthwright S , Shaffer S A , Landers J E , Glicksman M A , Bosco D A 
Published: December 2014

AbstractFused in sarcoma/translocated in liposarcoma (FUS/TLS or FUS) is a multifunctional RNA/DNA-binding protein that is pathologically associated with cancer and neurodegeneration. To gain insight into the vital functions of FUS and how a loss of FUS function impacts cellular homeostasis, FUS expression was reduced in different cellular models through RNA interference. Our results show that a loss of FUS expression severely impairs cellular proliferation and leads to an increase in phosphorylated histone H3, a marker of mitotic arrest. A quantitative proteomics analysis performed on cells undergoing various degrees of FUS knockdown revealed protein expression changes for known RNA targets of FUS, consistent with a loss of FUS function with respect to RNA processing. Proteins that changed in expression as a function of FUS knockdown were associated with multiple processes, some of which influence cell proliferation including cell cycle regulation, cytoskeletal organization, oxidative stress and energy homeostasis. FUS knockdown also correlated with increased expression of the closely related protein EWS (Ewing’s sarcoma). We demonstrate that the maladaptive phenotype resulting from FUS knockdown is reversible and can be rescued by re-expression of FUS or partially rescued by the small-molecule rolipram. These results provide insight into the pathways and processes that are regulated by FUS, as well as the cellular consequences for a loss of FUS function.