bluuebunny/crossref_metadata_2025_split huggingface dataset:
Imperative self-adjusting computation
Authors: Acar Umut A. , Ahmed Amal , Blume Matthias 
Published: August 2010

Self-adjusting computation enables writing programs that can automatically and efficiently respond to changes to their data (e.g., inputs). The idea behind the approach is to store all data that can change over time in modifiable references and to let computations construct traces that can drive change propagation. After changes have occurred, change propagation updates the result of the computation by re-evaluating only those expressions that depend on the changed data. Previous approaches to self-adjusting computation require that modifiable references be written at most once during execution---this makes the model applicable only in a purely functional setting.
In this paper, we present techniques for imperative self-adjusting computation where modifiable references can be written multiple times. We define a language SAIL (Self-Adjusting Imperative Language) and prove consistency, i.e., that change propagation and from-scratch execution are observationally equivalent. Since SAIL programs are imperative, they can create cyclic data structures. To prove equivalence in the presence of cycles in the store, we formulate and use an untyped, step-indexed logical relation, where step indices are used to ensure well-foundedness. We show that SAIL accepts an asymptotically efficient implementation by presenting algorithms and data structures for its implementation. When the number of operations (reads and writes) per modifiable is bounded by a constant, we show that change propagation becomes as efficient as in the non-imperative case. The general case incurs a slowdown that is logarithmic in the maximum number of such operations. We describe a prototype implementation of SAIL as a Standard ML library.
On the computational soundness of cryptographically masked flows
Authors: Laud Peeter 
Published: August 2010

To speak about the security of information flow in programs employing cryptographic operations, definitions based on computational indistinguish ability of distributions over program states have to be used. These definitions, as well as the accompanying analysis tools, are complex and error-prone to argue about. Cryptographically masked flows, proposed by Askarov, Hedin and Sabelfeld, are an abstract execution model and security definition that attempt to abstract away the details of computational security. This abstract model is useful because analysis of programs can be conducted using the usual techniques for enforcing non-interference.
In this paper we investigate under which conditions this abstract model is computationally sound, i.e. when does the security of a program in their model imply the computational security of this program. This paper spells out a reasonable set of conditions and then proposes a simpler abstract model that is nevertheless no more restrictive than the cryptographically masked flows together with these conditions for soundness.
A market-based bandwidth charging framework
Authors: Turner David Michael , Prevelakis Vassilis , Keromytis Angelos D. 
Published: August 2010

The increasing demand for high-bandwidth applications such as video-on-demand and grid computing is reviving interest in bandwidth reservation schemes. Earlier attempts did not catch on for a number of reasons, notably lack of interest on the part of the bandwidth providers. This, in turn, was partially caused by the lack of an efficient way of charging for bandwidth. Thus, the viability of bandwidth reservation depends on the existence of an efficient market where bandwidth-related transactions can take place. For this market to be effective, it must be efficient for both the provider (seller) and the user (buyer) of the bandwidth. This implies that: (a) the buyer must have a wide choice of providers that operate in a competitive environment, (b) the seller must be assured that a QoS transaction will be paid by the customer, and (c) the QoS transaction establishment must have low overheads so that it may be used by individual customers without a significant burden to the provider.
In order to satisfy these requirements, we propose a framework that allows customers to purchase bandwidth using an open market where providers advertise links and capacities and customers bid for these services. The model is close to that of a commodities market that offers both advance bookings (futures) and a spot market. We explore the mechanisms that can support such a model.
Stable Iteration Procedures in Metric Spaces which Generalize a Picard-Type Iteration
Authors: De la Sen M 
Published: August 2010

AbstractThis paper investigates the stability of iteration procedures defined by continuous functions acting on self-maps in continuous metric spaces. Some of the obtained results extend the contraction principle to the use of altering-distance functions and extended altering-distance functions, the last ones being piecewise continuous. The conditions for the maps to be contractive for the achievement of stability of the iteration process can be relaxed to the fulfilment of being large contractions or to be subject to altering-distance functions or extended altering functions.
Histopathologic and Immunohistochemical Characterization of Rash to Human Epidermal Growth Factor Receptor 1 (HER1) and HER1/2 Inhibitors in Cancer Patients
Authors: Nardone Beatrice , Nicholson Kimberly , Newman Marissa , Guitart Joan , Gerami Pedram , Talarico Nicholas , Yang Ximing J. , Rademaker Alfred , West Dennis P. , Lacouture Mario E. 
Published: August 2010

Abstract
Purpose: Human epidermal growth factor receptor (HER) 1 and HER 1/2 inhibitors have shown benefit against a wide range of solid tumors. However, their use is associated with rash in 40% to 90% of patients, which impacts quality of life and interrupts antineoplastic therapy. The pathologic characteristics of affected skin remain unclear, precluding development of rational therapies. The aim of this study was to evaluate differences in histologic and immunohistochemical alterations in rash caused by lapatinib, a dual HER1/2 inhibitor (HER1/2i), and the single HER1 inhibitors (HER1i) cetuximab, erlotinib, and panitumumab.
Experimental Design: For each of the four drugs, skin biopsies were collected and analyzed from 8 patients with rash (n = 32). Blinded independent histologic analysis and automated measurement of 17 skin biomarkers involved in proliferation, differentiation, and inflammation were conducted.
Results: Increased expression of pAKT and decreased dermal K16 and p27 for HER1/2i when compared with each of the HER1i were observed. In addition, decreased epidermal atrophy and follicular neutrophilic infiltrate were evidenced in the skin of patients on HER1/2i when compared with HER1i.
Conclusions: We found a lower inhibition of epidermal kinetics and decreased inflammation in HER1/2i-induced rash. These findings underscore differences in skin toxicity as related to specificity of HER blockade, concordant with clinical tolerability and decreased severity of skin toxicity seen with the HER1/2i lapatinib compared with the HER1 inhibitors cetuximab, erlotinib, and panitumumab. Clin Cancer Res; 16(17); 4452–60. ©2010 AACR.
Comparing Survival Curves Using an Easy to Interpret Statistic
Authors: Hess Kenneth R. 
Published: August 2010

Abstract
Here, I describe a statistic for comparing two survival curves that has a clear and obvious meaning and has a long history in biostatistics. Suppose we are comparing survival times associated with two treatments A and B. The statistic operates in such a way that if it takes on the value 0.95, then the interpretation is that a randomly chosen patient treated with A has a 95% chance of surviving longer than a randomly chosen patient treated with B. This statistic was first described in the 1950s, and was generalized in the 1960s to work with right-censored survival times. It is a useful and convenient measure for assessing differences between survival curves. Software for computing the statistic is readily available on the Internet. Clin Cancer Res; 16(20); 4912–3. ©2010 AACR.
Kryolab
Authors: Dumitriu Anna , Tenetz Antti , Lawrence Dave 
Published: August 2010

KryoLab is an installation and performance that brings together bioart, ice sculpture and sound, in an investigation of delicate relationships in the Arctic ecosystem. It traces our individual and collective journeys, in terms of investigative art/science research as well as in terms of being part of the experimental European/worldwide collaborative e-MobiLArt project—designed to encourage collaboration with scientists and with artists from other cultural backgrounds and geographic locations. This article briefly describes the KryoLab installation concept itself, and the collaboration process.
Multiscale Interactions in the Life Cycle of a Tropical Cyclone Simulated in a Global Cloud-System-Resolving Model. Part II: System-Scale and Mesoscale Processes*
Authors: Fudeyasu Hironori , Wang Yuqing , Satoh Masaki , Nasuno Tomoe , Miura Hiroaki , Yanase Wataru 
Published: August 2010

Abstract
The life cycle of Tropical Storm Isobel was simulated reasonably well in the Nonhydrostatic Icosahedral Atmospheric Model (NICAM), a global cloud-system-resolving model. The evolution of the large-scale circulation and the storm-scale structure change was discussed in Part I. Both the mesoscale and system-scale processes in the life cycle of the simulated Isobel are documented in this paper. In the preconditioned favorable environment over the Java Sea, mesoscale convective vortices (model MCVs) developed in the mesoscale convective systems (MCSs) and convective towers with cyclonic potential vorticity (PV) anomalies throughout the troposphere [model vortical hot towers (VHTs)] appeared in the model MCVs. Multiple model VHTs strengthened cyclonic PV in the interior of the model MCV and led to the formation of an upright monolithic PV core at the center of the concentric MCV (primary vortex enhancement). As the monolithic PV core with a warm core developed near the circulation center, the intensification and the increase in horizontal size of the cyclonic PV were enhanced through the system-scale intensification (SSI) process (the secondary vortex enhancement), leading to the genesis of Isobel over the Timor Sea. The SSI process can be well explained by the balanced dynamics.
After its genesis, the subsequent evolution of the simulated Isobel was controlled by both the external influence and the internal dynamics. Under the unfavorable environmental conditions, the development of asymmetric structure reduced the axisymmetric diabatic heating in the inner core and the SSI process became ineffective and the storm weakened. Later on, as the eyewall reformed as a result of the axisymmetrization of an inward-propagating outer spiral rainband, the SSI process became effective again, leading to the reintensification of Isobel. Therefore, the large-scale environmental flow provided the precondition for the genesis of Isobel and the triggering mechanism for subsequent storm-scale structure change as discussed in Part I. The system-scale and mesoscale processes, such as the evolution of MCVs and merging VHTs, were responsible for the genesis, while the eyewall processes were critical to the storm intensity change through the SSI process.
Deterioration of traditional dietary custom increases the risk of lifestyle-related diseases in young male Africans
Authors: Hamada Atsumi , Mori Mari , Mori Hideki , Muhihi Alfa , Njelekela Marina , Masesa Zablon , Mtabaji Jacob , Yamori Yukio 
Published: August 2010

Abstract

Background
Prevalence of metabolic syndrome (MS) is rapidly increasing worldwide. To investigate the spread of MS risks and its relationship with eating habits including fish intake, we carried out a health examination for young and middle-aged men.

Methods
The subjects were 97 healthy men (20 to 50 years) living in Mwanza, located on the shore of Lake Victoria in Tanzania. The health examination was conducted according to the basic protocol of WHO-CARDIAC (Car diovascular Di seases and A limentary C omparison) Study. This survey included anthropometric measurements, a dietary questionnaire, blood pressure measurement, and blood and 24-hour urine (24U) collection. Excretions of sodium, potassium and taurine (Tau) in 24U were estimated as the biomarkers of salt, vegetable and fish product intakes respectively.

Results
In this survey, 62.5 % of the young and 63.3% of the middle-aged adults had MS risks. The most prevalent MS risk factor was increased blood pressure (50.0% of young adults and 53.1% of the middle-aged). Tau excretions in 24U and n-3 fatty acid levels in plasma were significantly lower in young adults than those in the middle-aged (both P < 0.05). The eating frequencies of non-traditional foods such as donuts and ice cream showed negative correlations with age (r = -0.282, P < 0.01 and r = -0.246, P < 0.05), while salt intake positively correlated with age (r = 0.236, P < 0.05). Tau excretion in 24U was inversely correlated with atherosclerosis index (r = -0.306, P < 0.01) and fasting blood glucose (r = -0.284, P < 0.05).

Conclusions
Young adults in Mwanza had a decreased frequency of eating habit of fish products compared with the middle-aged as indicated by Tau excretion in 24U and n-3 fatty acid level in the plasma, and over half of young adults had one or more MS risks just as the middle-aged. The change in food habit of lowered fish intake and raised exotic food intake might be concluded to increase MS risks in young men.
Transcriptome responses to aluminum stress in roots of aspen (Populus tremula)
Authors: Grisel Nadine , Zoller Stefan , Künzli-Gontarczyk Marzanna , Lampart Thomas , Münsterkötter Martin , Brunner Ivano , Bovet Lucien , Métraux Jean-Pierre , Sperisen Christoph 
Published: August 2010

Abstract

Background
Ionic aluminum (mainly Al3+) is rhizotoxic and can be present in acid soils at concentrations high enough to inhibit root growth. Many forest tree species grow naturally in acid soils and often tolerate high concentrations of Al. Previously, we have shown that aspen (Populus tremula) releases citrate and oxalate from roots in response to Al exposure. To obtain further insights into the root responses of aspen to Al, we investigated root gene expression at Al conditions that inhibit root growth.

Results
Treatment of the aspen roots with 500 μM Al induced a strong inhibition of root growth within 6 h of exposure time. The root growth subsequently recovered, reaching growth rates comparable to that of control plants. Changes in gene expression were determined after 6 h, 2 d, and 10 d of Al exposure. Replicated transcriptome analyses using the Affymetrix poplar genome array revealed a total of 175 significantly up-regulated and 69 down-regulated genes, of which 70% could be annotated based on Arabidopsis genome resources. Between 6 h and 2 d, the number of responsive genes strongly decreased from 202 to 26, and then the number of changes remained low. The responses after 6 h were characterized by genes involved in cell wall modification, ion transport, and oxidative stress. Two genes with prolonged induction were closely related to the Arabidopsis Al tolerance genes ALS3 (for Al sensitive 3) and MATE (for multidrug and toxin efflux protein, mediating citrate efflux). Patterns of expression in different plant organs and in response to Al indicated that the two aspen genes are homologs of the Arabidopsis ALS3 and MATE.

Conclusion
Exposure of aspen roots to Al results in a rapid inhibition of root growth and a large change in root gene expression. The subsequent root growth recovery and the concomitant reduction in the number of responsive genes presumably reflect the success of the roots in activating Al tolerance mechanisms. The aspen genes ALS3 and MATE may be important components of these mechanisms.
Fucoidan present in brown algae induces apoptosis of human colon cancer cells
Authors: Kim Eun Ji , Park So Young , Lee Jae-Yong , Park Jung Han Yoon 
Published: August 2010

Abstract

Background
Fucoidan is a sulfated polysaccharide found in brown algae; it has been shown to exhibit a number of biological effects, including anti-tumor effects. In this study, we evaluated the effects of fucoidan on apoptosis in HT-29 and HCT116 human colon cancer cells.

Methods
HT-29 and HCT116 cells were cultured with various concentrations of fucoidan (0 - 20 μg/mL). Apoptosis was assayed via Hoechst staining and Annexin V staining followed by flow cytometric analysis. Western blot analyses and JC-1 staining were conducted to determine the levels of apoptosis-regulating proteins and mitochondrial membrane permeability, respectively.

Results
Fucoidan induced substantial reductions in viable cell numbers and apoptosis of HT-29 and HCT116 cells in a dose-dependent manner. In HT-29 cells, fucoidan also increased the levels of cleaved caspases-8, -9, -7, and -3, and cleaved poly (ADP-ribose) polymerase (PARP) levels. The levels of the X-linked inhibitor of apoptosis protein and survivin were attenuated in the fucoidan-treated cells. Fucoidan was also shown to enhance mitochondrial membrane permeability, as well as the cytochrome c and Smac/Diablo release from the mitochondria. Fucoidan increased the levels of the Bak and truncated Bid proteins, but reduced the levels of Mcl-1. Additionally, fucoidan increased the levels of the tumor necrosis factor-related apoptosis-inducing ligand, Fas and death receptor 5 proteins. The caspase-8 and -9 inhibitors Z-IETD-FMK and Z-LEHD-FMK induced a reduction in fucoidan-mediated apoptosis. Caspase-8 inhibitor inhibited the fucoidan-induced cleavage of Bid, caspases-9 and -3, and PARP.

Conclusion
The findings of this study indicate that fucoidan induces apoptosis in HT-29 and HCT116 human colon cancer cells, and that this phenomenon is mediated via both the death receptor-mediated and mitochondria-mediated apoptotic pathways. These results suggest that fucoidan may prove useful in the development of a colon cancer-preventive protocol.
The increase of alpha-melanocyte-stimulating hormone in the plasma of chronic fatigue syndrome patients
Authors: Shishioh-Ikejima Nobue , Ogawa Tokiko , Yamaguti Kouzi , Watanabe Yasuyoshi , Kuratsune Hirohiko , Kiyama Hiroshi 
Published: August 2010

AbstractBackgroundDespite extensive research, no reliable biological marker for chronic fatigue syndrome (CFS) has yet been identified. However, hyperactivation of melanotrophs in the pituitary gland and increased levels of plasma alpha-melanocyte-stimulating hormone (α-MSH) have recently been detected in an animal model of chronic stress. Because CFS is considered to be caused partly by chronic stress events, increased α-MSH plasma levels may also occur in CFS patients. We therefore examined α-MSH levels in CFS patients.MethodsFifty-five CFS patients, who were previously diagnosed within 10 years of with the disease, were enrolled in this study. Thirty healthy volunteers were studied as controls. Fasting bloods samples were collected in the morning and evaluated for their plasma levels of α-MSH, adrenocorticotropic hormone (ACTH), serum cortisol and dehydroepiandrosterone sulfate (DHEA-S). Mean levels of α-MSH were compared between the CFS and control groups using Welch'sttest.ResultsThe mean plasma α-MSH concentration in the CFS group (17.9 ± 1.0 pg/mL) was significantly higher than that in healthy controls (14.5 ± 1.0 pg/mL, p = 0.02). However, there was a wide range of values in the CFS group. The factors correlated with the plasma α-MSH values were analyzed using Spearman's rank correlation. A negative correlation was found between the duration of the CFS and the plasma α-MSH values (p = 0.04, rs= -0.28), but no correlations with ACTH, cortisol or DHEA-S levels were identified (p = 0.55, 0.26, 0.33, respectively). The CFS patients were divided into two groups: patients diagnosed for ≤ 5 years' duration, and those diagnosed for 5-10 years' duration. They were compared with the healthy controls using one-way ANOVA and Tukey-Kramer multiple comparison tests. The mean α-MSH concentration in the ≤ 5 years group was 20.8 ± 1.2 pg/mL, which was significantly higher than that in the healthy controls (p < 0.01). There was no significant difference between the 5-10 year group (15.6 ± 1.4 pg/mL) and the healthy controls.ConclusionsCFS patients with a disease duration of ≤ 5 years had significantly higher levels of α-MSH in their peripheral blood. α-MSH could be a potent biological marker for the diagnosis of CFS, at least during the first 5 years after onset of the disease.
Characterization of single chain antibody targets through yeast two hybrid
Authors: Vielemeyer Ole , Nizak Clément , Jimenez Ana Joaquina , Echard Arnaud , Goud Bruno , Camonis Jacques , Rain Jean-Christophe , Perez Franck 
Published: August 2010

Abstract

Background
Due to their unique ability to bind their targets with high fidelity, antibodies are used widely not only in biomedical research, but also in many clinical applications. Recombinant antibodies, including single chain variable fragments (scFv), are gaining momentum because they allow powerful in vitro selection and manipulation without loss of function. Regardless of the ultimate application or type of antibody used, precise understanding of the interaction between the antibody's binding site and its specific target epitope(s) is of great importance. However, such data is frequently difficult to obtain.

Results
We describe an approach that allows detailed characterization of a given antibody's target(s) using the yeast two-hybrid system. Several recombinant scFv were used as bait and screened against highly complex cDNA libraries. Systematic sequencing of all retained clones and statistical analysis allowed efficient ranking of the prey fragments. Multiple alignment of the obtained cDNA fragments provided a selected interacting domain (SID), efficiently narrowing the epitope-containing region.
Interactions between antibodies and their respective targets were characterized for several scFv. For AA2 and ROF7, two conformation-specific sensors that exclusively bind the activated forms of the small GTPases Rab6 and Rab1 respectively, only fragments expressing the entire target protein's core region were retained. This strongly suggested interaction with a non-linear epitope. For two other scFv, TA10 and SF9, which recognize the large proteins giantin and non-muscle myosin IIA, respectively, precise antibody-binding regions within the target were defined. Finally, for some antibodies, secondary targets within and across species could be revealed.

Conclusions
Our method, utilizing the yeast two-hybrid technology and scFv as bait, is a simple yet powerful approach for the detailed characterization of antibody targets. It allows precise domain mapping for linear epitopes, confirmation of non-linear epitopes for conformational sensors, and detection of secondary binding partners. This approach may thus prove to be an elegant and rapid method for the target characterization of newly obtained scFv antibodies. It may be considered prior to any research application and particularly before any use of such recombinant antibodies in clinical medicine.