Miracle-dz/UniFAR-FTUs huggingface dataset:
BRAF Inhibitor Treatment BRAF-Mutant Melanoma Patients during Growth Factor Serum Levels in Dynamics of Chemokine , Cytokine , and

The purpose of this study is to proﬁle the changes in the serum levels of a range of chemokines, cytokines, and growth and angiogenic factors in MAPK inhibitor–treated metastatic melanoma patients and to correlate these changes with clinical outcome and changes in melanoma tissue biopsies taken from the same patients. Forty-two chemokine, cytokine, angiogenic, and growth factors were measured in the sera of 20 BRAF inhibitor–treated and four combination BRAF and MEK inhibitor–treated metastatic melanoma patients using a multiplex chemokine assay. The changes were correlated with Ki-67 and CD8 + tumor-inﬁltrating lymphocytes in the tumor biopsies taken at the same time points, as well as clinical outcome, including response rate, progression-free survival, and overall survival. Serum levels of IFN- g , CCL4, and TNF- a were signiﬁcantly increased, whereas CXCL8 signiﬁcantly decreased from pretreatment (PRE) to early during treatment (EDT) serum samples. The decrease in serum CXCL8 levels from PRE to EDT signiﬁcantly correlated with decreases in markers of melanoma proliferation (Ki-67) and increases in cytotoxic tumor-inﬁltrating T cells in corresponding tumor biopsies. In addition, a greater fold reduction in CXCL8 serum levels from PRE to EDT serum samples was associated with decreased overall survival. These results suggest that BRAF inhibition causes decreased CXCL8 secretion from melanoma cells and induce an immune response against the tumor associated with increased IFN- g , CCL4, and TNF- a . Further studies are needed to determine if CXCL8 is predictive of response and to conﬁrm the functions of these chemokine and cytokine in BRAF -mutant melanoma under BRAF inhibition. (PRE value 2 EDT value). Fold-change of immunohistochemical (IHC) measurements from PRE to EDT were calculated as: (EDT value/PRE value). Wilcoxon signed-rank test was used to test for signiﬁcant changes in serum levels of chemokine and cytokine between treatment stages. Correlation analysis was performed using a Spearman rho test, and the Mann–Whitney U test was used to test for associations of scalar and categorical variables. Multivariate time to event analysis was conducted for continuous absolute PRE, EDT, raw change PRE–EDT change, and PRE–EDT fold change in serum levels of all chemokine and cytokine covariates while adjusting for serum 2 80˚C storage time using the Cox proportional hazards method. The following outcomes were investigated: PFS (deﬁned as the interval between commencement of the MAPKi and disease progression) and OS (deﬁned as the interval between commencement of the MAPKi and death). All patient deaths in this cohort were caused by melanoma. The storage duration for the serum was recorded and entered into any survival analyzes to adjust for degradation of analytes over time (34).
Hydrostatic pressures developed by osmotically swelling vesicles bound to planar membranes

When phospholipid vesicles bound to a planar membrane are osmotically swollen, they develop a hydrostatic pressure (delta P) and fuse with the membrane. We have calculated the steady-state delta P, from the equations of irreversible thermodynamics governing water and solute flows, for two general methods of osmotic swelling. In the first method, vesicles are swollen by adding a solute to the vesicle- containing compartment to make it hyperosmotic. delta P is determined by the vesicle membrane's permeabilities to solute and water. If the vesicle membrane is devoid of open channels, then delta P is zero. When the vesicle membrane contains open channels, then delta P peaks at a channel density unique to the solute permeability properties of both the channel and the membrane. The solute enters the vesicle through the channels but leaks out through the region of vesicle-planar membrane contact. delta P is largest for channels having high permeabilities to the solute and for solutes with low membrane permeabilities in the contact region. The model predicts the following order of solutes producing pressures of decreasing magnitude: KCl greater than urea greater than formamide greater than or equal to ethylene glycol. Differences between osmoticants quantitatively depend on the solute permeability of the channel and the density of channels in the vesicle membrane. The order of effectiveness is the same as that experimentally observed for solutes promoting fusion. Therefore, delta P drives fusion. When channels with small permeabilities are used, coupling between solute and water flows within the channel has a significant effect on delta P. In the second method, an impermeant solute bathing the vesicles is isosmotically replaced by a solute which permeates the channels in the vesicle membrane. delta P resulting from this method is much less sensitive to the permeabilities of the channel and membrane to the solute. delta P approaches the theoretical limit set by the concentration of the impermeant solute.
Applications of the MERIS algal pigment products in Belgian waters

Following validation activities and corresponding improvements in processing algorithms over the first few years of the MERIS mission, the algal1 and algal2 products are now considered as sufficiently mature for use in applications in Belgian waters. The utility of this product has been enhanced by the development of a number of multitemporal products including single point time series, multitemporal composites (monthly/3monthly means) and annual products such as the mean and 90 percentile concentrations and the timing of the spring bloom. Marine management applications include: support for the assessment of eutrophication status in the context of the Oslo and Paris Convention for the Prevention of Marine Pollution (OSPAR), optimisation of seaborne monitoring, detection of harmful algal blooms and support for aquaculture. More generally, the MERIS data is used in support of marine science including the validation of ecosystem models and may be used in the future for the estimation of air-sea carbon fluxes. The current status of these applications is described together with an assessment of the remaining scientific challenges as well as the future possibilities.
A brick wall, a locked door, and a bandit: a physical security metaphor for firewall warnings

We used an iterative process to design firewall warnings in which the functionality of a personal firewall is visualized based on a physical security metaphor. We performed a study to determine the degree to which our proposed warnings are understandable for users, and the degree to which they convey the risks and encourage safe behavior as compared to text warnings based on those from a popular personal firewall. The evaluation results show that our warnings facilitate the comprehension of warning information, better communicate the risk, and increase the likelihood of safe behavior. Moreover, they provide participants with a better understanding of both the functionality of a personal firewall and the consequences of their actions.
Exchangeable random variables

If Equation (1) be satisfied, then all sets S are equally likely under the null hypothesis. To obtain a permutation test that is both unbiased and most powerful, one need only select the set S so that its probability under the alternative >0 is a maximum. This is accomplished in most cases by rejecting the hypothesis for all values of the test statistic that lie in the upper tail of the permutation distribution. As research during the intervening half century has amply demonstrated, permutation tests should be used to do all of the following:
Using OODB Modeling to Partition a Vocabulary in Structurally and Semantically Uniform Concept Groups

Controlled vocabularies (CVs) are networks of concepts that unify disparate terminologies and facilitate the process of information sharing within an application domain. We describe a general methodology for representing an existing CV as an object-oriented database (OODB), called an object-oriented vocabulary repository (OOVR). A formal description of the OOVR methodology, which is based on a structural abstraction technique, is given, along with an algorithmic description and a number of theorems pertaining to some of the methodology's formal characteristics. An OOVR offers a two-level (concept level and schema level) view of a CV, with the schema-level view serving as an important abstraction that can aid in orientation to the CV's contents. While an OOVR can also assist in traversals of the CV, we have identified certain special CV configurations where such traversals can be problematic. To address this, we introduce - based on the original methodology - an enhanced OOVR methodology that utilizes both structural and semantic features to partition and model a CV's constituent concepts. With its basis in the notions of area and the recursively defined articulation concept, an enhanced OOVR representation provides users with an improved CV view comprising groups of concepts that are uniform both in their structure and semantics. An algorithmic description of the singly-rooted OOVR methodology and theorems describing some of its formal properties are given. The results of applying it to a large existing CV are discussed.
Airline Crew Recovery

An airline schedule rarely operates as planned. It is often disrupted by maintenance problems or severe weather conditions. In a typical day, several flights may be delayed or canceled, and aircraft and crews may miss the rest of their assigned flights. Airline coordinators have to find a minimal cost reassignment of aircraft and crews that satisfies all required safety rules, has little impact on passengers, and minimizes operational difficulties for the airline. The size of the entire schedule and the real-time nature of the problem rule out a full-scale optimization. It is necessary to reduce the complexity and the size of the problem before an optimization approach can be applied. In this paper, we focus on the problem of airline crew recovery. A new solution framework is developed, implemented, and tested. It provides, in almost real time, a recovery plan for reassigning crews to restore a disrupted crew schedule. Preprocessing techniques are applied to extract a subset of the schedule for rescheduling. A fast crew-pairing generator is built that enumerates feasible continuations of partially flown crew trips. Several branching strategies are presented that allow fast generation of integer solutions. We disturb the current schedule as little as possible, exploiting the fact that the planned schedule is optimal. The proposed framework has been implemented using tree-based data structures for efficient storage and data access. Computational results using a schedule from a major air carrier are presented.
Calcium consumption for osteoporosis prevention: knowledge, attitudes and behavior in the northeastern region, Thailand.

OBJECTIVE Identified Thai adults' knowledge and attitudes towards calcium and determined factors predicting calcium consumption. MATERIAL AND METHOD One thousand four hundred seventy five Thai adults, aged > or = 20 years old were interviewed, using a semi-structured questionnaire. Knowledge about role of calcium and good sources of calcium was measured using 17 questions. Attitudes towards calcium were measured with 10 opinion statements, using 7-point Likert scale (1 = strongly disagree to 7 = strongly agree). Calcium consumption, based on a 24-hour recall, was assessed using food frequency checklists and open-ended questions. RESULTS The median score for knowledge was 15 (IQR: 12, 16; total possible score: 17). The overall median of attitudinal score was 5.6 (IQR: 4.9, 6.1; cronbach's alpha = 0.80). Approximately 10.9% consumed adequate amounts of calcium (800 mg/day). CONCLUSION Factors significantly determining the likelihood an adequate intake of calcium were age < 35 years, support from peers and taking calcium-supplements.
The Cross-Category Effect

Although the cross-race effect (CRE) is a well-established phenomenon, both perceptual-expertise and social-categorization models have been proposed to explain the effect. The two studies reported here investigated the extent to which categorizing other people as in-group versus out-group members is sufficient to elicit a pattern of face recognition analogous to that of the CRE, even when perceptual expertise with the stimuli is held constant. In Study 1, targets were categorized as members of real-life in-groups and out-groups (based on university affiliation), whereas in Study 2, targets were categorized into experimentally created minimal groups. In both studies, recognition performance was better for targets categorized as in-group members, despite the fact that perceptual expertise was equivalent for in-group and out-group faces. These results suggest that social-cognitive mechanisms of in-group and out-group categorization are sufficient to elicit performance differences for in-group and out-group face recognition.
Game Theoretic Stochastic Routing for Fault Tolerance and Security in Computer Networks

We introduce the game-theoretic stochastic routing (GTSR) framework, a proactive alternative to today's reactive approaches to route repair. GTSR minimizes the impact of link and router failure by 1) computing multiple paths between source and destination and 2) selecting among these paths randomly to forward packets. Besides improving fault tolerance, the fact that GTSR makes packets take random paths from source to destination also improves security. In particular, it makes connection eavesdropping attacks maximally difficult as the attacker would have to listen on all possible routes. The approaches developed are suitable for network layer routing, as well as for application layer overlay routing and multipath transport protocols such as the stream control transmission protocol (SCTP). Through simulations, we validate our theoretical results and show how the resulting routing algorithms perform in terms of the security/fault-tolerant/delay/throughput trade-off. We also show that a beneficial side effect of these algorithms is an increase in throughput, as they make use of multiple paths.
NEUTROPHIL NAD(P)H OXIDASE IS REQUIRED FOR HEMORRHAGIC SHOCK-ENHANCED TLR2 UP-REGULATION IN ALVEOLAR MACROPHAGES IN RESPONSE TO LPS

Alveolar macrophages (AMs) play an important role in the development of posttrauma lung inflammation through initiating polymorphonuclear neutrophil (PMN) migration by direct interactions with PMN, which is in turn mediated by the expression of chemokines and cytokines. We have recently reported that hemorrhagic shock-activated PMN sensitize AM to bacteria LPS for the up-regulation of Toll-like receptor (TLR)2; in turn, this TLR2 up-regulation results in the amplification of expression of cytokines and chemokines in the AM in response to the bacterial products LPS and peptidoglycan, associated with enhanced PMN sequestration in the lung. We sought to address the mechanism underlying the augmentation of TLR2 in AM by shock-activated PMN. We found that hemorrhagic shock/resuscitation (shock) followed by a low dose of i.t. LPS markedly increased TLR2 mRNA expression in AM in wild-type (WT) mice. In contrast, in mice lacking the gp91phox subunit of nicotinamide adenine dinucleotide phosphate (reduced form) oxidase (gp91phox−/−) or in neutropenic WT mice, the increase in TLR2 mRNA was attenuated. Coculture of AM with PMN derived from WT-shocked mice caused a significantly higher level of TLR2 expression in the AM in response to LPS. However, this increase in TLR2 expression was less evident when the AMs were cocultured with PMN derived from gp91phox−/− mice subjected to shock. The antioxidant polyethylene glycol catalase markedly decreased MyD88-dependent activation of IL-1 receptor associated kinase 4 and TLR2 expression in the AM in response to LPS. Thus, PMN nicotinamide adenine dinucleotide phosphate (reduced form) oxidase sensitizes hemorrhagic shock-primed AM to LPS, at least in part via enhancing IL-1 receptor associated kinase 4 activity.
A novel class-dependent back-off scheme for Machine Type Communication in LTE systems

Machine Type Communication (MTC), which is also called as machine to machine communication over cellular mobile networks, has broad application prospects and market potential. However, due to massive concurrent data and control signaling transmitted by a lot of MTC user equipments (UEs), radio access network (RAN) congestion becomes an important issue. In this paper, we propose a novel class-dependent back-off scheme for LTE system to protect RAN from random access channel (RACH) overload. Numerical results show that the proposed scheme can effectively reduce the collision probability of random access and improve the throughput by 2%-5% with additional 100-200 packets access delay which is tolerable for most of the MTC applications.
Cost-Reliability Tradeoff in Licensed and Unlicensed Spectra Interoperable Networks With Guaranteed User Data Rate Requirements

Unlicensed spectra access holds the promise of alleviating licensed spectra scarcity and providing super high-rate mobile data services, which has been viewed as one of the key technologies of fifth generation (5G) cellular networks. In this paper, we first design a framework for 5G licensed and unlicensed spectra interoperable networks based on the cloud radio access network technology and the control/data decoupled architecture. Then, we investigate network-level cost-reliability tradeoff from two aspects. First, we study a fundamental tradeoff between the cost and the reliability by minimizing cost for a given reliability level. Second, we define a quality of experience efficiency utility as the complementary measure to characterize the cost and the reliability, offering an inherent tradeoff between them. Moreover, an interference power estimation method is proposed to more accurately estimate channel states to guarantee resource allocation effectiveness. Finally, we conduct extensive simulation study and demonstrate the effectiveness of the interference power estimation method.
Cooking Up Referring Expressions

This paper describes the referring expression generation mechanisms used in EPICURE, a computer program which produces natural language descriptions of cookery recipes. Major features of the system include: an underlying ontology which permits the representation of non-singular entities; a notion of discriminatory power, to determine what properties should be used in a description; and a PATR-like unification grammar to produce surface linguistic strings.
Microbial Genomics—Challenges and Opportunities: The 9th International Conference on Microbial Genomes

Genomic sequencing and analysis are in a period of “exponential growth. ” More than 60 eukaryotic and prokaryotic genomes have been completely sequenced, with analysis of more than 200 genome sequences currently under way ([www.jgi. doe.gov][1] ; [www.wit. integratedgenomics.com/GOLD/][2] ; [www.
Computer-Aided Approaches for Targeting HIVgp41

Virus-cell fusion is the primary means by which the human immunodeficiency virus-1 (HIV) delivers its genetic material into the human T-cell host. Fusion is mediated in large part by the viral glycoprotein 41 (gp41) which advances through four distinct conformational states: (i) native, (ii) pre-hairpin intermediate, (iii) fusion active (fusogenic), and (iv) post-fusion. The pre-hairpin intermediate is a particularly attractive step for therapeutic intervention given that gp41 N-terminal heptad repeat (NHR) and C‑terminal heptad repeat (CHR) domains are transiently exposed prior to the formation of a six-helix bundle required for fusion. Most peptide-based inhibitors, including the FDA‑approved drug T20, target the intermediate and there are significant efforts to develop small molecule alternatives. Here, we review current approaches to studying interactions of inhibitors with gp41 with an emphasis on atomic-level computer modeling methods including molecular dynamics, free energy analysis, and docking. Atomistic modeling yields a unique level of structural and energetic detail, complementary to experimental approaches, which will be important for the design of improved next generation anti-HIV drugs.
Load balancing and unbalancing for power and performance in cluster-based systems

In this paper we address power conservation for clusters of workstations or PCs. Our approach is to develop systems that dynamically turn cluster nodes on – to be able to handle the load imposed on the system efficiently – and off – to save power under lighter load. The key component of our systems is an algorithm that makes load balancing and unbalancing decisions by considering both the total load imposed on the cluster and the power and performance implications of turning nodes off. The algorithm is implemented in two different ways: (1) at the application level for a cluster-based, localityconscious network server; and (2) at the operating system level for an operating system for clustered cycle servers. Our experimental results are very favorable, showing that our systems conserve both power and energy in comparison to traditional systems.
AF relay-assisted MIMO/FSO/QAM systems in Gamma-Gamma fading channels

In this paper, the performance of amplify-and-forward (AF) relay-assisted multiple-input multiple-output free-space optical communication (MIMO/FSO) systems using sub-carrier intensity quadrature amplitude modulation (QAM) over Gamma-Gamma fading channels, which is represented for the case of strong atmospheric turbulence region, is studied. More specifically, an average symbol error rate (ASER) analytical expression for the AF relay-assisted MIMO/FSO/QAM systems is derived taking into account the strong atmospheric turbulence channel and the number of AF relaying stations with fixed gains. Numerical results qualitatively analyze the influence of the number of relaying stations, link distances, fixed gains and MIMO configurations on the performance of such systems.
RBF Volume Ray Casting on Multicore and Manycore CPUs

Modern supercomputers enable increasingly large N‐body simulations using unstructured point data. The structures implied by these points can be reconstructed implicitly. Direct volume rendering of radial basis function (RBF) kernels in domain‐space offers flexible classification and robust feature reconstruction, but achieving performant RBF volume rendering remains a challenge for existing methods on both CPUs and accelerators. In this paper, we present a fast CPU method for direct volume rendering of particle data with RBF kernels. We propose a novel two‐pass algorithm: first sampling the RBF field using coherent bounding hierarchy traversal, then subsequently integrating samples along ray segments. Our approach performs interactively for a range of data sets from molecular dynamics and astrophysics up to 82 million particles. It does not rely on level of detail or subsampling, and offers better reconstruction quality than structured volume rendering of the same data, exhibiting comparable performance and requiring no additional preprocessing or memory footprint other than the BVH. Lastly, our technique enables multi‐field, multi‐material classification of particle data, providing better insight and analysis.
Non-programmers identifying functionality in unfamiliar code: Strategies and barriers

Source code on the web is a widely available and potentially rich learning resource for non-programmers. However, unfamiliar code can be daunting to end-users without programming experience. This paper describes the results of an exploratory study in which we asked non-programmers to find and modify the code responsible for specific functionality within unfamiliar programs. We present two interacting models of how non-programmers approach this problem: the Task Process Model and the Landmark-Mapping model. Using these models, we describe code search strategies non-programmers employed and the difficulties they encountered. Finally, we propose guidelines for future programming environments that support non-programmers in finding functionality in unfamiliar programs.