Miracle-dz/UniFAR-FTUs huggingface dataset:
Survival benefit of combined curative resection of the stomach (D2 resection) and liver in gastric cancer patients with liver metastases.

BACKGROUND The benefit of surgical resection of liver metastases from gastric cancer has not been well established. The aim of this study was to evaluate the rationale for hepatic resection in patients with hepatic metastases from gastric cancer. METHODS Among 10 259 patients diagnosed with gastric adenocarcinoma in the Yonsei University Health System from 1995 to 2005, we reviewed the records of 58 patients with liver-only metastases from gastric cancer who underwent gastric resection regardless of hepatic surgery. RESULTS The overall 1-year, 3-year, and 5-year survival rates of 41 patients who underwent hepatic resection with curative intent were 75.3%, 31.7%, and 20.8%, respectively, and three patients survived >7 years. Of the 41 patients, 22 had complete resection and 19 had palliative resection. Between the curative and palliative resections, survival rates after curative intent were not different. The number of liver metastasis (solitary or multiple) was a marginally significant prognostic factor for survival. CONCLUSIONS Surgery for liver metastases arising from gastric adenocarcinoma is reasonable if complete resection seems feasible after careful preoperative staging, even if complete resection is not actually achieved. Hepatic resection should be considered as an option for gastric cancer patients with hepatic metastases.
Development of an Innovative Extension Model for Small Landholders - an Experiential Learning Journey

The Western Australia Small Landholder Information Service (SLIS) is an extension program that has grown out of a series of spatially focussed extension projects that sought behaviour change in areas given over to small landholdings. These projects highlighted that small landholders represented specific risks to agriculture and the environment. The small landholder has specific extension and information needs that differ from the needs of 'traditional' farmer clients engaged by agricultural extension programs. The Department of Agriculture and Food Western Australia recognised that there was a need to respond to the unique risks represented by small landholders and established an extension program to reduce the potential of these risks. The assumptions that underpinned the program in the planning phases were later confirmed by social, landuse planning and environmental impact research in a range of different locations (interstate and local). The SLIS employed a number of strategies to confirm assumptions and test efficacy of the extension campaign. The approach to continuously improve the extension model has been largely iterative and current social research investigating small landholders has been utilised. By necessity, the extension model has been reliant on the development and modification of a suite of tools and strategies for small landholder engagement and these are now being shared with national partners. The development of innovative partnerships for delivery has been integral to the program's success. The program has engaged more than 5,000 participants, many of whom had not previously sought support from the Department of Agriculture and Food. Most past participants in the program report that they have changed land management behaviours and moved to recommended land management practices. This paper describes the development of an innovative model for small landholders and explores the implications of this work in future program delivery. Key learnings: 1. A willingness to truly understand the client - the small landholder is different from mainstream farmers; 2. Where necessary, adapt and tailor an extension model(s) to suit the specific client group; 3. Be open to explore opportunities to synergistically deliver the extension package; 4. Have the courage to openly evaluate and then respond to resultant signals - back your judgement.
3D planning and trajectory optimization for real-time generation of smooth MAV trajectories

Complex indoor and outdoor missions for autonomous micro aerial vehicles (MAV) constitute a demand for fast generation of collision-free paths in 3D space. Often not all obstacles in an environment are known prior to the mission execution. Consequently, the ability for replanning during a flight is key for success. Our approach utilizes coarse grid-based path planning with an approximate model of flight dynamics to determine collision-free trajectories. To account for the flight dynamics and to mitigate discretization effects, these trajectories are further optimized with a gradient-based motion optimization method. We evaluate our method on an outdoor map with buildings and report trajectory costs and runtime results.
Feasibility of Seismic Characterization of Multiple Fracture Sets

Estimation of parameters of multiple fracture sets is often required for successful exploration and development of naturally fractured reservoirs. The goal of this paper is to determine the maximum number of fracture sets of a certain rheological type which, in principle, can be resolved from seismic data. The main underlying assumption is that an estimate of the complete effective stiffness tensor has been obtained, for example, from multiazimuth, multicomponent surface seismic and vertical seismic profiling (VSP) data. Although typically only a subset of the stiffness elements (or some of their combinations) may be available, this study helps to establish the limits of seismic fracture-detection algorithms. The number of uniquely resolvable fracture systems depends on the anisotropy of the host rock and the rheology and orientation of the fractures. Somewhat surprisingly, it is possible to characterize fewer vertical fracture sets than dipping ones, even though in the latter case the fracture dip has to be found from the data. For the simplest, rotationally invariant fractures embedded in either isotropic or transversely isotropic with a vertical symmetry axis (VTI) host rock, the stiffness tensor can be inverted for up to two vertical or four dipping fracture sets. In contrast, only one fracture set of the most general (microcorrugated) type, regardless of its orientation, is constrained by the effective stiffnesses. These results can be used to guide the development of seismic fracture-characterization algorithms that should address important practical issues of data acquisition, processing, and inversion for particular fracture models.
Limit Theorems for a Storage Process with a Random Release Rule

We consider a discrete time Storage Process Xn with a simple random walk input Sn and a random release rule given by a family {Ux, x ≥ 0} of random variables whose probability laws {Ux, x ≥ 0} form a convolution semigroup of measures, that is, μx × μy = μx + y The process Xn obeys the equation: X0 = 0, U0 = 0, Xn = Sn － USn, n ≥ 1. Under mild assumptions, we prove that the processes and are simple random walks and derive a SLLN and a CLT for each of them.
A model for wetland surface water dynamics

A mathematical model for overland flow through vegetated areas has been developed. Input information includes site topography and porosities, power law parameters for the velocity correlation, and the driving forces: precipitation, evapotranspiration, stream flows, groundwater recharge or discharge, and pumped additions. Depths and flow rates are then calculated as functions of position and time. A one-dimensional algorithm has been developed to execute these calculations. Numerical solutions to the nonlinear partial differential equations are accomplished using special finite difference approximations. The method permits long simulation times (several years), without significant material balance errors. The model and simulator have been validated using data from the Porter Ranch peatland located near Houghton Lake, Michigan.
Security under Uncertainty: Adaptive Attackers Are More Challenging to Human Defenders than Random Attackers

Game Theory is a common approach used to understand attacker and defender motives, strategies, and allocation of limited security resources. For example, many defense algorithms are based on game-theoretic solutions that conclude that randomization of defense actions assures unpredictability, creating difficulties for a human attacker. However, many game-theoretic solutions often rely on idealized assumptions of decision making that underplay the role of human cognition and information uncertainty. The consequence is that we know little about how effective these algorithms are against human players. Using a simplified security game, we study the type of attack strategy and the uncertainty about an attacker's strategy in a laboratory experiment where participants play the role of defenders against a simulated attacker. Our goal is to compare a human defender's behavior in three levels of uncertainty (Information Level: Certain, Risky, Uncertain) and three types of attacker's strategy (Attacker's strategy: Minimax, Random, Adaptive) in a between-subjects experimental design. Best defense performance is achieved when defenders play against a minimax and a random attack strategy compared to an adaptive strategy. Furthermore, when payoffs are certain, defenders are as efficient against random attack strategy as they are against an adaptive strategy, but when payoffs are uncertain, defenders have most difficulties defending against an adaptive attacker compared to a random attacker. We conclude that given conditions of uncertainty in many security problems, defense algorithms would be more efficient if they are adaptive to the attacker actions, taking advantage of the attacker's human inefficiencies.
Innate and acquired immunity intersect in a global view of the acute-phase response

Recognition of stereotypic chemical patterns by sentinel cells of the innate immune system provokes a transient deviation from homeostasis, the acute-phase response (APR). Although APR effectors have been identified individually, the complexity of the response suggested that emergent properties would be uncovered by a more comprehensive examination. Our global assessment revealed that ≈7% of genes in the mouse are mobilized in the hepatic APR to endotoxin. Extensive metabolic adjustments include suppression of pathways for cholesterol, fatty acid, and phospholipid synthesis. Increased expression of genes for innate defense was accompanied by coordinate induction of the MHC class I antigen presentation machinery, illustrating an intersection between innate and adaptive immunity.
Vision-based bin-picking: recognition and localization of multiple complex objects using simple visual cues

Vision-based bin-picking is increasingly more difficult as the complexity of target objects increases. We propose an efficient solution where complex objects are sufficiently represented by simple features/cues; thus invariance to object complexity is established. The region extraction algorithm utilized in our approach is capable of providing the focus of attention to the simple cues as a trigger toward recognition and pose estimation. Successful bin-picking experiments of industrial objects using stereo vision tools are presented.
Role of Exogenous and Endogenous Hormones in Endometrial Cancer

Endometrial carcinoma is the most common cancer of the female reproductive organs in the United States. International comparisons reveal that the incidence of endometrial cancer vary widely between different countries with the highest rates observed in North America and Northern Europe, intermediate rates in Eastern Europe and Latin America, and lowest rates in Asia and Africa. International variation in endometrial cancer rates may represent differences in the distribution of known risk factors, which include obesity, postmenopausal estrogen replacement, ovarian dysfunction, diabetes mellitus, infertility, nulliparity, and tamoxifen use. Most of the risk factors for endometrial cancer can be explained within the framework of the unopposed estrogen hypothesis, which proposes that exposure to estrogens unopposed by progesterone or synthetic progestins leads to increased mitotic activity of endometrial cells, increased number of DNA replication errors, and somatic mutations resulting in malignant phenotype. Although the impact of exogenous hormone replacement was intensively studied during the last two decades, less is known about the effects of endogenous hormones in endometrial cancer. A review of available experimental, clinical, and epidemiologic data suggests that in addition to estrogens, other endogenous hormones, including progesterone, androgens, gonadotropins, prolactin, insulin, and insulin‐like growth factors, may play a role in the pathogenesis of different histopathologic types of endometrial cancer.
ENaC-mediated alveolar fluid clearance and lung fluid balance depend on the channel-activating protease 1

Sodium transport via epithelial sodium channels (ENaC) expressed in alveolar epithelial cells (AEC) provides the driving force for removal of fluid from the alveolar space. The membrane‐bound channel‐activating protease 1 (CAP1/Prss8) activates ENaC in vitro in various expression systems. To study the role of CAP1/Prss8 in alveolar sodium transport and lung fluid balance in vivo, we generated mice lacking CAP1/Prss8 in the alveolar epithelium using conditional Cre‐loxP‐mediated recombination. Deficiency of CAP1/Prss8 in AEC induced in vitro a 40% decrease in ENaC‐mediated sodium currents. Sodium‐driven alveolar fluid clearance (AFC) was reduced in CAP1/Prss8‐deficient mice, due to a 48% decrease in amiloride‐sensitive clearance, and was less sensitive to β2‐agonist treatment. Intra‐alveolar treatment with neutrophil elastase, a soluble serine protease activating ENaC at the cell surface, fully restored basal AFC and the stimulation by β2‐agonists. Finally, acute volume‐overload increased alveolar lining fluid volume in CAP1/Prss8‐deficient mice. This study reveals that CAP1 plays a crucial role in the regulation of ENaC‐mediated alveolar sodium and water transport and in mouse lung fluid balance.
Pulotu: Database of Austronesian Supernatural Beliefs and Practices

Scholars have debated naturalistic theories of religion for thousands of years, but only recently have scientists begun to test predictions empirically. Existing databases contain few variables on religion, and are subject to Galton’s Problem because they do not sufficiently account for the non-independence of cultures or systematically differentiate the traditional states of cultures from their contemporary states. Here we present Pulotu: the first quantitative cross-cultural database purpose-built to test evolutionary hypotheses of supernatural beliefs and practices. The Pulotu database documents the remarkable diversity of the Austronesian family of cultures, which originated in Taiwan, spread west to Madagascar and east to Easter Island–a region covering over half the world’s longitude. The focus of Austronesian beliefs range from localised ancestral spirits to powerful creator gods. A wide range of practices also exist, such as headhunting, elaborate tattooing, and the construction of impressive monuments. Pulotu is freely available, currently contains 116 cultures, and has 80 variables describing supernatural beliefs and practices, as well as social and physical environments. One major advantage of Pulotu is that it has separate sections on the traditional states of cultures, the post-contact history of cultures, and the contemporary states of cultures. A second major advantage is that cultures are linked to a language-based family tree, enabling the use phylogenetic methods, which can be used to address Galton’s Problem by accounting for common ancestry, to infer deep prehistory, and to model patterns of trait evolution over time. We illustrate the power of phylogenetic methods by performing an ancestral state reconstruction on the Pulotu variable “headhunting", finding evidence that headhunting was practiced in proto-Austronesian culture. Quantitative cross-cultural databases explicitly linking cultures to a phylogeny have the potential to revolutionise the field of comparative religious studies in the same way that genetic databases have revolutionised the field of evolutionary biology.
Logical Systems: Towards Protocols for Web-Based Meaning Negotiation

Our thesis is that before Web-based agents can negotiate meanings, they need to agree on high-level protocols based on logical systems. The Semantic Web community is setting the stage for semantic interoperability among Web-based software agents by developing standard languages with well-defined semantics. But exactly how these languages might be used to negotiate meanings is an open question. The agent-oriented perspective of negotiation as a kind of deal-making does not seem to mesh with the perspective of Semantic Web community, which seems more inclined to fix meanings, rather than bargain over them. Fundamental to treatments of meanings on the Semantic Web is the ability of agents to perform logical inferences; therefore, any approach to Web-based meaning negotiation should, take into account those aspects of logic that have a bearing on logical inferences. Logical systems provide a general way of accounting for those aspects of an agent’s logical setup that have a bearing on inferences. An explicit taking into account of agents’ logical systems provides a suitably rich foundation on which to base protocols for meaning negotiation on the Web.
Diurnal variability of mesospheric ozone as measured by the UARS microwave limb sounder instrument: Theoretical and ground-based validations

Diurnal variability of mesospheric ozone as measured by the 183-GHz radiometer of the UARS microwave limb sounder (MLS) instrument for the northern midlatitudes in October 1991 and 1992 is compared with theoretical calculations of diurnal amplitudes produced by two photochemical models and with ground-based microwave measurements made from Bordeaux (France, 45°N) in October 1988, 1989, and 1990 and the Table Mountain Facility (California, 35°N) in October 1990. Great care has been taken in comparing all the data sets within the same frame, i.e., interpolating onto the same vertical grid (pressure or altitude), using the same units (concentration or mixing ratio) and degrading the vertical resolution of some data or models (convolution of the vertical profiles with appropriate averaging kernels). MLS diurnal variability generally agrees to within 10% with ground-based and model results at 0.5, 0.2, 0.1, and 0.05 hPa (approximately 55, 60, 65, and 70 km, respectively). Although modeled diurnal changes at 55 ± 8 km are closer to the ground-based Bordeaux measurements than to the MLS data at 45°N, MLS results are closer to ground-based Table Mountain Facility data at 35°N at 0.42 and 0.22 hPa (∼55 ± 8 and ∼60 ± 8 km, respectively) than to models. At 0.1 and 0.042 hPa, MLS diurnal changes are weaker than ground-based and model variations, but daytime O 3 mixing ratios are found to be in very good agreement for all data sets.
STBenchmark: towards a benchmark for mapping systems

A fundamental problem in information integration is to precisely specify the relationships, called mappings, between schemas. Designing mappings is a time-consuming process. To alleviate this problem, many mapping systems have been developed to assist the design of mappings. However, a benchmark for comparing and evaluating these systems has not yet been developed. We present STBenchmark, a solution towards a much needed benchmark for mapping systems. We first describe the challenges that are unique to the development of benchmarks for mapping systems. After this, we describe the three components of STBenchmark: (1) a basic suite of mapping scenarios that we believe represents a minimum set of transformations that should be readily supported by any mapping system, (2) a mapping scenario generator as well as an instance generator that can produce complex mapping scenarios and, respectively, instances of varying sizes of a given schema, (3) a simple usability model that can be used as a first-cut measure on the case of use of a mapping system. We use STBenchmark to evaluate four mapping systems and report our results, as well as describe some interesting observations.
Solving partial differential equations on a network of workstations

The use of a network of workstations as a single unit for speeding up computationally intensive applications is becoming a cost-effective alternative to traditional parallel computers. We present the implementation of an application-driven parallel platform for solving partial differential equations (PDEs) on this computing environment. The platform provides a general and efficient parallel solution for time-dependent PDEs and an easy-to-use interface that allows the inclusion of a wide range of parallel programming tools. We have used two different parallelization methods in this platform. The first method is a two-phase algorithm which uses the conventional technique of alternating computation and communication phases. The second method uses a novel pre-computation technique which allows overlapping of computation and communication. Both methods yield significant speedup. However the pre-computation technique is shown to be more efficient and scalable. <<ETX>>
MER41 Repeat Sequences Contain Inducible STAT1 Binding Sites

Chromatin immunoprecipitation combined with massively parallel sequencing methods (ChIP-seq) is becoming the standard approach to study interactions of transcription factors (TF) with genomic sequences. At the example of public STAT1 ChIP-seq data sets, we present novel approaches for the interpretation of ChIP-seq data. We compare recently developed approaches to determine STAT1 binding sites from ChIP-seq data. Assessing the content of the established consensus sequence for STAT1 binding sites, we find that the usage of “negative control” ChIP-seq data fails to provide substantial advantages. We derive a single refined probabilistic model of STAT1 binding sequences from these ChIP-seq data. Contrary to previous claims, we find no evidence that STAT1 binds to multiple distinct motifs upon interferon-gamma stimulation in vivo. While a large majority of genomic sites with high ChIP-seq signal is associated with a nucleotide sequence ressembling a STAT1 binding site, only a very small subset of the over 5 million potential STAT1 binding sites in the human genome is covered by ChIP-seq data. Furthermore a surprisingly large fraction of the ChIP-seq signal (5%) is absorbed by a small family of repetitive sequences (MER41). The observation of the binding of activated STAT1 protein to a specific repetitive element bolsters similar reports concerning p53 and other TFs, and strengthens the notion of an involvement of repeats in gene regulation. Incidentally MER41 are specific to primates, consequently, regulatory mechanisms in the IFN-STAT pathway might fundamentally differ between primates and rodents. On a methodological aspect, the presence of large numbers of nearly identical binding sites in repetitive sequences may lead to wrong conclusions about intrinsic binding preferences of TF as illustrated by the spacing analysis STAT1 tandem motifs. Therefore, ChIP-seq data should be analyzed independently within repetitive and non-repetitive sequences.