Miracle-dz/UniFAR-FTUs huggingface dataset:
Environmental Genome Shotgun Sequencing of the Sargasso Sea

We have applied “whole-genome shotgun sequencing” to microbial populations collected en masse on tangential flow and impact filters from seawater samples collected from the Sargasso Sea near Bermuda. A total of 1.045 billion base pairs of nonredundant sequence was generated, annotated, and analyzed to elucidate the gene content, diversity, and relative abundance of the organisms within these environmental samples. These data are estimated to derive from at least 1800 genomic species based on sequence relatedness, including 148 previously unknown bacterial phylotypes. We have identified over 1.2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity.
Combined effect of the direction of information transmission and the spatiality over sustaining cooperation

We propose an agent-based model to explore the joint effect of spatial distribution and the direction information transmission over cooperation's maintenance. Particularly, we study two information transmission modes: Horizontal (H) and Vertical (V) over fives spatial structures: grids 1D and 2D, Random Graphs, Small World Graphs, and Scale Free Networks. Our Results show that cooperation's dynamics for Vertical and Horizontal transmission are completely different. The effect over cooperation dynamics of Horizontal Transmission is not affected by the spatial distribution, while Vertical Transmission's effect is altered by spatiality. Particularly, cooperation dynamics are more sensible to Horizontal Transmission in Small World Graphs. Finally, looking at different Horizontal Transmission rates we found that for bigger rates the fewer cooperators survive.
Kernel Weaver: Automatically Fusing Database Primitives for Efficient GPU Computation

Data warehousing applications represent an emerging application arena that requires the processing of relational queries and computations over massive amounts of data. Modern general purpose GPUs are high bandwidth architectures that potentially offer substantial improvements in throughput for these applications. However, there are significant challenges that arise due to the overheads of data movement through the memory hierarchy and between the GPU and host CPU. This paper proposes data movement optimizations to address these challenges. Inspired in part by loop fusion optimizations in the scientific computing community, we propose kernel fusion as a basis for data movement optimizations. Kernel fusion fuses the code bodies of two GPU kernels to i) reduce data footprint to cut down data movement throughout GPU and CPU memory hierarchy, and ii) enlarge compiler optimization scope. We classify producer consumer dependences between compute kernels into three types, i) fine-grained thread-to-thread dependences, ii) medium-grained thread block dependences, and iii) coarse-grained kernel dependences. Based on this classification, we propose a compiler framework, Kernel Weaver, that can automatically fuse relational algebra operators thereby eliminating redundant data movement. The experiments on NVIDIA Fermi platforms demonstrate that kernel fusion achieves 2.89x speedup in GPU computation and a 2.35x speedup in PCIe transfer time on average across the micro-benchmarks tested. We present key insights, lessons learned, measurements from our compiler implementation, and opportunities for further improvements.
Measures of Cultural Competence in Nurses: An Integrative Review

Background. There is limited literature available identifying and describing the instruments that measure cultural competence in nursing students and nursing professionals. Design. An integrative review was undertaken to identify the characteristics common to these instruments, examine their psychometric properties, and identify the concepts these instruments are designed to measure. Method. There were eleven instruments identified that measure cultural competence in nursing. Of these eleven instruments, four had been thoroughly tested in either initial development or in subsequent testing, with developers providing extensive details of the testing. Results. The current literature identifies that the instruments to assess cultural competence in nurses and nursing students are self-administered and based on individuals' perceptions. The instruments are commonly utilized to test the effectiveness of educational programs designed to increase cultural competence. Conclusions. The reviewed instruments measure nurses' self-perceptions or self-reported level of cultural competence but offer no objective measure of culturally competent care from a patient's perspective which can be problematic. Comparison of instruments reveals that they are based on a variety of conceptual frameworks and that multiple factors should be considered when deciding which instrument to use.
Recent advances and new applications of computer vision (特集 デジタルメディア処理先端技術)

At Cambridge we have identified a number of possible applications and are now pioneering core technology in the main three areas of vision Reconstruction (3D shape recovery from uncalibrated images); Registration (human body detection and tracking for use in novel interfaces) and Recognition (object detection, segmentation and recognition in video). Our approach is predominantly geometric but includes modern practice in machine learning.
Algebraic $H_infty$ Design of Higher-Order Iterative Learning Controllers

This paper presents an Hinfin-based design technique for synthesis of higher-order iterative learning controllers (ILC) for plants subject to iteration-domain input/output disturbances and plant model uncertainty. Using a formulation of the higher-order ILC problem into a high-dimensional MIMO discrete-time system, it is shown how the addition of input/output disturbances and plant model uncertainty to the ILC problem can be cast into a standard Hinfin framework. An algebraic approach to solving the problem in this framework is presented, resulting in a sub-optimal controller that can achieve both stability and robust performance. The key observation is that Hinfin synthesis can be used for higher-order ILC design to achieve reliable performance in the presence of iteration-varying external disturbances and model uncertainty
[Autobiographical memory in aging].

Episodic memory deficits are characteristic of old subjects. However, few results concern studies of autobiographical memory, one of the most essential part of human memory. Usually remote, but not recent, memory is regarded as preserved in aging. This phenomenom is well known as the Ribot's law. We briefly present the recent models of autobiographical memory and we detail the different aspects of aging on the two components, either episodic or semantic, of autobiographical memory. The data are reviewed with respect to the different kinds of autobiographical memory assessments : cue-words technique, autobiographical verbal fluency and interview. In addition, we present the results from novel autobiographical memory tasks specially designed to be more valid and reliable than the previous neuropsychological tools by assessing the contribution of episodic and semantic memory systems to autobiographical performance viaexperimental paradigms (remember/know). This review shows that the Ribot's law is not confirmed in aging by contrast with Alzheimer's disease. Indeed, in older subjects, the performances on episodic autobiographical memory tests diminish with time interval, with a clear recency effect. Moreover, the episodic, but not the semantic, component of autobiographical memory is significantly altered in aging.
Functional interactions between alternatively spliced forms of Pax 6 in crystallin gene regulation and in haploinsuf ® ciency

Pax6 is essential for development of the eye, olfactory system, brain and pancreas. Haploinsuf®ciency of Pax6 causes abnormal eye development. Two forms of Pax6 protein, PAX6 and PAX6(5a), differ in a 14 amino acid insertion encoded by an alternatively spliced exon 5a in the N-terminal DNA-binding paired domain (PD), and they are simultaneously expressed. Here, we show that PAX6 and PAX6(5a) together synergistically activate transcription from promoters recognized by Pax6 PD and PD5a, but not by their homeodomain. This synergism promotes activation of transcription by c-Maf and MafA on the aB-crystallin promoter, and is required for transcriptional co-activation by RARb/RXRb and PAX6/PAX6(5a) on the gF-crystallin promoter. To determine the role of this synergism in haploinsuf®ciency, we tested four human missense (G18W, R26G, G64V and R128C) and one nonsense (R317X) mutants, with reporters driven by Pax6 PD consensus binding sites and the aB-crystallin promoter. The simultaneous activity of Pax6 proteins [PAX6, mutated PAX6, PAX6(5a) and mutated PAX6(5a)] modeling haploinsuf®ciency yielded results not predicted by properties of individual PAX6 or PAX6(5a). Taken together, these results indicate that complex ocular phenotypes due to Pax6 haploinsuf®ciency originate, at least partially, from functional interactions between alternatively spliced PAX6 and PAX6(5a) variants and other factors, e.g. MafA/c-
A low-power opportunistic communication protocol for wearable applications

Recent trends in wearable applications demand flexible architectures being able to monitor people while they move in free-living environments. Current solutions use either store-download-offline processing or simple communication schemes with real-time streaming of sensor data. This limits the applicability of wearable applications to controlled environments (e.g, clinics, homes, or laboratories), because they need to maintain connectivity with the base station throughout the monitoring process. In this paper, we present the design and implementation of an opportunistic communication framework that simplifies the general use of wearable devices in free-living environments. It relies on a low-power data collection protocol that allows the end user to opportunistically, yet seamlessly manage the transmission of sensor data. We validate the feasibility of the framework by demonstrating its use for swimming, where the normal wireless communication is constantly interfered by the environment.
Identification and Characterization of cis-Acting Elements Residing in the Walleye Dermal Sarcoma Virus Promoter

ABSTRACT Walleye dermal sarcoma virus (WDSV) is a complex retrovirus found associated with tumors that appear and regress on a seasonal basis. There are quantitative and qualitative differences in the amount of virus expression between developing and regressing tumors. To understand the role of host cell factors in WDSV expression, DNase I footprint analysis, electrophoretic mobility shift assays (EMSA), and reporter gene assays were employed. DNase I footprint analysis of the U3 region of the WDSV long terminal repeat with nuclear extract prepared from a walleye cell line revealed protection of an Oct1, AP1, Whn, and two E4BP4 sites. Additionally, three regions that contained no putative transcription factor binding sites were protected. EMSA confirmed the specific binding of the protected sites and revealed three additional sites, NF1, AP3, and LVa, not protected in DNase I footprint analysis. Site-directed mutagenesis of the individual sites, in the context of a luciferase reporter plasmid, revealed that the NF1, Oct1, AP1, E4BP4#2, AP3, and LVa sites contributed to transcription activation driven by the WDSV U3 region. Mutation of Novel#2 resulted in an increase in luciferase activity, suggesting the Novel#2 site may function to bind a negative regulator of transcription. Anti-Jun and anti-Fos antiserum specifically inhibited protein-DNA complex formation, indicating the presence of c-Jun and c-Fos in the walleye cell nuclear extracts and their participation in binding to the AP1 site. Interestingly, degenerative 15-bp repeats found in the U3 region are differentially protected in DNase I footprint analysis by the walleye cell line nuclear extract and regressing-tumor nuclear extract. EMSA utilizing the 15-bp repeat probe revealed that there are similarities of binding with W12 cell and developing-tumor nuclear extracts and that the binding differs from that observed with regressing-tumor nuclear extract.
Optimal Investment Management in a Port Project

This paper proposes a new method for valuing a major public investment project. The method allows also the study and determination of the optimal time to begin the investment. Such a project needs long-term investment, requires tools of analysis able to collect and systematize the future uncertainty, which is present in the evolution of the problem variables. Valuation is difficult and must take into account the large number of traffic variables, the cash flows function characteristics and the implicit real options in the investment decisions. We propose a new method based on an algorithm, which adds stochastic processes simulation and discrete scenario space generation. The algorithm not only allows us to approach the given problem but also it can be applied to another problems with similar characteristics.
Combined DWT-DCT Digital Image Watermarking

The proliferation of digitized media due to the rapid growth of networked multimedia systems, has created an urgent need for copyright enforcement technologies that can protect copyright ownership of multimedia objects. Digital image watermarking is one such technology that has been developed to protect digital images from illegal manipulations. In particular, digital image watermarking algorithms which are based on the discrete wavelet transform have been widely recognized to be more prevalent than others. This is due to the wavelets' excellent spatial localization, frequency spread, and multi-resolution characteristics, which are similar to the theoretical models of the human visual system. In this paper, we describe an imperceptible and a robust combined DWT-DCT digital image watermarking algorithm. The algorithm watermarks a given digital image using a combination of the Discrete Wavelet Transform (DWT) and the Discrete Cosine Transform (DCT). Performance evaluation results show that combining the two transforms improved the performance of the watermarking algorithms that are based solely on the DWT transform.
Translated and annotated version of the 2015-2020 National Mental Health Work Plan of the People's Republic of China

The following document is a translation of the 2015-2020 National Mental Health Work Plan of the People's Republic of China which was issued by the General Office of China's State Council on June 4, 2015. The original Chinese version of the document is available at the official government website: http://www.gov. cn/gongbao/content/2015/content_2883226. htm The translators have added annotations at the end of the document that provide background information to help contextualize content that may be unclear to readers unfamiliar with China and explain their decisions when translating terms that can have multiple interpretations.
Mining parameterized role-based policies

Role-based access control (RBAC) offers significant advantages over lower-level access control policy representations, such as access control lists (ACLs). However, the effort required for a large organization to migrate from ACLs to RBAC can be a significant obstacle to adoption of RBAC. Role mining algorithms partially automate the construction of an RBAC policy from an ACL policy and possibly other information. These algorithms can significantly reduce the cost of migration to RBAC. This paper defines a parameterized RBAC (PRBAC) framework in which users and permissions have attributes that are implicit parameters of roles and can be used in role definitions. Parameterization significantly enhances the scalability of RBAC, by allowing much more concise policies. This paper presents algorithms for mining such policies and reports the results of evaluating the algorithms on case studies. To the best of our knowledge, these are the first policy mining algorithms for a PRBAC framework. An evaluation on three small but non-trivial case studies demonstrates the effectiveness of our algorithms.
Ordered Stick-Breaking Prior for Sequential MCMC Inference of Bayesian Nonparametric Models

This paper introduces ordered stick-breaking process (OSBP), where the atoms in a stickbreaking process (SBP) appear in order. The choice of weights on the atoms of OSBP ensure that; (1) probability of adding new atoms exponentially decrease, and (2) OSBP, though non-exchangeable, admit predictive probability functions (PPFs). In a Bayesian nonparametric (BNP) setting, OSBP serves as a natural prior over sequential mini-batches, facilitating exchange of relevant statistical information by sharing the atoms of OSBP. One of the major contributions of this paper is SUMO, an MCMC algorithm, for solving the inference problem arising from applying OSBP to BNP models. SUMO uses the PPFs of OSBP to obtain a Gibbs-sampling based truncation-free algorithm which applies generally to BNP models. For large scale inference problems existing algorithms such as particle filtering (PF) are not practical and variational procedures such as TSVI (Wang & Blei, 2012) are the only alternative. For Dirichlet process mixture model (DPMM), SUMO outperforms TSVI on perplexity by 33% on 3 datasets with million data points, which are beyond the scope of PF, using only 3GB RAM.
Rhetorical Structure Analysis of Japanese Patent Claims using Cue Phrases

The most important part of patent specification is where the claims are written. It is common that claims written in Japanese are described in one sentence with peculiar style and are difficult to understand for ordinary people. We are investigating NLPtechnologies to improve readability of patent claims. To do so, it is necessary to present the structure of patent claims in a readable way. We found that there are several typical phrases used in claim descriptions and that they can be used as clues to analyze the rhetorical structure of patent claims. We propose a method to analyze the rhetorical structure of patent claims by using these cue phrases and report the result of evaluation.
Functionally Competent Cardiac Stem Cells Can Be Isolated From Endomyocardial Biopsies of Patients With Advanced Cardiomyopathies

Rationale: Two categories of cardiac stem cells (CSCs) with predominantly myogenic (mCSC) and vasculogenic (vCSC) properties have been characterized in the human heart. However, it is unknown whether functionally competent CSCs of both classes are present in the myocardium of patients affected by end-stage cardiac failure, and whether these cells can be harvested from relatively small myocardial samples. Objective: To establish whether a clinically relevant number of mCSCs and vCSCs can be isolated and expanded from endomyocardial biopsies of patients undergoing cardiac transplantation or left ventricular assist device implantation. Methods and Results: Endomyocardial biopsies were collected with a bioptome from the right side of the septum of explanted hearts or the apical LV core at the time of left ventricular assist device implantation. Two to 5 biopsies from each patient were enzymatically dissociated, and, after expansion, cells were sorted for c-kit (mCSCs) or c-kit and KDR (vCSCs) and characterized. mCSCs and vCSCs constituted 97% and 3% of the c-kit population, respectively. Population doubling time averaged 27 hours in mCSCs and vCSCs; 5×106 mCSCs and vCSCs were obtained in 28 and 41 days, respectively. Both CSC classes possessed significant growth reserve as documented by high telomerase activity and relatively long telomeres. mCSCs formed mostly cardiomyocytes, and vCSCs endothelial and smooth muscle cells. Conclusions: The growth properties of mCSCs and vCSCs isolated from endomyocardial biopsies from patients with advanced heart failure were comparable to those obtained previously from larger myocardial samples of patients undergoing elective cardiac surgery.
The three mouse multidrug resistance (mdr) genes are expressed in a tissue-specific manner in normal mouse tissues

The gene responsible for multidrug resistance (mdr), which encodes the P-glycoprotein, is a member of a multigene family. We have identified distinct mdr gene transcripts encoded by three separate mdr genes in the mouse. Expression levels of each mdr gene are dramatically different in various mouse tissues. Specific mdr RNA transcripts of approximately 4.5, 5, and 6 kilobases have been detected. Each of the mdr genes has a specific RNA transcript pattern. These results should be considered in relation to understanding the normal physiological function of the mdr multigene family.
The Research and Application on Business Tier Based on J2EE

After analyzing and researching on management system’s specific business in logistic enterprises based on J2EE model, this paper proposes the design scheme of business tier with the ideology of design pattern, makes more reasonable design and improvement to abstract domain model from the business tier in maximum, resultingly the whole system is more flexible, expandable and reusable.
Hypnosis and Distraction Differ in Their Effects on Cold Pressor Pain

Abstract On the bases of Hilgard's neodissociation theory and Spano's (1982) socio-cognitive theory, volunteers stringently selected for high (N = 10) and low (N = 10) hypnotizability were exposed to a cold pressor pain test during counterbalanced conditions of waking relaxation, distraction, and hypnosis. To better discriminate between hypnosis and distraction conditions, a new distraction procedure was developed involving the memorization of a sequence of colored lights. High hypnotizables showed significantly greater pain relief for hypnosis versus distraction or waking relaxation conditions. High hypnotizables also demonstrated significantly greater pain relief than low hypnotizables in response to hypnosis. Quantitative electroencephalographic (EEG) findings showed significantly greater high theta (5.5–7.5 Hz) activity for highs as compared to lows at parietal (P3) and occipital (01) sites during both hypnosis and waking relaxation conditions. The findings fail to support the socio-cognitive conceptualization of hypnotic behavior while providing additional evidence supporting the neo-dissociation theory and state based theories of hypnosis in general.
Estimates of DNA strand breakage in bottlenose dolphin (Tursiops truncatus) leukocytes measured with the Comet and DNA diffusion assays

The analysis of DNA damage by mean of Comet or single cell gel electrophoresis (SCGE) assay has been commonly used to assess genotoxic impact in aquatic animals being able to detect exposure to low concentrations of contaminants in a wide range of species. The aims of this work were 1) to evaluate the usefulness of the Comet to detect DNA strand breakage in dolphin leukocytes, 2) to use the DNA diffusion assay to determine the amount of DNA strand breakage associated with apoptosis or necrosis, and 3) to determine the proportion of DNA strand breakage that was unrelated to apoptosis and necrosis. Significant intra-individual variation was observed in all of the estimates of DNA damage. DNA strand breakage was overestimated because a considerable amount (~29%) of the DNA damage was derived from apoptosis and necrosis. The remaining DNA damage in dolphin leukocytes was caused by factors unrelated to apoptosis and necrosis. These results indicate that the DNA diffusion assay is a complementary tool that can be used together with the Comet assay to assess DNA damage in bottlenose dolphins.