Miracle-dz/UniFAR-FTUs huggingface dataset:
Building JACK : Developing Metrics for Use in Multi-Objective Optimal Data Allocation Strategies Technical Report UCSC-SSRC-1401 January 2014

Current file systems optimize for a single objective, often to the detriment of other objectives. This can result in an unbalanced system that does not reflect the needs of the system or its users. We suggest addressing the data allocation problem as a multi-objective optimization problem, using our general data placement framework, JACK. This provides us with a means of finding an optimal data allocation, tailored to the requirements of individual systems, requiring at most the specification of the relative importance of competing performance goals. For such an approach to be feasible, we need to define meaningful, yet observable, metrics for such a multiobjective optimization problem. We introduce the objectives we intend to optimize for and example metrics which can be used to gauge them. We provide a detailed description of how each metric was developed, using a data set provided by Los Alamos National Laboratory for evaluation. We also explain how the metrics enable the development of JACK, with the intent that others can make use of our metrics and develop their own metrics for additional performance goals.
Hematopoietic stem cell expansion and generation: the ways to make a breakthrough

Hematopoietic stem cell transplantation (HSCT) is the first field where human stem cell therapy was successful. Flooding interest on human stem cell therapy to cure previously incurable diseases is largely indebted to HSCT success. Allogeneic HSCT has been an important modality to cure various diseases including hematologic malignancies, various non-malignant hematologic diseases, primary immunodeficiency diseases, and inborn errors of metabolism, while autologous HSCT is generally performed to rescue bone marrow aplasia following high-dose chemotherapy for solid tumors or multiple myeloma. Recently, HSCs are also spotlighted in the field of regenerative medicine for the amelioration of symptoms caused by neurodegenerative diseases, heart diseases, and others. Although the demand for HSCs has been growing, their supply often fails to meet the demand of the patients needing transplant due to a lack of histocompatible donors or a limited cell number. This review focuses on the generation and large-scale expansion of HSCs, which might overcome current limitations in the application of HSCs for clinical use. Furthermore, current proof of concept to replenish hematological homeostasis from non-hematological origin will be covered.
Complement Is an Essential Component of the Immune Response to Adeno-Associated Virus Vectors

ABSTRACT Adeno-associated virus (AAV) vectors are associated with relatively mild host immune responses in vivo. Although AAV induces very weak innate immune responses, neutralizing antibodies against the vector capsid and transgene still occur. To understand further the basis of the antiviral immune response to AAV vectors, studies were performed to characterize AAV interactions with macrophages. Primary mouse macrophages and human THP-1 cells transduced in vitro using an AAV serotype 2 (AAV2) vector encoding green fluorescent protein did not result in measurable transgene expression. An assessment of internalized vector genomes showed that AAV2 vector uptake was enhanced in the presence of normal but not heat-inactivated or C3-depleted mouse/human serum. Enhanced uptake in the presence of serum coincided with increased macrophage activation as determined by the expression of NF-κB-dependent genes such as macrophage inflammatory protein 2 (MIP-2), interleukin-1β (IL-1β), IL-8, and MIP-1β. AAV vector serotypes 1 and 8 also activated human and mouse macrophages in a serum-dependent manner. Immunoprecipitation studies demonstrated the binding of iC3b complement protein to the AAV2 capsid in human serum. AAV2 did not activate the alternative pathway of the complement cascade and lacked cofactor activity for factor I-mediated degradation of C3b to iC3b. Instead, our results suggest that the AAV capsid also binds complement regulatory protein factor H. In vivo, complement receptor 1/2- and C3-deficient mice displayed impaired humoral immunity against AAV2 vectors, with a delay in antibody development and significantly lower neutralizing antibody titers. These results show that the complement system is an essential component of the host immune response to AAV.
Detection of residual cognitive function through non-spontaneous eye movement in a patient with advanced frontotemporal dementia

As dementia progresses, cognitive functions decline in patients, and caregivers and other support staff gradually lose the means to communicate with them. However, some caregivers believe that patients can still recognize their surroundings even when they show akinesis with mutism. In this study, we observed eye movements (preferential-looking paradigm) to detect the presence of residual cognitive functions in a patient with severe frontotemporal dementia (FTD). The subject was a 76-year-old female. At the time of observation, she had lost all spontaneous activities. Magnetic resonance imaging (MRI) imaging showed dense atrophy of the bilateral frontotemporal lobe, but the parieto-occipital lobe was preserved. A preferential-looking paradigm was used in the experiment, whereby two different faces (learned and non-learned) were simultaneously presented to the patient on a TV monitor. As a result, we found no significant differences in looking time between the two faces. However, when the saccade timing to the presented faces was examined, a much longer latency was observed for the right than the left side of the target faces. Even though the patient had lost capacity for spontaneous activity due to severe FTD, we were able to observe partial residual cognitive ability using the eye-movement paradigm.
Literature study on k-nearest neighbor query processing

User's locations and there interested are different. Collecting large amount of data to the user is very difficult. Sometime information is very sensitive; handling the information is very difficult task. Information storage also very big issue.so data owner does not make data accessible in all customers. It's allowed only paying customers. User send their current location points and want to know about nearest POIs in NN but data Owner does not have that much storage capacity so we are using cloud service. Cloud provides power full storage at low cost but Cloud is not fully trusted. So allow processing of NN queries in an untrusted outsourced environment, whereas at an equivalent time protective each the POI and querying users' positions. Our techniques based on mutable order preserving encoding (mOPE). It is a secure order-preserving encryption. We provide performance optimizations to decrease the computational cost.
Baculovirus-based expression of an insect viral protein in 12 different insect cell lines

SummaryThe ability of 12 unique lepidopteran insect cell lines, from Anticarsia gemmatalis, Heliothis virescens, Lymantria dispar (two lines), Mamestra brassica, Plutella xylostella, Spodoptera, frugigerda (two lines), and Trichoplusia ni (three lines) to support production of a recombinant polydnavirus (PDV) protein (GiPDV 1.1) expressed using the Bac-to-Bac™ baculovirus expression system was examined. Polydnavirus gene GiPDV 1.1 was cloned into the pFastBac baculovirus vector under the control of the polyhedron promoter, followed by generation of recombinant bacmid-GiPDV 1.1 by site-specific transposition. The ability of each insect cell line to support recombinant PDV gene expression was estimated using reverse transcriptase-polymerase chain reaction and Western blot. Each insect cell line infected with recombinant bacmid-GiPDV 1.1 and tested in this study was capable of supporting and producing recombinant protein. Teme course expression analysis showed that 72–96 h after transfection to be the optimal time for recombinant protein for each insect cell line.
Genome-Wide Identification and Expression Analysis of the WRKY Gene Family in Cassava

The WRKY family, a large family of transcription factors (TFs) found in higher plants, plays central roles in many aspects of physiological processes and adaption to environment. However, little information is available regarding the WRKY family in cassava (Manihot esculenta). In the present study, 85 WRKY genes were identified from the cassava genome and classified into three groups according to conserved WRKY domains and zinc-finger structure. Conserved motif analysis showed that all of the identified MeWRKYs had the conserved WRKY domain. Gene structure analysis suggested that the number of introns in MeWRKY genes varied from 1 to 5, with the majority of MeWRKY genes containing three exons. Expression profiles of MeWRKY genes in different tissues and in response to drought stress were analyzed using the RNA-seq technique. The results showed that 72 MeWRKY genes had differential expression in their transcript abundance and 78 MeWRKY genes were differentially expressed in response to drought stresses in different accessions, indicating their contribution to plant developmental processes and drought stress resistance in cassava. Finally, the expression of 9 WRKY genes was analyzed by qRT-PCR under osmotic, salt, ABA, H2O2, and cold treatments, indicating that MeWRKYs may be involved in different signaling pathways. Taken together, this systematic analysis identifies some tissue-specific and abiotic stress-responsive candidate MeWRKY genes for further functional assays in planta, and provides a solid foundation for understanding of abiotic stress responses and signal transduction mediated by WRKYs in cassava.
A Theory of Theories in Information Systems

The aim of this paper is to explore what is meant by ‘theory’ in Information Systems. Different conceptions of causality are discussed, as they are seen as key to understanding different types of theory. Five different types of theory are distinguished: (i) theory for analysing and describing, (ii) theory for understanding, (iii) theory for predicting, (iv) theory for explaining and predicting, and (v) theory for design and action. Illustrations of relevant work in Information Systems are provided, as are relevant research methods, and the form of contributions to knowledge in each. The limited discussion of the nature of theory in Information Systems indicates that further work is needed, particularly with respect to theory for design and action.
Fusion-based recommender system

Recommender systems have become a common way to help people navigate among increasingly more complex selection options. Various recommendation algorithms have been proposed and a lot of business solutions have been built for applications such as selecting books, cinema, video/TV program, restaurants, etc. However, there is no simply best approach due to the high complexity and uncertainty of the problem. Therefore, a recommender system usually includes multiple different recommenders and aggregates their recommendation results through a combiner. In this paper, we discussed combining recommenders in the framework of information fusion theory including rank fusion, decision fusion, Dempster-Shafer fusion and estimation fusion. Experiments results on the benchmark Movie-Lens dataset show that our proposed methods with fusion techniques leaded to significant performance improvements over the baselines models.
Color Signals in the Black Grouse (Tetrao tetrix): Signal Properties and Their Condition Dependency

Recent progress in techniques of quantifying between‐individual differences of color‐based ornaments has revealed undiscovered possibilities for research in sexual selection. We present how the color spectra data can be comprehensively used for studying the importance of sexual ornaments in the black grouse and how these ornaments are related to a male condition. For this, we used both correlative field and experimental data. Field data indicated that older males had more chromatic coloration than yearlings. Blue chroma of males was correlated with male mating success. We experimentally manipulated yearling birds with testosterone implants and found that testosterone‐implanted males had impaired expression of several sexual ornaments: 10 months after the implantation, both structural‐based blue and carotenoid‐based red eye comb coloration were diminished, as well as lyre (tail) length. However, the manipulation did not affect vital traits under natural selection (wing length or body mass). Our data indicate that structural color is an important trait in sexual selection in this lekking species. Importantly, the data also indicate that male sexual ornaments are more susceptible to environmental conditions than the other male traits, thus showing their heightened condition dependency compared with the other traits mediating the honesty of signaling.
Uniform Materials and the Multiplicative Decomposition of the Deformation Gradient in Finite Elasto-Plasticity

Abstract In this work we analyze the relation between the multiplicative decomposition F = F e F p of the deformation gradient as a product of the elastic and plastic factors and the theory of uniform materials. We prove that postulating such a decomposition is equivalent to having a uniform material model with two configurations – total φ and the inelastic φ1. We introduce strain tensors characterizing different types of evolutions of the material and discuss the form of the internal energy and that of the dissipative potential. The evolution equations are obtained for the configurations (φ, φ1) and the material metric g. Finally, the dissipative inequality for the materials of this type is presented. It is shown that the conditions of positivity of the internal dissipation terms related to the processes of plastic and metric evolution provide the anisotropic yield criteria.
Arctic circulation regimes

Between 1948 and 1996, mean annual environmental parameters in the Arctic experienced a well-pronounced decadal variability with two basic circulation patterns: cyclonic and anticyclonic alternating at 5 to 7 year intervals. During cyclonic regimes, low sea-level atmospheric pressure (SLP) dominated over the Arctic Ocean driving sea ice and the upper ocean counterclockwise; the Arctic atmosphere was relatively warm and humid, and freshwater flux from the Arctic Ocean towards the subarctic seas was intensified. By contrast, during anticylonic circulation regimes, high SLP dominated driving sea ice and the upper ocean clockwise. Meanwhile, the atmosphere was cold and dry and the freshwater flux from the Arctic to the subarctic seas was reduced. Since 1997, however, the Arctic system has been under the influence of an anticyclonic circulation regime (17 years) with a set of environmental parameters that are atypical for this regime. We discuss a hypothesis explaining the causes and mechanisms regulating the intensity and duration of Arctic circulation regimes, and speculate how changes in freshwater fluxes from the Arctic Ocean and Greenland impact environmental conditions and interrupt their decadal variability.
Software Metrics from the Algorithmic Perspective

In this paper, software metrics and processes of program development, verification and maintenance are analyzed in the context of the theory of algorithms. This study is aimed to support the development of high quality production-grade software. The process of program design as a transition from a problem to a program is studied. Analysis of the situation shows that there are different meanings of a problem solution. We formalize these meanings with the aim of better structuring and optimization of the program design process. On the base of algorithmic complexity and of the theory of programs in the sense of Halstead, we analyze qualities of programs represented by software metrics. A classification of software metrics is developed.
Voicing features for robust speech detection

Accurate speech activity detection is a challenging problem in the car environment where high background noise and high amplitude transient sounds are common. We investigate a number of features that are designed for capturing the harmonic structure of speech. We evaluate separately three important characteristics of these features: 1) discriminative power 2) robustness to greatly varying SNR and channel characteristics and 3) performance when used in conjunction with MFCC features. We propose a new features, the Windowed Autocorrelation Lag Energy (WALE) which has desirable properties.
CEO Overconfidence: An Alternative Explanation for Corporate Financing Decisions

In the well-established trade-off capital structure model, a rational CEO chooses to issue debt and equity depending on the costs and benefits of each. In this model, the optimal amount of debt and equity financing occurs when the dead-weight costs of bankruptcy exactly offset the tax saving benefits of debt. However, this rational decision-making theory does not provide an adequate explanation for empirical findings that companies often deviate from the presumably optimal levels of debt and equity issuance. As an alternative explanation for these capital structures, we examine the additional impact that CEO overconfidence appears to have on financing decisions. In order to measure overconfidence of CEOs, we employ a measure based on the percentage of optimistic press coverage a CEO receives relative to the percentage of optimistic press coverage that the company itself receives. We then gather data on net debt issuance and net equity issuance under the governance of each CEO, and regress these financing decisions on our measure of CEO overconfidence. We find weak evidence that what we term overconfident CEOs deem equity financing relatively more expensive than debt financing, and thereby maintain higher than expected leverage ratios. We focus our data analysis on financing decision data from the decade 19972007, and examine capital structure decisions arising from CEO overconfidence in conjunction with differentials by industry and the effects of the dividend tax cuts from the 2003 Jobs and Growth Tax Relief Reconciliation Act.
Analysis and Design of Reduced-Size Marchand Rat-Race Hybrid for Millimeter-Wave Compact Balanced Mixers in 130-nm CMOS Process

The analysis and design flow for reduced-size Marchand rat-race hybrids are presented in this paper. A simplified single-to-differential mode is used to analyze the Marchand balun, and the methodology to reduce the size of Marchand balun is developed. The 60-GHz CMOS singly balanced gate mixer and diode mixer using the reduced-size Marchand rat-race hybrid are implemented to verify the design methodology. The monolithic microwave integrated circuit mixers achieve comparable performance with a compact chip size among the reported 60-GHz CMOS mixers.
Renal Function in De Novo Liver Transplant Recipients Receiving Different Prolonged‐Release Tacrolimus Regimens—The DIAMOND Study

DIAMOND: multicenter, 24‐week, randomized trial investigating the effect of different once‐daily, prolonged‐release tacrolimus dosing regimens on renal function after de novo liver transplantation. Arm 1: prolonged‐release tacrolimus (initial dose 0.2mg/kg/day); Arm 2: prolonged‐release tacrolimus (0.15–0.175mg/kg/day) plus basiliximab; Arm 3: prolonged‐release tacrolimus (0.2mg/kg/day delayed until Day 5) plus basiliximab. All patients received MMF plus a bolus of corticosteroid (no maintenance steroids). Primary endpoint: eGFR (MDRD4) at Week 24. Secondary endpoints: composite efficacy failure, BCAR and AEs. Baseline characteristics were comparable. Tacrolimus trough levels were readily achieved posttransplant; initially lower in Arm 2 versus 1 with delayed initiation in Arm 3. eGFR (MDRD4) was higher in Arms 2 and 3 versus 1 (p = 0.001, p = 0.047). Kaplan–Meier estimates of composite efficacy failure‐free survival were 72.0%, 77.6%, 73.9% in Arms 1–3. BCAR incidence was significantly lower in Arm 2 versus 1 and 3 (p = 0.016, p = 0.039). AEs were comparable. Prolonged‐release tacrolimus (0.15–0.175mg/kg/day) immediately posttransplant plus basiliximab and MMF (without maintenance corticosteroids) was associated with lower tacrolimus exposure, and significantly reduced renal function impairment and BCAR incidence versus prolonged‐release tacrolimus (0.2mg/kg/day) administered immediately posttransplant. Delayed higher‐dose prolonged‐release tacrolimus initiation significantly reduced renal function impairment compared with immediate posttransplant administration, but BCAR incidence was comparable.
Detection of an H$\alpha$ Emission Line on a Quasar, RX J1759.4$+$6638, at Z = 4.3 with AKARI

We report on the detection of an H emission line in the low-resolution spectrum of a quasar, RX J1759.4+6638, at a redshift of 4.3 with the Infrared Camera (IRC) onboard AKARI. This is the first spectroscopic detection of an H emission line in a quasar beyond z = 4. The overall spectral energy distribution (SED) of RX J1759.4+6638 in the nearand mid-infrared wavelengths agrees with a median SED of the nearby quasars; also, the flux ratio of F (Ly )=F (H ) is consistent with those of previous reports for lower-redshift quasars.
Automatic corner detection of chess board for medical endoscopy camera calibration

Camera calibration can hardly be avoided in the context of image-based computer aid surgery. Due to the radial distortion of endoscopy lens, the first challenging task is to solve the parameters of distortion correcting. Today various calibration methods have been proposed where the corners on a planar checker board are used as the control points. However the manual method and interactive method of corner extraction for endoscopy are extremely time consuming and require too much labor. In this paper, an effective automatic corner detection method for endoscopy lens is proposed. It consists of the detection of image corners, and the sub pixel recognition of corners at the intersection of black and white squares. Experiments show the robustness of the proposed method which will reduce the time consuming for endoscopy camera calibration.
Equivalent Indels – Ambiguous Functional Classes and Redundancy in Databases

There is considerable interest in studying sequenced variations. However, while the positions of substitutions are uniquely identifiable by sequence alignment, the location of insertions and deletions still poses problems. Each insertion and deletion causes a change of sequence. Yet, due to low complexity or repetitive sequence structures, the same indel can sometimes be annotated in different ways. Two indels which differ in allele sequence and position can be one and the same, i.e. the alternative sequence of the whole chromosome is identical in both cases and, therefore, the two deletions are biologically equivalent. In such a case, it is impossible to identify the exact position of an indel merely based on sequence alignment. Thus, variation entries in a mutation database are not necessarily uniquely defined. We prove the existence of a contiguous region around an indel in which all deletions of the same length are biologically identical. Databases often show only one of several possible locations for a given variation. Furthermore, different data base entries can represent equivalent variation events. We identified 1,045,590 such problematic entries of insertions and deletions out of 5,860,408 indel entries in the current human database of Ensembl. Equivalent indels are found in sequence regions of different functions like exons, introns or 5' and 3' UTRs. One and the same variation can be assigned to several different functional classifications of which only one is correct. We implemented an algorithm that determines for each indel database entry its complete set of equivalent indels which is uniquely characterized by the indel itself and a given interval of the reference sequence.