Miracle-dz/UniFAR-FTUs huggingface dataset:
Natural Variation in Arabidopsis thaliana as a Tool for Highlighting Differential Drought Responses

To test whether natural variation in Arabidopsis could be used to dissect out the genetic basis of responses to drought stress, we characterised a number of accessions. Most of the accessions belong to a core collection that was shown to maximise the genetic diversity captured for a given number of individual accessions in Arabidopsis thaliana. We measured total leaf area (TLA), Electrolyte Leakage (EL), Relative Water Content (RWC), and Cut Rosette Water Loss (CRWL) in control and mild water deficit conditions. A Principal Component Analysis revealed which traits explain most of the variation and showed that some accessions behave differently compared to the others in drought conditions, these included Ita-0, Cvi-0 and Shahdara. This study relied on genetic variation found naturally within the species, in which populations are assumed to be adapted to their environment. Overall, Arabidopsis thaliana showed interesting phenotypic variations in response to mild water deficit that can be exploited to identify genes and alleles important for this complex trait.
Workflow principles applied to multi-solution analysis of dependable distributed systems

Real world dependable distributed systems are often heterogeneous, not only in their physical composition, but also from a modeling and analysis perspective. Indeed, different components may be modeled by using the most suitable modeling formalism and multisolution strategies may be applied to analyze the resulting multi-formalism model since no single solution method is adequate to solve all submodels. We present the architecture of an extensible multiformalism framework for the modeling and design of distributed dependable system. We show that the process needed to solve/analyze a model expressed through different formalisms may be described as it were a business process and executed by means of a workflow engine. We apply the proposed technique to a fault tolerant remote SCADA (supervisory control and data acquisition) system.
Automated lung nodule classification by artificial neural network and fuzzy inference system

Lung cancer is the most cause of death from all cancers being less survival rate according to various online cancer societies. The former medical studies showed that the early diagnosis of lung cancer with screening program is the way to decline mortality rate. Radiological examination takes a tremendous time and need many medical experts having a large number of images per patient. Consequently, the accuracy of examination results mainly depends on the skills of physicians. Computer-aided Detection (CAD) in radiology can provide a functional and advantageous way to physicians aiming at improving accuracy and assisting in early detection of cancer, saving the time of radiologists in exam evaluation of cancers. Our proposed CAD system has fulfilled these all tasks combining image processing and Artificial Neuro-Fuzzy Inference System (ANFIS); with 98% sensitivity of finding true lung nodules, 94.4% sensitivity and 85% accuracy of removing false detectives, and 87% sensitivity and 78% accuracy for cancerous nodules detection.
Excitation of solar-like oscillations across the HR diagram

Aims. We extend semi-analytical computations of excitation rates for solar oscillation modes to those of other solar-like oscillating stars to compare them with recent observations Methods. Numerical 3D simulations of surface convective zones of several solar-type oscillating stars are used to characterize the turbulent spectra as well as to constrain the convective velocities and turbulent entropy fluctuations in the uppermost part of the convective zone of such stars. These constraints, coupled with a theoretical model for stochastic excitation, provide the rate P at which energy is injected into the p-modes by turbulent convection. These energy rates are compared with those derived directly from the 3D simulations. Results. The excitation rates obtained from the 3D simulations are systematically lower than those computed from the semi-analytical excitation model. We find that Pmax ,t heP maximum, scales as (L/M) s where s is the slope of the power law and L and M are the mass and luminosity of the 1D stellar model built consistently with the associated 3D simulation. The slope is found to depend significantly on the adopted form of χk, the eddy time-correlation; using a Lorentzian, χ L , results in s = 2.6, whereas a Gaussian, χ G ,g ivess = 3.1. Finally, values of Vmax, the maximum in the mode velocity, are estimated from the computed power laws for Pmax and we find that Vmax increases as (L/M) sv . Comparisons with the currently available ground-based observations show that the computations assuming a Lorentzian χk yield a slope, sv, closer to the observed one than the slope obtained when assuming a Gaussian. We show that the spatial resolution of the 3D simulations must be high enough to obtain accurate computed energy rates.
How Emotions and Personality Effect the Utility of Alternative Decisions: A Terrorist Target Selection Case Study

The role of emotion modeling in the development of computerized agents has long been unclear. This is partially due to instability in the philosophical issues of the problem as psychologists struggle to build models for their own purposes, and partially due to the often-wide gap between these theories and that which can be implemented by an agent author. This paper describes an effort to use emotion models in part as a deep model of utility for use in decision theoretic agents. This allows for the creation of simulated forces capable of balancing a great deal of competing goals, and in doing so they behave, for better or for worse, in a more
Developing a feature weight self-adjustment mechanism for the CD-sIB algorithm

The sIB algorithm is one of the popular clustering algorithms due to its superior scalability and efficiency. The CD-sIB algorithm is proposed to solve the problem that the sIB algorithm can not handle Non co-occurrence data. It proposes a feature construction method to extend the dataset attributes with a binary transformation. However, the CD-sIB algorithm treats all features evenly and sets weights of all features equally. To address the issue, the paper proposes a feature weight self-adjustment mechanism for the CD-sIB algorithm. A weight-adjusting procedure is applied in the pre-processing stage. In the procedure, the weights of features are adjusted iteratively. The purpose of the feature self-adjusting mechanism is to simultaneously minimize the separations within clusters and maximize the separations between clusters. So that it can improve the quality of the clustering result. Experiments on the Non co-occurrence datasets show that the proposed algorithm based on the feature self-adjusting mechanism is superior to the CD-sIB algorithm.
Computational detection of transcriptional regulators of protein complexes in apoptosis

Apoptosis is a type of cell death mediated by different signaling pathways involving protein-protein interactions that eventually activate caspases, a family of proteases capable of degrading cellular proteins. In this study we identify genes that belong to 16 protein families known to be involved in apoptosis in 5 vertebrate genomes: human, mouse, rat, Danio zebrafish, and Fugu pufferfish. It is shown that most apoptotic pathways are conserved in these vertebrate genomes, whereas key genes of the Fasmediated extrinsic pathway have not yet been identified in zebrafish and pufferfish genomes. Sequence alignment indicates that the upstream regions are less conserved than the corresponding transcript sequences and the sequence identity further declines after masking out the repetitive elements in the upstream sequences. These data are critical for phylogenetic footprinting studies of apoptosis genes in vertebrate genomes. Based on 366 known protein-protein interactions covering 168 (-72%) human apoptosis genes, we assemble a protein interaction network. To facilitate human visualization and potentially help biologists in apoptosis research, a two-layer protein interaction network is built for each human apoptosis gene. Several known apoptotic complexes, such as apoptosome, DISC, inflammasome and TNFRI complex, are all visualized in the two-layer interaction networks. We hypothesize that these two-layer protein interaction networks may help infer other multi-protein complexes in apoptosis. Furthermore, we computationally identify putative transcription factor (TF) binding sites upstream of apoptosis genes, and use protein-protein interactions in conjunction with phylogenetic footprinting information for prediction filtering. Our results suggest that protein-protein interaction data could complement sequence conservation to reduce
Fast Algorithms for Finding O(Congestion + Dilation) Packet Routing Schedules

O(c+d) steps using constant-size queues, where c is the congestion of the paths in the network, and d is the length of the longest path. The proof, however, used the Lovász Local Lemma and was not constructive. In this paper, we show how to find such a schedule in time, with probability , for any positive constant β, where is the sum of the lengths of the paths taken by the packets in the network, and m is the number of edges used by some packet in the network. We also show how to parallelize the algorithm so that it runs in NC. The method that we use to construct the schedules is based on the algorithmic form of the Lovász Local Lemma discovered by Beck.
Antiproliferative effects of isoflavones on human cancer cell lines established from the gastrointestinal tract.

Seven isoflavones, biochanin A, daidzein, genistein, genistin, prunectin, puerarin, and pseudobaptigenin were tested for cytostatic and cytotoxic effects on 10 newly established cancer cell lines of the human gastrointestinal origin. Proliferation of HSC-41E6, HSC-45M2, and SH101-P4 stomach cancer cell lines was strongly inhibited by biochanin A and genistein, whereas other stomach, esophageal, and colon cancer lines were moderately suppressed by both compounds. Biochanin A and genistein were cytostatic at low concentrations (< 20 micrograms/ml for biochanin A, < 10 micrograms/ml for genistein) and were cytotoxic at higher concentrations (> 40 micrograms/ml for biochanin A, > 20 micrograms/ml for genistein). DNA fragmentation was observed at cytotoxic doses of both compounds, indicating the apoptotic mode of cell death by the compounds. Chromatin condensation and nuclear fragmentation of each cell line were also observed. The advent of apoptosis was dose dependent for both isoflavones. Biochanin A suppressed tumor growth of HSC-45M2 and HSC-41E6 lines in athymic nude mice. Our results suggest that two of isoflavone derivatives, biochanin A and genistein, inhibit the cell growth of stomach cancer cell lines in vitro through activation of a signal transduction pathway for apoptosis. Moreover, in vivo experiments demonstrate that biochanin A can be used as an anticancer agent.
PINCH-1 promotes Bcl-2-dependent survival signalling and inhibits JNK-mediated apoptosis in the primitive endoderm

Summary The focal adhesion (FA) protein PINCH-1 is required for the survival of primitive endoderm (PrE) cells. How PINCH-1 regulates this fundamental process is not known. Here, we use embryoid bodies (EBs) and isolated EB-derived PrE cells to investigate the mechanisms by which PINCH-1 promotes PrE survival. We report that loss of PINCH-1 in PrE cells leads to a sustained activity of JNK and the pro-apoptotic factor Bax. Mechanistically, the sustained JNK activation was due to diminished levels of the JNK inhibitory factor Ras suppressor protein-1 (RSU-1), whose stability was severely reduced upon loss of PINCH-1. Chemical inhibition of JNK attenuated apoptosis of PrE cells but failed to reduce Bax activity. The increased Bax activity was associated with reduced integrin signalling and diminished Bcl-2 levels, which were shown to inhibit Bax. Altogether our findings show that PINCH-1 is a pro-survival factor that prevents apoptosis of PrE cells by modulating two independent signalling pathways; PINCH-1 inhibits JNK-mediated apoptosis by stabilising the PINCH-1 binding protein RSU-1 and promotes Bcl-2-dependent pro-survival signalling downstream of integrins.
Genetic Evidence That Chain Length and Branch Point Distributions Are Linked Determinants of Starch Granule Formation in Arabidopsis1[W][OPEN]

Glucose polymers with both the right branching pattern and the right chain length distribution are required to produce semicrystalline starch granules. The major component of starch is the branched glucan amylopectin. Structural features of amylopectin, such as the branching pattern and the chain length distribution, are thought to be key factors that enable it to form semicrystalline starch granules. We varied both structural parameters by creating Arabidopsis (Arabidopsis thaliana) mutants lacking combinations of starch synthases (SSs) SS1, SS2, and SS3 (to vary chain lengths) and the debranching enzyme ISOAMYLASE1-ISOAMYLASE2 (ISA; to alter branching pattern). The isa mutant accumulates primarily phytoglycogen in leaf mesophyll cells, with only small amounts of starch in other cell types (epidermis and bundle sheath cells). This balance can be significantly shifted by mutating different SSs. Mutation of SS1 promoted starch synthesis, restoring granules in mesophyll cell plastids. Mutation of SS2 decreased starch synthesis, abolishing granules in epidermal and bundle sheath cells. Thus, the types of SSs present affect the crystallinity and thus the solubility of the glucans made, compensating for or compounding the effects of an aberrant branching pattern. Interestingly, ss2 mutant plants contained small amounts of phytoglycogen in addition to aberrant starch. Likewise, ss2ss3 plants contained phytoglycogen, but were almost devoid of glucan despite retaining other SS isoforms. Surprisingly, glucan production was restored in the ss2ss3isa triple mutants, indicating that SS activity in ss2ss3 per se is not limiting but that the isoamylase suppresses glucan accumulation. We conclude that loss of only SSs can cause phytoglycogen production. This is readily degraded by isoamylase and other enzymes so it does not accumulate and was previously unnoticed.
Analysis of Human Proteome Organization Plasma Proteome Project (HUPO PPP) reference specimens using surface enhanced laser desorption/ionization‐time of flight (SELDI‐TOF) mass spectrometry: Multi‐institution correlation of spectra and identification of biomarkers

We report on a multicenter analysis of HUPO reference specimens using SELDI‐TOF MS. Eight sites submitted data obtained from serum and plasma reference specimen analysis. Spectra from five sites passed preliminary quality assurance tests and were subjected to further analysis. Intralaboratory CVs varied from 15 to 43%. A correlation coefficient matrix generated using data from these five sites demonstrated high level of correlation, with values >0.7 on 37 of 42 spectra. More than 50 peaks were differentially present among the various sample types, as observed on three chip surfaces. Additionally, peaks at ∼9200 and ∼15 950 m/z were present only in select reference specimens. Chromatographic fractionation using anion‐exchange, membrane cutoff, and reverse phase chromatography, was employed for protein purification of the ∼9200 m/z peak. It was identified as the haptoglobin alpha subunit after peptide mass fingerprinting and high‐resolution MS/MS analysis. The differential expression of this protein was confirmed by Western blot analysis. These pilot studies demonstrate the potential of the SELDI platform for reproducible and consistent analysis of serum/plasma across multiple sites and also for targeted biomarker discovery and protein identification. This approach could be exploited for population‐based studies in all phases of the HUPO PPP.
Coordination of gaze shifts in primates: Brainstem inputs to neck and extraocular motoneuron pools

To, determine whether there are brainstem regions that provide common input to the motoneurons that move both the head and the eyes, we injected wheat germ agglutinin‐horseradish peroxidase complex (WGA‐HRP) into neck motoneuron pools at spinal level C2 (N = 3) and extraocular motoneuron pools in the abducens (N = 1) and oculomotor/trochlear (N = 1) nuclei of rhesus and fascicularis macaques. We also injected WGA‐HRP into spinal level C5‐7 (N = 1) of a fascicularis macaque for comparison.
State of Academic Knowledge on Toxicity and Biological Fate of Quantum Dots

Quantum dots (QDs), an important class of emerging nanomaterial, are widely anticipated to find application in many consumer and clinical products in the near future. Premarket regulatory scrutiny is, thus, an issue gaining considerable attention. Previous review papers have focused primarily on the toxicity of QDs. From the point of view of product regulation, however, parameters that determine exposure (e.g., dosage, transformation, transportation, and persistence) are just as important as inherent toxicity. We have structured our review paper according to regulatory risk assessment practices, in order to improve the utility of existing knowledge in a regulatory context. Herein, we summarize the state of academic knowledge on QDs pertaining not only to toxicity, but also their physicochemical properties, and their biological and environmental fate. We conclude this review with recommendations on how to tailor future research efforts to address the specific needs of regulators.
A Dynamic Provisioning Framework for Multi-tier Internet Applications in Virtualized Data Center

With the resurgence of virtualization technology, todaypsilas Internet data centers are shifting towards virtualized data centers. Internet applications tend to see dynamically varying workloads. To address the problem of performance management for multi-tier applications hosted in virtualized Internet data center, we propose a three-level automatic provisioning framework based on feedback control for multi-tier applications. Experiments demonstrate the effectiveness of our technique in SLA guarantees while obtaining improved resource utilization.
Nipped-A regulates intestinal stem cell proliferation in Drosophila

Adult stem cells uphold a delicate balance between quiescent and active states, a deregulation of which can lead to age-associated diseases such as cancer. In Drosophila, intestinal stem cell (ISC) proliferation is tightly regulated and mis-regulation is detrimental to intestinal homeostasis. Various factors are known to govern ISC behavior; however, transcriptional changes in ISCs during aging are still unclear. RNA sequencing of young and old ISCs newly identified Nipped-A, a subunit of histone acetyltransferase complexes, as a regulator of ISC proliferation that is upregulated in old ISCs. We show that Nipped-A is required for maintaining the proliferative capacity of ISCs during aging and in response to tissue-damaging or tumorigenic stimuli. Interestingly, Drosophila Myc cannot compensate for the effect of the loss of Nipped-A on ISC proliferation. Nipped-A seems to be a superordinate regulator of ISC proliferation, possibly by coordinating different processes including modifying the chromatin landscape of ISCs and progenitors. Summary: Balanced expression of Nipped-A prevents hyperproliferation of intestinal stem cells in aged Drosophila midguts, identifying Nipped-A as a novel regulator of stem cell proliferation.
On Embedding Uncertain Graphs

Graph data are prevalent in communication networks, social media, and biological networks. These data, which are often noisy or inexact, can be represented by uncertain graphs, whose edges are associated with probabilities to indicate the chances that they exist. Recently, researchers have studied various algorithms (e.g., clustering, classification, and k-NN) for uncertain graphs. These solutions face two problems: (1) high dimensionality: uncertain graphs are often highly complex, which can affect the mining quality; and (2) low reusability, where an existing mining algorithm has to be redesigned to deal with uncertain graphs. To tackle these problems, we propose a solution called URGE, or UnceRtain Graph Embedding. Given an uncertain graph G, URGE generates G's embedding, or a set of low-dimensional vectors, which carry the proximity information of nodes in G. This embedding enables the dimensionality of G to be reduced, without destroying node proximity information. Due to its simplicity, existing mining solutions can be used on the embedding. We investigate two low- and high-order node proximity measures in the embedding generation process, and develop novel algorithms to enable fast evaluation. To our best knowledge, there is no prior study on the use of embedding for uncertain graphs. We have further performed extensive experiments for clustering, classification, and k-NN on several uncertain graph datasets. Our results show that URGE attains better effectiveness than current uncertain data mining algorithms, as well as state-of-the-art embedding solutions. The embedding and mining performance is also highly efficient in our experiments.
Threshold-Voltage Reduction of FinFETs by Ta/Mo Interdiffusion Dual Metal-Gate Technology for Low-Operating-Power Application

In this paper, Ta/Mo interdiffusion dual metal-gate technology, which has an advantage in realizing dual gate work functions without etching of metals from the gate dielectrics, has been introduced for a FinFET. Gate-first fabrication of the FinFET was successfully implemented by optimizing the deposition and patterning of the Mo and Ta/Mo metal gates on the ultra- thin fin channels. The Ta/Mo-gated n-MOS and Mo-gated p-MOS FinFET exhibit symmetrical values of Vth (0.31/-0.36 V), which are desirable for FinFET CMOS circuit operation with enhanced current drivability, because the threshold voltage (Vth) is reduced due to Ta diffusion in the Ta/Mo gate. It was experimentally found that the Ta/Mo interdiffusion process causes no degradation in integrity of the gate dielectric or the carrier mobility. It was also confirmed that the Ta/Mo interdiffusion process is appropriate for a scaled gate length down to 100 nm.