Miracle-dz/UniFAR-FTUs huggingface dataset:
Modulation of Homology-Directed Repair in T98G Glioblastoma Cells Due to Interactions between Wildtype p53, Rad51 and HCMV IE1-72

Human cytomegalovirus (HCMV) is a ubiquitous pathogen capable of causing life threatening consequences in neonates and immune-compromised individuals. HCMV inflicts site-specific double strand breaks (DSBs) in the cellular genome. DNA damage infliction raises the corollary question of virus modulation of DNA repair. We recently reported HDR was stimulated in wt human foreskin fibroblasts (HFFs) during fully permissive infection or expression of the HCMV protein IE1-72 (IE72). These studies have been extended into semi-permissive T98G glioblastoma cells. T98Gs encode a mutant p53, which may contribute to their high baseline rate of HDR. We fully expected HCMV infection to increase HDR in T98Gs, similar to its effects in HFFs. Surprisingly in T98Gs HCMV infection, or sole expression of IE72, decreased HDR by two-fold. Transient expression of wt p53 in T98Gs also reduced HDR by two-fold. Dual transient expression of wt p53 and IE72 restored high baseline HDR levels. GST pulldown experiments revealed that both IE72 and wt p53 bound the important HDR protein, Rad51. We conclude that the expression of certain HCMV proteins can modulate HDR in an infected cell, dependent upon p53 status. We propose a model of the protein interactions explaining this behavior.
Distance-Integrated Combinatorial Testing

This paper proposes a novel approach to combinatorial test generation, which achieves an increase of not only the number of new combinations but also the distance between test cases. We applied our distance-integrated approach to a state-of-the-art greedy algorithm for traditional combinatorial test generation by using two distance metrics, Hamming distance, and a modified chi-square distance. Experimental results using numerous benchmark models show that combinatorial test suites generated by our approach using both distance metrics can improve interaction coverage for higher interaction strengths with low computational overhead.
Attention-Based Deep Distance Metric Learning for Aspect-Phrase Grouping

Aspect-phrase grouping is an important task for aspect finding in aspect-level sentiment analysis and it is a challenging problem due to polysemy and its context dependency. In this paper we propose an Attention-based Deep Distance Metric Learning (ADDML)method, which is more beneficial for clustering by considering aspect-phrase representation as well as context representation and their combination. Firstly, we feed word embeddings of aspect-phrases and its contexts into an attentionbased network to learn feature representation of contexts. Then, both of aspect-phrase embedding and context embedding as the input of a multilayer perceptron which is used to learn deep feature subspace, under which the distance of each intra-grouped pair is smaller and that of each intergrouped pair is bigger, respectively. After obtaining the learned representations, we use K-means to cluster them. Our extensive experimental study on four domain review datasets shows that the proposed method outperforms baseline methods.
Modeling developmental transitions in reasoning about false beliefs of others.

Reasoning about false beliefs of others develops with age. We present here an ACT-R model in order to show the developmental transitions. These start from a child’s reasoning from his/her own point of view (zero-order) to taking into consideration another agent’s beliefs (first-order), and later to taking into consideration another agent’s beliefs about again other agents’ beliefs (second-order). The model is based on a combination of rule-based and simulation approaches. We modeled the gradual development of reasoning about false beliefs of others by using activation of declarative knowledge instead of utility learning. Initially, in addition to the story facts, there is only one strategy chunk, namely a zero-order reasoning chunk, in declarative memory. The model retrieves this chunk each time it has to solve a problem. Based on the feedback, the model will strengthen a successful strategy chunk, or it will add or strengthen an alternative strategy if the current one failed.
Geographic Variations and Genetic Distance of Three Geographic Cyclina Clam (Cyclina sinensis Gmelin) Populations from the Yellow Sea

The gDNA isolated from Cyclina sinensis from Gochang (GOCHANG), Incheon (INCHEON) and a Chinese site (CHINESE), were amplified by PCR. Here, the seven oligonucleotide decamer primers (BION-66, BION-68, BION-72, BION-73, BION-74, BION-76, and BION-80) were used to generate the unique shared loci to each population and shared loci by the three cyclina clam populations. As regards multiple comparisons of average bandsharing value results, cyclina clam population from Chinese (0.763) exhibited higher bandsharing values than did clam from Incheon (0.681). In this study, the dendrogram obtained by the seven decamer primers indicates three genetic clusters: cluster 1 (GOCHANG 01~ GOCHANG 07), cluster 2 (INCHEON 08~INCHEON 14), cluster 3 (CHINESE 15~CHINESE 21). The shortest genetic distance that displayed significant molecular differences was between individuals 15 and 17 from the Chinese cyclina clam (0.049), while the longest genetic distance among the twenty-one cyclina clams that displayed significant molecular differences was between individuals GOCHANG no. 03 and INCHEON no. 12 (0.575). Individuals of Incheon cyclina clam population was somewhat closely related to that of Chinese cyclina clam population. In conclusion, our PCR analysis revealed a significant genetic distance among the three cyclina clam populations.
Which Model Better Fits the Role of Aire in the Establishment of Self-Tolerance: The Transcription Model or the Maturation Model?

The discovery of Aire-dependent transcriptional control of many tissue-restricted self-antigen (TRA) genes in thymic epithelial cells in the medulla (medullary thymic epithelial cells, mTECs) has raised the intriguing question of how the single Aire gene can influence the transcription of such a large number of TRA genes within mTECs. From a mechanistic viewpoint, there are two possible models to explain the function of Aire in this action. In the first model, TRAs are considered to be the direct target genes of Aire’s transcriptional activity. In this scenario, the lack of Aire protein within cells would result in the defective TRA gene expression, while the maturation program of mTECs would be unaffected in principle. The second model hypothesizes that Aire is necessary for the maturation program of mTECs. In this case, we assume that the mTEC compartment does not mature normally in the absence of Aire. If acquisition of the properties of TRA gene expression depends on the maturation status of mTECs, a defect of such an Aire-dependent maturation program in Aire-deficient mTECs can also result in impaired TRA gene expression. In this brief review, we will focus on these two contrasting models for the roles of Aire in controlling the expression of TRAs within mTECs.
Link and Location Based Routing Mechanism for Energy Efficiency in Wireless Sensor Networks

In Wireless Sensor Networks, sensed data are reported to the sink by the available nodes in the communication range. The sensed data should be reported to the sink with the frequency expected by the sink. In order to have a communication between source and sink, Link based routing is used. Link based routing aims to achieve an energy efficient and reliable routing path. This mechanism considers the status (current energy level in terms of Joules) of each node, link condition (number of transmissions that the Cluster Head (CH)and the Gateway (GW) candidates conducts) and the transmit power (power required for transmission in terms of Joules). A metric called Predicted Transmission Count (PTX) for each node is calculated using its status, link condition and transmit power. The node which has highest PTX will have the highest priority and it will be the potential candidate to act as CH or GW. Thus the selection of proper CH or GW reduces the energy consumption, and the network lifetime is increased.
Towards software analysis as a service

Throughout the years software engineers have come up with a myriad of specialized tools and techniques that focus on a certain type of analysis, such as metrics extraction, evolution tracking, co-change detection, bug prediction, all the way up to social network analysis of team dynamics. However, easy and straight forward synergies between these analyses/tools rarely exist because of their stand-alone nature, their platform dependence, their different input and output formats and the variety of systems to analyze. This significantly hampers their usage and reduces their acceptance by other researchers and software companies. To overcome this problem we propose a distributed and collaborative software analysis platform to enable a seamless interoperability of software analysis tools across platform, geographical and organizational boundaries. In particular, we devise software analysis tools as services that can be accessed and composed over the Internet. These distributed services shall be widely accessible through a software analysis broker where organizations and research groups can register and share their tools. To enable (semi)-automatic use and composition of these tools, they are classified and mapped into a software analysis taxonomy and adhere to specific meta-models and ontologies for their category of analysis.
High frequency of vitamin B12 deficiency in a Brazilian population

Abstract Objective There are few studies regarding vitamin B12 deficiency in developing countries. In Brazil, a late diagnosis of vitamin B12 deficiency progressing to severe neurological damage is common. Thus, the aim of the present study was to verify the frequency of vitamin B12 deficiency in two Brazilian populations (elderly and adult participants) and to compare different methods of vitamin B12 deficiency detection. Design Five hundred participants were recruited from health centres from south-east Brazil and were separated into two groups: 60 years old or more and 30–59 years old. Vitamin B12 and folate concentrations were measured using electrochemiluminescence immunoassay (ECI) and RIA. Methylmalonic acid (MMA) was measured by LC coupled to tandem MS. Full blood counts were acquired using standard methods. Results All participants had normal blood count results and mean cell volume less than 99 fl; none of them presented folate deficiency according to the results, which were all greater than 3 ng/ml. Cobalamin levels less than 200 pmol/l were identified by one of the two or by both methods in 7·2 % of the participants aged 60 years or more and 6·4 % of the participants aged 30–59 years. MMA levels were higher in older subjects (P = 0·007) compared with younger subjects. A greater correlation of MMA v. RIA was observed than of MMA v. ECI (P = 0·0017 v. P = 0·014). MMA quantification estimated that cobalamin deficiency was present in more than 11 % of the subjects for both studied groups. Conclusions The study shows that vitamin B12 deficiency is frequent in Brazilian adults and suggests that RIA is more sensitive than ECl for measuring cobalamin levels.
Image match using wavelet — Colour SIFT features

This paper presents a new technique for robust Image matching based on the combination of wavelet transform and Colour-SIFT (Scale Invariant Feature Transform). Low frequency and High frequency sub-bands of the image are extracted using wavelet transform and then colour SIFT method is used to extract colour feature descriptors. A wavelet basis having maximum statistical correlation with an image is chosen from a library of wavelets. A novel matching technique is used to validate true matches by establishing relationships between candidate matching features. The proposed method is tested on many image pairs with viewpoint changes, illumination changes and color information. Performance of this method is compared with Hue-SIFT and basic SIFT methods.
Design of monitor system for grain depots based on wireless sensor network

The safety of grain storage is a significant thing that concerns people's living quality and national economic development. It is exceedingly important for manager to timely master the grain storage condition. Improving the automation level of monitor system is the key to assure the safety of grain storage. A novel scheme of monitor system designed for grain depots is proposed based on wireless sensor network (WSN). This scheme utilizes sensor nodes deployed in barns, which compose an autonomous network, to collect environmental data of grain storage and then transmit them to remote control center by means of wireless and multi-hop communication. Due to using small, low cost sensor nodes and wireless communication, several problems in traditional monitor system are solved. These problems include large cable coverage, more opportunities of interference and lighting strike, high maintenance cost and so on. Consequently, the WSN-based system has good reliability, maintainability and cost effectiveness.
The Self-Reflective Functions of Inner Speech

The current chapter revisits an earlier account (2005) of how inner speech leads to self-reflection. Definitions, functions, neuroanatomy, and measurement of self-reflection and inner speech are first presented, followed by the detailed proposal suggesting that these two processes are connected in at least three possible ways. Empirical evidence supporting this proposal is discussed, as well as theoretical considerations pertaining to underlying mechanisms explaining how self-reflection and inner speech may interrelate. To illustrate, several self-referential tasks used in typical fMRI studies show a reliable activation of the left inferior frontal gyrus—the main brain area known to sustain inner speech; inner speech can reproduce (i.e. internalize) already existing social mechanisms leading to self-reflection. Some possible philosophical and clinical implications of the role played by inner speech in self-reflection are outlined in conclusion.
Prioritized Multi-layer Transmission for MIMO-OFDM Multiuser Broadcast Channel

In this paper, three different users, with three different qualities of service (QoSs) are allowed to share the same frequency using different space and modulation layers. A multiple-input multiple-output (MIMO) antenna transceiver combined with orthogonal frequency division multiplexing (OFDM) is implemented to allow spacefrequency multiple access. Moreover, the users’ symbols are allowed to share the same frequency via embedding their constellations in a hierarchical fashion (with nonhomogeneous constellation sizes). This ensures arbitrary QoS granularities and guarantees the same information transmission for each user. The latter characteristic can be exploited further to limit the multiuser interference (MUI) in conjunction with an optimized preand postfilter design. Simulation results show a fixed separation at different channel state information (CSI) accuracies.
Overview of orbital debris detection using spaceborne radar

Orbital debris in low-earth-orbit poses an increasing threat to humanpsilas space action. Spaceborne radar detection technique is a powerful complementarity for ground based radars or optical telescopes. The necessity of orbital debris detection using spaceborne radar is discussed; the design of spaceborne radar system is deeply studied on many aspects including operation frequency band, antenna type, observation mode, signal type, and location mode. Moreover, the space-based real-time radar signal processing technique for debris detection is analyzed in detail.
A Particular Bug Trap: Execution Replay Using Virtual Machines

Execution-replay (ER) is well known in the literature but has been restricted to special system architectures for many years. Improved hardware resources and the maturity of virtual machine technology promise to make ER useful for a broader range of development projects. This paper describes an approach to create a practical, generic ER infrastructure for desktop PC systems using virtual machine technology. In the created VM environment arbitrary application programs will run and be replayed unmodified, neither instrumentation nor recompilation are required.
Latent autoimmune diabetes of the adult: current knowledge and uncertainty

Patients with adult‐onset autoimmune diabetes have less Human Leucocyte Antigen (HLA)‐associated genetic risk and fewer diabetes‐associated autoantibodies compared with patients with childhood‐onset Type 1 diabetes. Metabolic changes at diagnosis reflect a broad clinical phenotype ranging from diabetic ketoacidosis to mild non‐insulin‐requiring diabetes, also known as latent autoimmune diabetes of the adult (LADA). This latter phenotype is the most prevalent form of adult‐onset autoimmune diabetes and probably the most prevalent form of autoimmune diabetes in general. Although LADA is associated with the same genetic and immunological features as childhood‐onset Type 1 diabetes, it also shares some genetic features with Type 2 diabetes, which raises the question of genetic heterogeneity predisposing to this form of the disease. The potential value of screening patients with adult‐onset diabetes for diabetes‐associated autoantibodies to identify those with LADA is emphasized by their lack of clinically distinct features, their different natural history compared with Type 2 diabetes and their potential need for a dedicated management strategy. The fact that, in some studies, patients with LADA show worse glucose control than patients with Type 2 diabetes, highlights the need for further therapeutic studies. Challenges regarding classification, epidemiology, genetics, metabolism, immunology, clinical presentation and treatment of LADA were discussed at a 2014 workshop arranged by the Danish Diabetes Academy. The presentations and discussions are summarized in this review, which sets out the current ideas and controversies surrounding this form of diabetes.
Genotyping‐by‐sequencing approaches to characterize crop genomes: choosing the right tool for the right application

Summary In the last decade, the revolution in sequencing technologies has deeply impacted crop genotyping practice. New methods allowing rapid, high‐throughput genotyping of entire crop populations have proliferated and opened the door to wider use of molecular tools in plant breeding. These new genotyping‐by‐sequencing (GBS) methods include over a dozen reduced‐representation sequencing (RRS) approaches and at least four whole‐genome resequencing (WGR) approaches. The diversity of methods available, each often producing different types of data at different cost, can make selection of the best‐suited method seem a daunting task. We review the most common genotyping methods used today and compare their suitability for linkage mapping, genomewide association studies (GWAS), marker‐assisted and genomic selection and genome assembly and improvement in crops with various genome sizes and complexity. Furthermore, we give an outline of bioinformatics tools for analysis of genotyping data. WGR is well suited to genotyping biparental cross populations with complex, small‐ to moderate‐sized genomes and provides the lowest cost per marker data point. RRS approaches differ in their suitability for various tasks, but demonstrate similar costs per marker data point. These approaches are generally better suited for de novo applications and more cost‐effective when genotyping populations with large genomes or high heterozygosity. We expect that although RRS approaches will remain the most cost‐effective for some time, WGR will become more widespread for crop genotyping as sequencing costs continue to decrease.
Vertebral Deformities and Functional Impairment in Men and Women

The objective of this study was to assess the prevalence and health effects of vertebral deformities in men and women. The study was carried out as part of the cross‐sectional baseline phase of The Rotterdam Study, a prospective population‐based cohort study of residents aged 55 years or over of a district of Rotterdam, The Netherlands. The prevalence of vertebral deformities according to a modification of the Eastell method and concomitant functional impairment were assessed in a random sample of 750 men and 750 women. The prevalence of moderate (grade I) vertebral deformities was 8 and 7% in men and women, respectively. For severe deformities (grade II), these percentages were 4 and 8%. In men, the prevalence of both moderate and severe deformities increased with age. In women, however, the prevalence of moderate vertebral deformities remained constant, opposite to a marked increase in severe deformities. Moderate vertebral deformity was significantly associated with impaired rising in men only. Severe vertebral deformity was associated with a significantly increased risk of general disability and the use of a walking aid in both men and women, impaired bending in men, and impaired rising in women. It is concluded that (1) vertebral deformities are only slightly less common in men than in women from the general population and (2) severe progression with age occurs in women only and (3) severe vertebral deformity is, particularly in men, related to functional impairment.
NEO PI-R Predictors of Alcohol Use and Alcohol-Related Problems

We investigated the relationships between Five-factor model domains and facets and drinking and alcohol-related problems. We also examined the moderating effects of gender. Two hundred students (99 men and 101 women) who had used alcohol in the past year completed self-report and interview assessments. Bivariate analyses demonstrated some significant relationships. In the multivariate analyses that controlled for gender, Neuroticism and Conscientiousness were linked to drinking, but only some of the facets from these domains had significant relationships to drinking. Facets of Extraversion and Agreeableness, but not these domains, were associated with drinking. Neuroticism and Conscientiousness and most of their facets were related to alcohol-related problems in the multivariate analyses. The interactions between gender and traits were not significant.
Transform domain Wyner-Ziv video coding with refinement of noise residue and side information

Distributed Video Coding (DVC) is a video coding paradigm which mainly exploits the source statistics at the decoder based on the availability of side information at the decoder. This paper considers feedback channel based Transform Domain Wyner-Ziv (TDWZ) DVC. The coding efficiency of TDWZ video coding does not match that of conventional video coding yet, mainly due to the quality of side information and inaccurate noise estimation. In this context, a novel TDWZ video decoder with noise residue refinement (NRR) and side information refinement (SIR) is proposed. The proposed refinement schemes are successively updating the estimated noise residue for noise modeling and side information frame quality during decoding. Experimental results show that the proposed decoder can improve the Rate- Distortion (RD) performance of a state-of-the-art Wyner-Ziv video codec for the set of test sequences.
Two-photon gateway in one-atom cavity quantum electrodynamics

Atoms absorb and emit resonant light photon by photon. However, an atom strongly coupled to the light field of a high-finesse optical resonator forms a new system with new characteristics, enabling the emission and absorption of photon pairs. The energy eigenstates of the coupled system form an anharmonic ladder of doublets, the so-called Jaynes-Cummings ladder. The first doublet, consisting of the two so-called normal modes, has been observed in various cavity QED systems. It can be explained classically using Maxwell equations as arising from the coupling of a classical dipole to a classical electromagnetic field. In contrast, the higher-order doublet has so far no classical analogue. It requires both the quantization of the atomic internal state as well as the quantization of light.