Miracle-dz/UniFAR-FTUs huggingface dataset:
A Reversible Histone H3 Acetylation Cooperates with Mismatch Repair and Replicative Polymerases in Maintaining Genome Stability

Mutations are a major driving force of evolution and genetic disease. In eukaryotes, mutations are produced in the chromatin environment, but the impact of chromatin on mutagenesis is poorly understood. Previous studies have determined that in yeast Saccharomyces cerevisiae, Rtt109-dependent acetylation of histone H3 on K56 is an abundant modification that is introduced in chromatin in S phase and removed by Hst3 and Hst4 in G2/M. We show here that the chromatin deacetylation on histone H3 K56 by Hst3 and Hst4 is required for the suppression of spontaneous gross chromosomal rearrangements, base substitutions, 1-bp insertions/deletions, and complex mutations. The rate of base substitutions in hst3Δ hst4Δ is similar to that in isogenic mismatch repair-deficient msh2Δ mutant. We also provide evidence that H3 K56 acetylation by Rtt109 is important for safeguarding DNA from small insertions/deletions and complex mutations. Furthermore, we reveal that both the deacetylation and acetylation on histone H3 K56 are involved in mutation avoidance mechanisms that cooperate with mismatch repair and the proofreading activities of replicative DNA polymerases in suppressing spontaneous mutagenesis. Our results suggest that cyclic acetylation and deacetylation of chromatin contribute to replication fidelity and play important roles in the protection of nuclear DNA from diverse spontaneous mutations.
A Fast and Efficient Entity Resolution Approach for Preserving Privacy in Mobile Data

With the advent of mobile networking and the widespread adoption of smartphone devices, a number of location-based services have emerged, where users actively participate by sharing and receiving mobility data. However, the collection and analysis of user mobility data, such as user location information and trajectory data, especially when exploited together with external sources, such as social networks that often provide rich and publicly available information, can reveal sensitive user information. This paper proposes an approach based on entity resolution which enables users to disclose their mobility information without compromising their privacy, even if these data are linked with external publicly available information. We present detailed experimental results using four real datasets to illustrate that our approach is practical, efficient and effectively preserves privacy by eliminating potential links among the data.
Modulation of Retinoid Signaling by a Cytoplasmic Viral Protein via Sequestration of Sp110b, a Potent Transcriptional Corepressor of Retinoic Acid Receptor, from the Nucleus

ABSTRACT Hepatitis C virus (HCV) core protein (core) plays a significant role in the development of chronic liver diseases caused by HCV infection. We have discovered that the core sensitized all-trans-retinoic acid (ATRA)-induced cell death in MCF-7 cells. Activation of retinoic acid receptor alpha (RARα)-mediated transcription by the core was also seen in all the cell lines tested. By use of a yeast two-hybrid system, we identified Sp110b as a candidate for a core-interacting cellular factor. Although the function of Sp110b has remained unknown, we observed that Sp110b interacts with RARα and suppresses RARα-mediated transcription. These data suggest that Sp110b is a transcriptional cofactor negatively regulating RARα-mediated transcription. RNA interference-mediated reduction of endogenous Sp110b levels depressed the ability of the core to activate RARα-mediated transcription, suggesting an essential role for Sp110b in this pathway. The normal nuclear subcellular localization of Sp110b was altered by molecular interaction with the core to the cytoplasmic surface of the endoplasmic reticulum. This evidence suggests a model in which the core sequesters Sp110b from the nucleus and inactivates its corepressor function to activate RARα-mediated transcription. These findings likely describe a novel system in which a cytoplasmic viral protein regulates host cell transcription.
Change in Bone Turnover and Hip, Non‐Spine, and Vertebral Fracture in Alendronate‐Treated Women: The Fracture Intervention Trial

We used data from the Fracture Intervention Trial to assess the relationship change in bone turnover after 1 year of alendronate or placebo treatment and subsequent hip, non‐spine, and spine fracture risk among 6186 postmenopausal women. In the alendronate group (n = 3105), greater reductions in one or more biochemical marker were associated with a lower risk of fracture.
Effects of different facets of paternal and maternal control behaviour on early adolescents' perceived academic competence

The purpose of this study was to examine how different aspects of paternal and maternal control behaviours influence the perceived academic competence of early adolescents indirectly via their engagement with school. The analyses are based on a longitudinal study with two waves that were separated by 12 months. The participants were 228 early adolescents (50.4% girls) with an average age of 11.62 years (SD = .41) at the outset. Structural equation modeling analyses using bootstrapping procedures revealed that parental supervision was indirectly related to the perceived academic competence of adolescents via their engagement with schools, whereas parental authoritarian control was only linked to engagement with school. The discussion focuses on the multifaceted nature of parental control and the importance of both parents for the academic success of adolescents.
The effect of incomplete information on the compromise effect

Most research on the compromise effect focuses on how consumers make their decisions in a complete information scenario; however, consumers generally lack sufficient information when they make purchase decisions. This research aims to explore the compromise effect with incomplete information. Three studies were conducted to examine the research hypotheses. The main findings was that consumers are more likely to choose the middle option when they have incomplete information than when they have complete information. Further, the compromise effect decreases when consumers can choose to defer their decision in an incomplete information scenario. Finally, the compromise effect decreases when consumers are asked to infer missing attribute values from the incomplete information.
Does a History of Alcohol Use Disorder Affect Response to Antidepressant Medication in Patients With Dysthymic Disorder?

ABSTRACT Background: Research on the relationship between depression and alcohol use disorder in remission has been scarce. The authors examined whether a lifetime history of alcohol use disorder affected response to antidepressant treatment of dysthymic disorder (DD) in adult outpatients. Methods: This is a secondary analysis of data from previous prospective medication trials. Data from 123 subjects with DD were included. Subjects were categorized into 2 groups: (1) no lifetime alcohol use disorder (NLAUD) (n = 99) and (2) lifetime alcohol use disorder (LAUD) (n = 24). None of the subjects met criteria for alcohol use disorder for 6 months prior to intake. Rating scales from baseline and after 8 weeks of pharmacotherapy were collected. Results: After 8 weeks of treatment, the NLAUD and LAUD groups did not differ in rates of response or remission, despite significantly higher baseline Hamilton Depression Rating Scale (HDRS)-24 scores in the LAUD group. We also found a greater decrease in symptoms in the LAUD group, as measured by the HDRS-24. Conclusions: Our preliminary findings suggest that DD in remitted alcoholics is at least as responsive to pharmacotherapy as DD in nonalcoholics and support adequate evaluation and treatment of DD in remitted alcoholic patients.
Application of random relaying of partitioned MDS codeword block to persistent relay CSMA over random error channels

We propose an incorporation of random relaying of MDS codeword blocks (RP-MDS), which has been proposed for multi-hop cooperative relay networks, to persistent relay CSMA (PRCSMA) over noisy channels. The proposed protocol elaborately employs the powerful error-correcting capability of MDS codes into cooperative communication systems and introduces the incremental redundancy concept to PRCSMA. A destination node can reinforce an error-correcting capability when it receives a new frame. The performance of the proposed protocol is compared to PRCSMA by means of computer simulation. Numerical results indicate that the proposed protocol can significantly reduce the duration of the cooperation phase and provide robust and stable performance against channel impairments.
Understanding mobile phone activities via retrospective review of visualizations of usage data

It can be very challenging to get an accurate understanding of mobile phone usage because of the difficulty of observing phone activity in a natural setting. We describe a retrospective methodology where participants review visualizations of their logged activity in an interview setting, and our lessons learned in applying this methodology in a study of user goals and journeys on mobile devices across apps.
No Such Effect? The Implications of Measurement Error in Self-Report Measures of Mobile Communication Use

Research on the social and psychological effects of mobile phone communication primarily is conducted using self-report measures of use. However, recent studies have suggested such measures of mobile phone communication use contain a significant amount of measurement error. This study compares the frequency of mobile phone use measured by self-report questions with error-free log data automatically collected through an Android smartphone application. Using data from 310 Android phone users in Japan, we investigate the extent to which nonrandom measurement error exists in self-report responses to questions about mobile phone use and predictors of this error. Our analysis shows that users generally overreport their frequency of mobile communication and that overestimation is better predicted by proxy measures of social activity than demographic variables. We further show an example of how overreporting can result in an overestimation of the effects of mediated communication on civic engagement. Finally, the value of behavioral log data in mediated communication research is discussed.
A 1-V 450-nW Fully Integrated Programmable Biomedical Sensor Interface Chip

This paper presents a fully integrated programmable biomedical sensor interface chip dedicated to the processing of various types of biomedical signals. The chip, optimized for high power efficiency, contains a low noise amplifier, a tunable bandpass filter, a programmable gain stage, and a successive approximation register analog-to-digital converter. A novel balanced tunable pseudo-resistor is proposed to achieve low signal distortion and high dynamic range under low voltage operations. A 53 nW, 30 kHz relaxation oscillator is included on-chip for low power consumption and full integration. The design was fabricated in a 0.35 mum standard CMOS process and tested at 1 V supply. The analog front-end has measured frequency response from 4.5 mHz to 292 Hz, programmable gains from 45.6 dB to 60 dB, input referred noise of 2.5 muVrms in the amplifier bandwidth, a noise efficiency factor (NEF) of 3.26, and a low distortion of less than 0.6% with full voltage swing at the ADC input. The system consumes 445 nA in the 31 Hz narrowband mode for heart rate detection and 895 nA in the 292 Hz wideband mode for ECG recording.
3D model retrieval using 2D cepstral descriptor of overlapping subbands

In this paper, a new 2D cepstral descriptor will be proposed for 3D model retrieval. In the proposed approach, the overlapping subband decomposition will be employed to divide each 2D spectrum into a number of overlapped subbands for further 2D cepstral descriptor extraction. Experiments conducted on the Princeton Shape Benchmark (PSB) database have shown that the proposed 2D cepstral descriptor yields better retrieval accuracy than traditional 2D cepstral descriptors and outperforms other state-of-the-art descriptors in terms of the discounted cumulative gain (DCG) score.
Mechanical testing of bones: the positive synergy of finite–element models and in vitro experiments

Bone biomechanics have been extensively investigated in the past both with in vitro experiments and numerical models. In most cases either approach is chosen, without exploiting synergies. Both experiments and numerical models suffer from limitations relative to their accuracy and their respective fields of application. In vitro experiments can improve numerical models by: (i) preliminarily identifying the most relevant failure scenarios; (ii) improving the model identification with experimentally measured material properties; (iii) improving the model identification with accurately measured actual boundary conditions; and (iv) providing quantitative validation based on mechanical properties (strain, displacements) directly measured from physical specimens being tested in parallel with the modelling activity. Likewise, numerical models can improve in vitro experiments by: (i) identifying the most relevant loading configurations among a number of motor tasks that cannot be replicated in vitro; (ii) identifying acceptable simplifications for the in vitro simulation; (iii) optimizing the use of transducers to minimize errors and provide measurements at the most relevant locations; and (iv) exploring a variety of different conditions (material properties, interface, etc.) that would require enormous experimental effort. By reporting an example of successful investigation of the femur, we show how a combination of numerical modelling and controlled experiments within the same research team can be designed to create a virtuous circle where models are used to improve experiments, experiments are used to improve models and their combination synergistically provides more detailed and more reliable results than can be achieved with either approach singularly.
Structured Learning from Data for Novelty Detection by Linear Programming

Novelty detection involves modeling the normal patterns for detecting any divergence from this behavior. Our recently proposed algorithm, Glabal&Local One Class Classifier (GLocal OCC), can solve this problem by maximizing the margin between the hyperplane and the origin through embedding the global information into the OCSVM framework. In this paper, we propose Linear Programming (LP) GLocal OCC (lpGLocal OCC) instead of the Quadratic Programming optimization to speed up GLocal OCC. By minimizing the average functional distance of the overall samples to the hyperplane, the lpGLocal OCC can attract the optimal hyperplane towards the centre of the data without using the origin anymore. Borrow off-the-shelf LP solver, this novel algorithm can be implemented easily and process solve large datasets rapidly. Results on benchmark datasets show that lpGLocal OCC not only has the comparable generalization power compared with the GLocal OCC besides its efficiency, but also has better generalization than (lp)OCSVM due to its structured learning approach.
Interference Mitigation Using Coordinated Backhaul Timing Allocation for LTE-Advanced Relay Systems

This paper proposes an inter-cell co-channel interference (CCI) mitigation method with the mixed deployment of evolved NodeBs (eNBs) and relay nodes (RNs) for Long Term Evolution (LTE)-Advanced systems studied in the 3rd Generation Partnership Project (3GPP). Supporting RNs for LTE-Advanced can increase coverage in areas without service, and also improve system capacity. Although RNs can improve system capacity by reusing identical frequency bands in macro and relay cells, this also causes additional CCI. To deal with this issue, we investigated three methods of mitigating CCI by differentiating the backhaul resource allocation timing among eNBs and RNs. Then, we evaluated these methods with a system level simulator. This confirmed improvement of both the received signal-to-interference ratio plus noise power patio (SINR) at user equipment (UE) and system capacity.
Brockett problem for systems with feedback delay

Abstract The Brockett problem is posed for systems with feedback delay in the form: what kind of time-varying controllers should be used to obtain asymptotic stability? Stabilization of delayed systems is a challenging task in control theory, since these systems usually have infinitely many poles. In this paper, the act-and-wait control concept is investigated as a possible technique to reduce the number of poles of systems with feedback delay. The Brockett problem is rephrased for the act-and-wait control system.
The Sch9 Kinase Regulates Conidium Size, Stress Responses, and Pathogenesis in Fusarium graminearum

Fusarium head blight caused by Fusarium graminearum is an important disease of wheat and barley worldwide. In a previous study on functional characterization of the F. graminearum kinome, one protein kinase gene important for virulence is orthologous to SCH9 that is functionally related to the cAMP-PKA and TOR pathways in the budding yeast. In this study, we further characterized the functions of FgSCH9 in F. graminearum and its ortholog in Magnaporthe oryzae. The ΔFgsch9 mutant was slightly reduced in growth rate but significantly reduced in conidiation, DON production, and virulence on wheat heads and corn silks. It had increased tolerance to elevated temperatures but became hypersensitive to oxidative, hyperosmotic, cell wall, and membrane stresses. The ΔFgsch9 deletion also had conidium morphology defects and produced smaller conidia. These results suggest that FgSCH9 is important for stress responses, DON production, conidiogenesis, and pathogenesis in F. graminearum. In the rice blast fungus Magnaporthe oryzae, the ΔMosch9 mutant also was defective in conidiogenesis and pathogenesis. Interestingly, it also produced smaller conidia and appressoria. Taken together, our data indicate that the SCH9 kinase gene may have a conserved role in regulating conidium size and plant infection in phytopathogenic ascomycetes.
Effects of age and IQ on paced auditory serial addition task (PASAT) performance

Abstract The Paced Auditory Serial Addition Task (PASAT) is a neuropsychological instrument used by clinicians and researchers to measure attention and information processing, to evaluate impairments, and to quantify changes in performance over time. The PASAT is sensitive to these subtle deficits in neurocognitive functioning. Clinical interpretation of test results requires comparison relative to the normal population. The present data, compiled from 526 normal, healthy US adults, represents the first published comprehensive normative study of the Levin modification of the PASAT. Analyses were conducted to assess the effect of the demographic variables of age, IQ, gender, race, and education on PASAT performance. Education and race had no significant effect. Gender exerted minimal statistical significance that was not considered clinically meaningful. Age and IQ did significantly affect PASAT test results. For both clinical and research purposes, the age and intellectual functioning of subjects must be .
Online Motion Estimation from Image and Inertial Measurements

We present two algorithms for estimating sensor motion from image and inertial measurements, which are suitable for use with inexpensive inertial sensors and in environments without known fiducials. The first algorithm is a batch method, which produces optimal estimates of the sensor motion, scene structure, and other parameters using measurements from the entire observation sequence simultaneously. The second algorithm recovers sensor motion, scene structure, and other parameters in an online manner, is suitable for use with long or “infinite” sequences, and handles sequences in which no feature is always visible. We also describe initial results from running each algorithm on a sequence for which ground truth is available. We show that while image measurements alone are not sufficient for accurate motion estimation from this sequence, both batch and online estimation from image and inertial measurements produce accurate estimates of the sensors’ motion.
Efficient hardware architecture for fast IP address lookup

A multigigabit IP router may receive several million packets per second from each input link. For each packet, the router needs to find the longest matching prefix in the forwarding table in order to determine the packet's next-hop. In this paper, we present an efficient hardware solution for the IP address lookup problem. We model the address lookup problem as a searching problem on a binary-trie. The binary-trie is partitioned into four levels of fixed size 255-node subtrees. We employ a hierarchical indexing structure to facilitate direct access to subtrees in a given level. It is estimated that a forwarding table with 40 K prefixes will consume 2.5 Mbytes of memory. The searching is implemented using a hardware pipeline with a minimum cycle of 12.5 ns if the memory modules are implemented using SRAM. A distinguishing feature of our design is that forwarding table entries are not replicated in the data structure. Hence, table updates can be done in constant time with only a few memory accesses.
The Psychologically Violent Parental Practices Inventory (PVPPI): English Translation

ABSTRACT This paper reports the translation and preliminary validation process of the Psychologically Violent Parental Practices Inventory (PVPPI). The original Francophone inventory was previously tested with 306 Francophone students recruited in fifth to ninth grade classes. Findings of the original study had suggested a coherent two-factor structure, good construct validity, and satisfactory internal consistency. The PVPPI was translated into English and tested on a convenience sample of 90 girls and boys recruited in fifth and sixth grade classes of two English schools in the Quebec City area. The psychometric properties of this translation seem to reproduce those of the original French inventory. On the whole, PVPPI appears to be a promising tool that could find practical, as well as scientific applications.