Miracle-dz/UniFAR-FTUs huggingface dataset:
Delayed Ras/PKA signaling augments the unfolded protein response

Significance The unfolded protein response (UPR) maintains protein-folding homeostasis in the endoplasmic reticulum (ER). The UPR is involved in diseases such as triple-negative breast cancer, developmental processes such as B-cell activation, and the decision to commit to apoptosis. In principle, the UPR could restore homeostasis to the ER by increasing folding capacity or reducing the load of newly synthesized proteins. Here we report that budding yeast augments the UPR with PKA signaling and reduces the load of newly synthesized proteins, a role functionally analogous to the PKR-like ER kinase (PERK) and regulated inositol-requiring enzyme 1 (IRE1)-dependent mRNA decay (RIDD) pathways in other organisms. Accounting for all the pathways that contribute to stress resistance is necessary to understand how perturbations, including targeted therapies, propagate through the cell. During environmental, developmental, or genetic stress, the cell’s folding capacity can become overwhelmed, and misfolded proteins can accumulate in all cell compartments. Eukaryotes evolved the unfolded protein response (UPR) to counteract proteotoxic stress in the endoplasmic reticulum (ER). Although the UPR is vital to restoring homeostasis to protein folding in the ER, it has become evident that the response to ER stress is not limited to the UPR. Here, we used engineered orthogonal UPR induction, deep mRNA sequencing, and dynamic flow cytometry to dissect the cell’s response to ER stress comprehensively. We show that budding yeast augments the UPR with time-delayed Ras/PKA signaling. This second wave of transcriptional dynamics is independent of the UPR and is necessary for fitness in the presence of ER stress, partially due to a reduction in general protein synthesis. This Ras/PKA-mediated effect functionally mimics other mechanisms, such as translational control by PKR-like ER kinase (PERK) and regulated inositol-requiring enzyme 1 (IRE1)-dependent mRNA decay (RIDD), which reduce the load of proteins entering the ER in response to ER stress in metazoan cells.
Jointly multi-user detection and channel estimation with genetic algorithm

This work aims at proposing the use of the evolutionary computation methodology in order to jointly solve the multi-user channel estimation (MuChE) and detection problems at its maximum-likelihood, both related to the direct sequence code division multiple access (DS/CDMA). The effectiveness of the proposed heuristic approach is proven by comparing performance and complexity merit figures with that obtained by traditional methods found in literature. Simulation results considering genetic algorithm (GA) applied to multipath, DS/CDMA and MuChE and multi-user detection (MuD) show that the proposed genetic algorithm multi-user channel estimation (GAMuChE) yields a normalized mean square error estimation (nMSE) inferior to 11%, under slowly varying multipath fading channels, large range of Doppler frequencies and medium system load, it exhibits lower complexity when compared to both maximum likelihood multi-user channel estimation (MLMuChE) and gradient descent method (GrdDsc). A near-optimum multi-user detector (MuD) based on the genetic algorithm (GAMuD), also proposed in this work, provides a significant reduction in the computational complexity when compared to the optimum multi-user detector (OMuD). In addition, the complexity of the GAMuChE and GAMuD algorithms were (jointly) analyzed in terms of number of operations necessary to reach the convergence, and compared to other jointly MuChE and MuD strategies. The joint GAMuChE–GAMuD scheme can be regarded as a promising alternative for implementing third-generation (3G) and fourth-generation (4G) wireless systems in the near future. Copyright © 2010 John Wiley & Sons, Ltd. (The material in this paper was presented in part at the ISSSTA'06 - IEEE International Symposium on Spread Spectrum Techniques and Applications, Manaus, Brazil, 2006.) (The main aim of this work is to propose the use of evolutionary computation methodology in order to jointly solve the multi-user channel estimation and detection problems at its maximum-likelihood. The effectiveness of the proposed genetic algorithm multi-user channel estimation (GAMuChE) was proven by evaluating performance and complexity merit figures. The GAMuChE yields an nMSE estimation inferior to 11%, under slowly varying multipath fading channels, large range Doppler (i.e., 1.85 Hz < fD < 277.78 Hz) and medium system load. )
Network Coding Based Multicast in Internet

Multicast transmission is a key technology in Internet, which can send the same information simultaneously to several receivers. A new multicast routing algorithm based on network coding is proposed in this paper, searching the routing groups from source to each receiver by using Dijkstra reduction network. Simulation results show that, compared with traditional multicast routing algorithms, performances of the routing algorithm are improved at a great extent in resource consumption and load balance, and are closer to minimum-cost multicast algorithm based on network coding. Finally, mathematic analysis indicates that the algorithm has lower computational complexity.
Layered Functional Network Analysis of Gene Expression in Human Heart Failure

Background Although dilated cardiomyopathy (DCM) is a leading cause of heart failure (HF), the mechanism underlying DCM is not well understood. Previously, it has been demonstrated that an integrative analysis of gene expression and protein-protein interaction (PPI) networks can provide insights into the molecular mechanisms of various diseases. In this study we develop a systems approach by linking public available gene expression data on ischemic dilated cardiomyopathy (ICM), a main pathological form of DCM, with data from a layered PPI network. We propose that the use of a layered PPI network, as opposed to a traditional PPI network, provides unique insights into the mechanism of DCM. Methods Four Cytoscape plugins including BionetBuilder, NetworkAnalyzer, Cerebral and GenePro were used to establish the layered PPI network, which was based upon validated subcellular protein localization data retrieved from the HRPD and Entrez Gene databases. The DAVID function annotation clustering tool was used for gene ontology (GO) analysis. Results The assembled layered PPI network was divided into four layers: extracellular, plasma membrane, cytoplasm and nucleus. The characteristics of the gene expression pattern of the four layers were compared. In the extracellular and plasma membrane layers, there were more proteins encoded by down-regulated genes than by up-regulated genes, but in the other two layers, the opposite trend was found. GO analysis established that proteins encoded by up-regulated genes, reflecting significantly over-represented biological processes, were mainly located in the nucleus and cytoplasm layers, while proteins encoded by down-regulated genes were mainly located in the extracellular and plasma membrane layers. The PPI network analysis revealed that the Janus family tyrosine kinase-signal transducer and activator of transcription (Jak-STAT) signaling pathway might play an important role in the development of ICM and could be exploited as a therapeutic target of ICM. In addition, glycogen synthase kinase 3 beta (GSK3B) may also be a potential candidate target, but more evidence is required. Conclusion This study illustrated that by incorporating subcellular localization information into a PPI network based analysis, one can derive greater insights into the mechanisms underlying ICM.
How Do Marketing Investments Benefit Brand Revenue Premiums

How do marketing investments (such as price promotions, new product introductions and advertising) contribute to a brand's revenue premium? Moreover, how do brand and category characteristics moderate the impact of the marketing investments on brand revenue premiums? In this paper, I address these questions with a large-scale econometric analysis of marketing investments and associated brand revenue premiums in the automobile industry. The results suggest that while investments in advertising and product innovations are successful in generating building long-run brand revenue premiums, investments in sales promotions are not. Interestingly, corporate branding strategies significantly enhance the revenue premium effects of new product introductions and brand advertising, relative to mixed and house-of-brands strategies. Moreover, the effectiveness of such investments from a brand revenue premium perspective are higher for leading brands with higher perceived appeal and quality, that are characterized by more pioneering innovations, but with narrower product-line breadth.
Generalizations of the distributed Deutsch–Jozsa promise problem

In the distributed Deutsch–Jozsa promise problem, two parties are to determine whether their respective strings x, y ∈ {0,1} n are at the Hamming distance H(x, y) = 0 or H(x, y) = $\frac{n}{2}$ . Buhrman et al. (STOC' 98) proved that the exact quantum communication complexity of this problem is O(log n) while the deterministic communication complexity is Ω(n). This was the first impressive (exponential) gap between quantum and classical communication complexity. In this paper, we generalize the above distributed Deutsch–Jozsa promise problem to determine, for any fixed $\frac{n}{2}$ ⩽ k ⩽ n, whether H(x, y) = 0 or H(x, y) = k, and show that an exponential gap between exact quantum and deterministic communication complexity still holds if k is an even such that $\frac{1}{2}$ n ⩽ k < (1 − λ)n, where 0 < λ < $\frac{1}{2}$ is given. We also deal with a promise version of the well-known disjointness problem and show also that for this promise problem there exists an exponential gap between quantum (and also probabilistic) communication complexity and deterministic communication complexity of the promise version of such a disjointness problem. Finally, some applications to quantum, probabilistic and deterministic finite automata of the results obtained are demonstrated.
The sway compensation trajectory for a biped robot

From 1970's, legged robots have attracted much attention of many researchers. In spite of this, it has been regarded that dynamically stable walking is very difficult to be tackled for any types of legged robots. For a trot gait for quadruped walking robots, we have proposed "the sway compensation trajectory". This method utilizes a lateral, longitudinal, and vertical motion of a robot body to keep a zero moment point (ZMP) on a diagonal line between support legs. In this paper, we develop the sway compensation trajectory for a biped robot, and show that dynamically stable walking is realized. This method makes it quite easy to design stable ZMP and COG (center of gravity) trajectories, which have been regarded as a very complicated and delicate problem. The effectiveness of the proposed method is verified through computer simulations and walking experiments by a humanoid robot, HOAP-1.
Graded Learning for Object Detection

Fort Collins, CO, June, 1999. (Published on Web). Graded Learning for Object Detection Francois Fleuret1 and Donald Geman2 Abstract Our goal is to detect all instances of a generic object class, such as a face, in greyscale scenes. The design of the algorithm is motivated by computational e ciency. The search is coarse-tone in both the exploration of poses and the representation of the object class. Starting from training examples, we recursively learn a hierarchy of spatial arrangements of edge fragments, graded by their size (sparsity). The arrangements have no a priori semantic or geometric interpretation. Instead, they are selected to be "decomposable": Each can be split into two correlated subarrangements, each of which can be further divided, etc. As a result, the probability of an arrangement of size k appearing on an object instance decays slowly with k. We demonstrate this both theoretically and in experiments in which detection means nding a su cient number of arrangements of various sizes.
Least periods of k-automatic sequences

Currie and Saari initiated the study of least periods of infinite words, and they showed that every integer n >= 1 is a least period of the Thue-Morse sequence. We generalize this result to show that the characteristic sequence of least periods of a k-automatic sequence is (effectively) k-automatic. Through an implementation of our construction, we confirm the result of Currie and Saari, and we obtain similar results for the period-doubling sequence, the Rudin-Shapiro sequence, and the paperfolding sequence.
DIABLO: a reliable, retargetable and extensible link-time rewriting framework

Modern software engineering techniques introduce an overhead to programs in terms of performance and code size. A traditional development environment, where only the compiler optimizes the code, cannot completely eliminate this overhead. To effectively remove the overhead, tools are needed that have a whole-program overview. Link-time binary rewriting is an effective technique for whole-program optimization and instrumentation. In this paper, we describe a novel framework to reliably perform link-time program transformations. This framework is designed to be retargetable, supporting multiple architectures and development toolchains. Furthermore it is extensible, which we illustrate by describing three different applications that are built on top of the framework.
Implementing Key Strategies for Successful Network Integration in the Quebec Substance-Use Disorders Programme

Background: Fragmentation and lack of coordination often occur among organisations offering treatment for individuals with substance-use disorders. Better integration from a system perspective within a network of organisations offering substance-use disorder services can be developed using various integration strategies at the administrative and clinical levels. This study aims to identify integration strategies implemented in Quebec substance-use disorder networks and to assess their strengths and limitations. Methods: A total of 105 stakeholders representing two regions and four local substance-use disorder networks participated in focus groups or individual interviews. Thematic qualitative and descriptive quantitative analyses were conducted. Results: Six types of service integration strategies have been implemented to varying degrees in substance-use disorder networks. They are: 1) coordination activities-governance, 2) primary-care consolidation models, 3) information and monitoring management tools, 4) service coordination strategies, 5) clinical evaluation tools and 6) training activities. Conclusion: Important investments have been made in Quebec for the training and assessment of individuals with substance-use disorders, particularly in terms of support for emergency room liaison teams and the introduction of standardised clinical evaluation tools. However, the development of integration strategies was insufficient to ensure the implementation of successful networks. Planning, consolidation of primary care for substance-use disorders and systematic implementation of various clinical and administrative integration strategies are needed in order to ensure a better continuum of care for individuals with substance-use disorders.
Instilling Values to Children in Conflict with the Law in a Youth Facility

This study investigates how values are instilled to children in conflict with the law (CICL) in a Philippines youth facility through the houseparent–resident relationship. Although a wealth of literature has examined the condition of child residents in youth rehabilitation institutions, little is known about the relationship between the child residents and the houseparents assigned to care for them, particularly, how the values the houseparents instil in the children impacts on their rehabilitation. Through an ethnographic study of a child facility and in-depth interviews of the CICL residents and their houseparents, the study presents a rich description of the kind of relationship between these carers and their wards. The totalizing effect of the institution is mitigated by the genial relationship between the houseparents and the child residents. In particular, the Filipino values of personalism as applied by the houseparents in their parenting tasks positively impacts on the child residents they are caring for. The findings gathered from this study will provide critical information on what values the social workers, caregivers, houseparents and other staff of a youth facility should impart to the CICL to help achieve the facility’s rehabilitative goals.
Research on binocular stereo video attention model based on human visual system

In order to solve the enormous pressure of the stereo video surveillance mass data storage and transmission, the human visual system(HVS) is introduced into the stereo video compressing coding by researchers, but the perception mechanism of inter-view and the inherent characteristics of monitoring the scene are neglected, hence the coding efficiency is affected. Therefore, this paper puts forward the surveillance-oriented binocular stereo video attention model for video coding. Firstly, the paper analyzes the binocular competition perception mechanism of stereo video, then, it builds up an attention model of binocular stereo video coding framework, lastly, it is applied perception rate allocation. It is expected that in the case of the same subjective quality, this research can reduce 20% of the coding bitrates to meet the professional needs of video surveillance system from 2D to stereo upgrade and updating.
A VAD-robust Multichannel Wiener Filter algorithm for noise reduction in hearing aids

The Speech Distortion Weighted Multichannel Wiener Filter (SDW-MWF) is a promising multi-microphone noise reduction technique, in particular for hearing aid applications. Its benefit over other techniques has been shown in several theoretical and experimental contributions. In theoretical studies, a single target speech source is commonly assumed, as this facilitates the analysis. In this contribution, we first prove that an algorithm, that implicitly assumes a single target speech source, is also more robust against estimation errors in the speech second order statistics, compared to a standard SDW-MWF algorithm. Secondly, as any SDW-MWF algorithm relies on a voice activity detector (VAD), a novel VAD-robust extension is also proposed. It is shown theoretically and through experiments with a realistic VAD that the new algorithm indeed achieves a good performance, even at low input SNR's where the VAD error rate is high.
Latent Frequency Synthesis for Behavioral Hard Disk Drive Access Time Models

Access time prediction is important for predicting hard disk drive latencies. Existing approaches use white-box models developed with expert knowledge and can take months to parameterize. Automatically learning behavior is much preferred, requiring less expertise, fewer assumptions, and less time. Black-box modeling has been attempted, but none have demonstrated per-request accuracy. Barriers to machine learning of access times include periodicity with high, unknown frequencies, and a discontinuous access time function. Previously, we showed that recognizing periodicity is crucial for accuracy. Unfortunately, Fourier analysis is expensive and ill-suited for this problem. In this paper, we demonstrate that the model can identify periods itself, bypassing Fourier analysis. We show that neural nets, given specific sinusoids as additional inputs, can predict access times, even across differing track lengths and thus differing periods. This removes a significant barrier and expands the range, although challenges remain. Removing discontinuities via a trigonometric transformation further reduces error.
The roles of phonation and F0 in Zhuang

Zhuang is a Tai-Kadai language spoken in the Guangxi province, China. The goal of this talk to describe dialectal differences in two varieties of Zhuang via phonetic measurements: phonation and F0. In particular, we will discuss findings from the creakiness detection algorithm and SSANOVA. We will also explore the concept of roughness as a psychoacoustic unit for discriminating creakiness.
Neoadjuvant capecitabine, bevacizumab and radiotherapy for locally advanced rectal cancer: results of a single-institute Phase I study

The aim of this Phase I clinical trial was to assess the feasibility and safety of capecitabine-based preoperative chemoradiotherapy (CRT) combined with bevacizumab and to determine the optimal capecitabine dose for Japanese patients with locally advanced rectal cancer. Patients with cT3/T4 rectal cancer were eligible. Bevacizumab was administered at 5 mg/kg intravenously on Days 1, 15 and 29. Capecitabine was administered on weekdays concurrently with pelvic radiotherapy at a daily dose of 1.8 Gy, totally to 50.4 Gy. Capecitabine was initiated at 825 mg/m2 twice daily at Dose Level 1, with a planned escalation to 900 mg/m2 twice daily at Dose Level 2. Within 6.1–10.3 (median, 9.4) weeks after the completion of the CRT, surgery was performed. Three patients were enrolled at each dose level. Regarding the CRT-related acute toxicities, all of the adverse events were limited to Grade 1. There was no Grade 2 or greater toxicity. No patient needed attenuation or interruption of bevacizumab, capecitabine or radiation. All of the patients received the scheduled dose of CRT. All of the patients underwent R0 resection. Two (33.3%) of the six patients had a pathological complete response, and five (83.3%) patients experienced downstaging. In total, three patients (50%) developed postoperative complications. One patient developed an intrapelvic abscess and healed with incisional drainage. The other two patients healed following conservative treatment. This regimen was safely performed as preoperative CRT for Japanese patients with locally advanced rectal cancer. The recommended capecitabine dose is 900 mg/m2 twice daily.
Response to letter regarding article, "TASER electronic control devices and cardiac arrests: coincidental or causal?".

We thank Dr Sheridan for his interest and wish to acknowledge his contributions to the understanding of the effects of the electronic control device (ECD). 1 There have, in fact, been published studies in which ECD probes were launched into the chests of volunteers. In 2 of these studies there was continuous echocardiographic monitoring to verify that there was no cardiac capture.2,3 The 63 volunteers received a total of 10 170 ECD pulses with no arrhythmias and no cardiac capture (in the 9450 with echo monitoring). Consistent with the study coauthored by Dr Sheridan, some of us have previously published that the risk of ventricular fibrillation (VF) induction is vanishingly small, if not …