Miracle-dz/UniFAR-FTUs huggingface dataset:
Vertical partitioning of relational OLTP databases using integer programming

A way to optimize performance of relational row store databases is to reduce the row widths by vertically partitioning tables into table fractions in order to minimize the number of irrelevant columns/attributes read by each transaction. This paper considers vertical partitioning algorithms for relational row-store OLTP databases with an H-store-like architecture, meaning that we would like to maximize the number of single-sited transactions. We present a model for the vertical partitioning problem that, given a schema together with a vertical partitioning and a workload, estimates the costs (bytes read/written by storage layer access methods and bytes transferred between sites) of evaluating the workload on the given partitioning. The cost model allows for arbitrarily prioritizing load balancing of sites vs. total cost minimization. We show that finding a minimum-cost vertical partitioning in this model is NP-hard and therefore the problem should obviously not be solved manually by a human DBA. We present two algorithms returning solutions in which single-sitedness of read queries is preserved while allowing column replication (which may allow a drastically reduced cost compared to disjoint partitioning). The first algorithm is a quadratic integer program that finds optimal minimum-cost solutions with respect to the model, and the second algorithm is a more scalable heuristic based on simulated annealing. Experiments show that the algorithms can reduce the cost of the model objective by 37% when applied to the TPC-C benchmark and the heuristic is shown to obtain solutions with costs close to the ones found using the quadratic program.
On the Emergence of Common Design Metaphors in Collaborative Design

This paper reports an observation of how designers work together to achieve integrated building design on the basis of individual contributions. A case study shows that the keystone of fruitfid collaboration lies in the projection of common images; and common design metaphors emerging from group interpretation of the common images can function as a communicative device, allowing for participants to collaborate effectively. A set of constraints on collaboration is identified via a situation-theoretical analysis of a scenario of collaborative design. As shown, the constraints derived have some implications for building collaboration-supporting tools.
Computation of Conformational Coupling in Allosteric Proteins

In allosteric regulation, an effector molecule binding a protein at one site induces conformational changes, which alter structure and function at a distant active site. Two key challenges in the computational modeling of allostery are the prediction of the structure of one allosteric state starting from the structure of the other, and elucidating the mechanisms underlying the conformational coupling of the effector and active sites. Here we approach these two challenges using the Rosetta high-resolution structure prediction methodology. We find that the method can recapitulate the relaxation of effector-bound forms of single domain allosteric proteins into the corresponding ligand-free states, particularly when sampling is focused on regions known to change conformation most significantly. Analysis of the coupling between contacting pairs of residues in large ensembles of conformations spread throughout the landscape between and around the two allosteric states suggests that the transitions are built up from blocks of tightly coupled interacting sets of residues that are more loosely coupled to one another.
ARB-NET: A novel adaptive monitoring platform for stacked mesh 3D NoC architectures

The emerging three-dimensional integrated circuits (3D ICs) offer a promising solution to mitigate the barriers of interconnect scaling in modern systems. In order to exploit the intrinsic capability of reducing the wire length in 3D ICs, 3D NoC-Bus Hybrid mesh architecture was proposed. Besides its various advantages in terms of area, power consumption, and performance, this architecture has a unique and hitherto previously unexplored way to implement an efficient system-wide monitoring network. In this paper, an integrated low-cost monitoring platform for 3D stacked mesh architectures is proposed which can be efficiently used for various system management purposes. The proposed generic monitoring platform called ARB-NET utilizes bus arbiters to exchange the monitoring information directly with each other without using the data network. As a test case, based on the proposed monitoring platform, a fully congestion-aware adaptive routing algorithm named AdaptiveXYZ is presented taking advantage from viable information generated within bus arbiters. Our extensive simulations with synthetic and real benchmarks reveal that our architecture using the AdaptiveXYZ routing can help achieving significant power and performance improvements compared to recently proposed stacked mesh 3D NoCs.
Loss of MyD88 alters neuroinflammatory response and attenuates early Purkinje cell loss in a spinocerebellar ataxia type 6 mouse model

Spinocerebellar ataxia type 6 (SCA6) is dominantly inherited neurodegenerative disease, caused by an expansion of CAG repeat encoding a polyglutamine (PolyQ) tract in the Cav2.1 voltage-gated calcium channel. Its key pathological features include selective degeneration of the cerebellar Purkinje cells (PCs), a common target for PolyQ-induced toxicity in various SCAs. Mutant Cav2.1 confers toxicity primarily through a toxic gain-of-function mechanism; however, its molecular basis remains elusive. Here, we studied the cerebellar gene expression patterns of young Sca6-MPI(118Q/118Q) knockin (KI) mice, which expressed mutant Cav2.1 from an endogenous locus and recapitulated many phenotypic features of human SCA6. Transcriptional signatures in the MPI(118Q/118Q) mice were distinct from those in the Sca1(154Q/2Q) mice, a faithful SCA1 KI mouse model. Temporal expression profiles of the candidate genes revealed that the up-regulation of genes associated with microglial activation was initiated before PC degeneration and was augmented as the disease progressed. Histological analysis of the MPI(118Q/118Q) cerebellum showed the predominance of M1-like pro-inflammatory microglia and it was concomitant with elevated expression levels of tumor necrosis factor, interleukin-6, Toll-like receptor (TLR) 2 and 7. Genetic ablation of MyD88, a major adaptor protein conveying TLR signaling, altered expression patterns of M1/M2 microglial phenotypic markers in the MPI(118Q/118Q) cerebellum. More importantly, it ameliorated PC loss and partially rescued motor impairments in the early disease phase. These results suggest that early neuroinflammatory response may play an important role in the pathogenesis of SCA6 and its modulation could pave the way for slowing the disease progression during the early stage of the disease.
Learning and Tracking Cyclic Human Motion

We present methods for learning and tracking human motion in video. We estimate a statistical model of typical activities from a large set of 3D periodic human motion data by segmenting these data automatically into "cycles". Then the mean and the principal components of the cycles are computed using a new algorithm that accounts for missing information and enforces smooth transitions between cycles. The learned temporal model provides a prior probability distribution over human motions that can be used in a Bayesian framework for tracking human subjects in complex monocular video sequences and recovering their 3D motion.
Micromilling: Material microstructure effects

Abstract Micromilling is one of the technologies that is currently widely used for the production of microcomponents and tooling inserts. To improve the quality and surface finish of machined microstructures the factors affecting the process dynamic stability should be studied systematically. This paper investigates the machining response of a metallurgically and mechanically modified material. The results of micromilling workpieces of an Al 5000 series alloy with different grain microstructures are reported. In particular, the machining response of three Al 5083 workpieces whose microstructure was modified through a severe plastic deformation was studied when milling thin features in microcomponents. The effects of the material microstructure on the resulting part quality and surface integrity are discussed and conclusions made about its importance in micromilling. The investigation has shown that through a refinement of material microstructure it is possible to improve significantly the surface integrity of the microcomponents and tooling cavities produced by micromilling.
Alcohol potently inhibits the kainate receptor-dependent excitatory drive of hippocampal interneurons

Kainate receptors (KA-Rs) are members of the glutamate-gated family of ionotropic receptors, which also includes N-methyl-d-aspartate (NMDA) and α-amino-3-hydroxy-5-methylisoxazole-4-propionate (AMPA) receptors. KA-Rs are important modulators of interneuron excitability in the CA1 region of the hippocampus. Activation of these receptors enhances interneuron firing, which robustly increases spontaneous inhibitory postsynaptic currents in pyramidal neurons. We report here that ethanol (EtOH) potently inhibits this KA-R-mediated effect at concentrations as low as those that can be achieved in blood after the ingestion of just 1–2 drinks (5–10 mM). Pressure application of kainate, in the presence of AMPA and NMDA receptor antagonists, evoked depolarizing responses in interneurons that triggered repetitive action potential firing. EtOH potently inhibited these responses to a degree that was sufficient to abolish action potential firing. This effect appears to be specific for KA-Rs, as EtOH did not affect action potential firing triggered by AMPA receptor-mediated depolarizing responses. Importantly, EtOH inhibited interneuron action potential firing in response to KA-R activation by synaptically released glutamate, suggesting that our findings are physiologically relevant. KA-R-dependent modulation of glutamate release onto pyramidal neurons was not affected by EtOH. Thus, EtOH increases excitability of pyramidal neurons indirectly by inhibiting the KA-R-dependent drive of γ-aminobutyric acid (GABA)ergic interneurons. We postulate that this effect may explain, in part, some of the paradoxical excitatory actions of this widely abused substance. The excitatory actions of EtOH may be perceived as positive by some individuals, which could contribute to the development of alcoholism.
Financial competitiveness of organic agriculture on a global scale

Significance Some recognize organic agriculture as being important for future global food security, whereas others project it to become irrelevant. Although organic agriculture is rapidly growing, it currently occupies only 1% of global cropland. Whether organic agriculture can continue to expand will likely be determined by whether it is economically competitive with conventional agriculture. Accordingly, we analyzed the financial performance of organic and conventional agriculture from 40 y of studies covering 55 crops grown on five continents. We found that, in spite of lower yields, organic agriculture was significantly more profitable than conventional agriculture and has room to expand globally. Moreover, with its environmental benefits, organic agriculture can contribute a larger share in sustainably feeding the world. To promote global food and ecosystem security, several innovative farming systems have been identified that better balance multiple sustainability goals. The most rapidly growing and contentious of these systems is organic agriculture. Whether organic agriculture can continue to expand will likely be determined by whether it is economically competitive with conventional agriculture. Here, we examined the financial performance of organic and conventional agriculture by conducting a meta-analysis of a global dataset spanning 55 crops grown on five continents. When organic premiums were not applied, benefit/cost ratios (−8 to −7%) and net present values (−27 to −23%) of organic agriculture were significantly lower than conventional agriculture. However, when actual premiums were applied, organic agriculture was significantly more profitable (22–35%) and had higher benefit/cost ratios (20–24%) than conventional agriculture. Although premiums were 29–32%, breakeven premiums necessary for organic profits to match conventional profits were only 5–7%, even with organic yields being 10–18% lower. Total costs were not significantly different, but labor costs were significantly higher (7–13%) with organic farming practices. Studies in our meta-analysis accounted for neither environmental costs (negative externalities) nor ecosystem services from good farming practices, which likely favor organic agriculture. With only 1% of the global agricultural land in organic production, our findings suggest that organic agriculture can continue to expand even if premiums decline. Furthermore, with their multiple sustainability benefits, organic farming systems can contribute a larger share in feeding the world.
Bell violations through independent bases games

In a recent paper, Junge and Palazuelos presented two two-player games exhibiting interesting properties. In their first game, entangled players can perform notably better than classical players. The quantitative gap between the two cases is remarkably large, especially as a function of the number of inputs to the players. In their second game, entangled players can perform notably better than players that are restricted to using a maximally entangled state (of arbitrary dimension). This was the first game exhibiting such a behavior. The analysis of both games is heavily based on non-trivial results from Banach space theory and operator space theory. Here we provide alternative proofs of these two results. Our proofs are arguably simpler, use elementary probabilistic techniques and standard quantum information arguments, and also give better quantitative bounds.
Audio–Visual Active Speaker Tracking in Cluttered Indoors Environments

We propose a system for detecting the active speaker in cluttered and reverberant environments where more than one person speaks and moves. Rather than using only audio information, the system utilizes audiovisual information from multiple acoustic and video sensors that feed separate audio and video tracking modules. The audio module operates using a particle filter (PF) and an information-theoretic framework to provide accurate acoustic source location under reverberant conditions. The video subsystem combines in 3-D a number of 2-D trackers based on a variation of Stauffer's adaptive background algorithm with spatiotemporal adaptation of the learning parameters and a Kalman tracker in a feedback configuration. Extensive experiments show that gains are to be expected when fusion of the separate modalities is performed to detect the active speaker.
Exploring Artifact Signals in Atom Probe Mass Spectra

A variety of artifact signals are commonly observed in atom probe tomography mass spectra. Some artifacts are immediately apparent (e.g. the background spectrum and peak tails), while some are more difficult to discern (e.g. DC field evaporation, ion feedback, and multi-hit detection events). A deeper understanding of mass spectrum artifacts should advance understanding of instrument behavior; produce more accurate analyses; help mitigate the effects of the artifacts; and provide ways to recover signal information that would otherwise be lost.
Capricate: A Fabrication Pipeline to Design and 3D Print Capacitive Touch Sensors for Interactive Objects

3D printing is widely used to physically prototype the look and feel of 3D objects. Interaction possibilities of these prototypes, however, are often limited to mechanical parts or post-assembled electronics. In this paper, we present Capricate, a fabrication pipeline that enables users to easily design and 3D print highly customized objects that feature embedded capacitive multi-touch sensing. The object is printed in a single pass using a commodity multi-material 3D printer. To enable touch input on a wide variety of 3D printable surfaces, we contribute two techniques for designing and printing embedded sensors of custom shape. The fabrication pipeline is technically validated by a series of experiments and practically validated by a set of example applications. They demonstrate the wide applicability of Capricate for interactive objects.
Metabolic Aberrations Impact Biophysical Integrity of Macromolecular Protein Pools in the Default Mode Network

The brain’s default mode network (DMN), having a high rate of basal energy metabolism, is vulnerable to altered glucose metabolism in type 2 diabetes mellitus (T2DM) due to insulin resistance and chronic hyperglycemia. Previous studies showed that functional connectivity and structural connectivity among the DMN nodal regions are compromised in T2DM. We applied magnetization transfer imaging to examine the impact of T2DM on the biophysical integrity of the DMN. The results showed that the biophysical integrity of macromolecular protein pools in the posterior cingulate cortex (PCC), a central DMN hub region, was selectively compromised in T2DM, whereas the other nodal regions of the DMN, including the medial prefrontal cortex, lateral inferior parietal cortex, precuneus, and medial and lateral temporal cortices, were biophysically intact compared with those of control subjects without diabetes. Furthermore, the degree of biophysical impairment of the PCC correlated with both hyperglycemia and vascular compromise, the two physiological hallmarks of diabetes. These new findings demonstrate that the PCC is vulnerable in the DMN and may shed light on the molecular neurobiology of T2DM and help to elucidate the pathophysiology of diabetes-related cognitive comorbidities and increased risk for dementia.
VizBlog : Discovering Conversations in the Blogosphere Candida

Web logs (or blogs) have become a means for citizens to share opinions and deliberate on local issues. However, the large number of blogs makes finding and exploring content of interest relatively difficult. We developed a tool that displays citizen-to citizen discussion in blogs and reveals some similarity across blog entries. Through association and content analysis, blog entries are linked to each other to form clusters of related local content. Users can navigate and explore online discussions by manipulating the graph, filtering content, and clicking on different parts of the graph. The visualization of online discussion can promote participation by highlighting ‘the buzz’ of popular topics and laying out the structure of conversations. In this demo, we will show our tool in use with a digest of regional Southwest Virginia blogs.
Association between Resistin Levels and All-Cause and Cardiovascular Mortality: A New Study and a Systematic Review and Meta-Analysis

Context Studies concerning the association between circulating resistin and mortality risk have reported, so far, conflicting results. Objective To investigate the association between resistin and both all-cause and cardiovascular (CV) mortality risk by 1) analyzing data from the Gargano Heart Study (GHS) prospective design (n=359 patients; 81 and 58 all-cause and CV deaths, respectively); 2) performing meta-analyses of all published studies addressing the above mentioned associations. Data Source and Study Selection MEDLINE and Web of Science search of studies reporting hazard ratios (HR) of circulating resistin for all-cause or CV mortality. Data Extraction Performed independently by two investigators, using a standardized data extraction sheet. Data Synthesis In GHS, adjusted HRs per one standard deviation (SD) increment in resistin concentration were 1.28 (95% CI: 1.07-1.54) and 1.32 (95% CI: 1.06-1.64) for all-cause and CV mortality, respectively. The meta-analyses included 7 studies (n=4016; 961 events) for all-cause mortality and 6 studies (n=4,187: 412 events) for CV mortality. Pooled HRs per one SD increment in resistin levels were 1.21 (95% CI: 1.03-1.42, Q-test p for heterogeneity<0.001) and 1.05 (95% CI: 1.01-1.10, Q-test p for heterogeneity=0.199) for all-cause and CV mortality, respectively. At meta-regression analyses, study mean age explained 9.9% of all-cause mortality studies heterogeneity. After adjusting for age, HR for all-cause mortality was 1.24 (95% CI: 1.06-1.45). Conclusions Our results provide evidence for an association between circulating resistin and mortality risk among high-risk patients as are those with diabetes and coronary artery disease.
X-Ray-emitting QSOs Ejected from Arp 220

Four compact ROSAT X-ray sources very close to the nearby ultraluminous infrared galaxy Arp 220 (IC 4553) have been identified as medium-redshift QSOs. The closest pair lying symmetrically across the galaxy have almost identical redshifts z = 1.25, 1.26. All of the evidence suggests that these QSOs have been ejected from Arp 220 and have large intrinsic redshifts.
Toward a gold standard for promoter prediction evaluation

Motivation: Promoter prediction is an important task in genome annotation projects, and during the past years many new promoter prediction programs (PPPs) have emerged. However, many of these programs are compared inadequately to other programs. In most cases, only a small portion of the genome is used to evaluate the program, which is not a realistic setting for whole genome annotation projects. In addition, a common evaluation design to properly compare PPPs is still lacking. Results: We present a large-scale benchmarking study of 17 state-of-the-art PPPs. A multi-faceted evaluation strategy is proposed that can be used as a gold standard for promoter prediction evaluation, allowing authors of promoter prediction software to compare their method to existing methods in a proper way. This evaluation strategy is subsequently used to compare the chosen promoter predictors, and an in-depth analysis on predictive performance, promoter class specificity, overlap between predictors and positional bias of the predictions is conducted. Availability: We provide the implementations of the four protocols, as well as the datasets required to perform the benchmarks to the academic community free of charge on request. Contact: yves.vandepeer@psb.ugent. be Supplementary information: Supplementary data are available at Bioinformatics online.
Proteomic Study of Differential Protein Expression in Mouse Lung Tissues after Aerosolized Ricin Poisoning

Ricin is one of the most poisonous natural toxins from plants and is classified as a Class B biological threat pathogen by the Centers for Disease Control and Prevention (CDC) of U.S.A. Ricin exposure can occur through oral or aerosol routes. Ricin poisoning has a rapid onset and a short incubation period. There is no effective treatment for ricin poisoning. In this study, an aerosolized ricin-exposed mouse model was developed and the pathology was investigated. The protein expression profile in the ricin-poisoned mouse lung tissue was analyzed using proteomic techniques to determine the proteins that were closely related to the toxicity of ricin. 2D gel electrophoresis, mass spectrometry and subsequent biological functional analysis revealed that six proteins including Apoa1 apolipoprotein, Ywhaz 14-3-3 protein, Prdx6 Uncharacterized Protein, Selenium-binding protein 1, HMGB1, and DPYL-2, were highly related to ricin poisoning.