Miracle-dz/UniFAR-FTUs huggingface dataset:
Susceptibility of various cells treated with interferon to the toxic effect of poly(rI).poly(rC) treatment.

Various cells were treated with interferon and then exposed to polyriboinosinic-polyribocytidylic acid complex [poly(rI). poly(rC)]. With mouse L cells, there was a marked cytotoxic effect from low doses of interferon and poly(rI.poly(rC), whereas chick embryo cells showed an effect only after high doses. When primate cells (LLC.Mk2,BSC.B, Vero and human embryo cells) were treated with human or monkey interferon, poly(rI). poly(rC) was not cytotoxic.
Regularized low-coherence overcomplete dictionary learning for sparse signal decomposition

This paper deals with learning an overcomplete set of atoms that have low mutual coherence. To this aim, we propose a new dictionary learning (DL) problem that enables a control on the amounts of the decomposition error and the mutual coherence of the atoms of the dictionary. Unlike existing methods, our new problem directly incorporates the mutual coherence term into the usual DL problem as a regularizer. We also propose an efficient algorithm to solve the new problem. Our new algorithm uses block coordinate descent, and updates the dictionary atom-by-atom, leading to closed-form solutions. We demonstrate the superiority of our new method over existing approaches in learning low-coherence overcomplete dictionaries for natural image patches.
Global Empirical Picture of Magnetospheric Substorms Inferred From Multimission Magnetometer Data

Magnetospheric substorms represent key explosive processes in the interaction of the Earth's magnetosphere with the solar wind, and their understanding and modeling are critical for space weather forecasting. During substorms, the magnetic field on the nightside is first stretched in the antisunward direction and then it rapidly contracts earthward bringing hot plasmas from the distant space regions into the inner magnetosphere, where they contribute to geomagnetic storms and Joule dissipation in the polar ionosphere, causing impressive splashes of aurora. Here we show for the first time that mining millions of spaceborne magnetometer data records from multiple missions allows one to reconstruct the global 3‐D picture of these stretching and dipolarization processes. Stretching results in the formation of a thin (less than the Earth's radius) and strong current sheet, which is diverted into the ionosphere during dipolarization. In the meantime, the dipolarization signal propagates further into the inner magnetosphere resulting in the accumulation of a longer lived current there, giving rise to a protogeomagnetic storm. The global 3‐D structure of the corresponding substorm currents including the substorm current wedge is reconstructed from data.
FOLFIRI Followed by FOLFOX6 or the Reverse Sequence in Advanced Colorectal Cancer: A Randomized GERCOR Study

PURPOSE In metastatic colorectal cancer, phase III studies have demonstrated the superiority of fluorouracil (FU) with leucovorin (LV) in combination with irinotecan or oxaliplatin over FU + LV alone. This phase III study investigated two sequences: folinic acid, FU, and irinotecan (FOLFIRI) followed by folinic acid, FU, and oxaliplatin (FOLFOX6; arm A), and FOLFOX6 followed by FOLFIRI (arm B). PATIENTS AND METHODS Previously untreated patients with assessable disease were randomly assigned to receive a 2-hour infusion of l-LV 200 mg/m2 or dl-LV 400 mg/m2 followed by a FU bolus 400 mg/m2 and 46-hour infusion 2,400 to 3,000 mg/m2 every 46 hours every 2 weeks, either with irinotecan 180 mg/m2 or with oxaliplatin 100 mg/m2 as a 2-hour infusion on day 1. At progression, irinotecan was replaced by oxaliplatin (arm A), or oxaliplatin by irinotecan (arm B). RESULTS Median survival was 21.5 months in 109 patients allocated to FOLFIRI then FOLFOX6 versus 20.6 months in 111 patients allocated to FOLFOX6 then FOLFIRI (P = .99). Median second progression-free survival (PFS) was 14.2 months in arm A versus 10.9 in arm B (P = .64). In first-line therapy, FOLFIRI achieved 56% response rate (RR) and 8.5 months median PFS, versus FOLFOX6 which achieved 54% RR and 8.0 months median PFS (P = .26). Second-line FOLFIRI achieved 4% RR and 2.5 months median PFS, versus FOLFOX6 which achieved 15% RR and 4.2 months PFS. In first-line therapy, National Cancer Institute Common Toxicity Criteria grade 3/4 mucositis, nausea/vomiting, and grade 2 alopecia were more frequent with FOLFIRI, and grade 3/4 neutropenia and neurosensory toxicity were more frequent with FOLFOX6. CONCLUSION Both sequences achieved a prolonged survival and similar efficacy. The toxicity profiles were different.
Analysis of Continuous Steering Movement Using a Motor-Based Quantification System

Continuous steering movement (CSM) of the upper extremity (UE) is an essential component of steering movement during vehicle driving. This study presents an integrated approach to examine the force exertion and movement pattern during CSM. We utilized a concept similar to the isokinetic dynamometer to measure the torque profiles during 180°/s constant-velocity CSM. During a steering cycle, the extremity movement can be divided into stance and swing phases based upon the hand contact information measured from the hand switch devices. Data from twelve normal young adults (six males and six females) showed that there are three typical profiles of force exertion. The two hands exhibit similar time expenditures but with asymmetric force exertions and contact times in both the clockwise (CW) and counterclockwise (CCW) steering cycles. Both hands contribute more force but with less contact time in their outward CSM directions (i.e., CW for the right hand and CCW for the left hand). These findings help us to further understand CSM and have a number of important implications for future practice in clinical training. Considerably more research is required to determine the roles of the various shoulder muscles during CSM at various speeds.
Simpler unsupervised POS tagging with bilingual projections

We present an unsupervised approach to part-of-speech tagging based on projections of tags in a word-aligned bilingual parallel corpus. In contrast to the existing state-of-the-art approach of Das and Petrov, we have developed a substantially simpler method by automatically identifying “good” training sentences from the parallel corpus and applying self-training. In experimental results on eight languages, our method achieves state-of-the-art results.
Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

We report a reparameterization of the glycosidic torsion χ of the Cornell et al. AMBER force field for RNA, χOL. The parameters remove destabilization of the anti region found in the ff99 force field and thus prevent formation of spurious ladder-like structural distortions in RNA simulations. They also improve the description of the syn region and the syn–anti balance as well as enhance MD simulations of various RNA structures. Although χOL can be combined with both ff99 and ff99bsc0, we recommend the latter. We do not recommend using χOL for B-DNA because it does not improve upon ff99bsc0 for canonical structures. However, it might be useful in simulations of DNA molecules containing syn nucleotides. Our parametrization is based on high-level QM calculations and differs from conventional parametrization approaches in that it incorporates some previously neglected solvation-related effects (which appear to be essential for obtaining correct anti/high-anti balance). Our χOL force field is compared with several previous glycosidic torsion parametrizations.
Grazing pressure versus environmental covariates: Effects on woody and herbaceous plant biodiversity on a limestone mountain in northern Tunisia

Mediterranean vegetation is characterized by high biodiversity and conservation value and grazing is controversial. We sampled woody and herbaceous plants on a limestone mountain with strong mesic-xeric gradients, ranked grazing pressure (on a scale of 1-4) and asked whether grazing had a significant effect on plant compositional abundance before and after controlling for environmental covariates. For woody species the shift in means among grazing classes was greater than for herbaceous species according to distance-based redundancy analysis (dbRDA). For herbaceous species differences in multivariate dispersion were greater among grazing classes. Both groups showed significant differences among grazing classes in multivariate location (permutational multivariate ANOVA), even after controlling for aspect. After taking into account biophysical covariates, grazing was not significant and the variation unique to grazing was small. According to best models in dbRDA, grazing was significant in two models for woody species, and all models for herbaceous species. For woody species, spatial variables were most important and confounded with grazing while for herbs, altitude, distance to road, slope, rock outcropping were important. Significant effects of grazing were found for forbs, Poaceae, and Geophytes but not woody and herbaceous legumes. We found a negative relationship between grazing intensity and beta diversity for herbs overall and especially Poaceae, but moderate grazing resulted in higher beta diversity for Geophytes and herbaceous legumes. Jebel Ichkeul provides a microcosm of similar conservation and management issues elsewhere in the Mediterranean. Carefully controlled grazing may enhance plant diversity and maintain the characteristics of maquis vegetation.
Do Imaging Biomarkers Relate to Outcome in Patients Treated with VEGF Inhibitors?

The management of solid tumors has been transformed by the advent of VEGF pathway inhibitors. Early clinical evaluation of these drugs has used pharmacodynamic biomarkers derived from advanced imaging such as dynamic MRI, computed tomography (CT), and ultrasound to establish proof of principle. We have reviewed published studies that used these imaging techniques to determine whether the same biomarkers relate to survival in renal, hepatocellular, and brain tumors in patients treated with VEGF inhibitors. Data show that in renal cancer, pretreatment measurements of Ktrans and early pharmacodynamic reduction in tumor enhancement and density have prognostic significance in patients treated with VEGF inhibitors. A weaker, but significant, relationship is seen with subtle early size change (10% in one dimension) and survival. Data from high-grade glioma suggest that pretreatment fractional blood volume and Ktrans were prognostic of overall survival. However, lack of control data with other therapies prevents assessment of the predictive nature of these biomarkers, and such studies are urgently required. Clin Cancer Res; 18(24); 6588–98. ©2012 AACR.
Points-of-Interest Mining from People's Photo-Taking Behavior

Millions of geo-tagged photos are becoming available due to the widespread of photo-sharing websites. These social medias capture attractive points-of-interest and contain interesting photo-taking patterns. Massive amount of these user-oriented data produces new challenges and understanding people's photo-taking behavior is of great importance for local tourism-related businesses. This paper analyzes geotagged photos from Flickr for Queensland, a tourismintensive and the second largest state in Australia. We report interesting points-of-interest patterns and discuss these findings.
Controllable Edge Feature Sharpening for Dental Applications

This paper presents a new approach to sharpen blurred edge features in scanned tooth preparation surfaces generated by structured-light scanners. It aims to efficiently enhance the edge features so that the embedded feature lines can be easily identified in dental CAD systems, and to avoid unnatural oversharpening geometry. We first separate the feature regions using graph-cut segmentation, which does not require a user-defined threshold. Then, we filter the face normal vectors to propagate the geometry from the smooth region to the feature region. In order to control the degree of the sharpness, we propose a feature distance measure which is based on normal tensor voting. Finally, the vertex positions are updated according to the modified face normal vectors. We have applied the approach to scanned tooth preparation models. The results show that the blurred edge features are enhanced without unnatural oversharpening geometry.
Accelerating Haskell array codes with multicore GPUs

Current GPUs are massively parallel multicore processors optimised for workloads with a large degree of SIMD parallelism. Good performance requires highly idiomatic programs, whose development is work intensive and requires expert knowledge. To raise the level of abstraction, we propose a domain-specific high-level language of array computations that captures appropriate idioms in the form of collective array operations. We embed this purely functional array language in Haskell with an online code generator for NVIDIA's CUDA GPGPU programming environment. We regard the embedded language's collective array operations as algorithmic skeletons; our code generator instantiates CUDA implementations of those skeletons to execute embedded array programs. This paper outlines our embedding in Haskell, details the design and implementation of the dynamic code generator, and reports on initial benchmark results. These results suggest that we can compete with moderately optimised native CUDA code, while enabling much simpler source programs.
Mixed Compressed Sensing Based on Random Graphs

Finding a suitable measurement matrix is an important topic in compressed sensing. Though the known random matrix, whose entries are drawn independently from a certain probability distribution, can be used as a measurement matrix and recover signal well, in most cases, we hope the measurement matrix imposed with some special structure. In this paper, based on random graph models, we show that the mixed symmetric random matrices, whose diagonal entries obey a distribution and non-diagonal entries obey another distribution, can be used to recover signal successfully with high probability.
Running Title : Protein-Protein Interaction Sites Predicting Protein-Protein Interaction Sites From Amino Acid Sequence

We describe an approach for computational prediction of protein-protein interaction sites using a support vector machine (SVM) classifier. Interface residues and other surface residues were extracted from 115 proteins derived from a set of 70 heterocomplexes in PDB. The SVM classifier was trained to predict whether or not a surface residue is located in the interface based on the identity of the target residue and its 10 sequence neighbors. The effectiveness of the approach was evaluated using 115 leave-one-out cross validation (jack-knife) experiments. In each experiment, an SVM classifier was trained using a set of 1250 randomly chosen interface residues and an equal number of non-interface residues from 114 of the 115 molecules. The resulting classifier was used to classify surface residues from the remaining molecule into interface and non-interface residues. The classifier in each experiment was evaluated in terms of several performance measures. In results averaged over 115 experiments, interface residues and non-interface residues were identified with relatively high specificity (71%) and sensitivity (67%), and with a correlation coefficient of 0.29 between predicted and actual class labels, indicating that the method performs substantially better than chance (zero correlation). We also investigated the classifier's performance in terms of overall interactions site recognition. In 80% of the proteins, the classifier recognized the interaction surface by identifying at least half of the interface residues, and in 98% of the proteins, at least 20% of the interface residues were correctly identified. The success of this approach was confirmed by examination of predicted interfaces in the context of the three-dimensional structures of representative complexes. This study demonstrates that an SVM classifier can be used to predict whether or not a surface residue is an interface residue using amino acid sequence information. Because surface residues can be identified based on their solvent accessible surface area (ASA), given recent progress in computational methods for predicting ASA from sequence, the approach described in this paper provides a basis for computational prediction of interaction sites in proteins for which only amino acid sequence information is available.
Rule induction performance in amnestic mild cognitive impairment and Alzheimer’s dementia: examining the role of simple and biconditional rule learning processes

ABSTRACT Introduction: Rule induction tests such as the Wisconsin Card Sorting Test require executive control processes, but also the learning and memorization of simple stimulus–response rules. In this study, we examined the contribution of diminished learning and memorization of simple rules to complex rule induction test performance in patients with amnestic mild cognitive impairment (aMCI) or Alzheimer’s dementia (AD). Method: Twenty-six aMCI patients, 39 AD patients, and 32 control participants were included. A task was used in which the memory load and the complexity of the rules were independently manipulated. This task consisted of three conditions: a simple two-rule learning condition (Condition 1), a simple four-rule learning condition (inducing an increase in memory load, Condition 2), and a complex biconditional four-rule learning condition—inducing an increase in complexity and, hence, executive control load (Condition 3). Results: Performance of AD patients declined disproportionately when the number of simple rules that had to be memorized increased (from Condition 1 to 2). An additional increment in complexity (from Condition 2 to 3) did not, however, disproportionately affect performance of the patients. Performance of the aMCI patients did not differ from that of the control participants. In the patient group, correlation analysis showed that memory performance correlated with Condition 1 performance, whereas executive task performance correlated with Condition 2 performance. Conclusions: These results indicate that the reduced learning and memorization of underlying task rules explains a significant part of the diminished complex rule induction performance commonly reported in AD, although results from the correlation analysis suggest involvement of executive control functions as well. Taken together, these findings suggest that care is needed when interpreting rule induction task performance in terms of executive function deficits in these patients.
Testing whether linear equations are causal: A free probability theory approach

We propose a method that infers whether linear relations between two high-dimensional variables X and Y are due to a causal influence from X to Y or from Y to X. The earlier proposed so-called Trace Method is extended to the regime where the dimension of the observed variables exceeds the sample size. Based on previous work, we postulate conditions that characterize a causal relation between X and Y. Moreover, we describe a statistical test and argue that both causal directions are typically rejected if there is a common cause. A full theoretical analysis is presented for the deterministic case but our approach seems to be valid for the noisy case, too, for which we additionally present an approach based on a sparsity constraint. The discussed method yields promising results for both simulated and real world data.
Preliminary findings on the effectiveness of ergonomic criteria for the evaluation of human-computer interfaces

The effectiveness of ergonomic criteria for the evaluation of user interfaces was assessed. Two groups of experts evaluated the interface of a musical database application. After an exploration-diagnosis phase, the participants evaluated the same interface states with or without ergonomic criteria. Preliminary results show that in the first phase, the number of usability problems detected and the proportions of usability problems with respect to the size of the aggregates were similar for both groups. In the second phase, the use of criteria increased both the evaluation diagnosis and the proportions of problems with respect to the size of the aggregates.
Assaying Aspects of Attention and Impulse Control in Mice Using the 5‐Choice Serial Reaction Time Task

First developed in the 1980s by Trevor Robbins in Cambridge to investigate attentional function in rats, the 5‐choice serial reaction time task involves continuous scanning by the subject across a spatial array of visual stimuli. On detecting a brief stimulus at one of five locations, the subject must make a nose poke in order to collect a reward. The task has also been conducted successfully in several strains of mice, including transgenic models. This unit presents the procedures required to run the task in mice, outlining the expected results at each stage of training and presenting examples of the most common manipulations used to dissociate behavior further.
Gesture Based Interaction NUI: An Overview

Touch, face, voice-recognition and movement sensors - all are part of an emerging field of computing often called natural user interface, or NUI. Interacting with technology in these humanistic ways is no longer limited to high-tech secret agents. Gesture recognition is the process by which gestures formed by a user are made known to the system. In completely immersive VR environments, the keyboard is generally not included, Technology incorporates face, voice, gesture, and object recognition to give users a variety of ways to interact with the console, all without needing a controller. This paper focuses on the emerging way of human computer interaction, Gesture recognition concept and gesture types.
Biosynthesis of the Halogenated Auxin, 4-Chloroindole-3-Acetic Acid1[W][OA]

Seeds of several agriculturally important legumes are rich sources of the only halogenated plant hormone, 4-chloroindole-3-acetic acid. However, the biosynthesis of this auxin is poorly understood. Here, we show that in pea (Pisum sativum) seeds, 4-chloroindole-3-acetic acid is synthesized via the novel intermediate 4-chloroindole-3-pyruvic acid, which is produced from 4-chlorotryptophan by two aminotransferases, TRYPTOPHAN AMINOTRANSFERASE RELATED1 and TRYPTOPHAN AMINOTRANSFERASE RELATED2. We characterize a tar2 mutant, obtained by Targeting Induced Local Lesions in Genomes, the seeds of which contain dramatically reduced 4-chloroindole-3-acetic acid levels as they mature. We also show that the widespread auxin, indole-3-acetic acid, is synthesized by a parallel pathway in pea.
Adaptive receive and transmit apodization for synthetic aperture ultrasound imaging

This paper suggests a framework for utilizing adaptive, data-dependent apodization weights on both the receiving and transmitting aperture for Synthetic Aperture (SA) ultrasound imaging. The suggested approach is based on the Minimum Variance (MV) beamformer and consists of two steps. A set of uniquely designed receive apodization weights are applied to pre-summed element data forming a set of adaptively weighted images; these are in SA literature conventionally referred to as low-resolution images. The adaptive transmit apodization is obtained by applying MV across the full set of single emission images before summation. The method is investigated using simulated SA ultrasound data obtained using Field II. Data of 13 point targets distributed at depths from 40 mm to 70 mm, and a 5.5 MHz, 64-element linear array transducer have been used. The investigation has shown that the introduction of adaptive apodization weights on the transmitting aperture provides a main-lobe reduction (estimated at -30 dB) by a factor of 1.8 compared to the method using adaptive apodization weights on the receiving aperture only.