nils-herrmann/clean_scirepeval huggingface dataset:
A Predictive Model for Music based on Learned Interval Representations

Connectionist sequence models (e.g., RNNs) applied to musical sequences suffer from two known problems: First, they have strictly “absolute pitch perception”. Therefore, they fail to generalize over musical concepts which are commonly perceived in terms of relative distances between pitches (e.g., melodies, scale types, modes, cadences, or chord types). Second, they fall short of capturing the concepts of repetition and musical form. In this paper we introduce the recurrent gated autoencoder (RGAE), a recurrent neural network which learns and operates on interval representations of musical sequences. The relative pitch modeling increases generalization and reduces sparsity in the input data. Furthermore, it can learn sequences of copy-and-shift operations (i.e. chromatically transposed copies of musical fragments)—a promising capability for learning musical repetition structure. We show that the RGAE improves the state of the art for general connectionist sequence models in learning to predict monophonic melodies, and that ensembles of relative and absolute music processing models improve the results appreciably. Furthermore, we show that the relative pitch processing of the RGAE naturally facilitates the learning and the generation of sequences of copy-and-shift operations, wherefore the RGAE greatly outperforms a common absolute pitch recurrent neural network on this task.
Global Increases in Individualism.

Individualism appears to have increased over the past several decades, yet most research documenting this shift has been limited to the study of a handful of highly developed countries. Is the world becoming more individualist as a whole? If so, why? To answer these questions, we examined 51 years of data on individualist practices and values across 78 countries. Our findings suggest that individualism is indeed rising in most of the societies we tested. Despite dramatic shifts toward greater individualism around the world, however, cultural differences remain sizable. Moreover, cultural differences are primarily linked to changes in socioeconomic development, and to a lesser extent to shifts in pathogen prevalence and disaster frequency.
Test case design for context-aware applications: Are we there yet?

Current software systems have increasingly implemented context-aware adaptations to handle the diversity of conditions of their surrounding environment. Therefore, people are becoming used to a variety of context-aware software systems (CASS). This context-awareness brings challenges to the software construction and testing because the context is unpredictable and may change at any time. Therefore, software engineers need to consider the dynamic context changes while testing CASS. Different test case design techniques (TCDT) have been proposed to support the testing of CASS. However, to the best of our knowledge, there is no analysis of these proposals on the advantages, limitations and their effective support to context variation during testing.  To gather empirical evidence on TCDT concerned with CASS by identifying, evaluating and synthesizing knowledge available in the literature.  To undertake a secondary study (quasi -Systematic Literature Review) on TCDT for CASS regarding their assessed quality characteristics, used coverage criteria, test type, and test technique.  From 833 primary studies published between 2004 and 2014, just 17 studies regard the design of test cases for CASS. Most of them focus on functional suitability. Furthermore, some of them take into account the changes in the context by providing specific test cases for each context configuration (static perspective) during the test execution. These 17 studies revealed five challenges affecting the design of test cases and 20 challenges regarding the testing of CASS. Besides, seven TCDT are not empirically evaluated.  A few TCDT partially support the testing of CASS. However, it has not been observed evidence on any TCDT supporting the truly context-aware testing, which that can adapt the expected output based on the context variation (dynamic perspective) during the test execution. It is an open issue deserving greater attention from researchers to increase the testing coverage and ensure users confidence in CASS.
Pseudo aptamer expands aptamer ’ s applications

Because of broad range of applications and distinctive properties of aptamer, the global market size was valued at USD 723.6 million in 2016 and is projected to grow at the compound annual growth rate (CAGR) of 28.2%,1 and expected to reach $8.91 Billion by 2025, growing rapidly. Aptamers and the derivatives are also referred to as “synthetic antibodies” or “chemical antibodies”2‒5 that are able to bind with high affinity and specificity to almost all types of molecules as well as antigens, cells. Because of their unique properties, aptamers have a wide range of applications, particularly in biological and medical sciences, including diagnosis, therapies, forensics, and biodefense.6‒9 So far, hundreds of aptamer reagents have been developed for the applications,10 which are faster, cheaper, and less or without the predictable problems associated with the production of recombinant antibodies. This review summarizes the resent technologies of modified analogous of aptamer, so called pseudo aptamers in this script.
phyloseq: A Bioconductor Package for Handling and Analysis of High-Throughput Phylogenetic Sequence Data

We present a detailed description of a new Bioconductor package, phyloseq, for integrated data and analysis of taxonomically-clustered phylogenetic sequencing data in conjunction with related data types. The phyloseq package integrates abundance data, phylogenetic information and covariates so that exploratory transformations, plots, and confirmatory testing and diagnostic plots can be carried out seamlessly. The package is built following the S4 object-oriented framework of the R language so that once the data have been input the user can easily transform, plot and analyze the data. We present some examples that highlight the methods and the ease with which we can leverage existing packages.
Categories for classification of aircraft flight model validation

One version of a stochastic computer simulation of airspace includes the implementation of complex, high-fidelity models of aircraft. Since the models are pre-existing, third-party developed products, these aircraft models require validation prior to implementation. Several methodologies are available to demonstrate the accuracy of these models and a variety of testers potentially involved, so a notation is proposed to describe the level of testing performed in the validation of a given model using seven fields, each making use of succinct notation. Rather than limiting those qualified to do this type of work or restrict the aircraft models available for use, this classification is proposed in order to allow for anyone to complete validation tasks and to allow for a wide variety of tasks during the course of validation, while keeping the ultimate user of the model easily and fully informed as to the level of testing done and the experience and qualifications of the tester.
Influence of FE model variability in predicting brain motion and intracranial pressure changes in head impact simulations

In order to create a useful computational tool that will aid in the understanding and perhaps prevention of head injury, it is important to know the quantitative influence of the constitutive properties, geometry and finite element formulations of the intracranial contents upon the mechanics of a head impact event. The University College Dublin Brain Trauma Model (UCDBTM)  has been refined and validated against a series of cadaver tests and the influence of different finite element formulations has been investigated. In total six different model configurations were constructed: (i) the baseline model, (ii) a refined baseline model which explicitly differentiates between grey and white neural tissue, (iii) a model with three elements through the thickness of the cerebrospinal fluid (CSF) layer, (iv) a model simulating a sliding boundary, (v) a projection mesh model (which also distinguishes between neural tissue) and (vi) a morphed model. These models have been compared against a cadaver test of Trosseille  and of Hardy . The results indicate that, despite the fundamental differences between these six model formulations, the comparisons with the experimentally measured pressures and relative displacements were largely consistent and in good agreement. These results may prove useful for those attempting to model real life accident scenarios, especially when the time to construct a patient specific model using traditional mesh generation approaches is taken into account.
US Intergroup Trial of Response-Adapted Therapy for Stage III to IV Hodgkin Lymphoma Using Early Interim Fluorodeoxyglucose-Positron Emission Tomography Imaging: Southwest Oncology Group S0816.

Four US National Clinical Trials Network components (Southwest Oncology Group, Cancer and Leukemia Group B/Alliance, Eastern Cooperative Oncology Group, and the AIDS Malignancy Consortium) conducted a phase II Intergroup clinical trial that used early interim fluorodeoxyglucose positron emission tomography (FDG-PET) imaging to determine the utility of response-adapted therapy for stage III to IV classic Hodgkin lymphoma.



The Southwest Oncology Group S0816 (Fludeoxyglucose F 18-PET/CT Imaging and Combination Chemotherapy With or Without Additional Chemotherapy and G-CSF in Treating Patients With Stage III or Stage IV Hodgkin Lymphoma) trial enrolled 358 HIV-negative patients between July 1, 2009, and December 2, 2012. A PET scan was performed after two initial cycles of doxorubicin, bleomycin, vinblastine, and dacarbazine (ABVD) and was labeled PET2. PET2-negative patients (Deauville score 1 to 3) received an additional four cycles of ABVD, whereas PET2-positive patients (Deauville score 4 to 5) were switched to escalated bleomycin, etoposide, doxorubicin, cyclophosphamide, vincristine, procarbazine, and prednisone (eBEACOPP) for six cycles. Among 336 eligible and evaluable patients, the median age was 32 years (range, 18 to 60 years), with 52% stage III, 48% stage IV, 49% International Prognostic Score 0 to 2, and 51% score 3 to 7.



Three hundred thirty-six of the enrolled patients were evaluable. Central review of the interim PET2 scan was performed in 331 evaluable patients, with 271 (82%) PET2-negative and 60 (18%) PET2-positive. Of 60 eligible PET2-positive patients, 49 switched to eBEACOPP as planned and 11 declined. With a median follow-up of 39.7 months, the Kaplan-Meier estimate for 2-year overall survival was 98% (95% CI, 95% to 99%), and the 2-year estimate for progression-free survival (PFS) was 79% (95% CI, 74% to 83%). The 2-year estimate for PFS in the subset of patients who were PET2-positive after two cycles of ABVD was 64% (95% CI, 50% to 75%). Both nonhematologic and hematologic toxicities were greater in the eBEACOPP arm than in the continued ABVD arm.



Response-adapted therapy based on interim PET imaging after two cycles of ABVD seems promising with a 2-year PFS of 64% for PET2-positive patients, which is much higher than the expected 2-year PFS of 15% to 30%.
Endurance Exercise and the Regulation of Skeletal Muscle Metabolism.

Almost a half century ago, regular endurance exercise was shown to improve the capacity of skeletal muscle to oxidize substrates to produce ATP for muscle work. Since then, adaptations in skeletal muscle mRNA level were shown to happen with a single bout of exercise. Protein changes occur within days if daily endurance exercise continues. Some of the mRNA and protein changes cause increases in mitochondrial concentrations. One mitochondrial adaptation that occurs is an increase in fatty acid oxidation at a given absolute, submaximal workload. Mechanisms have been described as to how endurance training increases mitochondria. Importantly, Pgc-1α is a master regulator of mitochondrial biogenesis by increasing many mitochondrial proteins. However, not all adaptations to endurance training are associated with increased mitochondrial concentrations. Recent evidence suggests that the energetic demands of muscle contraction are by themselves stronger controllers of body weight and glucose control than is muscle mitochondrial content. Endurance exercise has also been shown to regulate the processes of mitochondrial fusion and fission. Mitophagy removes damaged mitochondria, a process that maintains mitochondrial quality. Skeletal muscle fibers are composed of different phenotypes, which are based on concentrations of mitochondria and various myosin heavy chain protein isoforms. Endurance training at physiological levels increases type IIa fiber type with increased mitochondria and type IIa myosin heavy chain. Endurance training also improves capacity of skeletal muscle blood flow. Endurance athletes possess enlarged arteries, which may also exhibit decreased wall thickness. VEGF is required for endurance training-induced increases in capillary-muscle fiber ratio and capillary density.
Up in smoke: I. Smoke-derived germination cues for postfire annual,Nicotiana attenuata torr. Ex. Watson

Some postfire annuals with dormant seeds use heat or chemical cues from charred wood to synchronize their germination with the postfire environment. We report that wood smoke and polar extracts of wood smoke, but not the ash of burned wood, contain potent cue(s) that stimulate germination in the postfire annual plant,Nicotiana attenuata. We examined the responses of seeds from six populations of plants from southwest Utah to extracts of smoke and found the proportion of viable seeds that germinated in the presence of smoke cues to vary between populations but to be consistent between generations. With the most dormant genotypes, we examine three mechanisms by which smoke-derived chemical cues may stimulate germination (chemical scarification of the seed coat and nutritive- and signal-mediated stimulation of germination) and report that the response is consistent with the signal-mediated mechanism. The germination cue(s) found in smoke are produced by the burning of hay, hardwood branches, leaves, and, to a lesser degree, cellulose. Moreover, the cues are found in the common food condiment, “liquid smoke,” and we find no significant differences between brands. With a bioassay-driven fractionation of liquid smoke, we identified 71 compounds in active fractions by GC-MS and AA spectrometry. However, when these compounds were tested in pure form or in combinations that mimicked the composition of active fractions over a range of concentrations, they failed to stimulate germination to the same degree that smoke fractions did. Moreover, enzymatic oxidation of some of these compounds also failed to stimulate germination. In addition, we tested 43 additional compounds also reported from smoke, 85 compounds that were structurally similar to those reported from smoke and 34 compounds reported to influence germination in other species. Of the 233 compounds tested, 16 proved to inhibit germination at the concentrations tested, and none reproduced the activity of wood smoke. By thermally desorbing smoke produced by cellulose combustions that was trapped on Chromosorb 101, we demonstrate that the cue is desorbed between 125 and 150°C. We estimate that the germination cues are active at concentrations of less than 1 pg/seed and, due to their chromatographic behavior, infer that a number of different chemical structures are active. In separate experiments, we demonstrate that cues remain active for at least 53 days in soil under greenhouse conditions and that the application of aqucous extracts of smoke to soil containing seeds results in dramatic increases in germination of artificial seed banks. Hence, although the chemical nature of the germination cue remains elusive, the stability of the germination cues, their water-solubility, and their activity in low concentrations suggest that these cues could serve as powerful tools for the examination of dormant seed banks and the selective factors thought to be important in the evolution of postfire plant communities.
Mapping Large Loops with a Single Hand-Held Camera

This paper presents a method for Simultaneous Localization and Mapping (SLAM), relying on a monocular camera as the only sensor, which is able to build outdoor, closed-loop maps much larger than previously achieved with such input. Our system, based on the Hierarchical Map approach , builds independent local maps in real-time using the EKF-SLAM technique and the inverse depth representation proposed in . The main novelty in the local mapping process is the use of a data association technique that greatly improves its robustness in dynamic and complex environments. A new visual map matching algorithm stitches these maps together and is able to detect large loops automatically, taking into account the unobservability of scale intrinsic to pure monocular SLAM. The loop closing constraint is applied at the upper level of the Hierarchical Map in near real-time. We present experimental results demonstrating monocular SLAM as a human carries a camera over long walked trajectories in outdoor areas with people and other clutter, even in the more difficult case of forward-looking camera, and show the closing of loops of several hundred meters.
Acquired lymphangioma of the penis in a patient with severe phimosis.

presenting with bullous pemphigoid-like lesions.   Scabies associated with a bullous pemphigoid-like eruption.  Association of scabies with a bullous pemphigoid-like eruption.  Bullous scabies failing to respond to glucocorticoids, immunoglobulin, and cyclophosphamide. . 8 Nakamura E, Taniguchi H, Ohtaki N. A case of crusted scabies with a bullous pemphigoid-like eruption and nail involvement.  2006; 33: 196–201. 9 Galvany Rossell L, Salleras Redonnet M, Umbert Millet P. Bullous scabies responding to ivermectin therapy. Actas Dermosifiliogr 2010; 101: 81–84. 10 Gutte RM. Bullous scabies in an adult: a case report with review of literature.
Prediction and classification of Alzheimer disease based on quantification of MRI deformation

Detecting early morphological changes in the brain and making early diagnosis are important for Alzheimer's disease (AD). High resolution magnetic resonance imaging can be used to help diagnosis and prediction of the disease. In this paper, we proposed a machine learning method to discriminate patients with AD or mild cognitive impairment (MCI) from healthy elderly and to predict the AD conversion in MCI patients by computing and analyzing the regional morphological differences of brain between groups. Distance between each pair of subjects was quantified from a symmetric diffeomorphic registration, followed by an embedding algorithm and a learning approach for classification. The proposed method obtained accuracy of 96.5% in differentiating mild AD from healthy elderly with the whole-brain gray matter or temporal lobe as region of interest (ROI), 91.74% in differentiating progressive MCI from healthy elderly and 88.99% in classifying progressive MCI versus stable MCI with amygdala or hippocampus as ROI. This deformation-based method has made full use of the pair-wise macroscopic shape difference between groups and consequently increased the power for discrimination.
Fast Image Dehazing Method Based on Linear Transformation

Images captured in hazy or foggy weather conditions are seriously degraded by the scattering of atmospheric particles, which directly influences the performance of outdoor computer vision systems. In this paper, a fast algorithm for single image dehazing is proposed based on linear transformation by assuming that a linear relationship exists in the minimum channel between the hazy image and the haze-free image. First, the principle of linear transformation is analyzed. Accordingly, the method of estimating a medium transmission map is detailed and the weakening strategies are introduced to solve the problem of the brightest areas of distortion. To accurately estimate the atmospheric light, an additional channel method is proposed based on quad-tree subdivision. In this method, average grays and gradients in the region are employed as assessment criteria. Finally, the haze-free image is obtained using the atmospheric scattering model. Numerous experimental results show that this algorithm can clearly and naturally recover the image, especially at the edges of sudden changes in the depth of field. It can, thus, achieve a good effect for single image dehazing. Furthermore, the algorithmic time complexity is a linear function of the image size. This has obvious advantages in running time by guaranteeing a balance between the running speed and the processing effect.
NIS04-2: Detection of DNS Anomalies using Flow Data Analysis

The Domain Name System (DNS) is an essential network infrastructure component since it supports the operation of the Web, Email, Voice over IP (VoIP) and other business- critical applications running over the network. Events that compromise the security of DNS can have a significant impact on the Internet since they can affect its availability and its intended operation. This paper describes algorithms used to monitor and detect certain types of attacks to the DNS infrastructure using flow data. Our methodology is based on algorithms that do not rely on known signature attack vectors. The effectiveness of our solution is illustrated with real and simulated traffic examples. In one example, we were able to detect a tunneling attack well before the appearance of public reports of it.
The rôle of abscisic acid in root growth and gravireaction: A critical review

A brief account is given of the discovery of abscisic acid (ABA) in roots and root caps of higher plants as well as the techniques by which ABA may be demonstrated in these tissues. The remainder of the review is concerned with examining the rôle of ABA in the regulation of root growth. In this regard, it is well established that when ABA is supplied to roots their elongation is usually inhibited, although at low external concentrations a stimulation of growth may also be found. Fewer observations have been directed at exploring the connection between root growth and the level of naturally occurring, endogenous ABA. Nevertheless, the evidence here also suggests that ABA is an inhibitory regulator of root growth. Moreover, ABA appears to be involved in the differential growth that arises in response to a gravitational stimulus. Recent reports that deny a rôle for ABA in root gravitropism are considered inconclusive. The response of roots to osmotic stress and the changes in ABA levels which ensue, are summarised; so are the interrelations between ABA and other hormones, particularly auxin (e.g. indoleacetic acid); both are considered in the context of the root growth and development. Quantitative changes in auxin and ABA levels may together provide the root with a flexible means of regulating its growth.