nils-herrmann/clean_scirepeval huggingface dataset:
Turkish Language Resources: Morphological Parser, Morphological Disambiguator and Web Corpus

In this paper, we propose a set of language resources for building Turkish language processing applications. Specifically, we present a finite-state implementation of a morphological parser, an averaged perceptron-based morphological disambiguator, and compilation of a web corpus. Turkish is an agglutinative language with a highly productive inflectional and derivational morphology. We present an implementation of a morphological parser based on two-level morphology. This parser is one of the most complete parsers for Turkish and it runs independent of any other external system such as PCKIMMO in contrast to existing parsers. Due to complex phonology and morphology of Turkish, parsing introduces some ambiguous parses. We developed a morphological disambiguator with accuracy of about 98% using averaged perceptron algorithm. We also present our efforts to build a Turkish web corpus of about 423 million words.
Assembling short reads from jumping libraries with large insert sizes

Advances in Next-Generation Sequencing technologies and sample preparation recently enabled generation of high-quality jumping libraries that have a potential to significantly improve short read assemblies. However, assembly algorithms have to catch up with experimental innovations to benefit from them and to produce high-quality assemblies.



We present a new algorithm that extends recently described exSPAnder universal repeat resolution approach to enable its applications to several challenging data types, including jumping libraries generated by the recently developed Illumina Nextera Mate Pair protocol. We demonstrate that, with these improvements, bacterial genomes often can be assembled in a few contigs using only a single Nextera Mate Pair library of short reads.



Described algorithms are implemented in C++ as a part of SPAdes genome assembler, which is freely available at bioinf.spbau.ru/en/spades.




Supplementary data are available at Bioinformatics online.
A system for acquiring, processing, and rendering panoramic light field stills for virtual reality

We present a system for acquiring, processing, and rendering panoramic light field still photography for display in Virtual Reality (VR). We acquire spherical light field datasets with two novel light field camera rigs designed for portable and efficient light field acquisition. We introduce a novel real-time light field reconstruction algorithm that uses a per-view geometry and a disk-based blending field. We also demonstrate how to use a light field prefiltering operation to project from a high-quality offline reconstruction model into our real-time model while suppressing artifacts. We introduce a practical approach for compressing light fields by modifying the VP9 video codec to provide high quality compression with real-time, random access decompression.
 We combine these components into a complete light field system offering convenient acquisition, compact file size, and high-quality rendering while generating stereo views at 90Hz on commodity VR hardware. Using our system, we built a freely available light field experience application called Welcome to Light Fields featuring a library of panoramic light field stills for consumer VR which has been downloaded over 15,000 times.
Trust and Acceptance of Cloud Computing: A Revised UTAUT Model

Despite the fact that benefits of adopting cloud computing services and applications have become well known within the communities of information technology, adoption of such technology still facing various challenges. Currently, establishing trust is considered as the main barrier preventing individuals and enterprises adopting cloud solutions. Though, to best of our knowledge it has not been considered as a main factor when investigating cloud computing acceptance whereas the majority of studies in the literature focused mainly on finding out ways and approaches increasing trust of cloud computing solutions. Therefore, we present a revised Unified Theory of Acceptance and Use of Technology (UTAUT) where trust is considered as a main construct beside its original constructs.
Non-linear PCA: a missing data approach

Visualizing and analysing the potential non-linear structure of a dataset is becoming an important task in molecular biology. This is even more challenging when the data have missing values.



Here, we propose an inverse model that performs non-linear principal component analysis (NLPCA) from incomplete datasets. Missing values are ignored while optimizing the model, but can be estimated afterwards. Results are shown for both artificial and experimental datasets. In contrast to linear methods, non-linear methods were able to give better missing value estimations for non-linear structured data.



We applied this technique to a time course of metabolite data from a cold stress experiment on the model plant Arabidopsis thaliana, and could approximate the mapping function from any time point to the metabolite responses. Thus, the inverse NLPCA provides greatly improved information for better understanding the complex response to cold stress.



scholz@mpimp-golm.mpg.de.
Formal verification of a fully IEEE compliant floating point unit

In this thesis we describe the formal verification of a fully IEEE compliant floating point unit (FPU). The hardware is verified on the gate-level against a formalization of the IEEE standard. The verification is performed using the theorem proving system PVS. The FPU supports both single and double precision floating point numbers, normal and denormal numbers, all four IEEE rounding modes, and exceptions as required by the standard. Beside the verification of the combinatorial correctness of the FPUs we pipeline the FPUs to allow the integration into an out-of-order processor. We formally define the correctness criterion the pipelines must obey in order to work properly within the processor. We then describe a new methodology based on combining model checking and theorem proving for the verification of the pipelines.
The application of deep convolutional neural networks to ultrasound for modelling of dynamic states within human skeletal muscle

This paper concerns the fully automatic direct in vivo measurement of active and passive dynamic skeletal muscle states using ultrasound imaging. Despite the long standing medical need (myopathies, neuropathies, pain, injury, ageing), currently technology (electromyography, dynamometry, shear wave imaging) provides no general, non-invasive method for online estimation of skeletal intramuscular states. Ultrasound provides a technology in which static and dynamic muscle states can be observed non-invasively, yet current computational image understanding approaches are inadequate. We propose a new approach in which deep learning methods are used for understanding the content of ultrasound images of muscle in terms of its measured state. Ultrasound data synchronized with electromyography of the calf muscles, with measures of joint torque/angle were recorded from 19 healthy participants (6 female, ages: 30 ± 7.7). A segmentation algorithm previously developed by our group was applied to extract a region of interest of the medial gastrocnemius. Then a deep convolutional neural network was trained to predict the measured states (joint angle/torque, electromyography) directly from the segmented images. Results revealed for the first time that active and passive muscle states can be measured directly from standard b-mode ultrasound images, accurately predicting for a held out test participant changes in the joint angle, electromyography, and torque with as little error as 0.022°, 0.0001V, 0.256Nm (root mean square error) respectively.
CD69 gene is differentially regulated in T and B cells by evolutionarily conserved promoter-distal elements.

CD69 is a type II C-type lectin involved in lymphocyte migration and cytokine secretion. CD69 expression represents one of the earliest available indicators of leukocyte activation and its rapid induction occurs through transcriptional activation. In this study we examined the molecular mechanism underlying mouse CD69 gene transcription in vivo in T and B cells. Analysis of the 45-kb region upstream of the CD69 gene revealed evolutionary conservation at the promoter and at four noncoding sequences (CNS) that were called CNS1, CNS2, CNS3, and CNS4. These regions were found to be hypersensitive sites in DNase I digestion experiments, and chromatin immunoprecipitation assays showed specific epigenetic modifications. CNS2 and CNS4 displayed constitutive and inducible enhancer activity in transient transfection assays in T cells. Using a transgenic approach to test CNS function, we found that the CD69 promoter conferred developmentally regulated expression during positive selection of thymocytes but could not support regulated expression in mature lymphocytes. Inclusion of CNS1 and CNS2 caused suppression of CD69 expression, whereas further addition of CNS3 and CNS4 supported developmental-stage and lineage-specific regulation in T cells but not in B cells. We concluded CNS1-4 are important cis-regulatory elements that interact both positively and negatively with the CD69 promoter and that differentially contribute to CD69 expression in T and B cells.
Smart Integrated Renewable Energy Systems ( SIRES ) : A Novel Approach for Sustainable Development

Technical and economic aspects of the viability of SIRES (Smart Integrated Renewable Energy Systems) for sustainable development of remote and rural areas of the world are discussed. The hallmark of the proposed SIRES is the smart utilization of several renewable resources in an integrated fashion and matching of resources and needs a priori with the ultimate goal of “energization”, not just “electrification”. Historical background leading to this approach is succinctly presented along with a comprehensive schematic diagram. Modeling of various components and their collective use in optimizing SIRES with the aid of genetic algorithm are presented using a typical hypothetical example. SIRES is also compared with various approaches for rural development based on Annualized Cost of System (ACS) and installation costs. Implementation of SIRES will lead to overall sustainable development of rural communities.
Room-Temperature High-Performance H2S Sensor Based on Porous CuO Nanosheets Prepared by Hydrothermal Method.

Porous CuO nanosheets were prepared on alumina tubes using a facile hydrothermal method, and their morphology, microstructure, and gas-sensing properties were investigated. The monoclinic CuO nanosheets had an average thickness of 62.5 nm and were embedded with numerous holes with diameters ranging from 5 to 17 nm. The porous CuO nanosheets were used to fabricate gas sensors to detect hydrogen sulfide (H2S) operating at room temperature. The sensor showed a good response sensitivity of 1.25 with respond/recovery times of 234 and 76 s, respectively, when tested with the H2S concentrations as low as 10 ppb. It also showed a remarkably high selectivity to the H2S, but only minor responses to other gases such as SO2, NO, NO2, H2, CO, and C2H5OH. The working principle of the porous CuO nanosheet based sensor to detect the H2S was identified to be the phase transition from semiconducting CuO to a metallic conducting CuS.
Combining qualitative and quantitative research within mixed method research designs: a methodological review.

It has been argued that mixed methods research can be useful in nursing and health science because of the complexity of the phenomena studied. However, the integration of qualitative and quantitative approaches continues to be one of much debate and there is a need for a rigorous framework for designing and interpreting mixed methods research. This paper explores the analytical approaches (i.e. parallel, concurrent or sequential) used in mixed methods studies within healthcare and exemplifies the use of triangulation as a methodological metaphor for drawing inferences from qualitative and quantitative findings originating from such analyses.



This review of the literature used systematic principles in searching CINAHL, Medline and PsycINFO for healthcare research studies which employed a mixed methods approach and were published in the English language between January 1999 and September 2009.



In total, 168 studies were included in the results. Most studies originated in the United States of America (USA), the United Kingdom (UK) and Canada. The analytic approach most widely used was parallel data analysis. A number of studies used sequential data analysis; far fewer studies employed concurrent data analysis. Very few of these studies clearly articulated the purpose for using a mixed methods design. The use of the methodological metaphor of triangulation on convergent, complementary, and divergent results from mixed methods studies is exemplified and an example of developing theory from such data is provided.



A trend for conducting parallel data analysis on quantitative and qualitative data in mixed methods healthcare research has been identified in the studies included in this review. Using triangulation as a methodological metaphor can facilitate the integration of qualitative and quantitative findings, help researchers to clarify their theoretical propositions and the basis of their results. This can offer a better understanding of the links between theory and empirical findings, challenge theoretical assumptions and develop new theory.
An Evaluation of Yelp Dataset

Yelp is one of the largest online searching and reviewing systems for kinds of businesses, including restaurants, shopping, home services et al. Analyzing the real world data from Yelp is valuable in acquiring the interests of users, which helps to improve the design of the next generation system. This paper targets the evaluation of Yelp dataset, which is provided in the Yelp data challenge. A bunch of interesting results are found. For instance, to reach any one in the Yelp social network, one only needs 4.5 hops on average, which verifies the classical six degree separation theory; Elite user mechanism is especially effective in maintaining the healthy of the whole network; Users who write less than 100 business reviews dominate. Those insights are expected to be considered by Yelp to make intelligent business decisions in the future.
A demonstration of the Polaris poker system

Poker games provide a useful testbed for modern Artificial Intelligence techniques. Unlike many classical game domains such as chess and checkers, poker includes elements of imperfect information, stochastic events, and one or more adversarial agents to interact with. Furthermore, in poker it is possible to win or lose by varying degrees. Therefore, it can be advantageous to adapt ones’ strategy to exploit a weak opponent. A poker agent must address these challenges, acting in uncertain environments and exploiting other agents, in order to be highly successful. Arguably, poker games more closely resemble many real world problems than games with perfect information. In this brief paper, we outline Polaris, a Texas Hold’em poker program. Polaris recently defeated top human professionals at the Man vs. Machine Poker Championship and it is currently the reigning AAAI Computer Poker Competition winner in the limit equilibrium and no-limit events.
Links between two semisymmetric graphs on 112 vertices via association schemes

This paper provides a model of the use of computer algebra experimentation in algebraic graph theory. Starting from the semisymmetric cubic graph L on 112 vertices, we embed it into another semisymmetric graph N of valency 15 on the same vertex set. In order to consider systematically the links between L and N a number of combinatorial structures are involved and related coherent configurations are investigated. In particular, the construction of the incidence double cover of directed graphs is exploited. As a natural by-product of the approach presented here, a number of new interesting (mostly non-Schurian) association schemes on 56, 112 and 120 vertices are introduced and briefly discussed. We use computer algebra system GAP (including GRAPE and nauty), as well as computer package COCO.
Interactive Shadow Play Animation System

The paper describes a Chinese shadow play animation system based on Kinect. Users, without any professional training, can personally manipulate the shadow characters to finish a shadow play performance by their body actions and get a shadow play video through giving the record command to our system if they want. In our system, Kinect is responsible for capturing human movement and voice commands data. Gesture recognition module is used to control the change of the shadow play scenes. After packaging the data from Kinect and the recognition result from gesture recognition module, VRPN transmits them to the server-side. At last, the server-side uses the information to control the motion of shadow characters and video recording. This system not only achieves human-computer interaction, but also realizes the interaction between people. It brings an entertaining experience to users and easy to operate for all ages. Even more important is that the application background of Chinese shadow play embodies the protection of the art of shadow play animation. Gesture recognition, Kinect, shadow play animation, VRPN.
Acute iliofemoral venous thrombosis in patients with atresia of the inferior vena cava can be treated successfully with catheter-directed thrombolysis.

To assess the effectiveness and clinical outcomes of catheter-directed thrombolysis in patients with atresia of the inferior vena cava (IVC) and acute iliofemoral deep vein thrombosis (DVT).



From 2001 to 2009, 11 patients (median age, 32 y) with atresia of the IVC and acute iliofemoral DVT in 13 limbs were admitted for catheter-directed thrombolysis. Through a multiple-side hole catheter inserted in the popliteal vein, continuous pulse-spray infusion of tissue plasminogen activator and heparin was performed. Thrombolysis was terminated when all thrombus was resolved and venous outflow through the paravertebral collateral vessels was achieved. After thrombolysis, all patients received lifelong anticoagulation and compression stockings and were followed up at regular intervals.



Ultrasound or computed tomography revealed absence of the suprarenal segment of the IVC in two patients, and nine were diagnosed with absence of the infrarenal segment of the IVC. Median treatment time was 58 hours (range, 42-95 h). No deaths or serious complications occurred. Overall, complications were observed in four patients, one of whom required blood transfusion. Three patients were diagnosed with thrombophilia. Median follow-up was 37 months (range, 51 d to 96 mo). All patients had patent deep veins and one developed reflux in the popliteal fossa after 4 years. No thromboembolic recurrences were observed during follow-up.



Catheter-directed thrombolysis of patients with acute iliofemoral DVT and atresia of the IVC is a viable treatment option, as reasonable clinical outcomes can be obtained.
Virginal hypertrophy. Case report.

A 13-year-old girl with virginal hypertrophy (bilateral extensive juvenile hypertrophy) of the breasts is presented. Her breasts began to grow rapidly after puberty and reached an enormous size within a year. On examination, both breasts were greatly enlarged. Routine blood chemistry and the endocrinological investigations were normal. The computerized tomography scan of the sella was unremarkable. A bilateral reduction mammaplasty was performed, and histological analysis of the breast tissue revealed the diagnosis of virginal hypertrophy. After four months her breasts began to grow again, and a second mammaplasty was performed. After this operation, tamoxifen citrate was given to prevent recurrence for four months, and during the follow-up period of 20 months, no recurrence was noted.
The National Institute on Aging Health Disparities Research Framework.

Development of a new framework for the National Institute on Aging (NIA) to assess progress and opportunities toward stimulating and supporting rigorous research to address health disparities.



Portfolio review of NIA's health disparities research portfolio to evaluate NIA's progress in addressing priority health disparities areas.



The NIA Health Disparities Research Framework highlights important factors for health disparities research related to aging, provides an organizing structure for tracking progress, stimulates opportunities to better delineate causal pathways and broadens the scope for malleable targets for intervention, aiding in our efforts to address health disparities in the aging population.



The promise of health disparities research depends largely on scientific rigor that builds on past findings and aggressively pursues new approaches. The NIA Health Disparities Framework provides a landscape for stimulating interdisciplinary approaches, evaluating research productivity and identifying opportunities for innovative health disparities research related to aging.
Touch Your Heart: A Tone-aware Chatbot for Customer Care on Social Media

Chatbot has become an important solution to rapidly increasing customer care demands on social media in recent years. However, current work on chatbot for customer care ignores a key to impact user experience - tones. In this work, we create a novel tone-aware chatbot that generates toned responses to user requests on social media. We first conduct a formative research, in which the effects of tones are studied. Significant and various influences of different tones on user experience are uncovered in the study. With the knowledge of effects of tones, we design a deep learning based chatbot that takes tone information into account. We train our system on over 1.5 million real customer care conversations collected from Twitter. The evaluation reveals that our tone-aware chatbot generates as appropriate responses to user requests as human agents. More importantly, our chatbot is perceived to be even more empathetic than human agents.
Minimum Cost Path Problem for Plug-in Hybrid Electric Vehicles

We introduce a practically important and theoretically challenging problem: finding the minimum cost path for plug-in hybrid electric vehicles (PHEVs) in a network with refueling and battery switching stations, considering electricity and gasoline as sources of energy with different cost structures and limitations. We show that this problem is NP-complete even though its electric vehicle and conventional vehicle special cases are polynomially solvable. We propose three solution techniques: (1) a mixed integer quadratically constrained program that incorporates non-fuel costs such as vehicle depreciation, battery degradation and stopping, (2) a dynamic programming based heuristic and (3) a shortest path heuristic. We conduct extensive computational experiments using both real world road network data and artificially generated road networks of various sizes and provide significant insights about the effects of driver preferences and the availability of battery switching stations on the PHEV economics. In particular, our findings show that increasing the number of battery switching stations may not be enough to overcome the range anxiety of the drivers.