nils-herrmann/clean_scirepeval huggingface dataset:
Parallel Reservoir Computing Using Optical Amplifiers

Reservoir computing (RC), a computational paradigm inspired on neural systems, has become increasingly popular in recent years for solving a variety of complex recognition and classification problems. Thus far, most implementations have been software-based, limiting their speed and power efficiency. Integrated photonics offers the potential for a fast, power efficient and massively parallel hardware implementation. We have previously proposed a network of coupled semiconductor optical amplifiers as an interesting test case for such a hardware implementation. In this paper, we investigate the important design parameters and the consequences of process variations through simulations. We use an isolated word recognition task with babble noise to evaluate the performance of the photonic reservoirs with respect to traditional software reservoir implementations, which are based on leaky hyperbolic tangent functions. Our results show that the use of coherent light in a well-tuned reservoir architecture offers significant performance benefits. The most important design parameters are the delay and the phase shift in the system's physical connections. With optimized values for these parameters, coherent semiconductor optical amplifier (SOA) reservoirs can achieve better results than traditional simulated reservoirs. We also show that process variations hardly degrade the performance, but amplifier noise can be detrimental. This effect must therefore be taken into account when designing SOA-based RC implementations.
Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B.

High-throughput screening (HTS) of compound libraries is used to discover novel leads for drug development. When a structure is available for the target, computer-based screening using molecular docking may also be considered. The two techniques have rarely been used together on the same target. The opportunity to do so presented itself in a project to discover novel inhibitors for the enzyme protein tyrosine phosphatase-1B (PTP1B), a tyrosine phosphatase that has been implicated as a key target for type II diabetes. A corporate library of approximately 400 000 compounds was screened using high-throughput experimental techniques for compounds that inhibited PTP1B. Concurrently, molecular docking was used to screen approximately 235 000 commercially available compounds against the X-ray crystallographic structure of PTP1B, and 365 high-scoring molecules were tested as inhibitors of the enzyme. Of approximately 400 000 molecules tested in the high-throughput experimental assay, 85 (0.021%) inhibited the enzyme with IC50 values less than 100 microM; the most active had an IC50 value of 4.2 microM. Of the 365 molecules suggested by molecular docking, 127 (34.8%) inhibited PTP1B with IC50 values less than 100 microM; the most active of these had an IC50 of 1.7 microM. Structure-based docking therefore enriched the hit rate by 1700-fold over random screening. The hits from both the high-throughput and docking screens were dissimilar from phosphotyrosine, the canonical substrate group for PTP1B; the two hit lists were also very different from each other. Surprisingly, the docking hits were judged to be more druglike than the HTS hits. The diversity of both hit lists and their dissimilarity from each other suggest that docking and HTS may be complementary techniques for lead discovery.
The Optimization of an Intravaginal Ring Releasing Progesterone Using a Mathematical Model

Progering® is the only intravaginal ring intended for contraception therapies during lactation. It is made of silicone and releases progesterone through the vaginal walls. However, some drawbacks have been reported in the use of silicone. Therefore, ethylene vinyl acetate copolymer (EVA) was tested in order to replace it. EVA rings were produced by a hot-melt extrusion procedure. Swelling and degradation assays of these matrices were conducted in different mixtures of ethanol/water. Solubility and partition coefficient of progesterone were measured, together with the initial hormone load and characteristic dimensions. A mathematical model was used to design an EVA ring that releases the hormone at specific rate. An EVA ring releasing progesterone in vitro at about 12.05 ± 8.91 mg day−1 was successfully designed. This rate of release is similar to that observed for Progering®. In addition, it was observed that as the initial hormone load or ring dimension increases, the rate of release also increases. Also, the device lifetime was extended with a rise in the initial amount of hormone load. EVA rings could be designed to release progesterone in vitro at a rate of 12.05 ± 8.91 mg day−1. This ring would be used in contraception therapies during lactation. The use of EVA in this field could have initially several advantages: less initial and residual hormone content in rings, no need for additional steps of curing or crosslinking, less manufacturing time and costs, and the possibility to recycle the used rings.
Is the Canadian childhood obesity epidemic related to physical inactivity?

This study examined the relation among children's physical activity, sedentary behaviours, and body mass index (BMI), while controlling for sex, family structure, and socioeconomic status. Epidemiological study examining the relations among physical activity participation, sedentary behaviour (video game use and television (TV)/video watching), and BMI on a nationally representative sample of Canadian children. A representative sample of Canadian children aged 7–11 (N=7216) from the 1994 National Longitudinal Survey of Children and Youth was used in the analysis. Physical activity and sport participation, sedentary behaviour (video game use and TV/video watching), and BMI measured by parental report. Both organized and unorganized sport and physical activity are negatively associated with being overweight (10–24% reduced risk) or obese (23–43% reduced risk), while TV watching and video game use are risk factors for being overweight (17–44% increased risk) or obese (10–61% increased risk). Physical activity and sedentary behaviour partially account for the association of high socioeconomic status and two-parent family structure with the likelihood of being overweight or obese. This study provides evidence supporting the link between physical inactivity and obesity of Canadian children.
Analysis of wire tension control principles for highly dynamic applications in coil winding: Investigation of new tension control devices for noncicurlar orthocyclic coils

This paper comprises an overview of different aspects for wire tension control devices and algorithms according to the state of industrial use and state of research. Based on a typical winding task of an orthocyclic winding scheme, possible new principles for an alternative piezo-electric actuator and an electromechanical tension control will be derived and presented.
Protein unfolding by the mitochondrial membrane potential

Mitochondria can unfold importing precursor proteins by unraveling them from their N-termini. However, how this unraveling is induced is not known. Two candidates for the unfolding activity are the electrical potential across the inner mitochondrial membrane and mitochondrial Hsp70 in the matrix. Here, we propose that many precursors are unfolded by the electrical potential acting directly on positively charged amino acid side chains in the targeting sequences. Only precursor proteins with targeting sequences that are long enough to reach the matrix at the initial interaction with the import machinery are unfolded by mitochondrial Hsp70, and this unfolding occurs even in the absence of a membrane potential.
Review of Constructivism and Social Constructivism

Although constructivism is a concept that has been embraced recently, a great number of sociologists, psychologists, applied linguists, and teachers have provided varied definitions of this concept. Also many philosophers and educationalists such as Piaget, Vygotsky, and Perkins suggest that constructivism and social constructivism try to solve the problems of traditional teaching and learning. This research review represents the meaning and the origin of constructivism, and then discusses the role of leaning, teaching, learner, and teacher in the first part from constructivist perspective. In the second part, the paper discusses the same issues, as presented in the first part, from social constructivist perspective. The purpose of this research review is to make EFL teachers and EFL students more familiar with the importance and guidance of both constructivism and social constructivism perspectives.
Community assembly: when should history matter?

Community assembly provides a conceptual foundation for understanding the processes that determine which and how many species live in a particular locality. Evidence suggests that community assembly often leads to a single stable equilibrium, such that the conditions of the environment and interspecific interactions determine which species will exist there. In such cases, regions of local communities with similar environmental conditions should have similar community composition. Other evidence suggests that community assembly can lead to multiple stable equilibria. Thus, the resulting community depends on the assembly history, even when all species have access to the community. In these cases, a region of local communities with similar environmental conditions can be very dissimilar in their community composition. Both regional and local factors should determine the patterns by which communities assemble, and the resultant degree of similarity or dissimilarity among localities with similar environments. A single equilibrium in more likely to be realized in systems with small regional species pools, high rates of connectance, low productivity and high disturbance. Multiple stable equilibria are more likely in systems with large regional species pools, low rates of connectance, high productivity and low disturbance. I illustrate preliminary evidence for these predictions from an observational study of small pond communities, and show important effects on community similarity, as well as on local and regional species richness.
Predictive representations can link model-based reinforcement learning to model-free mechanisms

Humans and animals are capable of evaluating actions by considering their long-run future rewards through a process described using model-based reinforcement learning (RL) algorithms. The mechanisms by which neural circuits perform the computations prescribed by model-based RL remain largely unknown; however, multiple lines of evidence suggest that neural circuits supporting model-based behavior are structurally homologous to and overlapping with those thought to carry out model-free temporal difference (TD) learning. Here, we lay out a family of approaches by which model-based computation may be built upon a core of TD learning. The foundation of this framework is the successor representation, a predictive state representation that, when combined with TD learning of value predictions, can produce a subset of the behaviors associated with model-based learning, while requiring less decision-time computation than dynamic programming. Using simulations, we delineate the precise behavioral capabilities enabled by evaluating actions using this approach, and compare them to those demonstrated by biological organisms. We then introduce two new algorithms that build upon the successor representation while progressively mitigating its limitations. Because this framework can account for the full range of observed putatively model-based behaviors while still utilizing a core TD framework, we suggest that it represents a neurally plausible family of mechanisms for model-based evaluation.
A Solution for Internet of Things based on Blockchain Technology

Blockchain technology is a generic term for data organization structures, cryptography algorithms, distributed consensus mechanisms, and peer-to-peer communications that are used to implement distributed ledgers. Its core value lies in the establishment of mutual trust between non-coordinated participants. However, the current blockchain applications are inclined towards software and network, missing strong connection with the real world. The Internet of Things technology connects various smart devices and sensors to Internet to facilitate recognition and management of information. This paper presents a blockchain-based Internet of Things solution, where RFID chips with built-in asymmetric encryption algorithm and scanners uploading information directly to blockchain. Compared to traditional Internet of Things designs, the proposed solution combines the advantages of both decentralized blockchain, and the Waltonchain implementation demonstrates such advantages with both data security and application flexibility.
A preliminary validation of the Brief COPE instrument for assessing coping strategies among people living with HIV in China

The Brief COPE instrument has been utilized to conduct research on various populations, including people living with HIV (PLWH). However, the questionnaire constructs when applied to PLWH have not been subjected to thorough factor validation.



A total of 258 PLWH were recruited from two provinces of China. They answered questions involving the scales of three instruments: the Brief COPE, the Perceived Social Support Scale, and the Perceived Discrimination Scale for PLWH. Confirmatory factor analysis (CFA) and exploratory factor analysis (EFA) were conducted.



The CFA found a poor goodness of fit to the data. The subsequent EFA identified six preliminary factors, forming subscales with Cronbach's alphas, which ranged from 0.61 to 0.80. Significant correlation coefficients between the subscales and measures of perceived social support and perceived discrimination were reported, giving preliminary support to the validity of the new empirical factor structure.



This study showed that the original factor structure of the Brief COPE instrument, when applied to PLWH in China, did not fit the data. Thus, the Brief COPE should be applied to various populations and cultures with caution. The new factor structure established by the EFA is only preliminary and requires further validation.
Tip shaping in primary rhinoplasty: an algorithmic approach.

Underprojection and lack of tip definition often coexist. Techniques that improve both nasal tip refinement and projection are closely interrelated, and an algorithmic approach can be developed to improve the predictability of the dynamic changes that occur. Use of nondestructive and nonpalpable techniques that enhance nasal tip shape are emphasized.



A retrospective review of primary rhinoplasty patients was undertaken to delineate the precise role of preoperative analysis, intraoperative evaluation, and execution of specific surgical techniques in creating nasal tip refinement and projection. Specific case studies are used to demonstrate the efficacy and predictability of these maneuvers.



Successful tip refinement and projection depends on (1) proper preoperative analysis of the deformity; (2) a fundamental understanding of the intricate and dynamic relationships between tip-supporting structures that contribute to nasal tip shape and projection; and (3) execution of the operative plan using controlled, nondestructive, and predictable surgical techniques.



A simplified algorithmic approach to creating aesthetic nasal tip shape and projection in primary rhinoplasty has been established to aid the rhinoplasty surgeon in reducing the inherent unpredictability of combined techniques and improving long-term aesthetic outcomes.
The evolution of molecular markers — just a matter of fashion?

In less than half a century, molecular markers have totally changed our view of nature, and in the process they have evolved themselves. However, all of the molecular methods developed over the years to detect variation do so in one of only three conceptually different classes of marker: protein variants (allozymes), DNA sequence polymorphism and DNA repeat variation. The latest techniques promise to provide cheap, high-throughput methods for genotyping existing markers, but might other traditional approaches offer better value for some applications?
Enterprise information extraction: recent developments and open challenges

Information extraction (IE) - the problem of extracting structured information from unstructured text - has become an increasingly important topic in recent years. A SIGMOD 2006 tutorial  outlined challenges and opportunities for the database community to advance the state of the art in information extraction, and posed the following grand challenge: "Can we build a System R for information extraction?
 Our tutorial gives an overview of progress the database community has made towards meeting this challenge. In particular, we start by discussing design requirements in building an enterprise IE system. We then survey recent technological advances towards addressing these requirements, broadly categorized as: (1) Languages for specifying extraction programs in a declarative way, thus allowing database-style performance optimizations; (2) Infrastructure needed to ensure scalability, and (3) Development support for enterprise IE systems. Finally, we outline several open challenges and opportunities for the database community to further advance the state of the art in enterprise IE systems. The tutorial is intended for students and researchers interested in information extraction and its applications, and assumes no prior knowledge of the area.
Characterization of ischemic index using ultra-widefield fluorescein angiography in patients with focal and diffuse recalcitrant diabetic macular edema.

To explore the association of angiographic nonperfusion in focal and diffuse recalcitrant diabetic macular edema (DME) in diabetic retinopathy (DR).



A retrospective, observational case series of patients with the diagnosis of recalcitrant DME for at least 2 years placed into 1 of 4 cohorts based on the degree of DR.



A total of 148 eyes of 76 patients met the inclusion criteria at 1 academic institution. Ultra-widefield fluorescein angiography (FA) images and spectral-domain optical coherence tomography (SD OCT) images were obtained on all patients. Ultra-widefield FA images were graded for quantity of nonperfusion, which was used to calculate ischemic index. Main outcome measures were mean ischemic index, mean change in central macular thickness (CMT), and mean number of macular photocoagulation treatments over the 2-year study period.



The mean ischemic index was 47% (SD 25%; range 0%-99%). The mean ischemic index of eyes within Cohorts 1, 2, 3, and 4 was 0%, 34% (range 16%-51%), 53% (range 32%-89%), and 65% (range 47%-99%), respectively. The mean percentage decrease in CMT in Cohorts 1, 2, 3, and 4 were 25.2%, 19.1%, 11.6%, and 7.2%, respectively. The mean number of macular photocoagulation treatments in Cohorts 1, 2, 3, and 4 was 2.3, 4.8, 5.3, and 5.7, respectively.



Eyes with larger areas of retinal nonperfusion and greater severity of DR were found to have the most recalcitrant DME, as evidenced by a greater number of macular photocoagulation treatments and less reduction in SD OCT CMT compared with eyes without retinal nonperfusion. Areas of untreated retinal nonperfusion may generate biochemical mediators that promote ischemia and recalcitrant DME.
Agile SYSTEMS ENGINEERING versus AGILE SYSTEMS engineering

This paper explores recent developments in agile systems engineering. We draw a distinction between agility in the systems engineering process versus agility in the resulting system itself. In the first case the emphasis is on carefully exploring the space of design alternatives and to delay the freeze point as long as possible as new information becomes available during product development. In the second case we are interested in systems that can respond to changed requirements after initial fielding of the system. We provide a list of known and emerging methods in both domains and explore a number of illustrative examples such as the case of the Iridium satellite constellation or recent developments in the automobile industry.
Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication.

Little is known about the genetic changes that distinguish domestic cat populations from their wild progenitors. Here we describe a high-quality domestic cat reference genome assembly and comparative inferences made with other cat breeds, wildcats, and other mammals. Based upon these comparisons, we identified positively selected genes enriched for genes involved in lipid metabolism that underpin adaptations to a hypercarnivorous diet. We also found positive selection signals within genes underlying sensory processes, especially those affecting vision and hearing in the carnivore lineage. We observed an evolutionary tradeoff between functional olfactory and vomeronasal receptor gene repertoires in the cat and dog genomes, with an expansion of the feline chemosensory system for detecting pheromones at the expense of odorant detection. Genomic regions harboring signatures of natural selection that distinguish domestic cats from their wild congeners are enriched in neural crest-related genes associated with behavior and reward in mouse models, as predicted by the domestication syndrome hypothesis. Our description of a previously unidentified allele for the gloving pigmentation pattern found in the Birman breed supports the hypothesis that cat breeds experienced strong selection on specific mutations drawn from random bred populations. Collectively, these findings provide insight into how the process of domestication altered the ancestral wildcat genome and build a resource for future disease mapping and phylogenomic studies across all members of the Felidae.
File System Workload Analysis For Large Scale Scientific Com puting Applications

Parallel scientific applications require high-performanc e I/O support from underlying file systems. A comprehensive understanding of the expected workload is t herefore essential for the design of high-performance parallel file systems. We re-examine the w orkload characteristics in parallel computing environments in the light of recent technology ad vances and new applications. We analyze application traces from a cluster with hundreds o f nodes. On average, each application has only one or two typical request sizes. Large requests fro m several hundred kilobytes to several megabytes are very common. Although in some applications, s mall requests account for more than 90% of all requests, almost all of the I/O data are transferre d by large requests. All of these applications show bursty access patterns. More than 65% of write req uests have inter-arrival times within one millisecond in most applications. By running the same be nchmark on different file models, we also find that the write throughput of using an individual out p t file for each node exceeds that of using a shared file for all nodes by a factor of 5. This indicate s that current file systems are not well optimized for file sharing.
Interactive Skeleton Techniques for Enhancing Motion Dynamics in Key Frame Animation

A significant increase in the capability for controlling motion dynamics in key frame animation is achieved through skeleton control. This technique allows an animator to develop a complex motion sequence by animating a stick figure representation of an image. This control sequence is then used to drive an image sequence through the same movement. The simplicity of the stick figure image encourages a high level of interaction during the design stage. Its compatibility with the basic key frame animation technique permits skeleton control to be applied selectively to only those components of a composite image sequence that require enhancement.