Miracle-dz/UniFAR-FTUs huggingface dataset:
Boa: a link between worlds

The business models of software/platform as a service have contributed to developers dependence on the Internet. Developers can rapidly point each other and consumers to the newest software changes with the power of the hyper link. But, developers are not limited to referencing software changes to one another through the web. Other shared hypermedia might include links to: Stack Overflow, Twitter, and issue trackers. This work explores the software traceability of Uniform Resource Locators (URLs) which software developers leave in commit messages and software repositories. URLs are easily extracted from commit messages and source code. Therefore, it would be useful to researchers if URLs provide additional insight on project development. To assess traceability, manual topic labelling is evaluated against automated topic labelling on URL data sets. This work also shows differences between URL data collected from commit messages versus URL data collected from source code. As well, this work explores outlying software projects with many URLs in case these projects do not provide meaningful software relationship information. Results from manual topic labelling show promise under evaluation while automated topic labelling did not yield precise topics. Further investigation of manual and automated topic analysis would be useful.
A micro-tensile method for measuring mechanical properties of MEMS materials

Mechanical properties of micro-electro-mechanical systems (MEMS) materials are increasingly important with the wide use of miniaturized systems. This paper proposes a new method for measuring mechanical properties of thin films. This method is suitable for thin films with large strain (>5%) and can be applied to samples with different thicknesses. The S-shaped support springs of the test chip are able to improve the measurement accuracy. Specimens of Ni thin film, with a gauge section 50 µm wide, 100 µm long and 5 µm thick, were tested. The measured Young's modulus of Ni thin film is about 32 GPa and the tensile strength is about 750 MPa.
Mapping information policy frames: The politics of the digital millennium copyright act

Passage of the Digital Millennium Copyright Act (DMCA) was a significant milestone in congressional information policy legislation. However, the results were widely criticized in some circles as providing too much power to certain stakeholder groups. This paper uses computer-based content analysis and a theoretical taxonomy of information policy values to analyze congressional hearing testimony. The results of document coding were then analyzed using a variety of statistical tools to map how different stakeholders framed issues in the debate and determine if congressional value statements about the legislation conformed more closely to certain stakeholders. Results of the analysis indicate that significant differences in the use of information policy terms occurred across stakeholders, and showed varying degrees of convergence between congressional or other stakeholders when framing information policy issues.
Mutant Protein Kinase Cγ Found in Spinocerebellar Ataxia Type 14 Is Susceptible to Aggregation and Causes Cell Death*

Spinocerebellar ataxia type 14 (SCA14) is an autosomal dominant neurodegenerative disease characterized by various symptoms including cerebellar ataxia. Recently, several missense mutations in the protein kinase Cγ (γPKC) gene have been found in different SCA14 families. To elucidate how the mutant γPKC causes SCA14, we examined the molecular properties of seven mutant (H101Y, G118D, S119P, S119F, Q127R, G128D, and F643L) γPKCs fused with green fluorescent protein (γPKC-GFP). Wild-type γPKC-GFP was expressed ubiquitously in the cytoplasm of CHO cells, whereas mutant γPKC-GFP tended to aggregate in the cytoplasm. The insolubility of mutant γPKC-GFP to Triton X-100 was increased and correlated with the extent of aggregation. γPKC-GFP in the Triton-insoluble fraction was rarely phosphorylated at Thr514, whereas γPKC-GFP in the Triton-soluble fraction was phosphorylated. Furthermore, the stimulation of the P2Y receptor triggered the rapid aggregation of mutant γPKC-GFP within 10 min after transient translocation to the plasma membrane. Overexpression of the mutant γPKC-GFP caused cell death that was more prominent than wild type. The cytotoxicity was exacerbated in parallel with the expression level of the mutant. These results indicate that SCA14 mutations make γPKC form cytoplasmic aggregates, suggesting the involvement of this property in the etiology of SCA14.
MEASUREMENT OF CHARM MESON LIFETIMES

We report measurements of the D{sup 0} , D{sup +} , and D{sup +}{sub s} meson lifetimes using 3.7 fb{sup {minus}1} of e{sup +}e{sup {minus}} annihilation data collected near the {Upsilon}(4S) resonance with the CLEO detector. The measured lifetimes of the D{sup 0} , D{sup +} , and D{sup +}{sub s} mesons are 408.5{plus_minus}4.1{sup +3.5}{sub {minus}3.4} fs , 1033.6{plus_minus}22.1{sup +9.9}{sub {minus}12.7} fs , and 486.3{plus_minus}15.0{sup +4.9}{sub {minus}5.1} fs . The precisions of these lifetimes are comparable to those of the best previous measurements, and the systematic errors are very different. In a single experiment we find that the ratio of the D{sup +}{sub s} and D{sup 0} lifetimes is 1.19{plus_minus}0.04 . {copyright} {ital 1999} {ital The American Physical Society}
Attention, please! Expanding the GECO database

This paper describes current and future contents of the (GErman COnversations) conversations database and promotes investigating the role of attention in phonetics research. GECO is freely available for non-commercial use. It consists of conversations of high-audio quality between female subjects, together with results of personality tests of each participant, and participants’ ratings of each other and of the conversation. To our knowledge it is currently the largest German database of this type. This corpus will be doubled in size by adding more dialogs in the next two years, and these new speech data will be complemented by results of several attention tests. Some of these tests will follow established test paradigms, but we also suggest a new, less artificial paradigm for testing attention. We describe the existing GECO corpus as well as the future additions including the proposed test in this paper.
Comparative study of one-sided factorizations with multiple software packages on multi-core hardware

The emergence and continuing use of multi-core architectures require changes in the existing software and sometimes even a redesign of the established algorithms in order to take advantage of now prevailing parallelism. The Parallel Linear Algebra for Scalable Multi-core Architectures (PLASMA) is a project that aims to achieve both high performance and portability across a wide range of multi-core architectures. We present in this paper a comparative study of PLASMA's performance against established linear algebra packages (LAPACK and ScaLAPACK), against new approaches at parallel execution (Task Based Linear Algebra Subroutines - TBLAS), and against equivalent commercial software offerings (MKL, ESSL and PESSL). Our experiments were conducted on one-sided linear algebra factorizations (LU, QR and Cholesky) and used multi-core architectures (based on Intel Xeon EMT64 and IBM Power6). A performance improvement of 67% was for instance obtained on the Cholesky factorization of a matrix of order 4000, using 32 cores.
Maelstrom: Transparent Error Correction for Communication Between Data Centers

The global network of data centers is emerging as an important distributed systems paradigm-commodity clusters running high-performance applications, connected by high-speed “lambda” networks across hundreds of milliseconds of network latency. Packet loss on long-haul networks can cripple applications and protocols: A loss rate as low as 0.1% is sufficient to reduce TCP/IP throughput by an order of magnitude on a 1-Gb/s link with 50-ms one-way latency. Maelstrom is an edge appliance that masks packet loss transparently and quickly from intercluster protocols, aggregating traffic for high-speed encoding and using a new forward error correction scheme to handle bursty loss.
Skull-stripping with deformable organisms

Segmenting brain from non-brain tissue within magnetic resonance (MR) images of the human head, also known as skull-stripping, is a critical processing step in the analysis of neuroimaging data. Though many algorithms have been developed to address this problem, challenges remain. In this paper, we apply the “deformable organism” framework to the skull-stripping problem. Within this framework, deformable models are equipped with higher-level control mechanisms based on the principles of artificial life, including sensing, reactive behavior, knowledge representation, and proactive planning. Our new deformable organisms are governed by a high-level plan aimed at the fully-automated segmentation of various parts of the head in MR imagery, and they are able to cooperate in computing a robust and accurate segmentation. We applied our segmentation approach to a test set of human MRI data using manual delineations of the data as a reference “gold standard. ” We compare these results with results from three widely used methods using set-similarity metrics.
Cognitive diagnosis using item response models

In this paper, I will describe a particular approach to cognitive diagnosis that is centered on the idea of developmental assessment, and illustrate how data from this approach can be modeled using explanatory item response models. The developmental assessment approach starts with the idea of a progression of learning embodied in what are called progress variables. In a progress variable, student understanding is conceptualized as a continuum with successive levels of development. Effectively, these are seen as a series of student conceptions – this is the first layer of diagnosis. Then, student misconceptions are seen as particular diagnoses within the student conceptions, forming a second layer of diagnosis. Explanatory measurement is introduced as a way to formally model the psychometrics of this situation, using the Berkeley Evaluation and Assessment Research (BEAR) assessment system as a specific example. The discussion is illustrated with examples from student learning about selected topics in scien.
“It is not guaranteed that you will benefit”: True but misleading?

Background: Participants of early-phase intervention trials for serious conditions provide high estimates of likelihood of benefit, even when informed consent forms do not promise such benefits. However, some technically correct, negatively stated benefits statements—such as “it is not guaranteed that you will benefit”—could play a role in raising expectations of benefit because in ordinary English usage such statements denote a likely but not a certain-to-occur event. Methods: An experimental online survey of 584 English-speaking adults recruited online. They were randomized to receive one of two benefit statements (“not guaranteed” vs “some but very small chance”), using a hypothetical scenario of an early-phase clinical trial testing an intervention to treat amyotrophic lateral sclerosis. We assessed respondents’ willingness to consider participating in the amyotrophic lateral sclerosis trial, their estimates of likelihood of benefit, and their explanations for those estimates. Results: The two arms did not differ in willingness to consider participation in the amyotrophic lateral sclerosis trial. Those receiving “not guaranteed” benefit statement had higher estimates of benefit than those receiving “some but very small chance” statement (35.7% (standard deviation 20.2) vs 28.3% (standard deviation 22.0), p < 0.0001). A total of 43% of all respondents chose expressions of positive sentiment (hope and need to stay positive) as explanations of their estimates; these respondents’ estimates of benefit were higher than others but similar between the two arms. The effect of benefit statements was greatest among those who chose “Those are just the facts” as the explanation for their estimate (31.0% (standard deviation 22.4%) in “not guaranteed” arm vs 18.9% (standard deviation 21.0%) in comparison arm, p = 0.008). Conclusion: The use of “not guaranteed” language in benefit statements, when compared to “small but very small chance” language, appeared to increase the perception of likelihood of benefit of entering an early-phase trial, especially among those who view their estimates of benefits as “facts. ” Such “no guarantee” benefit statements may be misleading and should not be used in informed consent forms.
Mobile Re-Identification Based on Local Features Analysis

Nowadays, there is a growing interest in security applications using embedded smart cameras. Despite the rising attention to re-identifying the people in a non-overlapping embedded camera network, there exist no comparative evaluation of the existing schemes, specially facial representations. Though, facial features offer the advantage of remaining stable over much larger time intervals in contrast to commonly exploited features for person re-identification, such as whole body appearance. However, the challenge in using faces for such applications, apart from low captured face resolutions, is that their appearance is largely influenced by changes in illumination, pose, viewpoint, background and partial occlusions. Therefore, in this paper, we present a comparative study of facial local features for the task of person re-identification using embedded smart cameras in a realistic surveillance scenario. The experiments are performed on a novel data set which we make publicly available for future research in this area. The contributions of this work are as follows: 1) evaluation of eight baseline facial local features for person re-identification using embedded smart cameras; 2) an empirical study of the performance of person re-identification systems based on local facial features when fused with auxiliary information such as face shape, face skin color tone, hair color, and cloth color; 3) comparative study of single- and multi-shot approaches; 4) a novel data set using embedded cameras for person re-identification with properties unavailable in exiting data sets.
Microfluidic point-of-care diagnostics for resource-poor environments

Point-of-care (POC) diagnostics have tremendous potential to improve human health in remote and resource-poor settings. However, the design criteria for diagnostic tests appropriate in settings with limited infrastructure are unique and challenging. Here we present a custom optical reader which quantifies silver absorbance from heterogeneous immunoassays. The reader is simple, low-cost and suited for POC diagnostics.
Evaluating architecture and compiler design through static loop analysis

Using the MAQAO loop static analyzer, we characterize a corpus of binary loops extracted from common benchmark suits such as SPEC, NAS, etc. and several industrial applications. For each loop, MAQAO extracts low-level assembly features such as: integer and floating-point vectorization ratio, number of registers used and spill-fill, number of concurrent memory streams accessed, etc. The distributions of these features on a large representative code corpus can be used to evaluate compilers and architectures and tune them for the most frequently used assembly patterns. In this paper, we present the MAQAO loop analyzer and a characterization of the 4857 binary loops. We evaluate register allocation and vectorization on two compilers and propose a method to tune loop buffer size and stream prefetcher based on static analysis of benchmarks.
HLA‐A2‐restricted CTL epitopes of a novel lung cancer‐associated cancer testis antigen, cell division cycle associated 1, can induce tumor‐reactive CTL

Toward the development of a novel cancer immunotherapy, we have previously identified several tumor‐associated antigens (TAAs) and the epitopes recognized by human histocompatibility leukocyte (HLA)‐A2/A24‐restricted cytotoxic T lymphocyte (CTL). In this study, we tried to identify a TAA of lung cancer (LC) and its HLA‐A2 restricted CTL epitopes to provide a target antigen useful for cancer immunotherapy of LC. We identified a novel cancer testis antigen, cell division cycle associated gene 1 (CDCA1), overexpressed in nonsmall cell LC using a cDNA microarray analysis. The expression levels of CDCA1 were also increased in the majority of small cell LC, cholangiocellular cancer, urinary bladder cancer and renal cell cancers. We used HLA‐A2.1 transgenic mice to identify the HLA‐A2 (A*0201)‐restricted CDCA1 epitopes recognized by mouse CTL, and we investigated whether these peptides could induce CDCA1‐reactive CTLs from the peripheral blood mononuclear cells (PBMCs) of HLA‐A2‐positive donors and a NSCLC patient. Consequently, we found that the CDCA165–73 (YMMPVNSEV) peptide and CDCA1351–359 (KLATAQFKI) peptide could induce peptide‐reactive CTLs in HLA‐A2.1 transgenic mice. In HLA‐A2+ donors, in vitro stimulation of PBMC with these peptides could induce peptide‐reactive CTLs which killed tumor cell lines endogenously expressing both HLA‐A2 and CDCA1. As a result, CDCA1 is a novel cancer‐testis antigen overexpressed in LC, cholangiocellular cancer, urinary bladder cancer and renal cell cancers, and CDCA1 may therefore be an ideal TAA useful for the diagnosis and immunotherapy of these cancers. © 2008 Wiley‐Liss, Inc.
Viscosity-based height reflex for workspace augmentation for quadrupedal locomotion on rough terrain

We propose a reactive locomotion strategy, called height reflex, that is useful to address big elevation changes in the terrain (e.g. when a quadruped robot has to step down from a high platform). In these cases the swing leg can lose mobility creating issues in the subsequent steps. The height reflex is a foot trajectory replanning strategy that redistributes the swing motion (in a smart way) to the stance legs to “lower” the whole trunk and to aid the foothold searching motion. To spread the motion we exploit a massless link model of the robot with virtual dampers at the joints, which is used to replan the feet trajectories. The proposed approach is able to incorporate kinematic limits, it is easy-to-tune, computationally efficient and suitable for real-time implementations. The reflex is implemented and experimentally evaluated on the 80 kg hydraulic quadruped HyQ. With our approach we were able to address high steps, up to 24 cm which is 30% of HyQ leg length and 53% of its retractable leg range.
Systematic Design of Slow Light Waveguides

Light can propagate much slower in photonic crystal waveguides and plasmonic waveguides than in vacuum. Slow light propagation in waveguides shows broad prospects in the terabit communication systems. However, it causes severe signal distortions and displays large propagation loss. Moreover it is vulnerable to manufacturing disorders. This thesis aims to design novel waveguides to alleviate signal distortions and propagation loss using optimization methodologies, and to explore the design robustness with respect to manufacturing imperfections. To alleviate the signal distortions in waveguides, an optimization formulation is presented to tailor the slope of the dispersion curve. The design robustness is enforced by considering different manufacturing realizations in the optimization procedure. Both freeand fixed-topology (circular-hole based) slow light photonic crystal waveguides are obtained using two different parameterizations. Detailed comparisons show that the bandwidth of slow light propagation can be significantly enhanced by allowing irregular geometries in the waveguides. To mitigate the propagation loss due to scattering in the photonic crystal waveguides, an optimization problem is formulated to minimize the average propagation loss of the designed modes. The presented approach is employed to design a freetopology slow light waveguide. Numerical result illustrates that slow light propagation in the optimized waveguide displays significantly suppressed propagation loss while keeping the same bandwidth. The first optimization formulation is further employed to design slow light metaldielectric-metal plasmonic waveguides. It is shown that dispersionless slow light propagation is achieved in the optimized plasmonic waveguide. Further study reveals that the loss in metal can be compensated by integrating gain media in the optimized waveguide, while keeping negligible signal distortions.
Scaling up analytical queries with column-stores

As data analytics is used by an increasing number of applications, data analytics engines are required to execute workloads with increased concurrency, i.e., an increasing number of clients submitting queries. Data management systems designed for data analytics - a market dominated by column-stores - however, were initially optimized for single query execution, minimizing its response time. Hence, they do not treat concurrency as a first class citizen. In this paper, we experiment with one open-source and two commercial column-stores using the TPC-H and SSB benchmarks in a setup with an increasing number of concurrent clients submitting queries, focusing on whether the tested systems can scale up in a single node instance. The tested systems for in-memory workloads scale up, to some degree; however, when the server is saturated they fail to fully exploit the available parallelism. Further, we highlight the unpredictable response times for high concurrency.
A scalable and efficient user authentication scheme for cloud computing environments

Cloud computing is an emerging technology that is still unclear to many security problems and user authentication, access control, and ensuring the security of stored data in cloud servers are the most challenging issues in cloud-based environment. Accordingly, this paper offers an efficient and scalable user authentication scheme for cloud computing environment. It the suggested model, various tools and techniques have been introduced and used by using the concept of agent. Therefore, a client-based user authentication agent has been introduced to confirm identity of the user in client-side. Furthermore, a cloud-based software-as-a-service application has been used to confirm the process of authentication for unregistered devices. Moreover, there are two separate servers for storing authentication and cryptography resources from main servers to decrease the dependency of user authentication and encryption processes from main server. Cryptography agent was also introduced to encrypt resources before storing on cloud servers. In overall, the theoretical analysis of the suggested scheme shows that, designing this user authentication and access control model will enhance the reliability and rate of trust in cloud computing environments as an emerging and powerful technology in various industries.
IB2d: a Python and MATLAB implementation of the immersed boundary method

The development of fluid-structure interaction (FSI) software involves trade-offs between ease of use, generality, performance, and cost. Typically there are large learning curves when using low-level software to model the interaction of an elastic structure immersed in a uniform density fluid. Many existing codes are not publicly available, and the commercial software that exists usually requires expensive licenses and may not be as robust or allow the necessary flexibility that in house codes can provide. We present an open source immersed boundary software package, IB2d, with full implementations in both MATLAB and Python, that is capable of running a vast range of biomechanics models and is accessible to scientists who have experience in high-level programming environments. IB2d contains multiple options for constructing material properties of the fiber structure, as well as the advection-diffusion of a chemical gradient, muscle mechanics models, and artificial forcing to drive boundaries with a preferred motion.