gebhart/patrepeval huggingface dataset:
ChronoTwigger: A Visual Analytics Tool for Understanding Source and Test Co-evolution (2014)

Applying visual analytics to large software systems can help users comprehend the wealth of information produced by source repository mining. One concept of interest is the co-evolution of test code with source code, or how source and test files develop together over time. For example, understanding how the testing pace compares to the development pace can help test managers gauge the effectiveness of their testing strategy. A useful concept that has yet to be effectively incorporated into a co-evolution visualization is co-change. Co-change is a quantity that identifies correlations between software artifacts, and we propose using this to organize our visualization in order to enrich the analysis of co-evolution. In this paper, we create, implement, and study an interactive visual analytics tool that displays source and test file changes over time (co-evolution) while grouping files that change together (co-change). Our new technique improves the analyst's ability to infer information about the software development process and its relationship to testing. We discuss the development of our system and the results of a small pilot study with three participants. Our findings show that our visualization can lead to inferences that are not easily made using other techniques alone.
A Micromachined Electret-Based Transponder for In Situ Radiation Measurement (2006)

This letter reports on the development of a micromachined passive transponder for in situ measurement of ionizing radiation. gamma-ray exposure is remotely measured by monitoring the resonance frequency change correlated with a change in the surface charge of an electret. This is achieved through a micromachined capacitor with a movable plate that is partially filled with a Teflon electret and connected in parallel with an inductor, forming a passive LC tank (a microionization chamber, 1.5 cm in diameter and 3 mm in thickness). Test results show that an exposure of 60 000 R from Cs <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">137</sup> produces a 687-kHz resonance frequency shift (sensitivity of 11.45 kHz/kR)
Constraint-based image understanding system for aerial imagery interpretation (2003)

The authors describe a constraint-based image understanding system, named COBIUS, for aerial imagery interpretation. COBIUS consists of knowledge bases for domain objects spatial and temporal constraints, control strategies, blackboard areas to instantiate hypotheses of objects and constraints, and an image feature database to fuse results from multiple image segmentation modules. Domain-specific knowledge is represented in terms of generic temporal and spatial constraints. A set of generic constraint manipulation and hypothesis formation rules are used to perform formation, evaluation, propagation, and satisfaction of constraints and hypotheses. More importantly, constraints are represented hierarchically and are no different from the representation of domain objects. This representation avoids time-consuming graph matching processor for image interpretation and provides greater representation modularity. The processing example is presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Autologous Transplantation of Bone Marrow Cells Improves Damaged Heart Function (1999)

Background —Autologous bone marrow cells (BMCs) transplanted into ventricular scar tissue may differentiate into cardiomyocytes and restore myocardial function. This study evaluated cardiomyogenic differentiation of BMCs, their survival in myocardial scar tissue, and the effect of the implanted cells on heart function. Methods and Results —In vitro studies: BMCs from adult rats were cultured in cell culture medium (control) and medium with 5-azacytidine (5-aza, 10 μmol/L), TGFβ1 (10ng/mL), or insulin (1 nmol/L) (n=6, each group). Only BMCs cultured with 5-aza formed myotubules which stained positively for troponin I and myosin heavy chain. In vivo studies: a cryoinjury-derived scar was formed in the left ventricular free wall. At 3 weeks after injury, fresh BMCs (n=9), cultured BMCs (n=9), 5-aza–induced BMCs (n=12), and medium (control, n=12) were autologously transplanted into the scar. Heart function was measured at 8 weeks after myocardial injury. Cardiac-like muscle cells which stained positively for myosin heavy chain and troponin I were observed in the scar tissue of the 3 groups of BMC transplanted hearts. Only the 5-aza–treated BMC transplanted hearts had systolic and developed pressures which were higher ( P <0.05) than that of the control hearts. All transplanted BMCs induced angiogenesis in the scar. Conclusions —Transplantation of BMCs induced angiogenesis. BMCs cultured with 5-aza differentiated into cardiac-like muscle cells in culture and in vivo in ventricular scar tissue and improved myocardial function.
On cyclic MDS codes of length q over GF(q) (Corresp.) (1986)

It is shown that a cyclic code <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">C</tex> of length <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">q</tex> over GF <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">(q)</tex> is the maximum distance separable if and only if either <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1) q</tex> is a prime, in which case <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">C</tex> is equivalent, up to a coordinate permutation, to an extended Reed-Solomon code, or <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2) C</tex> is a trivial code of dimension <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k \in \{1, q - 1, q \}</tex> . Hence there exists a nontrivial cyclic extended Reed-Solomon code of length <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">q</tex> over GF <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">(q)</tex> if and only if <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">q</tex> is a prime.
Comparison of MRI Under-Sampling Techniques for Compressed Sensing with Translation Invariant Wavelets Using FastTestCS: A Flexible Simulation Tool (2016)

A sparsifying transform for use in Compressed Sensing (CS) is a vital piece of image reconstruction for Magnetic Resonance Imaging (MRI). Previously, Translation Invariant Wavelet Transforms (TIWT) have been shown to perform exceedingly well in CS by reducing repetitive line pattern image artifacts that may be observed when using orthogonal wavelets. To further establish its validity as a good sparsifying transform, the TIWT is comprehensively investigated and compared with Total Variation (TV), using six under-sampling patterns through simulation. Both trajectory and random mask based under-sampling of MRI data are reconstructed to demonstrate a comprehensive coverage of tests. Notably, the TIWT in CS reconstruction performs well for all varieties of under-sampling patterns tested, even for cases where TV does not improve the mean squared error. This improved Image Quality (IQ) gives confidence in applying this transform to more CS applications which will contribute to an even greater speed-up of a CS MRI scan. High vs low resolution time of flight MRI CS re-constructions are also analyzed showing how partial Fourier acquisitions must be carefully addressed in CS to prevent loss of IQ. In the spirit of reproducible research, novel software is introduced here as FastTestCS. It is a helpful tool to quickly develop and perform tests with many CS customizations. Easy integration and testing for the TIWT and TV minimization are exemplified. Simulations of 3D MRI datasets are shown to be efficiently distributed as a scalable solution for large studies. Comparisons in reconstruction computation time are made between the Wavelab toolbox and Gnu Scientific Library in FastTestCS that show a significant time savings factor of 60×. The addition of FastTestCS is proven to be a fast, flexible, portable and reproducible simulation aid for CS research.
Dynamic Expression of Long Non-Coding RNAs (lncRNAs) in Adult Zebrafish (2013)

Long non-coding RNAs (lncRNA) represent an assorted class of transcripts having little or no protein coding capacity and have recently gained importance for their function as regulators of gene expression. Molecular studies on lncRNA have uncovered multifaceted interactions with protein coding genes. It has been suggested that lncRNAs are an additional layer of regulatory switches involved in gene regulation during development and disease. LncRNAs expressing in specific tissues or cell types during adult stages can have potential roles in form, function, maintenance and repair of tissues and organs. We used RNA sequencing followed by computational analysis to identify tissue restricted lncRNA transcript signatures from five different tissues of adult zebrafish. The present study reports 442 predicted lncRNA transcripts from adult zebrafish tissues out of which 419 were novel lncRNA transcripts. Of these, 77 lncRNAs show predominant tissue restricted expression across the five major tissues investigated. Adult zebrafish brain expressed the largest number of tissue restricted lncRNA transcripts followed by cardiovascular tissue. We also validated the tissue restricted expression of a subset of lncRNAs using independent methods. Our data constitute a useful genomic resource towards understanding the expression of lncRNAs in various tissues in adult zebrafish. Our study is thus a starting point and opens a way towards discovering new molecular interactions of gene expression within the specific adult tissues in the context of maintenance of organ form and function.
Optimal video replication and placement on a cluster of video-on-demand servers (2003)

A cost-effective approach to building up scalable video-on-demand (VoD) servers is to couple a number of VoD servers together in a cluster. In this article, we study a crucial video replication and placement problem in a distributed storage VoD cluster for high quality and high availability services. We formulate it as a combinatorial optimization problem with objectives of maximizing the encoding bit rate and the number of replicas of each video and balancing the workload of the servers. It is subject to the constraints of the storage capacity and the outgoing network bandwidth of the servers. Under the assumption of single fixed encoding bit rate for all videos, we give an optimal replication algorithm and a bounded-placement algorithm for videos with different popularities. To reduce the complexity of the replication algorithm, we present an efficient algorithm that utilizes the Zipf-like video popularity distributions to approximate the optimal solution. For videos with scalable encoding bit rates, we propose a heuristic algorithm based on simulated annealing. We conduct a comprehensive performance evaluation of the algorithms and demonstrate their effectiveness via simulations over a synthetic workload set.
Hematopoietic cell kinase (HCK) as a therapeutic target in immune and cancer cells (2015)

The hematopoietic cell kinase (HCK) is a member of the SRC family of cytoplasmic tyrosine kinases (SFKs), and is expressed in cells of the myeloid and B-lymphocyte cell lineages. Excessive HCK activation is associated with several types of leukemia and enhances cell proliferation and survival by physical association with oncogenic fusion proteins, and with functional interactions with receptor tyrosine kinases. Elevated HCK activity is also observed in many solid malignancies, including breast and colon cancer, and correlates with decreased patient survival rates. HCK enhances the secretion of growth factors and pro-inflammatory cytokines from myeloid cells, and promotes macrophage polarization towards a wound healing and tumor-promoting alternatively activated phenotype. Within tumor associated macrophages, HCK stimulates the formation of podosomes that facilitate extracellular matrix degradation, which enhance immune and epithelial cell invasion. By virtue of functional cooperation between HCK and bona fide oncogenic tyrosine kinases, excessive HCK activation can also reduce drug efficacy and contribute to chemo-resistance, while genetic ablation of HCK results in minimal physiological consequences in healthy mice. Given its known crystal structure, HCK therefore provides an attractive therapeutic target to both, directly inhibit the growth of cancer cells, and indirectly curb the source of tumor-promoting changes in the tumor microenvironment.
miR-147, a microRNA that is induced upon Toll-like receptor stimulation, regulates murine macrophage inflammatory responses (2009)

Toll-like receptors (TLRs) are major receptors that enable inflammatory cells to recognize invading microbial pathogens. MicroRNAs are small non-coding RNAs that play important regulatory roles in a variety of biological processes. In this study, we found that a microRNA, miR-147, was induced upon stimulation of multiple TLRs and functioned as a negative regulator of TLR-associated signaling events in murine macrophages. We first demonstrated that the NMES1 transcript was a functional primary miR-147. miR-147 was induced in LPS-stimulated mouse macrophages and under in vivo conditions in the lungs of LPS-treated mice. Expression of miR-147 was greater after cellular activation by TLR4 than after engagement of either TLR2 or TLR3, suggesting that maximal induction of miR-147 required activation of both NF-kappaB and IRF3. TLR4-induced miR-147 expression was both MyD88- and TRIF-dependent. The miR-147 promoter was responsive to TLR4 stimulation and both NF-kappaB and STAT1alpha bound to the miR-147 promoter. miR-147 mimics or induced expression of miR-147 decreased, whereas miR-147 knockdown increased inflammatory cytokine expression in macrophages stimulated with ligands to TLR2, TLR3, and TLR4. These data demonstrate a negative-feedback loop in which TLR stimulation induces miR-147 to prevent excessive inflammatory responses.
Switching linear turbo equalizers with three vector of coefficients (2006)

We propose in this article the use of linear turbo equalization schemes in which the equalizer coefficients, for the sake of complexity reduction, are switched between three vectors of coefficients previously calculated. Techniques for choosing the switching point are developed and evaluated. Simulation results of performance comparison against the MMSE equalizer proposed in [1] are also provided. It is shown that the schemes herein described perform close to the MMSE equalizer, despite being much less complex.
Addressing the contractor selection problem using an evidential reasoning approach (2001)

Selecting the ‘best’ main contractor is a complex decision process for construction clients. It requires a large number of criteria to be simultaneously measured and evaluated. Many of these criteria are related to one another in a complex way and therefore, they very often conflict insofar as improvement in one often results in decline of another(s). Furthermore, as contractors' attributes are expressed in both quantitative and qualitative terms, decision‐makers have to base their judgements on both quantitative data and experiential subjective assessments. In this paper, the evidential reasoning (ER) approach (which is capable of processing both quantitative and qualitative measures) is applied as a means of solving the contractor selection problem (CSP). The process of building a multiple criteria decision model of a hierarchical structure is presented, in which both quantitative and qualitative information is represented in a unified manner. The CSP is then fully investigated using the ER approach. Both the advantages of applying this model in practice and the analysis process itself are discussed.
Extracellular DNA in natural environments: features, relevance and applications (2018)

Extracellular DNA (exDNA) is abundant in many habitats, including soil, sediments, oceans and freshwater as well as the intercellular milieu of metazoa. For a long time, its origin has been assumed to be mainly lysed cells. Nowadays, research is collecting evidence that exDNA is often secreted actively and is used to perform a number of tasks, thereby offering an attractive target or tool for biotechnological, medical, environmental and general microbiological applications. The present review gives an overview on the main research areas dealing with exDNA, depicts its inherent origins and functions and deduces the potential of existing and emerging exDNA-based applications. Furthermore, it provides an overview on existing extraction methods and indicates common pitfalls that should be avoided whilst working with exDNA.
Preparation of oligosaccharides from alginic acid by enzymic hydrolysis (1996)

For the purpose of production of oligosaccharides from alginates, a bacterium was isolated from seaweed, and then an enzyme which degraded alginates was obtained from the bacterium. A specific activity of the enzyme was shown in G-rich block and Na-alginate (Wako Co.) as a result of reaction between the enzyme and six types of alginates (G-rich block, M-rich block and 4 commercial Na-alginate). Degradation products were prepared from the Na-alginate (Wako Co.) by the enzyme. The oligosaccharides were fractioned by Sephadex G-25 and Bio-gel P-2 and identified on a thin layer chromatography (TLC). Degree of polymerization (DP) of the oligosaccharides was shown from 2.6 to 7.5.
Design of Multi-text English Reading Instruction Aiming at Cultural Awareness Cultivation (2022)

The reading classroom is a main place for English teaching and cultural awareness cultivation. However, the limitations of the traditional English reading class with single reading material cannot meet students’ needs of comparing and discriminating among different cultures, which leads to the fragmentation of students’ acquisition of cultural knowledge and a one-sided understanding of cultural phenomena. Considering this context, the author combines the elements of multi-text reading, takes the cultural awareness cultivation objectives in the new curriculum standard as the basis to construct a multi-text reading teaching framework aiming at the cultivation of cultural awareness which includes teaching objectives, teaching contents, teaching process, and teaching evaluation.
Preparation of Oxaliplatin-Deoxycholic Acid Derivative Nanocomplexes and <i>In Vivo</i> Evaluation of Their Oral Absorption and Tumor Growth Suppression (2015)

To prepare orally available oxaliplatin (OXA), nanocomplexes were formed by ionic conjugation of OXA with the deoxycholic acid derivative, Nalpha-deoxycholy-L-lysyl-methylester (DCK), as an oral absorption enhancer. We characterized the DCK-conjugated OXA nanocomplexes by differential scanning calorimetry, particle size determination, and morphological analysis. To evaluate the effects of DCK on the intestinal permeability of OXA, we assessed the solubilities and partition coefficients of OXA and the OXA/DCK nanocomplex, and then conducted in vitro artificial intestinal membrane and Caco-2 cell permeability studies. Finally, bioavailability in rats and tumor growth inhibition in the squamous cell carcinoma (SCC7) model after oral administration of the OXA/DCK nanocomplex were investigated compared to pure OXA. Analysis of the ionic complex formation of OXA with DCK revealed that OXA existed in an amorphous form within the complex, resulting in for- mation of nanocomp;exes (35.05 +/- 4.48 nm in diameter). The solubility of OXA in water was approximately 7.07 mg/mL, whereas the water solubility of OXA/DCK was approximately 2.04 mg/mL and its partition coefficient was approximately 1.2-fold higher than that of OXA. The in vitro intestinal membrane permeability of OXA was significantly enhanced by complex formation with DCK. An in vivo pharmacokinetic study revealed that the Cm value of the OXA/DCK nanocomplex was 3.18-fold higher than that of OXA (32.22 +/- 10.24 ng/mL), and the resulting oral bioavailability of the OXA/DCK nanocomplex was 39.3-fold more than that of OXA. Furthermore, the oral administration of OXA/DCK significantly inhibited tumor growth in SCC7-bearing mice, and maximally inhibited tumor volume by 54% compared to the control. These findings demonstrate the therapeutic potential of the OXA/DCK nanocomplex as an oral anti-cancer therapy because it improves the oral absorption of OXA, which may improve patient compliance and expand the therapeutic applications of OXA to the prevention of recurrence and metastasis.
A biodegradable ring enables growth of the native tricuspid annulus. (2011)

The implantation of a biodegradable ring does not restrict growth of the native TV annulus; this enabled its stabilization in proportion to the somatic growth in the majority of the children. The TV annulus began to change its dimension at six months postoperatively, which may coincide with its biodegradation. The rate of growth of the TV annulus differed from that in the normal population, and was proportional to the patient age. The increase in TV annulus diameter over time did not have any negative influence on the function of the repaired valve.
Authors’ response: SARS-CoV-2 detection by real-time RT-PCR (2020)

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DC-coupled burst-mode receiver with high sensitivity, wide dynamic range and short settling time for symmetric 10G-GPONs (2011)

This paper presents a high performance DC-coupled 10 Gbit/s APD-based optical burst-mode receiver (BM-RX) for symmetric 10G-GPONs. The BM-RX can handle upstream bursts with a loud/soft range wider than 24.0 dB, and the measured sensitivity is -30.0 dBm at BER = 10(-3) after a start of burst settling time no longer than 51 ns. This paper also investigates, for the first time, the inter-burst guard time required for a 10 Gbit/s BM-RX with auto-reset generation, while the PON operates upstream at a high raw BER and is using FEC.