gebhart/patrepeval huggingface dataset:
What programmers really want (2002)

This paper steps the reader through a needs assessment of programmers that was conducted by instructional designers. The assessment's purpose was to identify what learning support programmers need and want to successfully use a new software development kit (SDK). The paper includes the challenges the researchers encountered, the questions asked and the responses, the types of individuals interviewed, and the conclusions reached from the research. Recommendations also are presented. Those responsible with developing documentation, training, and other learning support systems for programmers may find this assessment helpful. Marketing, product development and customer support people may also find value in learning more about the needs of this unique audience.
Inverse association of cell adhesion regulator messenger RNA expression with metastasis in human colorectal cancer. (1996)

Alterations in several classes of adhesion molecules have been implicated in the progression of colorectal cancer. Cell adhesion regulator (CAR) has been identified as a regulator molecule of integrin-dependent cell adhesion. We have explored a possible involvement of the CAR gene in colorectal cancer. Reverse transcription-PCR revealed that CAR expression was detected in normal colonic cells, whereas it was decreased or undetectable in 6 of 13 (46.2%) human colon cancer cell lines. To further study the biological significance of CAR expression in colon cancer cells, a CAR expression vector was introduced into HT-29 cells, in which CAR is not expressed. Adhesion of HT-29 cells to extracellular matrix components was up-regulated by the introduction of CAR. In spite of similar growth properties with the controls, CAR-transfected HT-29 cells showed a significantly reduced spontaneous metastatic potential in nude mice. To determine whether these experimental results are of relevance with respect to actual human tumors, we investigated CAR expression in 30 surgical specimen pairs of human colorectal cancer and adjacent noncancerous tissue using semiquantitative reverse transcription-PCR. In 14 of 30 cases (46.7%), CAR expression in cancer was less than one-tenth of that in matched noncancerous tissue. The tumor:normal ratio of CAR expression was significantly lower in patients with lymph node metastasis than in those without it (P < 0.01) and in patients with distant metastasis than in those without it (P < 0.05). CAR expression was significantly lower in more advanced Dukes' stage tumors (P < 0.05). Our results suggest that down-regulation of CAR expression may play an important role in the progression and metastasis of colorectal cancer.
A self-reconfiguring IEEE 1687 network for fault monitoring (2016)

Efficient handling of faults during operation is highly dependent on the interval (latency) from the time embedded instruments detect errors to the time when the fault manager localizes the errors. In this paper, we propose a self-reconfiguring IEEE 1687 network in which all instruments that have detected errors are automatically included in the scan path. To enable self-reconfiguration, we propose a modified segment insertion bit (SIB) compliant to IEEE 1687. We provide time analyses on error detection and fault localization for single and multiple faults, and we suggest how the self-reconfiguring IEEE 1687 network should be designed such that time for error detection and fault localization is kept low and deterministic. For validation, we implemented and performed post-layout simulations for one self-reconfiguring network. We show that compared to previous schemes, our proposed network significantly reduces the fault localization time.
Molecular Biology: Promiscuous Chromosomal Proteins: Complexes About Sex (1996)

In the phenomenon of dosage compensation, the expression of genes from the entire X chromosome is adjusted to be equivalent between the two sexes. This is necessary because one sex usually has two X chromosomes, while the other has only one. In the Perspective, Kuroda and Villeneuve explain the findings in two reports in this issue of Science from Meyer and co-workers ( p. 1732 and p. 1736 ), in which subunits of a protein complex critical for dosage compensation are shown to be also used in the process of chromosome segregation during meiosis, suggesting that both occur by the regulated condensation of chromosomes.
Genetic tools for reliable gene expression and recombineering in <i>Pseudomonas putida</i> (2018)

Pseudomonas putida is a promising bacterial host for producing natural products, such as polyketides and nonribosomal peptides. In these types of projects, researchers need a genetic toolbox consisting of plasmids, characterized promoters, and techniques for rapidly editing the genome. Past reports described constitutive promoter libraries, a suite of broad host range plasmids that replicate in P. putida, and genome-editing methods. To augment those tools, we have characterized a set of inducible promoters and discovered that IPTG-inducible promoter systems have poor dynamic range due to overexpression of the LacI repressor. By replacing the promoter driving lacI expression with weaker promoters, we increased the fold induction of an IPTG-inducible promoter in P. putida KT2440 to 80-fold. Upon discovering that gene expression from a plasmid was unpredictable when using a high-copy mutant of the BBR1 origin, we determined the copy numbers of several broad host range origins and found that plasmid copy numbers are significantly higher in P. putida KT2440 than in the synthetic biology workhorse, Escherichia coli. Lastly, we developed a λRed/Cas9 recombineering method in P. putida KT2440 using the genetic tools that we characterized. This method enabled the creation of scarless mutations without the need for performing classic two-step integration and marker removal protocols that depend on selection and counterselection genes. With the method, we generated four scarless deletions, three of which we were unable to create using a previously established genome-editing technique.
An Ion-insensitive cAMP Biosensor for Long Term Quantitative Ratiometric Fluorescence Resonance Energy Transfer (FRET) Measurements under Variable Physiological Conditions (2011)

Ratiometric measurements with FRET-based biosensors in living cells using a single fluorescence excitation wavelength are often affected by a significant ion sensitivity and the aggregation behavior of the FRET pair. This is an important problem for quantitative approaches. Here we report on the influence of physiological ion concentration changes on quantitative ratiometric measurements by comparing different FRET pairs for a cAMP-detecting biosensor. We exchanged the enhanced CFP/enhanced YFP FRET pair of an established Epac1-based biosensor by the fluorophores mCerulean/mCitrine. In the case of enhanced CFP/enhanced YFP, we showed that changes in proton, and (to a lesser extent) chloride ion concentrations result in incorrect ratiometric FRET signals, which may exceed the dynamic range of the biosensor. Calcium ions have no direct, but an indirect pH-driven effect by mobilizing protons. These ion dependences were greatly eliminated when mCerulean/mCitrine fluorophores were used. For such advanced FRET pairs the biosensor is less sensitive to changes in ion concentration and allows consistent cAMP concentration measurements under different physiological conditions, as occur in metabolically active cells. In addition, we verified that the described FRET pair exchange increased the dynamic range of the FRET efficiency response. The time window for stable experimental conditions was also prolonged by a faster biosensor expression rate in transfected cells and a greatly reduced tendency to aggregate, which reduces cytotoxicity. These properties were verified in functional tests in single cells co-expressing the biosensor and the 5-HT(1A) receptor.
Use of synthetic peptides to confirm that the <i>Pseudomonas aeruginosa</i> PAK pilus adhesin and the <i>Candida albicans</i> fimbrial adhesin possess a homologous receptor‐binding domain (1996)

Pseudomonas aeruginosa PAK pili and Candida albicans fimbriae are adhesins present on the microbial cell surfaces which mediate binding to epithelial cell-surface receptors. The receptor-binding domain (adhesintope) of the PAK pilus adhesin has been shown previously to reside in the carboxy-terminal disulphide-bonded region of P. aeruginosa pilin (PAK128-144). The delineation of the C. albicans fimbrial adhesintope was investigated in these studies using synthetic peptides which correspond to the whole (PAK128-144) or part of (PAK134-140) adhesintope of the PAK pilus and their respective anti-peptide antisera and biotinylated PAK pili (Bt-PAK pili), fimbriae (Bt-fimbriae), P. aeruginosa whole cells (Bt-P. aeruginosa) and C. albicans whole cells (Bt-C. albicans). The results from these studies confirmed that a structurally conserved motif akin to the PAK(128-144) peptide sequence is present in C. albicans fimbrial adhesin and that the seven-amino-acid residue PAK(134-140) sequence plays an important role in forming the adhesintope for both P. aeruginosa PAK pilus and C. albicans fimbrial adhesins.
Sexuality, contraception and pregnancy in a high-school population. (1973)

Students in a middle-class and in an economically lower-class high school were surveyed regarding their attitudes and behavior with respect to sexuality, contraception, and pregnancy. A large majority of students approved of premarital intercourse for both sexes within the context of a loving relationship. The most important deterrent to sexual intercourse was fear of pregnancy. A majority of both sexes had had sexual intercourse. Forty percent of the sexually active had used no contraception on some occasions, and many of the remainder had used poor methods such as withdrawal or rhythm. The pregnancy rate was high-at least 20 percent in several of the sexually active subgroups. Parents were an infrequent source of information about sex. On the other hand, there was some evidence that students exposed to a sex education program retained useful information if it was relevant to their situation, and if they were appropriately motivated.A model for integrating the various aspects of this subject area is offered.
3D pose estimation and shape coding of moving objects based on statistical morphological skeleton (2002)

Recognition-based tracking and image coding methods are often based on different techniques. However, these techniques share the necessity of reliable and fast methods for the representation of the information content of the scene. In this paper, a method based on a lossy shape descriptor is presented which can be used for both recognition and coding purposes. The statistical morphological skeleton provides a noise-robust shape descriptor on which a further approximation phase is performed in order to improve the compression ratio. Then, it is possible to estimate the object's pose through a comparison of the shape descriptor with a set of object models stored in a database. An application to surveillance is presented where the obtained description is used to transmit shape information to a remote control center.
Viability of Human Corneal Endothelium Following Optisol-GS Storage (1995)

Corneas stored in Optisol-GS through 21 days at 4 degrees C maintain a high percentage of viable endothelial cells. There was no significant difference of endothelial viability between corneas stored in glass vials or in viewing chambers (Alcon). A 50% loss of endothelial viability occurred in moist chamber-stored corneas after 2 days and by 35 days in corneas stored in Optisol-GS.
Compact explicit MPC with guarantee of feasibility for tracking (2006)

This paper deals with the constrained model predictive control, and focuses on the reference tracking problem. The analysis of the feasibility limitations is done using explicit formulations of the multi-parametric optimizations and invariant sets theory. The enlargement of the set of feasible trajectories by using reference governor schemes is discussed. The main result is a compact piecewise affine law with guarantees of feasibility, constructed by mixing the explicit formulations of the predictive law and the reference adjustment mechanism.
Regulatory T cell (Treg) therapy (2019)

Milestones in the discovery and clinical translation of regulatory T cells (Tregs), a subset of suppressive T lymphocytes that hold the potential to treat autoimmune disorders and organ transplant rejection.
A partial structural repeat forms the heterodimer self-association site of all beta-spectrins (1994)

The self-polymerization of alpha beta-spectrin heterodimers to form tetramers and higher oligomers is central to its role as a membrane stabilizer and organizer. Mutations near the amino terminus of alpha I sigma 1-spectrin or the COOH terminus of beta I sigma 1-spectrin often lead to profound impairment heterodimer polymerization and to hemolytic disease of varying severity. Previous studies using an 80-kDa univalent fragment of alpha I sigma 1-spectrin have established that the amino-terminal segment of alpha I sigma 1-spectrin mediates the association of the alpha subunit with either intact heterodimers or with isolated beta-spectrin (beta I sigma 1). However, the nature of the self-association site in beta-spectrin has remained unclear. In the present study, native beta-spectrin and recombinant beta-spectrin peptides representing COOH-terminal portions of two alternative transcripts of the gene on chromosome 2 (beta I sigma 1 or "erythrocyte" spectrin and beta I sigma 2 or "muscle" spectrin), and one transcript of the gene on chromosome 14 (beta II sigma 1 or "beta G-fodrin") have been examined for their ability to bind either intact alpha beta-spectrin or the alpha I-spectrin 80-kDa univalent fragment. Deletion of the nonhomologous beta-spectrin sequence downstream of repeat 17 (spectrin domain III) had no discernible effect on binding. Truncations proximal to codon 2085 of beta I sigma 1-spectrin demonstrated a precipitous loss of activity, accounted for by a loss of both binding affinity and capacity. Further truncations to repeat 16 (codon 1979) restored binding activity to levels approximating that of the intact molecule. Repeat 16/17 and 17/16 chimeras displayed reduced binding activity. Collectively, these data indicate that the beta-subunit self-association site is highly sensitive to conformation, involves widespread interactions within the 17th repeat unit, is largely independent of sequences in domain III, and can be recreated by the deletion of all residues distal to the COOH end (codon 1979) of the 16th and presumably other spectrin sequence repeat units. All beta-spectrins appear to use this binding motif, regardless of the nature of the nonhomologous sequence in domain III.
Synthesis and Photochemical Properties of a Kainate Precursor and Activation of Kainate and AMPA Receptor Channels on a Microsecond Time Scale (1996)

Kainate and alpha-amino-3-hydroxy-5-methyl-4-isoxazolylpropionate (AMPA) receptors are transmembrane proteins that can form ion channels upon binding a specific ligand. The receptors are located at major excitatory synapses in the mammalian central nervous system. Kainate and AMPA receptors participate in many physiological activities of the brain, including learning and memory, and are involved in many neurological disorders. Elucidation of the mechanisms of receptor transmembrane channel formation, inhibition, and regulation is important in understanding fundamental central nervous system function and in designing potential therapeutic agents. Kainate can activate both kainate and AMPA receptors, leading to channel opening in the microsecond to millisecond time region. A newly developed laser pulse photolysis technique, with a microsecond time resolution, has been successfully used to study the chemical reactions of receptor proteins in the microsecond to millisecond time region. To apply the technique to kainate and AMPA receptors, a photolabile kainate precursor in which a caging group, the alpha-carboxy-2-nitrobenzyl group, is attached to the gamma-carboxyl group of kainic acid has been synthesized. The photolytic release of free kainate from the caged kainate on the microsecond time scale, initiated by a pulse of laser light at 308 nm, was measured. The quantum yield is 0.34 at pH 6.8 and room temperature. The half-life of the major component (approximately 86%) of the photolytic reaction is 45 microseconds, while that of the minor component (approximately 14%) is 0.7 ms. The effects of the caged kainate on kainate and AMPA receptors endogenously expressed in rat hippocampal neurons were also evaluated. Caged kainate (750 microM) did not activate the receptor channels, nor did it potentiate or inhibit the kainate response. Photolysis of the caged kainate by a pulse of 333-nm laser light resulted in a rapid rise (with a t1/2 of 0.4 ms) in the whole-cell current due to the opening of kainate-activated receptor channels. The results presented demonstrate that this kainate precursor is suitable for rapid chemical kinetic investigations of the kainate and AMPA receptors in the microsecond to millisecond time region.
Theoretical Framework for Eliminating Redundancy in Workflows (2009)

In this paper we look at combining and compressing a set of workflows, such that computation can be minimized. In this context, we look at two novel theoretical problems with applications in workflow systems and services research, which are duals of each other. The first problem looks at merging the maximum number of vertices in two DAGs (directed acyclic graphs) without creating a cycle. We prove that the dual of this problem is the problem of maximizing the length of the LCS (longest common subsequence) between all pairs of topological orderings of the two DAGs. This formulation generalizes to a new definition of LCS between complex structures like workflows or XML documents, which we call M-LCS. Subsequently, we present a taxonomy of the different kinds of problems in this set, and find the M-LCS solution for a tree and a chain with a dynamic programming algorithm. Along with this theoretical formulation, we implement the algorithms in C++ and run it on representative workflows. We evaluate the performance of the M-LCS algorithm on a set of random workflows and observe that it is substantially better than traditional AI based approaches.
Ambient RF Energy Harvesting From a Two-Way Talk Radio for Flexible Wearable Wireless Sensor Devices Utilizing Inkjet Printing Technologies (2015)

A complete design and additive fabrication process of flexible wearable radio-frequency (RF) energy harvesters for off-the-shelf 2 W two-way talk radios utilizing inkjet printing technology is discussed in this paper. As a result of numerous output dc power measurements of fabricated proof-of-concept prototypes, a maximum output power of 146.9 mW and 43.2 mW was achieved with an H-field and E-field harvester, respectively. Also, the effect of misalignment between receiver and hand-held radio on harvesting performance is discussed in detail. To verify their potential in real-world wearable autonomous RF modules, the operation of E- and H-field energy harvesters was verified by utilizing an LED and a microcontroller communication module under on-body and on-bottle conditions, and the effect of the energy harvesters on the performance of the harvested communication systems was inspected through received power measurements in an anechoic chamber.
A novel duplex real-time reverse transcriptase-polymerase chain reaction assay for the detection of hepatitis C viral RNA with armored RNA as internal control (2010)

The duplex real-time RT-PCR assay is an efficient and effective viral assay. It is comparable with the CAP/CTM assay with regard to the power of the test and is appropriate for blood-donor screening and laboratory diagnosis of HCV infection.
Suitability of tile-based rendering for low-power 3d graphics accelerators (2007)

In this dissertation, we address low-power high performance 3D graphics accelerator architectures. The purpose of these accelerators is to relieve the burden of graphical computations from the main processor and also to achieve a better energy efficiency than can be achieved by executing these computations on the main processor. Since external data traffic is a major source of power consumption and because usually the rasterization stage of the 3D graphics pipeline requires the highest amount of data traffic, in this dissertation we especially focus on this stage of the graphics pipeline. Another reason for focusing on the rasterization stage is that it requires more processing power than the other stages because the operations are pixel-based. A promising technique to reduce the external data traffic in the rasterization stage of the graphics pipeline is tile-based rendering. This technique decomposes a scene into tiles and renders the tiles one by one. This allows the color components and z values of one tile to be stored in small, on-chip buffers, so that only the pixels visible in the final scene need to be stored in the external framebuffer. Tile-based accelerators, however, require large scene buffers to store the primitives to be rendered. While there have been studies related to the tile-based rendering paradigm for high performance systems, we are specifically discussing the suitability of tile-based 3D graphics accelerators for low-power devices. In order to evaluate various low-power 3D graphics architectures we first present GraalBench, a set of 3D graphics workloads representative for contemporary and emerging mobile devices. Furthermore, we propose several scene and state management algorithms for tile-based renderers. Thereafter, we analyze the performance of tile-based renderers compared to that of traditional renderers and we also determine the influence of the tile size on the amount of the data-traffic required for the rasterization stage of a tile-based renderer. In order to reduce even more the data traffic between the main memory and graphics accelerators, and to exploit the high temporal and spatial locality of texture accesses, we have also investigated several cache structures. Our results show that the proposed algorithms for tile-based renderers can effectively decrease the data traffic and computational requirements for the rasterization stage of the 3D graphics pipeline.