gebhart/patrepeval huggingface dataset:
A rapid non-radioactive technique for measurement of repair synthesis in primary human fibroblasts by incorporation of ethynyl deoxyuridine (EdU) (2008)

Xeroderma pigmentosum (XP) is an autosomal recessive genetic disorder. Afflicted patients show extreme sun-sensitivity and skin cancer predisposition. XP is in most cases associated with deficient nucleotide excision repair (NER), which is the process responsible for removing photolesions from DNA. Measuring NER activity by nucleotide incorporation into repair patches, termed 'unscheduled DNA synthesis (UDS)', is one of the most commonly used assays for XP-diagnosis and NER research. We have established a rapid and accurate procedure for measuring UDS by replacement of thymidine with 5-ethynyl-2'-deoxyuridine (EdU). EdU incorporated into repair patches can be directly conjugated to fluorescent azide derivatives, thereby obviating the need for either radiolabeled thymidine or denaturation and antibody detection of incorporated bromodeoxyuridine (BrdU). We demonstrate that the EdU incorporation assay is compatible with conventional techniques such as immunofluorescent staining and labeling of cells with micro-latex beads. Importantly, we can complete the entire UDS assay within half a day from preparation of the assay coverslips; this technique may prove useful as a method for XP diagnosis.
<i>Shigella</i> applies molecular mimicry to subvert vinculin and invade host cells (2006)

Shigella flexneri, the causative agent of bacillary dysentery, injects invasin proteins through a type III secretion apparatus upon contacting the host cell, which triggers pathogen internalization. The invasin IpaA is essential for S. flexneri pathogenesis and binds to the cytoskeletal protein vinculin to facilitate host cell entry. We report that IpaA harbors two vinculin-binding sites (VBSs) within its C-terminal domain that bind to and activate vinculin in a mutually exclusive fashion. Only the highest affinity C-terminal IpaA VBS is necessary for efficient entry and cell-cell spread of S. flexneri, whereas the lower affinity VBS appears to contribute to vinculin recruitment at entry foci of the pathogen. Finally, the crystal structures of vinculin in complex with the VBSs of IpaA reveal the mechanism by which IpaA subverts vinculin's functions, where S. flexneri utilizes a remarkable level of molecular mimicry of the talin-vinculin interaction to activate vinculin. Mimicry of vinculin's interactions may therefore be a general mechanism applied by pathogens to infect the host cell.
Replicating real-time garbage collector for Java (2009)

Real-time Java is becoming a viable platform for real-time applications, bringing new challenges to a garbage collector. A real-time collector has to be incremental as not to cause deadline misses by suspending an application for too long. In particular, a real-time collector has to relocate objects in the heap, incrementally and transparently to the application. This is usually achieved via an indirection that has to be followed on every read and write to the heap.
On latching probability of particle induced transients in combinational networks (2002)

The question to what extent particle induced transients in combinational parts of a circuit propagate into memory elements is addressed in this paper An experimental method is presented in which the proportion of bit flips originating from heavy-ion hits in combinational logic is determined. It is proposed that a voltage pulse may only propagate through a limited number of transistor stages and still be latched. The proportion of all transients in combinational logic that were latched into registers was experimentally, estimated to be between 0.7/spl middot/10/sup -3/ and 2/spl middot/10/sup -3/ for a custom designed CMOS circuit. Very few multiple bit flips were observed during the experiments which indicates that the single bit flip model used in many high-level simulations is reasonable accurate.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
THREE <i>Alu</i> REPEATED SEQUENCES ASSOCIATED WITH A HUMAN GLANDULAR KALLIKREIN GENE (1988)

1. Recently the complete primary structure of a human glandular kallikrein gene, hGK-1, was reported. The present paper presents further structural information. 2. Associated with the gene were three Alu repeated sequences; one in the second intron and two approximately 0.4 kb and 1.2 kb upstream. 3. The 5' non-coding and 5' flanking DNA was highly homologous to that in the mouse genes. 4. Different polyadenylation signals are used in different human kallikrein genes.
[Development of atraumatic microneedles for use in ophthalmology]. (1989)

Measurement of the force interaction of the microneedle with the pierced material helps quantitatively estimate the microneedle functional characteristics and cut down the time for control. Flat microneedles with a trihedral point require the least pricking effort; the use of such needles is most desirable in suturing solid biological tissues (cornea, sclera, etc.). Experimental samples of Soviet ophthalmologic microneedles are not inferior to foreign ones. Employment of a mathematical model helps select the optimal combinations of the values of the geometrical parameters that will provide the least pricking effort.
Pattern Roughness Mitigation of 22 nm Lines and Spaces: The Impact of a H<sub>2</sub>Plasma Treatment (2014)

As the semiconductor industry pursues Moore's law, the demand to obtain smaller features continues. Extreme ultraviolet (EUV) lithography remains one of the primary options for sub-20 nm patterns. However, the technology struggles to meet the line width roughness (LWR) specifications. In this article, we present the significance of plasma treatment as a roughness smoothing technique. Two EUV photoresists with 22 nm lines are exposed to various plasma processes. We highlight the advantages of a hydrogen plasma treatment and its vacuum ultraviolet (VUV) emission as an optimal smoothing process and discuss the effect of photoresist thickness, initial LWR and the VUV plasma emission. Even though a H2 plasma treatment results in a successful reduction of LWR/LER, the target value of below 2nm is not yet achieved.
The mythical man-month (anniversary ed.) (1995)

Few books on software project management have been as influential and timeless as The Mythical Man-Month. With a blend of software engineering facts and thought-provoking opinions, Fred Brooks offers insight for anyone managing complex projects. These essays draw from his experience as project manager for the IBM System/360 computer family and then for OS/360, its massive software system. Now, 20 years after the initial publication of his book, Brooks has revisited his original ideas and added new thoughts and advice, both for readers already familiar with his work and for readers discovering it for the first time.The added chapters contain (1) a crisp condensation of all the propositions asserted in the original book, including Brooks' central argument in The Mythical Man-Month: that large programming projects suffer management problems different from small ones due to the division of labor; that the conceptual integrity of the product is therefore critical; and that it is difficult but possible to achieve this unity; (2) Brooks' view of these propositions a generation later; (3) a reprint of his classic 1986 paper No Silver Bullet; and (4) today's thoughts on the 1986 assertion, There will be no silver bullet within ten years. 0201835959B04262002
Broadband multi-frequency GNSS signal simulation with GPU (2016)

This work introduces an alternative architecture of a GNSS signal simulator, where the multiple GNSS services in the full GNSS bandwidth from L5 to L1 are generated and mixed in digital form. The digital-to-analog conversion and up-conversion to L-band is then applied to the single compounded wideband digital signal. The digital signal generation and mixing is implemented on a pair of strong GPUs with specially designed algorithms for massive parallel signal generation, mixing and quantization. Data transfer overlaps with the signal generation on both GPUs. The architecture uses up the full speed of the PCIe interface to transfer the signal to a broadband DAC-board and to reach high bandwidth for real-time generation. The digital part of the system was build up using low-cost mass-market components. The backbone of the system is a gaming PC system and two gaming-level graphic cards with total costs below 5000 €. The DAC conversion board and up-conversion need to reach high conversion rate and broad-band requirements, but it is only a single wide band channel to be processed without any inter-channel synchronization. The objective of the work was to reach real-time capability for a sufficient number of channels and GNSS signals to demonstrate viability of the concept. The potential and limits with respect to issues of signal quality, simulation settings flexibility and capacity to simulate important signal features were assessed as well.
Designing for Usability of an Adaptive Time Management Assistant (2009)

This case study article describes the iterative design process of an AI‐based mixed‐initiative calendaring tool with embedded artificial intelligence. We establish the specific types of assistance in which the target user population expressed interest, and we highlight our findings regarding the scheduling practices and the reminding preferences of these users. These findings motivated the redesign and enhancement of our intelligent system. Lessons learned from the study—namely, that AI systems must be usable to gain widespread adoption and retention and that simple problems that perhaps do not necessitate complex AI‐based solutions should not go unattended merely because of their inherent simplicity—conclude the article, along with a discussion of the importance of the iterative design process for any user adaptive system.
Blue-Prints, Synthesis and Applications of Glycopolymers. (1996)

本総説は最近「糖質ポリマー」と定義され、急速に拡大しているネオ複合糖質の合成と応用について書かれている。最も一般的に用いられている合成法に関する事柄を、その利点や欠点とともに議論した。単純なあるいは複雑なオリゴ糖連鎖をポリマーに導入することについても述べている。それに加えて、糖質ポリマー前駆体への酵素を用いたグリコシル化反応について、trans-シアリダーゼやエンド-β-D-N-アセチルグルコサミニダーゼを例に挙げて述べた。糖質ポリマーの主要な物性や生化学的性質を、応用を考慮して評価した。最近になって明かとなった、他のネオ複合糖質よりも糖質ポリマーが優れている多くの事柄に焦点をあてた。糖質ポリマーの応用が急速に発展しているため、特殊な要求に合ったポリマーが合成されるであろうことが予測されてきた。その結果、プロープやエフェクター分子を組み入れた糖質ポリマーの合成法によって得られるような、特別あつらえの性質を有するものが合成されてきている。最後に、特殊な糖残基を有する糖質ポリマーの幅広い応用について触れる。細胞培養、抗原決定基の確認、抗体の分類、免疫診断、細胞ターゲティング、あるいはインフルエンザウイルスなどの病原体の接着の阻害に使用される糖質ポリマーについて述べた。最近のいくつかの応用例は、糖質ポリマーが肺癌増殖の予後および抗炎症剤に用いられる可能性があることを示唆している。
Apolipoprotein B100 Exit from the Endoplasmic Reticulum (ER) Is COPII-dependent, and Its Lipidation to Very Low Density Lipoprotein Occurs Post-ER (2003)

Hepatic apolipoprotein B100 (apoB100) associates with lipids to form dense lipoprotein particles in the endoplasmic reticulum (ER) and is further lipidated to very low density lipoproteins (VLDL). Because the VLDL diameter can exceed 200 nm, classical ER-derived vesicles may be unable to accommodate VLDLs. Using hepatic membranes and cytosol to reconstitute ER budding, apoB100-containing vesicles sedimented distinct from those harboring more typical cargo but contained Sec23. Moreover, ER exit of apoB was inhibited by dominant-negative Sar1. Budding required Sar1 regardless of whether oleic acid (OA) was added to stimulate apoB lipidation; therefore, either large apoB100-lipoproteins reside in secretory vesicles, or full lipidation occurs post-ER. Using membranes from cells incubated in the presence or absence of OA, we determined that apoB100-lipoproteins in ER vesicles had not become lipidated to VLDLs. VLDL particles resided in the Golgi, but not the ER, after fractionation of OA-treated cells. We conclude that apoB100-lipoproteins exit the ER in COPII vesicles, but under conditions favorable for VLDL formation final lipid loading occurs post-ER.
Microseismic Monitoring Quality-Control (QC) Reports as an Interpretative Tool for Nonspecialists (2007)

Abstract In the oilfield industry microseismic monitoring is widely applied to determine induced fracture network geometry and stress changes in reservoirs. The basic result is usually a map of the distribution of the microseismic events describing the area influenced by injection/production of reservoir fluids, e.g hydraulic fracturing. As every microearthquake event, i.e. ‘dot’ on the map, is processed individually, it has its own level of location accuracy. To prevent any misinterpretations based on events with low accuracy, Quality-Control (QC-) reports can provide important information regarding location accuracy and other attributes which help in the overall interpretation of the maps, in addition to the standard event location. However, much of the information that is needed to assess the quality of the data is very specialized and technical, so that the figures presented in the QC- reports often appear complicated and are not easy to read for the non-specialist. By introducing easy-to-read figures that summarize the essential information, these reports have become more useful to the occasional user.
Use of hematopoietic growth factors in marrow transplantation (1994)

Results of clinical trials in bone marrow transplantation (BMT) patients have shown that morbidity associated with myelosuppressive chemo- or radiotherapy is reduced in patients receiving hematopoietic growth factors such as recombinant human granulocyte colony-stimulating factor or recombinant human granulocyte-macrophage colony-stimulating factor. Recombinant human granulocyte-macrophage colony-stimulating factor has been approved by the Food and Drug Administration to speed neutrophil recovery, to reduce the severity and duration of infection, and to shorten hospital stays of patients with lymphoid malignancy who undergo autologous BMT. Recombinant human granulocyte colony-stimulating factor is not approved by the Food and Drug Administration as therapy in BMT; however, results of phase I and phase II trials suggest similar beneficial effects in autologous BMT. Both molecules are well tolerated in patients undergoing autologous or allogeneic BMT. Other hematopoietic growth factors, such as recombinant Human macrophage colony-stimulating factor, recombinant human interleukin (rhIL)-3, rhIL-3-GM-CSF (rh-PIXY 321), rhIL-6, rhIL-1, rhc-kit ligand (rh-KL), and erythropoietin (rh-EPO), are also being studied singly or in combination in patients undergoing BMT. The use of hematopoietic growth factors in marrow transplantation is reviewed.
Quantitative measurement of the nanoparticle size and number concentration from liquid suspensions by atomic force microscopy (2014)

Microscopy techniques are indispensable to the nanoanalytical toolbox and can provide accurate information on the number size distribution and number concentration of nanoparticles (NPs) at low concentrations (ca. ppt to ppb range) and small sizes (ca. <20 nm). However, the high capabilities of microscopy techniques are limited by the traditional sample preparation based on drying a small volume of suspension of NPs on a microscopy substrate. This method is limited by low recovery of NPs (ca. <10%), formation of aggregates during the drying process, and thus, the complete misrepresentation of the NP suspensions under consideration. This paper presents a validated quantitative sampling technique for atomic force microscopy (AFM) that overcomes the above-mentioned shortcomings and allows full recovery and representativeness of the NPs under consideration by forcing the NPs into the substrate via ultracentrifugation and strongly attaches the NPs to the substrate by surface functionalization of the substrate or by adding cations to the NP suspension. The high efficiency of the analysis is demonstrated by the uniformity of the NP distribution on the substrate (that is low variability between the number of NPs counted on different images on different areas of the substrate), the high recovery of the NPs up to 71%) and the good correlation (R > 0.95) between the mass and number concentrations. Therefore, for the first time, we developed a validated quantitative sampling technique that enables the use of the full capabilities of microscopy tools to quantitatively and accurately determine the number size distribution and number concentration of NPs at environmentally relevant low concentrations (i.e. 0.34-100 ppb). This approach is of high environmental relevance and can be applied widely in environmental nanoscience and nanotoxicology for (i) measuring the number concentration dose in nanotoxicological studies and (ii) accurately measuring the number size distribution of NPs; both are key requirements for the implementation of the European Commission recommendation for definition of nanomaterials.
Mutational analysis of the active site of indoleglycerol phosphate synthase from<i>Escherichia coli</i> (1998)

Abstract Indoleglycerol phosphate synthase catalyzes the ring closure of 1‐(2‐carboxyphenylamino)‐1‐deoxyribulose 5′‐phosphate to indoleglycerol phosphate, the fifth step in the pathway of tryptophan biosynthesis from chorismate. Because chemical synthesis of indole derivatives from arylamino ketones requires drastic solvent conditions, it is interesting by what mechanism the enzyme catalyzes the same condensation reaction. Seven invariant polar residues in the active site of the enzyme from Escherichia coli have been mutated directly or randomly, to identify the catalytically essential ones. A strain of E. coli suitable for selecting and classifying active mutants by functional complementation was constructed by precise deletion of the trp C gene from the genome. Judged by growth rates of transformants on selective media, mutants with either S58 or S60 replaced by alanine were indistinguishable from the wild‐type, but R186 replaced by alanine was still partially active. Saturation random mutagenesis of individual codons showed that E53 was partially replaceable by aspartate and cysteine, whereas K114, E163, and N184 could not be replaced by any other residue. Partially active mutant proteins were purified and their steady‐state kinetic and inhibitor binding constants determined. Their relative catalytic efficiencies paralleled their relative complementation efficiencies. These results are compatible with the location of the essential residues in the active site of the enzyme and support a chemically plausible catalytic mechanism. It involves two enzyme‐bound intermediates and general acid‐base catalysis by K114 and E163 with the support of E53 and N184.
Real-Time Dense Stereo Matching With ELAS on FPGA-Accelerated Embedded Devices (2018)

For many applications in low-power real-time robotics, stereo cameras are the sensors of choice for depth perception as they are typically cheaper and more versatile than their active counterparts. Their biggest drawback, however, is that they do not directly sense depth maps; instead, these must be estimated through data-intensive processes. Therefore, appropriate algorithm selection plays an important role in achieving the desired performance characteristics. Motivated by applications in space and mobile robotics, we implement and evaluate a field programmable gate arrays (FPGA) accelerated adaptation of the efficient large-scale stereo (ELAS) algorithm. Despite offering one of the best tradeoffs between efficiency and accuracy, ELAS has only been shown to run at 1.5-3 fps on a high-end CPU. Our system preserves all intriguing properties of the original algorithm, such as the slanted plane priors, but can achieve a frame rate of 47 fps whilst consuming under 4 W of power. Unlike previous FPGA-based designs, we take advantage of both components on the CPU/FPGA system-on-chip to showcase the strategy necessary to accelerate more complex and computationally diverse algorithms for such low power, real-time systems.
Residential Building Retrofit through Numerical Simulation: A Case Study (2017)

This paper presents an energy conservation measures prioritization process of a residential Australian building. For this purpose, a simulation model of the building has been implemented and validated based on the information from the energy audit report. Further, a preliminary set of potential energy conservation measures has been identified according to specific information collected during the building survey phase. DesignBuilder software has been used as the simulation tool and yearly energy benefits have been quantified for each intervention. Finally, an economic assessment is conducted based on the most common economic tools (net present value, internal rate of return, profitability index and discounted payback period). As a consequence, a final building performance simulation has been conducted in order to properly quantify the potential energy benefit of the whole retrofit intervention. As results, this study highlights how arduous could be, in certain cases, to achieve a cost-effective retrofit intervention and how economic indexes could bring users to exclude a priori certain energy conservation measures during decision-making process even when these interventions are necessary to improve thermal comfort and energy efficiency.
Die Datengewinnung zur Analyse des Sicherheitsverhaltens (1990)

Die Analyse des Sicherheitsverhaltens erfordert eine theoretische Fundierung, an der sich die Interpretation von Ergebnissen zu orientieren hat. Eine Theorie besteht aus einer oder mehreren begründeten und falsifizierbaren Hypothesen. Eine Hypothese stellt die Verknüpfung zwischen zwischen zwei Variablen in Form von Wenn-Dann-Aussagen her. Hypothesen können sich auf strenge Gesetzmäβigkeiten beziehen, werden aber im Rahmen empirischer Analysen des Konsumentenverhaltens häufig auf ihre allgemeine Generalisierbarkeit überprüft.
PCR-based procedures to isolate insertion sites of DNA elements (2007)

During the past several years, retroviral insertional mutagenesis has been fruitfully applied to search for genes/pathways involved in tumorigenesis. Techniques used to identify proviral insertion sites are critical for fulfilling these projects. Although a variety of approaches have been described, an improvement over existing methods is required to recover every possible insertion site for cancer gene discovery, so-called saturation analysis. Here, we have described the development of two ligation-mediated PCR variants, SplinkTA-PCR (STA-PCR) and SplinkBlunt-PCR, for efficient isolation of insertion sites in retrovirus-induced leukemia. Our results demonstrated that these two protocols are complementary to each other and that they are better employed in combination for maximal cloning efficiency. These protocols are easy-to-use, reliable and efficient, and are readily applicable to large-scale cloning of insertion sites of provirus and other integrated DNA elements, as well as for detection and cloning of differential insertions unique to drug-resistant cells.
A lazy cache algorithm (1989)

This paper examines cache consistency conditions (safety conditions) for multiprocessor shared memory systems. It states and motivates a weaker condition than is normally required. An algorithm is presented that exploits the weaker condition to achieve greater concurrency. The paper concludes with a proof that the algorithm satisfies the safety condition.
Detection of Rare Allelic Variants of the Interferon-α <sub>2</sub> Gene in Human Genomic DNA (1995)

We have analyzed human donor DNA for the presence of sequences corresponding to allelic variants of the IFN-alpha 2 locus. Using both restriction enzyme digestion of PCR-amplified fragments and sequence analysis of these fragments, we have identified the three reported allelic variants, IFN-alpha 2a, IFN-alpha 2b, and IFN-alpha 2c, in genomic DNA derived from donors of African or Afro-Caribbean origin. This is the first report of the IFN-alpha 2a and IFN-alpha 2c alleles occurring in human donor DNA and supports the view that these are variants of the predominant IFN-alpha 2b allele rather than arising from mutations occurring in cultured cells.