gebhart/patrepeval huggingface dataset:
ParGeo: A Library for Parallel Computational Geometry (2022)

This paper presents ParGeo, a multicore library for computational geometry. ParGeo contains modules for fundamental tasks including $k$d-tree based spatial search, spatial graph generation, and algorithms in computational geometry. We focus on three new algorithmic contributions provided in the library. First, we present a new parallel convex hull algorithm based on a reservation technique to enable parallel modifications to the hull. We also provide the first parallel implementations of the randomized incremental convex hull algorithm as well as a divide-and-conquer convex hull algorithm in $\mathbb{R}^3$. Second, for the smallest enclosing ball problem, we propose a new sampling-based algorithm to quickly reduce the size of the data set. We also provide the first parallel implementation of Welzl's classic algorithm for smallest enclosing ball. Third, we present the BDL-tree, a parallel batch-dynamic $k$d-tree that allows for efficient parallel updates and $k$-NN queries over dynamically changing point sets. BDL-trees consist of a log-structured set of $k$d-trees which can be used to efficiently insert, delete, and query batches of points in parallel. On 36 cores with two-way hyper-threading, our fastest convex hull algorithm achieves up to 44.7x self-relative parallel speedup and up to 559x speedup against the best existing sequential implementation. Our smallest enclosing ball algorithm using our sampling-based algorithm achieves up to 27.1x self-relative parallel speedup and up to 178x speedup against the best existing sequential implementation. Our implementation of the BDL-tree achieves self-relative parallel speedup of up to 46.1x. Across all of the algorithms in ParGeo, we achieve self-relative parallel speedup of 8.1--46.61x.
Glutathione S-conjugate transport in hepatocytes entering the cell cycle is preserved by a switch in expression from the apical MRP2 to the basolateral MRP1 transporting protein (1999)

The multidrug resistance protein MRP1 and its isoform MRP2 are involved in ATP-dependent glutathione S-conjugate transport and have similar substrate specificities. MRP2 mediates hepatic organic anion transport into bile. The physiological function of MRP1 in hepatocytes is unknown. Previous results show that MRP1 expression is low in quiescent hepatocytes but increased after SV40 large T antigen immortalization, suggesting a relationship with cell proliferation. Therefore, we determined mrp1 and mrp2 expression in rat hepatocytes in relation to the cell cycle. By varying cell density we obtained cultures that are mainly in G1 (high density) or have progressed into the S-phase or beyond (low density). In both cultures mrp1 mRNA and protein levels are increased, concomitantly with the disappearance of mrp2. This switch from mrp2 to mrp1 occurs in the G1 phase of the cell cycle and is associated with a decreased cell polarity. Mrp1 is located on lateral membranes or on intracellular vesicles, depending on whether cell-cell contact is established. In both locations mrp1 contributes to cellular glutathione S-conjugate efflux and protects against oxidative stress-inducing quinones. We conclude that a switch in expression from the apically located mrp2 to the basolaterally located mrp1 preserves glutathione S-conjugate transport in hepatocytes entering the cell cycle and protects against certain cytotoxic agents.
Functional tethered bilayer membranes as a biosensor platform (2005)

Tethered bilayer lipid membranes (tBLMs) present a powerful kind of solid supported membranes that can be used to study membrane related processes. TBLMs offer a quasi-natural environment where membrane proteins can be embedded and investigated. A tBLM consists of a lipid bilayer that is coupled covalently via a spacer group to a solid support. This being an electrode, electrical characterization of the system is possible and potential bio-sensing applications arise. We have developed a whole series of tBLM systems that provide different spacer groups and have anchor groups to allow for the assembly either on gold or on oxide surfaces. They show excellent barrier properties in terms of electrical resistance and capacitance. Systems are characterized using a variety of surface analytical tools. Here, we present the incorporation of the ion carrier valinomycin into a membrane consisting of a new anchor lipid (DPTT). This molecule is a modification of a previously reported structure. The modification is based on a new generic approach in the synthesis, which allows for an easier access different molecules and is open to adaptation to various substrates
Diffusion of Naproanilide in Water from Bubbling Tablets and Formation of Its Metabolite NOP (1995)

著者らは水田用除草剤施用の省力化を目的とした発泡性錠剤の研究を行なっている。炭酸塩と固体酸を含有する小型のナプロアニリド発泡性錠剤 (NBT) を試作し, ガラス温室内に設置した水槽 (29cm×3.5m) を用いてナプロアニリド [2-(2-naphthyloxy) propionanilide] およびその加水分解産物であるNOP [2-(2-naphthyloxy) propionic acid] の挙動を調べた。水槽の一端にNBTを処理し, 処理後0.5hrのナプロアニリド水中濃度を調べたところ, 処理点から1.5m以内では0.06ppm以上のナプロアニリドが検出され, この範囲では水深2cmの方が6cmの場合より濃度が高かった (Fig. 1)。処理点から1mおよび2.5m離れた地点でのナプロアニリドおよびNOPの水中濃度を経時的に調べたところ, ナプロアニリドは1m地点では処理後0.5hrで, 2.5m地点では処理後4hrで最高の濃度に達した。1m地点では初期に水深2cmの方が6cmの場合よりも水中濃度が高いが, 後に水深による差はなくなった。また2.5m地点では, 水深6cmの方が2cmよりも濃度が高かった (Fig. 2)。この結果からナプロアニリドは処理点に近い場所では水深が浅い方が水中に高濃度存在し, 処理点から遠い場所へは, 水深が深い方が拡散しやすいと考えられる。またNOPは1m地点および2.5m地点で, 処理後48hrで最高の水中濃度を示した。この場合, どちらの地点でもナプロアニリドよりかなり高い水中濃度を示した。また水深2cmの方が6cmよりも濃度が高かった (Fig. 3)。NOPはナプロアニリド自身よりも水溶解度が高いため水中拡散性が高いと考えられる。次に処理後96hrの土壌表面のナプロアニリドおよびNOPの濃度を調べた。ナプロアニリドの土壌表面濃渡は, 処理点からの距離にかかわらず水深6cmの方が水深2cmよりも高かった。一方, NOPの濃度は処理点から1m以内では水深2cmの方が高く, それ以上離れた所では水深6cmの方が高かった (Fig. 4)。この結果から, これら2つの化合物は水深が深い方が水中を広く拡散し, 処理点から離れた地点でより多くの量が土壌表面に吸着されると考えられる。NBTのウリカワに対する除草効果は処理点に近く, 水深が深い方が高かった (Fig. 5)。処理後0.5hrのナプロアニリド水中濃度と除草効果の関係を調べたところ, 水中濃度が高いほど除草効果も高く, 最小致死濃度は水深6cmでは0.2ppm, 水深2cmでは0.35ppmであった (Fig. 6)。
[Retracted] Conservative Therapy vs. Endovascular Approach for Intracranial Vertebrobasilar Artery Trunk Large Aneurysms: A Prospective Multicenter Cohort Study (2022)

Compared with conservative treatment, endovascular treatment of the IVBTLAs may be associated with a lower incidence of SAEs, with higher 1-year, 3-year, and 5-year survival rates. Conservative therapy, giant aneurysm, and ischemic onset were associated with a high risk of SAEs.
ChemInform Abstract: CYCLOADDITION REACTIONS OF HETEROCUMULENES, XI. REACTIONS OF MONOMERIC AND DIMERIC TERT‐BUTYLCYANOKETENE WITH AZOMETHINES (1978)

Abstract Das Keten (II) reagiert mit den Azomethinen (Ia)‐(Ic) zu den Addukten (IIIa) ( + Isomeres (IVa)), (IIIb) (+ Isomeres (IVb)) bzw. (IIIc); aus (Id) wird ein analoges Addukt (V) erhalten.
La fermentación maloláctica: objetivos y variables de control (2006)

La fermentacion malolactica se produce en el vino como resultado de la actividad metabolica de ciertas cepas de bacterias lacticas bien adaptadas. La reduccion de la acidez del vino y la modificacion de su sabor, que se producen por esta fermentacion bacteriana, se suelen considerar beneficiosas para el vino. La ventaja de la induccion de la fermentacion malolactica (FML) por inoculacion de cepas seleccionadas de bacterias lacticas es doble; en primer lugar, mejora el control del tiempo y la velocidad de la conversion del acido malico y, en segundo lugar, ejerce una influencia positiva en el sabor y la calidad del vino. Los estudios sensoriales demuestran que los compuestos de sabor producidos por las bacterias del acido lactico provocan cambios reconocibles en las caracteristicas de sabor del vino (1). Varios estudios prueban que distintas cepas de bacterias malolacticas tienen distintos efectos sensoriales en el vino (1,2,3,4,5), pero la influencia de la programacion temporal de la incorporacion de las bacterias, asi como el nivel de inoculacion, no se terminan de comprender del todo.
ChemInform Abstract: C—H Functionalization in the Synthesis of Amino Acids and Peptides (2014)

Abstract Review: 107 refs.
Digital image watermarking for photo authentication in Thai national ID card (2012)

Problem of fake image in ID card spreads all over the world e.g. false Thai national ID card in Thailand. This problem is quite difficult to detect because appearances of human face always change. Digital image watermarking for photo authentication in Thai national ID card is therefore proposed in this paper to overcome such a problem. Basically, a watermark signal consisting of ID code is embedded into the owner's picture and printed on ID card. To authenticate a card holder, his shown ID card is taken by a camera in a handheld device, and the watermark detection process is carried out to verify whether the extracted watermark matches the ID code printed on the card. However in practice, distortions introduced to the taken photo directly affect accuracy of the extracted watermark. To minimize these distortions, image registration technique based on projective transformation is applied in order to improve the accuracy of the extracted watermark. Our proposed method is efficient and very practical to implement with the existing watermarking schemes, as shown in the experimental results.
Anion exchange membranes composed of perfluoroalkylene chains and ammonium-functionalized oligophenylenes (2015)

A novel series of ammonium-containing copolymers (QPAFs) were synthesized as anion exchange membranes for alkaline fuel cell applications.
Comparative Study of Surface Modification Treatment for Porous Titanium (2020)

Alkali treatment was found to be a suitable surface modification method for porous titanium, resulting in good mechanical strength and apatite formation ability in simulated body fluid.
Lymphomatoid papulosis types D and E: a multicentre series of the French Cutaneous Lymphomas Study Group (2021)

LyP D and E have distinct clinical findings and may be associated with other cutaneous lymphomas.
Systemic lupus erythematosus in Lebanon (1999)

The present study describes the clinical characteristics of patients with systemic lupus erythematosus (SLE) from the American University of Beirut Medical Center (AUBMC), one of the largest teaching hospitals in Lebanon. This is a retrospective chart review of 100 SLE patients seen over a 20 y period. There were 86 females and 14 males, with a median age of 26 y. 85 patients were Lebanese and 15 patients were Palestinians. The main clinical features were arthritis and/or arthralgias seen in 95% of our patients, followed by malar rash (52%), and renal involvement (50%). Of the hematological manifestations, thrombocytopenia was most commonly seen in 33% of patients, followed by leucopenia in 17% and hemolytic anemia in 10% Oral ulcers and serositis were both seen in 40% of patients. Less frequent manifestations included discoid lupus (19%), neuropsychiatric manifestations (19%), and photosensitivity (16%). Antinuclear antibodies were detected in 87% of patients, whereas anti-DNA antibodies were seen in 50% of cases. 25 patients (25%) had a false-positive VDRL. A comparison between our findings and 3 other Arab SLE groups revealed a higher incidence of oral ulcers, discoid lupus, articular manifestations, thrombocytopenia and false-positive VDRL, and a lower incidence of photosensitivity, leucopenia, neuropsychiatric manifestations, and anti-DNA antibodies.
ChainSmith: Automatically Learning the Semantics of Malicious Campaigns by Mining Threat Intelligence Reports (2018)

Modern cyber attacks consist of a series of steps and are generally part of larger campaigns. Large-scale field data provides a quantitative measurement of these campaigns. On the other hand, security practitioners extract and report qualitative campaign characteristics manually. Linking the two sources provides new insights about attacker strategies from measurements. However, this is a time-consuming task because qualitative measurements are generally reported in natural language and are not machine-readable. We propose an approach to bridge measurement data with manual analysis. We borrow the idea from threat intelligence: we define campaigns using a 4-stage model, and describe each stage using IOCs (indicators of compromise), e.g. URLs and IP addresses. We train a multi-class classifier to extract IOCs and further categorize them into different stages. We implement these ideas in a system called ChainSmith. Our system can achieve 91.9% precision and 97.8% recall in extracting IOCs, and can determine the campaign roles for 86.2% of IOCs with 78.2% precision and 80.7% recall. We run ChainSmith on 14,155 online security articles, from which we collect 24,653 IOCs. The semantic roles allow us to link manual attack analysis with large scale field measurements. In particular, we study the effectiveness of different persuasion techniques used on enticing user to download the payloads. We find that the campaign usually starts from social engineering and "missing codec" ruse is a common persuasion technique that generates the most suspicious downloads each day.
Antiwear Characteristics of Automatic Transmission Fluids (1989)

&lt;div class="htmlview paragraph"&gt;Automatic transmission fluids (ATFs) are required to possess a high level of antiwear (AW) characteristics in order to function properly in the multitude of applications where such products are used. Generally DEXRON&lt;sup&gt;®&lt;/sup&gt;-II&lt;span class="xref"&gt;*&lt;/span&gt; or MERCON&lt;sup&gt;®&lt;/sup&gt;&lt;span class="xref"&gt;**&lt;/span&gt; fluids have given good AW performance in the field.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;However, ATFs of different chemistries might exhibit different levels of AW performance. Experimental work with ATFs of different chemistries has shown wide differences in AW levels. Thus, tests were carried out with the GM power steering pump test, the vickers pump (MERCON&lt;sup&gt;®&lt;/sup&gt; procedure) test, the FZG Low-Speed Wear test, the CRC L-20 gear test and several industrial pump tests. The results show that significant amounts of metals in the product detract from some aspects of the AW properties, and an ashless formulation can be the best choice.&lt;/div&gt;
Understanding Ionic Liquids through Atomistic and Coarse-Grained Molecular Dynamics Simulations (2007)

Understanding the physical properties of ionic liquids (ILs) via computer simulation is important for their potential technological applications. The goal of our IL research is to obtain a unified understanding of the properties of ILs with respect to their underlying molecular structure. From atomistic molecular dynamics simulations, the many-body electronic polarization effect was found to be important for modeling ILs, especially their dynamics. The multiscale coarse-graining methodology has also been employed to increase the simulation speed by a factor of 100 or more, thereby making it possible to study the mesoscopic behavior of ILs by computer simulations. With these simulation techniques, ILs with an amphiphilic cation were found to exhibit a spatial heterogeneity due to the aggregation of their nonpolar alkyl tails. This spatial heterogeneity is a key feature in interpreting many physical phenomena of ILs, such as their heterogeneous self-diffusion and surface layering, as well as their surfactant-like micelles formed in IL/water mixtures.
Expression and quantitative variation of the low‐incidence blood group antigen He on some S‐s‐red cells (1996)

The finding of He on S-s- red cells provides direct evidence for the presence of an altered form of GPB in red cells previously thought to be devoid of this glycophorin. Quantitative variation in He antigen expression was observed in a subset of S-s- red cells.
Testicular histology in streptozotocin‐induced diabetes (1986)

The use of the streptozotocin rat model for diabetes has been questioned by the appearance of extrapancreatic cytotoxicity, notably renal and hepatic. In this study the model was made specific to diabetic, drug-induced, and starvation effects on parameters of testicular histology. Formulation of orthogonal contrast expressions permitted the statistical separation of these influences. Tubules from moderately diabetic animals showed frequent thinning, and premature desquamation of pachytene spermatocytes and early spermatids from the germinal epithelium. Results showed that only diabetes significantly decreased seminiferous tubule diameter and increased testicular blood vessel numbers. In addition, significant alteration from the control pattern of tubule stage distribution was noted, particularly at stages IX-XI. Due to the inclusion of a drug-treated but nondiabetic group, streptozotocin itself was shown to have no significant effect on these parameters.
Application of cross correlation to HREM images of surfaces (1987)

As the HREM becomes increasingly used for the study of dynamic localized phenomena, the development of techniques to recover the desired information from a real image is important. Often, the important features are not strongly scattering in comparison to the matrix material in addition to being masked by statistical and amorphous noise. The desired information will usually involve the accurate knowledge of the position and intensity of the contrast. In order to decipher the desired information from a complex image, cross-correlation (xcf) techniques can be utilized. Unlike other image processing methods which rely on data massaging (e.g. high/low pass filtering or Fourier filtering), the cross-correlation method is a rigorous data reduction technique with no a priori assumptions. We have examined basic cross-correlation procedures using images of discrete gaussian peaks and have developed an iterative procedure to greatly enhance the capabilities of these techniques when the contrast from the peaks overlap.
Framework for quality assessment of whole genome, cancer sequences (2017)

Abstract Working with cancer whole genomes sequenced over a period of many years in different sequencing centres requires a validated framework to compare the quality of these sequences. The Pan-Cancer Analysis of Whole Genomes (PCAWG) of the International Cancer Genome Consortium (ICGC), a project a cohort of over 2800 donors provided us with the challenge of assessing the quality of the genome sequences. A non-redundant set of five quality control (QC) measurements were assembled and used to establish a star rating system. These QC measures reflect known differences in sequencing protocol and provide a guide to downstream analyses of these whole genome sequences. The resulting QC measures also allowed for exclusion samples of poor quality, providing researchers within PCAWG, and when the data is released for other researchers, a good idea of the sequencing quality. For a researcher wishing to apply the QC measures for their data we provide a Docker Container of the software used to calculate them. We believe that this is an effective framework of quality measures for whole genome, cancer sequences, which will be a useful addition to analytical pipelines, as it has to the PCAWG project.
Abstract 2509: Human anti-MUC1 antibodies elicited by a prophylactic cancer vaccine for mAb and CAR-modified T cell immunotherapies (2015)

Abstract MUC1 is a tumor-associated protein that is abnormally expressed on human adenocarcinomas. In our recent clinical trial, individuals at-risk for colonic adenocarcinoma received a prophylactic MUC1 cancer vaccine. Many individuals responded to the vaccine by producing high titers of anti-MUC1 IgG antibodies (Kimura, 2013). We isolated a panel of these antibodies and are seeking to develop them as antibody and chimeric antigen receptor (CAR) T cell cancer immunotherapies. To this end we used a novel method combining proteomics and next-gen DNA sequencing to identify and recombinantly produce 12 high-affinity anti-MUC1 antibodies from the sera of vaccinated individuals. By ELISA we determined that the antibodies bind with high-affinity to diverse epitopes within the MUC1 vaccine peptide. We also found that several of the antibodies can stain MUC1+ pancreas, colon, and breast cancer cell lines, but not a cell line expressing normal MUC1. We then determined that the antibodies could stain MUC1+ human pancreas and colon tumor samples, but not normal tissues. Having established tumor-specificity we have begun assessing the antibodies in a series of functional assays. In preliminary in vitro testing we determined that several of the antibodies can be internalized by MUC1+ cells making them potential candidates for toxin delivery as antibody drug conjugates (ADCs). Additionally, we found that two of the antibodies are capable of efficiently performing complement-dependent cytotoxicity (CDC) on MUC1+ cells. Finally, we have constructed CAR lentiviral expression constructs using the variable regions of several of the antibodies as targeting domains and are testing their ability to mediate MUC1-specific T cell activation, cytokine production, and target cell lysis. As the antibodies are human-derived, indication of efficacy in pre-clinical testing has the potential to directly enable clinical trials and hopefully approval of these reagents for therapy of cancer patients. Citation Format: Jason J. Lohmueller, Shuji Sato, Wan Cheung Cheung, Isabel Chu, Lana Popova, Christopher A. Manning, Katherine Crosby, Christopher Grange, James D. Ham, Roberto D. Polakiewicz, Olivera J. Finn. Human anti-MUC1 antibodies elicited by a prophylactic cancer vaccine for mAb and CAR-modified T cell immunotherapies. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2509. doi:10.1158/1538-7445.AM2015-2509
An image-to-map loop closing method for monocular SLAM (2008)

In this paper we present a loop closure method for a handheld single-camera SLAM system based on our previous work on relocalization. By finding correspondences between the current image and the map, our system is able to reliably detect loop closures. We compare our algorithm to existing techniques for loop closure in single-camera SLAM based on both image-to-image and map-to-map correspondences and discuss both the reliability and suitability of each algorithm in the context of monocular SLAM.
Design of haptic guides for pre-positioning assistance of a comanipulated needle (2019)

In minimally-invasive procedures like biopsy, the physician has to insert a needle into the tissues of a patient to reach a target. Currently, this task is mostly performed manually and under visual guidance. However, manual needle insertion can result in a large final positioning error of the tip that might lead to misdiagnosis and inadequate treatment. A way to solve this limitation is to use shared control; a gesture-assistance paradigm that combines the cognitive skills of the operator with the precision, stamina and repeatability of a robotic or haptic device. In this paper, we propose to assist the physician with a haptic device that holds the needle and generates mechanical guides during the phase of manual needle pre-positioning. In the latter, the physician has to place the tip of the needle on a planned entry point, with a pre-defined angle of incidence. From this pre-operative information and also from intra-operative measurements, we propose to generate haptic cues, known as virtual fixtures, to guide the physician towards the desired position and orientation of the needle. It takes the form of five haptic guides, each one implementing virtual fixtures. We conducted a user study where those guides were compared to the unassisted reference gesture. The most constraining guide, in terms of assisted degrees of freedom, was highlighted as the one that provides the best results in terms of performance and user experience.