gebhart/patrepeval huggingface dataset:
Increased Throughput by Parallelization of Library Preparation for Massive Sequencing (2010)

We present a novel automated procedure that makes it possible to prepare 36 indexed libraries per person and day, which can be increased to up to 96 libraries processed simultaneously. The yield, speed and robust performance of the protocol constitute a substantial improvement to present manual methods, without the need of extensive equipment investments. The described procedure enables a considerable efficiency increase for small to midsize sequencing centers.
On improving information retrieval performance from structured, semi-structured and un-structured information sources (2005)

The field of unstructured data retrieval for simple data types such as text and structured data retrieval in relational data models for transactional processing has already been well researched and commercially developed. However, more complex data types and models such as XML (as semi-structured data), data warehouses (as structured data), images (as unstructured data), etc. pose additional research challenges. The goal of this work is to address such information retrieval performance issues and challenges. 
As XML is an evolving semi-structured data representation format, techniques for indexing and retrieval of XML data are drawing increasing attention. We have proposed a memory-efficient index structure and an efficient algorithm for incremental indexing of XML document collections. The experimental results show that our proposed index structure outperforms earlier schemes in terms of indexing time and storage requirements. 
Given the growth in size of image collections over the last few years, Content-Based Image Retrieval (CBIR) systems are required to effectively and efficiently access images using information contained in them. Perception-based image retrieval, on the other hand, plays an important role in overcoming some of the semantic problems associated with CBIR. We have proposed a method that uses the concept of Inverse Image Frequency for perception-based color image quantization to improve traditional quantization schemes. Additionally, a cluster-based approach for efficient CBIR that uses a similarity-preserving space transformation method is proposed. Our results show that it offers superior response time with sufficiently high retrieval accuracy. 
Lastly, for improving online analytical processing, our focus has been on the more challenging and evolving multidimensional data model. Earlier work does not completely address performance issues, such as query response time and view maintenance time, in data warehouses. We propose a hybrid approach for the selection of views that combines the improved response time of the static approach and the automated tuning capability of the dynamic approach. Experimental results show that the hybrid approach outperforms both the static and the dynamic approaches to view selection. 
For future work, we suggest the integration of our results in these different areas and the evaluation of their applicability to real-life multimodal systems applications.
Modulation of CD1d-restricted NKT cell responses by using N- acyl variants of α-galactosylceramides (2005)

A form of alpha-galactosylceramide, KRN7000, activates CD1d-restricted Valpha14-invariant (Valpha14i) natural killer (NK) T cells and initiates multiple downstream immune reactions. We report that substituting the C26:0 N-acyl chain of KRN7000 with shorter, unsaturated fatty acids modifies the outcome of Valpha14i NKT cell activation. One analogue containing a diunsaturated C20 fatty acid (C20:2) potently induced a T helper type 2-biased cytokine response, with diminished IFN-gamma production and reduced Valpha14i NKT cell expansion. C20:2 also exhibited less stringent requirements for loading onto CD1d than KRN7000, suggesting a mechanism for the immunomodulatory properties of this lipid. The differential cellular response elicited by this class of Valpha14i NKT cell agonists may prove to be useful in immunotherapeutic applications.
A comparison of the fragmentation thresholds and inertial cavitation doses of different ultrasound contrast agents (2003)

Contrast bubble destruction is important in several new diagnostic and therapeutic applications. The pressure threshold of destruction is determined by the shell material, while the propensity for of the bubbles to undergo inertial cavitation (IC) depends both on the gas and shell properties of the ultrasound contrast agent (UCA). The ultrasonic fragmentation thresholds of three specific UCAs (Optison, Sonazoid, and biSpheres), each with different shell and gas properties, were determined under various acoustic conditions. The acoustic emissions generated by the agents, or their derivatives, characteristic of IC after fragmentation, was also compared, using cumulated broadband-noise emissions (IC "dose"). Albumin-shelled Optison and surfactant-shelled Sonazoid had low fragmentation thresholds (mean = 0.13 and 0.15 MPa at 1.1 MHz, 0.48 and 0.58 MPa at 3.5 MHz, respectively), while polymer-shelled biSpheres had a significant higher threshold (mean = 0.19 and 0.23 MPa at 1.1 MHz, 0.73 and 0.96 MPa for thin- and thick-shell biSpheres at 3.5 MHz, respectively, p<0.01). At comparable initial concentrations, surfactant-shelled Sonazoid produced a much larger IC dose after shell destruction than did either biSpheres or Optison (p<0.01). Thick-shelled biSpheres had the highest fragmentation threshold and produced the lowest IC dose. More than two and five acoustic cycles, respectively, were necessary for the thin- and thick-shell biSpheres to reach a steady-state fragmentation threshold.
Synthesis of enantiopure chloroalcohols by enzymatic kinetic resolution (2006)

3-Alkenyl and heteroaryl chloroalcohols have been obtained in excellent enantiomeric excess (>99%) by enzymatic kinetic resolution using the haloalcohol dehalogenase HheC. Yields were close to the theoretical maximum for all substrates employed. Furthermore, the applicability of this methodology on multigram scale has been established.
Fast and accurate long-read alignment with Burrows–Wheeler transform (2010)

Abstract Motivation: Many programs for aligning short sequencing reads to a reference genome have been developed in the last 2 years. Most of them are very efficient for short reads but inefficient or not applicable for reads &amp;gt;200 bp because the algorithms are heavily and specifically tuned for short queries with low sequencing error rate. However, some sequencing platforms already produce longer reads and others are expected to become available soon. For longer reads, hashing-based software such as BLAT and SSAHA2 remain the only choices. Nonetheless, these methods are substantially slower than short-read aligners in terms of aligned bases per unit time. Results: We designed and implemented a new algorithm, Burrows-Wheeler Aligner's Smith-Waterman Alignment (BWA-SW), to align long sequences up to 1 Mb against a large sequence database (e.g. the human genome) with a few gigabytes of memory. The algorithm is as accurate as SSAHA2, more accurate than BLAT, and is several to tens of times faster than both. Availability: http://bio-bwa.sourceforge.net Contact: rd@sanger.ac.uk
Specific Monoclonal Antibodies against Leukocyte-restricted Cell Surface Molecule CD43 React with Nonhematopoietic Tumor Cells (1996)

CD43 is the major sialoglycoprotein found on the surface of cells of hemopoietic origin. Because CD43 is a typical member of the surface mucins, molecules that play a relevant role in tumor progression, we have addressed the expression of CD43 in nonhematopoietic tumor cells. For this purpose, we have tested a broad panel of anti-CD43 antibodies on tumors of different embryonic origins. Of the 17 anti-CD43 mAbs used, 9 reacted with leukocytes in paraffin-fixed formalin-embedded lymph node tissues. Two mAbs, BS1 and L10, stained 24 out of 31 (78%) nonhematopietic tumors analyzed; i.e. , some tumors were positive for both anti-bodies, and others were positive for either L10 or BS1. We have also found reactivity of these two anti-CD43 mAbs in 13 out of 20 metastases studied.
Isolation and Characterization of Ricin E from Castor Beans (1977)

A toxic protein, distinct from ricin D, was isolated from castor beans produced in Japan and referred to as ricin E. Ricin E was extracted from defatted meal of castor beans and purified by gel filtration through Sephadex G-75 column followed by DEAE- and CM-cellulose column chromatographies. Ricin E was found to be a glycoprotein and had two N-terminal amino acids, Ile and Ala, which were identical to those of ricin D. The molecular weight of ricin E was 64,000 by SDS-polyacrylamide gel electrophoresis and its sedimentation coefficient was 4.45 S. The isoelectric point of ricin E, estimated to be 8.8 by ampholine electrophoresis, was higher than that of ricin D. Ricin E had equal toxicity for mice and equal cytoagglutinating activity for Sarcoma 180 ascites tumor cells to those of ricin D, and this cytoagglutination was inhibited by galactose.
NEW REQUIREMENTS OF SUBJECTIVE VIDEO QUALITY ASSESSMENT METHODOLOGIES FOR 3DTV (2010)

International audience
Influence of interference coatings on the optical strength of semiconductor laser mirrors (1988)

Accurate analytic expressions are given and proven for the coefficients of reflection from a coating consisting of an arbitrary number of quarter-wave layers. These are used to show that the amplitude of the field at a cleaved mirror in a semiconductor laser decreases appreciably if the refractive indices of the neighboring layers in the interference coating differ substantially. The influence of these coatings on the output power of the laser radiation is studied. An analysis is made of the longitudinal field distribution inside a semiconductor laser and it is established that the true field at the mirrors differs appreciably from the averaged one.
Comparison of digital signal-signal beat interference compensation techniques in direct-detection subcarrier modulation systems (2016)

Single-polarization direct-detection transceivers may offer advantages compared to digital coherent technology for some metro, back-haul, access and inter-data center applications since they offer low-cost and complexity solutions. However, a direct-detection receiver introduces nonlinearity upon photo detection, since it is a square-law device, which results in signal distortion due to signal-signal beat interference (SSBI). Consequently, it is desirable to develop effective and low-cost SSBI compensation techniques to improve the performance of such transceivers. In this paper, we compare the performance of a number of recently proposed digital signal processing-based SSBI compensation schemes, including the use of single- and two-stage linearization filters, an iterative linearization filter and a SSBI estimation and cancellation technique. Their performance is assessed experimentally using a 7 × 25 Gb/s wavelength division multiplexed (WDM) single-sideband 16-QAM Nyquist-subcarrier modulation system operating at a net information spectral density of 2.3 (b/s)/Hz.
Limited proteolysis of the cellobiohydrolase I from Trichoderma reesei (1986)

Limited proteolysis of the cellobiohydrolase I (CBH I, 65 kDa) from Trichoderma reesei by papain yields a core protein (56 kDa) which is fully active against small, soluble substrates such as the chromophoric glycosides derived from the cellodextrins and lactose. Activity against an insoluble substrate, such as Avicel, is however completely lost and concomitantly decreased adsorption onto this microcrystalline cellulose is observed. The peptide (10 kDa), initially split off during proteolysis, is identified as the heavily glycosylated carboxy‐terminal of the native CBH I. Depending on the experimental conditions the core protein is further nicked in between disulfide bonds, but its properties and stability do not appreciably differ from those of intact CBH I. These results lead to the proposal of a bifunctional organisation of the CBH I: one domain, corresponding to the carboxyterminal, acts as a binding site for insoluble cellulose and the other, localised in the core protein, contains the active (hydrolytic) site.
Transfection of Leishmania enriettii and expression of chloramphenicol acetyltransferase gene. (1989)

We report a transient expression transfection system in Leishmania enriettii. A hybrid gene containing an intergenic region of the alpha-tubulin cluster and the bacterial chloramphenicol acetyltransferase (CAT; EC 2.3.1.28) gene is expressed after transfection of L. enriettii with the hybrid plasmid. The expression of the CAT gene is dependent on the presence of sequences from the alpha-tubulin gene. The hybrid gene is also active in Leishmania braziliensis and Leishmania major.
New surfaces for desorption electrospray ionization mass spectrometry: porous silicon and ultra‐thin layer chromatography plates (2006)

The performance of nanoporous silicon (pSi) and ultra-thin layer chromatography (UTLC) plates as surfaces for desorption electrospray ionization (DESI) was compared with that of polymethyl methacrylate (PMMA) and polytetrafluoroethylene (PTFE), both popular surfaces in previous DESI studies. The limits of detection (LODs) and other analytical characteristics for six different test compounds were determined using all four surfaces. The LODs for the compounds were in the fmol-pmol (pg-ng) range. The LODs with the pSi surface were further improved for each of the compounds when heat was applied to the surface during sample application which gave LODs as low as or lower than those achieved with PMMA and PTFE. The UTLC plates were successfully used as a rapid means of chromatographic separation prior to DESI-MS analysis. Another advantage achieved using the newer pSi and UTLC surfaces was increased speed of analysis, associated with drying of solution-phase samples. This took place immediately at the UTLC surface and it could be achieved rapidly by gently heating the pSi surface. The presence of salts in the sample did not cause suppression of the analyte signal with any of the surfaces.
Oestrogen receptors in mucinous carcinoma of the breast: an immunohistological study using paraffin wax sections. (1989)

An immunohistological method (Shintaku-Said method) for the demonstration of oestrogen receptors in routinely processed paraffin wax embedded tissue was applied to 19 cases of mucinous carcinoma of the breast. Seventeen (89%) tumours showed variable degrees of positivity and two were negative. In eight cases the receptors were also assayed biochemically using a dextran-coated charcoal method, and the results of the two methods showed good correlation. No difference in the distribution of positive and negative cases was noted between pure and mixed mucinous tumours, and in the latter group the pattern of staining of the mucinous elements was similar to that seen in the solid elements. It is concluded that the major advantage of this method is its ability to offer for study the distribution of the receptors in individual cells and specific histological structures. The results also indicate that most mucinous carcinomas of the breast are oestrogen receptor positive, irrespective of whether they are pure or mixed type.
Analytical molecular surface calculation (1983)

A computer algorithm is presented for calculating the part of the van der Waals surface of molecule that is accessible to solvent. The solvent molecule is modeled by a sphere. This sphere is, in effect, rolled over the molecule to generate a smooth outer-surface contour. This surface contour is made up of pieces of spheres and tori that join at circular arcs. The spheres, tori and arcs are defined by analytical expressions in terms of the atomic coordinates, van der Waals radii and the probe radius. The area of each surface piece may be calculated analytically and the surface may be displayed on either vector or raster computer-graphics systems. These methods are useful for studying the structure and interactions of proteins and nucleic acids.
Stem Cell Extracellular Vesicles: Extended Messages of Regeneration (2016)

Stem cells are critical to maintaining steady-state organ homeostasis and regenerating injured tissues. Recent intriguing reports implicate extracellular vesicles (EVs) as carriers for the distribution of morphogens and growth and differentiation factors from tissue parenchymal cells to stem cells, and conversely, stem cell-derived EVs carrying certain proteins and nucleic acids can support healing of injured tissues. We describe approaches to make use of engineered EVs as technology platforms in therapeutics and diagnostics in the context of stem cells. For some regenerative therapies, natural and engineered EVs from stem cells may be superior to single-molecule drugs, biologics, whole cells, and synthetic liposome or nanoparticle formulations because of the ease of bioengineering with multiple factors while retaining superior biocompatibility and biostability and posing fewer risks for abnormal differentiation or neoplastic transformation. Finally, we provide an overview of current challenges and future directions of EVs as potential therapeutic alternatives to cells for clinical applications.
Ionic Liquid Electrolytes for Safer Lithium Batteries (2016)

In this paper we report on the investigation of ionic liquid-based electrolytes with enhanced characteristics. In particular, we have studied ternary mixtures based on the lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) salt and two ionic liquids sharing the same cation (N-methyl-N-propyl pyrrolidinium, PYR13), but different anions, bis(trifluoromethanesulfonyl)imide (TFSI) and bis(fluorosulfonyl)imide (FSI). The LiTFSI-PYR13TFSI-PYR13FSI mixtures, found to be ionically dissociated, exhibit better ion transport properties (about 10-3 S cm-1 at -20°C) with respect to similar ionic liquid electrolytes till reported in literature. An electrochemical stability window of 5 V is observed in carbon working electrodes. Preliminary battery tests confirm the good performance of these ternary electrolytes with high-voltage NMC cathodes and graphite anodes. Ionic liquid electrolyte mixtures, PYR13TFSI, PYR13FSI. © The Author(s) 2016. Published by ECS.
Results of an Internet survey of myoelectric prosthetic hand users (2007)

The results of a survey of 54 persons with upper limb amputations who anonymously completed a questionnaire on an Internet homepage are presented. The survey ran for four years and the participants were divided into groups of females, males, and children. It was found that the most individuals employ their myoelectric hand prosthesis for 8 hours or more. However, the survey also revealed a high level of dissatisfaction with the weight and the grasping speed of the devices. Activities for which prostheses should be useful were stated to include handicrafts, personal hygiene, using cutlery, operation of electronic and domestic devices, and dressing/undressing. Moreover, additional functions, e.g., a force feedback system, independent movements of the thumb, the index finger, and the wrist, and a better glove material are priorities that were identified by the users as being important improvements the users would like to see in myoelectric prostheses.
Recent Progress in SFQ Device Technologies in Japan (2007)

Recent progress in single flux quantum (SFQ) device technologies in Japan is described, mainly focusing on those developed in the NEDO "Superconductors Network Device Project" which includes developments of both LTS and HTS devices. The advanced Nb process which consists of a planarized structure with nine Nb layers and 10 kA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> Josephson junctions (JJs) has been developed. This enables fabrication of chips including 100,000 JJs and operating frequency up to 80 GHz. We have also developed the CAD tool by which one can generate SFQ circuit layouts including about 400,000 JJs from logic descriptions. For demonstration of a small-scale switch system, a 4 times 4 switch chip, a 117 Gbps multi-chip-module (MCM) technology, and a packaging technology with 32-ch 10 Gbps I/Os to an MCM have been developed. By using the multilayer process with three HTS epitaxial layers and interface-engineered ramp-edge JJs, we demonstrated operation of SFQ circuits with up to 200 JJs. A variety of elementary SFQ circuits such as a T-FF and a 1:2 switch required for an A/D converter front-end circuit have been designed based on a new layout method, and their operation at 30-50 K has been confirmed. A prototype sampler system is being developed for demonstration of bandwidth over 100 GHz for optical input signals.
Fluorescence photobleaching‐based image standardization for fluorescence microscopy (2000)

A method is presented for the standardization of images acquired with fluorescence microscopy, based on the knowledge of spatial distributions proportional to the microscope's absolute excitation intensity and fluorescence detection efficiency distributions over the image field. These distributions are determined using a thin fluorescent test layer, employed under practically mono-exponential photobleaching conditions. It is demonstrated that these distributions can be used for (i) the quantitative evaluation of differences between both the excitation intensity and the fluorescence detection efficiency of different fluorescence microscopes and (ii) the standardization of images acquired with different microscopes, permitting the deduction of quantitative relationships between images obtained under different imaging conditions.
Coplanar ac discharges between cylindrical electrodes with a nanoporous alumina dielectric: Modular dielectric barrier plasma devices (2005)

Dielectric barrier discharges between coplanar Al rods having an /spl sim/2-/spl mu/m-thick layer of nanoporous alumina dielectric at the surface have been investigated. Rods 3 mm in diameter, 7 cm in length, and spaced by 5 mm produce stable and intense glow discharges in 50 torr of Ne when pairs of rods are driven by an alternating current (bipolar) waveform for which the peak voltage is /spl sim/460-510 V.
Immunotoxicity of monoclonal antibodies (2009)

Monoclonal antibodies (mAbs) are large molecules intended to bind to specific targets often expressed on the immune system, and to treat various immunopathological conditions. Therefore, mAbs can be considered to have a high potential for immunotoxicity, which is reflected in the clinical experience accumulated on mAbs-induced adverse effects related to immunosuppression, immunostimulation and hypersensitivity (immunogenicity). So far, non clinical immunotoxicity studies have been inadequate to address all safety issues in relation to the possible immunotoxicity of mAbs, because they are fraught with limitations and pitfalls primarily related to the lack of relevant animal species. In addition, clinical studies rarely include validated end-points dedicated to the prediction of immunotoxicity. With the ongoing development of mAbs as novel therapeutic strategies for a wide variety of diseases, efforts should be paid to improve our understanding of mAbs-induced immunotoxic effects and design dedicated strategies to assess their immunological safety, both non clinically and clinically.
Absorption of ultra-intense laser pulses (1992)

We use simulations to investigate the interaction of ultra-intense laser pulses with a plasma. With an intensity greater than ${10}^{18}$ W/${\mathrm{cm}}^{2}$, these pulses have a pressure greater than ${10}^{3}$ M bar and drive the plasma relativistically. Hole boring by the light beam is a key feature of the interaction. We find substantial absorption into heated electrons with a characteristic temperature of order the pondermotive potential. Other effects include a dependence on the polarization of the incident light, strong magnetic field generation, and a period of intense instability generation in the underdense plasma.