gebhart/patrepeval huggingface dataset:
An integrated method for spectrum extraction and compound identification from gas chromatography/mass spectrometry data (1999)

A method is presented for extracting individual component spectra from gas chromatography/mass spectrometry (GC/MS) data files and then using these spectra to identify target compounds by matching spectra in a reference library. It extends a published “model peak” approach which uses selected ion chromatograms as models for component shape. On the basis of this shape, individual mass spectral peak abundance profiles are extracted to produce a “purified” spectrum. In the present work, ion-counting noise is explicitly treated and a number of characteristic features of GC/MS data are taken into account. This allows spectrum extraction to be reliably performed down to very low signal levels and for overlapping components. A spectrum match factor for compound identification is developed that incorporates a number of new corrections, some of which employ information derived from chromatographic behavior. Test results suggest that the ability of this system to identify compounds is comparable to that of conventional analysis.
Non-Volatile Memories for Removable Media (2009)

NAND Flash memory has become the preferred nonvolatile choice for portable consumer electronic devices. Features such as high density, low cost, and fast write times make NAND perfectly suited for media applications where large files of sequential data need to be loaded into the memory quickly and repeatedly. When compared to a hard disk drive, a limitation of the Flash memory is the finite number of erase/write cycles: most of commercially available NAND products are guaranteed to withstand 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> programming cycles at most. As a consequence, special care (remapping, bad block management algorithms, etc.) has to be taken when hard-drive based, read/write intensive applications, such as operating systems, are migrated to Flash-memory based devices. One of the basic requirements of the consumer market for data storage is the portability of stored data from one device to the other. Flash cards are the actual solution. A Flash card is a nonvolatile ldquosystem in packagerdquo in which a NAND Flash memory is embedded with a dedicated controller. This paper presents the basic features of the NAND Flash memory and the basic architecture of Flash cards. We provide an outlook on opportunities and challenges of future Flash systems.
TOOL PAPER: ScalaBison Recursive Ascent-Descent Parser Generator (2010)

ScalaBison is a parser generator accepting bison syntax and generating a parser in Scala. The generated parser uses the idea of “recursive ascent-descent parsing,” that is, directly encoded generalized left-corner parsing. Of interest is that fact that the parser is generated from the LALR(1) tables created by bison, thus enabling extensions such as precedence to be handled implicitly.
G-Réseaux dans un environnement aléatoire (2000)

We study networks with positive and negative customers (or Generalized networks of queues and signals) in a random environment. This environment may change the arrival rates, the routing probabilities, the service rates and also the effect of signals. We prove that the steady-state distribution has a product form. This property is obtained as a corollary of a much more general result on multidimensional Markov chains.
Chemisch gesteuerte schrittweise Entfaltung von Einzelketten‐ Nanopartikeln (2016)

Abstract Die vorliegende Studie beschreibt die stufenweise, orthogonale und gleichzeitig pfadunabhängige Entfaltung von Einzelketten‐Nanopartikeln (ENPs), um aktive Kontrolle über die Faltungsdynamik von ENPs zu erlangen. Die Kompaktierung der NPs erfolgt zum einen über Wasserstoffbrücken und zum anderen durch Wirt‐Gast‐Wechselwirkungen. Um den Entfaltungsprozess zu untersuchen, wurden engverteilte Diblock‐ (AB) und Tetrablockcopolymere (ABCD) synthetisiert, welche orthogonale Faltungsmotive entlang der lateralen Kette beinhalten. In einem ersten Schritt wurde die Einzelkettenfaltung des AB‐Diblockcopolymersystems durch eine Wirt‐Gast‐Wechselwirkung von Benzo‐21‐Krone‐7 (B21K7, Wirt) mit einem sekundären Ammoniumsalz (AS, Gast) ausgelöst. Anschließend wurden die zwei orthogonalen Motive, bestehend aus Hamilton‐Wedge/Cyanursäure und B21K7/AS, in das Tetrablockcopolymersystem eingebaut. Zuletzt wurde, durch Zugabe spezieller Substrate, die orthogonale, stufenweise und pfadunabhängige Entfaltung der ENPs ausgelöst und untersucht. Die Faltung und Entfaltung wurde durch 1D‐ 1 H‐NMR‐Spektroskopie, dynamische Lichtstreuung (DLS) und diffusionsgeordnete NMR‐Spektroskopie (DOSY) charakterisiert und nachgewiesen.
Face and Object Recognition and Detection Using Colour Vector Quantisation (2002)

In this paper we present an approach to face and object detection and recognition based on an extension of the contentbased image retrieval method of Lu and Teng (1999). The method applies vector quantisation (VQ) compression to the image stream and uses Mahalonobis weighted Euclidean distance between VQ histograms as the measure of image similarity. This distance measure retains both colour and spatial feature information but has the useful property of being relatively insensitive to changes in scale and rotation. The method is applied to real images for face recognition and face detection applications. Tracking and object detection can be coded relatively efficiently due to the data reduction afforded by VQ compression of the data stream. Additional computational efficiency is obtained through a variation of the tree structured fast VQ algorithm also presented here. 1.
Optogenetic control of protein binding using light-switchable nanobodies (2020)

A growing number of optogenetic tools have been developed to reversibly control binding between two engineered protein domains. In contrast, relatively few tools confer light-switchable binding to a generic target protein of interest. Such a capability would offer substantial advantages, enabling photoswitchable binding to endogenous target proteins in cells or light-based protein purification in vitro. Here, we report the development of opto-nanobodies (OptoNBs), a versatile class of chimeric photoswitchable proteins whose binding to proteins of interest can be enhanced or inhibited upon blue light illumination. We find that OptoNBs are suitable for a range of applications including reversibly binding to endogenous intracellular targets, modulating signaling pathway activity, and controlling binding to purified protein targets in vitro. This work represents a step towards programmable photoswitchable regulation of a wide variety of target proteins.
Beam emittance measurements on multicusp ion sources (1996)

Multicusp ion sources are used for various applications. Presently, the implementation of this type of ion source is planned for the development of an ion beam lithography machine, which will be used for the projection of sub-0.2 μm patterns onto a wafer substrate. Since, for this application, a very good beam quality and a small ion energy spread are required, emittance measurements have been performed on a multicusp ion source for various source conditions. It is shown that the installation of proper capacitors between the extraction electrodes is necessary to avoid rf pickup, which otherwise leads to a distortion of the beam emittance. The influence of the magnetic filter field on the beam emittance has been investigated, and the beam emittance of a dc filament-discharge plasma has also been compared to that of a rf-generated plasma.
Plasma‐Aided Micro‐ and Nanopatterning Processes for Biomedical Applications (2006)

Abstract Summary: Micro‐ and nanofabrication methods are essential today in microelectronics, optoelectronics, catalysis, and analytics. Recent advances in biomaterials show that micro‐ and nanofeatures, either at the surface or embedded in materials, can drive specific responses both in in vivo and in vitro biological systems. With such an approach, scientists can understand better, and possibly exploit, biological responses stimulated by properly designed biomedical surfaces. Because of their versatility, plasma treatment, deposition, and etching processes are often part of procedures optimized to create micro‐ and nanofeatures of different shape, size, and position, onto and inside materials. Presented here are recent examples of such processes developed in our group for biomedical applications. Residuals of self‐assembled polystyrene (PS) beads (600 ± 50 nm in diameter) on NH 3 plasma‐treated PS substrate, after O 2 plasma etching. magnified image Residuals of self‐assembled polystyrene (PS) beads (600 ± 50 nm in diameter) on NH 3 plasma‐treated PS substrate, after O 2 plasma etching.
Notes on hyphomycetes. LVIII. Some dematiaceous taxa, including two undescribed species of Cladosporium, associated with biodeterioration of carpet, plaster and wallpaper (1988)

Volume: 32
Stem revision: special implant versus primary device. (2004)

The purpose of hip revision surgery is to relieve pain and restore hip function, while improving hip biomechanics and bone stock. The entity of bone stock impairment due to lysis indicates to the surgeon which revision stem he would preferably choose. Modern literature has described several options for stem revision, ranging from primary cemented/less implants in the case of limited proximal bone defects, to special revision stems where a massive femoral bone stock impairment is present. There are many classifications of the femoral bone-stock loss in the literature but most authors seem to agree that the treatment of minimal proximal defects should be performed with primary implant stems. The need to bridge a bigger bony gap makes distal fixation a good deal. Two options are described for this purpose: the Wagner stem and modular stems. Wagner's concept consists of a distal fixation based on the interference of the straight tapered titanium alloy stem at the level of the femoral isthmus, while longitudinal fins provide rotational stability. A wide variety of modular stems was lately developed to prevent major complication associated to the Wagner's stem, but some new problems arose from proximal overfill of the canal, difficult in assembly and fretting corrosion. Early experience with the new ZMR taper (Zimmer, Warsaw, IN, USA) modular revision stem is reported.
The classification of ethnic status using name information. (1988)

Methodology is developed to classify ethnic status by name using a simple probabilistic model. This method involves the consideration of four rules which may be used to classify individuals using three name components (first, middle and last names). In order to do this, conditional probabilities of ethnic status are estimated from a sample in which the ethnic status is known. Using a split sample technique the sensitivity and specificity of this methodology were examined in a data set of death registrations. Each of the classification rules performed well on the data from which they were constructed but were not as efficient when applied to another population. Nevertheless a model (linear), in which the sum of the conditional probabilities of each home component is used, achieved a sensitivity and specificity of 97% and 100% respectively in males and 89% and 100% in females.
DeepEfference: Learning to predict the sensory consequences of action through deep correspondence (2017)

As the human eyeball saccades across the visual scene, humans maintain egocentric visual positional constancy despite retinal motion identical to an egocentric shift of the scene. Characterizing the underlying biological computations enabling visual constancy can inform methods of robotic localization by serving as a model for intelligently integrating complimentary, heterogeneous information. Here we present DeepEfference, a bio-inspired, unsupervised, deep sensorimotor network that learns to predict the sensory consequences of self-generated actions. DeepEfference computes dense image correspondences [1] at over 500 Hz and uses only a single monocular grayscale image and a low-dimensional extra-modal motion estimate as data inputs. Designed for robotic applications, DeepEfference employs multi-level fusion via two parallel pathways to learn dense, pixel-level predictions and correspondences between source and target images. We present quantitative and qualitative results from the SceneNet RGBD [2] and KITTI Odometry [3] datasets and demonstrate an approximate runtime decrease of over 20,000% with only a 12% increase in mean pixel matching error compared to DeepMatching [4] on KITTI Odometry.
The Future of Annotation in a Digital (Paper) World (1998)

If order-making in the large is part of the institutional mission of libraries,&#13;\nthen order-making in the small???i.e., the informal work of annotating&#13;\nand organizing materials collected in the service of particular dayto-&#13;\nday work or pleasure???is part of the business of library patrons. This&#13;\ndiscussion focuses on just such activities; activities that stem from readers'&#13;\nengagements with texts, and possibly with each other, against a backdrop&#13;\nof real-world settings and practices. I hesitate to call digital library patrons&#13;\nusers, since that is the word computer scientists tend to use to hide the&#13;\ncharacteristics of what we hope is a diverse population.
Cell surface glycoconjugates of gingival fibroblasts exposed to dental plaque extract (1984)

The cell surface glycoconjugates of human gingival fibroblasts exposed in a culture to dental plaque extract were studied by surface labeling techniques and indirect immunoflurescennce. After 24 h of exposure, the fibroblast morphology changed from well‐spread to spindle‐like. This alteration was associated with a disappearance of the intercellular fibronectin (FN) network and most of the high molecular weight cell surface glycoproteins. These effects of the extract were prevented by heating. After prolonged treatment with the native extract, a 80 kd glycoprotein disappeared and a 140 kd glycoprotein was replaced by a 110 kd polypeptide, but the trypsin sensitive 55 kd glycoprotein remained on the surface of the treated cells. The protcolytic activity of the plaque extract degraded the FN to various fragments with a different molecular weight than previously obtained with several purified mammalian enzymes. After a 24 h incubation of the treated cells in a normal, serum supplemented medium, the normal surface characteristics and FN network were recovered. In the treated cells, the phosphorylation of the cell surface glycoproteins was increased as well as the activity of the hyaluronic acid synthetase. The results suggest that plaque extract has a dual role in affecting the behavior of gingival fibroblasts. First, the enzymatic degradation of the FN network and surface glycoproteins destroys the association between the extracellular matrix and the cytoskeleton. Second, heat‐stable components alter the cell surface phosphorylation. These changes are associated with an activation of the cells to produce hyaluronic acid, the most striking anabolic change obtained in treated cells.
Supplementary Figures from A New Triglycyl Peptide Linker for Antibody–Drug Conjugates (ADCs) with Improved Targeted Killing of Cancer Cells (2023)

&lt;p&gt;Supplementary Figures (S1-S4). Supplementary Figure S1: In vitro cytotoxic activities of tetraglycyl (Gly4), triglycyl (Gly3), diglycyl (Gly2), and valine-citrulline-glycine (VCG)-linked anti-EGFR ADCs and a triglycyl-linked non-binding antibody ADC in PC-9, Ca9-22, HSC-2, H1975, A-431, and OSC-19 cells (3-4 DAR ADCs). Supplementary Figure S2: In vitro cytotoxic activities of anti-EpCAM CX and SMCC ADCs toward a low EpCAM antigen-expressing cell line, RPMI 8226 (~50,000 EpCAM per cell). The CX ADCs tested included a conjugate with a typical payload number (3.9 maytansinoid molecules per antibody molecule; 3.9 DAR) and conjugates with high payload numbers (8 and 9.6 DAR). The SMCC ADC had a typical payload number (4.3 DAR). Supplementary Figure S3: Binding-competition ELISA of catabolites of CX ADC (DM-CX1 and DM-CX2) and SMCC ADC (lysine-SMCC-DM1): inhibition by catabolites toward binding of anti-maytansine antibody to immobilized BSA-maytansinoid conjugate. Supplementary Figure S4: Test of bystander cytotoxic activity of anti-EGFR-CX-DM1 or SPDB-DM4 conjugate in mixed culture of EGFR-positive (Ca9-22) and EGFR-negative (Ramos) cells.&lt;/p&gt;
Current role of spacers for prostate cancer radiotherapy (2015)

Radiotherapy is an established curative treatment method for prostate cancer. Optimal tumor control rates can only be achieved with high local doses, associated with a considerable risk of rectal toxicity. Apart from already widely adapted technical advances, as intensity-modulated radiation therapy, the application of spacers placed between the prostate and rectum has been increasingly used in the last years. Biodegradable spacers, including hydrogel, hyaluronic acid, collagen or an implantable balloon, can be injected or inserted in a short procedure under transrectal ultrasound guidance via a transperineal approach. A distance of about 1.0-1.5 cm is usually achieved between the rectum and prostate, excluding the rectal wall from the high isodoses. Several studies have shown well tolerated injection procedures and treatments. Apart from considerable reduction of rectal irradiation, a prospective randomized trial demonstrated a reduction of rectal toxicity after hydrogel injection in men undergoing prostate image-guided intensity-modulated radiation therapy. The results are encouraging for continuing evaluation in dose escalation, hypofractionation, stereotactic radiotherapy or re-irradiation trials in the future.
Memory safety without garbage collection for embedded applications (2005)

Traditional approaches to enforcing memory safety of programs rely heavily on run-time checks of memory accesses and on garbage collection, both of which are unattractive for embedded applications. The goal of our work is to develop advanced compiler techniques for enforcing memory safety with minimal run-time overheads. In this paper, we describe a set of compiler techniques that, together with minor semantic restrictions on C programs and no new syntax, ensure memory safety and provide most of the error-detection capabilities of type-safe languages, without using garbage collection, and with no run-time software checks, (on systems with standard hardware support for memory management). The language permits arbitrary pointer-based data structures, explicit deallocation of dynamically allocated memory, and restricted array operations. One of the key results of this paper is a compiler technique that ensures that dereferencing dangling pointers to freed memory does not violate memory safety, without annotations, run-time checks, or garbage collection , and works for arbitrary type-safe C programs. Furthermore, we present a new interprocedural analysis for static array bounds checking under certain assumptions. For a diverse set of embedded C programs, we show that we are able to ensure memory safety of pointer and dynamic memory usage in all these programs with no run-time software checks (on systems with standard hardware memory protection), requiring only minor restructuring to conform to simple type restrictions. Static array bounds checking fails for roughly half the programs we study due to complex array references, and these are the only cases where explicit run-time software checks would be needed under our language and system assumptions.
Ectopic and Serum Lipid Levels Are Positively Associated with Bone Marrow Fat in Obesity (2013)

Results of this study suggest that ectopic and serum lipid levels are positively associated with bone marrow fat in obese men and women.
Common missense mutation G1528C in long-chain 3-hydroxyacyl-CoA dehydrogenase deficiency. Characterization and expression of the mutant protein, mutation analysis on genomic DNA and chromosomal localization of the mitochondrial trifunctional protein alpha subunit gene. (1996)

Mitochondrial trifunctional protein (MTP) is a recently identified enzyme involved in mitochondrial beta-oxidation, harboring long-chain enoyl-CoA hydratase, long-chain 3-hydroxyacyl-CoA dehydrogenase (LCHAD) and long-chain 3-ketothiolase activity. A deficiency of this protein is associated with impaired oxidation of long-chain fatty acids which can lead to sudden infant death. Furthermore, it is clear that this inborn error of fatty acid oxidation is very frequent, second to medium chain acyl-CoA dehydrogenase deficiency. In most patients only the LCHAD activity of MTP is deficient with near normal activity of the two other enzyme activities of the complex. We recently described the occurrence of a frequent G1528C mutation in the cDNA coding for the a subunit of MTP. Using S. cerevisiae for expression of wild type and mutant protein we show that the G1528C mutation is directly responsible for the loss of LCHAD activity. Furthermore, we describe a newly developed method allowing identification of the G1528C mutation in genomic DNA. The finding of an 87% allele frequency of the G1528C mutation in 34 LCHAD deficient patients makes this a valuable test for prenatal diagnosis. Finally, we show that the gene encoding the alpha subunit of MTP is located on chromosome 2p24.1-23.3.
Controlled coupling of aminoglycoside antibiotics to proteins for use in homogeneous enzyme immunoassays (1984)

Selective N-acylation of aminoglycoside antibiotics with the N-hydroxysuccinimide ester of methyldithioacetic acid, followed by reaction with methanethiol or dithioerythritol, gives sulfhydryl labeled antibiotics. Alternatively, the nucleophilic sulfhydryl group is incorporated into an antibiotic by treatment with N-acetyl-d,l-homocysteine thiolactone. These derivatives couple readily with proteins that have previously been modified with bromoacetylglycyl groups to provide conjugates for use in the development of homogeneous enzyme immunoassays.
Spatially Resolved Thermoelectric Effects in Operando\n Semiconductor-Metal Nanowire Heterostructures (2020)

The thermoelectric properties of a nanoscale germanium segment connected by\naluminium nanowires are studied using scanning thermal microscopy. The\ngermanium segment of 168\\,nm length features atomically sharp interfaces to the\naluminium wires and is surrounded by an Al$_2$O$_3$ shell. The temperature\ndistribution along the self-heated nanowire is measured as a function of the\napplied electrical current, for both Joule and Peltier effects. An analysis is\ndeveloped that is able to extract the thermal and thermoelectric properties\nincluding thermal conductivity, the thermal boundary resistance to the\nsubstrate and the Peltier coefficient from a single measurement. Our\ninvestigations demonstrate the potential of quantitative measurements of\ntemperature around self-heated devices and structures down to the scattering\nlength of heat carriers.\n
Shot noise of a tunnel junction displacement detector (2004)

We study quantum-mechanically the frequency-dependent current noise of a tunnel-junction coupled to a nanomechanical oscillator. The cases of both dc and ac voltage bias are considered, as are the effects of intrinsic oscillator damping. The dynamics of the oscillator can lead to large signatures in the shot noise, even if the oscillator-tunnel junction coupling is too weak to yield an appreciable signature in the average current. Moreover, the modification of the shot noise by the oscillator cannot be fully explained by a simple classical picture of a fluctuating conductance.