gebhart/patrepeval huggingface dataset:
Analysis of pristanic acid β-oxidation intermediates in plasma from healthy controls and patients affected with peroxisomal disorders by stable isotope dilution gas chromatography mass spectrometry (1999)

In this paper we report the development of highly sensitive, selective, and accurate stable isotope dilution gas chromatography negative chemical ionization mass spectrometry (GC-NCI-MS) methods for quantification of peroxisomal beta-oxidation intermediates of pristanic acid in human plasma: 2,3-pristenic acid, 3-hydroxypristanic acid, and 3-ketopristanic acid. The carboxylic groups of the intermediates were converted into pentafluorobenzyl esters, whereas hydroxyl groups were acetylated and ketogroups were methoximized. Hereafter, the samples were subjected to clean-up by high performance liquid chromatography. Analyses were performed by selected monitoring of the carboxylate anions of the derivatives. Control values of all three metabolites were established (2,3-pristenic acid: 2-48 nm, 3-hydroxypristanic acid: 0.02-0.81 nm, 3-ketopristanic acid: 0.07-1.45 nm). A correlation between the concentrations of pristanic acid and its intermediates in plasma was found. The diagnostic value of the methods is illustrated by measurements of the intermediates in plasma from patients with peroxisomal disorders. It is shown that in generalized peroxisomal disorders, the absolute concentrations of 2,3-pristenic acid, 3-hydroxypristanic acid, and 3-ketopristanic acid were comparable to those in the controls, whereas relative to the pristanic acid concentrations these intermediates were significantly decreased. In bifunctional protein deficiency, elevated levels of 2,3-pristenic acid and 3-hydroxypristanic acid were found. 3-Ketopristanic acid, although within the normal range, was relatively low when compared to the high pristanic acid levels in these patients.-Verhoeven, N. M., D. S. M. Schor, E. A. Struys, E. E. W. Jansen, H. J. ten Brink, R. J. A. Wanders, and C. Jakobs. Analysis of pristanic acid beta-oxidation intermediates in plasma from healthy controls and patients affected with peroxisomal disorders by stable isotope dilution gas chromatography mass spectrometry.
Nonnegative Matrix and Tensor Factorization for Discussion Tracking (2009)

Abstract not provided.
A ubiquitin-protein ligase specific for type III protein substrates. (1990)

A previously studied species of ubiquitin-protein ligase contains specific sites for the binding of basic (Type I) and bulky hydrophobic (Type II) NH2-terminal amino acid residues of protein substrates. We now describe another enzyme that ligates ubiquitin specifically to proteins that have NH2-terminal residues other than the above two categories (Type III substrates). The new species of ligase, that we call E3 beta, is separable from the formerly described ligase (termed E3 alpha) by affinity chromatography on protein substrate columns. E3 beta was partially purified from extracts of rabbit reticulocytes and was shown to be required for the breakdown of Type III proteins. Apart from its different substrate specificity, it resembles E3 alpha in some physical properties, in a requirement for ubiquitin carrier protein (E2) for conjugate formation, and in its action to ligate multiple ubiquitin units to the substrate protein. The denatured derivative of bovine pancreatic ribonuclease is a specific substrate for E3 alpha, while that of ribonuclease S-protein is a good substrate for E3 beta. Since S-protein is formed by the removal from ribonuclease of NH2-terminal S-peptide, it is suggested that E3 beta interacts with an NH2-terminal determinant exposed in ribonuclease S-protein.
Prefrontal Theta Oscillations Are Modulated by Estradiol Status During Fear Recall and Extinction Recall (2021)

Our data show that neural oscillatory and peripheral correlates of heightened fear expression during fear recall and (impaired) extinction recall do not simply differ between sexes but depend on hormonal fluctuations within women.
Conformational Nanobodies Reveal Tethered Epidermal Growth Factor Receptor Involved in EGFR/ErbB2 Predimers (2015)

The epidermal growth factor receptor (EGFR) is a cell-surface receptor with a single transmembrane domain and tyrosine kinase activity carried by the intracellular domain. This receptor is one of the four members of the ErbB family including ErbB2, ErbB3, and ErbB4. Ligand binding, like EGF binding, induces a conformational rearrangement of the receptor and induces a homo/hetero dimerization essentially with ErbB family receptors that leads to the phosphorylation of the kinase domain, triggering a signaling cascade. EGFR can also form inactive dimers in a ligand-independent way through interactions between cytoplasmic domains. To date, the conformation of EGFR extracellular domain engaged in these inactive dimers remains unclear. In this study, we describe the successful selection and characterization of llama anti-EGFR nanobodies and their use as innovative conformational sensors. We isolated three different specific anti-EGFR clones binding to three distinct epitopes. Interestingly, the binding of all three nanobodies was found highly sensitive to ligand stimulation. Two nanobodies, D10 and E10, can only bind the ligand-free EGFR conformation characterized by an intramolecular tether between domains II and IV, whereas nanobody G10 binds both ligand-free and ligand activated EGFR, with an 8-fold higher affinity for the extended conformation in the presence of ligand. Here we took advantage of these conformational probes to reveal the existence of tethered EGFR in EGFR/ErbB2 predimers. These biosensors represent important tools allowing the determination of EGFR conformations and should help the design of relevant inhibitors.
Multiple Sclerosis Lesion Segmentation from Brain MRI via Fully Convolutional Neural Networks (2018)

Multiple Sclerosis (MS) is an autoimmune disease that leads to lesions in the central nervous system. Magnetic resonance (MR) images provide sufficient imaging contrast to visualize and detect lesions, particularly those in the white matter. Quantitative measures based on various features of lesions have been shown to be useful in clinical trials for evaluating therapies. Therefore robust and accurate segmentation of white matter lesions from MR images can provide important information about the disease status and progression. In this paper, we propose a fully convolutional neural network (CNN) based method to segment white matter lesions from multi-contrast MR images. The proposed CNN based method contains two convolutional pathways. The first pathway consists of multiple parallel convolutional filter banks catering to multiple MR modalities. In the second pathway, the outputs of the first one are concatenated and another set of convolutional filters are applied. The output of this last pathway produces a membership function for lesions that may be thresholded to obtain a binary segmentation. The proposed method is evaluated on a dataset of 100 MS patients, as well as the ISBI 2015 challenge data consisting of 14 patients. The comparison is performed against four publicly available MS lesion segmentation methods. Significant improvement in segmentation quality over the competing methods is demonstrated on various metrics, such as Dice and false positive ratio. While evaluating on the ISBI 2015 challenge data, our method produces a score of 90.48, where a score of 90 is considered to be comparable to a human rater.
Clustering of <i>Escherichia coli</i> Type‐1 Fimbrial Adhesins by Using Multimeric Heptyl α‐<scp>D</scp>‐Mannoside Probes with a Carbohydrate Core (2011)

Heptyl α-D-mannoside (HM) is a strong inhibitor of the FimH lectin that mediates the initial adhesion of the uropathogenic Escherichia coli (E. coli) to the bladder cells. We designed a set of multivalent HM ligands based on carbohydrate cores with structural valencies that range from 1 to 7. The chemical strategy used to construct the regular hydrophilic structures consisted of the repetition of a critical glucoside fragment. A primary amino group was grafted at the sugar reducing end to couple the multimers to a fluorescent label. A one-pot synthetic approach was developed to tether the ligands and the fluorescein isothiocyanate (FITC) probe to the scaffold simultaneously. Isothermal calorimetry with the monomeric FimH lectin revealed nanomolar affinities and saturation of all structurally available binding sites on the multivalent HM ligands. Direct titrations domain showed almost strict correlation of enthalpy-entropy compensation with increasing valency of the ligand, whereas reverse titration calorimetry demonstrated negative cooperativity between the first and the second binding site of the divalent heptyl mannoside. A multivalency effect was nevertheless observed by inhibiting the haemagglutination of type-1 piliated UTI89 E. coli, with a titer as low as 60 nM for the heptavalent HM ligand. An FITC-labeled HM trimer showed capture and cross-linking of living bacteria in solution, a phenomenon not previously described with low-valency ligands.
Visually tolerable tiling (VTT) for making a large-area flexible patterned surface (2014)

Large-area micro/nano-patterns on a flexible substrate were produced using the VTT (visually tolerable tiling) method, realizing invisible seam lines between small master tiles. This could be applied in the roll-to-roll imprinting process, producing large-area polarizers and microprism sheets without visible seam lines.
Ultra-Lightweight Mutual Authentication in the Vehicle Based on Smart Contract Blockchain: Case of MITM Attack (2020)

For quite a long time, purchasers have come to depend on the convenience and security and included security that a passive vehicle immobilizer framework offers. These frameworks comprise of a Passive Entry Passive Start (PEPS) innovation, conveyed by the driver, and a Smart Key Unit (SKU), mounted in the vehicle with regards to the principal parts of these frameworks. This paper for the first time shows the cyber vulnerability of PEPS in the vehicle against the man-in-the middle attack (MITM). It enables the hacker to open and begin the vehicle, although there was still a distance between the vehicle and the key. To stop this physical cyber attack, we propose a hearty ultra-lightweight common confirmation technique dependent on the radio frequency identification (RFID) convention that cooperates with a decentralized database to verify the PEPS. A secure blockchain based on smart contract is also developed which is compatible with the mutual authentication in the vehicle. A detailed security analysis is performed on an undefined vehicle to prove the high security of the proposed communication approach when facing MITM.
Characterization of Gradient Dominance and Regularity Conditions for Neural Networks (2017)

The past decade has witnessed a successful application of deep learning to solving many challenging problems in machine learning and artificial intelligence. However, the loss functions of deep neural networks (especially nonlinear networks) are still far from being well understood from a theoretical aspect. In this paper, we enrich the current understanding of the landscape of the square loss functions for three types of neural networks. Specifically, when the parameter matrices are square, we provide an explicit characterization of the global minimizers for linear networks, linear residual networks, and nonlinear networks with one hidden layer. Then, we establish two quadratic types of landscape properties for the square loss of these neural networks, i.e., the gradient dominance condition within the neighborhood of their full rank global minimizers, and the regularity condition along certain directions and within the neighborhood of their global minimizers. These two landscape properties are desirable for the optimization around the global minimizers of the loss function for these neural networks.
Detection of Hygiene-relevant Parameters from Cereal Grains based on Intelligent Image Interpretation and Data Mining. (2005)

We are going on to develop a novel method for the detection of hygiene-relevant parameters from grains of cereal crops based on intelligent image acquisition and interpretation methods as well as data mining method. We present our first case study that describes the data acquisition, the planned image analysis and interpretation method as well as the reasoning methods that can map the automatic acquired parameters of grain to the relevant hygiene parameters. The preliminary results show that with the new computer science methods it is possible to come up with new insights into the quality control of food stuff.
<title>Binary optic diffuser design</title> (2001)

This paper describes the fundamentals of diffractive optics diffuser design, with an emphasis on common pitfalls and important design decisions. In addition, several new design and fabrication methods are presented, which overcome many of the current limitations of multi-level diffractive diffusers. These designs include an easily fabricated white-light diffuser and a uniform, high-NA diffuser design.
Using probabilistic models of document retrieval without relevance information (1988)

Most probabilistic retrieval models incorporate information about the occurrence of index terms in relevant and non‐relevant documents. In this paper we consider the situation where no relevance information is available, that is, at the start of the search. Based on a probabilistic model, strategies are proposed for the initial search and an intermediate search. Retrieval experiments with the Cranfield collection of 1,400 documents show that this initial search strategy is better than conventional search strategies both in terms of retrieval effectiveness and in terms of the number of queries that retrieve relevant documents. The intermediate search is shown to be a useful substitute for a relevance feedback search. Experiments with queries that do not retrieve relevant documents at high rank positions indicate that a cluster search would be an effective alternative strategy.
HTGR fuel development: loading of uranium on carboxylic acid cation- exchange resins using solvent extraction of nitrate (1975)

phase over the nitrate ion concentration range of approx. 0.2 to 2.0 N. Estimates of thorium behavior and its separation from uranium can be calculated from these values and derived constants for the reaction system. In all tests, thorium was preferentially absorbed on the resin with separation factors, relative to uranium concentrations, greater than unity.
Outer Segments of Retinal Photoreceptors – A Review in the Light of Novel Findings (2014)

Aims: Recent studies have demonstrated that all molecules of the respiratory chain are present in the photoreceptor outer segment (see Calzia et al., Biol Cell 2013). Furthermore, our group (Roehlecke et al., PLoS One 2013) could show that, after blue light stress of the retina, the outer segments are significant sources of reactive oxygen species (ROS) ‐ even more so than the mitochondria in the inner segment. These two new findings have also important implications for degenerative diseases of the retina. Methodology: In this respect we revisited the literature regarding the photoreceptor reactions after blue light and radical stress. Furthermore, we refer to the common features of mitochondria and outer segments. Results: In the light of the recent findings many unique features of the photoreceptors get understandable: they are characterized by excessive oxygen consumption - even higher than that of other neuronal cells. Photoreceptors possess, in addition to their mitochondria ‐ rich neuronal component an outer segment packed with stacks of membrane discs harbouring the photo pigments, respiratory enzymes and enzymes of the visual cycle. Therapeutic use of red and near infrared light is often explained by ameliorating the
Dimpled Planar Lightguide Solar Concentrators (2010)

Lightguide concentrators show tremendous promise for thin form-factor, lightweight, and inexpensive replacements for the current generation of refractive and reflective solar concentrators. We propose a new type of structure for reducing optical losses and dramatically increasing the practical upper limit on concentration within micro-structured lightguide concentrators.
Effect of metal annealing on the Q-factor of metal- coated fused silica micro shell resonators (2015)

This paper reports on the effect of annealing thin metal films coated on high-Q fused silica shell resonators. While the ring-down time of some resonators improves with annealing, others degrade. Investigations include the effect of annealing on metal film stress, roughness, and elemental composition, as well as the effect of film thickness and roughness on quality factor. Increased tensile stress and film roughness are observed after annealing; it is suspected that these changes are due to formation of intermetallic grain boundaries that result in film densification and the formation of hillocks. Increasing film thickness reduces Q, though it is unlikely due to thermoelastic damping. Surface roughness tends to increase with film thickness, but does not appear to have a direct correlation with Q.
Microbial Production of Long-chain Dicarboxylic Acids from n-Alkanes Part II (1972)

Strain M-1 which was derived from Candida cloacae 310 as a mutant unable to assimilate dicarboxylic acid (DC) produced large amount of DCs from n-alkanes, as expected. It produced DCs with the same number of carbon atoms as those of n-alkanes used (9 to 18 carbon atoms). Among DCs produced, n-tetradecane ω, ω'-dicarboxylic acid (DC-16) from n-hexadecane (n-C16) was most abundantly accumulated and the highest level of DC-16, i.e., 29.3g/liter was obtained by resting cells. On the other hand, since the growth rate of strain M-1 on n-alkane markedly decreased in comparison with that of the parent strain, other carbon source which supported the growth of strain M-1 was necessary for the production of DC from n-alkane by growing cells. When acetic acid was used as carbon source for the growth in DC-16 production from n-C16, the highest level of DC-16, i.e., 21.8g/liter was obtained ofter 3 days' cultivation.
Crown ether derivatives of anthraquinone as ionophores in ion‐selective electrodes (1992)

Abstract 1,8‐anthraquinono‐18‐crown‐6 and 10‐[(2,4‐dinitrophenyl)azo]‐9‐hydroxy‐1,8‐anthraceno‐18‐crown‐6 were prepared from 1, 8‐dichloroanthraquinone and used in the development of ion‐selective electrodes. The electrodes based on 10‐[(2,4‐dinitrophenyl)azo]‐9‐hydroxy‐1,8‐anthraceno‐18‐crown‐6 displayed better selectivity for potassium over sodium and had fewer interferences. The differences and similarities between the ionophores, as well as the optimum conditions for the preparation of the electrodes are discussed.
Inhibition of Nuclear Factor κB Activation Attenuates Apoptosis Resistance in Lymphoid Cells (1998)

Death-inducing ligands (DILs) such as tumor necrosis factor alpha (TNFalpha) or the cytotoxic drug doxorubicin have been shown to activate a nuclear factor kappaB (NFkappaB)-dependent program that may rescue cells from apoptosis induction. We demonstrate here that TRAIL (TNF-related apoptosis-inducing ligand), a recently identified DIL, also activates NFkappaB in lymphoid cell lines in a kinetic similar to TNFalpha. NFkappaB activity is independent from FADD, caspases, and apoptosis induction. To study the influence of NFkappaB activity on apoptosis mediated by TRAIL, CD95, TNFalpha, or doxorubicin, NFkappaB activation was inhibited using the proteasome inhibitor N-acetyl-L-leucinyl-L-leucinyl-L-norleucinal or transient overexpression of mutant IkappaBalpha. Sensitivity for induction of apoptosis was markedly increased by these treatments in apoptosis sensitive cell lines. Moreover, both in cell lines and in primary leukemia cells that are resistant towards induction of apoptosis by DILs and doxorubicin, antagonization of NFkappaB activity partially restored apoptosis sensitivity. These data suggest that inhibition of NFkappaB activation may provide a molecular approach to increase apoptosis sensitivity in anticancer treatment.
Culture as Context for Intervention: Developing a Culturally Congruent Early Intervention Programme (2002)

Black South African children with hearing loss are affected by the issues facing the deaf population as well as those facing the Black population educationally, socially and vocationally. The cultural context in which the child exists will not only influence the acquisition of communication skills but also the context in which intervention occurs. It is imperative that early interventionists have insight into, and understanding of the ethnographic - and family characteristics that may influence responses to early intervention. A theoretical framework for the design and implementation of culturally congruent early intervention programs for young Black South African children with hearing loss is developed. The aim of this paper is to describe culture as a context for early intervention and to provide a cultural perspective of early intervention for young Black children with hearing loss. Based on these theoretical underpinnings, models are suggested and guidelines are formulated for early communication intervention for young Black South African children with
Application of logic cell arrays in design of self-clocked sequential circuits (2002)

A systematic method of design for asynchronous sequential circuits using logic cell arrays such as the XILINX 2000 or 3000 series is presented. In this method each state is represented by a separate flip-flop whose clock signal is generated locally. State machines of considerable size can be accommodated on a single chip and in most applications the outputs are readily available on the chip without the need for external decoding of the states. Problems of races and hazards, commonly associated with asynchronous circuits, are eliminated. The method is applied to the design of a VME bus requester, and the use of CAD packages to simulate such designs is discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Soft combining hybrid ARQ schemes application to reliable communications within 3G wireless networks (2004)

This paper deals with the application of hybrid automatic repeat request (H-ARQ) techniques to reliable data communications in wireless 3G networks. Basically, retransmission of coded data is endowed with soft combining schemes applied, respectively, to packet replicas, or to decoding algorithm outputs. By means of analytical derivations and simulations on UMTS environment, a noticeable bit error rate (BER) and, then, frame error rate (FER) improvements have been shown. A significant link throughput increase is also pointed out with a consequent reduced packet delivery delay and power wasting.
Multiple-frequency-tuned photonic bandgap microstrip structures (2000)

Photonic bandgap (PBG) structures in microstrip technology have been recently proposed as efficient Bragg reflectors. The periodic patterns employed until now were formed by a distribution of nonconnected holes (cermet topology) etched in the ground plane or drilled in the dielectric substrate, giving rise to single-frequency-tuned band reflectors. In this letter, a novel pattern that follows a continuous profile (network topology) is proposed to simultaneously reject multiple frequency bands. It is formed by the addition of various sinusoidal functions tuned at the design frequencies. Measurements performed for two-and three-frequency-tuned PBG microstrip prototypes show that multiple deep and wide stopbands can be obtained using these novel devices.
Use of Agrobacterium radiobacter in agricultural ecosystems. (1988)

Agrobacterium tumefaciens is a soil inhabitant that infects many dicotyledonous plants, causing crown gall disease. The success of Agrobacterium radiobacter K84 to control this disease in agroecosystems throughout the world has been impressive. This review describes the attributes of K84, its mechanism of control, its failures, and other alternative biocontrol agents.