gebhart/patrepeval huggingface dataset:
On Holo-Hilbert spectral analysis: a full informational spectral representation for nonlinear and non-stationary data (2016)

The Holo-Hilbert spectral analysis (HHSA) method is introduced to cure the deficiencies of traditional spectral analysis and to give a full informational representation of nonlinear and non-stationary data. It uses a nested empirical mode decomposition and Hilbert-Huang transform (HHT) approach to identify intrinsic amplitude and frequency modulations often present in nonlinear systems. Comparisons are first made with traditional spectrum analysis, which usually achieved its results through convolutional integral transforms based on additive expansions of an a priori determined basis, mostly under linear and stationary assumptions. Thus, for non-stationary processes, the best one could do historically was to use the time-frequency representations, in which the amplitude (or energy density) variation is still represented in terms of time. For nonlinear processes, the data can have both amplitude and frequency modulations (intra-mode and inter-mode) generated by two different mechanisms: linear additive or nonlinear multiplicative processes. As all existing spectral analysis methods are based on additive expansions, either a priori or adaptive, none of them could possibly represent the multiplicative processes. While the earlier adaptive HHT spectral analysis approach could accommodate the intra-wave nonlinearity quite remarkably, it remained that any inter-wave nonlinear multiplicative mechanisms that include cross-scale coupling and phase-lock modulations were left untreated. To resolve the multiplicative processes issue, additional dimensions in the spectrum result are needed to account for the variations in both the amplitude and frequency modulations simultaneously. HHSA accommodates all the processes: additive and multiplicative, intra-mode and inter-mode, stationary and non-stationary, linear and nonlinear interactions. The Holo prefix in HHSA denotes a multiple dimensional representation with both additive and multiplicative capabilities.
Biosynthesis of the Cyclotide MCoTI-II using an Engineered Intein (2006)

Cyclotides are an emerging family of naturally occurring circular mini-proteins ({approx}30-40 amino acids) characterized by six conserved Cys residues (forming 3 disulfide bridges) that create a topologically unique structure designated as a cyclic cysteine knot (CCK). The cysteine knot motif, which is embedded within the macrocylic backbone, is described as two disulfide bridges that form a ring that is penetrated by the third disulfide bridge. The cyclic backbone and CCK motif together confer cyclotides with a remarkable stability and resistance to proteolytic, chemical, and thermal degradation. Further, cyclotides are functionally diverse and display a wide range of functions including uterotonic activity, trypsin inhibition, cytotoxicity, neurotensin binding, anti-HIV, antimicrobial, and insecticidal activity. Together, these characteristics make cyclotides attractive candidates for both drug design and agricultural applications, both in their native forms and as molecular scaffolds for the incorporation of novel bioactivities. [1] The ability to manipulate production of cyclotides within biological systems is critical for mutagenesis studies, production of grafted products, and the mass production of cyclotides with novel activities. My adviser's hope is to achieve this capability by employing recombinant DNA expression techniques to generate large combinatorial libraries of cyclotides. The advantage in creating a biosynthetic library (containing {approx}10{sup 6}-10{sup 10} members/library vs. chemically based libraries with typical values ranging from {approx}10{sup 3}-10{sup 5} members/library) is that it can be lead to the in vivo application of biological screening and selection methodologies based on a specific clone's ability to affect certain cellular processes.
Diverse roles of invariant natural killer T cells in liver injury and fibrosis induced by carbon tetrachloride # (2008)

Natural activation of hepatic iNKT cells inhibits, whereas strong activation of iNKT cells by alpha-GalCer accelerates CCl(4)-induced acute liver injury, inflammation, and fibrosis. During chronic liver injury, hepatic iNKT cells are depleted and play a role in inhibiting liver fibrosis in the early stage but not the late stage of fibrosis.
Pharmacology of Calcium Channels in Cardiac Muscle, Vascular Muscle, and Neurons (1991)

The properties of voltage-dependent calcium channels in muscle cells and neurons have been studied using the whole-cell patch clamp technique. Cardiac muscle cells, vascular muscle cells, and neurons all have multiple types of calcium channels, and the different types have different pharmacological properties. The predominant calcium current in most cardiac and vascular muscle cells is carried through L-type calcium channels, which are potently and completely blocked by dihydropyridine drugs; the block is voltage-dependent, and is more potent at depolarized holding potentials where the calcium current is partly inactivated. In neurons, much less of the high-threshold calcium channel current is blocked by dihydropyridines, because much of it is carried through N-type calcium channels, which are not blocked by dihydropyridines but are blocked by the peptide toxin omega-conotoxin GVIA. In addition to L-type and N-type calcium channels, rat neurons have a third type of high-threshold calcium channel that is not blocked by either omega-conotoxin or dihydropyridines. Some neurons also have a fourth type of calcium current, a low threshold current carried by T-type calcium channels.
Destabilization of collagen in hide and leather by anionic surfactants. II. Calorimetry of the reaction of collagen with sulfates (1998)

Leather, a textile based on collagen, usually requires the addition of sulfated oils that have been recently found to cause instability when heated in critical manufacturing processes. Here reactions between collagen and sodium dodecyl sulfate (SDS), sulfated castor oil, or a synthetic sulfated oil are studied calorimetrically. Sodium lauryl sulfate below its critical micelle concentration (cmc) displayed an immediate exotherm due to equilibrium binding of the reagents with stoichiometry n = 12.6 ± 0.2, K = (2.02 ± 0.8) × 107 M−1, and enthalpy ΔH = 62 ± 2 Kcal/mol; and a delayed endotherm due to denaturation of collagen. The endotherms accompanying the reactions with sulfated oils with longer chains were smaller, with no apparent denaturation of collagen. The micellar nature of these surfactants was apparent from very large n for sulfated castor oil, 4082 ± 11 and a very small value of ΔH, 0.77 ± 0.01 cal/mol. The binding of sulfated castor oil at the polar bands of collagen crystallites, comprising extended molecules arranged side-by-side, was shown directly by electron microscopy. © 1998 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 36: 805–813, 1998
Association between radiation dose to neuronal progenitor cell niches and temporal lobes and performance on neuropsychological testing in children: a prospective study (2013)

These prospective data demonstrate a significant association between increasing RT dose to hippocampus and temporal lobes and decline in neurocognitive skills following cranial irradiation. These findings have important implications for trials, including RTOG 0933 (hippocampal-sparing whole brain radiation therapy for brain metastases).
Immunity and Tolerance to <i>Aspergillus</i> Involve Functionally Distinct Regulatory T Cells and Tryptophan Catabolism (2006)

The inherent resistance to diseases caused by Aspergillus fumigatus suggests the occurrence of regulatory mechanisms that provide the host with adequate defense without necessarily eliminating the fungus or causing unacceptable levels of host damage. In this study, we show that a division of labor occurs between functionally distinct regulatory T cells (Treg) that are coordinately activated by a CD28/B-7-dependent costimulatory pathway after exposure of mice to Aspergillus conidia. Early in infection, inflammation is controlled by the expansion, activation and local recruitment of CD4+CD25+ Treg capable of suppressing neutrophils through the combined actions of IL-10 and CTLA-4 on indoleamine 2,3-dioxygenase. The levels of IFN-gamma produced in this early phase set the subsequent adaptive stage by conditioning the indoleamine 2,3-dioxygenase-dependent tolerogenic program of dendritic cells and the subsequent activation and expansion of tolerogenic Treg, which produce IL-10 and TGF-beta, inhibit Th2 cells, and prevent allergy to the fungus. The coordinate activation of Treg may, however, be subverted by the fungus, as germinating conidia are capable of interfering with anti-inflammatory and tolerogenic Treg programs. Thus, regulation is an essential component of the host response in infection and allergy to the fungus, and its manipulation may allow the pathogen to overcome host resistance and promote disease.
A multicast mechanism with ordering on overlapping groups (2002)

The paper proposes a new mechanism for group communication which guarantees the total ordering of message delivery, especially the ordering on the members common to overlapping groups. The mechanism is based on a method which propagates messages to all destinations along trees. The approach has the following advantages over the propagation tree mechanism: (1) greater parallelism (messages can be sent to destinations by using broadcast networks); (2) less latency time (it takes less time to have a message reach all the destinations); and (3) more flexible to dynamic membership changes, (each change of process membership does not involve a restructuring of propagation trees).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The effects of ion implantation on the interdiffusion coefficients in In<i>x</i>Ga1−<i>x</i>As/GaAs quantum well structures (1993)

Photoluminescence coupled with repetitive thermal annealing has been used to determine the diffusion coefficients for intermixing in InxGa1−xAs/GaAs quantum wells and to study the subsequent effects of ion implantation on the intermixing. It is shown that following ion implantation there is a very fast interdiffusion process, which is independent of the implanted ion and that is thought to be due to the rapid diffusion of interstitials created during the implantation. Following this rapid process, it was found that neither gallium nor krypton ions had any effect on the subsequent interdiffusion coefficient. Following arsenic implantation in addition to the initial damage related process, an enhanced region of interdiffusion was observed with a diffusion coefficient that was an order of magnitude greater than that of an unimplanted control wafer. This enhanced process is thought to be due to the creation of group III vacancies by the arsenic atoms moving onto group V lattice sites. This fast process was present until the structure had broadened by about 75 Å when the diffusion coefficient returned to the unimplanted control value. The activation energy for the interdiffusion was measured over the temperature range 1050–750°C and a value of 3.7±0.1 eV was measured. This was found to be independent of the implanted ion.
Synthese von selektiv <i>N</i>‐ funktionalisierten Polyamin‐Derivaten (1993)

Synthesis of Selectively N ‐Functionalized Polyamine Derivatives A threefold differently protected derivative 8 of the triamine spermidine ( 2 ) has been prepared in three steps starting from propane‐1,3‐diamine ( 1 ). The protected spermidine derivative 8 was converted to its spermine analogue 12 , a useful polyamine intermediate. In a convergent way, the fourfold differently protected derivative 18 of the tetraamine spermine ( 3 ) has been obtained by coupling the two different and separately prepared propane‐1,3‐diamine units 15 and 17 . Spermidine derivative 19 and spermine derivative 20 , both selectively protected at both primary amino groups, have been Prepared from the free polyamines 2 and 3 , respectively, in a direct approach.
Iodine and iodine supported on polyvinylpyrrolidone as catalysts and reagents for alcoholysis, hydrolysis, and acetolysis of epoxides and thiiranes (1997)

Iodine and iodine supported on polyvinylpyrrolidone (betadine) have been used as catalysts for ring opening of epoxides and as reagent for ring-opening dimerization of thiiranes in alcohols, water, and acetic acid. The reactions occur with high regio-, chemo-, and stereoselectivity. The reaction of R-(+)-styrene oxide with I 2 supported on PVP in methanol was found to be very stereospecific and the product was isolated in 93% ee. Keywords: iodine, support, polyvinylpyrrolidone, ring opening, epoxides, thiiranes.
Multiple Discontinuous Ligand-mimetic Antibody Binding Sites Define a Ligand Binding Pocket in Integrin αIIbβ3 (2000)

Integrin alpha(IIb)beta(3), a platelet fibrinogen receptor, is critically involved in thrombosis and hemostasis. However, how ligands interact with alpha(IIb)beta(3) has been controversial. Ligand-mimetic anti-alpha(IIb)beta(3) antibodies (PAC-1, LJ-CP3, and OP-G2) contain the RGD-like RYD sequence in their CDR3 in the heavy chain and have structural and functional similarities to native ligands. We have located binding sites for ligand-mimetic antibodies in alpha(IIb) and beta(3) using human-to-mouse chimeras, which we expect to maintain functional integrity of alpha(IIb)beta(3). Here we report that these antibodies recognize several discontinuous binding sites in both the alpha(IIb) and beta(3) subunits; these binding sites are located in residues 156-162 and 229-230 of alpha(IIb) and residues 179-183 of beta(3). In contrast, several nonligand-mimetic antibodies (e.g. 7E3) recognize single epitopes in either subunit. Thus, binding to several discontinuous sites in both subunits is unique to ligand-mimetic antibodies. Interestingly, these binding sites overlap with several (but not all) of the sequences that have been reported to be critical for fibrinogen binding (e.g. N-terminal repeats 2-3 but not repeats 4-7, of alpha(IIb)). These results suggest that ligand-mimetic antibodies and probably native ligands may make direct contact with these discontinuous binding sites in both subunits, which may constitute a ligand-binding pocket.
Optimizing video search reranking via minimum incremental information loss (2008)

This paper is concerned with video search reranking - the task of reordering the initial ranked documents (video shots) to improve the search performance - in an optimization framework. Conventional supervised reranking approaches empirically convert the reranking as a classification problem in which each document is determined relevant or not, followed by reordering the documents according to the confidence scores of classification. We argue that reranking is essentially an optimization problem in which the ranked list is globally optimal if any two arbitrary documents from the list are correctly ranked in terms of relevance, rather than simply classifying a document into relevant or not. Therefore, we propose in this paper to directly optimize video search reranking from a novel viewpoint of information theory, that is, to identify an optimal set of correctly-ranked document pairs which maximally preserves the relevant information and simultaneously carries the irrelevant information as little as possible. The final reranked list is then directly recovered from this optimal set of pairs. Under the framework, we further propose an effective algorithm, called minimum incremental information loss (MIIL) reranking, to solve the optimization problem more practically. We conducted comprehensive experiments on automatic video search task over TRECVID 2005-2007 benchmarks, and showed significant and consistent improvements over the text search baseline and other reranking approaches.
Vale (1970)

John muir became the fifth editor of this journal in 1964. He had been educated at Newbury (an ancient foundation from which there had emerged a long series of classical scholars) and at Keble College, Oxford. There followed some years of teaching at Public and Grammar School before he was appointed a Lecturer at King's College, London. So far he had little or no experience of the duties, and trials, of editorship, but he did bring to the task outstanding qualities, which soon proved that a worthy successor to Geoffrey Hooker had been found. In fact, Muir has left his own mark on Greece & Rome . Now, after six fruitful years, the pressure of work as a University teacher, as well as his own researches and—far more important—the ties of family (he and Mrs. Muir have three fine sons) have made it necessary for him to resign. We shall remember him for his scholarly approach, his modesty and a charming sense of humour—a virtue not always evident in a literary critic (which of course he had to become). He has earned the gratitude of us all. We wish him well.
Quality control of inclusion bodies in Escherichia coli (2010)

alpha-glucosidase is fragmented before aggregation, but neither by proteolytic action on the IBs by the common major proteases, nor during downstream IB preparation. Different fragments co-aggregate in the process of IB formation together with the full-length product. Other intracellular proteases than ClpP or Lon must be responsible for fragmentation. Reaggregation of protease-stable alpha-glucosidase fragments during in situ disintegration of the existing IBs does not seem to occur.
Ultra-Lightweight Speech Separation via Group Communication (2020)

Model size and complexity remain the biggest challenges in the deployment of speech enhancement and separation systems on low-resource devices such as earphones and hearing aids. Although methods such as compression, distillation and quantization can be applied to large models, they often come with a cost on the model performance. In this paper, we provide a simple model design paradigm that explicitly designs ultra-lightweight models without sacrificing the performance. Motivated by the sub-band frequency-LSTM (F-LSTM) architectures, we introduce the group communication (GroupComm), where a feature vector is split into smaller groups and a small processing block is used to perform inter-group communication. Unlike standard F-LSTM models where the sub-band outputs are concatenated, an ultra-small module is applied on all the groups in parallel, which allows a significant decrease on the model size. Experiment results show that comparing with a strong baseline model which is already lightweight, GroupComm can achieve on par performance with 35.6 times fewer parameters and 2.3 times fewer operations.
Chemical Vapor Deposition of Monolayer Rhenium Disulfide (ReS<sub>2</sub>) (2015)

The direct synthesis of monolayer and multilayer ReS2 by chemical vapor deposition at a low temperature of 450 °C is reported. Detailed characterization of this material is performed using various spectroscopy and microscopy methods. Furthermore initial field-effect transistor characteristics are evaluated, which highlight the potential in being used as an n-type semiconductor.
Real‐time Volumetric Deformable Models for Surgery Simulation using Finite Elements and Condensation (1996)

Abstract This paper discusses the application of 3D solid volumetric Finite Element models to surgery simulation. In particular it introduces three new ideas for solving the problem of achieving real‐time performance for these models. The simulation system we have developed is described and we demonstrate real‐time deformation using the methods developed in the paper.
Functional Design Verification by Multi-Level Simulation (1984)

This paper introduces Intel's functional CAD design environment and methodology. The generation of an accurate behavioral model for use in systems design validation and for comparisons with lower-level components is described. The need for both an RTL and a schematics simulator in Intel's hierarchical design methodology is explained. Finally, the paper shows how these two simulators have been linked together in two ways for two different purposes: for RTL-schematics verification, and for very large logic simulation runs.
Functional coupling of SSTR4, a major hippocampal somatostatin receptor, to adenylate cyclase inhibition, arachidonate release and activation of the mitogen-activated protein kinase cascade. (1994)

Somatostatin has a modulatory role in regulating the membrane conductance in hippocampal neurons. To examine the signal transducing molecules involved in this process, we isolated the cDNA encoding the dominant rat hippocampal somatostatin receptor, SSTR4. Distribution of SSTR4 in the adult central nervous system was restricted to the hippocampus, cerebral cortex, striatum, hypothalamus, and thalamus, as determined by Northern blot analysis and in situ hybridization. In SSTR4-expressing Chinese hamster ovary cells, SSTR4 was functionally coupled not only to inhibition of adenylate cyclase, but also to activation of both arachidonate release and mitogen-activated protein (MAP) kinase cascade, with similar ED50 values. All of these pathways, including both MAP kinase kinase and MAP kinase activation, were completely blocked by pretreatment with pertussis toxin. On the other hand, neither inositol 1,4,5-trisphosphate synthesis nor intracellular Ca2+ mobilization was induced upon SSTR4 stimulation. These data indicate that the hippocampal functions of somatostatin might be mediated through diverse but selective second messenger systems activated via SSTR4 and reveal an unsuspected coupling of a neuronal SSTR subtype to a mitogenic signaling pathway. SSTR4, in addition, provides a useful system to study the Ca(2+)-independent, Gi-dependent (pertussis toxin-sensitive) pathway of MAP kinase activation.
Pharmacokinetics and pharmacodynamics of SB-240563, a humanized monoclonal antibody directed to human interleukin-5, in mild asthmatics (1999)

Clinical Pharmacology & Therapeutics (1999) 65, 147–147; doi:
Biodegradable polymers: Chymotrypsin degradation of a low molecular weight poly(ester‐urea) containing phenylalanine (1979)

Abstract A low molecular weight poly(ester urea), poly(L‐phenylalanine/ethylene glycol/1,6‐diisocyanatohexane), and a model diester diurea, dimethyldiphenylalaninehexamethylenediruea, were synthesized and found to be hydrolyzed by α‐chymotrypsin solutions at pH 7.8. After ten‐day exposure to 0.1 mg/ml enzyme solution at room temperature, 79.9% weight loss was observed for the model diester diurea (containing two ester linkages per molecule). A weight loss of 19.4% was observed for the poly(ester urea) of M̄ n 1930 (containing an average of eight ester linkages per molecule) after the same period of exposure. A poly(ester urea) of similar molecular weight, but derived from glycine instead of phenylalanine, was found to resist chymotrypsin hydrolysis.
Genetics of Parkinson's Disease (2012)

Fifteen years of genetic research in Parkinson's disease (PD) have led to the identification of several monogenic forms of the disorder and of numerous genetic risk factors increasing the risk to develop PD. Monogenic forms, caused by a single mutation in a dominantly or recessively inherited gene, are well-established, albeit relatively rare types of PD. They collectively account for about 30% of the familial and 3%-5% of the sporadic cases. In this article, we will summarize the current knowledge and understanding of the molecular genetics of PD. In brief, we will review familial forms of PD, basic genetic principles of inheritance (and their exceptions in PD), followed by current methods for the identification of PD genes and risk factors, and implications for genetic testing.