gebhart/patrepeval huggingface dataset:
Fiber coupling using graded-index rod lenses (1980)

The graded-index rod lens (GRIN lens) is useful in coupling between multimode optical fibers. Applications include connectors, switches, multiplexers, and branch couplers. In these devices, one GRIN lens collimates light from an input fiber, and a second lens collects the light and focuses it on an output fiber. This paper presents analyses of power losses in these devices resulting from lateral and angular misalignments and from the spacing between the lenses. It is found that the GRIN lens coupling system is very sensitive to angular alignment but is more tolerant of lateral errors and lens spacing.
Thermohaline circulation at three key sections in the North Atlantic over 1985–2002 (2005)

Efforts are presently underway to monitor the Thermohaline Circulation (THC) in the North Atlantic. A measuring strategy has been designed to monitor both the Meridional Overturning Circulation (MOC) in the subtropics and dense outflows at higher latitudes. To provide a historical context for these new observations, we diagnose an eddy‐permitting ocean model simulation of the period 1985–2002. We present time series of the THC, MOC and heat transport, at key hydrographic sections in the subtropics, the northeast Atlantic and the Labrador Sea. The simulated THC compares well with observations. We find considerable variability in the THC on each section, most strikingly in the Labrador Sea during the early 1990's, consistent with observed changes. Overturning in the northeast Atlantic declines by ∼20% over the 1990's, coincident with an increase in the subtropics. We speculate that MOC weakening may soon be detected in the subtropics, if the decline continues in mid‐latitudes.
New approach to voiced onset detection in speech signal and its application for frame error concealment (2008)

This paper presents a new approach for accurate detection of voiced onsets in a speech signal. The knowledge of the precise location of the beginning of a voiced segment has several potential applications in speech compression (e.g. source-controlled variable bitrate coding, classification-based frame erasure concealment). The proposed onset detection algorithm is based on Teager's energy operator applied on sub-bands. The technique has been integrated in the signal classifier of the VMR-WB speech coding standard used for frame erasure (FE) concealment. A subjective listening test using MUSHRA methodology showed an improvement in frame error conditions with respect to the legacy VMR-WB classification.
A Method for the Construction of Minimum-Redundancy Codes (1952)

An optimum method of coding an ensemble of messages consisting of a finite number of members is developed. A minimum-redundancy code is one constructed in such a way that the average number of coding digits per message is minimized.
Photoinactivation of Viruses in Human Fresh Plasma by Phenothiazine Dyes in Combination with Visible Light (1991)

We developed a photodynamic method to inactivate viruses in human fresh plasma. Single plasma bags were illuminated with visible light in the presence of low doses of phenothiazine dyes like methylene blue or toluidine blue. By this treatment the infectivity of different enveloped viruses including the causative agent of AIDS, HIV-1, was completely removable from the plasma. Non enveloped viruses, however, proved to be more stable. The activities of clotting factors and other plasma proteins were only slightly decreased. There was no indication that the procedure led to important structural modifications of plasma proteins. The dyes are photodynamically active at concentrations much lower than those at which they are therapeutically used as antidots in the treatment of methemoglobinemia.
Video-rate spectral imaging of gas leaks in the longwave infrared (2013)

We have recently constructed and tested a gas cloud imager which demonstrates the rst-ever video-rate detection (15 frames/sec) of gas leaks using an uncooled LWIR detector array. Laboratory and outdoor measurements, taken in collaboration with BP Products North America Inc. and IES Inc., show detection sensitivities comparable to existing cooled systems for detecting hydrocarbon gases. Gases imaged for these experiments include methane, propane, propylene, ethane, ethylene, butane, and iso-butylene, but any gases with absorption features in the LWIR band could potentially be detected, such as sarin and other toxic gases. These results show that practical continuous monitoring of gas leaks with uncooled imaging sensors is now possible.
Cloning and expression of a soluble sialidase from Chinese hamster ovary cells: sequence alignment similarities to bacterial sialidases (1994)

A cDNA encoding a soluble sialidase from Chinese hamster ovary (CHO) cells has been cloned and expressed. Completely degenerate oligonucleotide primers, which were based on the amino acid sequence of peptides obtained from the purified sialidase (Warner et al., Glycobiology, 3, 455-463, 1993), and the polymerase chain reaction, with single-stranded cDNA template, were employed to generate a unique oligonucleotide probe. The unique probe of 93 bp was used for screening a lambda gt 10 CHO cell cDNA library. A single clone, which contained a 1.4 kb insert, was isolated after screening 450,000 recombinants. The complete coding region of the protein, 1137 nucleotides, was contained in the isolated clone and it predicted a protein of 379 amino acids. The insert had a 186 bp 5' non-coding leader sequence and a 40 bp 3' non-coding region. No signal peptide was identified in the insert, suggesting a cytosolic localization for the protein. No significant primary sequence identities were observed when the deduced amino acid sequence of the CHO cell sialidase was compared with other mammalian proteins or microbial sialidases. However, the protein had significant sequence alignment similarity with several bacterial sialidases. Two 'Asp box' motifs in the CHO cell sialidase had a remarkable alignment positioning in the protein sequence with the similar motifs of the Salmonella LT2 and Clostridium perfringens sialidases. High levels of the enzyme were expressed in Spodoptera frugiperda cells infected with a modified Autographa californica nuclear polyhedrosis virus harbouring the sialidase cDNA.
PPARγ and PPARδ negatively regulate specific subsets of lipopolysaccharide and IFN-γ target genes in macrophages (2003)

Natural and synthetic agonists of the peroxisome proliferator-activated receptor gamma (PPARgamma) regulate adipocyte differentiation, glucose homeostasis, and inflammatory responses. Although effects on adipogenesis and glucose metabolism are genetically linked to PPARgamma, the PPARgamma dependence of antiinflammatory responses of these substances is less clear. Here, we have used a combination of mRNA expression profiling and conditional disruption of the PPARgamma gene in mice to characterize programs of transcriptional activation and repression by PPARgamma agonists in elicited peritoneal macrophages. Natural and synthetic PPARgamma agonists, including the thiazolidinedione rosiglitazone (Ro), modestly induced the expression of a surprisingly small number of genes, several of which were also induced by a specific PPARdelta agonist. The majority of these genes encode proteins involved in lipid homeostasis. In contrast, Ro inhibited induction of broad subsets of lipopolysaccharide and IFN-gamma target genes in a gene-specific and PPARgamma-dependent manner. At high concentrations, Ro inhibited induction of lipopolysaccharide target genes in PPARgamma-deficient macrophages, at least in part by activating PPARdelta. These studies establish overlapping transactivation and transrepression functions of PPARgamma and PPARdelta in macrophages and suggest that a major transcriptional role of PPARgamma is negative regulation of specific subsets of genes that are activated by T helper 1 cytokines and pathogenic molecules that signal through pattern recognition receptors. These findings support a physiological role of PPARgamma in regulating both native and acquired immune responses.
Optimization of fast block motion estimation algorithms (1997)

There are basically three approaches for carrying out fast block motion estimation: (1) fast search by a reduction of motion vector candidates; (2) fast block-matching distortion (BMD) computation; and (3) motion field subsampling. The first approach has been studied more extensively since different ways of reducing motion vector candidates may result in significantly different performance; while the second and third approaches can in general be integrated into the first one so as to further accelerate the estimation process. In this paper, we first formulate the design of good fast estimation algorithms based on motion vector candidate reduction into an optimization problem that involves the checking point pattern (CPP) design via minimizing the distance from the true motion vector to the closest checking point (DCCP). Then, we demonstrate through extensive studies on the statistical behavior of real-world motion vectors that the DCCP minimization can result in fast search algorithms that are very efficient as well as highly robust. To further utilize the spatiotemporal correlation of motion vectors, we develop an adaptive search scheme and a hybrid search idea that involves a fixed CPP and a variable CPP. Simulations are performed to confirm their advantages over conventional fast search algorithms.
Synthesis and Biological Evaluation of 1-Arylsulfonyl-5-(<i>N</i>-hydroxyacrylamide)indoles as Potent Histone Deacetylase Inhibitors with Antitumor Activity in Vivo (2012)

A series of 1-arylsulfonyl-5-(N-hydroxyacrylamide)indoles has been identified as a new class of histone deacetylase inhibitors. Compounds 8, 11, 12, 13, and 14 demonstrated stronger antiproliferative activities than 1 (SAHA) with GI(50) values ranging from 0.36 to 1.21 μM against Hep3B, MDA-MB-231, PC-3, and A549 human cancer cell lines. Lead compound 8 showed remarkable HDAC 1, 2, and 6 isoenzymes inhibitory activities with IC(50) values of 12.3, 4.0, 1.0 nM, respectively, which are comparable to 1. In in vivo efficacy evaluation against lung A549 xenograft model, 8 displayed better antitumor activity than compound 1.
Cell‐free expression as an emerging technique for the large scale production of integral membrane protein (2006)

Membrane proteins are highly underrepresented in structural data banks due to tremendous difficulties that occur upon approaching their structural analysis. Inefficient sample preparation from conventional cellular expression systems is in many cases the first major bottleneck. Preparative scale cell-free expression has now become an emerging alternative tool for the high level production of integral membrane proteins. Many toxic effects attributed to the overproduction of recombinant proteins are eliminated by cell-free expression as viable host cells are no longer required. A unique characteristic is the open nature of cell-free systems that offers a variety of options to manipulate the reaction conditions in order to protect or to stabilize the synthesized recombinant proteins. Detergents or lipids can easily be supplemented and membrane proteins can therefore be synthesized directly into a defined hydrophobic environment of choice that permits solubility and allows the functional folding of the proteins. Alternatively, cell-free produced precipitates of membrane proteins can efficiently be solubilized in mild detergents after expression. Highly valuable for structural approaches is the fast and efficient cell-free production of uniformly or specifically labeled proteins. A considerable number of membrane proteins from diverse families like prokaryotic small multidrug transporters or eukaryotic G-protein coupled receptors have been produced in cell-free systems in high amounts and in functionally active forms. We will give an overview about the current state of the art of this new approach with special emphasis on technical aspects as well as on the functional and structural characterization of cell-free produced membrane proteins.
Murine Sclerodermatous Graft-Versus-Host Disease, a Model for Human Scleroderma: Cutaneous Cytokines, Chemokines, and Immune Cell Activation (2002)

Murine sclerodermatous graft-vs-host disease (Scl GVHD) models human scleroderma, with prominent skin thickening, lung fibrosis, and up-regulation of cutaneous collagen mRNA. Fibrosis in Scl GVHD may be driven by infiltrating TGF-beta1-producing mononuclear cells. Here we characterize the origin and types of those cutaneous effector cells, the cytokine and chemokine environments, and the effects of anti-TGF-beta Ab on skin fibrosis, immune cell activation markers, and collagen and cytokine synthesis. Donor cells infiltrating skin in Scl GVHD increase significantly at early time points post-transplantation and are detectable by PCR analysis of Y-chromosome sequences when female mice are transplanted with male cells. Cutaneous monocyte/macrophages and T cells are the most numerous cells in Scl GVHD compared with syngeneic controls. These immune cells up-regulate activation markers (MHC class II I-A(d) molecules and class A scavenger receptors), suggesting Ag presentation by cutaneous macrophages in early fibrosing disease. Early elevated cutaneous mRNA expression of TGF-beta1, but not TGF-beta2 or TGF-beta3, and elevated C-C chemokines macrophage chemoattractant protein-1, macrophage inflammatory protein-1alpha, and RANTES precede subsequent skin and lung fibrosis. Therefore, TGF-beta1-producing donor mononuclear cells may be critical effector cells, and C-C chemokines may play important roles in the initiation of Scl GVHD. Abs to TGF-beta prevent Scl GVHD by effectively blocking the influx of monocyte/macrophages and T cells into skin and by abrogating up-regulation of TGF-beta1, thereby preventing new collagen synthesis. The Scl GVHD model is valuable for testing new interventions in early fibrosing diseases, and chemokines may be new potential targets in scleroderma.
A surface micromachined rotating micro-mirror normal to the substrate (2002)

An optical mirror for directing a laser parallel to the substrate surface has been designed and fabricated. The mirror consists of a 214 /spl mu/m/spl times/210 /spl mu/m, 3.5 /spl mu/m thick polysilicon plate, coated with a 0.5 /spl mu/m thick layer of gold. The mirror is connected to the substrate by 3 floating substrate hinges. Using microprobes, the mirror is lifted off of the substrate and up into a latch mechanism. The latch holds the mirror normal to the substrate. The floating substrate hinges are connected to a 200 /spl mu/m diameter circular 2.0 /spl mu/m thick polysilicon plate. This plate is mounted to the substrate via a rotating sliding anchor. The mirror is designed to be driven by an array of thermal actuators.
Porous Polymer Monoliths:  Preparation of Sorbent Materials with High-Surface Areas and Controlled Surface Chemistry for High-Throughput, Online, Solid-Phase Extraction of Polar Organic Compounds (1998)

Porous monolithic materials with high surface areas have been prepared from commercial 80% divinylbenzene. The pore properties of these materials are controlled by the type and composition of the porogenic solvent and by the percentage of cross-linking monomer (divinylbenzene) in the polymerization mixture. Surface area was found to increase with the divinylbenzene content of the monolith. Using high-grade divinylbenzene and a suitable porogenic solvent, monolithic materials with specific surface areas as high as 400 m2/g yet still permeable to liquids at reasonable back pressure were obtained for the first time. A macroporous material with hydrodynamic properties optimized for solid-phase extraction has been designed and its permeability and adsorption ability was demonstrated by adsorbing phenols at flow velocities that exceed those of current materials by a factor of 30. A unique set of polymerization conditions had to be developed to allow the incorporation of polar 2-hydroxylethyl methacrylate into the hydrophobic nonpolar backbone of the divinylbenzene monolithic material. This improves wettability while high-flow properties are maintained and unusually high recoveries of polar compounds are allowed.
Wavelet Thresholding via A Bayesian Approach (1998)

Summary We discuss a Bayesian formalism which gives rise to a type of wavelet threshold estimation in nonparametric regression. A prior distribution is imposed on the wavelet coefficients of the unknown response function, designed to capture the sparseness of wavelet expansion that is common to most applications. For the prior specified, the posterior median yields a thresholding procedure. Our prior model for the underlying function can be adjusted to give functions falling in any specific Besov space. We establish a relationship between the hyperparameters of the prior model and the parameters of those Besov spaces within which realizations from the prior will fall. Such a relationship gives insight into the meaning of the Besov space parameters. Moreover, the relationship established makes it possible in principle to incorporate prior knowledge about the function's regularity properties into the prior model for its wavelet coefficients. However, prior knowledge about a function's regularity properties might be difficult to elicit; with this in mind, we propose a standard choice of prior hyperparameters that works well in our examples. Several simulated examples are used to illustrate our method, and comparisons are made with other thresholding methods. We also present an application to a data set that was collected in an anaesthesiological study.
Ray casting architectures for volume visualization (1999)

Real-time visualization of large volume data sets demands high-performance computation, pushing the storage, processing and data communication requirements to the limits of current technology. General-purpose parallel processors have been used to visualize moderate-size data sets at interactive frame rates; however, the cost and size of these supercomputers inhibits the widespread use for real-time visualization. This paper surveys several special-purpose architectures that seek to render volumes at interactive rates. These specialized visualization accelerators have cost, performance and size advantages over parallel processors. All architectures implement ray casting using parallel and pipelined hardware. We introduce a new metric that normalizes performance to compare these architectures. The architectures included in this survey are VOGUE, VIRIM, Array-Based Ray Casting, EM-Cube and VIZARD II. We also discuss future applications of special-purpose accelerators.
Evaluation of Multidimensional Chromatography Coupled with Tandem Mass Spectrometry (LC/LC−MS/MS) for Large-Scale Protein Analysis:  The Yeast Proteome (2002)

Highly complex protein mixtures can be directly analyzed after proteolysis by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). In this paper, we have utilized the combination of strong cation exchange (SCX) and reversed-phase (RP) chromatography to achieve two-dimensional separation prior to MS/MS. One milligram of whole yeast protein was proteolyzed and separated by SCX chromatography (2.1 mm i.d.) with fraction collection every minute during an 80-min elution. Eighty fractions were reduced in volume and then re-injected via an autosampler in an automated fashion using a vented-column (100 microm i.d.) approach for RP-LC-MS/MS analysis. More than 162,000 MS/MS spectra were collected with 26,815 matched to yeast peptides (7,537 unique peptides). A total of 1,504 yeast proteins were unambiguously identified in this single analysis. We present a comparison of this experiment with a previously published yeast proteome analysis by Yates and colleagues (Washburn, M. P.; Wolters, D.; Yates, J. R., III. Nat. Biotechnol. 2001, 19, 242-7). In addition, we report an in-depth analysis of the false-positive rates associated with peptide identification using the Sequest algorithm and a reversed yeast protein database. New criteria are proposed to decrease false-positives to less than 1% and to greatly reduce the need for manual interpretation while permitting more proteins to be identified.
Type V Protein Secretion Pathway: the Autotransporter Story (2004)

Gram-negative bacteria possess an outer membrane layer which constrains uptake and secretion of solutes and polypeptides. To overcome this barrier, bacteria have developed several systems for protein secretion. The type V secretion pathway encompasses the autotransporter proteins, the two-partner secretion system, and the recently described type Vc or AT-2 family of proteins. Since its discovery in the late 1980s, this family of secreted proteins has expanded continuously, due largely to the advent of the genomic age, to become the largest group of secreted proteins in gram-negative bacteria. Several of these proteins play essential roles in the pathogenesis of bacterial infections and have been characterized in detail, demonstrating a diverse array of function including the ability to condense host cell actin and to modulate apoptosis. However, most of the autotransporter proteins remain to be characterized. In light of new discoveries and controversies in this research field, this review considers the autotransporter secretion process in the context of the more general field of bacterial protein translocation and exoprotein function.
A new social communication intervention for children with autism: pilot randomised controlled treatment study suggesting effectiveness (2004)

A Randomised Treatment Trial design of this kind in classical autism is feasible and acceptable to patients. This pilot study suggests significant additional treatment benefits following a targeted (but relatively non-intensive) dyadic social communication treatment, when compared with routine care. The study needs replication on larger and independent samples. It should encourage further RCT designs in this area.
Antibody-Induced Botulinum Toxin Therapy Failure: Can It Be Overcome by Increased Botulinum Toxin Doses? (2002)

In some patients treated with botulinum toxin type A (BT) therapy failure occurs due to the formation of antibodies against BT (BT-AB). We investigated whether increased BT doses can overcome this form of therapy failure. Eight patients with cervical dystonia, secondary BT therapy failure and evidence of BT-AB formation in the mouse diaphragm bioassay received BT test doses (Dysport, Ipsen Ltd., Maidenhead, Berks, UK) into one of their sternocleidomastoid muscles. Test doses were increased in three steps at 3-month intervals and their effect on the amplitude of the electromyographic activity of the sternocleidomastoid muscle under maximal isometric activation (M-EMG) was measured and compared to a control group. In step 1 (200 or 300 MU) the M-EMG reduction was 12 +/- 13% compared to 85 +/- 10% (200 MU) and 83 +/- 9% (300 MU) in the control group. In step 2 (400, 600 or 800 MU) the M-EMG reduction was 25 +/- 21% compared to 78 +/- 7% (400 MU) in the control group. In step 3 (1,600 or 1,800 MU) the M-EMG reduction was 24 plus minus 10%. Side effects were not observed in any of the patients studied. In 1 patient with partial secondary BT therapy failure, with a low BT-AB titre (0.0015 U/ml) and with a moderately pathological M-EMG reduction of 40% with 200 MU a normal M-EMG reduction of 71% could be regained with 800 MU. In three subsequent therapeutic injection series with quadrupled BT doses in all target muscles the original therapy outcome could be regained and maintained. Side effects or increasing BT-AB titres were not observed. Even massively increased BT doses cannot overcome BT-AB-induced complete secondary therapy failure. However, in patients with partial secondary therapy failure, low BT-AB titres and a moderately pathological M-EMG reduction, increased BT doses might regain and maintain normal BT efficacy without induction of side effects or increasing BT-AB titres.