gebhart/patrepeval huggingface dataset:
Effects of the nearest neighbors and the alloy matrix on SiH stretching vibrations in the amorphousSiOr:H (0<r<2) alloy system (1989)

Hydrogenated silicon suboxides, ${\mathrm{SiO}}_{\mathrm{r}}$:H, for alloy range (0&lt;r&lt;2) have been deposited by remote plasma-enhanced chemical vapor deposition (remote PECVD) under conditions in which hydrogen is incorporated predominantly in monohydride or SiH bonding configurations. We have investigated both the SiH bond-stretching and bond-bending absorption bands by infrared (ir) absorption spectroscopy as a function of r, the alloy composition. In this paper, we have focused on the bond-stretching absorption bands, and have modeled the shape of the bond-stretching band as a function of the alloy composition. There are four distinct local environments for the SiH group in the sub- oxides; these can be written as HSi-${\mathrm{Si}}_{3\mathrm{\ensuremath{-}}\mathrm{n}}$${\mathrm{O}}_{\mathrm{n}}$, for n=0--3. A sum of Gaussian functions, one for each environment, is used to synthesize the absorption in the SiH stretching band. The peak positions of these Gaussians are calculated by an induction model which includes both local and matrix (or alloy) effects; the amplitude weightings are determined from a random statistical model for the local bonding environments of the Si-O groups in the ${\mathrm{SiO}}_{\mathrm{r}}$ alloy. We find that the frequency shifts caused by changes in the matrix, and associated with different values of r, are comparable to the shifts associated with the different local environments. The combination of these effects serves to diminish the discreteness of subband features in the absorption spectrum.
Kinetic analysis of the interactions between Troponin C (TnC) and Troponin I (TnI) binding peptides: evidence for separate binding sites for the ‘structural’ N‐terminus and the ‘regulatory’ C‐terminus of TnI on TnC (2003)

The Ca(2+)/Mg(2+)-dependent interactions between TnC and TnI play a critical role in regulating the 'on' and 'off' states of muscle contraction as well as maintaining the structural integrity of the troponin complex in the off state. In the present study, we have investigated the binding interactions between the N-terminus of TnI (residues 1-40 of skeletal TnI) and skeletal TnC in the presence of Ca(2+) ions, Mg(2+) ions and in the presence of the C-terminal regulatory region peptides: TnI(96-115), TnI(96-131) and TnI(96-139). Our results show the N-terminus of TnI can bind to TnC with high affinity in the presence of Ca(2+) or Mg(2+) ions with apparent equilibrium dissociation constants of K(d(Ca(2+) ) ) = 48 nM and K(d(Mg(2+) ) ) = 29 nM. The apparent association and dissociation rate constants for the interactions were, k(on) = 4.8 x 10(5) M (-1) s(-1), 3.4 x 10(5) M (-1) s(-1) and k(off) = 2.3 x 10(-2) s(-1), 1.0 x 10(-2) s(-1) for TnC(Ca(2+)) and TnC(Mg(2+)) states, respectively. Competition studies between each of the TnI regions and TnC showed that both TnI regions can bind simultaneously to TnC while native gel electrophoresis and SEC confirmed the formation of stable ternary complexes between TnI(96-139) (or TnI(96-131)) and TnC-TnI(1-40). Further analysis of the binding interactions in the ternary complex showed the binding of the TnI regulatory region to TnC was critically dependent upon the presence of both TnC binding sites (i.e. TnI(96-115) and TnI(116-131)) and the presence of Ca(2+). Furthermore, the presence of TnI(1-40) slightly weakened the affinity of the regulatory peptides for TnC. Taken together, these results support the model for TnI-TnC interaction where the N-terminus of TnI remains bound to the C-domain of TnC in the presence of high and low Ca(2+) levels while the TnI regulatory region (residues 96-139) switches in its binding interactions between the actin-tropomyosin thin filament and its own sites on the N- and C-domain of TnC at high Ca(2+) levels, thus regulating muscle contraction.
Properties of mobile radio propagation above 400 MHz (1974)

This paper begins with a discussion of multipath interference. The spatial description of the field impinging upon a mobile radio antenna is derived and the power spectrum and other properties of the signal envelope are considered. Next, large scale variations of the average signal are discussed. Measurements of observed attenuation on mobile paths over both smooth and irregular terrain are summarized. The paper concludes with a discussion of methods of predicting the area of coverage from a base station.
Recombinant adeno‐associated virus (AAV) drives constitutive production of glutamate decarboxylase in neural cell lines (1999)

Many neurological disorders result directly or indirectly from the loss of inhibitory function. Engineering the production of GABA, an inhibitory neurotransmitter, may therefore be able at least partly to restore the lost inhibition seen in epilepsy, Parkinson's disease, or Huntington's disease. In this article, we describe a set of recombinant adeno-associated viruses (AAVs) that can deliver cDNAs encoding the GABA-producing enzyme, glutamate decarboxylase (GAD), directly into neural cells. We have characterized these recombinant AAVs in several cell lines derived from the CNS. These recombinant AAVs effectively transduced all neural cell lines, although with different efficiencies. Transduction occurred in both proliferating and nonproliferating cells, but actively proliferating cell lines had approximately six times greater transduction efficiency than nonproliferating cells. Furthermore, these AAVs maintained long-term expression of GAD in an astrocytic cell line for at least seven passages. These recombinant AAVs are promising vehicles for investigating the potential therapeutic effects of GABA in animal models of epilepsy and neurodegenerative diseases. J. Neurosci. Res. 57:137–148, 1999. © 1999 Wiley-Liss, Inc.
Inverse Spatially Offset Raman Spectroscopy for Deep Noninvasive Probing of Turbid Media (2006)

A new type of highly sensitive spatially offset Raman spectroscopy (SORS) developed for deep noninvasive probing of stratified turbid media is described. The technique, termed inverse SORS, permits much greater depths to be interrogated than those accessible with the conventional SORS approach. This is achieved by enhancing the sensitivity of the technique through the elimination of spectral distortions inherent to the conventional SORS methodology. The method also permits the use of higher laser powers in applications where intensity limits exist, such as when probing human tissue in vivo. In addition, the new approach possesses a much higher degree of flexibility, enabling on-the-spot tailoring of experimental conditions such as the magnitude and number of spatial offsets to individual samples. The scheme uses a reverse SORS geometry whereby Raman light is collected through fibers at the center of the probe and laser radiation is delivered to the sample through a beam in the shape of a ring. The method is demonstrated on a layered powder sample and several practical examples of its uses, presented for the first time, are also given. Potential applications include disease diagnosis, noninvasive probing of pharmaceutical products and chemicals through packaging, probing of polymers, biofilms or paints, and homeland security screening.
The Cambridge University spoken document retrieval system (1999)

This paper describes the spoken document retrieval system that we have been developing and assesses its performance using automatic transcriptions of about 50 hours of broadcast news data. The recognition engine is based on the HTK broadcast news transcription system and the retrieval engine is based on the techniques developed at City University. The retrieval performance over a wide range of speech transcription error rates is presented and a number of recognition error metrics that more accurately reflect the impact of transcription errors on retrieval accuracy are defined and computed. The results demonstrate the importance of high accuracy automatic transcription. The final system is currently being evaluated on the 1998 TREC-7 spoken document retrieval task.
Ligand-Specific Antibodies to Insulin-Like Growth Factors Suppress Intestinal Polyp Formation in Apc +/− Mice (2010)

Insulin-like growth factors (IGF-I and IGF-II) play important roles in intestinal tumorigenesis. To investigate the effectiveness of IGF-targeting strategies, we conducted an in vivo study using anti-mouse neutralizing antibodies IGF-I (KM3168) and IGF-II (KM1468). Six- and 10-week-old Apc(+/-) mice were given KM3168 and/or KM1468 i.p. at two doses (0.01 or 0.1 microg/g weight) once or twice weekly for 4 weeks. To clarify the source of IGFs in vivo, we evaluated the expression levels of IGFs in the liver, normal small intestine, and polyps of the small intestine of Apc(+/-) mice. The phosphorylation status of IGF signal-related molecules was examined using immunostaining to understand the mechanism underlying the effects of IGF-neutralizing antibody. The plasma half-life was 168 for KM3168 and 85 hours for KM1468. In two lineages of Apc(+/-) mice (Apc(1309) and Apc(Min/+)), a low dose (0.01 microg/g weight) of KM3168 and KM1468 significantly reduced the number of polyps when given once and twice weekly, respectively. Combined administration of the effective dose of each antibody had an additive effect. The liver was the main source of IGF-I, whereas the polyps of the small intestine and normal small intestine were the main source of IGF-II. IGF-neutralizing antibodies decreased the phosphorylation of IGF type 1 receptor and inhibited the signal transduction of the Akt pathway. These results suggest that IGF-I and IGF-II play important roles in polyp formation in Apc(+/-) mice and that specific antibodies to IGF-I and IGF-II may be promising antitumor agents.
Role of low-density lipoprotein receptor related protein 1 (LRP1) in CCN2/connective tissue growth factor (CTGF) protein transport in chondrocytes (2012)

Low-density lipoprotein receptor-related protein 1 (LRP1) is known to be a receptor for signal transmission and endocytosis. We have previously reported that LRP1 regulates WNT-β-catenin and protein kinase C signaling in chondrocytes, represses the hypertrophy of chondrocytes during endochondral ossification and that LRP1 is colocalized with a ligand, CCN family member 2 (CCN2; also known as connective tissue growth factor, CTGF), which conducts endochondral ossification, in chondrocytes. However, the role of LRP1 in the endocytic transport of CCN2 in chondrocytes is not yet understood. In the present study, we investigated the interaction between LRP1 and CCN2 during endocytic trafficking. Small interfering RNA (siRNA)-mediated knockdown of LRP1 in chondrocytic HCS-2/8 cells showed that the amount of exogenous CCN2 binding and/or incorporation was decreased in the LRP1 downregulated cells. Importantly, we observed that CCN2 internalization in chondrocytes was dependent on clathrin, and internalizated CCN2 was colocalized with an early or recycling endosome marker. Transcytosis of CCN2 through HCS-2/8 cells was confirmed by performing experiments with a trans-well apparatus, and the amount of transcytosed CCN2 was decreased by an LRP1 antagonist. These findings rule out possible leakage and confirm the crucial involvement of LRP1 during experimental transcytosis. Moreover, under hypoxic conditions that mimic the cartilaginous microenvironment, the level of LRP1 and the amount of transcytosed CCN2 increased, and these increases were neutralized by treatment with the LRP1 antagonist. The distribution of LRP1 and its antagonist in the growth plate in vivo was consistent with that of CCN2 in this tissue, which is produced by and transported by LRP1 from the chondrocytes in the prehypertrophic layer. These findings suggest that LRP1 mediates the transcytosis of CCN2, which might be a crucial event that determines the distribution of CCN2 in cartilage.
VEGF145, a Secreted Vascular Endothelial Growth Factor Isoform That Binds to Extracellular Matrix (1997)

A vascular endothelial growth factor (VEGF) mRNA species containing exons 1-6 and 8 of the VEGF gene was found to be expressed as a major VEGF mRNA form in several cell lines derived from carcinomas of the female reproductive system. This mRNA is predicted to encode a VEGF form of 145 amino acids (VEGF145). Recombinant VEGF145 induced the proliferation of vascular endothelial cells and promoted angiogenesis in vivo. VEGF145 was compared with previously characterized VEGF species with respect to interaction with heparin-like molecules, cellular distribution, VEGF receptor recognition, and extracellular matrix (ECM) binding ability. VEGF145 shares with VEGF165 the ability to bind to the KDR/flk-1 receptor of endothelial cells. It also binds to heparin with an affinity similar to that of VEGF165. However, VEGF145 does not bind to two additional endothelial cell surface receptors that are recognized by VEGF165 but not by VEGF121. VEGF145 is secreted from producing cells as are VEGF121 and VEGF165. However, VEGF121 and VEGF165 do not bind to the ECM produced by corneal endothelial cells, whereas VEGF145 binds efficiently to this ECM. Basic fibroblast growth factor (bFGF)-depleted ECM containing bound VEGF145 induces proliferation of endothelial cells, indicating that the bound VEGF145 is active. The mechanism by which VEGF145 binds to the ECM differs from that of bFGF. Digestion of the ECM by heparinase inhibited the binding of bFGF to the ECM and released prebound bFGF, whereas the binding of VEGF145 was not affected by heparinase digestion. It therefore seems that VEGF145 possesses a unique combination of biological properties distinct from those of previously characterized VEGF species.
VideoSense (2007)

With Internet delivery of video content surging to an unprecedented level, online video advertising is becoming increasingly pervasive. In this paper, we present a novel advertising system for online video service called VideoSense, which automatically associates the most relevant video ads with online videos and seamlessly inserts the ads at the most appropriate positions within each individual video. Unlike most current video-oriented sites that only display a video ad at the beginning or the end of a video, VideoSense aims to embed more contextually relevant ads at less intrusive positions within the video stream. Given an online video, VideoSense is able to detect a set of candidate ad insertion points based on content discontinuity and attractiveness, select a list of relevant candidate ads ranked according to global textual relevance, and compute local visual-aural relevance between each pair of insertion points and ads. To support contextually relevant and less intrusive advertising, the ads are expected to be inserted at the positions with highest discontinuity and lowest attractiveness, while the overall global and local relevance is maximized. We formulate this task as a nonlinear 0-1 integer programming problem and embed these rules as constraints. The experiments have proved the effectiveness of VideoSense for online video advertising.
Role of the Conformational Rigidity in the Design of Biomimetic Antimicrobial Compounds (2010)

When structural flexibility is a plus: A link between structural flexibility of biomimetic antimicrobials and their ability to penetrate into the hydrophobic core and disrupt the integrity of bacterial lipid model membranes has been established using liquid surface X-ray scattering techniques. Results indicate that the modes of interaction of flexible and conformationally restrained antimicrobials with the bacterial membranes are different (see picture).
Recent progress in sodium channel modulators for pain (2014)

Voltage-gated sodium channels (Navs) are an important family of transmembrane ion channel proteins and Nav drug discovery is an exciting field. Pharmaceutical investment in Navs for pain therapeutics has expanded exponentially due to genetic data such as SCN10A mutations and an improved ability to establish an effective screen sequence for example IonWorks Barracuda®, Synchropatch® and Qube®. Moreover, emerging clinical data (AZD-3161, XEN402, CNV1014802, PF-05089771, PF-04531083) combined with recent breakthroughs in Nav structural biology pave the way for a future of fruitful prospective Nav drug discovery.
Oxolanosterol oximes: dual-action inhibitors of cholesterol biosynthesis. (1994)

A series of oxolanosterol oximes and oxime ethers have been prepared as potential dual-action inhibitors of cholesterol biosynthesis. The synthesis of these oximes along with the evaluation of their ability to inhibit lanosterol 14 alpha-methyl demethylase (P450DM) and to suppress 3-hydroxy-3-methylglutaryl coenzyme. A reductase (HMGR) activity is presented. 3 beta-Hydroxylanost-7-en-15-one 15-oxime XIX was found to be an effective inhibitor of P450DM in rat liver microsomal preparations. In [14C]acetate incorporation studies using Chinese hamster ovary (CHO) cells, compound XIX was found to cause a dramatic reduction in the incorporation of acetate into C27 sterols with a concomitant increase in radiolabeled C30 sterols which is consistent with the inhibition of P450DM. In addition, 15-oxime XIX was shown to suppress HMGR activity in both wild-type CHO and P450DM-deficient (AR45) cells, indicating that suppression of HMGR is independent of any effects of this oxime on P450DM. In both cell lines, parallel declines in HMGR activity and HMGR protein levels were observed suggesting that compound XIX suppresses HMGR activity by regulation of gene expression. These results demonstrate that, as predicted, 15-oxime XIX is indeed a dual-action inhibitor of cholesterol biosynthesis which causes both the inhibition of P450DM and a reduction in HMGR activity.
Role for the Adenovirus IVa2 Protein in Packaging of Viral DNA (2001)

Although it has been demonstrated that the adenovirus IVa2 protein binds to the packaging domains on the viral chromosome and interacts with the viral L1 52/55-kDa protein, which is required for viral DNA packaging, there has been no direct evidence demonstrating that the IVa2 protein is involved in DNA packaging. To understand in greater detail the DNA packaging mechanisms of adenovirus, we have asked whether DNA packaging is serotype or subgroup specific. We found that Ad7 (subgroup B), Ad12 (subgroup A), and Ad17 (subgroup D) cannot complement the defect of an Ad5 (subgroup C) mutant, pm8001, which does not package its DNA due to a mutation in the L1 52/55-kDa gene. This indicates that the DNA packaging systems of different serotypes cannot interact productively with Ad5 DNA. Based on this, a chimeric virus containing the Ad7 genome except for the inverted terminal repeats and packaging sequence from Ad5 was constructed. This chimeric virus replicates its DNA and synthesizes Ad7 proteins, but it cannot package its DNA in 293 cells or 293 cells expressing the Ad5 L1 52/55-kDa protein. However, this chimeric virus packages its DNA in 293 cells expressing the Ad5 IVa2 protein. These results indicate that the IVa2 protein plays a role in viral DNA packaging and that its function is serotype specific. Since this chimeric virus cannot package its own DNA, but produces all the components for packaging Ad7 DNA, it may be a more suitable helper virus for the growth of Ad7 gutted vectors for gene transfer.
Aleutian mink disease parvovirus infection of mink peritoneal macrophages and human macrophage cell lines (1993)

Aleutian mink disease parvovirus (ADV) mRNAs are found in macrophages in lymph nodes and peritoneal exudate cells from ADV-infected mink. Therefore, we developed an in vitro infection system for ADV by using primary cultures of mink macrophages or macrophage cell lines. In peritoneal macrophage cultures from adult mink, virulent ADV-Utah I strain showed nuclear expression of viral antigens with fluorescein isothiocyanate-labeled ADV-infected mink serum, but delineation of specific viral proteins could not be confirmed by immunoblot analysis. Amplification of ADV DNA and production of replicative-form DNA were observed in mink macrophages by Southern blot analysis; however, virus could not be serially propagated. The human macrophage cell line U937 exhibited clear nuclear expression of viral antigens after infection with ADV-Utah I but not with tissue culture-adapted ADV-G. In U937 cells, ADV-Utah I produced mRNA, replicative-form DNA, virion DNA, and structural and nonstructural proteins; however, virus could not be serially passaged nor could [3H]thymidine-labeled virions be observed by density gradient analysis. These findings indicated that ADV-Utah I infection in U937 cells was not fully permissive and that there is another restricted step between gene amplification and/or viral protein expression and production of infectious virions. Treatment with the macrophage activator phorbol 12-myristate 13-acetate after adsorption of virus reduced the frequency of ADV-positive U937 cells but clearly increased that of human macrophage line THP-1 cells. These results suggested that ADV replication may depend on conditions influenced by the differentiation state of macrophages. U937 cells may be useful as an in vitro model system for the analysis of the immune disorder caused by ADV infection of macrophages.
Isoform Specific Interactions of Troponin I and Troponin C Determine pH Sensitivity of Myofibrillar Ca2+ Activation (1994)

We investigated whether differences in isoforms of troponin I (TnI) and troponin C (TnC) can account for the greater inhibition of Ca(2+)-dependent MgATPase activity by acidic pH in cardiac (c) than in fast skeletal (fs) myofilaments. We studied fast skeletal myofibrils from which whole Tn was extracted by displacement with excess fsTnT (the tropomyosin binding subunit of Tn) followed by reconstitution with TnC-TnI. Exchange of fsTnI with cTnI did not alter the effect of a drop in pH from 7.0 to 6.5 on the relation between pCa (-log[Ca2+]) and MgATPase activity of fast skeletal myofibrils. Exchange of fsTnC with cTnC did, however, induce an increase in the effect of this same pH change on Ca2+ activation. Yet, the pH sensitivity of Ca2+ activation of fast skeletal myofibrils containing cTnC was not as great as that of native cardiac myofibrils. However, when both fsTnC and fsTnI of fast skeletal myofibrils were replaced by cTnC-cTnI, there was a pH-induced shift in Ca2+ sensitivity similar to that of cardiac myofibrils. In studies using fluorescent probes, both pure fsTnC and pure cTnC showed decreased Ca2+ binding as pH was lowered. This decrease was potentiated in the fsTnC-fsTnI and cTnC-cTnI complexes. However, the effect of acidic pH was the same in fsTnC and the hybrid complex, fsTnC-cTnI, and in cTnC and the hybrid complex, cTnC-fsTnI. Thus, isoform specific interactions between TnI and TnC appear important in the differential response of skeletal and cardiac myofilaments to acidosis.
Basis picking for matching pursuits image coding (2005)

The novel 'Basis Picking' algorithm is applied to select dictionaries of 1D basis functions for coding of image data by Matching Pursuits. For both motion compensated residual images and normal still images, bases are picked with a hybrid Wavelet/Matching Pursuits image codec using 1D scanning. By successively adding bases one at a time from a set of 1289 candidates according to their ranked signal to residual ratio (SRR) performance, effective codebooks are constructed. These outperform traditional selection by ranked frequency of use from the same candidate bases over a range of compressions of both residuals and still images. This holds for both the training sets used for picking and other test images. Picked bases are also capable of good quality compression of still images, which was not previously thought to be feasible by matching pursuits.