gebhart/patrepeval huggingface dataset:
Temperature-Dependent Isotope Effects in Soybean Lipoxygenase-1:  Correlating Hydrogen Tunneling with Protein Dynamics (2002)

The hydrogen-atom transfer in soybean lipoxygenase-1 (SLO) exhibits a large kinetic isotope effect on k(cat) (KIE = 81) near room temperature and a very weak temperature dependence (E(act) = 2.1 kcal/mol). These properties are consistent with H small middle dot transfer that occurs entirely by a tunneling event. Mutants of SLO were prepared, and the temperature dependence of the KIE was measured, to test for alterations in the tunneling behavior. All mutants studied exhibit KIEs of similar, large magnitude at 30 degrees C, despite an up to 3 orders of magnitude change in k(cat). E(act) for two of the mutants (Leu(754) --> Ala, Leu(546) --> Ala) is larger than for wild-type (WT), and the KIE becomes slightly more temperature dependent. In contrast, Ile(553) --> Ala exhibits k(cat) and E(act) parameters similar to wild-type soybean lipoxygenase-1 (WT-SLO) for protiated substrate; however, the KIE is markedly temperature dependent. The behavior of the former two mutants could reflect increased reorganization energies (lambda), but the behavior of the latter mutant is inconsistent with this description. We have invoked a full H* tunneling model (Kuznetsov, A. M.; Ulstrup, J. Can. J. Chem. 1999, 77, 1085-1096) to explain the temperature dependence of the KIE, which is indicative of the extent to which distance sampling (gating) modulates hydrogen transfer. WT-SLO exhibits a very small E(act) and a nearly temperature-independent KIE, which was modeled as arising from a compressed hydrogen transfer distance with little modulation of the hydrogen transfer distance. The observations on the Leu(754) --> Ala and Leu(546) --> Ala mutants were modeled as arising from a slightly less compressed active site with greater modulation of the hydrogen transfer distance by environmental dynamics. Finally, the observed behavior of the Ile(553) --> Ala mutant indicates a relaxed active site with extensive involvement of gating to facilitate hydrogen transfer. We conclude that WT-SLO has an active site structure that is well organized to support hydrogen tunneling and that mutations perturb structural elements that support hydrogen tunneling. Modest alterations in active site residues increase lambda and/or increase the hydrogen transfer distance, thereby affecting the probability that tunneling can occur. These studies allow the detection and characterization of a protein-gating mode in catalysis.
Quantification of circulating endothelial and progenitor cells: comparison of quantitative PCR and four-channel flow cytometry (2008)

QPCR is more sensitive, but less specific than 4-channel flow cytometry for the detection of CEC/CEP cell types. However, both methods failed to reliably detect an increase of CEC/CEP in tumor patients. Thus, more specific CEC/CEP markers are needed to validate and improve the detection of these rare cell types by PCR-based assays.
VoiceLoop: Voice Fitting and Synthesis via a Phonological Loop (2017)

We present a new neural text to speech (TTS) method that is able to transform text to speech in voices that are sampled in the wild. Unlike other systems, our solution is able to deal with unconstrained voice samples and without requiring aligned phonemes or linguistic features. The network architecture is simpler than those in the existing literature and is based on a novel shifting buffer working memory. The same buffer is used for estimating the attention, computing the output audio, and for updating the buffer itself. The input sentence is encoded using a context-free lookup table that contains one entry per character or phoneme. The speakers are similarly represented by a short vector that can also be fitted to new identities, even with only a few samples. Variability in the generated speech is achieved by priming the buffer prior to generating the audio. Experimental results on several datasets demonstrate convincing capabilities, making TTS accessible to a wider range of applications. In order to promote reproducibility, we release our source code and models.
Profiling Environmental Chemicals for Activity in the Antioxidant Response Element Signaling Pathway Using a High Throughput Screening Approach (2012)

Our results support the robustness of using two different cell-based approaches for identifying compounds that induce ARE signaling. Together, these methods are useful for prioritizing chemicals for further in-depth mechanism-based toxicity testing.
CREB-2, a Cellular CRE-Dependent Transcription Repressor, Functions in Association with Tax as an Activator of the Human T-Cell Leukemia Virus Type 1 Promoter (1998)

The Tax protein of the human T-cell leukemia virus type 1 (HTLV-1) has been implicated in human T-cell immortalization. The primary function of Tax is to transcriptionally activate the HTLV-1 promoter, but Tax is also known to stimulate expression of cellular genes. It has been reported to associate with several transcription factors, as well as proteins not involved in transcription. To better characterize potential cellular targets of Tax present in infected cells, a Saccharomyces cerevisiae two-hybrid screening was performed with a cDNA library constructed from the HTLV-1-infected MT2 cell line. From this study, we found 158 positive clones representing seven different cDNAs. We focused our attention on the cDNA encoding the transcription factor CREB-2. CREB-2 is an unconventional member of the ATF/CREB family in that it lacks a protein kinase A (PKA) phosphorylation site and has been reported to negatively regulate transcription from the cyclic AMP response element of the human enkephalin promoter. In this study, we demonstrate that CREB-2 cooperates with Tax to enhance viral transcription and that its basic-leucine zipper C-terminal domain is required for both in vitro and in vivo interactions with Tax. Our results confirm that the activation of the HTLV-1 promoter through Tax and factors of the ATF/CREB family is PKA independent.
A marker for neoplastic progression of human melanocytes is a cell surface ectopeptidase. (1993)

Adenosine deaminase binding protein (ADAbp) is a cell surface glycoprotein that is expressed by normal melanocytes but not by melanoma, the malignant counterpart. ADAbp is specifically downregulated during malignant transformation of melanocytes. Recently, we have developed a system that progressively transforms melanocytes in vitro in defined steps. Transduction with v-Ha-ras oncogene followed by long-term culture leads to a cell phenotype and genotype that specifically mimics human melanoma. Loss of ADAbp expression occurred concomitantly with the emergence of growth factor independence and appearance of specific chromosomal abnormalities. The cellular function of ADAbp has not been defined. To characterize ADAbp, the mature 110-kD form was purified from human kidney. Five tryptic peptides from purified human ADAbp revealed 100% homology to a serine protease, human dipeptidyl peptidase IV (DPP IV), also known as CD26. DPP IV activity was detected in lysates from human melanocytes and renal carcinoma cells but not melanoma cells, and DPP IV activity could be specifically isolated from melanocytes by binding to ADA or to S27 monoclonal antibody against ADAbp. These findings show that ADAbp is a cell surface ectopeptidase that is tightly regulated during neoplastic transformation of melanocytes.
Initialisation for Visual Tracking in Urban Environments (2007)

Outdoor augmented reality systems often rely on GPS to cover large environments. Visual tracking approaches can provide more accurate location estimates but typically require a manual initialisation procedure. This paper describes the combination of both techniques to create an accurate localisation system that does not require any additional input for (re-)initialisation. The 2D GPS position together with average user height is used as an initial estimate for the visual tracking. The large gap in available GPS accuracy versus required accuracy for initialisation is overcome through a search procedure that tries to minimise search time by improving the likelihood of finding the correct estimate early. Re-initialisation of the visual tracking system after catastrophic failures is further improved by modelling the GPS error with a Gaussian process to provide a better estimate of the current location, thereby decreasing search time.
RTP Payload Format for the 1998 Version of ITU-T Rec. H.263 Video (H.263+) (1998)

This document specifies an RTP payload header format applicable to the
transmission of video streams generated based on the 1998 version of
ITU-T Recommendation H.263. [STANDARDS-TRACK]
On the use of high order derivatives for high performance alphabet recognition (2002)

In this paper I propose new feature vectors for automatic speech recognition. They are based on Mel-cepstrum vectors augmented by derivatives. In the literature, many systems using just two derivatives—delta and delta delta—are described. But none explores the use of higher order derivatives. This paper presents alphabet recognition results on the Isolet database, using feature vectors containing up to the fifth-order derivatives. For this paper I did not use the HTK toolkit proposed by Cambridge University. I developed my own HMM system. I show that with vectors incorporating all the derivatives up to the fifth one, 97.54% mean recognition accuracy was achieved, result which is comparable to the best published one on this database (97.6%), if the recognition accuracy confidence interval concerning this task (approximately 0.3%) is taken into account. It is important to note that this result was obtained without segmenting the speech files by an endpoint detection algorithm. This is an unfavourable experimental condition compared to previous published research works. As a consequence, my system is one of the most powerful systems ever implemented for alphabet recognition.
Calidad universitaria y la transición al empleo de los graduados universitarios (2001)

Aportacion al simposio calidad de la ensenanza y el aprendizaje en educacion superior. Congreso Nacional de Modelos de Investigacion Educativa (10o. 2001. La Coruna)
A low power VLSI architecture for mesh-based video motion tracking (2002)

This paper proposes a low-power very large-scale integration (VLSI) architecture for motion tracking. It uses a hierarchical adaptive structured mesh that generates a content-based video representation. The proposed mesh is a coarse-to-fine hierarchical two-dimensional mesh that is formed by recursive triangulation of the initial coarse mesh geometry. The structured mesh offers a significant reduction in the number of bits that describe the mesh topology. The motion of the mesh nodes represents the deformation of the video object. The architecture consists of motion estimation and motion compensation units. The motion estimation architecture generates a progressive mesh code and the motion vectors of the mesh nodes. It reduces the power consumption, uses a simpler approach for mesh construction, approximates the mesh nodes motion vector by using the three step search algorithm and uses a parallel motion estimation core to evaluate the mesh nodes motion vectors. Moreover, it maximizes the lifetime of the internal buffers. The motion compensation architecture uses a multiplication-free algorithm for affine transformation, which significantly reduces the complexity of the motion compensation architecture. Moreover, using pipelined affine units contributes to the power savings. The video motion compensation architecture processes a reference frame, mesh nodes and motion vectors to predict a video frame. It implements parallel threads in which each thread implements a pipelined chain of scalable affine units. This motion compensation algorithm allows the use of one simple warping unit to map a hierarchical structure. The affine unit warps the texture of a patch at any level of hierarchical mesh independently. The processor uses a memory serialization unit, which interfaces the memory to the parallel units. The architecture has been prototyped using top-down low-power design methodology. The performance analysis shows that this processor can be used in online object-based video applications such as in MPEG and VRML.
Alteration of a Single Amino Acid in Peroxisome Proliferator-Activated Receptor- (PPAR ) Generates a PPAR Phenotype (2000)

Three pharmacologically important nuclear receptors, the peroxisome proliferator-activated receptors (PPARs α,γ , and δ), mediate key transcriptional responses involved in lipid homeostasis. The PPARα and γ subtypes are well conserved from Xenopus to man, but the β/δ subtypes display substantial species variations in both structure and ligand activation profiles. Characterization of the avian cognates revealed a close relationship between chick (c) α and γ subtypes to their mammalian counterparts, whereas the third chicken subtype was intermediate to Xenopus (x) β and mammalian δ, establishing that β and δ are orthologs. Like xPPARβ, cPPARβ responded efficiently to hypolipidemic compounds that fail to activate the human counterpart. This provided the opportunity to address the pharmacological problem as to how drug selectivity is achieved and the more global evolutionary question as to the minimal changes needed to generate a new class of receptor. X-ray crystallography and chimeric analyses combined with...
Genomic Organization and Molecular Analysis of Virulent Bacteriophage 2972 Infecting an Exopolysaccharide-Producing Streptococcus thermophilus Strain (2005)

The Streptococcus thermophilus virulent pac-type phage 2972 was isolated from a yogurt made in France in 1999. It is a representative of several phages that have emerged with the industrial use of the exopolysaccharide-producing S. thermophilus strain RD534. The genome of phage 2972 has 34,704 bp with an overall G+C content of 40.15%, making it the shortest S. thermophilus phage genome analyzed so far. Forty-four open reading frames (ORFs) encoding putative proteins of 40 or more amino acids were identified, and bioinformatic analyses led to the assignment of putative functions to 23 ORFs. Comparative genomic analysis of phage 2972 with the six other sequenced S. thermophilus phage genomes confirmed that the replication module is conserved and that cos- and pac-type phages have distinct structural and packaging genes. Two group I introns were identified in the genome of 2972. They interrupted the genes coding for the putative endolysin and the terminase large subunit. Phage mRNA splicing was demonstrated for both introns, and the secondary structures were predicted. Eight structural proteins were also identified by N-terminal sequencing and/or matrix-assisted laser desorption ionization-time-of-flight mass spectrometry. Detailed analysis of the putative minor tail proteins ORF19 and ORF21 as well as the putative receptor-binding protein ORF20 showed the following interesting features: (i) ORF19 is a hybrid protein, because it displays significant identity with both pac- and cos-type phages; (ii) ORF20 is unique; and (iii) a protein similar to ORF21 of 2972 was also found in the structure of the cos-type phage DT1, indicating that this structural protein is present in both S. thermophilus phage groups. The implications of these findings for phage classification are discussed.
Dynamic Deviation Reduction-Based Volterra Behavioral Modeling of RF Power Amplifiers (2006)

A new representation of the Volterra series is proposed, which is derived from a previously introduced modified Volterra series, but adapted to the discrete time domain and reformulated in a novel way. Based on this representation, an efficient model-pruning approach, called dynamic deviation reduction, is introduced to simplify the structure of Volterra-series-based RF power amplifier behavioral models aimed at significantly reducing the complexity of the model, but without incurring loss of model fidelity. Both static nonlinearities and different orders of dynamic behavior can be separately identified and the proposed representation retains the important property of linearity with respect to series coefficients. This model can, therefore, be easily extracted directly from the measured time domain of input and output samples of an amplifier by employing simple linear system identification algorithms. A systematic mathematical derivation is presented, together with validation of the proposed method using both computer simulation and experiment
The polymicrobial hypothesis of bacterial vaginosis causation: a reassessment (2008)

The cause of bacterial vaginosis remains controversial. The two leading hypotheses are that Gardnerella vaginalis is the specific aetiologic agent versus the polymicrobial hypothesis that G. vaginalis acts in concert with other bacteria, principally anaerobes, to produce the disease. Here we reassess the prevailing polymicrobial hypothesis, finding it conceptually problematical. No host initiating factors as postulated have been identified, nor is there conclusive evidence that G. vaginalis lacks diagnostic specificity for the disease. The polymicrobial hypothesis, presupposing a unique disruption of vaginal microecology, is inconsistent with the epidemiological profile of the syndrome, which is that of a sexually transmitted disease. The epidemiological and clinical similarities between bacterial vaginosis and trichomoniasis suggest a similar pathogenetic process; i.e., primary causation by a specific agent, with secondary anaerobic activation and resultant amine production.
Imminent Oocyte Exhaustion and Reduced Follicular Recruitment Mark the Transition to Acyclicity in Aging C57BL/6J Mice (1983)

Quantitative cytological analyses of aging C57BL/6J mouse ovaries revealed that the populations of primordial and growing follicles were nearly exhausted by 13-14 months, the average age of ovulatory failure. Anovulatory animals of this age had, on the average, half the follicle number of their counterparts which were still ovulating. This result suggests that follicular depletion is a factor which contributes to the loss of ovarian cyclicity during aging. However, the considerable overlap of follicle number between the two groups suggests that other, possibly extraovarian, factors also influence the loss of ovulatory function. Although the numbers of follicles recruited for growth was much lower in ovaries from old cycling animals, the number of ova shed cyclically was generally within the range of younger individuals. The observed reduction in incidence of morphological atresia among medium-sized follicles may explain how ovulatory constancy is maintained virtually throughout the cyclical life of the ovary.
Microfluidic Enrichment of Mouse Epidermal Stem Cells and Validation of Stem Cell Proliferation In Vitro (2013)

Bulge stem cells reside in the lowest permanent portion of hair follicles and are responsible for the renewal of these follicles along with the repair of the epidermis during wound healing. These cells are identified by surface expression of CD34 and the α6-integrin. When CD34 and α6 double-positive cells are isolated and implanted into murine skin, they give rise to epidermis and hair follicle structures. The current gold standard for isolation of these stem cells is fluorescence-activated cell sorting (FACS) based on cell surface markers. Here, we describe an alternative method for CD34 bulge stem cell isolation: a microfluidic platform that captures stem cells based on cell surface markers. This method is relatively fast, requiring 30 min of time from direct introduction of murine skin tissue digestate into a two-stage microfluidic device to one-pass elution of CD34(+) enriched cells with a purity of 55.8% ± 5.1%. The recovered cells remain viable and formed colonies with characteristic morphologies. When grown in culture, enriched cells contain a larger α6(+) population than un-enriched cells.
Multiple Bcl-2 family members demonstrate selective dimerizations with Bax. (1995)

A family of Bcl-2-related proteins regulates cell death and shares highly conserved BH1 and BH2 domains. BH1 and BH2 domains of Bcl-2 were required for it to heterodimerize with Bax and to repress apoptosis. A yeast two-hybrid assay accurately reproduced this interaction and defined a selectivity and hierarchy of further dimerizations. Bax also heterodimerizes with Bcl-xL, Mcl-1, and A1. A Gly-159-->Ala substitution in BH1 of Bcl-xL disrupted its heterodimerization with Bax and abrogated its inhibition of apoptosis in mammalian cells. This suggests that the susceptibility to apoptosis is determined by multiple competing dimerizations in which Bax may be a common partner.
Hepatocyte Growth Factor Receptor Is a Coreceptor for Adeno-Associated Virus Type 2 Infection (2004)

After the first attachment of virus to the cell surface through a primary receptor, efficient entry of virus requires the presence of a coreceptor. For adeno-associated virus type 2 (AAV2) infection, heparan sulfate proteoglycan is supposed as the primary receptor, and alphavbeta5 integrin and FGFR1 are reported to act as coreceptors. In this study, we were able to demonstrate that hepatocyte growth factor receptor, c-Met, is also a coreceptor for AAV2 infection. AAV2-mediated transgene analyses revealed that c-Met expression significantly up-regulated transgene expression without increasing AAV2 cell binding. Moreover, a viral overlay assay elucidated the physical interaction between AAV2 and the beta subunit of c-Met. These data suggest that c-Met plays the role of coreceptor for AAV2 infection by facilitating AAV2 internalization into the cytoplasm.
Prevention of endotoxin shock by an antibody against leukocyte integrin β2through inhibiting production and action of TNF (1995)

Septic shock remains a serious disorder associated with high mortality. Accumulating evidence indicates that TNF is a major and essential mediator of endotoxin shock. We report here that administration of an antibody against CD18 dramatically reduced endotoxin-induced shock in rabbits as revealed by prevention of severe hypotension, metabolic acidosis and a pathological change suggestive of disseminated intravascular coagulation with concomitant inhibition of elevation of plasma TNF activity. The anti-CD18 antibody also inhibited the hypotension induced by administering recombinant TNF. Furthermore, an antibody against a ligand for CD18 complexes, intercellular adhesion molecule-1, also prevented TNF-induced shock as well as endotoxin shock in rabbits. These observations suggest that adhesion of leukocytes to endothelium may be of primary importance in the action of TNF as well as in the production of TNF in vivo and that the antibody against adhesion molecules could be of therapeutic benefit in life-threatening septic shock in humans.
Expression of bacteriophage T7 RNA polymerase in avian and mammalian cells by a recombinant fowlpox virus (1996)

The bacteriophage T7 RNA polymerase gene was integrated into the fowlpox virus genome under the control of the vaccinia virus early/late promoter, P7.5. The recombinant fowlpox virus, fpEFLT7pol, stably expressed T7 RNA polymerase in avian and mammalian cells, allowing transient expression of transfected genes under the control of the T7 promoter. The recombinant fowlpox virus expressing T7 RNA polymerase offers an alternative to the widely used vaccinia virus vTF7-3, or the recently developed modified vaccinia virus Ankara (MVA) T7 RNA polymerase recombinant, a highly attenuated strain with restricted host-range. Recombinant fowlpox viruses have the advantage that as no infectious virus are produced from mammalian cells they do not have to be used under stringent microbiological safety conditions.