gebhart/patrepeval huggingface dataset:
Activation of the human PAX6 gene through the exon 1 enhancer by transcription factors SEF and Sp1 (2001)

PAX6 is a transcription factor that plays a major role in ocular morphogenesis. PAX6 is expressed in the eye, central nervous system and pancreas. Two alternative promoters, P0 and P1, which are differentially regulated during development, drive PAX6 transcription. We identified a 57 bp cis-regulatory element in exon 1 of the human PAX6 gene exon 1 enhancer (EIE). EIE enhances P1-driven PAX6 expression. Three regions in E1E (E1E-1, E1E-2 and E1E-3) have sequence similarities with binding sites of transcription factors ARP-1, Isl-1 and SEF, respectively. As shown by electrophoretic mobility shift assays, E1E-3, but not E1E-1 or E1E-2, bound to proteins in nuclear extracts of human glioma cells and transcription factor SEF bound to E1E-3. As shown by transient transfection experiments, deletion or site-specific mutations in E1E-3 dramatically decreased P1 promoter activity. Mutations in E1E-2, however, did not affect function of the P1 promoter. Co-transfection of SEF and PAX6 promoter-reporter constructs showed that SEF up-regulates PAX6 gene expression through the P1 promoter. Two Sp1 sites in the E1E region were also shown to be important by transient co-transfection assays. Data from immunoprecipitation and transient transfection assays demonstrated that SEF and Sp1 interacted in vitro and may act together in vivo to regulate PAX6 expression.
Probable new species of Desulfovibrio isolated from a pyogenic liver abscess (1996)

A fastidious, slowly growing, spiral gram-negative bacterium was isolated from the liver abscess of an 82-year-old man with a 3-week history of febrile illness. The organism was an obligate anaerobe that grew at 37 and 42 degrees C but not at 25 degrees C. Its vibrioid or spiral morphology on Gram staining, rapid progressive motility, electron micrograph features, and biochemical tests were all consistent with the organism belonging to the genus Desulfovibrio. 16S rRNA gene sequencing of this organism demonstrated a 97% similarity to Desulfovibrio desulfuricans with 45 nucleotide differences, suggesting that it is a new species of Desulfovibrio.
Expression and Characterization of a Murine Enzyme Able to Cleave β-Carotene (2001)

Because animals are not able to synthesize retinoids de novo, ultimately they must derive them from dietary provitamin A carotenoids through a process known as carotene cleavage. The enzyme responsible for catalyzing carotene cleavage (beta-carotene 15,15'-dioxygenase) has been characterized primarily in rat intestinal scrapings. Using a recently reported cDNA sequence for a carotene cleavage enzyme from Drosophila, we identified a cDNA encoding a mouse homolog of this enzyme. When the cDNA was expressed in either Escherichia coli or Chinese hamster ovary cells, expression conferred upon bacterial and Chinese hamster ovary cell homogenates the ability to cleave beta-carotene to retinal. Several lines of evidence obtained upon kinetic analyses of the recombinant enzyme suggested that carotene cleavage enzyme interacts with other proteins present within cell or tissue homogenates. This was confirmed by pull-down experiments upon incubation of recombinant enzyme with tissue 12,000 x g supernatants. Matrix-assisted laser desorption ionization-mass spectrometry analysis of pulled-down proteins indicates that an atypical testis-specific isoform of lactate dehydrogenase associates with recombinant carotene cleavage enzyme. mRNA transcripts for the carotene cleavage enzyme were detected by reverse transcription-polymerase chain reaction in mouse testes, liver, kidney, and intestine. In situ hybridization studies demonstrated that carotene cleavage enzyme is expressed prominently in maternal tissue surrounding the embryo but not in embryonic tissues at 7.5 and 8.5 days postcoitus. This work offers new insights for understanding the biochemistry of carotene cleavage to retinoids.
Role of the transcriptional activator AppY in regulation of the cyx appA operon of Escherichia coli by anaerobiosis, phosphate starvation, and growth phase (1994)

Transcriptional lacZ fusions have been used to analyze the regulation of the appA operon of Escherichia coli. The appA operon contains the genes cyxA and cyxB, coding for the putative third cytochrome oxidase, and appA, encoding acid phosphatase. The analysis showed that the cyxAB and the appA genes are cotranscribed from a potentially strong promoter, Pcyx, located immediately upstream of cyxA and that the operon in addition contains an internal promoter, PappA, contributing significantly to the transcription of the appA gene. The two promoters were both induced by starvation for Pi and by entry into stationary phase. The cyx promoter was in addition found to be activated by anaerobic growth conditions. The product of the previously identified appY gene, which when present on a high-copy-number plasmid stimulates synthesis of acid phosphatase, was shown to activate the cyx promoter. An insertion mutation in the appY gene was constructed in vitro and recombined into the chromosome. The appY mutation eliminated induction of the cyx promoter by anaerobiosis and severely reduced induction of this promoter by phosphate starvation and upon entry into stationary phase but had no effect on induction of the appA promoter. The appY mutation had no effect on survival in stationary phase, nor did it have any effect on growth rate or yield under aerobic or anaerobic conditions. The possibility that AppY is a third global regulator of energy metabolism genes is discussed.
Phase II, Multicenter, Uncontrolled Trial of Single-agent Capecitabine in Patients With Non-clear Cell Metastatic Renal Cell Carcinoma (2011)

Capecitabine has clinical activity in MRCC patients who have non-clear cell histology and a good or intermediate prognosis. Additional prospective randomized trial comparing capecitabine with placebo is required.
The Hemagglutinin A Stem Antibody MEDI8852 Prevents and Controls Disease and Limits Transmission of Pandemic Influenza Viruses (2017)

MEDI8852, alone or with oseltamivir, shows promise for prophylaxis or therapy of group I and II IAVs with pandemic potential. Additionally, MEDI8852 blocked influenza transmission in ferrets, a unique finding among influenza-specific mAbs.
SiGeC: Band gaps, band offsets, optical properties, and potential applications (1998)

Studying the structural and photoluminescence properties of pseudomorphic Si1−yCy and Si1−x−yGexCy multiple quantum well (QW) structures on (001) Si substrates offer a quantitative characterization of the band gap and band offset shifts caused by C alloying for y&lt;3%. The main features of Si1−yCy alloys, which are a reduced lattice constant and a strong lowering of the conduction band energy, promise that C may serve as a counterpart to Ge in Si heteroepitaxy. The photoluminescent properties of Si1−yCy and SiGeC QWs are comparable to SiGe. Novel pseudomorphic Si1−yCy/SiGe coupled QW structures and Si1−yCy/Ge quantum dot structures result in a strong enhancement of the photoluminescent efficiency. The ternary SiGeC material system offers a higher degree of freedom in strain and band edge engineering of structures. We focus on our recent results on Si1−yCy and SiGeC QW layers embedded in Si concerning the growth by solid-source molecular beam epitaxy, structural properties, thermal stability, optical properties, and band offsets. The prospects of SiGeC alloys for realization of optoelectronic structures are discussed. First characteristics from 0.75 μm p-channel modulation-doped field-effect transistor devices containing an active SiGeC layer demonstrate good electrical properties.
Unprecedented Immunosuppressive Polyketides from <i>Daldinia eschscholzii</i>, a Mantis‐Associated Fungus (2008)

Heilkräftige Darmbewohner: Die Naturstoffe Dalesconol A (siehe Struktur rechts) und B wurden im Pilz Daldinia eschscholzii (Bild in der Mitte) gefunden, der aus dem Darm der Gottesanbeterin isoliert worden war. Ihre neuartigen Strukturen und biologischen Eigenschaften machen die Dalesconole zu vielversprechenden Leitverbindungen für die Entwicklung von Immunsuppressiva. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2008/z801284_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Generalization of a Result of Borwein and Ditor (1989)

D
An accurate model for power DMOSFETs including interelectrode capacitances (1991)

A SPICE-compatible circuit model for power MOSFETs is presented. It is based on device physics and uses a subcircuit representation. The interelectrode capacitances are modeled accurately as nonlinear functions of the applied biases. Various second-order effects relating to the gate capacitance model are discussed, and strategies are presented to include them in the model. The model parameters can be obtained from device measurements. The model is verified by comparing measured and simulated waveforms from a gate charge test circuit.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Low bit-rate video compression with neural networks and temporal subsampling (1996)

In this paper we describe a novel neural network technique for video compression, using a "point-process" type neural network model we have developed which is closer to biophysical reality and is mathematically much more tractable than standard models. Our algorithm uses an adaptive approach based upon the users' desired video quality Q, and achieves compression ratios of up to 500:1 for moving gray-scale images, based on a combination of motion detection, compression, and temporal subsampling of frames. This leads to a compression ratio of over 1000:1 for full-color video sequences with the addition of the standard 4:1:1 spatial subsampling ratios in the chrominance images. The signal-to-noise ratio ranges from 29 dB to over 34 dB. Compression is performed using a combination of motion detection, neural networks, and temporal subsampling of frames. A set of neural networks is used to adaptively select the desired compression of each picture block as a function of the reconstruction quality. The motion detection process separates out regions of the frame which need to be retransmitted. Temporal subsampling of frames, along with reconstruction techniques, lead to the high compression ratios.
Theoretical stability analysis of single-mode operation in uncontrolled mode-selection semiconductor lasers (1997)

An uncontrolled mode-selection laser is a laser containing an intracavity filter under which the cavity mode alignment is uncontrolled. We present a theoretical stability analysis of the single-mode operation of uncontrolled mode-selection semiconductor lasers. We find that to maximize the stability the cavity length and intracavity filter bandwidth must be minimized, and a specific, nonzero, linewidth enhancement parameter must be chosen. For a given cavity mode spacing to filter bandwidth ratio, a shorter cavity is more stable.
Fabrication of 3D InGaN/GaN structures providing semipolar GaN planes for efficient green light emission (2009)

Abstract A fabrication method for the formation of 3D GaN structures with reduced piezoelectric field is presented. Via optimized selective epitaxy the surface is just composed of hexagonally patterned semipolar {1 $ \bar 1 $ 01} or {11 $ \bar 2 $ 2} planes. GaN growth with less NH 3 at a higher growth speed, a doubled effective area and good light outcoupling properties compared to c‐plane growth are additional advantages of this effective technique. The high material quality is confirmed via PL measurements. No defect related optical transitions, often observed in non‐ and semipolar GaN, were found. An In‐GaN QW grown on these semipolar planes showed efficient green (522 nm) light emission in spite of a reduced influence of the quantum confined stark effect (QCSE) (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Discovering Commonness and Specificness for Human Action Recognition (2015)

Human action recognition remains a challenging problem though having been intensively researched for decades. Recently, many sparse coding based approaches have been proposed to advance the progress in this research field. However, most of these approaches aim to learn a more discriminative dictionary by incorporating various regularization terms so that sparse codes are more representative for better recognition performance. Instead, in this paper, we propose a novel discriminative dictionary learning method which recognizes the commonness and specificness among different action classes. That is, we aim to obtain a universal dictionary which consists of two parts, a shared dictionary for all action classes and a set of class-specific dictionaries. As a result, inter-class differences can be better characterized with sparse codes obtained from the class-specific dictionaries. In addition, group sparsity constraint is utilized to ensure that similar descriptors of the same action class have similar sparse codes and locality constraint is utilized to ensure data locality. The experimental results on the popular UCF sports dataset demonstrate that our proposed approach outperforms the state-of-the-art of related methods.
A New Class of Potent Reversible Inhibitors of Metallo-proteinases: C-terminal Thiol-peptides as Zinc-coordinating Ligands (2001)

A number of substrate analogous peptides containing a phosphoramidate, phosphonate ester, hydroxamate, carboxylate or sulfhydryl group are known to be inhibitors of thermolysin and other metalloproteinases. According to the specificity, most of the inhibitors mimic the prime site of the active center. Hitherto, peptidyl derivatives with a thiol group at the C-terminus have not been described. We have synthesized the protected cysteamides Ac-Ala-Ala-CA-SH and Z-Aa1-Aa2-CA-SH (Aa1: Ala, Pro; Aa2: Ala, Leu). The binding of these thiol peptide inhibitors to the metalloproteinases is characterized first by the coordination of the thiolate group of the inhibitor to the catalytic zinc ion and second by the subsite interaction of the peptide ligand in the active site of the enzyme. All peptide derivatives were competitive inhibitors of the zinc metalloproteinase thermolysin. The strongest inhibition was found with Z-Pro-Leu-CA-SH (Ki = 30 microM). Substitution of the N-protecting benzyloxycarbonyl residue towards the acetyl group in the peptide inhibitor, the inhibition constant decreased about 25 times.
Assessing a changepoint in a sequence of repeated measurements with application to a low-energy emission therapy sleep study (1993)

We describe a test statistic for a changepoint in a sequence of repeated measurements. This statistic is non-parametric, and may be motivated from either frequentist or Bayesian considerations. We apply this procedure to data arising from a clinical sleep study of low-energy emission therapy.
Glutathione Precursor N-Acetyl-Cysteine Modulates EEG Synchronization in Schizophrenia Patients: A Double-Blind, Randomized, Placebo-Controlled Trial (2012)

ClinicalTrials.gov NCT01506765.
Subpicosecond single-shot waveform measurement using temporal imaging (2003)

The recording of single-transient phenomena with a very large time-bandwidth product is a particularly challenging task. While many techniques have been developed to record ultrafast optical signals with sub 100 fs detail they often have practical limitations on the total amount of time that can be recorded or rely on sampling of a repetitive waveform. A waveform manipulation technique known as temporal imaging is being developed to overcome some of these limitations. Temporal imaging can expand an arbitrary optical waveform in time while maintaining the shape of the unknown envelope profile, thus allowing it to be recorded by a slower technology with a resolution improved by the magnification of the imaging system. We present here the first single-shot temporal images produced with an upconversion temporal imaging system and recorded with a streak camera.
Zusammenfassung (1993)

Die Zahl bekannter, formalisierter und durch den Computer unterstützter Methoden und Instrumente wächst ständig. Noch werden die Methoden und Instrumente vorwiegend für die Analyse und Rekonstruktion eingesetzt, doch eine zunehmende Zahl junger Architektinnen und Architekten benutzt sie als selbstverständliche intellektuelle Instrumente für die Tätigkeit des praktischen Entwurfs. Immer öfter tauchen in Publikationen Entwürfe bekannter Architekten auf, bei denen zumindest ein Teil der Präsentation die Verwendung eines Computers erkennen läßt. Interessant ist die Tatsache, daß die Verwendung des neuen Instruments durch bekannte Architekten einen höheren Abstraktionsgrad aufweist als die Beispiele weniger bekannter Architekten, die den Realitätsgrad möglichst hoch ansetzen [Gandelsonas 1991]. Am besten läßt sich das Eindringen des CAAD in Lehre und Praxis in den letzten entscheidenden Jahren wohl am Beispiel des ACS-Preises bei der jährlich stattfindenden Wiesbadener ACS-Messe nachverfolgen.
Intensifying Thermally Induced Ultrasound Emission (2002)

In a recent research, a new method of ultrasound emission was proposed. Though thermally induced ultrasound (TIU) emission proposed there has some notable features, the sound intensity and efficiency was very low in that report. In this paper we show methods to enhance the power and efficiency of TIU. The acoustic intensity can be heightened to be more than 1 kPa, and we can expect a non-contact actuator that gives manipulation force using radiation pressure. The most important key of the enhancement is concentrating electrical power both spatially and temporally. We show the principle and experimental results including radiation pressure generation.
Molecular Taxonomy of the Trichophyton rubrum Complex (2000)

The validity of taxa around Trichophyton rubrum was evaluated by a combination of phenetic and molecular methods. Morphological and physiological features were compared to results of sequencing of the internal transcribed spacer region of the ribosomal operon, PCR fingerprinting, and amplified fragment length polymorphism analysis. The 15 species and varieties investigated (Trichophyton circonvolutum, Trichophyton fischeri, Trichophyton fluviomuniense, Trichophyton glabrum, Trichophyton gourvilii, Trichophyton kanei, Trichophyton kuryangei, Trichophyton megninii, Trichophyton pedis, Trichophyton raubitschekii, Trichophyton rodhaini, Trichophyton rubrum var. nigricans, Trichophyton soudanense, Trichophyton violaceum var. indicum, and Trichophyton yaoundei) were reclassified or synonymized as T. rubrum or T. violaceum.
Alternative routes of aromatic catabolism in Pseudomonas acidovorans and Pseudomonas putida: gallic acid as a substrate and inhibitor of dioxygenases (1975)

When 3,4-dihydroxyphenylacetic acid (homoprotocatechuic acid) was added to Pseudomonase acidovorans growing at the expense of succinate, enzymes required for degrading homoprotocatechuate to pyruvate and succinate semialdehyde were strongly induced. These enzymes were effectively absent from cell extracts of the organism grown with 4-hydroxyphenylacetic acid, and this substrate was metabolized by the catabolic enzymes of the homogentisate pathway. Two separate ring-fission dioxygenases for 3,4,5-trihydroxybenzoic acid (gallic acid) were present in cell extracts of Pseudomonas putida when grown with syringic acid, and gallate was degraded by reactions associated with meta fission. One of the two gallate dioxygenases also attacked 3-O-methylgallic acid; the other, which did not, was induced when cells were exposed to gallate. This organism possessed ortho fission enzymes, including protocatechuate 3,4-dioxygenase (EC 1.13.11.3) and cis,cis-carboxymuconate-lactonizing enzyme (EC 5.5.1.2), after induction with 3,4-dihydroxybenzoic acid (protocatechuic acid). Gallate was a substrate for protocatechuate 3,4-dioxygenase, with a Vmax about 3% of that of protocatechuate and with an apparent Km slightly lower. Gallate was a powerful competitive inhibitor of protocatechuate oxidation.
Recent Development on Catalytic Reductive Amination and Applications (2008)

Reductive amination is one of the most useful and versatile methods for the preparation of amines in chemistry and biology. The present review focuses on the development of catalytic reductive amination from beginning to recent ones, where we have attempted to thoroughly illustrate an account of utility of various reagents including organocatalyst, symmetric and asymmetric (Ru, Rh, Ir) complexes, boron, tin or silicon reagents etc for enantio- and/or chemoselective reactions under different reaction conditions with emphasis on the yields of the reaction products and stability of the reagents used. Emerging applications of this reaction for the development of chiral ligands, pharmacologically active molecules, combinatorial scaffold, and key step in the total synthesis of some interesting natural products is also reviewed briefly. Keywords: Reductive Amination, organocatalyst
A constraint optimization framework for discovery of cellular signaling and regulatory networks (2011)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Computational and Systems Biology Program, 2011.
Synthesis of pipelined memory access controllers for streamed data applications on FPGA-based computing engines (2001)

Commercially available behavioral synthesis tools do not adequately support FPGA vendor-specific external memory interfaces making it extremely difficult to exploit pipelined memory access modes as well as application specific memory operations scheduling critical for high-performance solutions. This lack of support substantially increases the complexity and the burden on designers in the mapping of applications to FPGA-based computing engines. In this paper we address the problem of external memory interfacing and aggressive scheduling of memory operations by proposing a decoupled architecture with two components - one component captures the specific target architecture timing while the other component uses application specific memory access pattern information. Our results support the claim that it is possible to exploit application specific information and integrate that knowledge into custom schedulers that mix pipelined and non-pipelined access modes aimed at reducing the overhead associated with external memory accesses. The results also reveal that the additional design complexity of the scheduler, and its impact in the overall design is minimal.
Dynamic content web applications: Crash, failover, and recovery analysis (2009)

This work assesses how crashes and recoveries affect the performance of a replicated dynamic content web application. RobustStore is the result of retrofitting TPC-W's on-line bookstore with Treplica, a middleware for building dependable applications. Implementations of Paxos and Fast Paxos are at the core of Treplica's efficient and programmer-friendly support for replication and recovery. The TPC-W benchmark, augmented with faultloads and dependability measures, is used to evaluate the behaviour of RobustStore. Experiments apply faultloads that cause sequential and concurrent replica crashes. RobustStore's performance drops by less than 13% during the recovery from two simultaneous replica crashes. When subject to an identical faultload and a shopping workload, a five-replicas RobustStore maintains an accuracy of 99.999%. Our results display not only good performance, total autonomy and uninterrupted availability, they also show that it is simple to develop efficient recovery-oriented applications using Treplica.