gebhart/patrepeval huggingface dataset:
DNA array analyses of <i>Arabidopsis thaliana</i> lacking a vacuolar Na<sup>+</sup>/H<sup>+</sup> antiporter: impact of AtNHX1 on gene expression (2004)

AtNHX1, a vacuolar cation/proton antiporter of Arabidopsis, plays an important role in salt tolerance, ion homeostasis and development. We used the T-DNA insertional mutant of AtNHX1 (nhx1 plants) and Affymetrix ATH1 DNA arrays to assess differences in transcriptional profiles and further characterize the roles of a vacuolar cation/proton antiporter. Mature, soil-grown plants were used in this study to approximate typical physiological growing conditions. A comparison of plants grown in the absence of salt stress yielded many transcripts that were affected by the absence of the AtNHX1 vacuolar antiporter. Furthermore, changes in gene expression due to a non-lethal salt stress (100 mm NaCl) in the nhx1 plants were significantly different from the changes seen in wild-type plants. The nhx1 transcriptome was differentially affected when the plants were grown in the absence or presence of salt. In conclusion, in addition to the known role(s) of AtNHX1 on ion homeostasis, the vacuolar cation/proton antiporter plays a significant role in intracellular vesicular trafficking, protein targeting, and other cellular processes.
Lipases from psychrotropic antarctic bacteria (1990)

Properties of lipases excreted by 4 psychrotropic Moraxella strains from antarctic sea water have investigated. Despite an optimal cell generation time at 25°C, maximal lipase excretion essentially occurs at low temperatures. These enzymes are characterized by a shift of the apparent optimal activity towards low temperatures, by a reduction of the activation energy value and by a decrease in heat stability. These lipases are associated with lipopolysaccharides, forming high molecular weight complexes. One of the selected strain is able to express the antibiotic resistances carried by RP4, at both 4 and 25°C.
Wistar Rats and Premature Infants (1974)

Journal Article Wistar Rats and Premature Infants Get access C I Jarowski C I Jarowski Department of Allied Health and Industrial Science, St. John’s University, College of Pharmacy and Allied Health Professions, Jamaica, New York Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 38, Issue 3, 1 March 1974, Pages 479–483, https://doi.org/10.1080/00021369.1974.10861193 Published: 01 March 1974 Article history Received: 19 June 1973 Published: 01 March 1974
Pharmacokinetics of Py-Im Polyamides Depend on Architecture: Cyclic versus Linear (2012)

The pharmacokinetic properties of three pyrrole-imidazole (Py-Im) polyamides of similar size and Py-Im content but different shape were studied in the mouse. Remarkably, hairpin and cyclic oligomers programmed for the same DNA sequence 5'-WGGWWW-3' displayed distinct pharmacokinetic properties. Furthermore, the hairpin 1 and cycle 2 exhibited vastly different animal toxicities. These data provide a foundation for design of DNA binding Py-Im polyamides to be tested in vivo.
SOX2 and p63 colocalize at genetic loci in squamous cell carcinomas (2014)

The transcription factor SOX2 is an essential regulator of pluripotent stem cells and promotes development and maintenance of squamous epithelia. We previously reported that SOX2 is an oncogene and subject to highly recurrent genomic amplification in squamous cell carcinomas (SCCs). Here, we have further characterized the function of SOX2 in SCC. Using ChIP-seq analysis, we compared SOX2-regulated gene profiles in multiple SCC cell lines to ES cell profiles and determined that SOX2 binds to distinct genomic loci in SCCs. In SCCs, SOX2 preferentially interacts with the transcription factor p63, as opposed to the transcription factor OCT4, which is the preferred SOX2 binding partner in ES cells. SOX2 and p63 exhibited overlapping genomic occupancy at a large number of loci in SCCs; however, coordinate binding of SOX2 and p63 was absent in ES cells. We further demonstrated that SOX2 and p63 jointly regulate gene expression, including the oncogene ETV4, which was essential for SOX2-amplified SCC cell survival. Together, these findings demonstrate that the action of SOX2 in SCC differs substantially from its role in pluripotency. The identification of the SCC-associated interaction between SOX2 and p63 will enable deeper characterization the downstream targets of this interaction in SCC and normal squamous epithelial physiology.
Hybrid method for determining the parameters of condenser microphones from measured membrane velocities and numerical calculations (2009)

Typically, numerical calculations of the pressure, free-field, and random-incidence response of a condenser microphone are carried out on the basis of an assumed displacement distribution of the diaphragm of the microphone; the conventional assumption is that the displacement follows a Bessel function. This assumption is probably valid at frequencies below the resonance frequency. However, at higher frequencies the movement of the membrane is heavily coupled with the damping of the air film between membrane and backplate and with resonances in the back chamber of the microphone. A solution to this problem is to measure the velocity distribution of the membrane by means of a non-contact method, such as laser vibrometry. The measured velocity distribution can be used together with a numerical formulation such as the boundary element method for estimating the microphone response and other parameters, e.g., the acoustic center. In this work, such a hybrid method is presented and examined. The velocity distributions of a number of condenser microphones have been determined using a laser vibrometer, and these measured velocity distributions have been used for estimating microphone responses and other parameters. The agreement with experimental data is generally good. The method can be used as an alternative for validating the parameters of the microphones determined by classical calibration techniques.
Optimizing Memory Efficiency for Deep Convolutional Neural Networks on GPUs (2016)

Leveraging large data sets, deep Convolutional Neural Networks (CNNs) achieve state-of-the-art recognition accuracy. Due to the substantial compute and memory operations, however, they require significant execution time. The massive parallel computing capability of GPUs make them as one of the ideal platforms to accelerate CNNs and a number of GPU-based CNN libraries have been developed. While existing works mainly focus on the computational efficiency of CNNs, the memory efficiency of CNNs have been largely overlooked. Yet CNNs have intricate data structures and their memory behavior can have significant impact on the performance. In this work, we study the memory efficiency of various CNN layers and reveal the performance implication from both data layouts and memory access patterns. Experiments show the universal effect of our proposed optimizations on both single layers and various networks, with up to 27.9x for a single layer and up to 5.6x on the whole networks.
[Acute lymphoblastic leukemia accompanied by severe hypercalcemia; successful treatment with bisphosphonate]. (1995)

A 62-year-old woman was admitted to the hospital because of bone pain. Laboratory data showed blasts in the peripheral blood, hypercalcemia (corrected calcium 15.1 mg/dl) and an increased level of parathyroid hormone related-protein (PTHrP). Bone marrow aspiration revealed increased lymphoblasts (96.5%), indicating acute lymphoblastic leukemia (ALL, L1). Subsequent radiological examination disclosed bone infiltration of ALL. Although the hypercalcemia was successfully treated with bisphosphonate, the PTHrP level remained high. After chemotherapy, the blasts in the peripheral blood disappeared and the PTHrP level normalized. We hypothesize that in the present case the production of PTHrP by lymphoblasts resulted in the hypercalcemic state. Although ALL is rarely accompanied by hypercalcemia, this case might help us to understand the relationship between ALL and hypercalcemia.
Role of Room Temperature Sputtered High Conductive and High Transparent Indium Zinc Oxide Film Contacts on the Performance of Orange, Green, and Blue Organic Light Emitting Diodes (2011)

Abstract The core of this paper concerns the use of an amorphous transparent conductive oxide (a‐TCO), whose performance is on par with the classical indium tin oxide (ITO) films as a transparent contact in organic light emitting diodes (OLEDs). The main advantage of indium zinc oxide (IZO) films relies on their amorphous structure and high mobility that turns them likely to be used with high conductivity and high transmittance even at the infrared region. The mobility of IZO films (47.8 cm 2 · V −1 · s −1 ) surpasses the one exhibited by ITO films (26.4 cm 2 · V −1 · s −1 ), which along with its smoother surface and better current distribution plays an important role on OLEDs performance. Besides their similar turn‐on voltage, the devices using IZO anodes exhibit higher power efficiency than the ITO ones, which is 66, 18, and 62% for orange, green, and blue OLEDs, respectively. These results suggest that IZO can potentially be applied as an anode in full color displays based on OLEDs. magnified image
Real time implementation of a symbol timing recovery algorithm for a narrowband wireless modem (2002)

This paper examines some of the complexity issues arising in the real time implementation of the symbol timing subsystem of a narrowband wireless modem. The modem prototype has been designed for 4 kHz channels in the 220-222 MHz land mobile band. In an effort to achieve high bandwidth efficiency, the modem architecture employs transmitter diversity, pilot symbol assisted modulation, and trellis coded modulation. An experimental, non-real time system has been implemented and extensively field tested demonstrating bandwidth efficiencies in excess of 3 bits per second per Hz. The work on this project is focused on the real-time implementation of the baseband receiver functions using the Texas Instruments C54/spl times/ fixed point digital signal processor. Here we report on some of the performance/complexity tradeoffs present in the design of a DSP implementation of the digital filter and square symbol timing recovery algorithm.
Schizophrenic subjects with no history of admission to hospital (1995)

It has often been assumed that all subjects with schizophrenia will eventually be admitted to hospital and therefore little bias is introduced by restricting research to hospitalized subjects. Using the Lothian Psychiatric Case Register, 66 subjects were identified who had been diagnosed in Edinburgh as suffering from schizophrenia between 1978 and 1989 but had no history of hospital admission by December 1991. This represented an adjusted average of 6.7% of the estimated annual rate of first diagnosis of schizophrenia: the proportion of such patients did not change over the period. Using a case-control design, the index cases were compared with a control group of schizophrenic patients who had been admitted to hospital within 3 months of diagnosis. At the time of diagnosis, the cases were generally less disturbed with lower levels of violent behaviour and less evidence of neglect or hallucinations. They had a longer duration of illness prior to diagnosis, were more often diagnosed by a consultant and unemployed. In a follow-up study of the index cases, 59 (89%) were traced, of whom 6 (10%) were deceased. The outcome of the illness was heterogeneous although the course was often chronic. The general practitioner provided most of the care they received. The small proportion of such patients suggests that their exclusion from most published series does not seriously bias our picture of the natural history of schizophrenia. Moreover, as there was no increase in the proportion over the period, first admission rates for schizophrenia in Scotland are a reasonable approximation to incidence rates.
Silica-based, compact and variable-optical-attenuator integrated coherent receiver with stable optoelectronic coupling system (2012)

We demonstrate a compact and variable-optical-attenuator (VOA) integrated coherent receiver with a silica-based planar lightwave circuit (PLC). To realize the compact receiver, we integrate a VOA in a single PLC chip with polarization beam splitters and optical 90-degree hybrids, and employ a stable optoelectronic coupling system consisting of micro lens arrays and photodiode (PD) subcarriers with high-speed right-angled signal lines. We integrate a VOA and a coherent receiver in a 27x40x6 mm package, and successfully demodulate a 128-Gbit/s polarization division multiplexed (PDM) quadrature phase shift keying (QPSK) signal with a VOA-assisted wide dynamic range of more than 30 dB.
<i>Salmonella</i> -Type Heptaacylated Lipid A Is Inactive and Acts as an Antagonist of Lipopolysaccharide Action on Human Line Cells (2000)

The stimulation of both THP-1 and U937 human-derived cells by Salmonella lipid A preparations from various strains, as assessed by TNF-alpha induction and NF-kappaB activation, was found to be very low (almost inactive) compared with Escherichia coli lipid A, but all of the lipid As exerted strong activity on mouse cells and on Limulus gelation activity. Experiments using chemically synthesized E. coli-type hexaacylated lipid A (506) and Salmonella-type heptaacylated lipid A (516) yielded clearer results. Both lipid A preparations strongly induced TNF-alpha release and activated NF-kappaB in mouse peritoneal macrophages and mouse macrophage-like cell line J774-1 and induced Limulus gelation activity, although the activity of the latter was slightly weaker than that of the former. However, 516 was completely inactive on both THP-1 and U937 cells in terms of both induction of TNF-alpha and NF-kappaB activation, whereas 506 displayed strong activity on both cells, the same as natural E. coli LPS. In contrast to the action of the lipid A preparations, all the Salmonella LPSs also exhibited full activity on human cells. However, the polysaccharide portion of the LPS neither exhibited TNF-alpha induction activity on the cells when administered alone or together with lipid A nor inhibited the activity of the LPS. These results suggest that the mechanism of activation by LPS or the recognition of lipid A structure by human and mouse cells may differ. In addition, both 516 and lipid A from Salmonella were found to antagonize the 506 and E. coli LPS action that induced TNF-alpha release and NF-kappaB activation in THP-1 cells.
Face Recognition with the Karhunen-Loeve Transform (1991)

The major goal of this research was to investigate machine recognition of faces. The approach taken to achieve this goal was to investigate the use of Karhunen-Loe've Transform (KLT) by implementing flexible and practical code. The KLT utilizes the eigenvectors of the covariance matrix as a basis set. Faces were projected onto the eigenvectors, called eigenfaces, and the resulting projection coefficients were used as features. Face recognition accuracies for the KLT coefficients were superior to Fourier based techniques. Additionally, this thesis demonstrated the image compression and reconstruction capabilities of the KLT. This theses also developed the use of the KLT as a facial feature detector. The ability to differentiate between facial features provides a computer communications interface for non-vocal people with cerebral palsy. Lastly, this thesis developed a KLT based axis system for laser scanner data of human heads. The scanner data axis system provides the anthropometric community a more precise method of fitting custom helmets.
Preliminary radiographic observations of the tongue-repositioning manoeuvre (2006)

The tongue-repositioning manoeuvre (TRM) is a method to place the tongue in direct contact with the hard palate. The TRM makes use of voluntary generation of negative interocclusal pressure controlled by an intra-extraoral pressure indicator device in combination with an oral shield. The aim of the study was to investigate whether the TRM influences vertical tongue position and/or tongue-velum contact. Ninety consecutive patients (75 males, aged 26-76 years, and 15 females, aged 36-70 years) who presented with snoring and/or obstructive sleep apnoea (OSA) were examined at the University of Göttingen. Two cephalograms, with and without the TRM, were taken and traced. The data were analysed using Wilcoxon matched-pairs signed-rank test. Evaluation of the TRM demonstrated a significant increase (P < 0.01) of the mean tongue-velum contact from 6.3 to 24.5 mm and a significant decrease (P < 0.01) of the mean tongue-palate distance (12.3-3.1 mm) measured perpendicular to the nasal line. This was compatible with an intensification of posterior mouth closure and a contact position of the tongue with the palate.
Carboxylation of a polypentenamer and preparation of its hydrogenated derivatives (1979)

Abstract Carboxylated three‐membered ring derivatives of a polypentenamer (PP) that contained 82% trans and 17% cis double bonds were prepared by carbene addition of ethyldiazoacetate with a copper catalyst to the double bonds and subsequent hydrogenation of the residual unsaturation. In this way derivatives that contained approximately either 5 or 10 mole % three‐membered rings with ester side groups were obtained. These side groups were further reacted by hydrolysis or neutralization to form carboxylic acid and cesium salts of carboxylic acid. Reaction conditions were chosen so that no backbone degradation occurred and side reactions that led to crosslinking were avoided. The derivatives were characterized by gel permeation chromatography (GPC), thermal gravimetric analysis (TGA), differential scanning calorimetry (DSC), infrared (IR) spectroscopy, and nuclear magnetic resonance (NMR) spectroscopy. It was found that an increase in substituent concentration decreased the melting point ( T m ) in hydrogenated derivatives and increased the glass transition temperature ( T g ) in unhydrogenated derivatives. The cesium salts of carboxylic acid were the least thermally stable among those studied and the hydrogenated derivatives were generally more stable than the unhydrogenated.
Use of Amino Acid Composition to Predict Ligand-Binding Sites (2007)

A novel method for predicting the binding sites for druglike compounds on the surface of proteins was developed on the basis of the specific amino acid composition observed at the ligand-binding sites of ligand-protein complexes determined by X-ray analysis. A profile representing the preference of each of the 20 standard amino acids at the binding sites of druglike molecules was obtained for a small set of high-quality complex structures. An index termed propensity for ligand binding (PLB) was created from these profiles. The PLB index was used to predict the propensity of binding for 804 ligands at all potential binding sites on the proteins whose structures were determined by X-ray analysis. If the sites with the first two highest PLB indices are taken into consideration, the successfully predicted sites reached a high percentage of 86. The PLB prediction is relatively simple, but the validation study showed that it is both fast and accurate to detect ligand-binding sites, especially the binding sites of druglike molecules. Therefore, the PLB index can be used to predict the ligand-binding sites of uncharacterized protein structures and also to identify novel drug-binding sites of known drug targets.
Control of Silicon Dioxide Properties by RF Sputtering (1983)

We have examined the effect of simultaneously sputtered Teflon on the properties of sputtered silicon dioxide films. C‐V measurements show that positive ions in sputtered silicon dioxide can be compensated. It also shows that the compensation effect can be controlled by the negative voltage of bias sputtering during deposition.
Demonstration of a high repetition rate capillary discharge waveguide (2016)

A hydrogen-filled capillary discharge waveguide operating at kHz repetition rates is presented for parameters relevant to laser plasma acceleration (LPA). The discharge current pulse was optimized for erosion mitigation with laser guiding experiments and MHD simulation. Heat flow simulations and measurements showed modest temperature rise at the capillary wall due to the average heat load at kHz repetition rates with water-cooled capillaries, which is promising for applications of LPAs such as high average power radiation sources.
High speed 45nm gate length CMOSFETs integrated into a 90nm bulk technology incorporating strain engineering (2004)

A leading edge 90 nm logic bulk foundry technology with 45 nm gate length devices, incorporating strain engineering, is described in this paper. Gate length and dielectric scaling, along with optimized strain engineering, enable high performance devices, which are amongst the best reported to date. Short channel effect control down to 35 nm is demonstrated. Both NMOS and PMOS performance are improved through careful optimization of stress effects from both trench isolation and contact etch stop nitride film. Furthermore, analysis of the channel mobility and current enhancement is used to gain understanding of the stress mechanisms, and hence layout design practice should be optimized for performance.
Enhanced skin carcinogenesis in cyclin D1-conditional transgenic mice: cyclin D1 alters keratinocyte response to calcium-induced terminal differentiation. (2002)

Cyclin D1 is a critical gene involved in the regulation of progression through the G(1) phase of the cell cycle, thereby contributing to cell proliferation. Gene amplification and abnormal expression of Cyclin D1 have been described in several human cancers. To understand their biological significance in skin carcinogenesis, we established Cyclin D1-conditional transgenic mice with C57BL/6J background, in which skin-specific overexpression of Cyclin D1 transgene was observed. The mice were subjected to dimethylbenz[a]anthracene complete skin carcinogenesis studies. After 40 weeks of repeated administration of dimethylbenz[a]anthracene on the skin (once a week), all of the mice with high Cyclin D1 expression had papillomas, whereas only 9.5% of the control mice without the transgene developed papillomas. Primary cultured keratinocytes with induced Cyclin D1 transgene expression showed resistance to calcium-induced terminal differentiation and continued to replicate in vitro. These results clearly provide us with direct experimental evidence that overexpression of CyclinD1 induces excessive dermal cell proliferation via the altered differentiation state of keratinocytes. The conditional transgenic mice described here provide excellent in vivo and in vitro model systems to understand the role of cyclin D1 and deregulation of the cell cycle in carcinogenesis.
A Crystallization-Induced Asymmetric Transformation using Racemic Phenyl Alanine Methyl Ester Derivatives as Versatile Precursors to Prepare Amino Acids (2019)

L-Tyrosine and L-Dopa are the precursors in the biological synthesis of amine neurotransmitters. On the other hand, phenylalanine as an aromatic amino acid (AAA) is a precursor in the synthesis of L-Tyrosine and L-Dopa. For some substrates such as amino acids, resolution by the formation of diastereomers offers an attractive alternative. Among different methods in this case, crystallization-induced asymmetric transformation (CIAT) that is in situ racemization and selective crystallization of a reaction product can be a good choice. Using this method, preparation of L-Tyrosine and L-Dopa has been reported. In the synthetic route, racemic phenyl alanine methyl ester derivatives as versatile precursors were prepared by reducing azlactone derivatives with Mg in methanol as a reducing reagent and then in the resolution step (S)- enantiomer of L-Dopa (3,4-dihydroxyphenylalanine) and L-Tyrosine (4-hydroxyphenylalanine) were achieved via salt formation with (2R,3R)-tartaric acid in the presence of 5-nitro salicylaldehyde in good yield and high optical purity.