gebhart/patrepeval huggingface dataset:
Another twist in the transforming growth factor β-induced cell-cycle arrest chronicle (2003)

Members of the transforming growth factor β (TGF-β) superfamily of cytokines are important regulators of many fundamental cellular and developmental processes, including cell fate determination, proliferation, differentiation, migration, and apoptosis (1). TGF-β also harbors a paradoxical dual role in tumorigenesis. During early tumor development, TGF-β has tumor-suppressor-like activity because of its ability to inhibit cell-cycle progression and tumor growth. However, many late-stage, dedifferentiated tumor cells become refractory to the growth inhibition mediated by TGF-β, either because of genetic loss of TGF-β signaling components or downstream perturbation of the signaling pathway (2). In addition, late-stage tumors often display increased TGF-β expression (3), which is thought to enhance the motility and metastasis potential of these cells (4). Furthermore, although TGF-β is a potent growth inhibitor to most normal epithelial cells, it can also stimulate the proliferation of some fibroblastic cell lines, such as NIH 3T3 (5). The molecular mechanisms underlying the basis of these differential responses to TGF-β have not been elucidated. However, in this issue of PNAS, Bhowmick et al. (6) have now shed some light on an important clue of alternative signaling pathways involved in TGF-β-mediated growth regulation. By analyzing the paradoxical effects of TGF-β on epithelial cells versus fibroblasts, Bhowmick et al. (6) have uncovered a TGF-β growth-inhibitory pathway that links RhoA/p160ROCK to Cdc25A and at least partially explains the different response of epithelial cells and fibroblasts to TGF-β.

TGF-β signals through a heteromeric transmembrane complex composed of two type I and two type II receptor serine/threonine kinases (Fig. 1) (7). On TGF-β binding, the type I and type II receptors are brought together, resulting in the activation of the dormant kinase activity of the type I receptor. The activated type I receptor then propagates …
Restriction maps of the regions coding for methicillin and tobramycin resistances on chromosomal DNA in methicillin-resistant staphylococci (1989)

Chromosomal BamHI DNA fragments containing both the mecA gene encoding the penicillin-binding protein responsible for methicillin resistance and the aadD gene encoding 4',4"-adenylyltransferase responsible for tobramycin resistance were cloned from three methicillin- and tobramycin-resistant strains of Staphylococcus aureus and one strain of Staphylococcus epidermidis. Physical maps of the fragments were similar, suggesting their unique origin.
The ASYMMETRIC LEAVES2 Gene of Arabidopsis thaliana, Required for Formation of a Symmetric Flat Leaf Lamina, Encodes a Member of a Novel Family of Proteins Characterized by Cysteine Repeats and a Leucine Zipper (2002)

The ASYMMETRIC LEAVES2 (AS2) gene of Arabidopsis thaliana is involved in the establishment of the leaf venation system, which includes the prominent midvein, as well as in the development of a symmetric lamina. The gene product also represses the expression of class 1 knox homeobox genes in leaves. We have characterized the AS2 gene, which appears to encode a novel protein with cysteine repeats (designated the C-motif) and a leucine-zipper-like sequence in the amino-terminal half of the primary sequence. The Arabidopsis genome contains 42 putative genes that potentially encode proteins with conserved amino acid sequences that include the C-motif and the leucine-zipper-like sequence in the amino-terminal half. Thus, the AS2 protein belongs to a novel family of proteins that we have designated the AS2 family. Members of this family except AS2 also have been designated ASLs (AS2-like proteins). Transcripts of AS2 were detected mainly in adaxial domains of cotyledonary primordia. Green fluorescent protein-fused AS2 was concentrated in plant cell nuclei. Overexpression of AS2 cDNA in transgenic Arabidopsis plants resulted in upwardly curled leaves, which differed markedly from the downwardly curled leaves generated by loss-of-function mutation of AS2. Our results suggest that AS2 functions in the transcription of a certain gene(s) in plant nuclei and thereby controls the formation of a symmetric flat leaf lamina and the establishment of a prominent midvein and other patterns of venation.
Toward sustainable fuel cells (2016)

Improved fuel-cell catalysts require much less platinum for the same performance
Effects of the agricultural pesticides atrazine, deethylatrazine, endosulfan, and chlorpyrifos on an estuarine microbial food web (1999)

Abstract Aricultural pesticide runoff is a critical issue for many southeasternestuaries. The estuarine microbial food web plays an important role in nutrient cycling and transfer of nutrients to higher trophic levels. The present study examined the effects of agricultural pesticides on the estuarine microbial food web. Polyurethane foam substrates were used to collect microbial communities from a reference tidal creek in the North Inlet National Estuarine Research Reserve (Georgetown, SC, USA). Colonized substrates were brought into the laboratory and exposed to the following commonly used agricultural pesticides: atrazine (and a metabolite, deethylatrazine), endosulfan, and chlorpyrifos. Chlorophyll a, phototrophic carbon assimilation, dissolved oxygen, and phototrophic biovolume were significantly reduced at concentrations of 50 and 250 μg/L atrazine and deethylatrazine. Generally, inhibition of the phytoplankton resulted in increased bacterial abundance and productivity, whereas heterotrophic ciliate and flagellate abundances were not affected. Total bacterial abundance, but not heterotrophic bacterial productivity, was significantly reduced with endosulfan treatments of 1 and 10 μg/L. Endosulfan was primarily found to target the cyanobacteria. Changes in biomass reflected compositional shifts in the phototrophs. The abundance of heterotrophic ciliates and flagellates was significantly reduced at 10 μg/L chlorpyrifos. Bacterial abundance and productivity increased, whereas phototrophic variables decreased. Agricultural pesticides were found to alter both functional and structural aspects of the estuarine microbial food web.
Characteristics of negative-polarity DC superimposed nanosecond pulsed discharge and its applications (2019)

Non-thermal plasma generated by pulsed discharge is expected to efficiently treat combustion exhaust gases such as nitrogen oxide (NO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> ) and sulfur oxide (SOx) due to its high chemical activity. Nanosecond pulsed discharge which has voltage rise time and fall time of 2 ns, pulse width 5 ns and peak value of 60 kV, has been developed by our group. Nanosecond pulsed discharge mainly consists of streamer discharge phase, so that heat loss which caused by glow discharge is less, and plasma impedance is kept almost constant during the streamer discharge phase. Therefore, impedance matching between pulsed power supply and discharge load is possible. Applications on ozone generation and NO treatment using nanosecond pulsed discharge are reported with high energy efficiency compared to other discharge methods. However, the discharge mode transit to arc discharge phase sometimes. Also, for industrial applications, the plasma processing capacity leaves room to improve. It has also been reported that negative polarity nanosecond pulse discharges give better results depending on the plasma processing applications. In this study, negative polarity DC superimposed nanosecond pulsed discharge was suggested in order to improve the better performance of the nanosecond discharge plasma. Results of ozone generation using negative polarity DC superimposed nanosecond pulsed discharge have also been introduced.
Lust, lack of desire, and paraphilias: Some sthoughts and possible connections (1992)

How one develops specific sexual interests (desires, eroticisms, orientation, lust, preferences, etc.) is a basic and essentially unanswered question in sexology. The present paper explores a theoretical relationship between the the development of specific sexual interests and those individuals complaining of lack of desire. The ability of traditional sex therapy to intercede successfully in these problems is discussed.
A heat pulse technique for the determination of small‐scale flow directions and flow velocities in the streambed of sand‐bed streams (2011)

Abstract The hyporheic zone (HZ) has the capability to eliminate and attenuate nutrients and contaminants in riverine systems. Biogeochemical reactions and the potential elimination of contaminants are strongly controlled by the flow paths and dynamics in the HZ. Nevertheless, an easily applicable method for the field determination of flow patterns in the HZ is still lacking. Therefore, a heat pulse technique, which traces the movement of a short heat pulse in the upper part of the HZ and other sand beds, was developed. Five rods are vertically driven into the sediment of the streambed; one rod with a heater as point source located in about 10‐cm sediment depth and four rods with four temperature sensors in 3 cm distance, arranged concentrically with 7 cm diameter around the heating rod. Subsequently, a heat pulse is applied and the resulting breakthrough curves are indicative of flow velocities and flow directions in the streambed. A rough data analysis procedure is also suggested. In addition, laboratory experiments were performed to test the heat pulse technique. These experiments were validated based on coupled numerical modelling of flow and heat transport. First field tests of the method prove that the method is easily applicable under field conditions. These first field tests showed highly complex flow patterns with flow velocities from 1·8 to 4·9 cm min −1 and flow directions from parallel to surface flow to opposite to surface flow. This suggests the need for a robust method to quantify hyporheic flow patterns in situ . Copyright © 2011 John Wiley &amp; Sons, Ltd.
Energy-scalable OFDM transmitter design and control (2006)

Orthogonal Frequency Division Multiplexing (OFDM) is the modulation of choice for broadband wireless communications. Unfortunately, it comes at the cost of a very low energy efficiency of the analog transmitter. Numerous circuit-level and signal processing techniques have been proposed to improve that energy efficiency. However more disruptive improvement can be achieved at system-level, capitalizing on energy-scalable design and circuit reconfiguration to match the user requirements and operation environment. We describe the design of such an energy-scalable reconfigurable transmitter as well as its control strategy. Based on measurement carried out on the physical realization of this transmitter, the benefit of system-level energy management is shown. Energy-efficiency scalability ranges over 30%, which translates in an average system-level energy improvement of up to 40% compared to a non-scalable system.
Soluble forms of herpes simplex virus glycoprotein D bind to a limited number of cell surface receptors and inhibit virus entry into cells (1990)

Herpes simplex virus type 1 (HSV-1) and HSV-2 plaque production was inhibited by treating cells with soluble forms of HSV-1 glycoprotein D (gD-1t) and HSV-2 glycoprotein D (gD-2t). Both glycoproteins inhibited entry of HSV-1 and HSV-2 without affecting virus adsorption. In contrast, a soluble form of HSV-2 glycoprotein B had no effect on virus entry into cells. Specific binding of gD-1t and gD-2t to cells was saturable, and approximately 4 x 10(5) to 5 x 10(5) molecules bound per cell. Binding of gD-1t was markedly reduced by treating cells with certain proteases but was unaffected when cell surface heparan sulfate glycosaminoglycans were enzymatically removed or when the binding was carried out in the presence of heparin. Together, these results suggest that gD binds to a limited set of cell surface receptors which may be proteins and that these interactions are essential for subsequent virus entry into cells. However, binding of gD to its receptors is not required for the initial adsorption of virus to the cell surface, which involves more numerous sites (probably including heparan sulfate) than those which mediate gD binding.
Modeling and Verifying Configuration in Service Deployment (2006)

When deploying a service, software systems required by the service should be configured correctly. However, since software has tens or hundreds of configuration parameters and the parameters of different software may have simple or complex, explicit or implicit dependencies and constraints, to configure multiple software systems in service deployment becomes a difficult, error-prone and time-consuming task. In this paper, we propose a model based approach to automated configuration. Motivated by two real cases found in IBM software products and solutions, our approach has three contributions. Firstly, a meta-model of configuration, called software resource configuration model, is defined for integrating configuration parameters and experiences of different software into a global model. Secondly, a set of configuration rules are designed for verifying incorrect configuration that violates constraints specified by service deployment engineers. Thirdly, a supporting tool, called Comfort, is implemented and evaluated by the motivating cases
04 and A007-sulfatide antibodies bind to embryonic Schwann cells prior to the appearance of galactocerebroside; regulation of the antigen by axon-Schwann cell signals and cyclic AMP (1990)

In the rat sciatic nerve, the relationship between Schwann cells, axons, the extracellular matrix and perineurial sheath cells undergoes extensive modification between embryo day 15 and the onset of myelination during the first postnatal day. Little is known about molecular changes in Schwann cells in this important prenatal period. In the present paper, we use immunofluorescence to study the prenatal development and postnatal regulation of the antigen(s) recognized by the 04 monoclonal antibody and a well-characterized rat monoclonal antibody to sulfatide, A007. We show that, in a series of immunochemical tests, the 04 antibody recognizes only sulfatide in neonatal and adult rat nerves. Both antibodies first bind to Schwann cells in the sciatic nerve at embryo day 16-17, and all Schwann cells bind both antibodies at birth. In the adult nerve, both nonmyelin-forming and myelin-forming cells are labelled with the antibodies. Schwann cells dissociated from embryo day 15 nerves and cultured in the absence of axons develop neither 04 nor A007 binding on schedule, and 04-positive and A007-positive Schwann cells from postnatal nerves lose the ability to bind these antibodies during the first few days in culture. Schwann cells in the distal stump of transected nerves also sharply down-regulate cell surface binding of 04. High numbers of 04-positive or A007-positive Schwann cells reappear in cultures treated with agents that mimic or elevate intracellular cAMP. We conclude that two anti-sulfatide antibodies 04 and A007, recognize an antigen, probably sulfatide, that appears very early in Schwann cell development (one to two days prior to galactocerebroside) but is nevertheless subject to upregulation by axonal contact or elevation of intracellular cAMP.
Candida albicansCell Wall Proteins (2008)

The Candida albicans cell wall maintains the structural integrity of the organism in addition to providing a physical contact interface with the environment. The major components of the cell wall are fibrillar polysaccharides and proteins. The proteins of the cell wall are the focus of this review. Three classes of proteins are present in the candidal cell wall. One group of proteins attach to the cell wall via a glycophosphatidylinositol remnant or by an alkali-labile linkage. A second group of proteins with N-terminal signal sequences but no covalent attachment sequences are secreted by the classical secretory pathway. These proteins may end up in the cell wall or in the extracellular space. The third group of proteins lack a secretory signal, and the pathway(s) by which they become associated with the surface is unknown. Potential constituents of the first two classes have been predicted from analysis of genome sequences. Experimental analyses have identified members of all three classes. Some members of each class selected for consideration of confirmed or proposed function, phenotypic analysis of a mutant, and regulation by growth conditions and transcription factors are discussed in more detail.
Generation of two-cycle pulses and octave-spanning frequency combs in a dispersion-flattened micro-resonator (2013)

We show that octave-spanning Kerr frequency combs with improved spectral flatness of comb lines can be generated in dispersion-flattened microring resonators. The resonator is formed by a strip/slot hybrid waveguide, exhibiting a flat and low anomalous dispersion between two zero-dispersion wavelengths that are separated by one octave from near-infrared to mid-infrared. Such flattened dispersion profiles allow for the generation of mode-locked frequency combs, using relatively low pump power to obtain two-cycle cavity solitons on a chip, associated with the octave-spanning comb bandwidth. The wavelength dependence of the optical loss and of the coupling coefficient and thus wavelength dependent Q-factor are also considered.
Thiol‐ene/acrylate substrates for softening intracortical electrodes (2013)

Neural interfaces have traditionally been fabricated on rigid and planar substrates, including silicon and engineering thermoplastics. However, the neural tissue with which these devices interact is both 3D and highly compliant. The mechanical mismatch at the biotic-abiotic interface is expected to contribute to the tissue response that limits chronic signal recording and stimulation. In this work, novel ternary thiol-ene/acrylate polymer networks are used to create softening substrates for neural recording electrodes. Thermomechanical properties of the substrates are studied through differential scanning calorimetry and dynamic mechanical analysis both before and after exposure physiological conditions. This substrate system softens from more than 1 GPa to 18 MPa on exposure to physiological conditions: reaching body temperature and taking up less than 3% fluid. The impedance of 177 µm(2) gold electrodes electroplated with platinum black fabricated on these substrates is measured to be 206 kΩ at 1 kHz. Specifically, intracortical electrodes are fabricated, implanted, and used to record driven neural activity. This work describes the first substrate system that can use the full capabilities of photolithography, respond to physiological conditions by softening markedly after insertion, and record driven neural activity for 4 weeks.
Phase I Evaluation of Prolonged-Infusion Gemcitabine With Mitoxantrone for Relapsed or Refractory Acute Leukemia (2002)

PURPOSE: To ascertain the maximum tolerated duration of infusion of gemcitabine at 10 mg/m 2 /min in combination with mitoxantrone at 12 mg/m 2 daily for 3 days in the treatment of acute leukemia. PATIENTS AND METHODS: Thirty-four patients were enrolled. Stratum I consisted of 26 patients, median age 50 years (range, 25 to 71 years), with relapsed or refractory leukemia. Stratum II contained eight patients, median age 62.5 years (range, 38 to 83 years), who had received fewer than three cycles of myelotoxic therapy for chronic myeloid leukemia or myelodysplasia that had evolved into leukemia. Patients received mitoxantrone at 12 mg/m 2 daily for 3 days. After the first mitoxantrone dose, gemcitabine was provided intravenously at 10 mg/m 2 /min with the duration adjusted by following a continuous reassessment model. RESULTS: Severe myelosuppression, and stomatitis or esophagitis were the most common hematologic and nonhematologic dose-limiting toxicities. Several patients developed febrile neutropenia, nausea, or vomiting. In both strata, the maximum recommended duration of infusion of gemcitabine was 12 hours (7,200 mg/m 2 ). The mean steady-state concentration of gemcitabine was 24.72 μmol/L and varied over a fivefold range among patients. Overall response rates in this phase I trial for strata I and II were 42% and 63%, respectively. CONCLUSION: Prolonged-infusion gemcitabine at a fixed dose rate of 10 mg/m 2 /min for 12 hours with 12 mg/m 2 /d mitoxantrone for 3 days is a tolerable induction regimen and achieves plasma concentrations sufficient for maximal intracellular activation. Stomatitis or esophagitis should be anticipated; however, this regimen may induce significant responses in patients with difficult-to-treat leukemias.
Quantitative assessment of olfactory receptors activity in immobilized nanosomes: a novel concept for bioelectronic nose (2006)

We describe how mammalian olfactory receptors (ORs) could be used as sensing elements of highly specific and sensitive bioelectronic noses. An OR and an appropriate G(alpha) protein were co-expressed in Saccharomyces cerevisiae cells from which membrane nanosomes were prepared, and immobilized on a sensor chip. By Surface Plasmon Resonance, we were able to quantitatively evaluate OR stimulation by an odorant, and G protein activation. We demonstrate that ORs in nanosomes discriminate between odorant ligands and unrelated odorants, as in whole cells. This assay also provides the possibility for quantitative assessment of the coupling efficiency of the OR with different G(alpha) subunits, without the interference of the cellular transduction pathway. Our findings will be useful to develop a new generation of electronic noses for detection and discrimination of volatile compounds, particularly amenable to micro- and nano-sensor formats.
Vasomotor Control of the Liver Circulation (1930)

Our present knowledge of the vasomotor control of the liver circulation is curiously inadequate. In due time the evidence for this conclusion will be reviewed in detail; now we wish merely to record a summary of the results which have been obtained during the last couple of years in a study of this problem, using cats under chloralose anesthesia and the liver plethysmograph previously referred to., The peripheral vagus has no effect on liver volume; we have stimulated it in the neck (after denervating the heart according to Cannon's method), below the heart in the thorax and after emerging through the diaphragm. The postganglionic fibers of the hepatic plexus constrict not only the terminals of the hepatic artery but also those of the portal vein. The preganglionic fibers of the splanchnic (left) have exactly the same effect on liver volume, either by way of the artery or portal vein, as stimulation of the postganglionic fibers in the hepatic plexus. Reflex pressor responses are accompanied by decreased liver volume; depressor reflexes produce dilation in the liver. If, however, the liver is denervated by cutting the fibers of the hepatic plexus, its volume then follows passively the general blood pressure. During the generalized vasomotor activity induced by asphyxia (rebreathing the air in a small balloon) the liver constricts powerfully during the rise of general blood pressure and remains constricted even as the heart begins to fail. If it is denervated, however, it dilates for a time as the general blood pressure is rising; but before this has reached its maximum the liver often begins to constrict maximally. This delayed constriction may be prevented by removal of the adrenals; then the denervated liver volume passively follows the general blood pressure throughout the course of the asphyxia.