gebhart/patrepeval huggingface dataset:
Self-routing optical crossbar switch (1990)

A self-routing optical crossbar switch in which wavelengths of tag light represent the information of destination address by using an optically addressable spatial light modulator as the 3-D crossbar switch along with a wavelength filter for tag light. A BSO (Bi/sub 12/SiO/sub 20/) spatial light modulator was used to perform a 1*2 self-routing switching experiment with two different wavelengths of tag light. The implementation to scale-up the throughput of the switch is also presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Gaussian Interference Channel Capacity to Within One Bit (2008)

The capacity of the two-user Gaussian interference channel has been open for 30 years. The understanding on this problem has been limited. The best known achievable region is due to Han and Kobayashi but its characterization is very complicated. It is also not known how tight the existing outer bounds are. In this work, we show that the existing outer bounds can in fact be arbitrarily loose in some parameter ranges, and by deriving new outer bounds, we show that a very simple and explicit Han-Kobayashi type scheme can achieve to within a single bit per second per hertz (bit/s/Hz) of the capacity for all values of the channel parameters. We also show that the scheme is asymptotically optimal at certain high signal-to-noise ratio (SNR) regimes. Using our results, we provide a natural generalization of the point-to-point classical notion of degrees of freedom to interference-limited scenarios.
Prediction of endoplasmic reticulum resident proteins using fragmented amino acid composition and support vector machine (2017)

We found that out of 124 proteins of the training dataset, only 66 proteins had endoplasmic reticulum retention signals, which shows that these signals are not an absolute necessity for endoplasmic reticulum resident proteins to remain inside the endoplasmic reticulum. This observation also strongly indicates the role of additional factors in retention of proteins inside the endoplasmic reticulum. Our proposed predictor, ERPred, is a signal independent tool. It is tuned for the prediction of endoplasmic reticulum resident proteins, even if the query protein does not contain specific ER-retention signal.
Self-Assembly of the Recombinant Capsid Protein of a Swine Norovirus into Virus-Like Particles and Evaluation of Monoclonal Antibodies Cross-Reactive with a Human Strain from Genogroup II (2008)

Noroviruses (NoVs) are responsible for the majority of gastroenteritis outbreaks in humans. Recently, NoV strains which are genetically closely related to human genogroup II (GII) NoVs have been detected in fecal specimens from swine. These findings have raised concern about the possible role of pigs as reservoirs for NoVs that could infect humans. To better understand the epidemiology of swine NoVs in both the swine and the human populations, rapid immunoassays are needed. In this study, baculovirus recombinants were generated to express the capsid gene of a swine NoV GII genotype 11 (GII.11) strain which self-assembled into virus-like particles (VLPs). Subsequently, the purified VLPs were used to evoke monoclonal antibodies (MAbs) in mice. A panel of eight promising MAbs was obtained and evaluated for their ability to bind to heterologous VLPs, denaturated antigens, and truncated capsid proteins. The MAbs could be classified into two groups: two MAbs that recognized linear epitopes located at the amino-terminal half (shell domain) of the swine NoV GII.11 VLPs and that cross-reacted with human GII.4 NoV VLPs. The other six MAbs bound to conformational epitopes and did not cross-react with the human GII.4 VLPs. To our knowledge, this is the first report on the characterization of MAbs against swine NoVs. The swine NoV VLPs and the MAbs described here may be further used for the design of diagnostic reagents that could help increase our knowledge of the prevalence of NoV infections in pigs and the possible role of pigs as reservoirs for NoVs.
All SMILES Variational Autoencoder (2019)

Variational autoencoders (VAEs) defined over SMILES string and graph-based representations of molecules promise to improve the optimization of molecular properties, thereby revolutionizing the pharmaceuticals and materials industries. However, these VAEs are hindered by the non-unique nature of SMILES strings and the computational cost of graph convolutions. To efficiently pass messages along all paths through the molecular graph, we encode multiple SMILES strings of a single molecule using a set of stacked recurrent neural networks, pooling hidden representations of each atom between SMILES representations, and use attentional pooling to build a final fixed-length latent representation. By then decoding to a disjoint set of SMILES strings of the molecule, our All SMILES VAE learns an almost bijective mapping between molecules and latent representations near the high-probability-mass subspace of the prior. Our SMILES-derived but molecule-based latent representations significantly surpass the state-of-the-art in a variety of fully- and semi-supervised property regression and molecular property optimization tasks.
Expression of alpha-(1,3)-fucosyltransferases which synthesize sialyl Le(x) and sialyl Le(a), the carbohydrate ligands for E- and P-selectins,in human malignant cell lines. (1993)

Transcripts of alpha-(1,3)-fucosyltransferases in human epithelial cancer and leukemia cell lines were analyzed by Northern blotting and reverse transcriptase mediated-polymerase chain reaction using specific probes and primers which can discriminate between the transcripts derived from the four alpha-(1,3)-fucosyltransferase genes Fuc-TIII, IV, V, and VI. Flow cytometric analysis of the sialyl Le(x) and sialyl Le(a) antigens was also performed on the same cell lines. The sialyl Le(x) antigen was expressed on 14 of 15 epithelial cancer cell lines, and the sialyl Le(a) antigen was detected on 8 of them. The message of Fuc-TIII was detected in most of the epithelial cancer cell lines (14 of 15), which correlated with the surface expression of these carbohydrate determinants. In addition, the messages of Fuc-TIV and Fuc-TVI were detected in most epithelial cancer cell lines, while the message of Fuc-TV was undetectable in most of them. On the other hand, all leukemia cell lines were positively stained for sialyl Le(x), but none of them was stained for sialyl Le(a) in flow cytometry. The messages of Fuc-TIV++ were detected in all leukemia cell lines tested. Small quantities of Fuc-TIII, V, and/or VI messages were also detected in some leukemia cell lines in reverse transcriptase mediated-polymerase chain reaction analysis. These studies indicate that alpha-(1,3)-fucosyltransferase activities in epithelial cancer and leukemia cell lines are mixtures of multiple molecular species of alpha-(1,3)-fucosyltransferases. It is natural that epithelial cancer cells contain a significant amount of Fuc-TIII mRNA and leukemia cell lines contain Fuc-TIV mRNA, since their normal counterparts, normal epithelial cells and leukocytes, respectively, are known to contain these fucosyltransferases. The unexpectedly frequent occurrence of Fuc-TIV mRNA in epithelial cancer cell lines may be related to their retro-differentiation associated with tumorigenesis. Another unexpected finding was a weak but significant expression of the alpha-(1,3)-fucosyltransferases Fuc-TIII, V, and/or VI in leukemia cell lines detected by reverse transcriptase mediated-polymerase chain reaction analysis. Since these enzymes are known to be capable of synthesizing the sialyl Le(x) determinant, this finding implies a possibility that some of them may be involved in the synthesis of sialyl Le(x) in leukemia cells.
Photoinduced oxidation of sea salt halides by aromatic ketones: a source of halogenated radicals (2009)

Abstract. The interactions between triplet state benzophenone and halide anion species (Cl
Twelve random access strategies for the fiber optic networks (1988)

Twelve random-access strategies that do not constrain the distance or transmission rate of a network, and can use the capabilities of fiber-optic components, are described and compared. The twelve strategies consist of three protocols, each of which can use two timing arrangements and two network-access devices. The three protocols are the standard ALOHA protocol, LCSMA, and LCSMA/CD. The last two protocols operate on linear-unidirectional networks and use local information at the transmitter to increase the throughput of the system. The networks considered have a common point that all transmitted signals pass through before being received. This makes two timing arrangements possible; a slotted system or an unslotted system. The taps on the network can be either passive or active.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The epidermal growth factor receptor tyrosine kinase in liver epithelial cells (1989)

Epidermal growth factor (EGF) activates the intrinsic tyrosine-specific protein kinase of its receptor (EGF-R). We studied the effect of EGF-dependent EGF-R internalization on receptor autophosphorylation and on the appearance of tyrosine phosphoproteins in rat liver epithelial cells. Peak receptor autophosphorylation activity (3- to 6-fold over basal) was found in homogenates of EGF-treated cells at times when the majority of receptors (greater than 90%) had been internalized but not yet degraded (15 to 30 min). Stimulated activity persisted for at least 2 h if EGF-R degradation was blocked by methylamine or 18 degrees C incubation. Detection of stimulated autophosphorylation in homogenates of cells treated with EGF in culture required detergent in the assay. Detergent was not necessary to detect stimulated autophosphorylation when EGF was added directly to homogenates of untreated cells. Immunoblots using antibodies against phosphotyrosine (p-Tyr) demonstrated that EGF treatment of intact cells increased the p-Tyr content of at least seven proteins (EGF-R, 115, 100, 75, 66, 57, and 52 kDa) within 5 s. Incubation of intact cells with EGF at 0 degrees C to prevent endocytosis still resulted in tyrosine phosphorylation of these seven proteins. In contrast, several substrates (120, 78, and 38 kDa) showed delayed increases (45-90 s) in tyrosine phosphorylation at 37 degrees C; their phosphorylation was even slower at 18 degrees C and did not occur at 0 degrees C. In cells incubated with EGF at 18 degrees C or in the presence of methylamine, EGF-R p-Tyr in the intact cell was lost by 2 h even though receptor was not degraded and still exhibited enhanced autophosphorylation in the homogenate assay. These findings suggest that tyrosine phosphorylation in response to EGF occurs predominantly during the initial stages of endocytosis and is mediated for the most part by ligand-receptor complexes at the cell surface. A subset of phosphorylations may require intracellular movement.
Characterization of Ehrlichia risticii binding, internalization, and proliferation in host cells by flow cytometry (1993)

The binding, internalization, and proliferation of Ehrlichia risticii in P388D1 cells and equine polymorphonuclear (PMN) leukocytes were studied by immunofluorescent staining and flow cytometric analysis. The binding of ehrlichiae to P388D1 cells at 4 degrees C was dose dependent, and the antigens of bound organisms were susceptible to pronase treatment. Additionally, the binding of ehrlichiae to P388D1 cells was diminished when either P388D1 cells or ehrlichiae were treated with 1% paraformaldehyde for 30 min or 0.25% trypsin for 15 min. These results indicate that the ehrlichial ligand and host cell receptor are likely surface proteins. Following incubation at 37 degrees C, bound E. risticii and/or its antigens were removed with pronase and indirect immunofluorescent staining in the presence of saponin was used to examine intracellular ehrlichiae. Our results indicate that E. risticii was internalized into P388D1 cells within 3 h and proliferated by 48 h of incubation. The microfilament-disrupting agent cytochalasin D and the transglutaminase inhibitor monodansylcadaverine were used to differentiate between phagocytosis (sensitive to cytochalasin) and receptor-mediated endocytosis (sensitive to monodansylcadaverine) of E. risticii by P388D1 cells. In concentrations that produced distinctive morphological changes and inhibited phagocytosis of polystyrene latex beads, cytochalasin D did not suppress the infectivity of E. risticii. Binding, internalization, or proliferation of E. risticii was not affected by cytochalasin D. However, monodansylcadaverine inhibited infection of E. risticii in a dose-dependent manner. The agent did not affect the attachment of ehrlichiae to host cells, but it did suppress internalization and proliferation. These results suggest that E. risticii is internalized by receptor-mediated endocytosis and that productive infection by E. risticii does not depend on phagocytosis by the P388D1 cells. Although E. risticii did not bind to the surface of equine PMN leukocytes at 4 degrees C, organisms were taken up by this cell at 37 degrees C. E. risticii, however, failed to survive in equine PMN leukocytes.
The Temperature at the Ocean-Air Interface (1967)

A simple theory is presented to account for the difference between the temperature at the ocean-air interface and that of the water at a depth of about one meter. Except in very light winds and intense solar radiation the mean temperature difference ΔT is expected to be of the formwhere q is the sum of the sensible, latent, and long-wave radiative heat flux from ocean to atmosphere and τ/ρw is the kinematic stress. No data are available to test this prediction. The influence of slicks and solar insolation on interface temperature is also briefly discussed.
Bureaucracy and Development in the Sudan (1989)

With good education and a relatively high functional capability, Sudanese Public servants have had the potential to playa major role in the political and socio-economic development of their country. Unfortunately, all development plans since independence have failed to achieve their goals. This failure was caused by administrative inefficiency and obsolete structures, bureaucratic infighting, and the lack of co-ordination, leading to poor implemention and execution of government policies.
Autophagy genes function sequentially to promote apoptotic cell corpse degradation in the engulfing cell (2012)

Apoptotic cell degradation is a fundamental process for organism development, and impaired clearance causes inflammatory or autoimmune disease. Although autophagy genes were reported to be essential for exposing the engulfment signal on apoptotic cells, their roles in phagocytes for apoptotic cell removal are not well understood. In this paper, we develop live-cell imaging techniques to study apoptotic cell clearance in the Caenorhabditis elegans Q neuroblast lineage. We show that the autophagy proteins LGG-1/LC3, ATG-18, and EPG-5 were sequentially recruited to internalized apoptotic Q cells in the phagocyte. In atg-18 or epg-5 mutants, apoptotic Q cells were internalized but not properly degraded; this phenotype was fully rescued by the expression of autophagy genes in the phagocyte. Time-lapse analysis of autophagy mutants revealed that recruitment of the small guanosine triphosphatases RAB-5 and RAB-7 to the phagosome and the formation of phagolysosome were all significantly delayed. Thus, autophagy genes act within the phagocyte to promote apoptotic cell degradation.
Theory of the Performance of Porous Fuel Cell Electrodes (1966)

A theoretical analysis of the polarization mechanisms in a porous fuel cell electrode was made employing a model consisting of a single pore coated by a thin film of electrolyte. The analysis accounted for those polarizations associated with transport of electrolyte species, transport of dissolved gas, chemical reaction at the solid‐liquid interface, and ohmic losses in the electrolyte. The theory was compared with data from biporous nickel electrodes operating on oxygen in 80% at temperatures ranging from 300° to 500°F.
Design of Integrated Risk Management-Based Dynamic Driving Control of Automated Vehicles (2017)

This paper describes the design of a fully automated driving algorithm for automated driving in complex urban scenarios and motorways with a satisfactory safety level. The proposed algorithm consists of the following three steps: surround recognition, motion planning, and vehicle control. The surround recognition system consists of three main modules: object classification, vehicle/non-vehicle tracking and dynamic drivable area determination. All system modules utilize information from potentially commercializable sensors such as vision sensors, radars, lidar and vehicle sensors. The objective of the motion planning module is to derive an optimal trajectory as a function of time and the surround recognition results. A dynamic drivable area is represented as a complete driving corridor that leads to the destination while making sure all objects are outside the left or right corridor bounds. In the case of moving objects such as other traffic participants, their behaviors are anticipated within the dynamic drivable area. The optimal trajectory planning uses the dynamic drivable area as a safety constraint and computes a trajectory in which the vehicle stays in its safe bounds considering the driver?s pattern and characteristics based on predicted risk potential. The developed algorithm has been evaluated by computer simulation and vehicle tests on urban roads and motorways.
A flow aggregation method for the scalable and efficient quality of service support in Next Generation Networks (2013)

The services in the Next Generation Network (NGN) will be created on demand by the customers and will require end-to-end Quality of Service (QoS) for each flow. A very significant component for the end-to-end QoS support in the Internet is the packet schedulers in the routers. The complexity of the packet scheduling algorithms increases with the number of flows. As a solution, flow aggregation decreases the number of flows processed by the scheduler. The previous work in the literature proves that if the flow aggregator is fair, the end-to-end delay bounds of the aggregated flows are preserved and suggests limiting the service rate for the aggregate flow to achieve fairness in the expense of a lower utilization of the network resources. In this paper, we present a new method for flow aggregation, which relaxes this limit on the aggregate service rate, to increase the link utilization. We analytically show that our aggregation method is fair. Consequently, the end-to-end delay bounds in the network are preserved. In addition, we provide simulation results to demonstrate the decreased average delay of the aggregated flow.
Analysis of vibration signals for condition monitoring of power switching equipment using wavelet transform (2002)

A transient vibration signal processing technique jointly utilising wavelet transforms and a neural network has been developed. A nondecimated wavelet transform is employed as the wavelet band energy feature extractor and decimated wavelet transform as the envelope feature extractor for primary vibration signals. The feature patterns prepared from the output of the two feature extractors are used to train a self-organising map (SOM) for fault detection on power switching equipment. From the present investigation, it is concluded that wavelet-based feature extractor permits the extraction of essential features from transient vibration signals. Normalised quantisation error (NQE) of SOM is introduced to quantify the deviation of a vibration signal and its template. Numerical results show that NQE can be used as an effective indicator for faults occurring in a power switching device.
H<sup>+</sup>‐coupled nutrient, micronutrient and drug transporters in the mammalian small intestine (2007)

The H(+)-electrochemical gradient was originally considered as a driving force for solute transport only across cellular membranes of bacteria, plants and yeast. However, in the mammalian small intestine, a H(+)-electrochemical gradient is present at the epithelial brush-border membrane in the form of an acid microclimate. Over recent years, a large number of H(+)-coupled cotransport mechanisms have been identified at the luminal membrane of the mammalian small intestine. These transporters are responsible for the initial stage in absorption of a remarkable variety of essential and non-essential nutrients and micronutrients, including protein digestion products (di/tripeptides and amino acids), vitamins, short-chain fatty acids and divalent metal ions. Proton-coupled cotransporters expressed at the mammalian small intestinal brush-border membrane include: the di/tripeptide transporter PepT1 (SLC15A1); the proton-coupled amino-acid transporter PAT1 (SLC36A1); the divalent metal transporter DMT1 (SLC11A2); the organic anion transporting polypeptide OATP2B1 (SLC02B1); the monocarboxylate transporter MCT1 (SLC16A1); the proton-coupled folate transporter PCFT (SLC46A1); the sodium-glucose linked cotransporter SGLT1 (SLC5A1); and the excitatory amino acid carrier EAAC1 (SLC1A1). Emerging research demonstrates that the optimal intestinal absorptive capacity of certain H(+)-coupled cotransporters (PepT1 and PAT1) is dependent upon function of the brush-border Na(+)-H(+) exchanger NHE3 (SLC9A3). The high oral bioavailability of a large number of pharmaceutical compounds results, in part, from absorptive transport via the same H(+)-coupled cotransporters. Drugs undergoing H(+)-coupled cotransport across the intestinal brush-border membrane include those used to treat bacterial infections, hypercholesterolaemia, hypertension, hyperglycaemia, viral infections, allergies, epilepsy, schizophrenia, rheumatoid arthritis and cancer.
Concise and Enantioselective Synthesis of Fmoc-Pmp(Bu<sup>t</sup>)<sub>2</sub>-OH and Design of Potent Pmp-Containing Grb2-SH2 Domain Antagonists (2003)

[reaction: see text] L-Phosphonomethylphenylalanine (L-Pmp) is an important phosphatase-resistant pTyr analogue. A most concise and stereoselective approach to the synthesis of the suitably protected Fmoc-Pmp(Bu(t))(2)-OH was developed in order to incorporate the functionally significant L-Pmp residue into peptides and peptidomimetics efficiently using standard Fmoc protocol. With this key building block, we are able to efficiently synthesize a series of potent Pmp-containing Grb2-SH2 domain antagonists, which can be used as chemotherapeutic leads for the treatment of erbB2-overexpressed breast cancer.
Research toward optical-fiber transmission systems (1973)

The fundementals of optical fiber transmission systems including the fiber transmission medium, sources suitable for use as a carrier, modulation and detection techniques, and some system design considerations are reviewed. The advent of low-loss optical fibers brings new dimensions to optical communication prospects. Fibers may soon be used much as wire pairs of coaxial cable are now used in communication systems. Transmission losses as low as 2 dB/km have been achieved. Experimental repeaters for fiber systems with 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-9</sup> error rate at about 300-Mb/s pulse rate have been reported. Fiber cabling and splicing are among the problems requiring new ideas in order to make feasible an operable system.