gebhart/patrepeval huggingface dataset:
A novel phosphatase upregulated inAkp3knockout mice (2007)

Reexamination of the Akp3(-/-) mouse intestine showed that, despite the lack of intestinal alkaline phosphatase (IAP), the Akp3(-/-) gut still had considerable alkaline phosphatase (AP) activity in the duodenum and ileum. This activity is due to the expression of a novel murine Akp6 gene that encodes an IAP isozyme expressed in the gut in a global manner (gIAP) as opposed to duodenum-specific IAP (dIAP) isozyme encoded by the Akp3 gene. Phylogenetically, gIAP is similar to the rat IAP I isozyme. Kinetically, gIAP displays a 5.7-fold reduction in catalytic rate constant (k(cat)) and a 30% drop in K(m), leading to a 4-fold reduction k(cat)/K(m) compared with dIAP, and these changes in enzymatic properties can all be attributed to a crucial R317Q substitution. Western and Northern blot analyses document the expression of Akp6 in the gut, from the duodenum to the ileum, and it is upregulated in the jejunum and ileum of Akp3(-/-) mice. Developmentally, Akp3 expression is turned on during postnatal days 13-15 and exclusively in the duodenum, whereas Akp6 and Akp5 are expressed from birth throughout the gut with enhanced expression at weaning. Posttranslational modifications of gIAP have a pronounced effect on its catalytic properties. Given the low catalytic efficiency of gIAP, its upregulation during fat feeding, its sequence similarity with rat IAP I, and the fact that rat IAP I has been implicated in the upregulation of surfactant-like particles during fat intake, it appears likely that gIAP may have a role in mediating the accelerated fatty acid intake observed in Akp3(-/-) mice fed a high-fat diet.
Techniques in Quantification and Localization of Gene Expression (2000)

Basic Methods.- 1. Basic Flow Cytometry Instrumentation.- Instrumentation.- Overview.- Delivery of Sample.- Light Source and Signal Detection.- Data Analysis.- Gating.- Color Compensation.- Conclusion.- 2. Fixation for In Situ Molecular Analysis.- Types of Fixatives.- Cells.- Tissue.- 3. A Method for Reduction of Green Wavelength Autofluorescence Emission in Cellular Preparations.- Protocols-Flow Cytometry.- Trypan Blue with Surface Staining.- Surface Stain Plus In Situ Hybridization.- Surface Label Plus In Situ PCR or RT-PCR.- 4. Gene Quantification: Choosing the Target.- Fresh Cells and Tissue.- Quantification of Gene Expression Prior to In Situ Analysis.- 5. Detection and Quantification of Cytokine-Producing Cells by Immunostaining.- Materials.- Methods.- Procedure 1: Cytokine Detection of Individual Cells Smeared on Slides Using Immunostaining.- Quantification of Individual Cytokine-Producing Cells by Automated Computerized Image Analysis (ACIA).- Assessment of Cell Size, Intensity of Signal, and Enumeration of Individual Cytokine-Producing Cells.- Procedure 2: Immunofluorescent Staining of Cytokine-Producing Cells in Suspension.- Procedure 3. Cytokine Detection in Tissue Using Immunohistochemistry.- Troubleshooting.- 6. In Situ Hybridization Using the bDNA Technology.- Materials and Methods.- Reagents.- Preparation of Cytospin Slides.- Pretreatment of Slides Prior to Hybridization.- Hybridization and Signal Development.- Results and Discussion.- Conclusions.- Acknowledgments.- Specific Applications.- 7. Kaposi's Sarcoma-Associated Human Herpes Virus Eight: Localization of Viral Gene Expression and Viral Latency.- Materials and Methods.- Clinical Samples.- Solution-Based PCR and Serologic Assays.- In Situ Hybridization.- In Situ Polymerase Chain Reaction.- Results.- Discussion.- 8. Pathogenetic Mechanisms of Animal Orbiviruses That Cause Disease at Low Copy Number.- Materials and Methods.- Experimental Design.- Clinical Samples.- Virus Isolation.- Immunochemistry.- Nested Reverse Transcription Polymerase Chain Reaction.- In Situ Hybridization.- Reverse Transcription In Situ Polymerase Chain Reaction.- Results.- Clinicopathologic Features.- Isolation and Typing of Viruses.- Tissue Distribution and Cellular Localization of Viral Proteins and Nucleic Acids.- Discussion.- 9. Localization of Hepatitis C Virus Using Reverse Transcriptase Fluorescence In Situ 5' Nuclease Assay.- Determining the Localization Method.- Detection of Gene Expression in Specific Cell Types.- 10. Simultaneous Quantification and Localization of HIV gag-pol Expression Using Ultrasensitive Fluorescence In Situ Hybridization.- 11. Quantification and Localization of Gene Expression: Future Directions.
Crossed-beam spectral interferometry: a simple, high-spectral-resolution method for completely characterizing complex ultrashort pulses in real time (2006)

We present a high-spectral-resolution and experimentally simple version of spectral interferometry using optical fibers and crossed beams, which we call SEA TADPOLE. Rather than using collinear unknown and reference pulses separated in time to yield spectral fringes-and reduced spectral resolution-as in current versions, we use time-coincident pulses crossed at a small angle to generate spatial fringes. This allows the extraction of the spectral phase with the full spectrometer resolution, which allows the measurement of much longer and more complex pulses. In fact, SEA TADPOLE achieves spectral super-resolution, yielding the pulse spectrum with even better resolution. Avoiding collinear beams and using fiber coupling also vastly simplify alignment. We demonstrate SEA TADPOLE by measuring a chirped pulse, a double pulse separated by 14 ps, and a complex pulse comprising two trains of pulses with a time-bandwidth product of ~400.
Glass Surfaces Grafted with High-Density Poly(ethylene glycol) as Substrates for DNA Oligonucleotide Microarrays (2005)

Surfaces carrying a dense layer of poly(ethylene glycol) (PEG) were prepared, characterized, and tested as substrates for DNA oligonucleotide microarrays. PEG bis(amine) with a molecular weight of 2000 was grafted onto silanized glass slides bearing aldehyde groups. After grafting, the terminal amino groups of the PEG layer were derivatized with the heterobifunctional cross-linker succinimidyl 4-[p-maleimidophenyl]butyrate to permit the immobilization of thiol-modified DNA oligonucleotides. The stepwise chemical modification was validated with X-ray photoelectron spectroscopy. Goniometry indicated that the PEG grafting procedure reduced surface inhomogeneities present after the silanization step, while atomic force microscopy and ellipsometry confirmed that the PEG layer was dense and monomolecular. Hybridization assays using DNA oligonucleotides and fluorescence imaging showed that PEG grafting improved the yield in hybridization 4-fold compared to non-PEGylated maleimide-derivatized surfaces. In addition, the PEG layer reduced the nonspecific adsorption of DNA by a factor of up to 13, demonstrating that surfaces with a dense PEG layer represent suitable substrates for DNA oligonucleotide microarrays.
Les toxines bactériennes recombinantes: de nouveaux vecteurs pour la vaccination ? (2000)

Les lymphocytes T cytotoxiques CD8 + (CTL) sont des composants-cles de la reponse immunitaire. Ils reconnaissent de courts peptides antigeniques de 8 a 10 acides amines, associes aux molecules du complexe majeur d'histocompatibilite de classe I (CMH-I). Ces peptides sont generalement issus de la degradation de proteines cytosoliques. De ce fait, l'activation de reponses des CTL requiert, dans la majorite des cas, la synthese ou l'introduction prealable de la proteine antigenique dans le cytosol des cellules presentatrices d'antigenes. De nouvelles strategies ont ete recemment developpees pour delivrer les antigenes dans ces cellules. Ces strategies sont fondees sur les capacites naturelles de toxines bacteriennes a penetrer dans les cellules eucaryotes. Il est maintenant possible, en utilisant des toxines recombinantes genetiquement detoxifiees, de delivrer des antigenes heterologues dans les cellules presentatrices d'antigenes et d'activer ainsi des reponses CTL specifiques et protectrices in vivo. Dans cet article, nous discuterons les perspectives de ces nouvelles strategies vaccinales.
Tryptophan fluorescence as a probe of placental ribonuclease inhibitor binding to angiogenin (1989)

The binding of human placental ribonuclease inhibitor (PRI) to angiogenin, a human protein that induces neovascularization, occurs with a 1:1 stoichiometry and is accompanied by a 50% increase in tryptophan fluorescence. In contrast, the binding of PRI to bovine pancreatic RNase A or to angiogenin oxidized at its single tryptophan residue results in a quenching of fluorescence. These observations suggest that there is a change in the local environment of Trp-89 of angiogenin. Quenching experiments with acrylamide are consistent with the view that Trp-89 is exposed in the native protein and becomes less accessible upon formation of the complex with PRI. Stopped-flow kinetic measurements monitoring the fluorescence enhancement indicate a two-step mechanism for the binding of PRI to angiogenin. The first step involves rapid formation of an enzyme-inhibitor complex, EI, followed by a slower isomerization of EI to a tight enzyme-inhibitor complex, EI*: (Formula: see text). In 0.1 M NaCl at pH 6 and 25 degrees C, the values of K1 and K2 are 0.53 microM and 97 s-1, respectively. The apparent second-order rate constant of association at protein concentrations much less than K1 is approximated by K2/K1 and equals 1.8 X 10(8) M-1 s-1. The corresponding value for the association of PRI with RNase A is only slightly higher, 3.4 X 10(8) M-1 s-1. The effects of pH and sodium chloride concentration on the association rate of PRI with angiogenin suggest the importance of ionizable groups and ionic interactions, respectively, in the association process.(ABSTRACT TRUNCATED AT 250 WORDS)
Source model for transform video coder and its application. I. Fundamental theory (1997)

A source model describing the relationship between bits, distortion, and quantization step sizes of a large class of block-transform video coders is proposed. This model is initially derived from the rate-distortion theory and then modified to match the practical coders and real image data. The realistic constraints such as quantizer dead-zone and threshold coefficient selection are included in our formulation. The most attractive feature of this model is its simplicity in its final form. It enables us to predict the bits needed to encode a picture at a given distortion or to predict the quantization step size at a given bit rate. There are two aspects of our contribution: one, we extend the existing results of rate-distortion theory to the practical video coders, and two, the nonideal factors in real signals and systems are identified, and their mathematical expressions are derived from empirical data. One application of this model, as shown in the second part of this paper, is the buffer/quantizer control on a CCITT P/spl times/64 k coder with the advantage that the picture quality is nearly constant over the entire picture sequence.
Ryanodine receptor antibodies are associated with severe myasthenia gravis (1996)

Sera from 32 thymoma patients, 29 of them with myasthenia gravis (MG), were tested for the presence of circulating antibodies to the ryanodine receptor (RyR) in Western blot RyR is a channel protein essential for the excitation‐contraction coupling in skeletal muscle. MG severity was scored according to the Osserman classification during 1–17 years of follow‐up (mean 7 years). Fifteen patients (14 MG and 1 non‐MG) were RyR‐antibody positive. RyR‐positive patients had a significantly higher frequency of invasive thymomas ( p = 0.01), and also a more severe MG than RyR‐antibody negative patients ( p = 0.04). The use of immunosuppressive drugs at latest follow‐up was more frequent in RyR‐antibody positive than in RyR‐antibody negative patients ( p = 0.02). Thus the presence of RyR‐antibodies in thymoma patients is associated with a more severe disease and can be used as a prognostic marker.
Long-Term Survival for Patients With Non–Small-Cell Lung Cancer With Intratumoral Lymphoid Structures (2008)

The density of mature DCs was found to be a better predictor of clinical outcome than the other parameters tested. The number of tumor-infiltrating mature DCs may identify patients with early-stage NSCLC who have a high risk of relapse.
Mixing rates for the alternating Gibbs sampler over restricted Boltzmann machines and friends (2016)

Alternating Gibbs sampling is a modification of classical Gibbs sampling where several variables are simultaneously sampled from their joint conditional distribution. In this work, we investigate the mixing rate of alternating Gibbs sampling with a particular emphasis on Restricted Boltzmann Machines (RBMs) and variants.
A background timing-skew calibration technique for time-interleaved analog-to-digital converters (2006)

This paper presents a background timing-skew calibration technique for time-interleaved analog-to-digital converters (ADCs). The timing skew between any two adjacent analog-digital (A/D) channels is detected by counting the number of zero crossings of the ADCs input while randomly alternating their sampling sequence. Digitally controlled delay units are adjusted to minimize the timing skews among the A/D channels caused by the mismatches among the clock routes. The calibration behaviors, including converging speed and timing jitter, are theoretically analyzed and verified with simulations. A 6-bit 16-channel ADC is used as an example.
Induction of apoptosis by human amylin in RINm5F islet β‐cells is associated with enhanced expression of p53 and p21WAF1/CIP1 (1999)

Human amylin (10 microM) significantly inhibited RINm5F islet beta-cell proliferation and evoked apoptosis associated with typical degenerative ultrastructural changes and DNA fragmentation, whereas rat amylin did not. Time course analysis showed that human amylin elicited apoptosis in a passage-dependent manner. Expression of the apoptosis-related genes p53, bcl-2 and WAF1/CIP1 was examined using Northern blots. mRNAs corresponding to p53 and to p21WAF/CIP1 were remarkably increased following human amylin treatment, whereas no change in bcl-2 was detected. Our data suggest a role of p53 and p21 in human amylin-induced beta-cell apoptosis. Furthermore, cells with higher proliferative potential (lower passage) were found to be more susceptible to apoptosis and to induction of p53, suggesting that beta-cells with different proliferation rates respond differently to human amylin, and that human amylin may be more toxic to proliferating cells.
Dendritic nanocarriers based on hyperbranched polymers (2015)

Hyperbranched polymers are obtained through one-step polymerization reactions and exhibit properties that are very similar to those of perfect dendrimer analogues. Therefore, hyperbranched polymers are a suitable alternative for perfect dendrimers as building blocks for dendritic nanocarrier systems. With regard to using soluble hyperbranched polymers as carrier systems, their flexible chains are a major benefit as they can adopt and compartment guest molecules. Upon encapsulation, the properties of the host decides the fate of the guest, e.g., solubility, but the host can also shield a guest from the environment and protect it, e.g., from degradation and deactivation. With regard to the advantages of using hyperbranched polymers as nanocarrier systems and their scalable synthesis, we will discuss different types of hyperbranched polymers and their application as nanocarrier systems for drugs, dyes, and other guest molecules.
AC Electric Field Communication for Human-Area Networking (2010)

We have proposed a human-area networking technology that uses the surface of the human body as a data transmission path and uses an AC electric field signal below the resonant frequency of the human body. This technology aims to achieve a “touch and connect” intuitive form of communication by using the electric field signal that propagates along the surface of the human body, while suppressing both the electric field radiating from the human body and mutual interference. To suppress the radiation field, the frequency of the AC signal that excites the transmitter electrode must be lowered, and the sensitivity of the receiver must be raised while reducing transmission power to its minimally required level. We describe how we are developing AC electric field communication technologies to promote the further evolution of a human-area network in support of ubiquitous services, focusing on three main characteristics, enabling-transceiver technique, application-scenario modeling, and communications quality evaluation. Special attention is paid to the relationship between electro-magnetic compatibility evaluation and regulations for extremely low-power radio stations based on Japan's Radio Law.
Precision mapping of quantitative trait loci. (1994)

Adequate separation of effects of possible multiple linked quantitative trait loci (QTLs) on mapping QTLs is the key to increasing the precision of QTL mapping. A new method of QTL mapping is proposed and analyzed in this paper by combining interval mapping with multiple regression. The basis of the proposed method is an interval test in which the test statistic on a marker interval is made to be unaffected by QTLs located outside a defined interval. This is achieved by fitting other genetic markers in the statistical model as a control when performing interval mapping. Compared with the current QTL mapping method (i.e., the interval mapping method which uses a pair or two pairs of markers for mapping QTLs), this method has several advantages. (1) By confining the test to one region at a time, it reduces a multiple dimensional search problem (for multiple QTLs) to a one dimensional search problem. (2) By conditioning linked markers in the test, the sensitivity of the test statistic to the position of individual QTLs is increased, and the precision of QTL mapping can be improved. (3) By selectively and simultaneously using other markers in the analysis, the efficiency of QTL mapping can be also improved. The behavior of the test statistic under the null hypothesis and appropriate critical value of the test statistic for an overall test in a genome are discussed and analyzed. A simulation study of QTL mapping is also presented which illustrates the utility, properties, advantages and disadvantages of the method.
Object-oriented database management systems: concepts and issues (1991)

Requirements imposed on both the object data model and object management by the support of complex objects are outlined. The basic concepts of an object-oriented data model are discussed. They are objects and object identifiers, aggregation, classes and instantiation mechanisms, metaclasses, and inheritance. Object-oriented models are compared with semantic, relational, and Codasyl models. Object-oriented query languages and query processing are considered. Some operational aspects of data management in object-oriented systems are examined. Schema evolution is discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
An IEEE 1588 time synchronization testbed for assessing power distribution requirements (2010)

Wide-area monitoring (WAM) applications for power distribution rely on accurate global time synchronization. Furthermore, there is interest in replacing current time synchronization methods such as Inter Range Instrumentation Group (IRIG), with distributed time synchronization protocols that utilize the data communication lines eliminating the need for dedicated timing signals within the substation. By understanding the factors impacting synchronization performance, the testbed facilitates the characterization of metrics needed to meet industry requirements. The testbed provides an experimental venue to explore IEEE 1588 Precision Time Protocol (PTP) technologies and determine how new features and requirements for time synchronization can impact the performance of next-generation power distribution applications. Initial results indicate PTP has the capabilities to support an accurate and scalable time synchronization solution given the components are interoperable.
New Directions in the Synthesis of Glycopeptide Mimetics (1999)

Structural and functional mimetics of naturally occurring glycopeptides are attractive synthetic targets owing to their potential as biological tools and therapeutic agents. The syntheses of C- and S-glycopeptides, glycopeptoids, and oxime- (figure) and thioether-linked glycopeptides have now been realized, and many of these mimetics are currently undergoing biological evaluation.
On-line trajectory generation: Nonconstant motion constraints (2012)

A concept of on-line trajectory generation for robot motion control systems enabling instantaneous reactions to unforeseen sensor events was introduced in a former publication. This previously proposed class of algorithms requires constant kinematic motion constraints, and this paper extends the approach by the usage of time-variant motion constraints, such that low-level trajectory parameters can now abruptly be changed, and the system can react instantaneously within the same control cycle (typically one millisecond or less). This feature is important for instantaneous switchings between state spaces and reference frames at sensor-dependent instants of time, and for the usage of the algorithm as a control submodule in a hybrid switched robot motion control system. Real-world experimental results of two sample use-cases highlight the practical relevance of this extension.
Laser-produced lithium plasma as a narrow-band extended ultraviolet radiation source for photoelectron spectroscopy (1998)

Extended ultraviolet (EUV) emission characteristics of a laser-produced lithium plasma are determined with regard to the requirements of x-ray photoelectron spectroscopy. The main features of interest are spectral distribution, photon flux, bandwidth, source size, and emission duration. Laser-produced lithium plasmas are characterized as emitters of intense narrow-band EUV radiation. It can be estimated that the lithium Lyman-alpha line emission in combination with an ellipsoidal silicon/molybdenum multilayer mirror is a suitable EUV source for an x-ray photoelectron spectroscopy microscope with a 50-meV energy resolution and a 10-mum lateral resolution.
A Primer on Vacuum Pressure Measurement (2009)

It's often said that we live at the bottom of a sea of air. Looking more closely at the atmosphere around us it is composed of a variety of molecules such as nitrogen, oxygen, water vapor, carbon dioxide, argon and a host of other natural and manmade substances. The density of this mixture of molecules is determined by such factors as the total depth of the atmosphere, ambient temperature, altitude and meteorological conditions. At the microscopic level, the molecules are in motion and the combined force exerted by this vibrating mass of molecules on a surface is something we call pressure.