gebhart/patrepeval huggingface dataset:
Sugar-Sensing by Chiral Orientation of Dimeric Boronic-Acid-Appended Porphyrins Which Show Selectivity for Glucose and Xylose (1996)

Abstract 5,10,15,20-Tetrakis(4-boronylphenyl)porphyrin (1) and 5,10,15,20-tetrakis[N-(2- or 4-boronylphenyl)methyl-pyridinium]porphyrin (o-2 or p-2) formed a 1:1 complex, which gave specific exciton-coupling bands in CD spectroscopy only in the presence of glucose and xylose among monosaccharides. The structural examination established that only these monosaccharides can bridge two porphyrins by covalent-bond formation with boronic acids and twist them asymmetrically.
Quantum Wires and Dots (2005)

This chapter contains sections titled: Further confinement Schrödinger's equation in quantum wires Infinitely deep rectangular wires Simple approximation to a finite rectangular wire Circular cross-section wire Quantum boxes Spherical quantum dots Non-zero angular momentum states Approaches to pyramidal dots Matrix approaches Finite difference expansions Density of states
Isolation, Purification, and Characterization of a Collagen-associated Serpin, Caspin, Produced by Murine Colon Adenocarcinoma Cells (1998)

A 45-kDa serpin secreted by a murine colon adenocarcinoma cell line, colon26, was isolated, purified, and characterized. It was found to bind specifically to type I collagen with high affinity and to type III collagen with lower affinity. Immunohistochemical studies of murine embryonic tissues showed a specific distribution of this collagen-associated serpin, named caspin, in relation to the formation of bone, cartilage, teeth, and basement membrane. The expression of caspin in high and low lung metastatic subclones of colon26 cell lines was inversely correlated with their metastatic capacity: low lung metastatic cells secreted higher amounts of caspin than their high lung metastatic counterparts. Caspin also demonstrated high homology with human pigment epithelium-derived factor/early population doubling level cDNA-1, which reportedly induces neuronal differentiation of human retinoblastoma cells and is expressed in association with G0 growth arrest. These findings suggest that caspin/pigment epithelium-derived factor/early population doubling level cDNA-1 is a novel factor that might play a crucial role in embryogenesis and tumor metastasis through binding to the extracellular matrix.
Transaction Processing: Concepts and Techniques (1992)

From the Publisher:
The key to client/server computing.
Transaction processing techniques are deeply ingrained in the fields of databases and operating systems and are used to monitor, control and update information in modern computer systems. This book will show you how large, distributed, heterogeneous computer systems can be made to work reliably. Using transactions as a unifying conceptual framework, the authors show how to build high-performance distributed systems and high-availability applications with finite budgets and risk.

The authors provide detailed explanations of why various problems occur as well as practical, usable techniques for their solution. Throughout the book, examples and techniques are drawn from the most successful commercial and research systems. Extensive use of compilable C code fragments demonstrates the many transaction processing algorithms presented in the book. The book will be valuable to anyone interested in implementing distributed systems or client/server architectures.
MitoPark mice mirror the slow progression of key symptoms and L‐DOPA response in Parkinson's disease (2009)

The MitoPark mouse, in which the mitochondrial transcription factor Tfam is selectively removed in midbrain dopamine (DA) neurons, is a genetic model for Parkinson's disease (PD) that replicates the slow and progressive development of key symptoms. To further validate this model, we have extended both behavioral and biochemical analyses in these animals. We found that vertical movements decline earlier and faster than horizontal movements, possibly modeling the early occurrence of axial, postural instability in PD. L-DOPA induces different locomotor responses depending on the age: in young MitoPark mice the L-DOPA-induced motor activation is small; middle-aged MitoPark mice respond in a dose-dependent manner to L-DOPA, whereas aged MitoPark mice display a double-peaked locomotor response to a high dose of L-DOPA that includes an intermittent period of very low motor activity, similar to the 'on-off' phenomenon in PD. To correlate behavior with biochemical data, we analyzed monoamine levels in three different brain areas that are highly innervated by the DA system: striatum, anterior cortex and olfactory bulb. DA levels declined earlier and faster in striatum than in cortex; only at the latest time-point analyzed, DA levels were found to be significantly lower than control levels in the olfactory bulb. Interestingly, the ratio between homovanillic acid (HVA) and DA differed between regions over time. In striatum and olfactory bulb, the ratio increased steeply indicating increased DA turnover. In contrast, the ratio decreased over time in cortex, revealing important differences between DA cells in substantia nigra and the ventral tegmental area.
Detection of multiallele polymorphisms within gene sequences by GC-clamped denaturing gradient gel electrophoresis. (1992)

The ability to efficiently detect DNA polymorphisms is essential for the completion of a high-resolution polymorphic linkage map of the human genome. Currently the most informative polymorphisms are the multiallelic dinucleotide repeat polymorphisms. However, many gene sequences lack an associated dinucleotide repeat sequence. We used GC-clamped denaturing gradient gel electrophoresis to screen for DNA polymorphisms in the following six gene sequences: MCC, p53, prealbumin (transthyretin), rhodopsin, S-antigen, and TGF-alpha. A single-base sequence polymorphism was identified in each of these gene sequences. Some of these polymorphisms were multiallelic and highly informative. Our results demonstrate the value of denaturing gradient gel electrophoresis for both identifying and analyzing human DNA polymorphisms. The ability to detect highly informative polymorphisms within gene sequences will greatly contribute to a gene-based polymorphic linkage map.
Geographical topic discovery and comparison (2011)

This paper studies the problem of discovering and comparing geographical topics from GPS-associated documents. GPS-associated documents become popular with the pervasiveness of location-acquisition technologies. For example, in Flickr, the geo-tagged photos are associated with tags and GPS locations. In Twitter, the locations of the tweets can be identified by the GPS locations from smart phones. Many interesting concepts, including cultures, scenes, and product sales, correspond to specialized geographical distributions. In this paper, we are interested in two questions: (1) how to discover different topics of interests that are coherent in geographical regions? (2) how to compare several topics across different geographical locations? To answer these questions, this paper proposes and compares three ways of modeling geographical topics: location-driven model, text-driven model, and a novel joint model called LGTA (Latent Geographical Topic Analysis) that combines location and text. To make a fair comparison, we collect several representative datasets from Flickr website including Landscape, Activity, Manhattan, National park, Festival, Car, and Food. The results show that the first two methods work in some datasets but fail in others. LGTA works well in all these datasets at not only finding regions of interests but also providing effective comparisons of the topics across different locations. The results confirm our hypothesis that the geographical distributions can help modeling topics, while topics provide important cues to group different geographical regions.
Quantification of HDL2 and HDL3 cholesterol by the Vertical Auto Profile-II (VAP-II) methodology (1997)

Of the several existing methods for quantification of major subspecies of high density lipoprotein (HDL), HDL2 and HDL3, the methods based upon double precipitation are particularly useful for large-scale studies or for routine assay because of their high speed and low cost. The Vertical Auto Profile-II (VAP-II) method developed in our laboratory primarily for the direct single test measurement of cholesterol (C) in all major lipoproteins, including Lp[a] and IDL, is rapid, highly sensitive, and suitable for large-scale studies. Here we describe the modification of this procedure so as to be able to quantify both HDL2- and HDL3-C in addition to all major lipoproteins without any additional assay steps, time, or cost. The VAP-II procedure was validated by comparison with four other methods using plasma samples obtained from 35 healthy subjects: 1) HDL-VAP-II (a variation of the VAP-II procedure designed specifically to separate HDL subspecies); 2) dextran sulfate (DS)/Mg2+ double precipitation method performed at Northwest Lipid Research Laboratories (NWLRL), Seattle, WA; 3) 4-30% polyacrylamide-agarose (4/30 PAA) nondenaturing gradient gel electrophoresis (GGE); and 4) analytical ultracentrifugation (AUC), with both GGE and AUC performed at the Donner Laboratory, University of California at Berkeley. Both HDL2- and HDL3-C measurements by VAP-II correlated well with the measurements by all comparison methods (r for HDL3-C: HDL-VAP-II, 0.948; NWLRL, 0.947; GGE, 0.861; and AUC, 0.706, and r for HDL2-C: HDL-VAP-II, 0.867; NWLRL, 0.854; GGE, 0.885; and AUC, 0.721). The measurements of HDL2- and HDL3-C by the VAP-II method are reproducible, with the long-term between-rotor CV of 5.0% for HDL3-C and 9.0% for HDL2-C.
A Sub-Microwatt Low-Noise Amplifier for Neural Recording (2007)

In this paper we present a pre-amplifier designed for neural recording applications. Extremely low power dissipation is achieved by operating in an open-loop configuration, restricting the circuit to a single current branch, and reusing current to improve noise performance. Our amplifier exhibits 3.5 microVrms of input-referred noise and has a digitally-controlled gain between 36 dB and 44 dB. The amplifier is AC-coupled, with a pass-band from 0.3 Hz to 4.7 kHz. The circuit is implemented in a 0.5 microm SOI Bi-CMOS process and consumes 805nA from a 1.0V supply, corresponding to a noise efficiency factor (NEF) of 1.8, which is the lowest reported NEF to date.
Image non-uniformity in magnetic resonance imaging: its magnitude and methods for its correction (1987)

Image non-uniformity in magnetic resonance imaging (MRI) is a recognised problem when using surface coils but is rarely mentioned with respect to standard head coils, yet it can be a source of error in clinical interpretation of images. Figure 1 demonstrates the type of artefacts due to image non-uniformity for a large, homogeneous solution of water and copper sulphate. The image was acquired in the coronal section using a standard head coil, and vertical (i.e. read direction) and horizontal (i.e. phase encode direction) pixel intensity profiles through the centre of the image are illustrated. The standard deviation of pixel intensities, expressed as a percentage of the mean value, is greater than ±27% along the 23 cm length of this phantom. Figure 2 demonstrates how these image nonuniformities can affect the sagittal image of a normal volunteer. The display window width and level have been chosen to produce optimum visual contrast at the level of the cerebellum and brain stem but, as a result to image non-uniformity, this produces pronounced loss of signal in the signal in the neck and the vault of the skull. Quantitative and even qualitative comparison of pixel intensities across the image in the vertical direction (along the spine for example) are certainly invalid without some form of non-uniformity correction. Image quality assurance measurements, for example using phantoms to determine plane shape and thickness, will also be affected by this problem.
Mutations of temperature sensitivity in R plasmid pSC101 (1977)

Temperature-sensitive (Ts) mutant plasmids isolated from tetracycline resistance R plasmid pSC101 were investigated for their segregation kinetics and deoxyribonucleic acid (DNA) replication. The results fit well with the hypothesis that multiple copies of a plasmid are distributed to daughter cells in a random fashion and are thus diluted out when a new round of plasmid DNA replication is blocked. When cells harboring type I mutant plasmids were grown at 43 degrees C in the absence of tetracycline, antibiotic-sensitive cells were segregated after a certain lag time. This lag most likely corresponds to a dilution of plasmids existing prior to the temperature shift. The synthesis of plasmid DNA in cells harboring type I mutant plasmids was almost completely blocked at 43 degrees C. It seems that these plasmids have mutations in the gene(s) necessary for plasmid DNA replication. Cells haboring a type II mutant plasmid exhibited neither segregation due to antibiotic sensitivity nor inhibition of plasmid DNA replication throughout cultivation at high temperature. It is likely that the type II mutant plasmid has a temperature-sensitive mutation in the tetracycline resistance gene. Antibiotic-sensitive cells haboring type III mutant plasmids appeared at high frequency after a certain lag time, and the plasmid DNA synthesis was partially suppressed at the nonpermissive temperature. They exhibited also a pleiotrophic phenotype, such as an increase of drug resistance level at 30 degrees C and a decrease in the number of plasmid genomes in a cell.
Analysis of Proteins and Proteomes by Mass Spectrometry (2001)

A decade after the discovery of electrospray and matrix-assisted laser desorption ionization (MALDI), methods that finally allowed gentle ionization of large biomolecules, mass spectrometry has become a powerful tool in protein analysis and the key technology in the emerging field of proteomics. The success of mass spectrometry is driven both by innovative instrumentation designs, especially those operating on the time-of-flight or ion-trapping principles, and by large-scale biochemical strategies, which use mass spectrometry to detect the isolated proteins. Any human protein can now be identified directly from genome databases on the basis of minimal data derived by mass spectrometry. As has already happened in genomics, increased automation of sample handling, analysis, and the interpretation of results will generate an avalanche of qualitative and quantitative proteomic data. Protein-protein interactions can be analyzed directly by precipitation of a tagged bait followed by mass spectrometric identification of its binding partners. By these and similar strategies, entire protein complexes, signaling pathways, and whole organelles are being characterized. Posttranslational modifications remain difficult to analyze but are starting to yield to generic strategies.
Tumor Regression in Mice by Delivery of Bcl-2 Small Interfering RNA with Pegylated Cationic Liposomes (2008)

The pharmacokinetics and antitumor activity of pegylated small interfering RNA (siRNA)/cationic liposome complexes were studied after systemic administration to mice. We designed pegylated-lipid carriers for achieving increased plasma concentrations of RNA and hence improved accumulation of RNA in tumors by the enhanced permeability and retention effect. We compared the pharmacokinetics of siRNA complexed with liposomes incorporating pegylated lipids with longer (C-17 or C-18), shorter (C-12 to C-16), or unsaturated (C-18:1) acyl chains. When longer acyl chains were used, the plasma concentrations of siRNA obtained were dramatically higher than when shorter or unsaturated chains were used. This may be explained by the higher gel-to-liquid-crystalline phase-transition temperature (Tc) of lipids with longer acyl chains, which may form more rigid liposomes with reduced uptake by the liver. We tested a siRNA that is sequence specific for the antiapoptotic bcl-2 mRNA complexed with a pegylated liposome incorporating a C-18 lipid (PEG-LIC) by i.v. administration in a mouse model of human prostate cancer. Three-fold higher accumulation of RNA in the tumors was achieved when PEG-LIC rather than nonpegylated liposomes was used, and sequence-specific antitumor activity was observed. Our siRNA/PEG-LIC complex showed no side effects on repeated administration and the strength of its antitumor activity may be attributed to its high uptake by the tumors. Pegylation of liposomes improved the plasma retention, uptake by s.c. tumors, and antitumor activity of the encapsulated siRNA. PEG-LIC is a promising candidate for siRNA cancer therapy.
Sitagliptin pretreatment in diabetes patients presenting with acute coronary syndrome: results from the Acute Coronary Syndrome Israeli Survey (ACSIS) (2013)

Our data suggests that chronic treatment with DPP4i may have cardioprotective effects in diabetes patients presenting with acute coronary syndrome.
Oleamide: An Endogenous Sleep-inducing Lipid and Prototypical Member of a New Class of Biological Signaling Molecules (1998)

Oleamide is an endogenous fatty acid primary amide that accumulates in the cerebrospinal fluid under conditions of sleep deprivation and induces physiological sleep in animals. A review covering its discovery, its implications, and the emerging biology surrounding its discovery is presented. Consistent with its role as a prototypical member of a new class of biological signaling molecules, enzymatic regulation of endogenous concentrations of oleamide have been characterized or proposed. Fatty acid amide hydrolase (FAAH) is an integral membrane protein that degrades oleamide and potent inhibitors with physiological sleep-inducing properties have been disclosed. The characterization, cloning, and neuronal distribution of FAAH have been detailed and the enzyme was found to possess the ability to hydrolyze a range of fatty acid amides including anandamide which serves as the endogenous ligand for the cannabinoid receptor. An additional endogenous substance with REM sleep-inducing properties, 2-octyl gamma-bromoacetoacetate, was characterized as a potent FAAH inhibitor. Oleamide has been shown to modulate serotonergic neurotransmission and inhibit intercellular gap junction communication and detailed studies of its well defined and selective structural features required for activity have been disclosed.
Enforced TAL-1 expression stimulates primitive, erythroid and megakaryocytic progenitors but blocks the granulopoietic differentiation program. (1998)

In human adult hematopoiesis, the TAL-1 gene is up- and down-modulated in erythropoiesis and granulopoiesis, respectively [G. L. Condorelli et al., Blood, 86: 164-175, 19951. Here, it is shown that, in a hematopoietic progenitor cell (HPC) unilineage differentiation culture, tal-1 is induced and then expressed, in a sustained manner, in the megakaryopoietic lineage, whereas it is barely or not detected in the monocytopoietic series. We have investigated the role of enforced tal-1 expression by retroviral transfer into HPCs [erythroid burst-forming units and megakaryocytic and granulomonocytic colony-forming units (CFUs)], primitive HPCs (high proliferative potential colony-forming cells), and putative hematopoietic stem cells (HSCs), assayed as long-term culture initiating cells. TAL-1 overexpression induces an increase of erythroid burst-forming unit colony number and size and megakaryocytic CFU colony number and an inhibition of granulomonocytic CFU and granulocytic CFU (CFU-G) but not monocytic CFU colony number; conversely, TAL-1 mutants with defective heterodimerizing or DNA-binding domains do not exert these effects at a significant level. Although it does not affect long-term culture initiating cells, exogenous TAL-1 causes a significant proliferative stimulus on primary and secondary high proliferative potential colony-forming cells. In conclusion, exogenous tal-1 exerts differential and stage- and lineage-specific effects on the HPC/HSC differentiation/proliferation gene programs. Thus, it induces a stimulatory effect at the level of erythroid and megakaryocytic HPCs, while exerting a selective proliferative action on downstream erythropoiesis. Furthermore, it induces differential effects on the myeloid series: the partial blockade of CFU-G differentiation is possibly linked to the sharp down-modulation of endogenous TAL-1 expression at the level of the CFU-G-to-granulopoietic precursor differentiation step; in contrast, no significant effect is observed on monocytic CFU colony formation. Finally, the stimulatory effect on primitive HPCs but not putative stem cells suggests subtle differences in the effects exerted by tal-1 overexpression on primitive HPC/HSC subsets in adult life.
The hyperbox (1991)

A hyperbox is a 2-dimensional depiction of an N-dimensional box (rectangular parallelepiped). This paper defines the visual syntax of hyperboxes, states some properties, and sketches two applications. Hyperboxes can be evocative visual names for tensors or multidimensional arrays in visual programming languages. They can also be used to simultaneously display all pairwise relationships in an N-dimensional dataset. We show that this can be helpful in choosing a sequence of dimension-reducing transformations that preserve interesting properties of the dataset.
Muscle acetylcholine receptor biosynthesis. Regulation by transcript availability. (1987)

The expression of the muscle nicotinic acetylcholine receptor (AChR) on the cell surface entails a complex biosynthetic pathway, involving the expression and assembly of four subunits. The amount of AChR on the cell surface changes throughout muscle development and upon muscle denervation. We have examined the regulatory role of transcript levels on surface AChR expression by RNA blot analysis. During myogenesis of the fusing mouse muscle cell line C2, which expresses an embryonic type of receptor, changes in the rate of appearance of cell surface AChR have been assayed by 125I-alpha-bungarotoxin binding. The maximal increase in the rate of appearance of cell surface AChR occurs upon cell fusion, closely following the maximal increase in transcript levels for the alpha-, beta-, gamma-, and delta-AChR subunits. AChR alpha-, beta-, gamma-, and delta-subunit gene transcript levels have also been examined in innervated and denervated rat and mouse muscle. Muscle denervation results in an increase of transcripts for all four subunits. However, the amount of beta-subunit transcript in innervated rat skeletal muscle is high relative to the other subunit transcripts, and increases less than the other subunit transcripts upon denervation. Our results indicate that, during myogenesis and upon denervation, the availability of AChR subunit transcripts for translation plays a regulatory role in surface AChR appearance.
Heterocyclic Prostaglandins. IV. Synthesis of 8-Aza-11-deoxyprostaglandin E<SUB>1</SUB> and Its Related Compounds (1980)

Synthesis of 8-azaprostanoids (1a-e and 15a-e) from 5-hydroxymethyl-2-pyrrolidinone (3) was described. Acetylation of 3 and subsequent alkylation with methyl 7-iodoheptanoate yielded N-alkylated compound (7), which was converted into 5-hydro-xymethyl derivative (10) after selective hydrolysis. The same compound (10) was also conveniently prepared from 3 after ethoxyethylation and alkylation followed by treatment with acidic methanol. The Collins oxidation of 10 provided an aldehyde (11) which served as a key intermediate. The wittig reaction of 11 with various dimethyl 2-oxo-phosphonates yielded the corresponding enones (12a-e), which were reduced by sodium borohydride, followed by the separation of C15-epimers and alkaline hydrolysis, to give moderate yields of 1a-e, and 15a-e.