gebhart/patrepeval huggingface dataset:
Oxidative stress, age-related neurodegeneration, and the potential for neurotrophic treatment. (1995)

Amyotrophic lateral sclerosis, Parkinson's disease, and Alzheimer's disease are major human neurodegenerative disorders, the etiologies for which remain unknown. Although a unique subset of neurons is particularly affected in each of the three diseases, they have several intriguing overlapping similarities. Evidence is reviewed supporting the hypothesis that these diseases result from an inability to protect against accumulated damage by free radicals due to oxidative stress. If oxidative stress underlies or exacerbates the etiology of these diseases, then agents that effectively attenuate brain tissue lipid peroxidation or otherwise limit free radical damage may hold promise for the treatment of these neurodegenerative diseases. Although antioxidant chemical supplementation may provide effective therapy, the most effective therapy for neurodegenerative diseases may be treatment with specific neurotrophic, survival-promoting proteins. For example, brain-derived neurotrophic factor promotes survival of spinal motor neurons and mesencephalic dopaminergic neurons. One mechanism through which these proteins may exert their protection may be by stimulating endogenous defenses against oxidative stress and damage by free radicals. This hypothesis is being tested in several laboratories and provides exciting direction both for basic neurobiological research and therapeutic drug discovery.
Accessing multiple mirror sites in parallel: using Tornado codes to speed up downloads (1999)

Mirror sites enable client requests to be serviced by any of a number of servers, reducing load at individual servers and dispersing network load. Typically, a client requests service from a single mirror site. We consider enabling a client to access a file from multiple mirror sites in parallel to speed up the download. To eliminate complex client-server negotiations that a straightforward implementation of this approach would require, we develop a feedback-free protocol based on erasure codes. We demonstrate that a protocol using fast Tornado codes can deliver dramatic speedups at the expense of transmitting a moderate number of additional packets into the network. This scalable solution extends naturally to allow multiple clients to access data from multiple mirror sites simultaneously. The approach applies naturally to wireless networks and satellite networks as well.
Cloning and structure analysis of the rat apolipoprotein A-1 cDNA (1984)

Apolipoprotein A-I, the major protein in mammalian high-density lipoprotein, acts as a cofactor for lecithin-cholesterol acyltransferase during the formation of cholesterol ester and as such, is thought to promote cholesterol efflux from peripheral cells to the liver. In this paper, we report the partial purification of rat liver apolipoprotein A-I mRNA by a polysome immunoadsorption technique, and its cDNA cloning. Isolation of two overlapping cDNA clones enabled us to derive the whole rat apolipoprotein A-I cDNA coding sequence. Comparison of the deduced protein sequence with its human counterpart reveals a striking homology between the prepropeptide precursors. Both mature protein amino-terminal regions are very homologous, suggesting that this particular domain could be involved in lipid/protein binding or lecithin-cholesterol acyltransferase activation.
Characterization of Complex Quantum Dynamics with a Scalable NMR Information Processor (2005)

We present experimental results on the measurement of fidelity decay under contrasting system dynamics using a nuclear magnetic resonance quantum information processor. The measurements were performed by implementing a scalable circuit in the model of deterministic quantum computation with only one quantum bit. The results show measurable differences between regular and complex behavior and for complex dynamics are faithful to the expected theoretical decay rate. Moreover, we illustrate how the experimental method can be seen as an efficient way for either extracting coarse-grained information about the dynamics of a large system or measuring the decoherence rate from engineered environments.
Footloose: A Case for Physical Eventual Consistency and Selective Conflict Resolution. (2003)

Users are increasinglyinundatedwith small devices with communicationand storage capabilities. Unfortunately, the user is still responsible for reconciling all of the devices whenever a change is made. We present Footloose, a usercentered data store that can share data and reconcile conflicts across diverse devices. Footloose is an optimistic system based on physical eventual consistency—consistency based on the movement of devices—and selective conflict resolution—which allows conflicts to flow through devices that cannot resolve the conflict to devices the can. Using these techniques, Footloose can present consistent views of data on the devices closest to the user without user interaction.
Secondary hyperalgesia persists in capsaicin desensitized skin (2000)

Several lines of evidence suggest that secondary hyperalgesia to punctate mechanical stimuli arises from central sensitization to the input from primary afferent nociceptors. Conventional C-fiber nociceptors respond to heat stimuli and yet heat hyperalgesia is absent in the region of secondary hyperalgesia. This evidence suggests that the central sensitization to nociceptor input does not involve heat sensitive nociceptors. To test this hypothesis, we investigated whether desensitization of heat sensitive nociceptors by topical application of capsaicin led to an alteration in the secondary hyperalgesia. Two 2x2 cm areas on the volar forearm, separated by 1 cm, were treated in 10 healthy volunteers. One of the areas was desensitized by treatment with 10% topical capsaicin (6 h/day for 2 days). The other site served as vehicle control. Hyperalgesia was produced 2 days later by an intradermal injection of capsaicin (50 microg, 10 microl) at a point midway between the two treatment areas. Secondary hyperalgesia to noxious mechanical stimuli was investigated by using a blade probe (32 and 64 g) attached to a computer-controlled mechanical stimulator. In the area of topical capsaicin treatment, there was a marked increase in heat pain threshold and decrease in heat pain ratings indicating a pronounced desensitization of heat sensitive nociceptors. However, touch threshold and pain to pinching stimuli were not significantly altered. The intradermal capsaicin injection led to the development of a similar degree of secondary hyperalgesia at both the vehicle and capsaicin treatment areas. These results indicate that capsaicin insensitive nociceptive afferents play a dominant role not only in normal mechanical pain but also in secondary hyperalgesia to noxious mechanical stimuli.
Recent Developments in Olefin Cross‐Metathesis (2003)

Among the many types of transition-metal-catalyzed C-C bond-forming reactions, olefin metathesis has come to the fore in recent years owing to the wide range of transformations that are possible with commercially available and easily handled catalysts. Consequently, olefin metathesis is now widely considered as one of the most powerful synthetic tools in organic chemistry. Until recently the intermolecular variant of this reaction, cross-metathesis, had been neglected despite its potential. With the evolution of new catalysts, the selectivity, efficiency, and functional-group compatibility of this reaction have improved to a level that was unimaginable just a few years ago. These advances, together with a better understanding of the mechanism and catalyst-substrate interactions, have brought us to a stage where more and more researchers are employing cross-metathesis reactions in multistep procedures and in the synthesis of natural products. The recent inclusion of alkynes and hindered bicyclic olefins as viable substrates for bimolecular metathesis coupling, the discovery of enantioselective cross-metathesis and cross-metathesis in water, and the successful marriage of metathesis and solid-phase organic synthesis has further widened the scope of this versatile reaction.
Raltitrexed treatment promotes systemic inflammatory reaction in patients with colorectal carcinoma (2002)

We studied longitudinally inflammatory reactions and serum C-reactive protein (S-CRP) levels in 52 colorectal cancer patients treated with a median of six 3-weekly cycles of raltitrexed 1.5-3.0 mg m(-2) combined with oral carmofur (1-hexylcarbomoyl-5-fluorouracil) 300-400 mg m(-2) on cycle days 2-14. Thirty-nine (75%) of these patients had fever on days 2 to 9 after receiving raltitrexed, 49 (94%) had fatigue Gr. > or = 1, and 49 (94%) elevated S-CRP without a documented infection. The systemic inflammatory composite score (consists of body temperature, fatigue, S-CRP, interleukin-6 (S-IL-6), S-IL-8, and tumour necrosis factor-alpha (S-TNF alpha) levels) was calculated in a cross-sectional one-cycle study involving 60 colorectal cancer patients treated with single-agent raltitrexed, raltitrexed and carmofur, or 5-fluorouracil-based chemotherapy (n=20 in each group). The median S-CRP, S-IL-6, and S-TNF alpha levels were higher 7 days after giving raltitrexed (57 vs 23 mg l(-1), 64 vs 10 ng l(-1), and 11 vs 10 ng l(-1), respectively) or raltitrexed+carmofur (142 vs 10 mg l(-1), 64 vs 10 ng l(-1), and 16 vs 9 ng l(-1), respectively) than at baseline (P<0.01 for each comparison), but not when 5-fluorouracil-based regimens were administered. These findings suggest that colorectal cancer patients treated with raltitrexed may develop drug-related systemic inflammation, which may be difficult to discriminate from infection.
A Chasm Between Two Vanguards: Near Encounters of Russian Emigre Marxists and Dadaism in Switzerland (2017)

In the year 1916, Switzerland was an island of peace in a sea of belligerence. Surrounded by Germany, France, and Italy, Switzerland was one of the few European counties to maintain its neutrality during the war that transformed Europe into a graveyard. It also became an ideal sanctuary for those who opposed the brutality and strident nationalism of World War I. Ever since the defeat of the 1905 Revolution in Russia, Switzerland had acted as an ideal place of refuge for members of the Russian Social Democratic Labor Party (the RSDLP, a Marxist party founded in 1898). This party sought to overthrow the Russian autocracy and further the cause of an internationalist revolution based upon Marxist principles of creating a society where "the free development of each is the condition for the free development of all."
Quantitative surface normal measurement by a wavefront camera (2012)

A compact wavefront camera that allows users to quantitatively measure the intensity and wavefront at a remote object plane is reported. The camera is built from a chip-scale wavefront sensor that we previously developed. By measuring the wavefront of the image and calibrating the wavefront relationship between the image and object planes, the wavefront at the object plane can be computed and the surface normal of the object can be derived. We built a prototype camera and calibrated the wavefront relationship. In a proof-of-concept experiment, a set of concave mirrors with different focal lengths (50-200 mm), were imaged. The results agree well with their expected values. To demonstrate the application of the camera, we applied this method to measure the deformation of a microfluidic channel under pressure.
Human T cell clones recognize two abundant Mycobacterium tuberculosis protein antigens expressed in Escherichia coli. (1987)

Human T cells reactive to Mycobacterium tuberculosis were cloned from peripheral blood mononuclear cells (PBMC) of four tuberculosis patients by using whole irradiated bacilli as the in vitro stimulatory agent. Twenty-two T cell clones (CD4+) were tested for their reactivity to 12 different mycobacterial species and showed a distribution from limited to broad cross-reactivity. These T cell clones were also tested for their reactivity to three abundant M. tuberculosis proteins of 65, 19, and 14 kD, each expressed from recombinant DNA in Escherichia coli. The three proteins were expressed from DNA clones that were previously isolated from a lambda gt11 genomic DNA library of M. tuberculosis by using monoclonal antibodies directed against this pathogen. A T cell clone from one patient was stimulated by an E. coli lysate containing the 65 kD antigen, and a T cell clone from a second patient was stimulated by an E. coli lysate containing the 19 kD antigen in an in vitro proliferation assay. Both T cell clones showed very limited cross-reactivity when tested against other mycobacteria. We conclude that some patients with tuberculosis exhibit a T cell response to the 65 and 19 kD M. tuberculosis proteins defined by these isolated genes.
Multi-angle lensless digital holography for depth resolved imaging on a chip (2010)

A multi-angle lensfree holographic imaging platform that can accurately characterize both the axial and lateral positions of cells located within multi-layered micro-channels is introduced. In this platform, lensfree digital holograms of the micro-objects on the chip are recorded at different illumination angles using partially coherent illumination. These digital holograms start to shift laterally on the sensor plane as the illumination angle of the source is tilted. Since the exact amount of this lateral shift of each object hologram can be calculated with an accuracy that beats the diffraction limit of light, the height of each cell from the substrate can be determined over a large field of view without the use of any lenses. We demonstrate the proof of concept of this multi-angle lensless imaging platform by using light emitting diodes to characterize various sized microparticles located on a chip with sub-micron axial and lateral localization over approximately 60 mm(2) field of view. Furthermore, we successfully apply this lensless imaging approach to simultaneously characterize blood samples located at multi-layered micro-channels in terms of the counts, individual thicknesses and the volumes of the cells at each layer. Because this platform does not require any lenses, lasers or other bulky optical/mechanical components, it provides a compact and high-throughput alternative to conventional approaches for cytometry and diagnostics applications involving lab on a chip systems.
RNA binding specificity of aDrosophilasnRNP protein that shares sequence homology with mammalian U1-A and U2-B’ proteins (1992)

We have characterized a recombinant Drosophila melanogaster RNA binding protein, D25, by virtue of its antigenic relationship to mammalian U1 and U2 small nuclear ribonucleoprotein (U snRNP) proteins. Sequence analysis revealed that D25 bears strong similarity to both the human U1 snRNP-A (U1-A) and U2 snRNP-B" (U2-B") proteins. However, at residues known to be critical for the RNA binding specificities of U1-A and U2-B" D25 sequence is more similar to U2-B". Using direct RNA binding assays D25 selected U1 RNA from either HeLa or Drosophila Kc cell total RNA. Furthermore, D25 bound U1 RNA when transfected into mammalian cells. Thus, D25 appears to be a Drosophila homolog of the mammalian U1-A protein, despite its sequence similarity to U2-B".
Analysis of log-periodic folded dipole array (1992)

The admittance matrix of a reentrant folded dipole is derived, its equivalent circuit is evaluated, and a mathematical model is presented. These results, when combined with mutual coupling theory and an iterative network computation can lead to the evaluation of all element excitation coefficients. This, then, allows far-field radiation pattern predictions of a log-periodic folded dipole backfire array and permits tolerance analysis and optimization of antenna dimensions for best gain and sidelobes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Glutathione-Mediated Delivery and Release Using Monolayer Protected Nanoparticle Carriers (2006)

We demonstrate here the effective delivery of a dye payload into cells using 2-nm core gold nanoparticles, with release occurring via place exchange of glutathione onto the particle surface. In vitro experiments demonstrate effective release of drug analogues upon addition of glutathione. Cell culture experiments show rapid uptake of nanoparticle and effective release of payload. The role of glutathione in the release process was demonstrated through improved payload release upon transient increase in glutathione levels achieved via introduction of glutathione ethyl ester into the cell.
Real vs. artefactual absences in species distributions: tests for Oryzomys albigularis (Rodentia: Muridae) in Venezuela (2003)

Abstract Aim Numerous geographical information system (GIS)‐based techniques for estimating a species’ potential geographical distribution now exist. While a species’ potential distribution is more extensive than its documented range, the lack of records from some suitable regions may simply derive from inadequate sampling there. Using occurrence records of both the study species and the more inclusive overall target group, I propose a progression of statistical models to evaluate apparent absences in species distributions. Location Northern Venezuela. Methods Employing data from the Smithsonian Venezuelan Project (a large set of standardized mammalian inventories undertaken across Venezuela), I tested distributional hypotheses for the sigmodontine rodent Oryzomys albigularis ( Tomes, 1860 ). Those inventories collected O. albigularis in two of the five major montane regions of northern Venezuela (the Cordillera de Mérida/Macizo de El Tamá and Cordillera de la Costa Central). I used the Genetic Algorithm for Rule‐Set Prediction (GARP) to estimate the species’ potential distribution in northern Venezuela. Then, based on all collection localities from the Smithsonian Venezuelan Project, I determined the probability that the absence of O. albigularis from the three regions of potential presence where it was not documented (the Serranía de Perijá, Lara–Falcón highlands, and Cordillera de la Costa Oriental) could be the result of inadequate sampling. Results and main conclusions All statistical models indicated that the sampling efforts of the Smithsonian Venezuelan Project were insufficient to demonstrate conclusively the absence of O. albigularis from any of the three regions lacking records. Indeed, a subsequent compilation of specimens from ten natural history museums confirmed its presence in the Serranía de Perijá and the Lara–Falcón highlands. Tests using empirical sampling effort and taking human modification of the landscape into account most closely fulfilled the assumptions required for the tests. By providing a framework for bringing additional quantitative rigour to studies of species distributions, these methods will probably prove of wide applicability to other systems.
Bioinformatics: sequence and genome analysis (2001)

Preface Chapter 1. Historical introduction and overview Chapter 2. Collecting and storing sequences in the laboratory Chapter 3. Alignment of pairs of sequences Chapter 4. Introduction to probability and statistical analysis of sequence alignments Chapter 5. Multiple sequence alignment Chapter 6. Sequence database searching for similar sequences Chapter 7. Phylogenetic prediction Chapter 8. Prediction of RNA secondary structure Chapter 9. Gene prediction and regulation Chapter 10. Protein classification and structure prediction Chapter 11. Genome analysis Chapter 12. Bioinformatics programming using Perl and Perl modules Chapter 13. Analysis of microarrays
Selection and identification of single domain antibody fragments from camel heavy‐chain antibodies (1997)

Functional heavy-chain gamma-immunoglobulins lacking light chains occur naturally in Camelidae. We now show the feasibility of immunising a dromedary, cloning the repertoire of the variable domains of its heavy-chain antibodies and panning, leading to the successful identification of minimum sized antigen binders. The recombinant binders are expressed well in E. coli, extremely stable, highly soluble, and react specifically and with high affinity to the antigens. This approach can be viewed as a general route to obtain small binders with favourable characteristics and valuable perspectives as modular building blocks to manufacture multispecific or multifunctional chimaeric proteins.
An artificial liver sinusoid with a microfluidic endothelial‐like barrier for primary hepatocyte culture (2007)

Primary hepatocytes represent a physiologically relevant model for drug toxicity screening. Here, we created a biologically inspired artificial liver sinusoid with a microfluidic endothelial-like barrier having mass transport properties similar to the liver acinus. This unit consisted of a cord of hepatocytes (50 x 30 x 500 microm) fed by diffusion of nutrients across the microfluidic endothelial-like barrier from a convective transport vessel (10 nL/min). This configuration sustained rat and human hepatocytes for 7 days without an extracellular matrix (ECM) coating. Experiments with the metabolism mediated liver toxicant diclofenac showed no hepatotoxicity after 4 h and an IC(50) of 334 +/- 41 microM after 24 h.
High-resolution observations of the Lyman alpha sky background (1977)

The first high-resolution observations of the Lyman alpha sky background, obtained with a spectrometer on the Copernicus satellite, are examined. The high-resolution observations presented allow the first direct measurement of the heliocentric velocity of the local interstellar medium. The high resolution of the spectrometer and the projection of the earth's orbital velocity along the line of sight made it possible to separate the weak extraterrestrial background feature from the intense geocoronal emission line. The observations also contain considerable information about the Lyman alpha emission from the geocorona. The data permit limits to be placed on the temperature of the gas that produces the background feature.
TALE nucleases and next generation GM crops (2011)

Site-specific and adaptable DNA binding domains are essential modules to develop genome engineering technologies for crop improvement. Transcription activator-like effectors (TALEs) proteins are used to provide a highly specific and adaptable DNA binding modules. TALE chimeric nucleases (TALENs) were used to generate site-specific double strand breaks (DSBs) in vitro and in yeast, Caenorhabditis elegans, mammalian and plant cells. The genomic DSBs can be generated at predefined and user-selected loci and repaired by either the non-homologous end joining (NHEJ) or homology dependent repair (HDR). Thus, TALENs can be used to achieve site-specific gene addition, stacking, deletion or inactivation. TALE-based genome engineering tools should be powerful to develop new agricultural biotechnology approaches for crop improvement. Here, we discuss the recent research and the potential applications of TALENs to accelerate the generation of genomic variants through targeted mutagenesis and to produce a non-transgenic GM crops with the desired phenotype.
Effective mass and mobility of holes in strained Si/sub 1-x/Ge/sub x/ layers on (1992)

The directional density-of-state effective masses of the valence bands of a strained Si/sub 1-x/Ge/sub x/ layer for the
Antigenically Distinct Populations of Neisseria gonorrhoeaei Isolation and Characterization of the Responsible Determinants (1974)

Journal Article Antigenically Distinct Populations of Neisseria gonorrhoeaei Isolation and Characterization of the Responsible Determinants Get access Michael A. Apicella Michael A. Apicella From the Division of Infectious Diseases, Department of Medicine, State University of New York, Buffalo, New York Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Infectious Diseases, Volume 130, Issue 6, December 1974, Pages 619–625, https://doi.org/10.1093/infdis/130.6.619 Published: 01 December 1974 Article history Received: 03 May 1974 Revision received: 26 July 1974 Published: 01 December 1974