gebhart/patrepeval huggingface dataset:
Genetics of the serine cycle in Methylobacterium extorquens AM1: cloning, sequence, mutation, and physiological effect of glyA, the gene for serine hydroxymethyltransferase (1994)

The gene (glyA) of Methylobacterium extorquens AM1 encoding serine hydroxymethyltransferase (SHMT), one of the key enzymes of the serine cycle for C1 assimilation, was isolated by using a synthetic oligonucleotide with a sequence based on amino acid sequence conserved in SHMTs from different sources. The amino acid sequence deduced from the gene revealed high similarity to those of known SHMTs. The cloned gene was inactivated by insertion of a kanamycin resistance gene, and recombination of this insertion derivative with the wild-type gene produced an SHMT null mutant. Surprisingly, this mutant had lost its ability to grow on C1 as well as on C2 compounds but was still able to grow on succinate. The DNA fragment containing glyA was shown not to be linked with fragments carrying serine cycle genes identified earlier, making it the fourth chromosomal region of M. extorquens AM1 to be indicated as being involved in C1 assimilation.
Visualization, direct isolation, and transplantation of midbrain dopaminergic neurons (2001)

To visualize and isolate live dopamine (DA)-producing neurons in the embryonic ventral mesencephalon, we generated transgenic mice expressing green fluorescent protein (GFP) under the control of the rat tyrosine hydroxylase gene promoter. In the transgenic mice, GFP expression was observed in the developing DA neurons containing tyrosine hydroxylase. The outgrowth and cue-dependent guidance of GFP-labeled axons was monitored in vitro with brain culture systems. To isolate DA neurons expressing GFP from brain tissue, cells with GFP fluorescence were sorted by fluorescence-activated cell sorting. More than 60% of the sorted GFP(+) cells were positive for tyrosine hydroxylase, confirming that the population had been successfully enriched with DA neurons. The sorted GFP(+) cells were transplanted into a rat model of Parkinson's disease. Some of these cells survived and innervated the host striatum, resulting in a recovery from Parkinsonian behavioral defects. This strategy for isolating an enriched population of DA neurons should be useful for cellular and molecular studies of these neurons and for clinical applications in the treatment of Parkinson's disease.
Bone Marrow Stromal Stem Cells: Nature, Biology, and Potential Applications (2001)

Bone marrow stromal cells are progenitors of skeletal tissue components such as bone, cartilage, the hematopoiesis-supporting stroma, and adipocytes. In addition, they may be experimentally induced to undergo unorthodox differentiation, possibly forming neural and myogenic cells. As such, they represent an important paradigm of post-natal nonhematopoietic stem cells, and an easy source for potential therapeutic use. Along with an overview of the basics of their biology, we discuss here their potential nature as components of the vascular wall, and the prospects for their use in local and systemic transplantation and gene therapy.
Effects of Clostridium difficile toxins given intragastrically to animals (1985)

We examined the activities of Clostridium difficile toxin preparations given intragastrically to hamsters, mice, and rats. The culture filtrate from a highly toxigenic strain of C. difficile caused hemorrhage and accumulation of fluid in the small intestine and cecum, diarrhea, and death in hamsters and mice. In rats, the culture filtrate caused only a small amount of fluid accumulation and slight hemorrhage along the small intestine. When toxin A was removed from the culture filtrate, the filtrate lost its activity. Preparations of homogeneous toxin A caused a response similar to that observed after the administration of culture filtrate. Hamsters were more sensitive to toxin A than mice or rats were. When hamsters were given multiple low doses of toxin A 1 week apart at a concentration which singly caused no response, they became ill and died, indicating that the toxin may have long-term effects. High amounts of toxin B did not cause any significant response when given intragastrically, unless initially mixed with low amounts of toxin A or given to hamsters with bruised ceca. These results suggest that toxins A and B act synergistically and that the action of toxin B may occur via the tissue damage caused by toxin A.
Lysis of Plasma Clots by Urokinase-Soluble Urokinase Receptor Complexes (1998)

Single-chain urokinase plasminogen activator (scuPA), the unique form secreted by cells, expresses little intrinsic plasminogen activator activity. scuPA can be activated by proteolytic cleavage to form a two-chain enzyme (tcuPA), which is susceptible to inhibition by plasminogen activator inhibitor type I (PAI-1). scuPA is also activated when it binds to its cellular receptor (uPAR), in which case the protein remains as a single chain molecule with less susceptibility to PAIs. Fibrin clots are invested with PAI-1 derived from plasma and from activated platelets. Therefore, we compared the fibrinolytic activity of complexes between scuPA and recombinant soluble uPAR (suPAR) to that of scuPA, tcuPA, and tcuPA/suPAR complexes. scuPA/suPAR complexes mediated the lysis of plasma-derived fibrin clots 14-fold more extensively than did equimolar concentrations of scuPA and threefold more extensively than did tcuPA or tcuPA/suPAR, respectively. The enhanced catalytic activity of scuPA/suPAR required that all three domains of the receptor be present, correlated with its PAI-1 resistance, was not dependent on fibrin alone, and required a plasma cofactor that was identified as IgG. Human IgG bound specifically to suPAR and scuPA/suPAR as determined by using affinity chromatography and immunoprecipitation. Plasma depleted of IgG lost most of its capacity to promote the fibrinolytic activity of scuPA/suPAR, and the activity of the complex was restored by adding plasma concentrations of purified IgG. These studies indicate that scuPA/suPAR can function as a plasminogen activator in a physiological milieu. © 1998 by The American Society of Hematology.
Improving depth estimation from a plenoptic camera by patterned illumination (2015)

Plenoptic (light-field) imaging is a technique that allows a simple CCD-based imaging device to acquire both spatially and angularly resolved information about the “light-field” from a scene. It requires a microlens array to be placed between the objective lens and the sensor of the imaging device<sup>1</sup> and the images under each microlens (which typically span many pixels) can be computationally post-processed to shift perspective, digital refocus, extend the depth of field, manipulate the aperture synthetically and generate a depth map from a single image. Some of these capabilities are rigid functions that do not depend upon the scene and work by manipulating and combining a well-defined set of pixels in the raw image. However, depth mapping requires specific features in the scene to be identified and registered between consecutive microimages. This process requires that the image has sufficient features for the registration, and in the absence of such features the algorithms become less reliable and incorrect depths are generated. The aim of this study is to investigate the generation of depth-maps from light-field images of scenes with insufficient features for accurate registration, using projected patterns to impose a texture on the scene that provides sufficient landmarks for the registration methods.
Induction of Defective and Temperate Bacteriophages in Caulobacter (1970)

Summary Bacteriophage-like particles were induced from 6 of 21 strains of stalked bacteria, using mitomycin C or ultraviolet irradiation as the inducing agents. The phage inductions were observed in strains of Caulobacter crescentus, C. vibrioides and C. bacteroides. The phage-like particles were observed, using electron microscopy. Two of the phage-like entities, tentatively designated defective phages, could not be propagated on any of 21 potential host strains tested, nor did they possess bacteriocin activity. Host strains which permitted lytic cycles of phage replication were found for four induced phages.These bacteriophages contained double-stranded DNA. The bacterial strains from which they were induced were [resistant to infection by their respective phage. Four bacterial strains were treated with specific antiphage serum, but clones so treated retained their capacity to produce the phages. The inefficacy of antiphage serum in curing the bacteria of phage suggested that these Caulobacter strains were lysogenic.
Parallel FPGA Programming over Backplane Chassis (2000)

For systems with a large number of FPGAs, where a design is instantiated across multiple FPGAs in a chassis, an efficient mechanism of programming the FPGA devices is needed. The mechanism described herein allows multiple FPGAs to be programmed across a backplane. Only a single configuration PROM is required to store the configuration for the multiple instances of the design. When the system boots, all FPGAs are programmed in parallel. This design is applicable to any system which contains a multiple board system which has instances of identical FPGA implementations distributed across the boards. Signal integrity of signals is considered.
Angiotensin-(1–7) Induces Peripheral Antinociception through Mas Receptor Activation in an Opioid-Independent Pathway (2012)

The G protein-coupled receptor Mas was recently described as an angiotensin-(1-7) [Ang-(1-7)] receptor. In the present study, we demonstrate an antinociceptive effect of Ang-(1-7) for the first time. Additionally, we evaluated the anatomical localization of Mas in the dorsal root ganglia using immunofluorescence. This is the first evidence indicating that this receptor is present in sensitive neurons. The antinociceptive effect was demonstrated using the rat paw pressure test. For this test, sensitivity is increased by intraplantar injection of prostaglandin E(2). Ang-(1-7) administered locally into the right hind paw elicited a dose-dependent antinociceptive effect. Because the higher dose of Ang-(1-7) did not produce an effect when injected into the contralateral paw, this effect was considered local. The specific antagonist for the Mas receptor, A-779, inhibited the peripheral antinociception induced by exposure to 4 μg/paw Ang-(1-7) in a dose-dependent manner. The highest dose completely reversed the antinociceptive effect induced by Ang-(1-7), suggesting that the Mas receptor is an obligatory component in this process and that other angiotensin receptors may not be involved. When injected alone, the antagonist was unable to induce hyperalgesia or antinociception. Alternatively, naloxone was unable to inhibit the antinociceptive effect induced by Ang-(1-7), suggesting that endogenous opioid peptides may not be involved in this response. These data provide the first anatomical basis for the physiological role of Ang-(1-7) in the modulation of pain perception via Mas receptor activation in an opioid-independent pathway. Taken together, these results provide new perspectives for the development of a new class of analgesic drugs.
Multiple Mechanisms Regulate Subcellular Localization of Human CDC6 (2001)

CDC6 is a protein essential for DNA replication, the expression and abundance of which are cell cycle-regulated in Saccharomyces cerevisiae. We have demonstrated previously that the subcellular localization of the human CDC6 homolog, HsCDC6, is cell cycle-dependent: nuclear during G(1) phase and cytoplasmic during S phase. Here we demonstrate that endogenous HsCDC6 is phosphorylated during the G(1)/S transition. The N-terminal region contains putative cyclin-dependent kinase phosphorylation sites adjoining nuclear localization sequences (NLSs) and a cyclin-docking motif, whereas the C-terminal region contains a nuclear export signal (NES). In addition, we show that the observed regulated subcellular localization depends on phosphorylation status, NLS, and NES. When the four putative substrate sites (serines 45, 54, 74, and 106) for cyclin-dependent kinases are mutated to alanines, the resulting HsCDC6A4 protein is localized predominantly to the nucleus. This localization depends upon two functional NLSs, because expression of HsCDC6 containing mutations in the two putative NLSs results in predominantly cytoplasmic distribution. Furthermore, mutation of the four serines to phosphate-mimicking aspartates (HsCDC6D4) results in strictly cytoplasmic localization. This cytoplasmic localization depends upon the C-terminal NES. Together these results demonstrate that HsCDC6 is phosphorylated at the G(1)/S phase of the cell cycle and that the phosphorylation status determines the subcellular localization.
Computer generation of spectra of graphs: Applications to C60 clusters and other systems (1988)

Abstract A computer code based on the Givens–Householder matrix diagonalization method is used to calculate the spectra of graphs containing a large number of vertices. The code is most general in that it can handle graphs containing 200 or more vertices. Further, the code can be used to generate the spectra of weighted graphs. The program requires as input only the neighborhood table of the graph. The spectra of many graphs are generated for the first time in less than a few minutes of computer time. Applications to a number of chemical systems including two forms (foot and hand) of the recently synthesized C 60 cluster and the effect of bond alternation on these systems are discussed. In addition, the spectra of square and honeycomb lattices and the characteristic polynomials of the foot and hand forms of the C 60 cluster are obtained.
Comparative effectiveness of nafcillin or cefazolin versus vancomycin in methicillin-susceptible Staphylococcus aureus bacteremia (2011)

Receipt of nafcillin or cefazolin was protective against mortality compared to vancomycin even when therapy was altered after culture results identified MSSA. Convenience of vancomycin dosing may not outweigh the potential benefits of nafcillin or cefazolin in the treatment of MSSA bacteremia.
Average-rate optimal PSAM transmissions over time-selective fading channels (2002)

Enabling linear minimum-mean square error (LMMSE)-based estimation of random time-selective channels, pilot-symbol-assisted modulation (PSAM) has well-documented merits as a fading counter-measure boosting bit-error rate performance. We design average-rate optimal PSAM transmissions by maximizing a tight lower bound of the average channel capacity. Relying on a simple closed-form expression of this bound in terms of the LMMSE channel estimator variance, we obtain PSAM transmissions with optimal spacing of pilot symbols and optimal allocation of the transmit-power budget between pilot and information symbols. Equi-powered transmitted symbols, channels with special Doppler spectra, and analytical and simulation based comparisons of possible alternatives shed more light on information-theoretic aspects of PSAM-based transmissions.
Vaccination against type 1 diabetes (2011)

The clinical onset of type 1 diabetes or autoimmune diabetes occurs after a prodrome of islet autoimmunity. The warning signals for the ensuing loss of pancreatic islet beta cells are autoantibodies against insulin, GAD65, IA-2 and ZnT8, alone or in combinations. Autoantibodies against, for example, insulin alone have only a minor risk of type 1 diabetes. However, progression to clinical onset is increased by the induction of multiple islet autoantibodies. At the time of clinical onset, insulitis may be manifest, which seems to reduce the efficacy of immunosuppression. Autoantigen-specific immunotherapy with alum-formulated GAD65 (Diamyd(®)) shows promise to reduce the loss of beta-cell function after the clinical onset of type 1 diabetes. The mechanisms are unclear but may involve the induction of T regulatory cells, which may suppress islet autoantigen reactivity. Past and ongoing clinical trials have been safe. Future clinical trials, perhaps as combination autoantigen-specific immunotherapy, may increase the efficacy in preventing the clinical onset in subjects with islet autoantibodies or preserve residual beta-cell function in patients newly diagnosed with type 1 diabetes.
A portable interface for on-the-fly instruction space modification (1991)

Applications such as incremental linking must modify instruction space during program execution. Whenever instruction space is modified, machine-dependent systems issues such as instruction caching must be dealt with properly. However, there are no standard idioms for signaling a change to the instruction space. This paper discusses issues for instruction space allocation and coherence, describes a portable interface for modifying instruction space, and examines the details of several implementations of the interface.
Computer Coordination With Popular Music: A New Research Agenda (2018)

Computer accompaniment is now a well-established field of study, but nearly all work in this area assumes a Western classical music tradition in which timing is considered a flexible framework that performers manipulate for expression. This has important implications for the music, accompaniment, and performance style, and therefore the fundamental design of automatic accompaniment systems. Popular music has a very different set of assumptions and requirements for (human or computer) performers. In particular, the tempo is generally very stable, which would appear to simplify the synchronization problem, but synchronization must be quite precise and the music is not strictly notated, making coordination more difficult. The practical requirements for computer coordination with popular music create many problems that have not been addressed by research or practice. Some preliminary investigations in this area are reported, and future opportunities for research are discussed.
Experimental study of spectrum sensing based on energy detection and network cooperation (2006)

Spectrum sensing has been identified as a key enabling functionality to ensure that cognitive radios would not interfere with primary users, by reliably detecting primary user signals. Recent research studied spectrum sensing using energy detection and network cooperation via modeling and simulations. However, there is a lack of experimental study that shows the feasibility and practical performance limits of this approach under real noise and interference sources in wireless channels. In this work, we implemented energy detector on a wireless testbed and measured the required sensing time needed to achieve the desired probability of detection and false alarm for modulated and sinewave-pilot signals in low SNR regime. We measured the minimum detectable signal levels set by the receiver noise uncertainties. Our experimental study also measured the sensing improvements achieved via network cooperation, identified the robust threshold rule for hard decision combining and quantified the effects of spatial separation between radios in indoor environments.
Protein tyrosine kinases in malignant melanoma (2000)

Protein tyrosyl phosphorylation is an essential component in intracellular signalling, with diverse and crucial functions including mediation of cell proliferation, survival, death, differentiation, migration and attachment. It is regulated by the balance between the activities of protein tyrosine kinases (PTKs) and protein tyrosine phosphatases. A number of PTKs are encoded by proto-oncogenes or viral oncogenes, and are thus strongly implicated in cancer. While a role for PTKs in human melanoma is less firmly established, human melanomas or melanoma cells have been reported to contain more tyrosine phosphate than normal melanocytes, and some receptor PTKs (EPH-A2/ ECK and EPH-B3) are overexpressed in over 90% of melanoma cell lines. Other specific PTKs are also frequently overexpressed, including KDR and fibroblast growth factor receptor-4 (FGF-R4), while, interestingly, yet others, such as KIT and FES, are consistently downregulated in melanoma cell lines. All of these differentially expressed PTKs are candidates for gene products important in melanoma development. In addition, PTKs expressed in significant amounts in both benign and malignant melanocytes, such as insulin-like growth factor-1 receptor (IGF1-R), FGF-R1, HER2/NEU and FAK, are likely to play a role in melanoma genesis and progression.
CpG oligodeoxynucleotides trigger protective and curative Th1 responses in lethal murine leishmaniasis. (1998)

Synthetic oligodeoxynucleotides containing CpG dinucleotides (CpG-ODN) mimic the immunostimulatory qualities of bacterial DNA. We asked whether immunostimulation by CpG-ODN predisposes for a commitment toward a Th1 vs a Th2 response in Leishmania major infection, a model for a lethal Th2-driven disease, in BALB/c mice. CpG-ODN induced Th1 effector T cells in vitro and conveyed protective immunity to disease-prone BALB/c mice in vivo. Conversion to a Th1-driven resistant phenotype was associated with IL-12 production and maintained the expression of IL-12R beta2-chains. Most strikingly, CpG-ODN were even curative when given as late as 20 days after lethal L. major infection, indicating that CpG-ODN revert an established Th2 response. These findings imply an important role of bacterial DNA and CpG-ODN in the instruction of adaptive immune responses. They also point to the therapeutic potential of CpG-ODN in redirecting curative Th1 responses in Th2-driven disorders.
Mutations that increase the affinity of a translational repressor for RNA (1994)

The coat protein of the RNA bacteriophage MS2 is a specific RNA binding protein that represses translation of the viral replicase gene during the infection cycle. As an approach to characterizing the RNA-binding site of coat protein we have isolated a series of coat mutants that suppress the effects of a mutation in the translational operator. Each of the mutants exhibits a super-repressor phenotype, more tightly repressing both the mutant and wild-type operators than does the wild-type protein. The variant coat proteins were purified and subjected to filter binding assays to determine their affinities for the mutant and wild-type operators. Each protein binds the operators from 3 to 7.5-fold more tightly than normal coat protein. The amino acid substitutions seem to extend the normal binding site by introducing new interactions with RNA.
A high performance 4×4 inch AMLCD for avionic applications (2002)

Image Quest has developed a flight quality, high resolution, full color, high luminance, wide temperature range display module based on Active Matrix LCD (AMLCD) technology that has excellent contrast in full sunlight. The display is well suited for use in electronic replacements for the electro-mechanical 5ATI (five inch case size) flight indicators and offers greatly improved display format flexibility, operating reliability and display contrast in all ambient lighting conditions as well as attractive cost advantages. The display module is very close to meeting the predetermined design goals.