gebhart/patrepeval huggingface dataset:
Genomic Stability of Murine Leukemia Viruses Containing Insertions at the Env-3′ Untranslated Region Boundary (2001)

Retroviruses containing inserts of exogenous sequences frequently eliminate the inserted sequences upon spread in susceptible cells. We have constructed replication-competent murine leukemia virus (MLV) vectors containing internal ribosome entry site (IRES)-transgene cassettes at the env-3' untranslated region boundary in order to examine the effects of insert sequence and size on the loss of inserts during viral replication. A virus containing an insertion of 1.6 kb replicated with greatly attenuated kinetics relative to wild-type virus and lost the inserted sequences in a single infection cycle. In contrast, MLVs containing inserts of 1.15 to 1.30 kb replicated with kinetics only slightly attenuated compared to wild-type MLV and exhibited much greater stability, maintaining their genomic integrity over multiple serial infection cycles. Eventually, multiple species of deletion mutants were detected simultaneously in later infection cycles; once detected, these variants rapidly dominated the population and thereafter appeared to be maintained at a relative equilibrium. Sequence analysis of these variants identified preferred sites of recombination in the parental viruses, including both short direct repeats and inverted repeats. One instance of insert deletion through recombination with an endogenous retrovirus was also observed. When specific sequences involved in these recombination events were eliminated, deletion variants still arose with the same kinetics upon virus passage and by apparently similar mechanisms, although at different locations in the vectors. Our results suggest that while lengthened, insert-containing genomes can be maintained over multiple replication cycles, preferential deletions resulting in loss of the inserted sequences confer a strong selective advantage.
Cooperation, Deterrence, and the Ecology of Regulatory Enforcement (1984)

An ecological model based on evolutionary game theory is developed to analyze the role of egoistic cooperation in regulatory enforcement. The model demonstrates that socially beneficial cooperation depends on 1) a combination of cooperative and deterrence routines in an enforcement strategy that is at once vengeful and forgiving, 2) firms concerned enough about future enforcement encounters to forgo short-term gains from evasion, and 3) institutional arrangements that provide suitable sanctions and cost tradeoffs for existing enforcement and evasion technologies in the particular enforcement arena. Factors limiting the advantage of cooperation are also reviewed, and other applications of the model are suggested.
[Abnormal behavior and adaptation problems in dogs and cats and their pharmacologic control]. (1998)

Small animal practitioners are increasingly confronted with patients showing adaptation related problems (ARP) which are expressed as disturbed or abnormal behavior (DAB). As a result, practitioners are asked increasingly to euthanize animals which seemingly cannot be socialized. In healthy dogs and cats, three main causes for DAB can be detected: refusal of obedience because of the drive for dominance; anxiety and frustration; and geriatric DAB. Increasingly, disease conditions not readily diagnosed can cause DAB, especially hypothyroidism. Influencing and contributing factors to DAB are breed, sex, experiences as a puppy, behavior of owners, changes in the pet's environment. ARPs may also cause disturbances in the condition of skin and fur, e.g. atopic dermatitis, pruritus sine materia, lick granuloma, and of the intestinal organs (vomiting, irritated bowel syndrome) and may result in an immune deficiency. Therapeutic approaches include behavioral therapy, surgical or hormonal castration with progestins or antiandrogens, substitution with thyroxin in cases with hypothyroidism, and/or the use of psychopharmaca, most prominently of modern antidepressiva like amitriptyline; buspirone; clomipramine and fluoxetine, but also of selegiline, a mono-aminoxydase inhibitor. These compounds, among other effects, are elevating prolactin levels. This seems to allow to formulate a working hypothesis: in the canine species, prolactin is obviously a hormone enabling socialization; hence all drugs which safely cause an increase in prolactin production might be suitable to manage or control ARPs and DAB in the dog, but also in the cat. Higher levels of prolactin than those required for socialization, as seen in nursing bitches or some clinically overt cases of pseudopregnancy, may cause maternal aggression and can be controlled with prolactin inhibitors, if needed.
Normal cellular counterparts of B cell chronic lymphocytic leukemia (1987)

In an attempt to compare B cell chronic lymphocytic leukemia (B-CLL) with its normal cellular counterpart, the cell surface phenotype of 100 cases of B-CLL was determined by using a panel of monoclonal antibodies (MoAbs) directed against B cell-restricted and -associated antigens. The majority of B-CLL cells expressed Ia, B4 (CD19), B1 (CD20), B2 (CD21), surface immunoglobulin (sIg), and T1 (CD5) but lacked C3b (CD35) receptors. In contrast, the overwhelming majority of small unstimulated B cells expressed Ia, B4, B1, B2, sIg, and C3b receptors but lacked detectable T1. Small numbers of weakly sIg+ cells could be identified in peripheral blood and tonsil that coexpressed the B1 and T1 antigens. Approximately 16% of fetal splenocytes coexpressed B1, T1, weak sIg, B2, and Ia but lacked C3b receptors and therefore closely resembled most B-CLL cells. With the phenotypic differences between the majority of small unstimulated B cells and B-CLL cells, we examined normal in vitro activated B cells and B-CLL cells for the expression of B cell-restricted and -associated activation antigens. Of 20 cases examined, virtually all expressed B5, and approximately 50% of the cases expressed interleukin-2 receptors (IL-2R) and Blast-1. Normal B cells were activated with either anti-Ig or 12–0-tetradecanoylphorbol- beta-acetate (TPA) and then were examined for coexpression of B1, T1, and the B cell activation antigens B5 and IL-2R. Only cells activated with TPA coexpressed B1 and T1 as well as B5 and IL-2R. B cells activated with either anti-Ig or TPA proliferated in the presence of IL- 2, whereas B-CLL cells did not, although they all expressed the identical 60-kilodalton proteins by immunoprecipitation. These studies are consistent with the notion that B-CLL resembles several minor subpopulations of normal B cells including a population of B cells that are activated in vitro directly through the protein kinase C pathway.
The line of action (2013)

The line of action is a conceptual tool often used by cartoonists and illustrators to help make their figures more consistent and more dramatic. We often see the expression of characters---may it be the dynamism of a super hero, or the elegance of a fashion model---well captured and amplified by a single aesthetic line. Usually this line is laid down in early stages of the drawing and used to describe the body's principal shape. By focusing on this simple abstraction, the person drawing can quickly adjust and refine the overall pose of his or her character from a given viewpoint. In this paper, we propose a mathematical definition of the line of action (LOA), which allows us to automatically align a 3D virtual character to a user-specified LOA by solving an optimization problem. We generalize this framework to other types of lines found in the drawing literature, such as secondary lines used to place arms. Finally, we show a wide range of poses and animations that were rapidly created using our system.
Molecularly chemisorbed intermediates to oxygen adsorption on Pt(111): A molecular beam and electron energy-loss spectroscopy study (1999)

High translational energy adsorption of oxygen on the (111) surface of platinum was examined with electron energy loss spectroscopy (EELS) and molecular beam techniques. EEL spectra indicate that over an incident energy range of 0.2–1.37 eV and on a Pt(111) surface held at 77 K, oxygen adsorbs in an associative chemisorbed state—yielding to the dissociated state only after sufficient substrate heating. Simple direct dissociation appears negligible for all incident kinetic energies studied. At near-zero surface coverages, exclusive population of the peroxolike molecular precursor is observed for adsorption at these high translational energies, while both superoxolike and peroxolike forms are detected for low energy adsorption (0.055 eV). This peculiarity represents evidence that translational energy is effective in differentially populating reaction intermediates and provides better quantification of potential energy barriers to dissociation. We estimate the activation barrier for dissociation from the peroxolike precursor to be approximately 0.29 eV. Initial adsorption probability measurements over a wide range of surface temperatures and high incident kinetic energies corroborate a molecular chemisorption mediated mechanism.
Frequency-domain equalization of mobile radio and terrestrial broadcast channels (2002)

For mobile radio and terrestrial broadcast applications, we compare orthogonal frequency-division multiplexing (OFDM) and single-carrier transmission with frequency-domain equalization. With respect to our earlier results, we include channel coding and frequency-domain interleaving which are necessary for OFDM systems on multipath fading channels characterized by deep notches in the signal spectrum. Our results indicate that a single-carrier system with a frequency-domain equalizer achieves similar performance to coded-OFDM, while alleviating the carrier synchronization and nonlinear distortion problems inherent to this technique.
Wnt Signaling Regulates Hemopoiesis Through Stromal Cells (2001)

Hemopoietic cells develop in a complex milieu that is made up of diverse components, including stromal cells. Wnt genes, which are known to regulate the fate of the cells in a variety of tissues, are expressed in hemopoietic organs. However, their roles in hemopoiesis are not well characterized. In this study, we examined the roles of Wnt proteins in hemopoiesis using conditioned medium containing Wnt-3a. This conditioned medium dramatically reduced the production of B lineage cells and myeloid lineage cells, except for macrophages in the long-term bone marrow cultures grown on stromal cells, although the sensitivity to the conditioned medium differed, depending on the hemopoietic lineage. In contrast, the same conditioned medium did not affect the generation of B lineage or myeloid lineage cells in stromal cell-free conditions. These results suggested that Wnt proteins exert their effects through stromal cells. Indeed, these effects were mimicked by the expression of a stabilized form of beta-catenin in stromal cells. In this study, we demonstrated that Wnt signaling regulates hemopoiesis through stromal cells with selectivity and different degrees of the effect, depending on the hemopoietic lineage in the hemopoietic microenvironment.
Associations of Hormones and Menopausal Status With Depressed Mood in Women With No History of Depression (2006)

Transition to menopause and its changing hormonal milieu are strongly associated with new onset of depressed mood among women with no history of depression.
Measurement of optical distances by optical spectrum modulation (1994)

The spectral interferometry technique is outlined and its application to axial eye length measurement is discussed. First results obtained from glass plates are presented.
Advanced illumination techniques for GPU-based volume raycasting (2009)

Volume raycasting techniques are important for both visual arts and visualization. They allow efficient generation of visual effects and visualization of scientific data obtained by tomography or numerical simulation. Volume-rendering techniques are also effective for direct rendering of implicit surfaces used for soft-body animation and constructive solid geometry. The focus of this course is on volumetric illumination techniques that approximate physically based light transport in participating media. Such techniques include interactive implementation of soft and hard shadows, ambient occlusion, and simple Monte Carlo-based approaches to global illumination, including translucency and scattering.
The amino acid sequence of penicillinase from Bacillus licheniformis (1969)

of L-tyrosine methyl ester shows the presence of a group in the enzyme having a pK value of approx. 9.5. This group could conceivably be a thiol group, as the enzyme is known to be inactivated on storage and is reactivated by the addition of reduced thiols. In keeping with this hypothesis the enzyme was found to be inactivated by iodoacetamide at pH 7-5, and this inactivation is prevented by the addition of adenosine 3'-phosphate 5'-sulphato- phosphate, but not L-tyrosine methyl ester, to the alkylation mixture.
Controlled Synthesis of Iron Oxide Nanoparticles over a Wide Size Range (2009)

We report on the effect of using decanoic acid as capping ligand on the synthesis of iron oxide nanoparticles by thermal decomposition of an organic iron precursor in organic medium. This procedure allowed us to control the particle size within 5 nm and about 30 nm by modifying the precursor-to-capping ligand ratio in a systematic fashion and to further expand the particle size range up to about 50 nm by adjusting the final synthesis temperature. The nanoparticles also showed high saturation magnetization of about 80-83 emu/g at low temperature, almost size-independent and close to the value for the bulk counterpart. Decanoic acid-coated nanoparticles were transferred to water by using tetramethylammonium hydroxide, which allowed further coating with silica in a tetraethyl orthosilicate solution. Consequently, these iron oxide nanoparticles are tunable in size and highly magnetic, and they could become suitable candidates for various biomedical applications such as contrast agents for magnetic resonance imaging and magnetic carriers for drug delivery.
Aptamer affinity chromatography: combinatorial chemistry applied to protein purification. (1999)

The systematic evolution of ligands by exponential enrichment process is a combinatorial chemistry method that allows the identification of specific oligonucleotide sequences, known as aptamers, that bind to a desired target molecule with high affinity and specificity. Here, a DNA-aptamer specific for human L-selectin was immobilized to a chromatography support to create an affinity column. This column was effectively applied as either the first or second step in the purification of a recombinant human L-selectin-Ig fusion protein from Chinese hamster ovary cell-conditioned medium. The fusion protein was efficiently bound to the column and efficiently eluted by gentle elution schemes. Application of the aptamer column as the initial purification step resulted in a 1500-fold purification with an 83% single step recovery. These results demonstrate that oligonucleotide aptamers can be effective affinity purification reagents.
The grass leaf developmental gradient as a platform for a systems understanding of the anatomical specialization of C4 leaves (2011)

C(4) photosynthesis relies on spatial and quantitative specializations of common features of leaf anatomy, including venation pattern, bundle sheath cell and chloroplast differentiation, plasmodesmatal abundance, and secondary cell wall enhancement. It has thus far been challenging to dissect the molecular basis for these C(4)-specific alterations in spatial and quantitative patterns of regulation. The target downstream networks of genes and protein interactions that produce these fundamental anatomical features in both C(4) and C(3) species are poorly understood. The developing leaves of monocot grasses provide a base-to-tip gradient of developmental stages that can provide the platform for comprehensive molecular and anatomical data that can yield a better understanding both of the regulators and the targets that produce C(4) patterns, through a variety of gene discovery and systems analysis strategies.
Value of subthalamic nucleus local field potentials recordings in predicting stimulation parameters for deep brain stimulation in Parkinson's disease (2010)

Online spectral analysis of LFPs recorded from the DBS electrode may help identify the optimal therapeutic target in the STN region for DBS.
The West Nile Virus Outbreak of 1999 in New York: The Flushing Hospital Experience (2000)

West Nile Virus (WNV) is a mosquito-borne flavivirus, which has been known to cause human infection in Africa, the Middle East, and southwestern Asia. It has also been isolated in Australia and sporadically in Europe but never in the Americas. Clinical features include acute fever, severe myalgias, headache, conjunctivitis, lymphadenopathy, and a roseolar rash. Rarely is encephalitis or meningitis seen. During the month of August 1999, a cluster of 5 patients with fever, confusion, and weakness were admitted to the intensive care unit of the same hospital in New York City. Ultimately 4 of the 5 developed flaccid paralysis and required ventilatory support. Three patients with less-severe cases presented shortly thereafter. With the assistance of the New York City and New York State health departments and the Centers for Disease Control and Prevention, these were documented as the first cases of WNV infection on this continent.
Analysis of the origin of marrow cells in bone marrow transplant recipients using a Y-chromosome-specific in situ hybridization assay (1989)

A Y-chromosome-specific in situ hybridization assay was used to assess the frequency with which host bone marrow cells are retained after marrow grafting. The majority of patients (74%) showed the presence of both host and donor marrow cells when assayed 14 days after transplant. By 84 days posttransplant only 4% of the patients retained host marrow cells. Only 1 of 19 evaluable patients analyzed over 1 year posttransplant showed minimal retention of host cells. No statistical correlation was found between retention of host cells posttransplant and the development of relapse or acute or chronic graft-versus-host disease. Pretransplant conditioning regimen, HLA-matching, diagnosis, disease status at transplant, ABO-matching, and patient age also showed no correlation with the retention of host cells posttransplant.
Vaginoplasty using amnion. (1986)

Fifteen patients with various developmental and acquired abnormalities of the vagina were treated by the application of human amnion over a mold after surgical dissection of a space for the new vagina or enlargement of an existing but strictured one. Excellent results were achieved in cases of complete and partial vaginal agenesis, and there was improvement in all of the patients with vaginal strictures.
Epigenetic Regulation by Long Noncoding RNAs (2012)

Recent studies show that transcription of the mammalian genome is not only pervasive but also enormously complex. It is estimated that an average of 10 transcription units, the vast majority of which make long noncoding RNAs (lncRNAs), may overlap each traditional coding gene. These lncRNAs include not only antisense, intronic, and intergenic transcripts but also pseudogenes and retrotransposons. Do they universally have function, or are they merely transcriptional by-products of conventional coding genes? A glimpse into the molecular biology of multiple emerging lncRNA systems reveals the "Wild West" landscape of their functions and mechanisms and the key problems to solve in the years ahead toward understanding these intriguing macromolecules.
Human Bone Marrow Activates the Akt Pathway in Metastatic Prostate Cells through Transactivation of the α-Platelet–Derived Growth Factor Receptor (2007)

The factors regulating the bone tropism of disseminated prostate cancer cells are still vaguely defined. We report that prostate cancer cells that metastasize to the skeleton respond to human bone marrow with a robust stimulation of the phosphatidylinositol 3-kinase/Akt pathway, whereas prostate cells that lack bone-metastatic potential respond negligibly. The majority of this Akt activation is dependent on alpha-platelet-derived growth factor receptor (alpha-PDGFR) signaling, which was shown using the small-molecule inhibitor of PDGFR signaling AG1296. Low concentrations of PDGF-AA and PDGF-BB found in bone marrow aspirates, which were detected by ELISA, do not account for the high levels of alpha-PDGFR signaling. Additionally, neutralizing PDGF binding using a alpha-PDGFR-specific antibody (IMC-3G3) failed to produce a significant inhibition of bone marrow-induced Akt activation. However, the inhibitory effect of IMC-3G3 rivaled that of AG1296 when incubation was done under conditions that stimulated alpha-PDGFR internalization. We conclude that alpha-PDGFR is activated by multiple soluble factors contained within human bone marrow, in addition to its natural ligands, and this transactivation is dependent on receptor localization to the plasma membrane. Therefore, alpha-PDGFR expression may provide select prostate phenotypes with a growth advantage within the bone microenvironment.
Network-Resource Isolation for Virtualization Nodes (2012)

One key requirement for achieving network virtualization is resource isolation among slices (virtual networks), that is, to avoid interferences between slices of resources. This paper proposes two methods, per-slice shaping and per-link policing for network-resource isolation (NRI) in terms of bandwidth and delay. These methods use traffic shaping and traffic policing, which are widely-used traffic control methods for guaranteeing QoS. Per-slice shaping utilizes weighted fair queuing (WFQ) usually applied to a fine-grained flow such as a flow from a specific server application to a user. Since the WFQ for fine-grained flows requires many queues, it may not scale to a large number of slices with a large number of virtual nodes. Considering that the purpose of NRI is not thoroughly guaranteeing QoS but avoiding interferences between slices, we believe per-slice (not per virtual link) shaping satisfies our objective. In contrast, per-link policing uses traffic policing per virtual link. It requires less resource and achieves less-strict but more-scalable isolation between hundreds of slices (500 to 700 slices in estimation). Our results show that both methods perform NRI well but the performance of the former is better in terms of delay. Accordingly, per-slice shaping (with/without policing) is effective for delay-sensitive services while per-link policing may be sufficiently used for the other types of services.