gebhart/patrepeval huggingface dataset:
SWEPT VOLUMES: FUNDATION, PERSPECTIVES, AND APPLICATIONS (2006)

A survey of swept volume concepts and methods is presented. It consolidates and relates seemingly different terminology and methods. The methods are divided into five major categories: method with envelope theory, method with sweep differential equation (SDE)/sweep envelope differential equation (SEDE), method with Jacobian rank deficiency, Voxel-based method, and free-form solids' sweeping methods. Commentary is provided on three fronts, concerning the advantages and pitfalls of individual methods, the different classes of methods, and the field of swept volumes as a whole. The characteristics of the most significant methods are summarized. The applicability of this seemingly simple formulation to the fields of solid modeling, robotics, manufacturing automation, and visualization is demonstrated through results reported by the authors, each in their own field.
Saturable CD14-dependent binding of fluorescein-labeled lipopolysaccharide to human monocytes (1997)

We used rough lipopolysaccharide (ReLPS) to construct a fluorescein-labeled LPS (FITC-LPS) with a very high labeling efficiency that bound to isolated human monocytes in a CD14-dependent fashion and that in this respect behaved indistinctively from native LPS. The CD14-dependent binding could be inhibited either by a 1,000-fold excess of unlabeled LPS or by polymyxin B, bactericidal/permeability-increasing protein, cationic protein 18, or soluble CD14. Although this FITC-LPS preparation no longer possessed the ability to prime neutrophils for the production of reactive oxygen species or to stimulate human monocytes to produce tumor necrosis factor, activation of the Limulus amoebocyte lysate cascade was comparable to activation by native LPS. Binding to monocytes was enhanced by human pooled serum (HPS) or LPS-binding protein (LBP) for LPS concentrations up to 100 ng/ml and was completely CD14 dependent. For LPS concentrations exceeding 100 ng/ml, binding was still partially CD14 dependent, but not HPS or LBP dependent. CD14-dependent association of LPS with monocytes was shown to be totally saturable. In conclusion, we found an HPS- or LBP-dependent binding of FITC-LPS to monocytes that was CD14 dependent at up to 100 ng of LPS per ml, and saturation of binding was shown.
Induction of IL-1Ra in Resistant and Responsive Hepatitis C Patients Following Treatment with IFN-con1 (2002)

Hepatitis C virus (HCV) infection is resistant to interferon-alpha (IFN-alpha) in some patients. The mechanism of this resistance is unknown. Interleukin-1 receptor antagonist (IL-1Ra) is induced by IFN-alpha and is a good indicator of IFN activity. In the current study, we compared IL-1Ra levels in rapid virologic responders and flat responders who showed resistance to IFN. Three groups of patients were examined, including those who received a single dose of consensus IFN (IFN-con1), patients who received daily IFN-con1 for 1 week, and patients who received IFN-con1 daily for 24 weeks. Serum IL-1Ra, IL-6, and HCV RNA were measured serially in all groups. Serum IL-1Ra levels increased rapidly in all patients with hepatitis C after IFN-alpha administration, irrespective of their virologic response. IL-1Ra levels remained elevated at 1 week but were similar to baseline by week 2 of treatment in patients receiving continuous therapy. IL-6 levels also increased acutely but rose more slowly than IL-1Ra levels. The increase in IL-1Ra and IL-6 observed in both flat and rapid virologic responders indicates that IFN receptors are functioning in patients with IFN-resistant hepatitis C and that the lack of response is related to other virologic or immunologic factors.
Evaluation of the Therapeutic Usefulness of Botulinum Neurotoxin B, C1, E, and F Compared with the Long Lasting Type A (2003)

Seven types (A-G) of botulinum neurotoxin (BoNT) target peripheral cholinergic neurons where they selectively proteolyze SNAP-25 (BoNT/A, BoNT/C1, and BoNT/E), syntaxin1 (BoNT/C1), and synaptobrevin (BoNT/B, BoNT/D, BoNT/F, and BoNT/G), SNARE proteins responsible for transmitter release, to cause neuromuscular paralysis but of different durations. BoNT/A paralysis lasts longest (4-6 months) in humans, hence its widespread clinical use for the treatment of dystonias. Molecular mechanisms underlying these distinct inhibitory patterns were deciphered in rat cerebellar neurons by quantifying the half-life of the effect of each toxin, the speed of replenishment of their substrates, and the degradation of the cleaved products, experiments not readily feasible at motor nerve endings. Correlation of target cleavage with blockade of transmitter release yielded half-lives of inhibition for BoNT/A, BoNT/C1, BoNT/B, BoNT/F, and BoNT/E (31, 25, approximately 10, approximately 2, and approximately 0.8 days, respectively), equivalent to the neuromuscular paralysis times found in mice, with recovery of release coinciding with reappearance of the intact SNAREs. A limiting factor for the short neuroparalytic durations of BoNT/F and BoNT/E is the replenishment of synaptobrevin or SNAP-25, whereas pulse labeling revealed that extended inhibition by BoNT/A, BoNT/B, or BoNT/C1 results from longevity of each protease. These novel findings could aid development of new toxin therapies for patients resistant to BoNT/A and effective treatments for human botulism.
LOCALIZATION OF ANTIGEN IN TISSUE CELLS (1950)

The fate of the capsular polysaccharide of Friedländer B bacillus in the mouse after its intravenous administration was studied by means of homologous antibody labelled with fluorescein. The results indicate that this acid polysaccharide, like pneumococcal polysaccharide, types II and III, was rapidly taken up by phagocytic cells throughout the body, where it persisted in decreasing concentration for more than 33 days. It was widely distributed in the capillary endothelium and on collagenous fibres in all organs. It made a transient appearance in or on lymphocytes in the spleen and lymph nodes. It was found in the hepatic epithelium and in the bile; in the juxtaglomerular segment of the distal renal tubule and in an occasional cast in the lumens of collecting tubules; in the epithelium of some uterine glands; and in cells in the steroid-secreting tissues of the ovary, suprarenal cortex, and perhaps of the testis. In joints the synovial membranes contained large amounts of antigen, and some also penetrated into cartilage cells adjacent to the joint cavity. Osteoblasts and a few osteocytes also took up the polysaccharide. When administered by inhalation, the polysaccharide was found in high concentration in the pulmonary macrophages but could not be found constantly in other lung elements.
Antiadhesive Effects of GRN163L—An Oligonucleotide N3′→P5′ Thio-Phosphoramidate Targeting Telomerase (2007)

We determined previously that a novel human telomerase RNA (hTR) antagonist, GRN163L, inhibited the tumorigenic potential of A549-luciferase (A549-luc) lung cancer cells in vitro and in vivo. Further studies revealed that A549-luc cells were also morphologically altered by GRN163L. A549-luc cells treated before cell attachment with a single dose of GRN163L only weakly attached to the substrate and remained rounded, whereas control mismatch-treated cells exhibited typical epitheloid appearance and adhesion properties. These morphologic changes were independent of hTR expression and telomerase inhibition and were unrelated to telomere length. This effect is dependent on the molecular properties of the lipid moiety, the phosphorothioate backbone, and the presence of triplet-G sequences within the GRN163L structure. Altered adhesion was manifested by a 50% reduction in rapid cellular attachment and a 3-fold decrease in total cell spreading surface area. Administration of a single dose of GRN163L (15 mg/kg) at the time of cell inoculation, using an in vivo model of lung cancer metastasis, resulted in significant reductions in tumor burden at days 13, 20, and 27 of tumor progression. Thus, the potent antimetastatic effects of GRN163L may be related, in part, to the antiadhesive effects of this novel cancer therapeutic conferred via specific structural determinants and that these effects are independent of telomerase inhibition or telomere shortening.
Gene transfer to Clostridium cellulolyticum ATCC 35319 (2000)

Although much is known about the bacterial cellulosome and its various protein components, their contributions to bacterial growth on cellulose and the process of cellulolysis in vivo cannot currently be assessed. To remedy this, the authors have developed gene transfer techniques for Clostridium cellulolyticum ATCC 35319. Firstly, transfer of Tn1545 has been obtained using an Enterococcus faecalis donor. Secondly, IncP-mediated conjugative mobilization of plasmids from Escherichia coli donors has also been achieved. The yield of transconjugants in both cases was low and was probably limited by the suboptimal growth conditions that must of necessity be employed for the co-culture of oligotrophic C. cellulolyticum with copiotrophic donors. A restriction endonuclease was detected in crude extracts of C. cellulolyticum. This enzyme, named CCE:I, is an isoschizomer of MSP:I (HPA:II). Electro-transformation was employed to establish plasmids containing the replication functions of pAMss1 (En. faecalis), pIM13 (Bacillus subtilis), pCB102 (Clostridium butyricum), pIP404 (Clostridium perfringens) and pWV01 (Lactococcus lactis subsp. cremoris) in C. cellulolyticum. Transformants were only obtained if the DNA was appropriately methylated on the external C of the sequence 5'-CCGG-3' using either BSU:FI methylase in vivo or MSP:I methylase in vitro. Plasmids based on the pAMss1 and pIM13 replicons were more stably maintained than one based on the pCB102 replicon. Selection of transformants on solid medium led to low apparent transformation efficiencies (approx. 10(2) transformants per microg DNA) which might, in part, reflect the low plating efficiency of the organism. Selection of transformants in liquid medium led to a higher apparent yield of transformants (between 10(5) and 10(7) transformants per microg DNA). The methods developed here will pave the way for functional analysis of the various cellulosome components in vivo.
CD56+ Cells Induce Steroid Resistance in B Cells Exposed to IL-15 (2004)

Interleukin-2 can induce steroid resistance in T cells. IL-15 shares biological activities with IL-2, as both cytokines use IL-2Rgamma for signal transduction. We therefore sought to determine whether IL-15 contributes to induction of PBMC corticosteroid resistance. Surprisingly, we found that incubation of unfractionated PBMC with IL-15 for 48 h resulted in the inhibition of glucocorticoid receptor (GCR) nuclear translocation in response to dexamethasone (DEX) treatment in CD19-positive B cells significantly greater than CD19-negative non-B cells (p < 0.01). However, pure B cells incubated with IL-15 responded normally with nuclear translocation of GCR in response to steroids, but failed to translocate GCR when they were grown in the presence of CD19(-) cells. Coculture of B cells with CD3(+) (T cells), CD14(+) (monocytes), or CD56(+) (NK and NKT cells) in the presence of IL-15 revealed that only CD56(+) cells contributed to the steroid insensitivity of B cells. IL-15 stimulation significantly increased production of IL-4 by CD56(+) cells (p < 0.02). Treatment of purified B cells with combination IL-15/IL-4 resulted in abrogation of glucocorticoid receptor nuclear translocation and the inability of DEX to suppress cytokine production by B cells. In the presence of IL-4-neutralizing Ab, when B cells were cocultured with CD56(+) cells and IL-15, the B cells were found to be steroid sensitive, i.e., DEX induced GCR nuclear translocation. This study demonstrates that B cells develop steroid resistance in the presence of CD56(+) cells after IL-15 stimulation. Furthermore, IL-15 and IL-4 have the capacity to induce B cell insensitivity to steroids.
From Lentiviruses to Lentivirus Vectors (2003)

Although a member of the lentivirus group, the equine infectious anemia virus (EIAV) was the first nonplant virus discovered in the first decade of the 20th century (), lentiviruses were considered as rather mysterious viruses until the isolation of the human immunodeficiency virus type 1 (HIV-1) occurred at the beginning of 1980s. Lentiviruses are enveloped viruses carrying two copies of single-strand positive (i.e., codifying) RNA and are considered the ethiologic agents of acquired immunodeficiency syndromes for a broad range of animal species, such as humans, primates, cats, horses, sheep, and goats. Such syndromes develop in multiorgan diseases and share a long period of incubation (with viral persistence despite a potent immunological response) and a fatal outcome. The name lentiviruses (from Latin, lenti, slow) originated from the uniquely prolonged incubation period (i.e., from months to years) needed for the infecting virus to induce the disease, a feature joining the most popular lentivirus, HIV-1, with a large number of nonprimates lentiviruses. Lentiviruses belong to the Lentiviridae subfamily of the Retroviridae family, which also includes the Oncoviridae, for the most part viruses inducing cell transformation, and the Spumaviridae, viruses establishing persistent as well as nonpathogenic infections (a deeper treatment of this topic can be found in ref. ).
Enabling FPGAs in the cloud (2014)

Cloud computing is becoming a major trend for delivering and accessing infrastructure on demand via the network. Meanwhile, the usage of FPGAs (Field Programmable Gate Arrays) for computation acceleration has made significant inroads into multiple application domains due to their ability to achieve high throughput and predictable latency, while providing programmability, low power consumption and time-to-value. Many types of workloads, e.g. databases, big data analytics, and high performance computing, can be and have been accelerated by FPGAs. As more and more workloads are being deployed in the cloud, it is appropriate to consider how to make FPGAs and their capabilities available in the cloud. However, such integration is non-trivial due to issues related to FPGA resource abstraction and sharing, compatibility with applications and accelerator logics, and security, among others. In this paper, a general framework for integrating FPGAs into the cloud is proposed and a prototype of the framework is implemented based on OpenStack, Linux-KVM and Xilinx FPGAs. The prototype enables isolation between multiple processes in multiple VMs, precise quantitative acceleration resource allocation, and priority-based workload scheduling. Experimental results demonstrate the effectiveness of this prototype, an acceptable overhead, and good scalability when hosting multiple VMs and processes.
An unexpected N-terminal loop in PD-1 dominates binding by nivolumab (2017)

Cancer immunotherapy by targeting of immune checkpoint molecules has been a research 'hot-spot' in recent years. Nivolumab, a human monoclonal antibody targeting PD-1, has been widely used clinically since 2014. However, the binding mechanism of nivolumab to PD-1 has not yet been shown, despite a recent report describing the complex structure of pembrolizumab/PD-1. It has previously been speculated that PD-1 glycosylation is involved in nivolumab recognition. Here we report the complex structure of nivolumab with PD-1 and evaluate the effects of PD-1 N-glycosylation on the interactions with nivolumab. Structural and functional analyses unexpectedly reveal an N-terminal loop outside the IgV domain of PD-1. This loop is not involved in recognition of PD-L1 but dominates binding to nivolumab, whereas N-glycosylation is not involved in binding at all. Nivolumab binds to a completely different area than pembrolizumab. These results provide the basis for the design of future inhibitory molecules targeting PD-1.
Increased plasma serotonin following treatment with flavone-8-acetic acid, 5,6-dimethylxanthenone-4-acetic acid, vinblastine, and colchicine: relation to vascular effects. (1997)

A number of antitumor agents are known to cause selective reduction in tumor blood flow, leading in some cases to tumor necrosis and growth delay. These agents include flavone acetic acid (FAA), an antitumor agent with high experimental but no clinical antitumor activity, 5,6-dimethylxanthenone-4-acetic acid (DMXAA), a highly active analogue of FAA, endotoxin, vinblastine, and colchicine. We find here that plasma concentrations of serotonin (5-hydroxytryptamine) and its metabolite 5-hydroxyindole acetic acid (5-HIAA) are increased following administration of these agents. Mice were injected with each at the maximum tolerated dose and, at various times later, blood samples were taken, cells and platelets removed by centrifugation, and serotonin and 5-HIAA concentrations were measured by high performance liquid chromatography. FAA and DMXAA induced six- and sevenfold increases in serotonin and 5-HIAA, respectively, with maximal levels 4 h after drug administration. 8-Methylxanthenone-4-acetic acid, an inactive analogue of DMXAA, failed to increase serotonin and caused only a small increase in 5-HIAA. Endotoxin, vinblastine, and colchicine each caused increases in serotonin and 5-HIAA between 2 and 6 h after drug administration. The mitotic poison paclitaxel, despite inducing growth delays of Colon 38 tumors, did not induce tumor necrosis and caused no increase in serotonin or 5-HIAA up to 6 h. The effect of the presence of subcutaneous Colon 38 tumors was tested and found not to affect the induction of increases in serotonin and 5-HIAA by DMXAA and colchicine. We suggest that the increases in plasma serotonin and its metabolite are a result of drug-induced vascular effects in host tissues, and that measurement of these compounds provides a potential means of monitoring drugs exerting vascular effects.
Treatment of Angina Pectoris by Electrical Stimulation of the Carotid-Sinus Nerves (1969)

Radiofrequency carotid-sinus nerve stimulators implanted for treatment of incapacitating angina pectoris, unrelieved by intensive medical management, produced appreciable symptomatic improvement in 13 of 17 patients: nearly all episodes of angina were terminated by activation of the stimulator, and prophylactic use increased intensity and duration of exercise that could be performed. After long-term use exercise capacity was increased in many patients even when the stimulator was not activated. Two had no benefit, and two died. Prophylactic use during exercise lowered mean arterial pressure an average of 18 mm of mercury (p less than 0.001) in 13 of the 15 survivors, but heart rate was reduced by an average of only 4 beats per minute. The other two showed no hemodynamic response. The principal physiologic factor in the relief of angina appears to be a decrease in arterial pressure, which reduces a major determinant of myocardial oxygen consumption and re-establishes the balance between myocardial oxygen demands and supply.
Morphine via nitric oxide modulates beta-amyloid metabolism: a novel protective mechanism for Alzheimer's disease. (2005)

Ab and morphine/NO each inhibit the production of the other. This suggests that a deficiency of basal NO or endogenous morphine may trigger drastically reduced levels of basal NO. The outcome is chronic vasoconstriction and brain hypoperfusion and eventual neuronal death. This novel theorized mechanism for AD supports an increasingly-accepted vascular pathological hypothesis for the disease.
Monotheism and Its Discontents: Religious Violence and the Bible (1998)

Monotheism and Its Discontents: Religious Violence and the Bible The Curse of Cain: The Violent Legacy of Monotheism. By Regina M. Schwartz. Chicago: University of Chicago Press, 1997. 211 pages. $22.95. Brian K. Smith Brian K. Smith Brian K Smith is Professor of Religious Studies at the University of California, Riverside, Riverside, CA 92521. Search for other works by this author on: Oxford Academic Google Scholar Journal of the American Academy of Religion, Volume 66, Issue 2, SUMMER 1998, Pages 403–412, https://doi.org/10.1093/jaarel/66.2.403 Published: 01 July 1998
Photoluminescence emission spectra of Makrofol® DE 1-1 upon irradiation with ultraviolet radiation (2016)

Photoluminescence (PL) emission spectra of Makrofol® DE 1-1 (bisphenol-A based polycarbonate) upon irradiation with ultraviolet radiation of different wavelengths were investigated. The absorption-and attenuation coefficient measurements revealed that the Makrofol® DE 1-1 is characterized by high absorbance in the energy range 6.53–4.43 eV but for a lower energy than 4.43 eV, it is approximately transparent. Makrofol® DE 1-1 samples were irradiated with ultraviolet radiation of wavelength in the range from 250 (4.28 eV) to 400 (3.10 eV) nm in step of 10 nm and the corresponding photoluminescence (PL) emission spectra were measured with a spectrofluorometer. It is found that the integrated counts and the peak height of the photoluminescence emission (PL) bands are strongly correlated with the ultraviolet radiation wavelength. They are increased at the ultraviolet radiation wavelength 280 nm and have maximum at 290 nm, thereafter they decrease and diminish at 360 nm of ultraviolet wavelength. The position of the PL emission band peak was red shifted starting from 300 nm, which increased with the increase the ultraviolet radiation wavelength. The PL bandwidth increases linearly with the increase of the ultraviolet radiation wavelength. When Makrofol® DE 1-1 is irradiated with ultraviolet radiation of short wavelength (UVC), the photoluminescence emission spectra peaks also occur in the UVC but of a relatively longer wavelength. The current new findings should be considered carefully when using Makrofol® DE 1-1 in medical applications related to ultraviolet radiation.
Hierarchical Bayesian inference in the visual cortex (2003)

Traditional views of visual processing suggest that early visual neurons in areas V1 and V2 are static spatiotemporal filters that extract local features from a visual scene. The extracted information is then channeled through a feedforward chain of modules in successively higher visual areas for further analysis. Recent electrophysiological recordings from early visual neurons in awake behaving monkeys reveal that there are many levels of complexity in the information processing of the early visual cortex, as seen in the long-latency responses of its neurons. These new findings suggest that activity in the early visual cortex is tightly coupled and highly interactive with the rest of the visual system. They lead us to propose a new theoretical setting based on the mathematical framework of hierarchical Bayesian inference for reasoning about the visual system. In this framework, the recurrent feedforward/feedback loops in the cortex serve to integrate top-down contextual priors and bottom-up observations so as to implement concurrent probabilistic inference along the visual hierarchy. We suggest that the algorithms of particle filtering and Bayesian-belief propagation might model these interactive cortical computations. We review some recent neurophysiological evidences that support the plausibility of these ideas.