gebhart/patrepeval huggingface dataset:
Embedded deformation for shape manipulation (2007)

We present an algorithm that generates natural and intuitive deformations via direct manipulation for a wide range of shape representations and editing scenarios. Our method builds a space deformation represented by a collection of affine transformations organized in a graph structure. One transformation is associated with each graph node and applies a deformation to the nearby space. Positional constraints are specified on the points of an embedded object. As the user manipulates the constraints, a nonlinear minimization problem is solved to find optimal values for the affine transformations. Feature preservation is encoded directly in the objective function by measuring the deviation of each transformation from a true rotation. This algorithm addresses the problem of "embedded deformation" since it deforms space through direct manipulation of objects embedded within it, while preserving the embedded objects' features. We demonstrate our method by editing meshes, polygon soups, mesh animations, and animated particle systems.
Look-Ahead Processors (1975)

Methods of achieving look-ahead in processing units are discussed. An optimality criterion is proposed, and several schemes are compared against the optimum under varying assumptions. These schemes include existing and proposed machine organizations, and theoretical treatments not mentioned before in this context. The problems of eliminating associative searches in the processor control and the handling of loop-forming decisions are also considered. The inherent limitations of such processors are discussed. Finally, a number of enhancements to look-ahead processors is qualitatively surveyed.
An Overview of the SHS Technique and Applications (2007)

The concepts of Spatial Heterodyne Spectroscopy (SHS) are described, and trade-offs to be considered in applications are reviewed. SHS instruments in use and in development for ground- and space-based applications will be highlighted.
Nonviral RNA Transfection to Transiently Modify T Cells with Chimeric Antigen Receptors for Adoptive Therapy (2012)

Redirecting T cells with a chimeric antigen receptor (CAR) of predefined specificity showed remarkable efficacy in the adoptive therapy trials of malignant diseases. The CAR consists of a single chain fragment of variable region (scFv) antibody targeting domain covalently linked to the CD3ζ signalling domain of the T cell receptor complex to mediate T cell activation upon antigen engagement. By using an antibody-derived targeting domain a CAR can potentially redirect T cells towards any target expressed on the cell surface as long as a binding domain is available. Antibody-mediated targeting moreover circumvents MHC restriction of the targeted antigen, thereby broadening the potential of applicability of adoptive T cell therapy. While T cells were so far genetically modified by viral transduction, transient modification with a CAR by RNA transfection gained increasing interest during the last years. This chapter focuses on methods to modify human T cells from peripheral blood with a CAR by electroporation of in vitro transcribed RNA and to test modified T cells for function for use in adoptive immunotherapy.
Transmission Electron Microscopic Study of Cross-Sectional Morphologies of Core−Corona Polymeric Nanospheres (2000)

Ultrathin cross sections of core−corona polymeric nanospheres, which were prepared by the free-radical polymerization of methacrylate-terminated poly(ethylene glycol) (MA-PEG) as a hydrophilic macromonomer and styrene (St) as a hydrophobic comonomer in a ethanol/water (4/1, v/v) mixed solvent, were observed by using transmission electron microscopy (TEM). Conditions of the preparation of nanosphere-embedded resins, the cutting rate by a microtome for cross-section preparation, and staining with osmium tetraoxide were optimized in order to analyze cross-sectional morphologies of the nanospheres clearly. Nanospheres prepared showed a core−corona structure in all cases. The corona layer thickness was constant at around 6 nm when we used the same macromonomer (Mn 996), even if we altered the size in the nanosphere to 133, 272, and 1530 nm by altering the monomer ratio (St/MA-PEG 20/1, 50/1, and 200/1, respectively, mol/mol). The thickness increased from 6.7 to 17 nm with an increase in the molecular weight of a macromonomer from Mn 996 to 4250, although the size decreased from 373 to 204 nm with an increase in it. TEM observations in the present study led us to have further structural understanding of core−corona nanospheres that had various technological and biomedical applications.
Sustained Small Interfering RNA-Mediated HumanImmunodeficiency Virus Type 1 Inhibition in PrimaryMacrophages (2003)

Small interfering RNAs (siRNAs) can induce potent gene silencing by degradation of cognate mRNA. However, in dividing cells, the silencing lasts only 3 to 7 days, presumably because of siRNA dilution with cell division. Here, we investigated if sustained siRNA-mediated silencing of human immunodeficiency virus type 1 (HIV-1) is possible in terminally differentiated macrophages, which constitute an important reservoir of HIV in vivo. CCR5, the major HIV-1 coreceptor in macrophages, and the viral structural gene for p24 were targeted either singly or in combination. When transfected 2 days prior to infection, both CCR5 and p24 siRNAs effectively reduced HIV-1 infection for the entire 15-day period of observation, and combined targeting of both genes abolished infection. To investigate whether exogenously introduced siRNA is maintained stably in macrophages, we tested the kinetics of siRNA-mediated viral inhibition by initiating infections at various times (2 to 15 days) after transfection with CCR5 and p24 siRNAs. HIV suppression mediated by viral p24 siRNA progressively decreased and was lost by day 7 posttransfection. In contrast, viral inhibition by cellular CCR5 knockdown was sustained even when transfection preceded infection by 15 days, suggesting that the continued presence of target RNA may be needed for persistence of siRNA. The longer sustenance of CCR5 relative to p24 siRNA in uninfected macrophages was also confirmed by detection of internalized siRNA by modified Northern blot analysis. We also tested the potential of p24 siRNA to stably silence HIV in the setting of an established infection where the viral target gene is actively transcribed. Under these circumstances, long-term suppression of HIV replication could be achieved with p24 siRNA. Thus, siRNAs can induce potent and long-lasting HIV inhibition in nondividing cells such as macrophages.
Cyanobacterium aponinum, a new Cyanoprokaryote from the microbial mat of Euganean thermal springs (Padua, Italy) (2007)

A form of coccoid cyanobacterium, collected in Euganean thermal springs from cyanobacteria mats and ascribed to the Cyanobacterium genus has been described. Morphological, ultrastructural, pigment composition and molecular data characterizing this taxon are compared with other species included in the genus Cyanobacterium. The phylogenetic position of this strain has been investigated using 16S rDNA and ITS rDNA as molecular markers and the maximum likelihood and neighbour-joining methods. These results suggest that although the isolate shared features with a Japanese thermal strain (Cyanobacterium sp. MBIC10216), it might be considered a different taxon from previously described Cyanobacterium. For this strain the name Cyanobacterium aponinum is proposed.
IP to X.121 address mapping for DDN (1991)

This memo defines a standard way of converting IP addresses to CCITT
X.121 addresses and is the recommended standard for use on the
Internet, specifically for the Defense Data Network (DDN). This memo
provides information for the Internet community. It does not specify
an Internet standard.
Functional Characteristic of Snake Venom Disintegrins: Potential Therapeutic Implication (2005)

Snake venom disintegrins are the natural products that have been investigated as potent inhibitors of various integrins. Functionally, disintegrins can be divided into three groups according to their integrin selectivity and presence of specific, active motifs. This classification includes RGD-disintegrins, MLD-disintegrins, and KTS-disintegrins. RGD-disintegrins have been the most intensively investigated, and their research resulted in design and synthesis of new pharmaceutical compounds, eptifibatide and tirofiban that are currently being evaluated for the therapy of acute coronary ischaemic syndrome. MLD- and KTS-disintegrins are specific for leukocyte integrins and collagen receptors, respectively, and are being investigated in the new fields of pharmaceutical research. This review summarizes the biological activities of snake venom disintegrins, as well as discusses their potential in the study of the pharmacology of various human diseases.
Changes in Plasma Ghrelin Concentration Immediately after Gastrectomy in Patients with Early Gastric Cancer (2004)

Although the majority of circulating ghrelin originates from the stomach, no prospective study of the proportion of ghrelin derived from the stomach has been reported. Patients with early gastric cancer who underwent gastric resection were divided into three groups according to the extent and site of gastric resection: subtotal gastrectomy group (n = 24), proximal gastrectomy group (n = 4), and total gastrectomy group (n = 12). Patients with advanced gastric cancer who underwent gastrojejunostomy without gastrectomy served as the bypass group (n = 5). Blood samples were collected from all patients preoperatively, at 1 h after gastric resection or gastrojejunostomy, and on postoperative d 1, 3, and 7. The plasma ghrelin level was determined in all samples and expressed as a percentage of the preoperative level. In the bypass group, no significant drop in the ghrelin level was observed at 1 h after gastrojejunostomy, and the ghrelin level remained stable through postoperative d 7. In the subtotal gastrectomy group, the ghrelin concentration reached a nadir of 38.8 +/- 12.9% of preoperative levels at 1 h after gastric resection and then gradually increased to 88.1 +/- 13.2% by postoperative d 7. In the proximal gastrectomy group, the nadir ghrelin level was 24.5 +/- 15.4% at 1 h after gastric resection and was followed by a gradual recovery. However, the recovery rate was slower than that in the subtotal gastrectomy group, with the ghrelin level reaching only 47.6 +/- 18.8% by postoperative d 7 (P < 0.05). In the total gastrectomy group, the nadir ghrelin level was 28.6 +/- 11.1% at 1 h after gastric resection and remained at 30.0 +/- 13.2% until postoperative d 7. These results suggest that compensatory ghrelin production can occur in the remnant stomach after the surgical removal of part of the stomach and that the proximal fundus is more important than the distal antrum and body in terms of the capacity for ghrelin production. The principal site of ghrelin production is clearly the stomach, which contributes 70% of the circulating ghrelin concentration.
Damage to red blood cells during whole blood storage (2020)

Storage of WB results in changes associated with the pRBC storage lesion but not for all parameters tested. The relative rate of hemolysis (indexed by free hemoglobin and microparticles) and oxidative stress was similar to that of pRBCs. However, the absolute level of hemolysis products were lower due to lower hematocrit of stored WB units. The clinical significance of these findings requires further investigation.
Senescent mesenchymal stem cells promote colorectal cancer cells growth via galectin-3 expression (2015)

Senescent MSCs may alter the tissue microenvironment and affect nearby malignant cells via cytokine secretion, and galectin-3 is an important mediator of senescent AD-MSC-mediated stimulation of colon cancer cell growth. Therefore, thorough assessment of AD-MSCs prior to their implementation in clinical practice is warranted.
Transposon Mutagenesis of Pseudomonas solanacearum: Isolation of Tn5-Induced Avirulent Mutants (1985)

Summary: Transposon mutagenesis in a tomato isolate of Pseudomonas solanacearum (strain Kourou) is reported, using Tn7 and Tn5 inserted in suicide conjugative plasmids. Whereas Tn7 integrates at high frequency in a particular site of the the genome, Tn5 appears to transpose much more randomly, allowing isolation of auxotrophic mutants with a frequency of 0.35%. The mutants showed a wide range of nutritional requirements. Following Tn5 mutagenesis, screening of 8250 clones on axenic tomato seedlings led to the isolation of 12 avirulent mutants. Southern blot analysis revealed that, for avirulent mutants, insertion of Tn5 occurred in at least 10 different EcoRI restriction fragments. Additional independent insertions of IS50 were also detected in four of these mutants. For each mutant, transformation experiments demonstrated that the Tn5-encoded kanamycin resistance and the avirulent phenotype are linked. Based on their ability or inability to induce a collapse of tobacco leaf parenchyma, and on the timing of reaction of the plant, avirulent mutants have been divided in to two and possibly three groups.
RTP801 Is Elevated in Parkinson Brain Substantia Nigral Neurons and Mediates Death in Cellular Models of Parkinson's Disease by a Mechanism Involving Mammalian Target of Rapamycin Inactivation (2006)

The molecules underlying neuron loss in Parkinson's disease (PD) are essentially unknown, and current therapies focus on diminishing symptoms rather than preventing neuron death. We identified RTP801 as a gene whose transcripts were highly induced in a cellular model of PD in which death of neuronal catecholaminergic PC12 cells was triggered by the PD mimetic 6-OHDA. Here, we find that RTP801 protein is also induced in this and additional cellular and animal PD models. To assess the relevance of these observations to PD, we used immunohistochemistry to compare RTP801 expression in postmortem brains from PD and control patients. For all PD brains examined, expression was highly elevated within neuromelanin-containing neurons of the substantia nigra but not in cerebellar neurons. Evaluation of the potential role of RTP801 induction in our cellular model revealed that RTP801 overexpression is sufficient to promote death but does not further elevate death caused by 6-OHDA. Furthermore, RTP801 induction is requisite for death in our cellular PD models and in 6-OHDA-treated cultured sympathetic neurons in that its knockdown by short hairpin RNAs (shRNAs) is protective. The mechanism by which 6-OHDA and RTP801 induce neuron death appears to involve repression of mammalian target of rapamycin (mTOR) kinase activity, and such death is inhibited by shRNAs targeting TSC2 (tuberous sclerosis complex), a protein with which RTP801 interacts to block mTOR activation. Our findings thus suggest that the elevation of RTP801 we detect in PD substantia nigral neurons may mediate their degeneration and death and that RTP801 and its signaling cascade may be novel potential therapeutic targets for the disease.
The heat-stable toxin I gene from Escherichia coli 18D (1990)

The heat-stable toxin I gene in the human Escherichia coli isolate 18D is the estA1 allele. The gene is not part of a composite transposon, but inspection of the flanking DNA sequences suggests that it was at one time part of a transposon. The hypothetical transposon originated from an event other than the occurrence that formed Tn1681.
Second-Generation Anti–Carcinoembryonic Antigen Designer T Cells Resist Activation-Induced Cell Death, Proliferate on Tumor Contact, Secrete Cytokines, and Exhibit Superior Antitumor Activity In vivo : A Preclinical Evaluation (2008)

An advanced generation of anti-CEA designer T cells is described with features that promise a more potent and enduring antitumor immune response in vivo. These preclinical data qualify the human use of this agent that is currently undergoing trial in patients with CEA+ cancers.
An immunodominant class I-restricted cytotoxic T lymphocyte determinant of human immunodeficiency virus type 1 induces CD4 class II-restricted help for itself. (1990)

We have observed that a peptide corresponding to an immunodominant epitope of the HIV-1 envelope protein recognized by class I MHC-restricted CD8+ CTL can also induce T cell help for itself. The help is necessary for restimulation of CTL precursors in vitro with peptide alone in the absence of exogenous lymphokines, can be removed by depletion of CD4+ T cells, and can be replaced by exogenous IL-2. Whereas the CTL in BALB/c or B10. D2 mice are restricted by the class I molecule Dd, the Th cells are restricted by the class II molecule Ad, and the help can be blocked by anti-Ad mAb. To examine the genetic regulation of the induction of help, we studied B10.A mice that share the class I Dd molecule, but have different class II molecules, Ak and Ek. Spleen cells of immune B10.A mice behave like CD4-depleted BALB/c spleen cells in that they cannot be restimulated in vitro by the peptide alone, but can with peptide plus IL-2. Therefore, in the absence of exogenous lymphokines, peptide-specific help is necessary for restimulation with this immunodominant CTL epitope peptide, and in H-2d mice, this peptide stimulates help for itself as well as CTL. We speculate on the implications of these findings for the immunodominance of this peptide in H-2d mice, and for the selective advantage of pairing certain class I and class II molecules in an MHC haplotype.
Midkine, a Heparin-Binding Growth/Differentiation Factor, Exhibits Nerve Cell Adhesion and Guidance Activity for Neurite Outgrowth In Vitro (1996)

By means of a baculovirus expression system, a large amount of mouse midkine (MK) was produced. The protein was purified to homogeneity by heparin-Sepharose column chromatography. The purified protein was of a mature type; the signal peptide was cleaved at the expected site. To examine the neurite-guiding activity of MK, rat embryonic brain cells (embryonic days 17-18) were cultured on plates coated with purified MK in a grid pattern. The cells attached to and extended their neurites along the substrate pattern. This interaction was strongly inhibited by heparin, but not by other glycosaminoglycans. Treatment of the cells with heparitinase was effective for inhibiting their adhesion to the substrate. These data suggest that the heparin-like domain on cell surface heparan sulfate proteoglycan is the primary site for MK binding upon interaction with nerve cells.
Novel η3-Vinylcarbene Complexes Derived from Ruthenium-Based Olefin Metathesis Catalysts (2001)

Electron-rich, disubstituted alkynes react with (H2IMes)(PCy3)(Cl)2RuCHPh (1; H2IMes = 1,3-dimesityl-4,5-dihydroimidazol-2-ylidene) to form phosphine-free η3-vinylcarbene complexes. An X-ray diffraction study on (H2IMes)(Cl)2Ru[η3-(CHPh)(CPh)(CPh)] (2) confirms the unusual structure. These complexes are relevant to the mechanisms of olefin metathesis and alkyne polymerization.
Stress-Associated Endoplasmic Reticulum Protein 1 (Serp1)/Ribosome-Associated Membrane Protein 4 (Ramp4) Stabilizes Membrane Proteins during Stress and Facilitates Subsequent Glycosylation (1999)

Application of differential display to cultured rat astrocytes subjected to hypoxia allowed cloning of a novel cDNA, termed stress-associated endoplasmic reticulum protein 1 (SERP1). Expression of SERP1 was enhanced in vitro by hypoxia and/or reoxygenation or other forms of stress, causing accumulation of unfolded proteins in endoplasmic reticulum (ER) stress, and in vivo by middle cerebral artery occlusion in rats. The SERP1 cDNA encodes a 66-amino acid polypeptide which was found to be identical to ribosome-associated membrane protein 4 (RAMP4) and bearing 29% identity to yeast suppressor of SecY 6 protein (YSY6p), suggesting participation in pathways controlling membrane protein biogenesis at ER. In cultured 293 cells subjected to ER stress, overexpression of SERP1/RAMP4 suppressed aggregation and/or degradation of newly synthesized integral membrane proteins, and subsequently, facilitated their glycosylation when the stress was removed. SERP1/RAMP4 interacted with Sec61alpha and Sec61beta, which are subunits of translocon, and a molecular chaperon calnexin. Furthermore, Sec61alpha and Sec61beta, but not SERP1/RAMP4, were found to associate with newly synthesized integral membrane proteins under stress. These results suggest that stabilization of membrane proteins in response to stress involves the concerted action of a rescue unit in the ER membrane comprised of SERP1/RAMP4, other components of translocon, and molecular chaperons in ER.
An unusual pathway of excitation energy deactivation in carotenoids: Singlet-to-triplet conversion on an ultrafast timescale in a photosynthetic antenna (2001)

Carotenoids are important biomolecules that are ubiquitous in nature and find widespread application in medicine. In photosynthesis, they have a large role in light harvesting (LH) and photoprotection. They exert their LH function by donating their excited singlet state to nearby (bacterio)chlorophyll molecules. In photosynthetic bacteria, the efficiency of this energy transfer process can be as low as 30%. Here, we present evidence that an unusual pathway of excited state relaxation in carotenoids underlies this poor LH function, by which carotenoid triplet states are generated directly from carotenoid singlet states. This pathway, operative on a femtosecond and picosecond timescale, involves an intermediate state, which we identify as a new, hitherto uncharacterized carotenoid singlet excited state. In LH complex-bound carotenoids, this state is the precursor on the reaction pathway to the triplet state, whereas in extracted carotenoids in solution, this state returns to the singlet ground state without forming any triplets. We discuss the possible identity of this excited state and argue that fission of the singlet state into a pair of triplet states on individual carotenoid molecules constitutes the mechanism by which the triplets are generated. This is, to our knowledge, the first ever direct observation of a singlet-to-triplet conversion process on an ultrafast timescale in a photosynthetic antenna.
Nanocomposite of chitosan and silver oxide and its antibacterial property (2007)

Abstract An aqueous emulsion of chitosan nanoparticles encapsulating silver oxide is prepared from silver nitrate and chitosan. The nanoparticles are positively charged with an average diameter of 300 nm. The dried particle has a spherical shape with a 100 nm diameter. The emulsion is applied onto cotton and delivers a durable antibacterial activity against S. aureus and E. coli , after 20 washings. The coefficient of friction of the treated fabric is similar to that of the untreated cotton fabric. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 2008