gebhart/patrepeval huggingface dataset:
Coherent Hierarchical Culling: Hardware Occlusion Queries Made Useful (2004)

Abstract We present a simple but powerful algorithm for optimizing the usage of hardware occlusion queries in arbitrary complex scenes. Our method minimizes the number of issued queries and reduces the delays due to the latency of query results. We reuse the results of occlusion queries from the last frame in order to initiate and schedule the queries in the next frame. This is done by processing nodes of a spatial hierarchy in a front‐to‐back order and interleaving occlusion queries with rendering of certain previously visible nodes. The proposed scheduling of the queries makes use of spatial and temporal coherence of visibility. Despite its simplicity, the algorithm achieves good culling efficiency for scenes of various types. The implementation of the algorithm is straightforward and it can be easily integrated in existing real‐time rendering packages based on common hierarchical data structures. Categories and Subject Descriptors (according to ACM CCS): I.3.7 [Computer Graphics]: Three‐Dimensional Graphics and Realism
Nanobodies as modulators of inflammation: potential applications for acute brain injury (2014)

Nanobodies are single domain antibodies derived from llama heavy-chain only antibodies (HCAbs). They represent a new generation of biologicals with unique properties: nanobodies show excellent tissue distribution, high temperature and pH stability, are easy to produce recombinantly and can readily be converted into different formats such as Fc-fusion proteins or hetero-dimers. Moreover, nanobodies have the unique ability to bind molecular clefts, such as the active site of enzymes, thereby interfering with the function of the target protein. Over the last decade, numerous nanobodies have been developed against proteins involved in inflammation with the aim to modulate their immune functions. Here, we give an overview about recently developed nanobodies that target immunological pathways linked to neuroinflammation. Furthermore, we highlight strategies to modify nanobodies so that they can overcome the blood brain barrier and serve as highly specific therapeutics for acute inflammatory brain injury.
Embryogenesis of the enteric ganglia in normal mice and in mice that develop congenital aganglionic megacolon (1973)

ABSTRACT Embryological studies on the mouse indicate that, contrary to the classical concept, all the enteric ganglia are from a single, vagal, neural crest source. The immature ganglion cells first enter the gut by way of the newly formed vagal outgrowth at 10 days gestation. The neuroblasts then migrate down the gut in a cranio-caudal direction, being replaced by more neuroblasts from the vagus. By 15 days 12 h the process is complete and ganglion cells are present throughout the gut. The process is continuous and there is no evidence of a lumbosacral origin for any of the intramural ganglia. In mice which develop aganglionic megacolon the process is basically the same except that the neuroblasts appear to migrate at a slower rate than normal. The result is that the migration of the neuroblasts and the elongation of the gut are out of phase so the migrating neuroblasts cannot reach the end of the gut, despite the fact they migrate 6 – 7 days longer than normal.
Formation of Tetra(ethylene oxide) Terminated Si−C Linked Monolayers and Their Derivatization with Glycine:  An Example of a Generic Strategy for the Immobilization of Biomolecules on Silicon (2005)

Surface modification with oligo(ethylene oxide) functionalized monolayers terminated with reactive headgroups constitutes a powerful strategy to provide specific coupling of biomolecules with simultaneous protection from nonspecific adsorption on surfaces for the preparation of biorecognition interfaces. To date, oligo(ethylene oxide) functionalized monolayer-forming molecules which can be activated for attachment of biomolecules but which can selectively form monolayers onto hydrogen terminated silicon have yet to be developed. Here, self-assembled monolayers (SAMs) containing tetra(ethylene oxide) moieties protected with tert-butyl dimethylsilyl groups were formed by thermal hydrosilylation of alkenes with single-crystal Si(111)-H. The protection group was used to avoid side reactions with the hydride terminated silicon surface. Monolayer formation was carried out using solutions of the alkene in the high-boiling-point solvent 1,3,5-triethylbenzene. The protecting group was removed under very mild acidic conditions to yield a free hydroxyl functionality, a convenient surface moiety for coupling of biological entities via carbamate bond formation. The chemical composition and structure of the monolayers before and after deprotection were characterized by X-ray photoelectron spectroscopy (XPS) and X-ray reflectometry. To demonstrate the utility of this surface for covalent modification, two reagents were compared and contrasted for their ability to activate the surface hydroxyl groups for coupling of free amines, carbonyl diimidazole (CDI), and disuccinimidyl carbonate (DSC). Analysis of XP spectra before and after activation by CDI or DSC, and after subsequent reaction with glycine, provided quantitative information on the extent of activation and overall coupling efficiencies. CDI activated surfaces gave poor coupling yields under various conditions, whereas DSC mediated activation followed by aminolysis at neutral pH was found to be an efficient method for the immobilization of amines on tetra(ethylene oxide) modified surfaces.
Modulation of Oncogenic Phenotype in Human Glioma Cells by Cytomegalovirus IE1–Mediated Mitogenicity (2008)

Recent evidence indicates that human cytomegalovirus (HCMV) infection occurs in a high percentage of human malignant gliomas in vivo, as the HCMV immediate early-1 (IE1) protein is detected in >90% of these tumors. The HCMV IE1 protein is essential for viral infection and has potent trans-activating and oncomodulatory properties. To investigate a potential role of HCMV in glioma biology, we stably expressed the HCMV IE1 gene product in immortalized and malignant human glial cells. Here we show that stable IE1 expression can differentially affect the growth of human glioblastoma cells, resulting in either growth proliferation or arrest. IE1 expression led to dysregulation of phosphatidylinositol 3-kinase/AKT activity, Rb phosphorylation, and expression of the p53 family of proteins. In U87 and U118 glioblastoma cells, IE1 induced cellular proliferation paralleled by reduction in steady-state expression level of Rb and p53 family proteins (including p53, p63, or p73) and simultaneous induction of the phosphatidylinositol 3-kinase/AKT signaling pathway. In contrast, IE1 expression in LN229 and U251 glioblastoma cells and immortalized human astrocytes was associated with increased expression of p53 family proteins, accompanied by growth arrest or lack of enhanced proliferation. Moreover, IE1 promoted cell cycle entry and DNA synthesis of human glioma cells on both stable expression in tumor-derived cell lines as well as transient expression in primary glioblastoma cells. These findings indicate that HCMV IE1 can significantly affect important oncogenic signaling pathways in glioblastoma cells.
Homology probing: identification of cDNA clones encoding members of the protein-serine kinase family. (1987)

Mixed oligonucleotide probes were used to screen a HeLa cDNA library for clones encoding amino acid contiguities whose conservation is characteristic of the protein-serine kinase family. Eighty thousand clones were screened, from which 19 were identified as showing strong hybridization to two distinct probes. Four clones were chosen for characterization by partial DNA sequence analysis and 3 of these were found to encode amino acid sequences typical of protein-serine kinases. One deduced amino acid sequence shares 72% identity with rabbit skeletal muscle phosphorylase kinase gamma-subunit, while another is closely related to the yeast protein-serine kinases CDC2 in Schizosaccharomyces pombe and CDC28 in Saccharomyces cerevisiae. This screening approach should have applications in the identification of clones encoding previously unknown or poorly characterized members of other protein families.
Optimized complementary 40 V power LDMOS-FETs use existing fabrication steps in submicron CMOS technology (2002)

This paper discusses development of state-of-the-art complementary isolated lateral 40 V rated power MOSFETs. The goals of this project were to provide BV specific devices for use with an existing merged VLSI technology. Devices meeting this goal were fabricated in a production manufacturing environment with no extra cost added to the process. The p-channel FET has a BV=60 V, and R/sub s/p=2.71 m/spl Omega/ cm/sup 2/ @V/sub gs/=15 V, and for the n-channel FET, BV=47 V and R/sub sp/=0.67 m/spl Omega/cm/sup 2/ @V/sub gs/=15 V. These devices are seen to be very competitive solutions with advanced integral on-chip intelligence.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Synthesis and spectral studies of 2‐mercaptobenzimidazole derivatives. I (1982)

Abstract The syntheses of some 2‐mercaptobenzimidazole (I) derivatives have been described. While preparing such compounds it has been observed that I reacts predominantly as the thione under anhydrous reaction conditions, and as the thiol in the presence of an alkali. Strutures of all of the nine compounds have been established with the help of spectral methods including 13 C nmr spectroscopy of the two compounds (II and III).
Beyond Independence: Conditions for the Optimality of the Simple Bayesian Classifier. (1996)

The simple Bayesian classifier (SBC) is commonly thought to assume that attributes are independent given the class, but this is apparently contradicted by the surprisingly good performance it exhibits in many domains that contain clear attribute dependences. No explanation for this has been proposed so far. In this paper we show that the SBC does not in fact assume attribute independence, and can be optimal even when this assumption is violated by a wide margin. The key to this finding lies in the distinction between classification and probability estimation: correct classification can be achieved even when the probability estimates used contain large errors. We show that the previously-assumed region of optimality of the SBC is a second-order infinitesimal fraction of the actual one. This is followed by the derivation of several necessary and several sufficient conditions for the optimality of the SBC. For example, the SBC is optimal for learning arbitrary conjunctions and disjunction...
The molecular biology of apoptosis. (1996)

All multicellular organisms have mechanisms for killing their own cells, and use physiological cell death for defence, development, homeostasis, and aging. Apoptosis is a morphologically recognizable form of cell death that is implemented by a mechanism that has been conserved throughout evolution from nematode to man. Thus homologs of the genes that implement cell death in nematodes also do so in mammals, but in mammals the process is considerably more complex, involving multiple isoforms of the components of the cell death machinery. In some circumstances this allows independent regulation of pathways that converge upon a common end point. A molecular understanding of this mechanism may allow design of therapies that either enhance or block cell death at will.
A Hox gene mutation that triggers nonsense-mediated RNA decay and affects alternative splicing during Drosophila development (2003)

Nonsense mutations are usually assumed to affect protein function by generating truncated protein products. Nonetheless, it is now clear that these mutations affect not just protein synthesis but also messenger RNA stability. The surveillance mechanism responsible for the detection and degradation of 'nonsense' RNA messages is termed nonsense-mediated RNA decay (NMD). Essential biochemical components of the NMD machinery have been defined in several species. Here we identify the Drosophila orthologue of one of these factors, Upf1, and document its expression during embryogenesis. To test whether NMD acts during Drosophila development, we make use of a mutation that introduces a stop codon into a variably spliced exon of the Hox gene Ultrabithorax (Ubx). Using real-time quantitative RT-PCR we demonstrate that Ubx transcripts containing the premature stop codon are expressed at lower levels than their wild type counterpart. Unexpectedly, we also find that the same mutation significantly increases the levels of a Ubx splicing isoform that lacks the exon containing the premature termination codon. These findings indicate that NMD is operational during Drosophila development and suggest that nonsense mutations may affect development by altering the spectrum of splicing products formed, as well as by reducing or eliminating protein synthesis.
Might Microdosing Psychedelics Be Safe and Beneficial? An Initial Exploration (2019)

Albert Hoffman suggested that low doses of LSD might be an appropriate alternative to Ritalin. Following this possibility, a systematic exploration of the effects of "microdoses," comprising hundreds of lengthy descriptive reports, was undertaken. Based on these reports, using a psychedelic in the microdose range (10 micrograms) every three days was determined to be safe across a wide variety of individuals and conditions. Over 18 months, more than a thousand individuals from 59 countries did a daily evaluation of negative and positive emotional state using the PANAS checklist plus written reports for between one week and four months. Participant reports suggested that spaced but repeated microdoses were followed by improvements in negative moods, especially depression, and increases in positive moods. Increased energy, improved work effectiveness, and improved health habits were observed in clinical and non-clinical populations. Smaller samples described alleviation of symptoms in migraine headaches, pre-menstrual syndromes, traumatic brain injury, shingles, and other conditions not previously associated with psychedelic use.
InP Layer Grown on (001) Silicon Substrate by Epitaxial Lateral Overgrowth (1995)

An InP epitaxial layer with a dislocation-free area was obtained for the first time on (001) Si substrate by using the epitaxial lateral overgrowth (ELO) technique. Most etch pits appeared in the region over the seed area on the ELO stripe. This indicates that the SiO 2 film between the lateral overgrowth layer and the substrate prevented the propagation of the dislocations from the substrate to the lateral overgrowth layer. Spatially resolved photoluminescence showed that the optical quality of an InP ELO layer grown on Si was almost the same as that of a homoepitaxially grown InP layer and that the ELO technique is also useful to relieve stress caused by both the lattice mismatch and the difference in thermal expansion coefficient.
Le morte du tumour: Histological features of tumor destruction in chemo-resistant cancers following intravenous infusions of pathotropic nanoparticles bearing therapeutic genes (2007)

The pathotropic targeting of therapeutic nanoparticles to cancerous lesions is an innovative concept that has recently been reduced to practice in clinical trials for the treatment of metastatic cancer. Previously, we reported that intravenous infusions of Rexin-G, a pathotropic nanoparticle (or vector) bearing a cyto-ablative construct, induced tumor regression, reduced tumor burden, and improved survival, while enhancing the overall quality-of-life of patients with otherwise intractable chemotherapy-resistant cancers. In this report, we describe the major histopathological and radiologic features that are characteristic of solid tumors under the destructive influences of Rexin-G administered as a single therapeutic agent. To further promote tumor eradication and enhance cancer survival, we explored the potential of an auxiliary gene transfer strategy, specifically intended to induce a localized cancer auto-immunization in addition to assisting in acute tumor destruction. This immunization strategy uses Rexin-G in combination with Reximmune-C, a tumor targeted expression vector bearing a granulocyte macrophage-colony stimulating factor (GM-CSF) gene. Intravenous infusions of Rexin-G were given first to induce apoptosis and necrosis in the metastatic tumor nodules, thus exposing tumor neo-antigens, followed by Reximmune-C infusions, intended to recruit immune cells discretely into the same compartments (or lesions). The intent of this two-step approach is to bring a complement of cells involved in humoral and cell-mediated immunity in close proximity to the immunizing tumor antigens in a concerted effort to assist in tumor eradication and to promote a cancer vaccination in situ. Herein, we also describe the distinctive histopathologic and immunocytochemical features of tumors in terminal cancer patients who received Rexin-G infusions in combination with Reximmune-C. In addition to documenting the first histological indications of clinical efficacy achieved by this novel personalized approach to cancer vaccination, we discuss new methods and strategies for advancing its therapeutic utility. Taken together with the clinical data, these histological studies serve as valuable landmarks for medical oncology, and as definitive benchmarks for the emerging field of cancer gene therapy.
Mini-αB-Crystallin:  A Functional Element of αB-Crystallin with Chaperone-like Activity (2006)

Alpha-crystallin is a member of the family of small heat-shock proteins (sHSP) and is composed of two subunits, alphaA-crystallin and alphaB-crystallin, which exhibit molecular chaperone-like properties. In a previous study, we found that residues 70-88 in alphaA-crystallin can function like a molecular chaperone by preventing the aggregation and precipitation of denaturing substrate proteins [Sharma, K. K., et al. (2000) J. Biol. Chem. 275, 3767-3771]. In this study, we show that the complementary sequence in alphaB-crystallin, residues 73-92 (DRFSVNLDVKHFSPEELKVK), is the functional chaperone site of alphaB-crystallin. Like the mini-alphaA-crystallin chaperone, the mini-alphaB-crystallin chaperone interacts with 1,1'-bi(4-anilino) naphthalene-5,5'-disulphonic acid (bis-ANS) and also possesses significant beta-sheet and random coil structure. Deletion of four residues (DRFS) from the N-terminus or deletion of C-terminus LKVK residues from the 73-92 peptide abolishes the chaperone-like activity against denaturing alcohol dehydrogenase. However, removal of DRFS or HFSPEELKVK is necessary to completely abolish the antiaggregation property of the peptide in insulin reduction assay. Substitution of Asp at a site corresponding to D80 in alphaB-crystallin with d-Asp or beta-Asp results in a significant loss of chaperone-like activity. Kynurenine modification of His in the peptide abolishes the antiaggregation property of the mini-chaperone. These data suggest that the 73-92 region in alphaB-crystallin is one of the substrate binding sites during chaperone activity.
<title>New effect in ionic polymeric gels: the ionic flexogelectric effect</title> (1995)

Reported are a number of quantitative observations and analytical modeling of a new effect in ionic polymeric gels such as poly(2-acrylamido-2-methylpropanesulfonic acid) or PAMPS, polyacrylic acid plus sodium acrylate cross-linked with bisacrylamide (PAAM), or various chemically doped combinations of polyacrylic acid plus polyvinyl alcohol (PAA-PVA). This new effect, hereafter, referred to as `flexogelectric effect' is basically the inverse of the effect originally reported in 1965 by three GE researchers, namely, Hamlen, Kent, and Shafer in which the imposition of an electric field on an ionic polymeric gel fiber produced extension or contraction. Here it is shown, both theoretically and experimentally, that mechanically induced nonhomogeneous deformations, and in particular bending of strips of such ionic gels, can produce an electric field and the associated voltage. For typical samples of such gels (4 X 4 X 40 mm) with copper or platinum foil electrodes snugly contacting a pair of opposite sides (4 X 40 mm) of the strip, the difference in voltage measured between the electrodes for extreme bending configurations of the gel is typically in the 10s of millivolts range. This voltage difference which is quite significant for many engineering applications, such as large strain and deformation sensing, is still an order of magnitude smaller than the voltage necessary to induce similar deformations in the gel itself. A plausible explanation is also presented for such discrepancies.
<title>Liquid-xenon-jet laser-plasma source for EUV lithography</title> (2001)

The liquid-xenon-jet laser-plasma source is one of the extreme-ultraviolet (EUV) source technologies under development for EUV lithography. This paper discuss the basic, demanding, requirements of a source for EUV lithography including high in-band EUV power, absence of mirror contamination and high stability. It is further discussed how the liquid-xenon-jet can meet these requirements, and specifically how the ability to operate the plasma far from any mechanical details such as the nozzle will facilitate high power operation with low resulting mirror degradation. Furthermore, a new laser-to-EUV conversion efficiency result of 0.55%/(2%BW 2pisr) at lambda=13.45 nm is presented together with a detailed description of the method for calibrated EUV-power measurement.
Two-element phased array of antiguided vertical-cavity lasers (1999)

We demonstrate antiguided coupling of two adjacent vertical-cavity surface-emitting lasers (VCSELs), obtaining a 1×2 phase-locked array at 869 nm. The lateral index modification required for antiguiding is achieved by a patterned 3 nm etch performed between two epitaxial growths. In contrast with prior coupled VCSELs, adjacent antiguided VCSELs can emit in phase and produce a single on-axis lobe in the far field. Greater than 2 mW of in-phase output power is demonstrated with two VCSELs separated by 8 μm. Moreover, phase locking of two VCSELs separated by 20 μm is observed, indicating the possibility of a promising class of optical circuits based upon VCSELs that interact horizontally and emit vertically.
Dephosphorylation of activated protein kinase C contributes to downregulation by bryostatin (1996)

We show that bryostatin 1 (Bryo) rapidly produces an inactive, incompetent 76-kDa form of protein kinase C-alpha (PKC-alpha) in the LLC-MK2 line of renal epithelial cells. Bryo, like phorbol 12-myristate 13-acetate (PMA), acutely activated PKC, as indicated by autophosphorylation and translocation of PKC-alpha, the predominant PMA-sensitive isoform expressed by the cells. Bryo concomitantly increased the 32P labeling of 80-kDa PKC-alpha by autophosphorylation and produced a 76-kDa form of PKC-alpha that lacked detectable 32P. The 76-kDa form was in the particulate rather than the cytosolic fraction, which suggests that it was produced from activated kinase. Alkaline phosphatase treatment of immunoprecipitated PKC-alpha converted the 80-kDa form to 76 kDa, but it had no effect on the mobility of the 76-kDa form, suggesting that it was not phosphorylated. Pulse-chase labeling of PKC-alpha with [35S]Met/Cys indicated that there is a precursor-product relationship between the 80- and 76-kDa forms, respectively. Inhibition of protein synthesis had no effect on the production of 76-kDa PKC-alpha by Bryo. PMA also produced 76-kDa PKC-alpha but was less potent and efficacious than Bryo. Bryo produced a more rapid loss of 80-kDa PKC-alpha protein and total Ca(2+)- and phospholipid-dependent PKC activity than PMA. The 76-kDa form is inactive and incompetent because it lacked detectable 32P under conditions that strongly autophosphorylated the 80-kDa form. We suggest that dephosphorylation predisposes PKC to proteolysis, and greater production of the 76-kDa form explains the more efficient downregulation of the kinase by Bryo vs. PMA.