gebhart/patrepeval huggingface dataset:
Ig heavy chain protein controls B cell development by regulating germ-line transcription and retargeting V(D)J recombination. (1994)

The membrane-associated form of Ig heavy chain (mu) protein has been implicated as a critical regulator of B cell development. Mutant mice unable to produce the membrane form of mu protein fail to produce mature B cells. Splenic B cells from mice transgenic for a functionally rearranged Ig mu gene show a marked decrease in endogenous heavy chain gene rearrangement. We have analyzed the effects of a human mu transgene on the regulation of V(D)J recombination during B cell development in the mouse fetal liver. We found that mu transgenic and wild-type littermate mice begin kappa light chain gene rearrangement at the same time during development but the transgenic mice show a striking increase in the frequency of kappa gene rearrangement. The transgenic mice also show an increase in the levels of a germ-line kappa gene transcript known to be associated with kappa gene rearrangement. D-to-JH heavy chain gene rearrangement is unaffected throughout development by the presence of the mu transgene. Endogenous heavy chain gene V-to-DJH rearrangement occurs with similar frequency in transgenic and nontransgenic fetal livers during midgestation but is reduced in late gestation mu transgenic fetal liver. We show that this decrease in rearrangement is associated with a decrease in unrearranged VH gene transcription. Furthermore, we show that changes in the frequencies of rearranged kappa and mu genes are accompanied by changes in the frequencies of dsDNA breaks, a V(D)J recombination reaction intermediate associated with each of these loci. We propose that membrane-associated mu protein regulates B cell development by signaling a change in the pattern of unrearranged Ig gene transcriptional activity, thereby retargeting the V(D)J recombinase.
A method for gene enrichment based on the avidin-biotin interaction. Application to the Drosophila ribosomal RNA genes (1977)

A method of enriching, from the total DNA of an organism, for long DNA strands carrying a particular gene is described. The purified RNA corresponding to the gene is covalently attached to biotin via a cytochrome c bridge. This modified RNA is hybridized to the total DNA. Those DNA strands which hybridize are separated from all the other DNA, using the avidin-biotin interaction, by one of two methods. Avidin is covalently attached to submicroscopic polymer spheres; the complexes of avidin spheres with the DNA: RNA-biotin hybrids band in CsCl at a much lower buoyant density than does free DNA. Alternatively, the DNA:RNA-biotin hybrids are isolated by affinity chromatography on an avidin-solid support column. These methods have been used to prepare long single strands of Drosophila ribosomal DNA (rDNA) in high yield and 42 to 80% pure.
α v β 3 Integrin Expression in Normal and Atherosclerotic Artery (1995)

Recent evidence suggests that alpha v beta 3 integrin is a critical molecule in several processes involved in atherosclerosis progression and in restenosis, eg, smooth muscle cell (SMC) migration and angiogenesis. While several ligands for this integrin are known to be present in atherosclerotic plaque, little is known about the presence of alpha v beta 3 integrin at this site. In the present study, we have examined alpha v beta 3 expression in normal and atherosclerotic arteries. Thirty-six coronary artery segments from the recipient hearts of 24 patients undergoing heart transplantation were classified into two groups: nonatherosclerotic diffuse intimal thickening (DIT) and atherosclerotic plaques. Serial frozen sections were examined immunohistochemically with four different monoclonal antibodies directed against human alpha v beta 3 complex or the beta 3 subunit and with cell markers for SMCs, macrophages, and endothelial cells. The endothelium along the lumen of both DIT and plaque arteries showed high expression of alpha v beta 3. The media of both DIT and plaque arteries showed less intense but extensive expression of alpha v beta 3. Immunoprecipitation and reverse-transcribed polymerase chain reaction (RT-PCR) analyses performed on extracts from the aortic media confirmed the presence of alpha v beta 3 in the media. In the intima of both DIT and plaque arteries, alpha v beta 3 expression generally colocalized with SMCs but rarely with macrophages. The microvessels in the adventitia as well as in the plaque showed prominent expression of alpha v beta 3, in contrast to low expression in similar-sized microvessels of the skin.(ABSTRACT TRUNCATED AT 250 WORDS)
Comparative characterization of the iga gene encoding IgA1 protease in Neisseria meningitidis, Neisseria gonorrhoeae and Haemophilus influenzae (1995)

Cloning and sequencing of the IgA1 protease gene (iga) from Neisseria meningitidis strain HF13 showed an overall structure equivalent to iga genes from Neisseria gonorrhoeae and Haemophilus influenzae, although no region corresponding to the gonococcal alpha-peptide was evident. An additional 18 N. meningitidis and 3 H. influenzae iga genes were amplified by the polymerase chain reaction technique and sequenced corresponding approximately to the N-terminal half of the mature enzyme. Comparative analyses of a total of 29 iga genes showed that pathogenic Neisseria have iga genes with a significantly lower degree of heterogeneity than H. influenzae iga genes. Recombinational events indicated by mosaic-like structures corresponding to those found among N. gonorrhoeae protease genes were detected among N. meningitidis iga genes. One region showed characteristic differences in sequence and length which correlated with each of the different cleavage specificities. Meningococci were extremely conserved in this region with no evidence of recombination between isolates of different cleavage specificities. Sequences further downstream showed no obvious relationship with enzyme cleavage type. This region consisted of conserved areas interspersed with highly variable areas. Amino acid sequence homologies in the variable regions of meningococci reflected the antigenic types defined by using polyclonal neutralizing antibodies.
Quantum photoyield of diamond(111)—A stable negative-affinity emitter (1979)

Quantum photoyield and secondary-electron distributions are presented for an unreconstructed diamond (111) surface (type-$\mathrm{II}b$, gem-quality blue-white semiconductor). This chemically inert surface exhibits a negative electron affinity, resulting in a stable quantum yield that increases linearly from photothreshold (5.5 eV) to \ensuremath{\sim}20% at 9 eV, with a very large yield of \ensuremath{\sim}40%-70% for $13\ensuremath{\lesssim}h\ensuremath{\nu}\ensuremath{\lesssim}35$ eV. For all photon energies, secondary-electron energy distributions show a dominant \ensuremath{\sim}0.5-eV-wide emission peak at the conduction-band minimum (${\ensuremath{\Delta}}_{1}^{min}=5.50\ifmmode\pm\else\textpm\fi{}0.05$ eV above the valence-band maximum ${{\ensuremath{\Gamma}}_{25}}^{\ensuremath{'}}$). In contrast with recent self-consistent calculations [J. Ihm, S. G. Louie, and M. L. Cohen, Phys. Rev. B 17, 769 (1978)] no occupied intrinsic surface states with ionization energies in the fundamental gap (the Fermi level was 1 eV above ${{\ensuremath{\Gamma}}_{25}}^{\ensuremath{'}}$) were observed. Likewise, the measured photothreshold (${E}_{\mathrm{vac}}\ensuremath{-}{{\ensuremath{\Gamma}}_{25}}^{\ensuremath{'}}$) is significantly smaller than calculated (7.0\ifmmode\pm\else\textpm\fi{}0.7 eV).
Role of Solvent-Host Interactions That Lead to Very Large Swelling of Hybrid Frameworks (2007)

An unusually large expansion upon solvent adsorption occurs without apparent bond breaking in the network of a series of isoreticular chromium(III) or iron(III) diarboxylates labeled MIL-88A to D [dicarbox = fumarate (88A); terephthalate (1,4-BDC) (88B); 2,6-naphthalenedicarboxylate (2,6-NDC) (88C); and 4-4'-biphenyldicarboxylate (4-4'-BPDC) (88D)]. This reversible "breathing" motion was analyzed in terms of cell dimensions (extent of breathing), movements within the framework (mechanism of transformation), and the interactions between the guests and the skeleton. In situ techniques show that these flexible solids are highly selective absorbents and that this selectivity is strongly dependent on the nature of the organic linker.
YRRL motifs in the cytoplasmic domain of the thrombopoietin receptor regulate receptor internalization and degradation (2008)

Thrombopoietin (Tpo), acting through the c-Mpl receptor, promotes the survival and proliferation of hematopoietic stem and progenitor cells and drives megakaryocyte differentiation. The proproliferation and survival signals activated by Tpo must therefore be tightly regulated to prevent uncontrolled cell growth. In this work, we determined the mechanisms that control Tpo-stimulated c-Mpl internalization and defined the processes leading to its degradation. Stimulation of BaF-Mpl cells with Tpo leads to rapid, clathrin-dependent endocytosis of the receptor. Using small interfering RNA (siRNA), we found that inhibition of adaptor protein 2 (AP2), which mediates endocytosis of transmembrane proteins, strongly attenuates Tpo-stimulated c-Mpl internalization. AP2 interacts with YXXPhi motifs and we identified 2 such motifs in c-Mpl (Y(8)RRL and Y(78)RRL) and investigated Tpo-stimulated internalization of receptors bearing point mutations at these sites. After Tpo stimulation, internalization was greatly reduced in c-Mpl Y(78)F and c-Mpl Y(8+78)F, and these cell lines also exhibited increased proliferation and increased strength and duration of Jak2, STAT5, AKT, and ERK1/2 activation in response to Tpo. We also found that the Y(8)RRL motif regulates Tpo-stimulated lysosomal degradation of c-Mpl. Our data establishes that c-Mpl cytoplasmic YRRL motifs are responsible for both Tpo-mediated internalization via interactions with AP2 and lysosomal targeting after endocytosis.
Artificial evolution for computer graphics (1991)

This paper describes how evolutionary techniques of variation and selection can be used to create complex simulated structures, textures, and motions for use in computer graphics and animation. Interactive selection, based on visual perception of procedurally generated results, allows the user to direct simulated evolutions in preferred directions. Several examples using these methods have been implemented and are described. 3D plant structures are grown using fixed sets of genetic parameters. Images, solid textures, and animations are created using mutating symbolic lisp expressions. Genotypes consisting of symbolic expressions are presented as an attempt to surpass the limitations of fixed-length genotypes with predefined expression rules. It is proposed that artificial evolution has potential as a powerful tool for achieving flexible complexity with a minimum of user input and knowledge of details.
The use of urokinase in the anterior chamber of the eye (1964)

From the Croydon Eye Unit, London
Evolution reveals a glutathione-dependent mechanism of 3-hydroxypropionic acid tolerance (2014)

Biologically produced 3-hydroxypropionic acid (3 HP) is a potential source for sustainable acrylates and can also find direct use as monomer in the production of biodegradable polymers. For industrial-scale production there is a need for robust cell factories tolerant to high concentration of 3 HP, preferably at low pH. Through adaptive laboratory evolution we selected S. cerevisiae strains with improved tolerance to 3 HP at pH 3.5. Genome sequencing followed by functional analysis identified the causal mutation in SFA1 gene encoding S-(hydroxymethyl)glutathione dehydrogenase. Based on our findings, we propose that 3 HP toxicity is mediated by 3-hydroxypropionic aldehyde (reuterin) and that glutathione-dependent reactions are used for reuterin detoxification. The identified molecular response to 3 HP and reuterin may well be a general mechanism for handling resistance to organic acid and aldehydes by living cells.
Determining the efficacy of the herbicides endothal and diquat on the aquatic weed sagittaria in irrigation channels (2013)

Sagittaria (Sagittaria platyphylla (Engelmann) J.G. Smith) is an emergent aquatic weed that has invaded irrigation systems throughout northern Victoria and southern New South Wales. In earth irrigation channels and drains it impedes water flow, reducing hydraulic capacity and limiting the efficiency of modernised water delivery systems. Currently, there are limited effective control options for sagittaria. This paper describes a field trial to determine the effectiveness of winter applications of the herbicides endothal and diquat in controlling sagittaria, in static irrigation channels. Endothal provided excellent control of both the emergent and submerged forms of sagittaria during winter conditions. Diquat, with and without a gelling agent, was ineffective.
Polygraph: Automatically Generating Signatures for Polymorphic Worms (2005)

It is widely believed that content-signature-based intrusion detection systems (IDS) are easily evaded by polymorphic worms, which vary their payload on every infection attempt. In this paper, we present Polygraph, a signature generation system that successfully produces signatures that match polymorphic worms. Polygraph generates signatures that consist of multiple disjoint content substrings. In doing so, Polygraph leverages our insight that for a real-world exploit to function properly, multiple invariant substrings must often be present in all variants of a payload; these substrings typically correspond to protocol framing, return addresses, and in some cases, poorly obfuscated code. We contribute a definition of the polymorphic signature generation problem; propose classes of signature suited for matching polymorphic worm payloads; and present algorithms for automatic generation of signatures in these classes. Our evaluation of these algorithms on a range of polymorphic worms demonstrates that Polygraph produces signatures for polymorphic worms that exhibit low false negatives and false positives.
Transgenic Monkeys Produced by Retroviral Gene Transfer into Mature Oocytes (2001)

Transgenic rhesus monkeys carrying the green fluorescent protein (GFP) gene were produced by injecting pseudotyped replication-defective retroviral vector into the perivitelline space of 224 mature rhesus oocytes, later fertilized by intracytoplasmic sperm injection. Of the three males born from 20 embryo transfers, one was transgenic when accessible tissues were assayed for transgene DNA and messenger RNA. All tissues that were studied from a fraternal set of twins, miscarried at 73 days, carried the transgene, as confirmed by Southern analyses, and the GFP transgene reporter was detected by both direct and indirect fluorescence imaging.
Autoantibody to heat-shock protein 90 can mediate protection against systemic candidosis. (1991)

Epitope mapping shows that patients recovering from systemic infection with Candida albicans produce antibodies against both fungal-specific and conserved epitopes of the heat-shock protein (hsp) 90. In a mouse model of systemic candidosis, mortality was halved by prior administration of sera from two infected patients containing antibodies to hsp 90. One of these patients had no other candidal antibodies detectable on immunoblotting. The protective effect was mediated by the immunoglobulin fraction of the immune serum. It was not observed with a normal human serum. A mouse monoclonal antibody raised against one of the conserved peptide epitopes suggested that an autoantibody to hsp 90 could mediate protection against systemic candidosis in the animal model.
Human interleukin 17–producing cells originate from a CD161+CD4+ T cell precursor (2008)

We demonstrate that CD161 is a highly up-regulated gene in human interleukin (IL) 17 T helper cell (Th17) clones and that all IL-17-producing cells are contained in the CD161(+) fraction of CD4(+) T cells present in the circulation or in inflamed tissues, although they are not CD1-restricted natural killer T cells. More importantly, we show that all IL-17-producing cells originate from CD161(+) naive CD4(+) T cells of umbilical cord blood, as well as of the postnatal thymus, in response to the combined activity of IL-1 beta and IL-23. These findings implicate CD161 as a novel surface marker for human Th17 cells and demonstrate the exclusive origin of these cells from a CD161(+)CD4(+) T cell progenitor.
Metal screen‐film detector MTF at megavoltage x‐ray energies (1979)

The MTF of metal screen film detectors used in radiation treatment verification has been measured at 4 and 8 MV x-ray energies. The results show that lead screens provide better resolution than copper screens, and a single-emulsion film offers considerable advantage over the traditional double-emulsion film. A rear lead screen was found to seriously degrade the resolution properties of a front lead screen single-emulsion film detector. The detector MTF was found to be energy dependent. In general, both the low and the high spatial frequency response decreased with increasing x-ray energy. This, in part, accounts for the noticeable image quality difference between 4 and 8 MV radiographs.
Formation of polyesters consisting of medium-chain-length 3-hydroxyalkanoic acids from gluconate by Pseudomonas aeruginosa and other fluorescent pseudomonads (1990)

Pseudomonas aeruginosa PAO and 15 other strains of this species synthesized a polyester with 3-hydroxydecanoate as the main constituent (55 to 76 mol%) if the cells were cultivated in the presence of gluconate and if the nitrogen source was exhausted; 3-hydroxyhexanoate, 3-hydroxyoctanoate, and 3-hydroxydodecanoate were minor constituents of the polymer. The polymer was deposited in granules within the cell and amounted to 70% of the cell dry matter in some strains. Among 55 different strains of 41 Pseudomonas species tested, P. aureofaciens (21.6% of cellular dry matter), P. citronellolis (78.0%), P. chlororaphis (8.5%), P. marginalis (11.4%), P. mendocina (50.7%), P. putida (33.5%), and Pseudomonas sp. strain DSM 1650 (54.6%) accumulated this type of polymer at significant levels (greater than 5%) during cultivation on gluconate. In two strains of P. facilis and P. fluorescens, as well as in one strain of P. syringae, this polymer was detected as a minor constituent (much less than 5%). All other strains accumulated either poly(3-hydroxybutyrate) or a polymer consisting mainly of 3-hydroxyoctanoate with octanoate but no polyester with gluconate as the carbon source. Only a few species (e.g., P. stutzeri) were unable to accumulate poly(hydroxyalkanoic acids) (PHA) at all. These results indicated that the formation of PHA depends on a pathway which is distinct from all other known PHA-biosynthetic pathways. The polyesters accumulated by gluconate- or octanoate-grown cells of recombinant strains of P. aeruginosa and P. putida, which harbored the Alcaligenes eutrophus poly(3-hydroxybutyrate)biosynthetic genes, contained 3-hydroxybutyrate as an additional constituent.
Transepithelial Corneal Collagen Cross-Linking in Keratoconus (2010)

A limited but favorable effect of transepithelial CXL was noted on keratoconic eyes, without complications. The effect appears to be less pronounced than described in the literature after CXL with de-epithelialization.
Effect of aromatic substitution on phase behavior of blends of halogenated polystyrene and conventional polystyrene (2001)

Miscibility phase behavior in blends of poly(bromostyrene) with polystyrene (PS) has been investigated by means of time-resolved light scattering, optical microscopy, and DSC. Cloud point phase diagrams of blends of conventional PS with poly-(2-bromostyrene) (P2BrS), poly-(3-bromostyrene), and poly-(4-bromostyrene) of comparable molecular weights were established by light scattering. Of particular interest is the fact that ortho, meta, and para substitutions in the styrenic aromatic rings of poly(bromostyrene) show profound effects on the composition–temperature phase diagrams of their blends with PS, exhibiting a lower critical-solution temperature (LCST), an upper critical solution temperature (UCST), and combined LCST/UCST diagrams, respectively. Poly-(2-chlorostyrene) exhibits an LCST behavior very close to that of the P2BrS blend, suggesting that these types of halogen atoms may be inconsequential to phase behavior. A similar study has been extended to a PS blend containing commercial brominated PS (66 mol % bromine substitution) to determine what location of bromine substitution is crucial for miscibility enhancement in the flame-retardant brominated PS blends. © 2001 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 39: 1605–1615, 2001
General rules for the packing of hydrogen-bonded crystals as derived from the analysis of squaric acid anions: aminoaromatic nitrogen base co-crystals (2001)

Preparation and single-crystal X-ray structure determination of three co-crystals of hydrogen squarate, HSQ(-), with 2-aminopyrimidine, 3-aminopyridine and 4-aminopyridine, and one of squarate, SQ(2-), with 8-aminoquinoline are reported. Their crystal packings are analyzed and discussed in terms of the intermolecular O--H...O, N--H...O/N and C--H...O hydrogen bonds formed. Although the fine details of the supramolecular architecture are barely rationalizable, the comparative analysis of the data makes it possible to suggest some simple rules that may be of general application for the packing of hydrogen-bonded crystals, i.e. Rule 1: 'All hydrogen-bond acceptors available in a molecule will be engaged in hydrogen bonding as far as there are available donors'; Rule 2: 'The hydrogen-bond acceptors will be saturated in order of decreasing strength of the hydrogen bonds formed'.
Revised equations for calculating CO2 production from doubly labeled water in humans (1993)

The Schoeller model for calculating rate of CO2 production (rCO2) from doubly labeled water (DLW) relies on the assumption that deuterium and oxygen-18 overestimate body water by 4 and 1%, respectively. However, the deuterium-to-oxygen-18 dilution space ratio (DSR) varies considerably, and it is unknown whether this is due to analytical or biological sources. From 161 published values in adult humans, we derived a mean DSR of 1.0427 +/- 0.0218. Propagation of error suggests that analytical uncertainty accounts for 20-50% of the observed variation in the DSR, whereas reliability testing in vivo and in vitro demonstrate that 70-100% of observed interindividual variation in the DSR can be attributed to analytical uncertainty. The discrepancy between propagated error and experimental reliability suggest that it is unwise to rely on propagation of error when evaluating sources of error in DLW. The new constant of 1.0427 was used to revise existing equations for calculating rCO2 from DLW. Compared with the existing equation, the revised equation improved the accuracy (-0.38 vs. +10.3%) and the precision (9.3 vs 10.7%) of rCO2 calculations in previously published validation studies. We conclude that 1) variation in the oxygen-18-to-deuterium DSR is primarily influenced by analytical noise and warrants use of a fixed ratio, 2) existing equations should be revised because the original DSR may have been underestimated, and 3) the modified equations improve the accuracy and precision of rCO2 calculated from DLW.