gebhart/patrepeval huggingface dataset:
A lamin A protein isoform overexpressed in Hutchinson–Gilford progeria syndrome interferes with mitosis in progeria and normal cells (2007)

Hutchinson-Gilford progeria syndrome (HGPS) is a rare genetic disorder characterized by dramatic premature aging. Classic HGPS is caused by a de novo point mutation in exon 11 (residue 1824, C --> T) of the LMNA gene, activating a cryptic splice donor and resulting in a mutant lamin A (LA) protein termed "progerin/LADelta50" that lacks the normal cleavage site to remove a C-terminal farnesyl group. During interphase, irreversibly farnesylated progerin/LADelta50 anchors to the nuclear membrane and causes characteristic nuclear blebbing. Progerin/LADelta50's localization and behavior during mitosis, however, are completely unknown. Here, we report that progerin/LADelta50 mislocalizes into insoluble cytoplasmic aggregates and membranes during mitosis and causes abnormal chromosome segregation and binucleation. These phenotypes are largely rescued with either farnesyltransferase inhibitors or a farnesylation-incompetent mutant progerin/LADelta50. Furthermore, we demonstrate that small amounts of progerin/LADelta50 exist in normal fibroblasts, and a significant percentage of these progerin/LADelta50-expressing normal cells are binucleated, implicating progerin/LADelta50 as causing similar mitotic defects in the normal aging process. Our findings present evidence of mitotic abnormality in HGPS and may shed light on the general phenomenon of aging.
The single-electron transistor (1992)

The discovery of periodic conductance oscillations as a function of charge density in very small transistors has led to a new understanding of the behavior of electrons in such small structures. It has been demonstrated that, whereas a conventional transistor turns on only once as electrons are added to it, submicronsize transistors, isolated from their leads by tunnel junctions, turn on and off again every time an electron is added. This unusual behavior is primarily the result of the quantization of charge and the Coulomb interaction between electrons on the small transistor. However, recent experiments demonstrate that the quantization of energy is important as well.
Liver fat-storing cell clones obtained from a CCl4-cirrhotic rat are heterogeneous with regard to proliferation, expression of extracellular matrix components, interleukin-6, and connexin 43. (1993)

We suggest that clonal heterogeneity of FSC may occur in vivo. Since each of the clones expresses a unique phenotype, these FSC clones could be excellent models to study the role of defined extracellular matrices on the expression of liver specific genes by cultured hepatocytes.
Coronavirus IBV: Removal of Spike Glycopolypeptide S1 by Urea Abolishes Infectivity and Haemagglutination but Not Attachment to Cells (1986)

Urea has been used to remove the S1 spike glycopolypeptide from avian infectious bronchitis virus (IBV) strains M41 and Beaudette, without removing the S2 spike-anchoring glycopolypeptide. Reduction of the pH to 2.9 did not cause release of S1 although some S1 was released spontaneously from IBV Beaudette at pH 7.4. Virus that lacked S1 was no longer infectious or able to cause haemagglutination (HA). However, radiolabelled IBV that lacked S1 attached to erythrocytes and chick kidney cells to the same or similar extent as did intact virus. Treatment of IBV with a phospholipase C preparation, required to make IBV cause HA, did not increase binding of IBV to erythrocytes. The results indicate that while the attachment to cells of virus that lacks S1 is qualitatively different from that of intact virus, the decline in infectivity is the consequence of the loss of some other spike function.
Interleukin-10 prevents spontaneous death of germinal center B cells by induction of the bcl-2 protein. (1994)

In this study, we show that IL-10 enhances in vitro the viability of purified splenic B cells. There was a two- to threefold increase in recovery of viable cells during a 15-d culture period in the presence of IL-10. This effect was abolished by neutralizing antibodies to IL-10. The survival of large splenic B cells, which mostly represent follicular center cells, was similarly increased. The in vitro rescue from spontaneous death of the latter cells is known to involve a bcl-2-dependent pathway. We therefore investigated whether IL-10 might affect bcl-2 expression. Unseparated B cells as well as large splenic B cells displayed a strong expression of bcl-2 protein by immunofluorescence at days 2-7 of culture in the presence of IL-10. Other lymphokines such as IL-2 and IL-4 were able to trigger only a transient and faint expression of bcl-2; moreover, this effect was abolished by anti-IL-10 mAb. Inasmuch as activated B cells can produce their own IL-10, this lymphokine may play a crucial role in relieving from apoptosis those B cells that encounter their antigen in B cell follicles.
A FAAH-Regulated Class of N-Acyl Taurines That Activates TRP Ion Channels (2006)

Fatty acid amide hydrolase (FAAH) is an integral membrane enzyme that catabolizes several bioactive lipids in vivo. Most of the physiological substrates of FAAH characterized to date belong to the N-acyl ethanolamine (NAE) class of fatty acid amides, including the endocannabinoid anandamide, the anti-inflammatory lipid N-palmitoyl ethanolamine, and the satiating factor N-oleoyl ethanolamine. We recently identified a second structural class of fatty acid amides regulated by FAAH in vivo: the N-acyl taurines (NATs). Global metabolite profiling revealed high concentrations of long chain (> or = C20) saturated NATs in the central nervous system (CNS) of FAAH(-/-) mice. Here, we use metabolite profiling to characterize the FAAH-NAT system in peripheral mouse tissues. Livers and kidneys of FAAH(-/-) mice possessed dramatic elevations in NATs, which, in contrast to those detected in the CNS, were enriched in polyunsaturated acyl chains (e.g., C20:4, C22:6). Peripheral NATs rose more than 10-fold within 1 h following pharmacological inactivation of FAAH and reached levels up to approximately 5000 pmol/g tissue (C22:6 in kidney), implicating a constitutive and highly active pathway for NAT metabolism in which FAAH plays an integral part. Interestingly, NATs were found to activate multiple members of the transient receptor potential (TRP) family of calcium channels, including TRPV1 and TRPV4, which are both expressed in kidney. The dramatic elevation in endogenous levels of NATs following acute or chronic inactivation of FAAH, in conjunction with the pharmacological effects of these lipids on TRP channels, suggests the existence of a second major lipid signaling system regulated by FAAH in vivo.
3D indoor scene modeling from RGB-D data: A survey (2015)

3D scene modeling has long been a fundamental problem in computer graphics and computer vision. With the popularity of consumer-level RGB-D cameras, there is a growing interest in digitizing real-world indoor 3D scenes. However, modeling indoor 3D scenes remains a challenging problem because of the complex structure of interior objects and poor quality of RGB-D data acquired by consumer-level sensors. Various methods have been proposed to tackle these challenges. In this survey, we provide an overview of recent advances in indoor scene modeling techniques, as well as public datasets and code libraries which can facilitate experiments and evaluation.
CD8 T Cell Priming in the Presence of IFN-α Renders CTLs with Improved Responsiveness to Homeostatic Cytokines and Recall Antigens: Important Traits for Adoptive T Cell Therapy (2012)

Previous mouse and human studies have demonstrated that direct IFN-α/β signaling on naive CD8 T cells is critical to support their expansion and acquisition of effector functions. In this study, we show that human naive CD8 T cells primed in the presence of IFN-α possess a heightened ability to respond to homeostatic cytokines and to secondary Ag stimulation, but rather than differentiating to effector or memory CTLs, they preserve nature-like phenotypic features. These are qualities associated with greater efficacy in adoptive immunotherapy. In a mouse model of adoptive transfer, CD8 T cells primed in the presence of IFN-α are able to persist and to mediate a robust recall response even after a long period of naturally driven homeostatic maintenance. The long-lasting persistence of IFN-α-primed CD8 T cells is favored by their enhanced responsiveness to IL-15 and IL-7, as demonstrated in IL-15(-/-) and IL-7(-/-) recipient mice. In humans, exposure to IFN-α during in vitro priming of naive HLA-A2(+) CD8 T cells with autologous dendritic cells loaded with MART1(26-35) peptide renders CD8 T cells with an improved capacity to respond to homeostatic cytokines and to specifically lyse MART1-expressing melanoma cells. Furthermore, in a mouse model of melanoma, adoptive transfer of tumor-specific CD8 T cells primed ex vivo in the presence of IFN-α exhibits an improved ability to contain tumor progression. Therefore, exposure to IFN-α during priming of naive CD8 T cells imprints decisive information on the expanded cells that can be exploited to improve the efficacy of adoptive T cell therapy.
Dolichol phosphate mannose synthase is required in vivo for glycosyl phosphatidylinositol membrane anchoring, O mannosylation, and N glycosylation of protein in Saccharomyces cerevisiae. (1990)

Glycosyl phosphatidylinositol (GPI) anchoring, N glycosylation, and O mannosylation of protein occur in the rough endoplasmic reticulum and involve transfer of precursor structures that contain mannose. Direct genetic evidence is presented that dolichol phosphate mannose (Dol-P-Man) synthase, which transfers mannose from GDPMan to the polyisoprenoid dolichol phosphate, is required in vivo for all three biosynthetic pathways leading to these covalent modifications of protein in yeast cells. Temperature-sensitive yeast mutants were isolated after in vitro mutagenesis of the yeast DPM1 gene. At the nonpermissive temperature of 37 degrees C, the dpm1 mutants were blocked in [2-3H]myo-inositol incorporation into protein and accumulated a lipid that could be radiolabeled with both [2-3H]myo-inositol and [2-3H]glucosamine and met existing criteria for an intermediate in GPI anchor biosynthesis. The likeliest explanation for these results is that Dol-P-Man donates the mannose residues needed for completion of the GPI anchor precursor lipid before it can be transferred to protein. Dol-P-Man synthase is also required in vivo for N glycosylation of protein, because (i) dpm1 cells were unable to make the full-length precursor Dol-PP-GlcNAc2Man9Glc3 and instead accumulated the intermediate Dol-PP-GlcNAc2Man5 in their pool of lipid-linked precursor oligosaccharides and (ii) truncated, endoglycosidase H-resistant oligosaccharides were transferred to the N-glycosylated protein invertase after a shift to 37 degrees C. Dol-P-Man synthase is also required in vivo for O mannosylation of protein, because chitinase, normally a 150-kDa O-mannosylated protein, showed a molecular size of 60 kDa, the size predicted for the unglycosylated protein, after shift of the dpm1 mutant to the nonpermissive temperature.
Synthesis and evaluation of (+) and (−)‐2,2‐difluorocitrate as inhibitors of rat‐liver ATP‐citrate lyase and porcine‐heart aconitase (1991)

The enantiomers (+) and (−)‐2,2‐difluorocitrate have been synthesized. Both are good inhibitors of ATP‐citrate lyase, showing competitive inhibition against citrate, with K is = 0.7 μM for (+)‐2,2‐difluorocitrate and 3.2 μM for (−)‐2,2‐difluorocitrate. The inhibition patterns with either ATP or CoA as the varied substrate were uncompetitive and mixed, respectively, but with much weaker inhibition constants. Neither isomer undergoes carbon‐carbon bond cleavage as a substrate and there is no evidence of irreversible time‐dependent inactivation. When ATP‐citrate lyase is incubated with CoA and difluorocitrate, the maximal intrinsic ATPase rate is 10% of the citrate‐induced rate for the (+)‐enantiomer and 2% for the (−)‐enantiomer. 19 F‐NMR studies confirm that only the (+)‐enantiomer is chemically processed. The effects of the difluorocitrate enantiomers on the reaction catalysed by aconitase were examined. (−)‐2,2‐Difluorocitrate is a competitive inhibitor against citrate ( K is = 1.5 μM), whereas the (+)‐enantiomer is a relatively poor mixed inhibitor ( K i &gt; 300 μM). The (−)‐enantiomer irreversibly inactivates aconitase at 1.1 min ‐1 · mM ‐1 at 25°C and pH 7.4, whereas no irreversible inhibition is seen with the (+)‐enantiomer. Therefore, it would be expected that the (+)‐enantiomer would slow the rate of acetyl‐CoA synthesis in vivo , without inhibiting the citric acid cycle.
Perturbed glial scaffold formation precedes axon tract malformation in Drosophila mutants (1993)

The longitudinal glia (LG), progeny of a single glioblast, form a scaffold that presages the formation of longitudinal tracts in the ventral nerve cord (VNC) of the Drosophila embryo. The LG are used as a substrate during the extension of the first axons of the longitudinal tract. I have examined the differentiation of the LG in six mutations in which the longitudinal tracts were absent, displaced, or interrupted to determine whether the axon tract malformations may be attributable to disruptions in the LG scaffold. Embryos mutant for the gene prospero had no longitudinal tracts, and glial differentiation remained arrested at a preaxonogenic state. Two mutants of the Polycomb group also lacked longitudinal tracts; here the glia failed to form an oriented scaffold, but cytological differentiation of the LG was unperturbed. The longitudinal tracts in embryos mutant for slit fused at the VNC midline and scaffold formation was normal, except that it was medially displaced. Longitudinal tracts had intersegmental interruptions in embryos mutant for hindsight and midline. In hindsight, there were intersegmental gaps in the glial scaffold. In midline, the glial scaffold retracted after initial extension. LG morphogenesis during axonogenesis was abnormal in midline. Commitment to glial identity and glial differentiation also occurred before scaffold formation. In all mutants examined, the early distribution of the glycoprotein neuroglian was perturbed. This was indicative of early alterations in VNC pattern present before LG scaffold formation began. Therefore, some changes in scaffold formation may have reflected changes in the placement and differentiation of other cells of the VNC. In all mutants, alterations in scaffold formation preceded longitudinal axon tract formation.
<title>Motion modeling and estimation for very low bit rate video coding</title> (1995)

In video coding at high compression rates, e.g., in very low bit rate coding, every transmitted bit carries a significant amount of information that is related either to motion parameters or to intensity residual. As demonstrated in the SIM-3 coding scheme, a more precise motion model leads to improved quality of coded images when compared with the H.261 coding standard. In this paper, we present some of our recent results on the modeling and estimation of motion of the compression and post-processing of typical videophone ('head-and- shoulders') image sequences. We describe a block-based motion estimation that attempts to optimize the overall bit budget for intensity residual, motion and overhead information. We compare simulation results for this scheme with full-search block matching in the context of the H.261 coding. Then, we discuss a region-based motion estimation that exploits segmentation maps obtained from an MDL-based (minimum description length) algorithm. We compare experimentally several algorithms for the compression of such maps. Finally, we describe motion-compensated interpolation that takes into account pixel acceleration. We show experimentally a major performance improvement of the constant- acceleration model over the usual constant-velocity models. This is a very promising technique for post-processing in the receiver to improve reconstruction of frames dropped in the transmitter.
Resonant-cavity-enhanced high-speed Si photodiode grown by epitaxial lateral overgrowth (1999)

We report a resonant cavity Si photodiode grown by merged epitaxial lateral overgrowth. At a reverse bias of 5 V, the dark current was 2.7 pA and the bandwidth exceeded 34 GHz. The peak quantum efficiencies ranged from 42% at 704 nm to 31% at 836 nm. This is the highest speed reported for a Si p-i-n photodiode and the highest bandwidth-efficiency product for any Si-based photodetector.
High-Throughput Screening for Induced Point Mutations (2001)

With the completion of genome sequencing projects, emphasis in genomics has shifted from analyzing sequences to understanding gene function, and effective reverse genetic strategies are increasingly in demand. Here we report adaptations of the targeting induced local lesions in genomes (TILLING)
Protein solubility characteristics of commercial soy protein products (2003)

Abstract Solubility characteristics of commerical soy protein products (flours, concentrates, and isolates) were determined under various conditions. From the solubility profiles at various pH values and NaCl concentrations, soy protein isolates can be divided into three groups. One group had high solubility near the pl. Another group had low solubility near the pl, but high solubility at pH 11. The third group had low solubility even at pH 11. Except for the hydrolyzed products, the protein solubilities of the soy protein products at various salt concentrations were very low. Temperature did not significantly affect the protein solubility, although a few products showed more than a 20% increase at temperatures &gt;50°C. Soy protein concentrates and soy protein isolates showed similar solubility profiles. The proteins in all commercial products (except flours) tested were denatured, as evident from the solubility profiles in the presence of salt and the enthalpy values from DSC.
Evaluation of serum CEA, CYFRA21-1 and CA125 for the early detection of colorectal cancer using longitudinal preclinical samples (2015)

CEA is elevated in a significant proportion of individuals with preclinical CRC, but would not be useful alone as a screening tool. This work sets a baseline from which to develop panels of biomarkers which combine CEA for improved early detection of CRC.
Novel Sequence-Ordered Polymers by Transformation of Polymer Backbone:  Quantitative and Regioselective Insertion of Thiiranes into Poly(S-aryl Thioester) (1999)

Novel sequence-ordered poly(S-alkyl thioester)s were synthesized on the basis of transformation of a backbone of the poly(S-aryl thioester) (P-1) using the regioselective insertion of thiiranes. The insertion reaction of 3-butoxypropylene sulfide (BPS) into P-1 using catalysts such as tetrabutylammonium chloride (TBAC), tetrabutylphosphonium chloride, or 18-crown-6-ether/potassium chloride in DMAc at 70 °C for 6 h proceeded completely and regioselectively to provide an ordered poly(S-alkyl thioester) (P-2a) with a new sequence. The molecular weight of P-2a was reasonably higher than that of the starting polymer P-1. The structure of P-2a including a head-to-tail sequence of BPS unit was well-characterized by IR, 1H NMR, 13C NMR spectroscopies, GPC, and elemental analysis. Various sequence-ordered poly(S-alkyl thioester)s were successfully synthesized by the insertion reaction of 3-phenoxypropylene sulfide, BPS, or cyclohexene sulfide using the TBAC catalyst under the same conditions. It was demonstrated that the transformation of the polymer backbone because of the regioselective insertion of thiiranes using quaternary onium salts was a useful method for achieving the synthesis of sequence-ordered polymers.
<title>Ultimate sensitivity of time-resolved optoacoustic detection</title> (2000)

The major limitation in sensitivity of the optical tomography is associated with strong optical attenuation in human tissues. Opto-acoustic tomography overcomes this limitation utilizing detection of acoustic waves instead of detection of transmitted photons. Exceptional sensitivity of the opto-acoustic tomography allows early detection of small tumors located dep in human tissues, such as breast. This paper demonstrates that an optimally designed opto-acoustic imaging system can detect early 1-mm tumors with minimal blood content of only 7 percent at the depth of up to 7-cm within the breast attenuating laser irradiation 3.3 times per each 1-cm of its depth. A theoretical consideration of the ultimate sensitivity of piezo-detection in a wide ultrasonic frequency band is developed. The detection sensitivity is presented as a function of the ultrasonic frequency, tumor dimensions and optical absorption coefficient. Comparative analysis of piezo and optical interferometric detection of opto-acoustic transients is presented. The theoretical models of piezo detection were developed for the open-circuit and short-circuit schemes of operation. The ultimate sensitivity limited by thermal noise of electric capacitor of the piezo-element was estimated. It was shown that the limit of detection depends on the frequency band, the electric capacity of the transducer and the sped of sound in the piezo-element. Comparative analysis of various piezo-materials was made from the point of view of their utility for sensitive opto-acoustic detection.
The use of mRNA display to select high-affinity protein-binding peptides (2001)

We report the use of "mRNA display," an in vitro selection technique, to identify peptide aptamers to a protein target. mRNA display allows for the preparation of polypeptide libraries with far greater complexity than is possible with phage display. Starting with a library of approximately 10(13) random peptides, 20 different aptamers to streptavidin were obtained, with dissociation constants as low as 5 nM. These aptamers function without the aid of disulfide bridges or engineered scaffolds, yet possess affinities comparable to those for monoclonal antibody-antigen complexes. The aptamers bind streptavidin with three to four orders of magnitude higher affinity than those isolated previously by phage display from lower complexity libraries of shorter random peptides. Like previously isolated peptides, they contain an HPQ consensus motif. This study shows that, given sufficient length and diversity, high-affinity aptamers can be obtained even from random nonconstrained peptide libraries. By engineering structural constraints into these ultrahigh complexity peptide libraries, it may be possible to produce binding agents with subnanomolar binding constants.
Adaptive artificial impedance surface conformal antennas (2009)

Moving platforms, like manned and unmanned aerial vehicles, require adaptable directive antennas for both communication and radar applications. The integration of these antennas into the body of the platform drives significant development time and expense, and in many cases adversely affects the overall vehicle performance by adversely affecting its aerodynamics or weight. Being able to integrate the antenna function directly in the skin of the platform will result in simpler better performing vehicles. We have developed an AIB with which we have used to demonstrate 2D electronic beam steering. These results show how AIB technology can be utilized for the realization of next generation conformal, electrically steerable directive antennas.