gebhart/patrepeval huggingface dataset:
The LIM-domain binding protein Ldb1 and its partner LMO2 act as negative regulators of erythroid differentiation (1997)

The nuclear LIM domain protein LMO2, a T cell oncoprotein, is essential for embryonic erythropoiesis. LIM-only proteins are presumed to act primarily through protein-protein interactions. We, and others, have identified a widely expressed protein, Ldb1, whose C-terminal 76-residues are sufficient to mediate interaction with LMO2. In murine erythroleukemia cells, the endogenous Lbd1 and LMO2 proteins exist in a stable complex, whose binding affinity appears greater than that between LMO2 and the bHLH transcription factor SCL. However, Ldb1, LMO2, and SCL/E12 can assemble as a multiprotein complex on a consensus SCL binding site. Like LMO2, the Ldb1 gene is expressed in fetal liver and erythroid cell lines. Forced expression of Ldb1 in G1ER proerythroblast cells inhibited cellular maturation, a finding compatible with the decrease in Ldb1 gene expression that normally occurs during erythroid differentiation. Overexpression of the LMO2 gene also inhibited erythroid differentiation. Our studies demonstrate a function for Ldb1 in hemopoietic cells and suggest that one role of the Ldb1/LMO2 complex is to maintain erythroid precursors in an immature state.
Phase I/II Trial of Bevacizumab and Radiotherapy for Locally Advanced Inoperable Colorectal Cancer: Vasculature-Independent Radiosensitizing Effect of Bevacizumab (2009)

The combination of radiotherapy with bevacizumab is feasible and results in a high rate of durable complete responses in patients with LA/I-CRC. Radiosensitization may occur through a direct effect on tumor cells followed by a wide scale suppression of transcription factors and genes involved in DNA repair and proliferation.
DNA Vaccines Encoding Viral Glycoproteins Induce Nonspecific Immunity and Mx Protein Synthesis in Fish (2000)

Protective immunity by vaccination with plasmid DNA encoding a viral glycoprotein (G) has long been assumed to result from the induction of a specific immune response. We report here that the initial protection may be due to the induction of alpha/beta interferon, with long-term protection due to a specific response to the encoded viral G. DNA vaccines encoding the Gs of three serologically unrelated fish rhabdoviruses were used to vaccinate rainbow trout against a lethal challenge with infectious hematopoietic necrosis virus (IHNV). All three vaccines, each encoding the G gene of either IHNV (IHNV-G), snakehead rhabdovirus (SHRV) (SHRV-G), or spring viremia of carp virus (SVCV) (SVCV-G), elicited protective immunity against IHNV. Vaccinated fish were challenged at 30 or 70 days postvaccination with lethal doses of IHNV. At 30 days postvaccination, only 5% of fish that had received any of the G vaccines died, whereas more than 50% of the control fish succumbed to virus challenge. When fish were vaccinated and challenged at 70 days postvaccination, only 12% of the IHNV-G-vaccinated fish died compared to 68% for the SHRV-G- and 76% for the SVCV-G-vaccinated fish. Assays for trout Mx protein, an indicator of alpha/beta interferon induction, showed that only fish vaccinated with a G-containing plasmid produced high levels of Mx protein in the kidneys and liver. Interestingly, at day 7 after virus challenge, all of the fish vaccinated with the IHNV-G plasmid were negative for Mx, but the SHRV-G- and SVCV-G-vaccinated fish still showed detectable levels of Mx. These results suggest that DNA vaccines in fish induce an early, nonspecific antiviral protection mediated by an alpha/beta interferon and, later, a specific immune response.
Syntheses of 6-substituted 7,8,9,10-tetrahydrophenanthridin-7-ones through sulfur extrusion. (1985)

6-Substituted 7, 8, 9, 10-tetrahydrophenanthridin-7-ones were synthesized by dehydrative cyclization and concomitant sulfur extrusion of 3-(2-acylaminophenylthio)-2-cyclohexen-1-ones with polyphosphoric acid.
Head Group Specificity in the Requirement of Phosphatidylcholine Biosynthesis for Very Low Density Lipoprotein Secretion from Cultured Hepatocytes (1989)

We have demonstrated that hepatic very low density lipoprotein (VLDL) secretion requires active phosphatidylcholine (PC) synthesis via either the CDP-choline pathway or phosphatidylethanolamine (PE) methylation pathway (Yao, Z., and Vance, D.E. (1988) J. Biol. Chem. 263, 2998-3004). In the present work, the head group specificity of phospholipid synthesis required for lipoprotein secretion was investigated in cultured hepatocytes isolated from choline-deficient rats. When N-monomethylethanolamine (0.1 mM) or N,N-dimethylethanolamine (0.1 mM) was added to the culture medium, the cells synthesized correspondingly phosphatidylmonomethylethanolamine (PMME) or phosphatidyldimethylethanolamine (PDME). However, the synthesis of PDME could correct the impaired VLDL secretion only to a limited extent, whereas the synthesis of PMME inhibited VLDL secretion. Although dimethylethanolamine did not promote VLDL secretion as well as choline, dimethylethanolamine altered the increased triacylglycerol synthesis in the choline-deficient cells as effectively as choline. Supplementation of the culture medium with ethanolamine (0.1 mM) had little effect on cellular PE or PC levels, nor was normal VLDL secretion resumed. However, the amounts of cellular PC and PE were both decreased when the medium was supplemented with N-monomethylethanolamine or N,N-dimethylethanolamine. These results suggest that the choline head group moiety of PC is specifically required for normal VLDL secretion and cannot be replaced with ethanolamine, monomethylethanolamine, or dimethylethanolamine. In addition, the impaired VLDL secretion from the choline-deficient hepatocytes could also be corrected by supplementation of betaine (0.2 mM) and homocysteine (0.2 mM), indicating the utilization of a methyl group from betaine for PC formation via methylation of PE.
Derivative method for phase retrieval in off-axis quantitative phase imaging (2012)

We present a method for phase retrieval in off-axis interferometric systems. By numerically calculating the transverse 1st and 2nd order derivatives of the interferogram, we show that one can directly retrieve the quantitative phase image, without the need for Fourier or Hilbert transformations. Because of this, the method is significantly faster than the current approaches. We illustrate our method using biological specimen data from three different off-axis quantitative phase imaging techniques.
Atrophy-related ubiquitin ligases atrogin-1 and MuRF-1 are associated with uterine smooth muscle involution in the postpartum period (2006)

The regulation of cell size depends on a delicate balance between protein synthesis and breakdown. Skeletal and cardiac muscle adapt to hormonal and neuronal stimuli and can rapidly hypertrophy and atrophy; however, the extent to which these processes occur in smooth muscle is less clear. Atrophy in striated muscle results from enhanced protein breakdown and is associated with a common transcriptional profile and activation of the ubiquitin-proteasome pathway, including induction of the muscle-specific ubiquitin protein ligases atrogin-1 and muscle ring-finger protein 1 (MuRF-1). Here we show that atrogin-1 is also expressed in smooth muscle, and that both atrogin-1 and MuRF-1 are upregulated in the uterus following delivery, as rapid involution occurs. While these two genes are similarly induced in all types of muscle during rapid loss of cell mass, other striated muscle atrophy-specific transcriptional changes are not observed during uterine involution, suggesting different underlying molecular mechanisms. These results raise the possibility that activation of atrogin-1 and MuRF-1 may be a common general adaptation in cells undergoing a rapid reduction in size.
Development and Field Tests on Prototype of Leg Penetration Monitor System To Avoid the Punch-Through Accidents of Jackup Rigs (1990)

ABSTRACT Punch-through accidents with offshore jackup drilling rigs could bring on more serious damages than ever as the rigs become larger in size and go toward deeper and severer waters. There has been a pressing demand from the field for systems that minimize the possibility of such accidents. This paper reports the development and the field tests on the prototype of a Leg Penetration Monitor System (LPMS) which has been conceived to prevent punch-through accidents on jackup drilling rigs, based on the design already described in the previous paper1. Using prototypes, the following two kinds of field tests were carried out, and the test results confirmed the propriety of the system reported below. Test (A): Cone penetration and data processing tests Test (B): Acoustic sensing system tests in measurements of water depth, air gap, coordinates of sea-bottom transducer, leg penetration and small leg displacement. INTRODUCTION It is reported that some 20 percent of major jackup rig accidents occurred worldwide have been caused by some sorts of leg troubles, including punch-throughs (P-T) of the footings. Once a P-T happens on a leg, it likely causes damage to the leg structure and/or the associated jacking unit, or it even threatens losses of the rig and life. Particularly, the recent trend toward heavier jackups being built to cope with deeper and harsher seas of operation will translate into more serious consequences once a P-T accident takes place. An effective system, therefore, is vehemently awaited in the field that would possibly predict and provide preventive measures against the occurrence of a P-T accident on a jackup rig, thereby assuring safe drilling and development activities at sea. The previous paper1 reported the results of a study which finally led to the successful development of two P-T preventive measures. These countermeasures were: Strata Data Monitor System (SDMS) and Vertical Position Monitor System (VPMS). The SDMS allows to precisely know the properties of seabed soil through a device which, mounted on the rig itself, surveys the seabed nearby or immediately beneath the leg footings (spud cans), evaluates the safety of the sea floor on to rest the legs, and even suggests safe preloading procedures by computing the bearing capacity of the site. The VPMS acquires, monitors and records data on the water depth and the vertical position of the platform with respect to the sea floor during the jacking up/down and preloading operations. These two systems altogether are referred to in thispaper as the Leg Penetration Monitor System (LPMS). Figure 1 shows an outline configuration of the SDMS. Three cone-penetrometers that survey the seabed immediately underneath the leg footings are illustrated in the figure. An outline configuration of the VPMS is presented in Figure 2. Eight acoustic transducers are arranged in their respective locations in the following quantity and at the following known or unknown coordinates.
Oscillator array dynamics with broadband N-port coupling networks (1994)

This paper considers the analysis of an oscillator array with an arbitrary coupling network, described in terms of N-port circuit parameters. A Kurokawa analysis is used to transform the frequency domain network description into a set of equations for the oscillator amplitude and phase dynamics. The results reduce to previous work with "loosely" coupled Van der Pol oscillators, provided that the coupling network satisfies a broadband condition: the Q-factor of the coupling network must be much smaller than that of the oscillator. The theory is verified using a new coupling structure and a six-element patch oscillator array operating at 4 GHz, which produced a 70/spl deg/ scanning range using a phase-shifterless technique.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Sulfation is rate limiting in the futile cycling between estrone and estrone sulfate in enriched periportal and perivenous rat hepatocytes. (2001)

The metabolic activities and tissue binding of estrone (E1) and estrone sulfate (E1S) on futile cycling were examined. Desulfation of E1S in the 9000g supernatant fraction (S9) of periportal (PP) and perivenous (PV) rat hepatocytes were of similar V (2.9 +/- 1.0 and 2.4 +/- 0.9 nmol/min/mg of S9 protein), K (30.4 +/- 8.3 and 34.8 +/- 6.6 microM), and desulfation intrinsic clearances (V/K of 77 and 55 microl/min/10(6) cells). The intrinsic clearance towards E1 sulfation (1 microM) in cytosolic preparations of PV hepatocytes was 4 times that of PP hepatocytes (V/K of 26.4 +/- 9.5 versus 6.1 +/- 2.2 microl/min/mg of cytosolic protein or 13 +/- 5 versus 3.1 +/- 1.1 microl/min/10(6) cells). The observation was consistent with the immunolocalization of estrogen sulfotransferase (PV/PP ratio of 3.4 +/- 1.1) but not hydroxysteroid sulfotransferase (PV/PP ratio of 0.29 +/- 0.21) nor phenol sulfotransferase (PV/PP ratio of 1.13 +/- 0.23). Upon incubation of E1S (1-125 microM) with hepatocytes (30 min), higher concentrations of E1S and E1 were observed within PP than in PV cells, and saturation was evident at the higher concentrations. Based on the in vitro metabolic and tissue binding parameters for E1S and E1 and the published zonal uptake clearances of E1S (116 microl/min/10(6) cells), fitting revealed that uptake of E1 (1484 and 1463 microl/min/10(6) cells) by PP and PV cells was rapid and similar, and E1 sulfation was the slowest step in futile cycling. The greater metabolism of E1 in PV region led to higher levels of E1 and E1S in PP hepatocytes, and the nonlinear uptake, binding, and vesicular accumulation of E1S resulted in different t(1/2) values for E1S and E1.
Real-Time Illegal Parking Detection System Based on Deep Learning (2017)

The increasing illegal parking has become more and more serious. Nowadays the methods of detecting illegally parked vehicles are based on background segmentation. However, this method is weakly robust and sensitive to environment. Benefitting from deep learning, this paper proposes a novel illegal vehicle parking detection system. Illegal vehicles captured by camera are firstly located and classified by the famous Single Shot MultiBox Detector (SSD) algorithm. To improve the performance, we propose to optimize SSD by adjusting the aspect ratio of default box to accommodate with our dataset better. After that, a tracking and analysis of movement is adopted to judge the illegal vehicles in the region of interest (ROI). Experiments show that the system can achieve a 99% accuracy and real-time (25FPS) detection with strong robustness in complex environments.
Neural Network Training with Highly Incomplete Datasets (2021)

Neural network training and validation rely on the availability of large high-quality datasets. However, in many cases only incomplete datasets are available, particularly in health care applications, where each patient typically undergoes different clinical procedures or can drop out of a study. Since the data to train the neural networks need to be complete, most studies discard the incomplete datapoints, which reduces the size of the training data, or impute the missing features, which can lead to artefacts. Alas, both approaches are inadequate when a large portion of the data is missing. Here, we introduce GapNet, an alternative deep-learning training approach that can use highly incomplete datasets. First, the dataset is split into subsets of samples containing all values for a certain cluster of features. Then, these subsets are used to train individual neural networks. Finally, this ensemble of neural networks is combined into a single neural network whose training is fine-tuned using all complete datapoints. Using two highly incomplete real-world medical datasets, we show that GapNet improves the identification of patients with underlying Alzheimer's disease pathology and of patients at risk of hospitalization due to Covid-19. By distilling the information available in incomplete datasets without having to reduce their size or to impute missing values, GapNet will permit to extract valuable information from a wide range of datasets, benefiting diverse fields from medicine to engineering.
The bcl-2 candidate proto-oncogene product is a 24-kilodalton integral-membrane protein highly expressed in lymphoid cell lines and lymphomas carrying the t(14;18) translocation. (1989)

We have identified a 24-kilodalton protein that is the product of the human bcl-2 gene, implicated as an oncogene because of its presence at the site of t(14;18) translocation breakpoints. The Bcl-2 protein was detected by specific, highly sensitive rabbit antibodies and was shown to be present in a number of human lymphoid cell lines and tissues, as well as in mouse B cells transfected with a bcl-2 cDNA construct. Characterization of the Bcl-2 protein demonstrated that it has a lipophilic nature and is associated with membrane structures, probably by means of its hydrophobic carboxy-terminal membrane-spanning domain. In t(14;18)-carrying cell lines, the protein is predominantly localized to the perinuclear endoplasmic reticulum, with a minor fraction in the plasma membrane. These properties, together with the observations that Bcl-2 does not have a characteristic signal peptide and is not glycosylated, suggest that it is an integral-membrane protein that spans the bilayer at its C-terminal hydrophobic region but is exposed only at the cytoplasmic surface. The relative abundance of the Bcl-2 protein in various human lymphoid cell lines correlated with transcription of the bcl-2 gene. The protein was abundant in all t(14;18)-carrying cell lines and lymphomas and was also found at lower levels in pre-B-cell lines and nonmalignant lymphoid tissues that do not carry t(14;18) translocations. These results suggest that the Bcl-2 protein is functional in normal B lymphocytes and that a quantitative difference in its expression may play a role in the pathogenesis of lymphomas carrying the t(14;18) translocation.
Quantitative immunofluorescence mapping reveals little functional coclustering of proteins within platelet α-granules (2011)

Platelets are small anucleate blood cells that aggregate to seal leaks at sites of vascular injury and are important in the pathology of atherosclerosis, acute coronary syndromes, rheumatoid arthritis, cancer, and the regulation of angiogenesis. In all cases, platelet aggregation requires release of stored proteins from α-granules. However, how proteins with potentially antagonistic functions are packaged within α-granules is controversial. One possibility is the packaging of functional agonists and antagonists into different α-granule populations. By quantitative immunofluorescence colocalization, we found that pair-wise comparisons of 15 angiogenic-relevant α-granule proteins displayed little, if any, pattern of functional coclustering. Rather, the data suggested a Gaussian distribution indicative of stochastic protein delivery to individual granules. The apparent physiologic paradox raised by these data may be explained through alternate mechanisms, such as differential content release through incomplete granule fusion or dampened and balanced regulatory networks brought about by the corelease of antagonistic factors.
Development of antibody fragments for immunotherapy of prion diseases (2008)

Prions are infectious proteins responsible for a group of fatal neurodegenerative diseases called TSEs (transmissible spongiform encephalopathies) or prion diseases. In mammals, prions reproduce themselves by recruiting the normal cellular protein PrP(C) and inducing its conversion into the disease-causing isoform denominated PrP(Sc). Recently, anti-prion antibodies have been shown to permanently cure prion-infected cells. However, the inability of full-length antibodies and proteins to cross the BBB (blood-brain barrier) hampers their use in the therapy of TSEs in vivo. Alternatively, brain delivery of prion-specific scFv (single-chain variable fragment) by AAV (adeno-associated virus) transfer delays the onset of the disease in infected mice, although protection is not complete. We investigated the anti-prion effects of a recombinant anti-PrP (D18) scFv by direct addition to scrapie-infected cell cultures or by infection with both lentivirus and AAV-transducing vectors. We show that recombinant anti-PrP scFv is able to reduce proteinase K-resistant PrP content in infected cells. In addition, we demonstrate that lentiviruses are more efficient than AAV in gene transfer of the anti-PrP scFv gene and in reducing PrP(Sc) content in infected neuronal cell lines. Finally, we have used a bioinformatic approach to construct a structural model of the D18scFv-PrP(C) complex. Interestingly, according to the docking results, Arg(PrP)(151) (Arg(151) from prion protein) is the key residue for the interactions with D18scFv, anchoring the PrP(C) to the cavity of the antibody. Taken together, these results indicate that combined passive and active immunotherapy targeting PrP might be promising strategies for therapeutic intervention in prion diseases.
A cryptic 65-kilobase-pair transposonlike element isolated from Bacteroides uniformis has homology with Bacteroides conjugal tetracycline resistance elements (1990)

A 65-kilobase-pair element, XBU4422, which has some transposonlike characteristics but carries no known antibiotic resistance genes, has been isolated from Bacteroides uniformis 0061. XBU4422 was trapped on Bacteroides-Escherichia coli shuttle vectors during experiments in which one of the conjugal Bacteroides tetracycline resistance (Tcr) elements was being used to mobilize the shuttle vectors to Bacteroides recipients. Results of Southern hybridization experiments showed that XBU4422 is normally integrated in the B. uniformis 0061 chromosome and is found only in some strains. Insertion of XBU4422 in the shuttle vectors was site specific and orientation specific. Nonmobilizable vectors that had acquired XBU4422 became transmissible and could be transferred to Bacteroides or E. coli recipients. In B. uniformis transconjugants, the XBU4422 insertion in the vectors was usually intact, but XBU4422 was always lost in matings with E. coli, Bacteroides thetaiotaomicron, or B. ovatus. The loss of XBU4422 did not visibly alter the vector; in the case of E. coli, the loss of the insertion appeared to be RecA dependent. Although XBU4422 carried no antibiotic resistances, it shared regions of homology with six conjugal Bacteroides Tcr elements; this homology was strongest with the ends of XBU4422. Using a strain of B. thetaiotaomicron that contains no XBU4422-hybridizing sequences, we showed that the ends of XBU4422 were probably reacting with the ends of the Tcr elements. These results provide the first direct evidence that the Tcr elements, like XBU4422, are integrated in the chromosome and that insertion of the least some Tcr elements, such as TcrEmr DOT, is relatively site specific.
Evidence for an ancient selective sweep in the MHC class I gene repertoire of chimpanzees (2002)

MHC class I molecules play an essential role in the immune defense against intracellular infections. The hallmark of the MHC is its extensive degree of polymorphism at the population level. However, the present comparison of MHC class I gene intron variation revealed that chimpanzees have experienced a severe repertoire reduction at the orthologues of the HLA-A, -B, and -C loci. The loss of variability predates the (sub)speciation of chimpanzees and did not effect other known gene systems. Therefore the selective sweep in the MHC class I gene may have resulted from a widespread viral infection. Based on the present results and the fact that chimpanzees have a natural resistance to the development of AIDS, we hypothesize that the selective sweep was caused by the chimpanzee-derived simian immunodeficiency virus (SIVcpz), the closest relative of HIV-1, or a closely related retrovirus. Hence, the contemporary chimpanzee populations represent the offspring of AIDS-resistant animals, the survivors of a HIV-like pandemic that took place in the distant past.