gebhart/patrepeval huggingface dataset:
Identification and Characterization of a Soybean Ethylene-Responsive Element-Binding Protein Gene Whose mRNA Expression Changes During Soybean Cyst Nematode Infection (2002)

Ethylene-responsive element-binding proteins (EREBPs) are members of a family of plant transcription factors. Conserved EREBP domains of these proteins bind to the GCC box, an ethylene-responsive promoter element found in many pathogenesis-related (PR) genes. Using degenerate primers to the EREBP domain from diverse plant species, an EREBP homolog was isolated from a soybean cDNA library. Gel mobility-shift assays revealed that the translation product of this cDNA bound specifically to GCC box sequences. We, therefore, named this gene Glycine max ethylene-responsive element-binding protein 1 (GmEREBP1), i.e., a gene coding for the first confirmed GCC box-binding protein of soybean. GmEREBP1 mRNA abundance was analyzed by RNA blot hybridizations in soybean roots and shoots of cultivars Corsoy 79 and Hartwig, which are susceptible and resistant, respectively, to the soybean cyst nematode (Heterodera glycines). These analyses revealed that GmEREBP1 is expressed in a root-preferential manner and that GmEREBP1 mRNA abundance is changed after H. glycines infection. GmEREBP1 mRNA abundance decreased in infected (susceptible) 'Corsoy 79' roots, whereas it increased in abundance in infected (resistant) 'Hartwig' roots. Furthermore, ethephon treatment repressed GmEREBP1 mRNA accumulation in both cultivars, whereas wounding increased expression in both cultivars. These changes in mRNA steady-state levels suggest that GmEREBP1 plays a role in soybean-H. glycines interactions.
Therapeutic Activity of Lenalidomide in Mantle Cell Lymphoma and Indolent Non-Hodgkin’s Lymphomas (2012)

Mantle cell lymphoma (MCL) comprises 3-10% of NHL, with survival times ranging from 3 and 5 years. Indolent lymphomas represent approximately 30% of all NHLs with patient survival largely dependent on validated prognostic scores. High response rates are typically achieved in these patients with current first-line chemoimmunotherapy. However, most patients will eventually relapse and become chemorefractory with poor outcome. Alternative chemoimmunotherapy regimens are often used as salvage strategy and stem cell transplant remains an option for selected patients. However, novel approaches are urgently needed for patients no longer responding to conventional chemotherapy. Lenalidomide is an immunomodulatory drug with activity in multiple myeloma, myelodisplastic syndrome and chronic lymphoproliferative disorders. In phase II studies of indolent NHL and MCL lenalidomide has shown activity with encouraging response rates, both as a single agent and in combination with other drugs. Some of these responses may be durable. Optimal dose of lenalidomide has not been defined yet. The role of lenalidomide in the therapeutic armamentarium of patients with indolent NHL or MCL will be discussed in the present paper.
Labeling of monoclonal antibodies with rhenium-186 using the MAG3 chelate for radioimmunotherapy of cancer: a technical protocol. (1993)

A detailed technical protocol is provided for reproducible and aseptical production of stable 186Re-monoclonal antibody conjugates. Labeled Mab E48 IgG and its F(ab')2 fragment which are promising candidates for radioimmunotherapy of squamous cell carcinoma of the head and neck were used for evaluation. S-benzoylmercaptoacetyltriglycine (S-benzoyl-MAG3) was used as a precursor. Rhenium-186-MAG3 was prepared via a unique solid-phase synthesis, after which known strategies for esterification and conjugation to Mab IgG/F(ab')2 were applied. The biodistribution of 186Re-E48 F(ab')2 in tumor-bearing nude mice was found to be comparable to that of analogously labeled 99mTc-E48 F(ab')2 or 131I-E48 F(ab')2, indicating that the intrinsic behavior of the antibody remains preserved when using this labeling technique. Radiolytic decomposition of 186Re-E48 IgG/F(ab')2 solutions of 10 mCi.ml-1 was effectively reduced by the antioxidant ascorbic acid. Upon increase of the Re-MAG3 molar amount, a conjugation of seven to eight Re-MAG3 molecules per Mab molecule was generally the maximum ratio that could chemically be obtained. Such a ratio did not impair the immunoreactivity or alter the in vivo biodistribution characteristics of the immunoconjugate, making this labeling procedure suitable for general clinical application.
Feature-based image metamorphosis (1992)

A new technique is presented for the metainorphosix of one digital image into another.The approach gives the animator high-level control of the viNual effect by providing natural fuature-ba5ed specilication and interaction.When used effectively.this technique can give the illuxion that the photographed or computer generated subject.saretran*formingi n at1uid.furrealixtic.and oftendraniatic way Comparisons with existing methods are diawn, and the advantages and dEadvantages of each are examined.The new method is then extended tO accommodate keyIramed transiormations between image 5equence.1-u motion image LT(,rk.Several e.amples are illustrated w'ith rexulting images.Ke>'uords:
Ligand Effects and Kinetic Investigations of Sterically Accessible 2-Pyridonate Tantalum Complexes for Hydroaminoalkylation (2017)

The synthesis of a series of structurally varied pyridonate-supported tantalum amido complexes and their catalytic reactivity in the intermolecular α-alkylation of unprotected secondary amines are described. Both terminal and internal alkenes can undergo this hydroaminoalkylation reaction to give selectively substituted secondary amine products. The reactivity profiles of 3- and 6-substituted pyridonate tantalum complexes, [(2-pyridonate)Ta(NMe2)3Cl], and a triflato pyridonate tantalum complex, [(2-pyridonate)Ta(NMe2)3OTf], were evaluated to analyze ligand effects. The deprotonation and complexation of commercially available 3-methyl-2-pyridone and 2-pyridone readily yielded effective, catalytically active tantalum complexes, displaying reactivity with both terminal and internal alkene substrates. Kinetic studies and deuterium labeling experiments reveal a complex kinetic profile and provide evidence for off-cycle equilibria that dominate catalytic activity and provide guidance for future catalyst development.
Analysis of gene expression in human bullous keratopathy corneas containing limiting amounts of RNA. (1999)

Smart cDNA synthesis and nucleic acid arrays were combined and validated for the first time to identify differential gene expression in normal and diseased corneas. These techniques require very little RNA such as that equivalent to a half of a single cornea, which is useful when the amount of tissue is limiting. Altered expression of adhesive proteins beta6 integrin and beta-catenin may be related to the formation of epithelial bullae and microcystic changes in PBK patients.
In Vivo Footprinting Analysis of the Hepatic Control Region of the Human Apolipoprotein E/C-I/C-IV/C-II Gene Locus (1996)

Expression of both the apolipoprotein (apo)E and apoC-I genes in the liver is specified by a 319-nucleotide hepatic control region (HCR-1) that is located 15 kilobase pairs downstream of the apoE gene and 5 kilobase pairs downstream of the apoC-I gene. In vivo footprint analysis of HCR-1 in intact nuclei revealed several liver-specific protein-binding sites that were not detectable by in vitro methods. In addition to three previously identified in vitro footprints, four in vivo footprints were identified in a region of HCR-1 that is required for directing gene expression to hepatocytes. Prominent liver-specific DNase I-hypersensitive sites were associated with these footprints. Liver-specific nuclear protein binding to these sites was confirmed by oligonucleotide gel-retention assays. The in vivo analysis also identified a cluster of nuclear protein-binding sites in the Alu family repeat segment adjacent to the domain required for liver expression. Micrococcal nuclease digestion indicated the presence of a nucleosome in the central domain of HCR-1 in liver chromatin that was in phase with the nucleosome location in tissues that did not express the transgene. These results suggest that HCR-1 functions in a highly structured chromatin environment requiring a complex interaction of liver-enriched transcription factors.
Synthesis of (±)‐Strychnofoline via a Highly Convergent Selective Annulation Reaction (2006)

Studies aimed at preparing (+/-)-strychnofoline by total synthesis are detailed. The route described makes use of a recently developed MgI(2)-mediated ring-expansion reaction of spiro[cyclopropan-1,3'-oxindole] with a cyclic disubstituted aldimine. The ring-expansion product was formed as a single diastereoisomer in 55 % yield, possessing the same stereochemical pattern found in strychnofoline. In addition, our synthetic effort has led to the development of new reaction methodology to access 3,4-disubstituted cyclic aldimines.
Systematic Analysis of Sequences and Expression Patterns of Drought-Responsive Members of the HD-Zip Gene Family in Maize (2011)

Our results reveal a comprehensive overview of the maize HD-Zip gene family and provide the first step towards the selection of Zmhdz genes for cloning and functional research to uncover their roles in maize growth and development.
Protein cross‐linking by peroxidase: Possible mechanism for sclerotization of insect cuticle (1987)

Abstract Incubation of test proteins with horseradish peroxidase in the presence of hydrogen peroxide and a catechol resulted in polymerization and precipitation of test proteins. SDS‐PAGE readily revealed the generation of dimers, trimers, and higher oligomers in the reaction mixture. With the exception of 3,4‐dihydroxyphenylalanine, dopamine, and norepinephrine, most other catechols tested participated in protein polymerization. The inability of these three catechols to accomplish polymerization is attributed to their high rate of intramolecular cyclization, which results in melanin formation. Radioactive studies with [ 3 H]N‐acetyldopamine clearly reveal both intermolecular and intramolecular cross‐linking of test proteins by peroxidase. Based on these studies a possible mechanism for sclerotization and the biological significance of peroxidase in cuticle is discussed.
Hydroxyurea: effects on hemoglobin F production in patients with sickle cell anemia [see comments] (1992)

Patients with sickle cell anemia were treated with daily doses of hydroxyurea, to assess pharmacokinetics, toxicity, and increase in fetal hemoglobin (Hb) production in response to the drug. Plasma hydroxyurea clearances were not a useful guide to maximum tolerated doses of the drug. The mean daily single oral dose that could be maintained for at least 16 weeks was 21 mg/kg (range, 10 to 35 mg/kg). Among 32 patients, last HbF levels were 1.9% to 26.3% (mean, 14.9%) with increases in HbF over initial values of 1.4% to 20.2% (mean, 11.2%). The most significant predictors of last HbF were last plasma hydroxyurea level, initial white blood count and initial HbF concentration. Last HbF was not related to beta globin haplotype or alpha globin gene number. No serious toxicity was encountered. Clinically significant bone marrow depression was avoided, and chromosome abnormalities after 2 years of treatment were no greater than those observed before treatment. The period of observation has been too short to evaluate the risk of carcinogenesis. Patient's red cells developed striking macrocytosis. Median red cell Hb concentrations did not change. Hb concentrations increased, on average 1.2 g/dL, but serum erythropoietin levels increased. Patients' body weights increased, and some returned to work or school, but no conclusions regarding therapeutic efficacy could be drawn from this uncontrolled open-label study.
Frustum PointNets for 3D Object Detection from RGB-D Data (2018)

In this work, we study 3D object detection from RGBD data in both indoor and outdoor scenes. While previous methods focus on images or 3D voxels, often obscuring natural 3D patterns and invariances of 3D data, we directly operate on raw point clouds by popping up RGB-D scans. However, a key challenge of this approach is how to efficiently localize objects in point clouds of large-scale scenes (region proposal). Instead of solely relying on 3D proposals, our method leverages both mature 2D object detectors and advanced 3D deep learning for object localization, achieving efficiency as well as high recall for even small objects. Benefited from learning directly in raw point clouds, our method is also able to precisely estimate 3D bounding boxes even under strong occlusion or with very sparse points. Evaluated on KITTI and SUN RGB-D 3D detection benchmarks, our method outperforms the state of the art by remarkable margins while having real-time capability.
Calcium and Vitamin D Requirements of Enterally Fed Preterm Infants (2013)

Bone health is a critical concern in managing preterm infants. Key nutrients of importance are calcium, vitamin D, and phosphorus. Although human milk is critical for the health of preterm infants, it is low in these nutrients relative to the needs of the infants during growth. Strategies should be in place to fortify human milk for preterm infants with birth weight <1800 to 2000 g and to ensure adequate mineral intake during hospitalization and after hospital discharge. Biochemical monitoring of very low birth weight infants should be performed during their hospitalization. Vitamin D should be provided at 200 to 400 IU/day both during hospitalization and after discharge from the hospital. Infants with radiologic evidence of rickets should have efforts made to maximize calcium and phosphorus intake by using available commercial products and, if needed, direct supplementation with these minerals.
Xenotransplantation (1999)

The success of organ transplantation has led to an ever-increasing shortfall between the demand for organs and the supply. This has led to extensive investigation of the possible use of animals, especially the pig, as organ donors. However, a number of major barriers to successful xenotransplantation exist. These include immunological, physiological, anatomical, infectious and ethical problems. Of the immunological problems, the most immediate is hyperacute rejection of the organ caused by natural cytotoxic antibodies in man directed at the galactose alpha-1,3-galactose antigen present in all mammals except man, old world monkeys and the great apes. It is in this area in which genetic engineering has been applied most assiduously and essentially this problem is solved, at least in theory. However, many other problems remain to be resolved before xenotransplantation is likely to become a clinical reality.
Imaging Human Mesolimbic Dopamine Transmission with Positron Emission Tomography: I. Accuracy and Precision of D2 Receptor Parameter Measurements in Ventral Striatum (2001)

Dopamine transmission in the ventral striatum (VST), a structure which includes the nucleus accumbens, ventral caudate, and ventral putamen, plays a critical role in the pathophysiology of psychotic states and in the reinforcing effects of virtually all drugs of abuse. The aim of this study was to assess the accuracy and precision of measurements of D(2) receptor availability in the VST obtained with positron emission tomography on the high-resolution ECAT EXACT HR+ scanner (Siemens Medical Systems, Knoxville, TN, U.S.A.). A method was developed for identification of the boundaries of the VST on coregistered high-resolution magnetic resonance imaging scans. Specific-to-nonspecific partition coefficient (V(3)") and binding potential (BP) of [(11)C]raclopride were measured twice in 10 subjects, using the bolus plus constant infusion method. [(11)C]Raclopride V(3)" in the VST (1.86 +/- 0.29) was significantly lower than in the dorsal caudate (DCA, 2.33 +/- 0.28) and dorsal putamen (DPU, 2.99 +/- 0.26), an observation consistent with postmortem studies. The reproducibility of V(3)" and BP were appropriate and similar in VST (V(3)" test-retest variability of 8.2% +/- 6.2%, intraclass correlation coefficient = 0.83), DCA (7.7% +/- 5.1%, 0.77), DPU (6.0% +/- 4.1%, 0.71), and striatum as a whole (6.3% +/- 4.1%, 0.78). Partial volume effects analysis revealed that activities in the VST were significantly contaminated by counts spilling over from the adjacent DCA and DPU: 70% +/- 5% of the specific binding measured in the VST originated from D(2) receptors located in the VST, whereas 12% +/- 3% and 18% +/- 3% were contributed by D(2) receptors in the DCA and DPU, respectively. Thus, accuracy of D(2) receptor measurement is improved by correction for partial voluming effects. The demonstration of an appropriate accuracy and precision of D(2) receptor measurement with [(11)C]raclopride in the VST is the first critical step toward the use of this ligand in the study of synaptic dopamine transmission at D(2) receptors in the VST using endogenous competition techniques.
B cell depletion in diffuse progressive systemic sclerosis: safety, skin score modification and IL-6 modulation in an up to thirty-six months follow-up open-label trial (2010)

ISRCTN77554566.
Borverbindungen, XXII1) Darstellung von Pyrrolyl‐(1)‐boranen (1970)

Abstract Alkyl‐pyrrolyl‐(1)‐borane R 3 ‐ n B Pyrrn n 1 und 2 [n=1 bzw. 2; Pyrr auch Indolyl‐(1) und Carbazolyl‐(9); s. Tab. 1, S. 881 gewinnt man durch Aminolyse von Alkyldiboranen bzw. Trialkylboranen sowie durch Reaktion von Chloralkylboranen mit Alkalimetall‐pyrrolen.Die Aminolyse von Triäthyl‐ und Tripropylboran läß sich durch Pivalinsäure‐Derivate beschleunigen. Tripyrrolylboran ( 3 ) entsteht aus Triäthylamin‐boran und Pyrrol. – Von 1 und 2 werden die Molekulargewichte massenspektrometrisch bestimmt und die IR ‐ sowie 1 H‐NMR‐Daten angegeben. ‐ Die Verbindungen 1 bilden i. Vak. mit Pyridinbase unzersetzt destillierbare Addukte, die Pyridin‐dialkyl‐pyrrolylborane 4 (s. Tab. 2, S .89). Aus 4 können Dialkyl‐pyrrolylborane 1 mit Diäthyläther‐BF 3 wieder freigesetzt werden.
A highly pitch scalable 3D vertical gate (VG) NAND flash decoded by a novel self-aligned independently controlled double gate (IDG) string select transistor (SSL) (2012)

Despite vertical stacking, the lateral scaling of 3D NAND Flash is critically important because otherwise >;16 stacking layers are needed to be cost competitive to 20nm 2D NAND. In this work, we propose a 3D vertical gate (VG) NAND using a self-aligned independently controlled double gate (IDG) string select transistor (SSL) decoding method. The IDG SSL provides excellent program inhibit and read selection without any penalty of cell size increase, making our 3D VG NAND cell as scalable as conventional 2D NAND. We present the world's first <; 50nm (37.5nm) half-pitch 3D NAND. The BL decoding and page operation methods are illustrated in detail. This highly pitch scalable VG with IDG SSL approach provides a very cost competitive 3D NAND.
High-speed synthetic aperture microscopy for live cell imaging (2011)

We present a high-speed synthetic aperture microscopy for quantitative phase imaging of live biological cells. We measure 361 complex amplitude images of an object with various directions of illumination covering an NA of 0.8 in less than one-thirteenth of a second and then combine the images with a phase-referencing method to create a synthesized phase image. Because of the increased depth selectivity, artifacts from diffraction that are typically present in coherent imaging are significantly suppressed, and lateral resolution of phase imaging is improved. We use the instrument to demonstrate high-quality phase imaging of live cells, both static and dynamic, and thickness measurements of a nanoscale cholesterol helical ribbon.
Downregulation of cytolytic activity of human effector cells by transgenic expression of human PD-ligand-1 on porcine target cells (2010)

Cellular rejection is a relevant hurdle for successful pig-to-primate xenotransplantation. We have shown previously that the induction of a human anti-pig T cell response (in vitro activation of CD4(+) T cells) can be suppressed by the overexpression of human negative costimulatory ligands (e.g. programmed death receptor ligand, PD-L1) on pig antigen presenting cells. Here, we asked whether PD-L1 mediated enhancement of negative signaling might also be efficient during the effector phase of human anti-pig cellular immune responses. The porcine B-cell line L23 was transfected with human PD-L1, and clones were selected stably expressing PD-L1 with low, medium, or high density. Mock-transfected L23 cells were effectively lysed by human cytotoxic effector cells (IL-2 activated CD8(+) T cells and CD56(+) cells). The lytic potential of the effectors decreased with increasing levels of PD-L1 and was reduced by about 50% in L23-PD-L(high) targets. A proportion of activated CD8(+) effector cells underwent apoptosis when exposed to PD-L1 expressing L23 cells. These data suggest that the overexpression of PD-L1 on target cells may (a) trigger negative signals in effector cells that prevent the release of cytolytic molecules and/or (b) induce apoptosis in the attacking effector cells thereby protecting targets from destruction.
ERK MAP Kinase Links Cytokine Signals to Activation of Latent HIV-1 Infection by Stimulating a Cooperative Interaction of AP-1 and NF-κB (1999)

Human immunodeficiency virus type 1 (HIV-1) can establish latent infection following provirus integration into the host genome. NF-kappaB plays a critical role in activation of HIV-1 gene expression by cytokines and other stimuli, but the signal transduction pathways that regulate the switch from latent to productive infection have not been defined. Here, we show that ERK1/ERK2 mitogen-activated protein kinase (MAPK) plays a central role in linking signals at the cell surface to activation of HIV-1 gene expression in latently infected cells. MAPK was activated by cytokines and phorbol 12-myristate 13-acetate in latently infected U1 cells. The induction of HIV-1 expression by these stimuli was inhibited by PD98059 and U0126, which are specific inhibitors of MAPK activation. Studies using constitutively active MEK or Raf kinase mutants demonstrated that MAPK activates the HIV-1 long terminal repeat (LTR) through the NF-kappaB sites. Most HIV-1 inducers activated NF-kappaB via a MAPK-independent pathway, indicating that activation of NF-kappaB is not sufficient to explain the activation of HIV-1 gene expression by MAPK. In contrast, all of the stimuli activated AP-1 via a MAPK-dependent pathway. NF-kappaB and AP-1 components c-Fos and c-Jun were shown to physically associate by yeast two-hybrid assays and electrophoretic mobility shift assays. Coexpression of NF-kappaB and c-Fos or c-Jun synergistically transactivated the HIV-1 LTR through the NF-kappaB sites. These studies suggest that MAPK acts by stimulating AP-1 and a subsequent physical and functional interaction of AP-1 with NF-kappaB, resulting in a complex that synergistically transactivates the HIV-1 LTR. These results define a mechanism for signal-dependent activation of HIV-1 replication in latently infected cells and suggest potential therapeutic strategies for unmasking latent reservoirs of HIV-1.