gebhart/patrepeval huggingface dataset:
E2a-Pbx1 Induces Aberrant Expression of Tissue-Specific and Developmentally Regulated Genes When Expressed in NIH 3T3 Fibroblasts (1997)

The E2a-Pbx1 oncoprotein contains the transactivation domain of E2a joined to the DNA-binding homeodomain (HD) of Pbx1. In mice, E2a-Pbx1 transforms T lymphoblasts and fibroblasts and blocks myeloblast differentiation. Pbx1 and E2a-Pbx1 bind DNA as heterodimers with other HD proteins whose expression is tissue specific. While the transactivation domain of E2a is required for all forms of transformation, DNA binding by the Pbx1 HD is essential for blocking myeloblast differentiation but dispensable for fibroblast or T-lymphoblast transformation. These properties suggest (i) that E2a-Pbx1 causes cellular transformation by activating gene transcription, (ii) that transcription of E2a-Pbx1 target genes is normally regulated by ubiquitous Pbx proteins and tissue-specific partners, and (iii) that DNA-binding mutants of E2a-Pbx1 activate a subset of all gene targets. To test these predictions, genes induced in NIH 3T3 fibroblasts by E2a-Pbx1 were identified and examined for tissue- and stage-specific expression and their differential abilities to be upregulated by E2a-Pbx1 in NIH 3T3 fibroblasts and myeloblasts and by a DNA-binding mutant of E2a-Pbx1 in NIH 3T3 cells. Of 12 RNAs induced by E2a-Pbx1, 4 encoded known proteins (a J-C region of the immunoglobulin kappa light chain, natriuretic peptide receptor C, mitochondrial fumarase, and the 3',5'-cyclic nucleotide phosphodiesterase, PDE1A) and 5 encoded new proteins related to angiogenin, ion channels, villin, epidermal growth factor repeat proteins, and the human 2.19 gene product. Expression of many of these genes was tissue specific or developmentally regulated, and most were not expressed in fibroblasts, indicating that E2a-Pbx1 can induce ectopic expression of genes associated with lineage-specific differentiation.
Image registration under translation and rotation in two-dimensional planes using Fourier slice theorem (2015)

Image recognition in the presence of both rotation and translation is a longstanding problem in correlation pattern recognition. Use of log polar transform gives a solution to this problem, but at a cost of losing the vital phase information from the image. The main objective of this paper is to develop an algorithm based on Fourier slice theorem for measuring the simultaneous rotation and translation of an object in a 2D plane. The algorithm is applicable for any arbitrary object shift for full 180° rotation.
Segmental Pedicle Screwing for Idiopathic Scoliosis Using Computer-assisted Surgery (2008)

In the navigation group, a tendency to lateral perforation at the concave side and medial perforation at the convex side was noted, like in the control group. Use of the navigation system significantly reduced the screw misplacement rate for rotated vertebrae as compared with the control group. Separate registration is recommended for rotated vertebrae when possible.
Relationship between mevalonate and mitogenesis in human fibroblasts stimulated with platelet-derived growth factor. (1984)

Relationships between mevalonate and DNA synthesis were explored in quiescent human fibroblasts stimulated with human platelet-derived growth factor (PDGF). Studies of others have indicated that mevalonate, or a product of mevalonate other than cholesterol, is essential for DNA replication. The present studies were designed to determine whether there was a critical time in the cell cycle when mevalonate was necessary for later DNA synthesis to occur. Compactin and mevinolin, inhibitors of hydroxymethylglutaryl CoA reductase, were employed to block both the synthesis of mevalonate and of DNA. Compactin inhibited the sharp peak of DNA synthesis which occurs in cells 24 h after PDGF addition in a concentration-dependent manner. This suppression of DNA synthesis was not prevented by low density lipoprotein but was fully reversed by mevalonate. Compactin inhibited DNA synthesis when the inhibitor was present during the time interval 10-20 h after PDGF addition. Its presence only in the interval before 10 h or after 20 h had no effect. Conversely, mevalonate could fully overcome the compactin block in DNA synthesis when present during the period of from 10-20 h after PDGF addition. Mevalonate present only before 10 h or after 20 h had no effect. When mevalonate was added to mevinolin-blocked cells for the interval 10-15 h after PDGF, the mevinolin block of DNA synthesis was 68% overcome; in contrast, only 20% of the reversal of the mevinolin block was seen when mevalonate was added from 15-20 h. Addition of mevalonate for only the 2-h interval of from 10-12 h after PDGF overcame the mevinolin block of DNA synthesis (assayed at 24 h) by 50%. The results show that there is a critical time period, several h before S phase, when PDGF-stimulated cells require mevalonate in order for DNA synthesis to proceed at 24 h. This critical period comprised the interval of approximately 10-20 h after PDGF addition and especially the early part of this interval.
Abstract 4210: Oxidative stress, DNA damage, and apoptosis mediated by arsenic trioxide in lung carcinoma cells (2011)

Abstract Lung cancer is one of the most lethal and common of cancers in the world, causing up to 3 million deaths annually. Arsenic trioxide (ATO) has been used in the treatment of relapsed/refractory acute promyelocytic leukemias. However, its effects on lung cancer are not known. We hypothesize that ATO may also have a bioactivity against lung cancer, and its mechanisms of action may involve apoptosis, DNA damage and changes in stress-related proteins in lung cancer cells. Using lung cancer (A549) cells as test model, mthe effects of ATO were examined by 6-diamidine-2 phenylindole (DAPI) nuclear staining for apoptosis, commet assay for genotoxicity ane western blotanalysis for stress protein (Hsp 70 and cfos) expression. Morphological changes of apoptosis (condensed chromatin and apoptotic bodies) were observed with DAPI and cell shrinkage and membrane blebbing without DAPI at 4 and 6µg/ml of ATO. The comet assay data revealed that DNA damage was significant as indicated by increased of the precent of DNA damage, tailmoment and tail length. There was significant increase in Hsp70 expression and significant decrease in cfos in ATO-treated cells compared to controls. ATO is cytotoxic to lung cancer cells and its toxicity is mediated via oxidative stress and DNA damage leading to apoptosis. However, further studies are warranted to understand its specific molecular mechanisms of toxicity. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4210. doi:10.1158/1538-7445.AM2011-4210
Binding of Pinoline on the 5‐Hydroxytryptamine Transporter: Competitive Interaction with [<sup>3</sup>H] Citalopram (1997)

Pinoline (6-methoxy-1,2,3,4-tetrahydro-beta-carboline) is a naturally occurring compound in the mammalian body which inhibits 5-hydroxytryptamine (5-HT) uptake and exerts antidepressant-like behavioural effects in rats. The present study investigates the effects of pinoline on [3H]citalopram binding to the 5-HT transporter on rat brain. Our experiments revealed that pinoline inhibits [3H]citalopram binding with IC50 1255 +/- 167 nM and Ki 572 +/- 76 nM; Hill coefficient for inhibition was close to 1. In saturation experiments, pinoline co-incubated with [3H]citalopram, increased dose-dependently the Kd value but had no effect on the Bmax value of [3H]citalopram binding. Micromolar concentrations of pinoline did not have influence on the dissociation rate of specifically bound [3H]citalopram. Binding parameters of [3H]citalopram did not differ significantly in cerebral cortex and hippocampus of rats treated for 10 days with pinoline or vehicle. These results indicate that pinoline did not have any modulative influence on the activity of 5-HT transporter and it interacts competitively with citalopram on the substrate recognition site of the 5-HT transporter.
Intraspinal Transplantation of CD34+ Human Umbilical Cord Blood Cells after Spinal Cord Hemisection Injury Improves Functional Recovery in Adult Rats (2004)

The present study was designed to compare the functional outcome of the intraspinal transplantation of CD34+ human umbilical cord blood (CB) cells with that of human bone marrow stromal (BMS) cells in adult rats with spinal cord injury. Sixty adult Wistar rats were subjected to left spinal cord hemisection, and then divided into three groups randomly. The control group received an injection of PBS without cells, while the two other groups of rats received a transplantation of 5 x 10(5) CD34+ CB or BMS cells, respectively. Functional outcome was measured using the modified Tarlov score at days 1, 7, 14, 21, and 28 after transplantation. A statistically significant improvement in functional outcome and survival rate in the experimental groups of rats was observed compared with the control group. Rats that received CD34+ CB cells achieved a better improvement in functional score than those that received BMS cells at days 7 and 14 after transplantation. Histological evaluation revealed that bromodeoxyuridine (BrdU)-labeled CD34+ CB and BMS cells survived and migrated into the injured area. Some of these cells expressed glial fibriliary acidic protein (GFAP) or neuronal nuclear antigen (NeuN). Our data demonstrate for the first time that intraspinal transplantation of human CD34+ CB cells provides benefit in function recovery after spinal cord hemisection in rats and suggest that CD34+ CB cells may be an excellent choice of cells as routine starting material of allogenic and autologous transplantations for the treatment of spinal cord injury.
Prophylactic Pharmacological Treatment of Chronic Daily Headache (2000)

There is a great variety of pharmacological treatments available for chronic daily headache. Only the antidepressants have been extensively studied. Other medications may be used if these fail. Recommendations based on our experience at the Headache Unit of the Montefiore Medical Center are outlined here.
Development of a Direct-Measurement Thin-Film Heat Flux Array (2006)

T-cell activation is a consequence of the clonotypic T-cell antigen receptor (TCR) binding to an antigen followed by signal transduction via the invariant subunits of the TCR/CD3 complex. gamma delta TCR cells are a small subset of T cells that populate both the epithelial and lymphoid tissues and have unique antigen specificity and function. However, the composition of invariant chains within the gamma delta TCR/CD3 complex has not been well characterized. Here we report that, unlike the majority of alpha beta T cell, gamma delta T cells isolated from spleen and intestinal epithelial tissue express high levels of the gamma chain of the high-affinity receptor for IgE (Fc epsilon RI gamma) as one invariant subunit of their TCR/CD3 complex. Fc epsilon RI gamma exists as both a homodimer and a heterodimer associated with the TCR zeta chain. Moreover, stimulation of the gamma delta TCR results in rapid tyrosine phosphorylation of Fc epsilon RI gamma. Our results suggest that utilization of distinct receptor signaling components may enable the coupling of antigen stimulation to the activation of different signal transduction pathways in alpha beta and gamma delta T cells.
Inequivalent classes of interference experiments with non-Abelian anyons (2001)

We present a theoretical analysis of inequivalent classes of interference experiments with non-Abelian anyons using an idealized Mach-Zender-type interferometer. Because of the non-Abelian nature of the braid group action one has to distinguish the different possibilities in which the experiment can be repeated, which lead to different interference patterns. We show that each setup will, after repeated measurement, lead to a situation where the two-particle (or multiparticle) state gets locked into an eigenstate of some well-defined operator. Also, the probability to end up in such an eigenstate is calculated. Some representative examples are worked out in detail.
Stable porphyrin Zr and Hf metal–organic frameworks featuring 2.5 nm cages: high surface areas, SCSC transformations and catalyses (2015)

Two isostructural porphyrin Zr and Hf metal-organic frameworks (<b>FJI-H6</b> and <b>FJI-H7</b>) are rationally synthesized, and are constructed from 2.5 nm cubic cages. Notably, they both possess high water and chemical stability and can undergo single-crystal to single-crystal transformations to embed Cu<sup>2+</sup> ions into the open porphyrin rings. <b>FJI-H6</b> has a high BET surface area of 5033 m<sup>2</sup> g<sup>-1</sup>. Additionally, they exhibit promising catalytic abilities to convert CO<sub>2</sub> and epoxides into cyclic carbonates at ambient conditions.
Gentamicin Dosing Errors With Four Commonly Used Nomograms (1982)

Four methods for calculating gentamicin sulfate dosage requirements were evaluated in 96 patients and compared with an individualized method. The pharmacokinetic parameters of gentamicin were determined from serum concentration time data and used to calculate individualized dosage regimens. Doses were determined in each patient using the "predictive methods" (Sarubbi-Hull, Dettli, "rule of eights," and Chan). Resultant serum concentrations were calculated from doses arrived at by each method. These dosing methods resulted in a large proportion of patients with subtherapeutic or potentially toxic concentrations, or both. The Dettli and Chan methods produced therapeutic concentrations in more patients than the Sarubbi-Hull and rule of eights methods. Desired therapeutic concentrations were attained in significantly more patients with the individualized method than with the predictive methods, and, in addition, larger doses were required. The use of predictive dosage methods should be followed with serum concentration determinations and dosage adjustment to ensure therapeutic concentrations early in treatment.
Enhanced Green Fluorescent Protein as an Efficient Reporter Gene for Retroviral Transduction of Human Multipotent Lymphoid Precursors (1998)

Owing to its autofluorescence properties, green fluorescent protein (GFP) has aroused increasing interest as a marker system for many research applications. In this study we investigated the suitability of the "enhanced" GFP (EGFP), a mutant version of GFP optimized for flow cytometry and microscopy detection, as a reporter gene for retroviral transduction protocols. EGFP was shown to display a bright and stably maintained emission pattern in transfected GP+envAm12 packaging cells. Stable fluorescent emission was observed as well after transduction in NIH 3T3 fibroblasts and in the human Jurkat T cell line, in which EGFP was shown to confer no deleterious effect or growth disadvantage on the expressing cells. Moreover, EGFP expression could be detected after short-term retroviral exposure, thus allowing a rapid and quantitative retroviral titering assay, alternative to the standard colony-formation procedure. Most importantly, we showed the feasibility of EGFP as a marker gene in retroviral-mediated transduction of primary lymphoid precursors. In particular, transduction of CD34+CD1- human thymocytes by short-term cocultivation yielded up to 30% of EGFP-expressing cells, while maintaining CD34 expression levels. Finally, when cultured under multicytokine-supported conditions, such transduced intrathymic progenitors were shown to efficiently generate lymphoid-related dendritic cells, which displayed a distinct EGFP expression. Therefore, because of its rapid and easy detectability and its nontoxic characteristics, EGFP proves itself to be a valuable reporter gene by allowing the transduction of multipotential progenitors and by being compatible with the developmental programs of lymphoid lineage generation.
Synthesis of folded pipelined architectures for multirate DSP algorithms (1998)

In this paper we formalize a novel multirate folding transformation which is a tool used to systematically synthesize control circuits for pipelined VLSI architectures which implement multirate algorithms. Although multirate algorithms contain decimators and expanders which change the effective sample rate of a discrete-time signal, multirate folding time-multiplexes the multirate algorithm to hardware in such a manner that the resulting synchronous architecture requires only a single-clock signal. Multirate folding equations are derived and these equations are used to address two related issues. The first issue is memory requirements in folded architectures. We derive expressions for the minimum number of registers required by a folded architecture which implements a multirate algorithm. The second issue is retiming. Based on the noble identities of multirate signal processing, we derive retiming for folding constraints which indicate how a multirate data-flow graph must be retimed for a given schedule to be feasible. The techniques introduced in this paper can be used to synthesize architectures for a wide variety of digital signal processing applications which are based on multirate algorithms, such as signal analysis and coding based on subband decompositions and wavelet transforms.
Vaccines and Therapeutics Against Hantaviruses (2020)

Hantaviruses (HVs) are rodent-transmitted viruses that can cause hantavirus cardiopulmonary syndrome (HCPS) in the Americas and hemorrhagic fever with renal syndrome (HFRS) in Eurasia. Together, these viruses have annually caused approximately 200,000 human infections worldwide in recent years, with a case fatality rate of 5-15% for HFRS and up to 40% for HCPS. There is currently no effective treatment available for either HFRS or HCPS. Only whole virus inactivated vaccines against HTNV or SEOV are licensed for use in the Republic of Korea and China, but the protective efficacies of these vaccines are uncertain. To a large extent, the immune correlates of protection against hantavirus are not known. In this review, we summarized the epidemiology, virology, and pathogenesis of four HFRS-causing viruses, HTNV, SEOV, PUUV, and DOBV, and two HCPS-causing viruses, ANDV and SNV, and then discussed the existing knowledge on vaccines and therapeutics against these diseases. We think that this information will shed light on the rational development of new vaccines and treatments.
Improving Hydraulic Fracturing of Shale Formations by Acidizing (2013)

Abstract Acidizing as a stimulation technique does not always yield the desired sustainable conductivity especially compared to hydraulic fracturing. In addition to that, hydraulic fracturing provides a great contact with shale formations due to its deeper developed conductivity that is sustained by the existence of proppant. However, hydraulic fracture conductivity declines because of a variety of reasons: increasing effective stress, proppant fatigue due to stress cycling, and digenesis. Here, we studied the potential of combining the benefits of propped hydraulic fracturing and acidizing by introducing low concentrations of acid slugs in the hydraulic fracture treatment of shale formations. The acid slugs intended to improve the micro-fracture conductivity deep in the formation and near the wellbore. Experiments using low concentrations of HCl (up to 3 wt% active HCl) showed a great enhancement in oil recovery factors and shale porosity. The treatment was carried out at 200°F. Furthermore, the effect of the HCl treatment on samples from Mancos, Eagle Ford, Barnett, and Marcellus shale formations was examined. The samples used were 2.54-3.81 cm in diameter and 0.76-5.08 cm in length. The porosity measurements on the cores before the treatment range from 0.23-7.7% versus 0.2-35.8% after the treatment. Spontaneous imbibitions showed recovery factors of 2.5-13% from non-treated samples against 4-53% from the treated samples. The treated samples were saturated with more oil compared to the non-treated samples due to the improvement in porosity and permeability by the acid treatment. CT scan images also have been taken for the samples pre and post the acid treatments to show the effect of the treatment on the porosity and cracks distribution along the cores. Our study clearly demonstrates that injecting slugs of low concentrations of HCl near and away from the wellbore adds permanent improved conductivity to hydraulic fracturing that is resulted from the partial dissolution of calcite.
428. The chemistry of bacteria. Part V. Some acylindoles (1957)

J. A. Ballantine, C. B. Barrett, R. J. S. Beer, B. G. Boggiano, S. Eardley, B. E. Jennings and A. Robertson, J. Chem. Soc., 1957, 2227 DOI: 10.1039/JR9570002227
GCN4 protein, a positive transcription factor in yeast, binds general control promoters at all 5' TGACTC 3' sequences. (1986)

The GCN4 gene is required for the general amino acid control derepression response in yeast. GCN4 protein protects a repeated sequence motif in the 5'-untranslated region of HIS4, HIS3, ILV1, and ILV2 genes subject to general control. At low concentrations of GCN4, only certain repeats in these genes are bound. The repeats differ slightly from the 5' TGACTC 3' consensus core sequence, and the selective binding of some sites at low GCN4 concentrations is related to the relative affinity of these sites to GCN4. Using purified GCN4 protein obtained from an overproducing strain of Escherichia coli, we were able to obtain complete protection of all of the repeat elements in these four genes at high GCN4 concentrations. Analysis of the relative binding constant to the 15 repeated sequences protected by GCN4 shows that the optimal binding site for GCN4 is 5' RRTGACTC 3' followed by a short stretch of thymidines. Another protein, present mostly in yeast nuclear extracts, binds to the HIS4 promoter at a site overlapping one of the GCN4 binding sites. This protein is displaced from its binding site at high GCN4 concentrations.
Cyclization and Self-Organization in Polymerization of Trialkoxysilanes (2001)

Sol−gel polymerization of organotrialkoxysilanes RSi(OR‘)3 and formation of silsesquioxane (SSQO) structures was followed using SEC, 29Si NMR, and both small- and wide-angle X-ray scattering. Evolution of the SSQO structure is controlled by the competition between intermolecular polycondensation and cyclization. A strong tendency to buildup of polyhedral cyclic oligomersmainly octamer “cages” and larger cagelike structureswas found to grow with increasing size of substituent R. As a result, long substituents prevent gelation of the trifunctional system and increase stability of the SSQO. Because of incompatibility of the polyhedral SSQO framework and pendant organic chains, microphase separation takes place and spontaneous self-organization occurs. A micellar arrangement of compact SSQO domains with a correlation distance corresponding to the size of the substituent is formed, and the ordering is promoted by increasing length of the organic chain. The most organized arrangement was observed with the trialkoxysilanes substituted with long PEO chains which crystallize and force the SSQO cages to align in the lamellar structure.