gebhart/patrepeval huggingface dataset:
The effect of viral regulatory protein expression on gene delivery by human immunodeficiency virus type 1 vectors produced in stable packaging cell lines (1997)

We describe the generation of stable human immunodeficiency virus type 1 (HIV-1)-packaging lines that constitutively express high levels of HIV-1 structural proteins in either a Rev-dependent or a Rev-independent fashion. These cell lines were used to assess gene transfer by using an HIV-1 vector expressing the hygromycin B resistance gene and to study the effects of Rev, Tat, and Nef on the vector titer. The Rev-independent cell lines were created by using gag-pol and env expression vectors that contain the Mason-Pfizer monkey virus (MPMV) constitutive transport element (CTE). Vector titers approaching 10(4) CFU/ml were routinely obtained with these cell lines, as well as with the Rev-dependent cell lines, with HeLa-CD4 cells as targets. The presence of Nef and Tat in the producer cell each increased the vector titer 5- to 10-fold. Rev, on the other hand, was absolutely essential for gene transfer, unless the MPMV CTE was present in the vector. In that case, by using the Rev-independent cell lines for packaging, Rev could be completely eliminated from the system without a reduction in vector titer.
Cytosol-to-lysosome Transport of Free Polymannose-type Oligosaccharides (1999)

In hepatocellular carcinoma HepG2 cells, free polymannose-type oligosaccharides appearing in the cytosol during the biosynthesis and quality control of glycoproteins are rapidly translocated into lysosomes by an as yet poorly defined process (Saint-Pol, A., Bauvy, C., Codogno, P., and Moore, S. E. H. (1997) J. Cell Biol. 136, 45-59). Here, we demonstrate an ATP-dependent association of [2-3H]mannose-labeled Man5GlcNAc with isolated rat liver lysosomes. This association was only observed in the presence of swainsonine, a mannosidase inhibitor, which was required for the protection of sedimentable, but not nonsedimentable, Man5GlcNAc from degradation, indicating that oligosaccharides were transported into lysosomes. Saturable high affinity transport (Kuptake, 22.3 microM, Vmax, 7.1 fmol/min/unit of beta-hexosaminidase) was dependent upon the hydrolysis of ATP but independent of vacuolar H+/ATPase activity. Transport was inhibited strongly by NEM and weakly by vanadate but not by sodium azide, and, in addition, the sugar transport inhibitors phloretin, phloridzin, and cytochalasin B were without effect on transport. Oligosaccharide import did not show absolute specificity but was selective toward partially demannosylated and dephosphorylated oligosaccharides, and, furthermore, inhibition studies revealed that the free reducing GlcNAc residue of the oligosaccharide was of critical importance for its interaction with the transporter. These results demonstrate the presence of a novel lysosomal free oligosaccharide transporter that must work in concert with cytosolic hydrolases in order to clear the cytosol of endoplasmic reticulum-generated free oligosaccharides.
Effects of H2O on Atomic Hydrogen Generation in Hydrogen Plasma (1993)

The effects of water vapor added to hydrogen plasma were investigated by measuring the relative concentrations of hydrogen atoms in the plasma and in the downstream. The added water vapor increased the concentration of hydrogen atoms in the downstream to an amount 80 times greater than that without addition of water vapor. The relative concentration of hydrogen atoms generated from water-vapor-added hydrogen gas was only slightly decreased in the downstream. To clarify the role of water vapor, we examined the behavior of oxygen atoms and OH radicals. As a result, it was revealed that water vapor passivated the quartz surface and the recombination of hydrogen atoms was prevented.
Joint profiling of DNA and proteins in single cells to dissect genotype-phenotype associations in leukemia (2021)

Studies of acute myeloid leukemia rely on DNA sequencing and immunophenotyping by flow cytometry as primary tools for disease characterization. However, leukemia tumor heterogeneity complicates integration of DNA variants and immunophenotypes from separate measurements. Here we introduce DAb-seq, a technology for simultaneous capture of DNA genotype and cell surface phenotype from single cells at high throughput, enabling direct profiling of proteogenomic states in tens of thousands of cells. To demonstrate the approach, we analyze the disease of three patients with leukemia over multiple treatment timepoints and disease recurrences. We observe complex genotype-phenotype dynamics that illustrate the subtlety of the disease process and the degree of incongruity between blast cell genotype and phenotype in different clinical scenarios. Our results highlight the importance of combined single-cell DNA and protein measurements to fully characterize the heterogeneity of leukemia.
Effect of rapid eye movement-related obstructive sleep apnea on adherence to continuous positive airway pressure (2018)

Objective Rapid eye movement (REM)-related obstructive sleep apnea (OSA) is characterized by respiratory events such as apnea and hypopnea predominately or exclusively during REM sleep. Several studies have revealed clinical predictors of adherence to the use of continuous positive airway pressure (CPAP). However, the effect of REM-related OSA on adherence to CPAP use remains unclear. Therefore, we investigated the effects of REM-related OSA on adherence to CPAP use 6 months after treatment initiation. Methods We enrolled 161 patients in this study and divided them into 3 groups: the good adherence, poor adherence, and dropout groups. We compared polysomnographic data and clinical findings, including those regarding morbidity of REM-related OSA, among the three groups to identify predictors of adherence to CPAP use. Results None of the 43 patients in the good adherence group had REM-related OSA. Multivariate logistic regression analysis of the good adherence and dropout groups indicated that REM-related OSA was the only factor associated with adherence to CPAP use (odds ratio, 41.984; 95% confidence interval, 2.257-781.007). Conclusions REM-related OSA is a reliable risk factor for dropout from CPAP therapy.
BH3-only protein Bik is involved in both apoptosis induction and sensitivity to oxidative stress in multiple myeloma (2010)

ours results suggest that Bik has a role in both, apoptosis induction and sensitivity to oxidative stress in myeloma cells. Small BH3 mimetic molecules should be considered for further apoptosis-based therapy in myeloma cells expressing endogenous Bik/Bcl-2 complexes.
Two Steps Forward, One Step Back- Or Vice Versa: Labor Rights Under Free Trade Agreements from NAFTA, Through Jordan, via Chile, to Latin America, and Beyond (2002)

The U.S.-Jordan agreement, in turn, has provided a model for U.S. trade promotion authority ("TPA") legislation. It links free trade and labor rights as a condition of limiting legislative procedure in consideration of a trade agreement to an up or down "fast-track" vote without possibility of amendment."I Pursuant to the Bipartisan Trade Promotion Authority Act ("BTPAA"), sub regional and regional free trade agreements are under negotiation in addition to the bilateral agreements just mentioned.
Total Synthesis and Stereochemistry of Uncialamycin (2007)

Die Geheimnisse des Uncialamycins entschlüsselt: Die Totalsynthese der C26-Epimere der kürzlich entdeckten Endiin-Naturstoffe ermöglicht die stereochemische Zuordnung und weitere Untersuchungen dieses hoch wirksamen Antibiotikums. Schlüsselschritte sind die Addition einer Acetylid- an eine Pyridiniumspezies, die intramolekulare Endiinbildung und eine Hauser-Anellierung zum Aufbau der Anthrachinoneinheit.
Homology-Dependent Maternal Inhibition of Developmental Excision of Internal Eliminated Sequences in Paramecium tetraurelia (1998)

Thousands of single-copy internal eliminated sequences (IESs) are excised from the germ line genome of ciliates during development of the polygenomic somatic macronucleus, following sexual events. Paramecium IESs are short, noncoding elements that frequently interrupt coding sequences. No absolutely conserved sequence element, other than flanking 5'-TA-3' direct repeats, has been identified among sequenced IESs; the mechanisms of their specific recognition and precise elimination are unknown. Previous work has revealed the existence of an epigenetic control of excision. It was shown that the presence of one IES in the vegetative macronucleus results in a specific inhibition of the excision of the same element during the development of a new macronucleus, in the following sexual generation. We have assessed the generality and sequence specificity of this transnuclear maternal control by studying the effects of macronuclear transformation with 13 different IESs. We show that at least five of them can be maintained in the new macronuclear genome; sequence specificity is complete both between genes and between different IESs in the same gene. In all cases, the degree of excision inhibition correlates with the copy number of the maternal IES, but each IES shows a characteristic inhibition efficiency. Short internal IES-like segments were found to be excised from two of the IESs when excision between normal boundaries was inhibited. Available data suggest that the sequence specificity of these maternal effects is mediated by pairing interactions between homologous nucleic acids.
<title>Chemically amplified resist process for 0.25-um-generation photomasks</title> (1996)

A chemically amplified negative electron beam resist process is developed for fabricating 0.25 micrometers devices 4X magnification reticles. In order to improve a critical dimension (CD) uniformity on reticles, a precise temperature controllability in post exposure baking is realized. Dry etching for Cr is also adopted for getting an appropriate pattern fidelity down to submicron on reticles to meet requirements for such an optical proximity effect correction. Under the optimized process conditions, a CD uniformity of 16 nm in 3 (sigma) is achieved on reticles. A CD linearity of down to 0.8 micrometers on the reticles is ensured as well. Actual 0.25 micrometers device reticle production results show that the CD mean variation is controlled within +/- 43 nm. It is confirmed that an advanced 4X reticle fabrication process for 0.25 micrometers device generation is realized.
Early investigational drugs targeting PPAR-α for the treatment of metabolic disease (2015)

There is still a need for new drugs to treat atherogenic dyslipidemia. The highly potent and selective PPAR-α agonist K-877 has shown beneficial effects on atherogenic dyslipidemia and absence of some adverse effects seen with fibrates. The dual PPAR-α/PPAR-δ agonist GFT-505 has shown favorable results in improving atherogenic dyslipidemia and insulin resistance and appears to be a potential candidate for the treatment of NAFLD. Long-term trials are needed to assess the safety and efficacy of these new agents for cardiovascular and liver outcomes.
Okapi at TREC (1994)

City submitted two runs each for the automatic ad hoc, very large collection track, automatic routing and Chinese track; and took part in the interactive and filtering tracks. The method used was : expansion using terms from the top documents retrieved by a pilot search on topic terms. Additional runs seem to show that we would have done better without expansion. Twor runs using the method of city96al were also submitted for the Very Large Collection track. The training database and its relevant documents were partitioned into three parts. Working on a pool of terms extracted from the relevant documents for one partition, an iterative procedure added or removed terms and/or varied their weights. After each change in query content or term weights a score was calculated by using the current query to search a second protion of the training database and evaluating the results against the corresponding set of relevant documents. Methods were compared by evaluating queries predictively against the third training partition. Queries from different methods were then merged and the results evaluated in the same way. Two runs were submitted, one based on character searching and the other on words or phrases. Much of the work involved investigating plausible methods of applying Okapi-style weighting to phrases
Principles of Explanatory Debugging to Personalize Interactive Machine Learning (2015)

How can end users efficiently influence the predictions that machine learning systems make on their behalf? This paper presents Explanatory Debugging, an approach in which the system explains to users how it made each of its predictions, and the user then explains any necessary corrections back to the learning system. We present the principles underlying this approach and a prototype instantiating it. An empirical evaluation shows that Explanatory Debugging increased participants' understanding of the learning system by 52% and allowed participants to correct its mistakes up to twice as efficiently as participants using a traditional learning system.
3-(4-Aroyl-1-methyl-1H-2-pyrrolyl)-N-hydroxy-2-propenamides as a New Class of Synthetic Histone Deacetylase Inhibitors. 2. Effect of Pyrrole-C2 and/or -C4 Substitutions on Biological Activity (2004)

Previous SAR studies (Part 1: Mai, A.; et al. J. Med. Chem. 2003, 46, 512-524) performed on some portions (pyrrole-C4, pyrrole-N1, and hydroxamate group) of 3-(4-benzoyl-1-methyl-1H-pyrrol-2-yl)-N-hydroxy-2-propenamide (1a) highlighted its 4-phenylacetyl (1b) and 4-cynnamoyl (1c) analogues as more potent compounds in inhibiting maize HD2 activity in vitro. In the present paper, we investigated the effect on anti-HD2 activity of chemical substitutions performed on the pyrrole-C2 ethene chains of 1a-c, which were replaced with methylene, ethylene, substituted ethene, and 1,3-butadiene chains (compounds 2). Biological results clearly indicated the unsubstituted ethene chain as the best structural motif to get the highest HDAC inhibitory activity, the sole exception to this rule being the introduction of the 1,3-butadienyl moiety into the 1a chemical structure (IC50(2f) = 0.77 microM; IC50(1a) = 3.8 microM). IC50 values of compounds 3, prepared as 1b homologues, revealed that between benzene and carbonyl groups at the pyrrole-C(4) position a hydrocarbon spacer length ranging from two to five methylenes is well accepted by the APHA template, being that 3a (two methylenes) and 3d (five methylenes) are more potent (2.3- and 1.4-fold, respectively) than 1b, while the introduction of a higher number of methylene units (see 3e,f) decreased the inhibitory activities of the derivatives. Particularly, 3a (IC50 = 0.043 microM) showed the same potency as SAHA in inhibiting HD2 in vitro, and it was 3000- and 2.6-fold more potent than sodium valproate and HC-toxin and was 4.3- and 6-fold less potent than trapoxin and TSA, respectively. Finally, conformationally constrained forms of 1b,c (compounds 4), prepared with the aim to obtain some information potentially useful for a future 3D-QSAR study, showed the same (4a,b) or higher (4c,d) HD2 inhibiting activities in comparison with those of the reference drugs. Molecular modeling and docking calculations on the designed compounds performed in parallel with the chemistry work fully supported the synthetic effort and gave insights into the binding mode of the more flexible APHA derivatives (i.e., 3a). Despite the difference of potency between 1b and 3a in the enzyme assay, the two APHA derivatives showed similar antiproliferative and cytodifferentiating activities in vivo on Friends MEL cells, being that 3a is more potent than 1b in the differentiation assay only at the highest tested dose (48 microM).
Oriented single-crystal diamond cones and their arrays (2003)

One of the major problems in material science has been the difficulty in modification of the most endurable material, diamond, due to its extreme hardness and chemical inertness. Here, we report the development of a conical structure of diamond by performing bias-assisted reactive ion etching in hydrogen plasma. The diamond cones produced by this method are uniformly distributed over large areas on silicon substrates. Each cone was identified to be a single crystal with an apical angle as small as 28° and a very sharp tip (tip radii ∼2 nm). Their [001] axes are perpendicular to the substrate surface and parallel to each other. Such striking structures of individual single-crystal diamond cones and their arrays, in addition to their scientific value, may lead to a breakthrough in the design of high-performance mechanical and electronic devices.
RNA editing of a miRNA precursor: FIGURE 1. (2004)

Micro RNAs comprise a large family of small, functional RNAs with important roles in the regulation of protein coding genes in animals and plants. Here we show that human and mouse miRNA22 precursor molecules are subject to posttranscriptional modification by A-to-I RNA editing in vivo. The observed editing events are predicted to have significant implications for the biogenesis and function of miRNA22 and might point toward a more general role for RNA editing in the regulation of miRNA gene expression.
TRP channel–associated factors are a novel protein family that regulates TRPM8 trafficking and activity (2015)

TRPM8 is a cold sensor that is highly expressed in the prostate as well as in other non-temperature-sensing organs, and is regulated by downstream receptor-activated signaling pathways. However, little is known about the intracellular proteins necessary for channel function. Here, we identify two previously unknown proteins, which we have named "TRP channel-associated factors" (TCAFs), as new TRPM8 partner proteins, and we demonstrate that they are necessary for channel function. TCAF1 and TCAF2 both bind to the TRPM8 channel and promote its trafficking to the cell surface. However, they exert opposing effects on TRPM8 gating properties. Functional interaction of TCAF1/TRPM8 also leads to a reduction in both the speed and directionality of migration of prostate cancer cells, which is consistent with an observed loss of expression of TCAF1 in metastatic human specimens, whereas TCAF2 promotes migration. The identification of TCAFs introduces a novel mechanism for modulation of TRPM8 channel activity.
Molecular cloning of human CREB-2: an ATF/CREB transcription factor that can negatively regulate transcription from the cAMP response element. (1992)

The cAMP response element (CRE) is an octanucleotide motif (TGACGTCA) that mediates diverse transcriptional regulatory effects. In this report we describe the isolation and characterization of a full-length cDNA that encodes a CRE binding protein called CREB-2. Like other ATF/CREB transcription factors, the 351-amino acid CREB-2 protein contains a COOH-terminal leucine-zipper motif and an adjacent basic domain. CREB-2 mRNA is expressed ubiquitously in human tumor cell lines and mouse organs suggesting that it is involved in regulating transcription in a wide variety of cell types. Overexpression of CREB-2 resulted in a consistent and significant repression of CRE-dependent transcription in CV-1 cells. Deletional analyses localized the transcriptional repressor activity of CREB-2 to a 102-amino acid COOH-terminal region (amino acids 249-351) that contains the leucine-zipper and basic domains of the molecule. These results demonstrate that CRE-dependent transcription can be both positively and negatively regulated by structurally related members of the ATF/CREB family.
Temporal data management (1999)

A wide range of database applications manage time-varying information. Existing database technology currently provides little support for managing such data. The research area of temporal databases has made important contributions in characterizing the semantics of such information and in providing expressive and efficient means to model, store, and query temporal data. This paper introduces the reader to temporal data management, surveys stale-of-the-art solutions to challenging aspects of temporal data management, and points to research directions.
Structure of the ternary signaling complex of a TGF-β superfamily member (2006)

The crystal structure of the complete signaling complex formed between bone morphogenetic protein 2 (BMP-2) and the extracellular domains (ECDs) of its type I receptor [bone morphogenetic protein receptor type Ia (BMPR-Ia)-ECD] and its type II receptor [activin receptor type II (ActRII)-ECD] shows two fundamental structural constraints for receptor assembly. First, the homodimeric BMP-2 ligand assembles two pairs of each receptor symmetrically, where each of the receptor ECDs does not make physical contact. Therefore, conformational communication between receptor ECDs, if any, should be propagated through the central ligand. Second, the type I and II receptor interfaces of the complex, when compared with those of binary complexes such as BMP-2/BMPR Ia-ECD, BMP-7/ActRII-ECD, and activin/ActRIIb-ECD, respectively, show there are common sets of positions repeatedly used by both ligands and receptors. Therefore, specificity-determining amino acid differences at the receptor interfaces should also account for the disparity in affinity of individual receptors for different ligand subunits. We find that a specific mutation to BMP-2 increases its affinity to ActRII-ECD by 5-fold. These results together establish that the specific signaling output is largely determined by two variables, the ligand-receptor pair identity and the mode of cooperative assembly of relevant receptors governed by the ligand flexibility in a membrane-restricted manner.
Vasculogenesis and Angiogenesis: Molecular and Cellular Controls (2003)

Angiogenesis characterizes embryonic development, but also occurs in adulthood in physiological situations such as adaptation to muscle exercise, and in pathological conditions like cancer. Major advances have been made in understanding the molecular mechanisms responsible for vasculogenesis and angiogenesis, largely due to the use of "knock-out mice", i.e. mice in which the gene coding for the protein under investigation has been inactivated. Interestingly, the same growth factors and their receptors are equally involved in the different aspects of vasculogenesis and angiogenesis during development and in adulthood. This review aims to describe in detail their respective roles and how interactions between them lead to a newly formed vessel.
An Augmented Lagrangian Method for Total Variation Video Restoration (2011)

This paper presents a fast algorithm for restoring video sequences. The proposed algorithm, as opposed to existing methods, does not consider video restoration as a sequence of image restoration problems. Rather, it treats a video sequence as a space-time volume and poses a space-time total variation regularization to enhance the smoothness of the solution. The optimization problem is solved by transforming the original unconstrained minimization problem to an equivalent constrained minimization problem. An augmented Lagrangian method is used to handle the constraints, and an alternating direction method is used to iteratively find solutions to the subproblems. The proposed algorithm has a wide range of applications, including video deblurring and denoising, video disparity refinement, and hot-air turbulence effect reduction.