gebhart/patrepeval huggingface dataset:
Direct correlation between a negative autoregulatory response element at the cap site of the herpes simplex virus type 1 IE175 (alpha 4) promoter and a specific binding site for the IE175 (ICP4) protein (1988)

In transient-expression assays, the IE175 (alpha 4) promoter region of herpes simple virus is down-regulated after cotransfection with DNA encoding its own protein product (IE175 or ICP4). The inhibition by IE175 proved to be highly specific for its own promoter region and did not act on either the herpes simplex virus type 1 IE110 (alpha 0) or human cytomegalovirus major immediate-early promoters. Furthermore, the inhibition was still exhibited by IE175 effector plasmids driven by strong heterologous promoters and therefore must be a direct autoregulatory response that cannot be explained by promoter competition effects. In gel mobility retardation assays with infected-cell nuclear extracts, a prominent and specific DNA-protein complex was formed with DNA fragments containing sequences from -108 to +30 in the IE175 promoter region. This activity was not present in mock-infected samples. Even stronger binding occurred with a fragment containing sequences from -128 to +120 in the IE110 promoter, but this second locus was not associated with any detectable response phenotype in cotransfection assays. Supershift experiments with an anti-IE175 monoclonal antibody confirmed the presence of the IE175 protein in both DNA-protein complexes. In the IE175 promoter, specific binding correlated closely with the presence of an intact autoregulatory signal near the cap site as judged by the loss of both activities in a 3'-deleted promoter fragment lacking sequences from -7 to +30. Insertion of a cloned 30-mer synthetic oligonucleotide sequence from positions -8 to +18 in IE175 restored both IE175 binding activity and the down-regulation phenotype. Direct shift-up assays with a similar 30-base-pair (bp) oligonucleotide containing 21 bp from positions -75 to -55 of IE110 (which encompasses a consensus ATCGTC motif) also produced a specific DNA-protein complex containing the IE175 protein. This ATCGTC motif proved to be a necessary component of both the IE110 and IE175 binding sites, but was insufficient on its own for complex formation. Finally, deletion of 2 bp from positions -3 and -4 within the ATCGTC sequence in the IE175 cap site region abolished both binding activity and the IE175-dependent autoregulation phenotype.
Introduction to Macroergonomics (2000)

The origin and development of macroergonomics as an identifiable sub-discipline of human factors/ergonomics is reviewed. The concept of macroergonomics, including the underlying empirically developed sociotechnical systems model, is summarized. The relation of macro-to micro-ergonomics, and the synergism that is possible when the two are harmonized and consistent with the organization's sociotechnical characteristics, is explained.
Acetylation of Nuclear Hormone Receptor-Interacting Protein RIP140 Regulates Binding of the Transcriptional Corepressor CtBP (2001)

CtBP (carboxyl-terminal binding protein) participates in regulating cellular development and differentiation by associating with a diverse array of transcriptional repressors. Most of these interactions occur through a consensus CtBP-binding motif, PXDLS, in the repressor proteins. We previously showed that the CtBP-binding motif in E1A is flanked by a Lys residue and suggested that acetylation of this residue by the p300/CBP-associated factor P/CAF disrupts the CtBP interaction. In this study, we show that the interaction between CtBP and the nuclear hormone receptor corepressor RIP140 is regulated similarly, in this case by p300/CBP itself. CtBP was shown to interact with RIP140 in vitro and in vivo through a sequence, PIDLSCK, in the amino-terminal third of the RIP140 protein. Acetylation of the Lys residue in this motif, demonstrated in vivo by using an acetylated RIP140-specific antibody, dramatically reduced CtBP binding. Mutation of the Lys residue to Gln resulted in a decrease in CtBP binding in vivo and a loss of transcriptional repression. We suggest that p300/CBP-mediated acetylation disrupts the RIP140-CtBP complex and derepresses nuclear hormone receptor-regulated genes. Disruption of repressor-CtBP interactions by acetylation may be a general mode of gene activation.
Balloon angioplasty enhances the expression of angiotensin II AT1 receptors in neointima of rat aorta. (1992)

Angiotensin II is a vasoactive peptide and may act as a growth factor in vascular smooth muscle cells. Experimental injury of the rat aorta causes rapid migration of medial smooth muscle cells and their proliferation resulting in the formation of neointima. We have examined, using quantitative autoradiography, the expression of angiotensin II receptor subtypes AT1 and AT2, and angiotensin-converting enzyme, in the neointima formed in the rat thoracic aorta 15 d after balloon-catheter injury. In contrast to the normal aortic wall, which contained both AT1 and AT2 receptors (80% and 20%, respectively), neointimal cells expressed almost exclusively angiotensin II AT1 receptors. The apparent number of these receptors was fourfold higher in the neointima compared to that in the normal aortic wall. The affinities of the neointimal receptors to angiotensin II or to the AT1 receptor antagonist, losartan, were not different from those in the normal aortic wall. Angiotensin-converting enzyme binding in the neointima was not different from that in the media of the uninjured aorta. Our data suggest that angiotensin II AT1 receptors may have a significant role in injury-induced vascular smooth muscle proliferation and migration.
Correlation of TACC3, FGFR3, MMSET and p21 expression with the t(4;14)(p16·3;q32) in multiple myeloma (2004)

The t(4;14)(p16;q32) translocation seen in c. 18% of newly diagnosed multiple myeloma (MM) cases, results in FGFR3 activation and creation of an IGH/MMSET fusion transcript. We have recently shown that FGFR3 is activated in only 75% of t(4;14)(+) cases, suggesting that alternative genes near the breakpoint may be involved in the transforming event. The gene, TACC3, located just 50 kb telomeric of FGFR3, with transforming capacity, therefore represented a candidate gene. Using a real-time quantitative polymerase chain reaction-based approach on a cohort of 54 patients, we found a statistically significant, twofold increase in TACC3 expression in t(4;14)(+) cases. TACC3, MMSET and p21 values were positively correlated in all cases and, of particular interest, six patient samples [three t(4;14)(-), three t(4;14)(+)] samples showed a joint up-regulation of TACC3, MMSET and p21. Although a poor prognosis is linked with elevated MMSET expression, an extended follow-up period will be required to evaluate the significance of elevated TACC3 and p21 expression in this subgroup of MM.
Replication of the B19 Parvovirus in Human Bone Marrow Cell Cultures (1986)

The B19 parvovirus is responsible for at least three human diseases. The virus was successfully propagated in suspension cultures of human erythroid bone marrow from patients with hemolytic anemias; release of newly synthesized virus into the supernatants of infected cultures was observed. This culture system allowed study at a molecular level of events associated with the B19 life cycle. The B19 parvovirus replicated through high molecular weight intermediate forms, linked through a terminal hairpin structure. B19 replication in vitro was highly dependent on the erythropoietic content of cultures and on addition of the hormone erythropoietin.
Cardiolipin content in P19 embryonal carcinoma cells (2014)

Dissertação de mestrado em Bioquímica, apresentada ao Departamento de Ciências da Vida da Faculdade de Ciências e Tecnologia da Universidade de Coimbra
Inversion of Lipase Stereospecificity for Fluorogenic Alkyldiacyl Glycerols (1995)

We synthesized enantiomeric 1‐ O ‐alkyl‐2,3‐diacyl‐ sn ‐glycerol and 3‐ O ‐alkyl‐1,2‐diacyl‐ sn ‐glycerol containing pyrene as a fluorescent reporter and the trinitrophenylamino residue as a fluorescence quencher; both reporter groups were covalently bound to the ω end of the acyl chains at positions sn ‐2 and sn ‐3(1), respectively. The fluorescence of the intact substrate molecules was very low. Chemical or enzymic release of the fatty acyl chains lead to fluorescence dequenching. The rate of lipolysis could be measured from the time‐dependent increase in fluorescence intensity. We used the respective substrates for the continuous determination of activity and stereopreference of four different microbial lipases from Chromobacterium viscosum, Candida rugosa, Pseudomonas sp., Rhizopus arrhizus , as well as cutinase from Fusarium solani and lipoprotein lipase from bovine milk. The stereopreference of the lipases depended, in general, on how the substrate was solubilized in the reaction medium. All lipases under investigation preferentially hydrolysed the sn ‐1 acyl ester bond, if the lipid analog was dispersed in albumin‐containing Tris/HCl buffer in the absence of detergent or organic solvent. In mixtures of 1:1 (by vol.) water/ethanol, the enzymes showed higher activity toward the sn ‐3 acyl ester bond, except for lipoprotein lipase which preferred the sn ‐1 acyl isomer under all conditions tested. Different stereopreferences were observed with the different lipases if the substrate was solubilized by amphiphiles (micelles of N ‐dodecyl‐ N,N ‐dimethyl‐3‐ammonio‐1‐propanesulfonate). C. rugosa lipase and F. solani cutinase showed high stereopreference for the sn ‐3 acyl ester, whereas Pseudomonas sp. lipase and C. viscosum lipase hydrolysed both enantiomers at similar rates. From spectroscopic studies, it can be inferred that the conformation of the fluorescent lipids is probably similar in water, mixtures of water and organic solvents, and in micelles. The possible effects of reaction conditions on substrate accessibility and enzyme conformation on stereoselectivity of the respective lipases are discussed.
How to Exchange Secrets with Oblivious Transfer (1981)

As this paper puts forward the notion of “Oblivious Transfers” and is a well-known and frequently cited paper, I felt I should typeset the manuscript, and here is the result. While typesetting, I tried to stick to the original manuscript as much as possible. However, there were some cases, such as a few typos or punctuation marks, which were changed. As in many papers on cryptography, Alice and Bob play the role of participants of the given cryptographic protocols. For the sake of readability, Alice’s and Bob’s messages were printed in red and blue ink, respectively. This work was carefully proofread by my colleague Y. Sobhdel (sobhdel@ce.sharif.edu). Thanks also to H. M. Moghaddam for mentioning a minor mistake in an earlier version. That said, I will be thankful if you inform me of any possible mistakes.
Ligand discovery using encoded combinatorial libraries. (2000)

Solid-phase combinatorial synthesis using split-pool or direct divide methods allows large libraries of complex molecules to be generated. Encoding techniques used during synthesis allow the identities of the products to be determined readily. An overview of this process and its application to ligand discovery are presented, along with comparisons to alternative approaches. Libraries are classified depending upon their intended use as discovery libraries (for broad screening), targeted libraries (for structure-based screening) and optimization libraries (for activity improvement). Biological assays can be performed on the solid support that is used in synthesis, or in solution under in vitro or in vivo conditions, with readouts indicative of either receptor binding or biological activity. This approach has led to numerous examples of successful ligand discovery.
Epitope Determinants of a Chimpanzee Fab Antibody That Efficiently Cross-Neutralizes Dengue Type 1 and Type 2 Viruses Map to Inside and in Close Proximity to Fusion Loop of the Dengue Type 2 Virus Envelope Glycoprotein (2004)

The epitope determinants of chimpanzee Fab antibody 1A5, which have been shown to be broadly reactive to flaviviruses and efficient for cross-neutralization of dengue virus type 1 and type 2 (DENV-1 and DENV-2), were studied by analysis of DENV-2 antigenic variants. Sequence analysis showed that one antigenic variant contained a Gly-to-Val substitution at position 106 within the flavivirus-conserved fusion peptide loop of the envelope protein (E), and another variant contained a His-to-Gln substitution at position 317 in E. Substitution of Gly(106)Val in DENV-2 E reduced the binding affinity of Fab 1A5 by approximately 80-fold, whereas substitution of His(317)Gln had little or no effect on antibody binding compared to the parental virus. Treatment of DENV-2 with beta-mercaptoethanol abolished binding of Fab 1A5, indicating that disulfide bridges were required for the structural integrity of the Fab 1A5 epitope. Binding of Fab 1A5 to DENV-2 was competed by an oligopeptide containing the fusion peptide sequence as shown by competition enzyme-linked immunosorbent assay. Both DENV-2 antigenic variants were shown to be attenuated, or at least similar to the parental virus, when evaluated for growth in cultured cells or for neurovirulence in mice. Fab 1A5 inhibited low pH-induced membrane fusion of mosquito C6/36 cells infected with DENV-1 or DENV-2, as detected by reduced syncytium formation. Both substitutions in DENV-2 E lowered the pH threshold for membrane fusion, as measured in a fusion-from-within assay. In the three-dimensional structure of E, Gly(106) in domain II and His(317) in domain III of the opposite E monomer were spatially close. From the locations of these amino acids, Fab 1A5 appears to recognize a novel epitope that has not been mapped before with a flavivirus monoclonal antibody.
Time and frequency offset estimation for distributed multiple-input multiple-output orthogonal frequency division multiplexing systems (2010)

This study addresses the problem of time and frequency offset estimation in the case of the delays, and the frequency offsets of all the transmitter/receiver pairs are different for distributed multiple-input multiple-output orthogonal frequency division multiplexing (MIMO–OFDM) systems. A new training structure is designed and an efficient time and frequency offset estimator is proposed. With the symmetric conjugate property of the preamble, the timing metric proposed has an impulse shape, making the time offset estimation accurate. Using the repetition property of the preamble, iterative frequency offset estimation algorithm proposed can acquire a high precision and a wide estimation range. To distinguish different transmit antennas, the preamble is weighted by pseudo-noise (PN) sequences with low cross-correlations. The analysis and the simulation results show that the proposed estimator offers an accurate estimation on the different time delays and frequency offsets caused by the distributed transmitters of the MIMO–OFDM system. This is a situation that the conventional estimators cannot handle as far.
Glycosphingolipids of various human ovarian tumors: a significantly high expression of I3SO3GalCer and Lewis antigen in mucinous cystadenocarcinoma. (1992)

Among several human ovarian tumors, which include mucinous cystadenocarcinoma, serous cystadenocarcinoma, and clear cell adenocarcinoma, the mucinous cystadenocarcinoma showed a unique glycosphingolipid composition. In particular, more than 90% of the acidic glycosphingolipids in the mucinous cystadenocarcinoma is comprised of sulfolipids, which are hardly detected in normal ovary and are contained in concentrations of less than 40% in the other type of ovarian tumors. By means of negative ion fast atom bombardment mass spectrometry and gas liquid chromatography, the major sulfolipid in mucinous cystadenocarcinoma is confirmed to be I3SO3-GalCer with N-cerebronoyl phytosphingosine, that which contrasts with I3SO3-GalCer with N-nonhydroxy fatty acyl sphingosine as the major molecular species in the other ovarian cancers. In mucinous cystadenocarcinoma, galactosylceramide is found in the relatively high concentration and is also composed of N-cerebronoyl phytosphingosine. In addition, the concentrations of glycolipids with Le(a) and Le(b) antigenicities are significantly higher in mucinous cystadenocarcinoma than those in normal ovary and the other ovarian tumors.
Assay of ribonucleotide reduction in nucleotide‐permeable hamster cells (1978)

Abstract Ribonucleotide reduction was measured in Chinese hamster ovary cells made permeable to nucleotides by treatment with the detergent Tween‐80. When compared to the respective ribonucleotide reductase activity in partially purified cell extracts, CDP and GDP reductase activities in permeabilized cells responded in a similar fashion to dithiothreitol, pH, MgCl 2 , FeCl 3 , substrate concentration and the presence of positive or negative allosteric effectors. At low protein concentrations both CDP and GDP reduction with whole cells increased linearly with cell number and was greater than the activity in corresponding cell extracts. Permeabilized cells were used to measure the level of CDP and GDP reductase in a hamster cell line resistant to the cytotoxic effects of hydroxyurea. The hydroxyurea‐resistant cell line contained four to ten times more CDP and GDP reductase activity compared to parental or revertant cell lines. The permeabilized cell assay was also used to measure CDP and GDP reductase activities in Chinese hamster ovary cells synchronized by isoleucine starvation. CDP reductase activity was low in G1 arrested cells but increased 10‐fold by 16 hours after the readdition of isoleucine to the growth medium. GDP reductase, which is present at much higher levels, is similarly induced after isoleucine addition, but only by 2‐fold. The maximum activity of both CDP and GDP reductase occurred from 14 to 16 hours after isoleucine addition, which corresponded to the period of maximum DNA synthesis.
Cellular injury and neuroinflammation in children with chronic intractable epilepsy (2009)

Our results suggest that active neuroinflammation and marked cellular injury occur in pediatric epilepsy and may play a common pathogenic role or consequences in childhood epilepsy of diverse etiologies. Our findings support the concept that immunomodulation targeting activated microglia and astrocytes may be a novel therapeutic strategy to reduce neurological morbidity and prevent intractable epilepsy.
The Wnt co-receptors Lrp5 and Lrp6 are essential for gastrulation in mice (2004)

Recent work has identified LDL receptor-related family members, Lrp5 and Lrp6, as co-receptors for the transduction of Wnt signals. Our analysis of mice carrying mutations in both Lrp5 and Lrp6 demonstrates that the functions of these genes are redundant and are essential for gastrulation. Lrp5;Lrp6 double homozygous mutants fail to establish a primitive streak, although the anterior visceral endoderm and anterior epiblast fates are specified. Thus, Lrp5 and Lrp6 are required for posterior patterning of the epiblast, consistent with a role in transducing Wnt signals in the early embryo. Interestingly, Lrp5(+/-);Lrp6(-/-) embryos die shortly after gastrulation and exhibit an accumulation of cells at the primitive streak and a selective loss of paraxial mesoderm. A similar phenotype is observed in Fgf8 and Fgfr1 mutant embryos and provides genetic evidence in support of a molecular link between the Fgf and Wnt signaling pathways in patterning nascent mesoderm. Lrp5(+/-);Lrp6(-/-) embryos also display an expansion of anterior primitive streak derivatives and anterior neurectoderm that correlates with increased Nodal expression in these embryos. The effect of reducing, but not eliminating, Wnt signaling in Lrp5(+/-);Lrp6(-/-) mutant embryos provides important insight into the interplay between Wnt, Fgf and Nodal signals in patterning the early mouse embryo.
A Hierarchical Latent Variable Encoder-Decoder Model for Generating Dialogues (2017)

Sequential data often possesses hierarchical structures with complex dependencies between sub-sequences, such as found between the utterances in a dialogue. To model these dependencies in a generative framework, we propose a neural network-based generative architecture, with stochastic latent variables that span a variable number of time steps. We apply the proposed model to the task of dialogue response generation and compare it with other recent neural-network architectures. We evaluate the model performance through a human evaluation study. The experiments demonstrate that our model improves upon recently proposed models and that the latent variables facilitate both the generation of meaningful, long and diverse responses and maintaining dialogue state.
The transmission of geminiviruses by Bemisia tabaci (1994)

Abstract The cosmopolitan whitefly species, Bemisia tabaci (Gennadius) and Trialeurodes taporariorum (Westwood) have always been regarded as pests to a large range of worldwide crops. Both species are capable of transmitting plant viruses, with T. vaporariorum being the vector of only a few ‘clostero’‐like viruses and B. tabaci the vector of viruses in several groups. The largest group of viruses transmitted by B. tabaci are the geminiviruses and B. tabaci is known to transmit around 60 members. Until recently, B. tabaci had been associated with only a limited range of host plants within any one region, although its total potential host range was large. Virus transmission was confined within the plant host range of each regional population of B. tabaci. The emergence of the polyphagous ‘B’ biotype of B. tabaci with its increased host range of more than 600 plant species, has resulted in geminiviruses infecting previously unaffected crops. As the ‘B’ biotype spreads further into Europe, European field and glasshouse crops have been shown to be susceptible to whitefly‐transmitted viruses already endemic to other parts of the world. More than 20 colonies of B. tabaci , including both ‘B’ and non‐‘B’ biotypes from disparate global locations have been compared for their ability to transmit more than 20 geminiviruses. All but two highly host‐specific colonies were capable of transmitting most geminiviruses tested. However, some viruses were transmitted more efficiently than others. The virus coat protein or capsid is essential for vector recognition and transmission. By comparing transmissible viruses at the molecular level to viruses that are no longer whitefly‐transmissible, the active epitope on the virus coat protein could be identified for designing future virus control strategies.
Rituximab Therapy in Hematologic Malignancy Patients With Circulating Blood Tumor Cells: Association With Increased Infusion-Related Side Effects and Rapid Blood Tumor Clearance (1999)

Rituximab administration in patients who have a high number of tumor cells in the blood may have an increased likelihood of severe initial infusion-related reactions. These data also suggest that rituximab may have activity in a variety of other lymphoid neoplasms, such as chronic lymphocytic leukemia and B-cell prolymphocytic leukemia.
Voltage Divider and its Application in the Two-stage Power Architecture (2006)

An ultra-high power density DC/DC converter with fixed conversion ratio is proposed for the two-stage power architecture in the area of power management for the processor based power systems, including server, desktop, laptop, and other battery powered portable applications. Without the magnetic component inside, its power density has been scaled up by an order over the conventional approach. In addition, it also features the capability of holding ultra-high efficiency within whole load range, which is promising to the battery life extension in the laptop, 1 kw/inch/sup 3/ power density and 98% efficiency have been demonstrated in 120W and 60W DC/DC prototypes designed for two-stage VRs.