gebhart/patrepeval huggingface dataset:
Sequence requirements for ligand binding and cell surface expression of the Tac antigen, a human interleukin-2 receptor. (1988)

Discrete peptide domains within the primary sequence of cell-surface receptor glycoproteins are believed to regulate not only their function but also their targeting to the cell membrane. To identify sequence elements required for intracellular transport and ligand binding by the human Tac interleukin-2 (IL-2) receptor, we prepared expression plasmids encoding a series of artificially mutated or naturally occurring variants of the Tac cDNA. In particular, we sought to further delineate the functional role of the sequences contributed by each of the eight exons that together encode the Tac protein. Deletion of exons 5 through 8 of the receptor had no detectable effect on IL-2 binding or intracellular transport of the Tac protein, and resulted in secreted forms of this IL-2-binding protein. Removal of sequences corresponding to all of exon 4 ablated IL-2 binding activity yet still permitted transport to the cell surface. In contrast, partial deletion of exon 4 sequences resulted in proteins that not only lacked IL-2 binding activity but also were sequestered within the endoplasmic reticulum. Removal of one or both of the N-linked glycosylation sites present in the Tac protein did not impair receptor transport or ligand binding. These results demonstrate that exon 4 of the Tac gene encodes amino acid residues that play an important role in regulating both the intracellular transport and function of this IL-2 receptor.
SHIV-162P3 Infection of Rhesus Macaques Given Maraviroc Gel Vaginally Does Not Involve Resistant Viruses (2011)

Maraviroc (MVC) gels are effective at protecting rhesus macaques from vaginal SHIV transmission, but breakthrough infections can occur. To determine the effects of a vaginal MVC gel on infecting SHIV populations in a macaque model, we analyzed plasma samples from three rhesus macaques that received a MVC vaginal gel (day 0) but became infected after high-dose SHIV-162P3 vaginal challenge. Two infected macaques that received a placebo gel served as controls. The infecting SHIV-162P3 stock had an overall mean genetic distance of 0.294±0.027%; limited entropy changes were noted across the envelope (gp160). No envelope mutations were observed consistently in viruses isolated from infected macaques at days 14-21, the time of first detectable viremia, nor selected at later time points, days 42-70. No statistically significant differences in MVC susceptibilities were observed between the SHIV inoculum (50% inhibitory concentration [IC(50)] 1.87 nM) and virus isolated from the three MVC-treated macaques (MVC IC(50) 1.18 nM, 1.69 nM, and 1.53 nM, respectively). Highlighter plot analyses suggested that infection was established in each MVC-treated animal by one founder virus genotype. The expected Poisson distribution of pairwise Hamming Distance frequency counts was observed and a phylogenetic analysis did not identify infections with distinct lineages from the challenge stock. These data suggest that breakthrough infections most likely result from incomplete viral inhibition and not the selection of MVC-resistant variants.
Electronically addressable SnO2 inverted opal gas sensors fabricated on interdigitated gold microelectrodes (2003)

Electronically addressable thin films of tin oxide gas sensors with well-defined opaline microstructures and reproducible sensor-to-sensor responses have been fabricated on interdigitated gold microelectrodes through self-assembly growth of a monodisperse polystyrene latex film onto the electrodes followed by infiltration of tin tert-butoxide and calcination of the film.
Diagnostic power of diffuse reflectance spectroscopy for targeted detection of breast lesions with microcalcifications (2012)

Microcalcifications geographically target the location of abnormalities within the breast and are of critical importance in breast cancer diagnosis. However, despite stereotactic guidance, core needle biopsy fails to retrieve microcalcifications in up to 15% of patients. Here, we introduce an approach based on diffuse reflectance spectroscopy for detection of microcalcifications that focuses on variations in optical absorption stemming from the calcified clusters and the associated cross-linking molecules. In this study, diffuse reflectance spectra are acquired ex vivo from 203 sites in fresh biopsy tissue cores from 23 patients undergoing stereotactic breast needle biopsies. By correlating the spectra with the corresponding radiographic and histologic assessment, we have developed a support vector machine-derived decision algorithm, which shows high diagnostic power (positive predictive value and negative predictive value of 97% and 88%, respectively) for diagnosis of lesions with microcalcifications. We further show that these results are robust and not due to any spurious correlations. We attribute our findings to the presence of proteins (such as elastin), and desmosine and isodesmosine cross-linkers in the microcalcifications. It is important to note that the performance of the diffuse reflectance decision algorithm is comparable to one derived from the corresponding Raman spectra, and the considerably higher intensity of the reflectance signal enables the detection of the targeted lesions in a fraction of the spectral acquisition time. Our findings create a unique landscape for spectroscopic validation of breast core needle biopsy for detection of microcalcifications that can substantially improve the likelihood of an adequate, diagnostic biopsy in the first attempt.
Structural and ligand-binding analysis of the YAP-binding domain of transcription factor TEAD4 (2018)

The oncoprotein YAP (Yes-associated protein) requires the TEAD family of transcription factors for the up-regulation of genes important for cell proliferation. Disrupting YAP–TEAD interaction is an attractive strategy for cancer therapy. Targeting TEADs using small molecules that either bind to the YAP-binding pocket or the palmitate-binding pocket is proposed to disrupt the YAP–TEAD interaction. There is a need for methodologies to facilitate robust and reliable identification of compounds that occupy either YAP-binding pocket or palmitate-binding pocket. Here, using NMR spectroscopy, we validated compounds that bind to these pockets and also identify the residues in mouse TEAD4 (mTEAD4) that interact with these compounds. Flufenamic acid (FA) was used as a positive control for validation of palmitate-binding pocket-occupying compounds by NMR. Furthermore, we identify a hit from a fragment screen and show that it occupies a site close to YAP-binding pocket on the TEAD surface. Our results also indicate that purified mTEAD4 can catalyze autopalmitoylation. NMR studies on mTEAD4 revealed that exchanges exist in TEAD as NMR signal broadening was observed for residues close to the palmitoylation site. Mutating the palmitoylated cysteine (C360S mutant) abolished palmitoylation, while no significant changes in the NMR spectrum were observed for the mutant which still binds to YAP. We also show that FA inhibits TEAD autopalmitoylation. Our studies highlight the utility of NMR spectroscopy in identifying small molecules that bind to TEAD pockets and reinforce the notion that both palmitate-binding pocket and YAP-binding pocket are targetable.
Mutation of <i>toxB</i> and a Truncated Version of the <i>efa-1</i> Gene in <i>Escherichia coli</i> O157:H7 Influences the Expression and Secretion of Locus of Enterocyte Effacement-Encoded Proteins but not Intestinal Colonization in Calves or Sheep (2004)

Enterohemorrhagic Escherichia coli (EHEC) strains comprise a broad group of bacteria, some of which cause attaching and effacing (AE) lesions and enteritis in humans and animals. Non-O157:H7 EHEC strains contain the gene efa-1 (referred to in previous publications as efa1), which influences adherence to cultured epithelial cells. An almost identical gene in enteropathogenic E. coli (lifA) mediates the inhibition of lymphocyte proliferation and proinflammatory cytokine synthesis. We have shown previously that significantly lower numbers of EHEC O5 and O111 efa-1 mutants are shed in feces following experimental infection in calves and that these mutants exhibit reduced adherence to intestinal epithelia compared with isogenic wild-type strains. E. coli O157:H7 strains lack efa-1 but encode a homolog on the pO157 plasmid (toxB/l7095) and contain a truncated version of the efa-1 gene (efa-1'/z4332 in O island 122 of the EDL933 chromosome). Here we report that E. coli O157:H7 toxB and efa-1' single and double mutants exhibit reduced adherence to cultured epithelial cells and show reduced expression and secretion of proteins encoded by the locus of enterocyte effacement (LEE), which plays a key role in the host-cell interactions of EHEC. The activity of LEE1, LEE4, and LEE5 promoters was not significantly altered in E. coli O157:H7 strains harboring toxB or efa-1' mutations, indicating that the effect on the expression of LEE-encoded secreted proteins occurs at a posttranscriptional level. Despite affecting type III secretion, mutation of toxB and efa-1' did not significantly affect the course of fecal shedding of E. coli O157:H7 following experimental inoculation of 10- to 14-day-old calves or 6-week-old sheep. Mutation of tir caused a significant reduction in fecal shedding of E. coli O157:H7 in calves, indicating that the formation of AE lesions is important for colonization of the bovine intestine.
Solution‐Phase Mixture Synthesis with Fluorous Tagging En Route: Total Synthesis of an Eight‐Member Stereoisomer Library of Passifloricins (2006)

Doppelter Spaß: Eine neue Methode mit doppelter Markierung wurde verwendet, um acht individuelle Stereoisomere von Passifloricin über ein intermediär auftretendes Paar von quasi-isomeren Vierkomponentenmischungen zu synthetisieren. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2006/z600041_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Room temperature strong coupling effects and polariton lasing under electrical injection (2014)

When an emitter is placed in a resonant cavity, then in the strong coupling regime of light-matter interaction the degeneracy between the emitter and cavity photon is lifted, giving rise to two light-matter entangled eigenstates separated by a characteristic interaction energy (Rabi splitting) Ω <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">VRS</sub> . These are the lower and upper exciton-polariton branches, which are the normal modes of the system. Upon suitable excitation, a coherent state of exciton-polaritons is generated by polariton-phonon scattering and eventual stimulated polariton-polariton scattering, which is a phase coherent process and is the relevant gain mechanism. The coherent polariton state generates coherent light by spontaneous radiative recombination. This inversionless process of coherent emission has been termed polariton lasing. An electrically pumped GaAs-based polariton laser was demonstrated for the first time recently by Bhattacharya et al. [1] and Schneider et al. [2]. Because of the small exciton binding energy of excitons in the In <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.1</sub> Ga <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.9</sub> As quantum wells in the devices, operation had to be restricted to cryogenic temperatures (10-30 K). We report here, for the first time, high temperature electrically pumped polariton lasers using different material systems. In the first, where the emitter is a single Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.31</sub> Ga <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.69</sub> As/Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.41</sub> Ga <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.59</sub> As quantum well, operation is demonstrated at 155 K. Room temperature operation is demonstrated with a GaN-based microcavity device.
Vine Performance and Wine Quality for Four Red Wine Grape Cultivars Grown for Three Growing Seasons in Erie County, Pennsylvania (1978)

Replicated field trials for four red wine grape cultivars (cvs) were initiated in the spring of 1967 at The Pennsylvania State University Field Research Laboratory located in North East, Pennsylvania. The principal objectives were to determine whether cvs other than Catawba and Delaware could be grown commercially in Pennsylvania and produce table wines of acceptable quality exhibiting a "vinifera-like" character. Consistent wine evaluations were made from 1971 through 1973 for these four cvs: Chancellor (Seibel 7053), Chelois (Seibel 10878), DeChaunac (Seibel 9549), and Landot 4511. These trials revealed that at least four cvs can be grown commercially along the southern shore of Lake Erie in Pennsylvania and produce high-quality table wines with a "vinifera-like" character. The cv Chancellor consistently produced a wine of excellent quality. Wines of DeChaunac and Chelois were of high quality, and musts of Landot 4511 fermented into wines of acceptable quality. Average yield of fruit from vines of these four cvs ranged 19.0 metric tons per hectare (t/ha), for Chelois, to 15.3 t/ha, for Landot 4511. Soluble solids of the musts were lowest for DeChaunac (18.5%) and highest for Landot 4511 (19.4%). Total acidity values, expressed as tartaric acid, were lowest for Landot 4511 (0.90 g/100 g of must) and highest for Chancellor (1.13 g/100 g). Average vine vigor for these cvs ranged from 0.6 kg of cane wood per vine (kg/v), for Chancellor, to 1.7 kg/v, for Landot 4511.
Visual clutter reduction in zoomable proportional point symbol maps (2018)

Proportional point symbols are commonly used in map displays. However, when such displays are zoomed out, the available map space shrinks and consequently symbols overlap and the display suffers from visual clutter. Therefore, solutions are needed to reduce visual clutter in zoomable map displays that contain proportional point symbols. The authors add to the body of knowledge through the investigation of the performance of three solutions: aggregation of unit areas, the displacement of overlapping symbols, and modified symbolization; four variations of modified symbolization are examined in detail. The original study begins with a consideration of the strengths and weaknesses of the solutions, with an emphasis on information loss. Thereafter, user sessions with 165 participants are arranged to gain empirical evidence of the performance of the solutions. The results reveal that although participants zoom out the map to zoom levels that implement visual clutter reduction techniques, they tend to zoom in the map and pan it to examine specific areas. Moreover, they willingly use the map with aggregated unit areas in cases when the solution facilitates task accomplishment. A certain amount of skepticism attaches to the solution that displaces overlapping symbols.
Study of non-diffracting light beams from broad-stripe edge-emitting semiconductor lasers (2010)

Broad-stripe edge-emitting semiconductor lasers have been used to obtain propagation-invariant (nondiffracting) light beams with powers and diameters of the central ray acceptable for optical manipulation and tweezing. The results of investigations of the propagation of Bessel beams generated from broad-stripe lasers with spectrally selective resonator show that the spatial homogeneity of emission plays a much greater role than the temporal coherence in the formation of Bessel beams. The main factors limiting the length of non-diffracting beam propagation (without distortion of the central ray) are the astigmatism and multimode character of laser radiation.
Dynamic spectrum access in cognitive radio networks (2006)

Since the 1930's, the Federal Communications Commission (FCC) has con trolled the radio frequency energy spectrum. They license segments to particular users in particular geographic areas. A few, small, unlicensed bands were left open for anyone to use as long as they followed certain power regulations. With the recent boom in personal wireless technologies, these unlicensed bands have become crowded with everything from wireless networks to digital cordless phones. 
To combat the overcrowding, the FCC has been investigating new ways to manage RF resources. The basic idea is to let people use licensed frequencies, provided they can guarantee interference perceived by the primary license holders will be minimal. With advances in software and cognitive radio, practical ways of doing this are on the horizon. In 2003 the FCC released a memorandum seeking comment on the interference temperature model for controlling spectrum use. Analyzing the viability of this model and developing a medium access protocol around it are the main goals of this dissertation. 
A system implementing this model will measure the current interference temperature before each transmission. It can then determine what bandwidth and power it should use to achieve a desired capacity without violating an interference ceiling called the interference temperature limit. 
If a system consisting of interference sources, primaxy licensed users, and secondary unlicensed users is modeled stochastically, we can obtain some interesting results. In particular, if impact to licensed users is defined by a fractional decrease in coverage area, and this is held constant, the capacity achieved by secondary users is directly proportional to the number of unlicensed nodes, and is actually independent of the interference and primary users' transmissions. Using the basic ideas developed in the system analysis, Interference Temperature Multiple Access, a physical and data-link layer implementing the interference temperature model, was formulated, analyzed, and simulated. 
Overall, the interference temperature model is a viable approach for dynamic spectrum access, and ITMA is a concrete technique implementing it. With the help of cognitive radios, we can reform spectrum policy and have significantly more room to innovate, ushering in a new era of high-speed personal wireless communications.
A Resource Assignment Study on Wireless OFDMA Systems (2008)

In this article, we study the time-frequency scheduling for Orthogonal Frequency Division Multiple Access (OFDMA) systems. A number of OFDMA schedulers in the literature divides the scheduling problem into two steps: the resource allocation and the resource assignment. While the resource allocation optimizes various metrics, the resource assignment deals mostly with spectral efficiency and is almost service independent. We compare the some resource assignment algorithms in the literature and some proposed by us in fairness, spectral efficiency and ability to mantain the Quality of Service (QoS) requirements.
Liquid‐ and Liquid/Liquid‐Phase Reactions: Sections 4.3–4.4 (2004)

4.3 Aromatic Electrophilic Substitution 4.3.1 Nitrodehydrogenation – Nitration of Aromatics 4.3.1.1 Drivers for Performing Aromatic Nitrations in Micro Reactors 4.3.1.2 Beneficial Micro Reactor Properties for Aromatic Nitrations 4.3.1.3 Aromatic Nitration Reactions Investigated in Micro Reactors 4.3.1.4 Experimental Nitration Protocols in Micro Reactors 4.3.1.5 Typical Results 4.3.2 Diazotization + Arylazodehydrogenation – Diazonium Salt Formation + Diazo Coupling (Azo Chemistry) 4.3.2.1 Drivers for Performing Azo Chemistry in Micro Reactors 4.3.2.2 Beneficial Micro Reactor Properties for Azo Chemistry 4.3.2.3 Azo Chemistry Investigated in Micro Reactors 4.3.2.4 Experimental Protocols 4.3.2.5 Typical Results 4.3.3 Alkoxyborondehydro Substitution – Arylboron Formation 4.3.3.1 Drivers for Performing Arylboron Formation in Micro Reactors 4.3.3.2 Beneficial Micro Reactor Properties for Arylboron Formation 4.3.3.3 Arylboron Formation Investigated in Micro Reactors 4.3.3.4 Experimental Protocols 4.3.3.5 Typical Results 4.4 Aliphatic Electrophilic Substitution 4.4.1 Keto–Enol Tautomerism – Isomerization of Allyl Alcohols 4.4.1.1 Drivers for Performing Isomerization of Allyl Alcohols in Micro Reactors 4.4.1.2 Beneficial Micro Reactor Properties for Isomerization of Allyl Alcohols 4.4.1.3 Isomerization of Allyl Alcohols Investigated in Micro Reactors 4.4.1.4 Experimental Protocols 4.4.1.5 Typical Results
Adeno-associated virus gene expression inhibits cellular transformation by heterologous genes. (1987)

In this paper we report that adeno-associated virus (AAV) genomes inhibit stable transformation by several dominant selectable marker genes upon cotransfection into mouse tissue culture cells. Cotransfection of AAV genomes also inhibited the expression of pSV2cat in transient assays. In both cases, the inhibitory effect was independent of AAV DNA replication but required the AAV p5 and p19 genes, which encode proteins required for AAV DNA replication and regulation of AAV gene expression. Finally, addition of a cloned E4 gene in the transfection experiments partially blocked the AAV-mediated inhibitory activities.
Control of Gene Expression by the Retinoic Acid-Related Orphan Receptor Alpha in HepG2 Human Hepatoma Cells (2011)

Retinoic acid-related Orphan Receptor alpha (RORα; NR1F1) is a widely distributed nuclear receptor involved in several (patho)physiological functions including lipid metabolism, inflammation, angiogenesis, and circadian rhythm. To better understand the role of this nuclear receptor in liver, we aimed at displaying genes controlled by RORα in liver cells by generating HepG2 human hepatoma cells stably over-expressing RORα. Genes whose expression was altered in these cells versus control cells were displayed using micro-arrays followed by qRT-PCR analysis. Expression of these genes was also altered in cells in which RORα was transiently over-expressed after adenoviral infection. A number of the genes found were involved in known pathways controlled by RORα, for instance LPA, NR1D2 and ADIPOQ in lipid metabolism, ADIPOQ and PLG in inflammation, PLG in fibrinolysis and NR1D2 and NR1D1 in circadian rhythm. This study also revealed that genes such as G6PC, involved in glucose homeostasis, and AGRP, involved in the control of body weight, are also controlled by RORα. Lastly, SPARC, involved in cell growth and adhesion, and associated with liver carcinogenesis, was up-regulated by RORα. SPARC was found to be a new putative RORα target gene since it possesses, in its promoter, a functional RORE as evidenced by EMSAs and transfection experiments. Most of the other genes that we found regulated by RORα also contained putative ROREs in their regulatory regions. Chromatin immunoprecipitation (ChIP) confirmed that the ROREs present in the SPARC, PLG, G6PC, NR1D2 and AGRP genes were occupied by RORα in HepG2 cells. Therefore these genes must now be considered as direct RORα targets. Our results open new routes on the roles of RORα in glucose metabolism and carcinogenesis within cells of hepatic origin.