gebhart/patrepeval huggingface dataset:
Intervening sequence between the leader region and the nucleopcapsid gene of vesicular stomatitis virus RNA (1980)

The base sequence at the 3' end of vesicular stomatitis virus RNA was determined by using terminal labels and chemical RNA sequencing. The leader RNA was complementary to 47 bases at the 3' terminus, whereas the nucleocapsid gene (N) began 51 nucleotides from the 3' end of the genomic RNA. The intervening bases were 3'...GAAA...5' for the Indiana serotype and 3'...GAAAA...5' for the New Jersey serotype. The complements of these bases did not appear in either the leader RNA or the N mRNA. This sequence may function as a stop signal or cleavage site during transcription. Furthermore, processing or termination at this sequence must be inhibited during the production of full-length RNA plus-sense strands (replication). We recently found similar sequences approximately 46 to 48 nucleotides from the 3' ends of several defective interfering particle RNAs where the short defective interfering particle transciption products terminate. This sequence is present also at the end of the polymerase (L) gene.
Spectrum-Analysis and Neural Networks for Imaging to Detect and Treat Prostate Cancer (2001)

Conventional B-mode ultrasound currently is the standard means of imaging the prostate for guiding prostate biopsies and planning brachytherapy to treat prostate cancer. Yet B-mode images do not adequately display cancerous lesions of the prostate. Ultrasonic tissue-type imaging based on spectrum analysis of radiofrequency (rf) echo signals has shown promise for overcoming the limitations of B-mode imaging for visualizing prostate tumors. This method of tissue-type imaging utilizes nonlinear classifiers, such as neural networks, to classify tissue based on values of spectral parameter and clinical variables. Two- and three-dimensional images based on these methods demonstrate potential for guiding prostate biopsies and targeting radiotherapy of prostate cancer. Two-dimensional images are being generated in real time in ultrasound scanners used for real-time biopsy guidance and have been incorporated into commercial dosimetry software used for brachytherapy planning. Three-dimensional renderings show promise for depicting locations and volumes of cancer foci for disease evaluation to assist staging and treatment planning, and potentially for registration or fusion with CT images for targeting external-beam radiotherapy.
Analysis of the interchannel response in a MEMS 1 × N^2 wavelength-selective switch (2007)

A theoretical model based on Fourier optics and the power-coupling overlap integral is built to investigate the interchannel response in a micro-electro-mechanical systems 1xN(2) wavelength-selective switch. The simulation results demonstrate that the interchannel response depends significantly on the output port location and the radius of curvature of the micromirrors. For the output originally aligned with the input along the dispersion direction, it is possible to achieve interchannel-response suppression by rotating the two-dimensional (2D) collimator array by a slight angle, e.g., 20 degrees. Experimental results under different conditions are also shown.
Transformation of human umbilical cord blood T cells by human T-cell leukemia/lymphoma virus. (1983)

Several isolates of human T-cell leukemia/lymphoma virus (HTLV) were transmitted to normal human T cells obtained from the umbilical cord blood of newborns. T cells from seven specimens were immortalized by infection with different HTLV isolates and their properties were compared with those of activated uninfected normal T cells grown in the presence of T-cell growth factor (TCGF) and with those of HTLV-positive neoplastic T-cell lines derived from patients with T-cell malignancies. The HTLV-infected cells generally belonged to a class of mature T cells (OKT4+ and Leu 3A+) and differed from the normal uninfected cells in that they could be propagated in culture indefinitely; possessed altered morphology, including convoluted nuclei and some bi- and multinucleated giant cells; formed large clumps in culture; demonstrated a diminished requirement for TCGF; had an increased density of TCGF receptors; often became completely independent of exogenous TCGF; and expressed HLA-DR determinants. These properties of the HTLV-infected cord blood T cells contrasted to those of uncultured cord blood T cells and of cord blood cells stimulated with mitogen and grown with TCGF but resembled the characteristics of T-cell lines established previously from patients with HTLV-associated T-cell malignancies. This in vitro system offers a unique opportunity to study the basic mechanism involved in abnormal growth and neoplastic transformation of a specific class of human T cells.
Sensor and Map-Aided Cooperative Beam Tracking for Optical V2V Communications (2020)

This paper focuses on advanced pointing strategies enabling high data-rate directional vehicular communications. New emerging technologies aim to meet the challenging performance requirements of enhanced Vehicle-to-Everything (eV2X) applications by using highly collimated beams, which must rely on a very precise beam alignment. In this work, Free-Space Optics (FSO) is considered, and a system architecture is introduced together with algorithms for an accurate alignment of laser beam. The presented architecture exploits on-board sensor data sharing among vehicles to predict the pointing directions for FSO, thus counteracting the detrimental effect of motion, vibrations and tilting of vehicles. A solution is proposed for an accurate prediction of the FSO pointing direction, based on the sharing of vehicle kinematic data over a parallel wireless control link, augmented by prior information extracted from digital maps of the driving environment. Simulation results point out the challenges of a FSO V2V communication and highlight the feasibility of the proposed solution, considering both state of the art technology and future perspective hardware.
Summarizing biological literature with BioSumm (2010)

BioSumm is a summarization environment that supports user queries on online repositories of scientific publications by providing abstract descriptions of focused document groups. The summarization approach is driven by a grading function which evaluates the occurrences of domain dictionary terms.
Synthesis and Photoluminescent Properties of Violet Emitting 5,6‐Diphenylfuro[2,3‐d]pyrimidine Derivatives. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Effects of an outreach and internal navigation program on breast cancer diagnosis in an urban cancer center with a large African‐American population (2008)

The outreach initiatives and internal patient navigation appear to have improved stage at diagnosis. To determine whether specific patients presented earlier as a result of specific community outreach initiatives, prospective work is underway to measure the effects of these interventions on potential stage migration. Similarly, prospective data are being collected to determine whether Patient Navigators influence treatment and appointment adherence as well as the underlying reasons for barriers to specific interventions in this underserved minority population.
Cobalt(<scp>ii</scp>)-bridged triphenylamine and terpyridine-based donor–acceptor coordination polymer as an efficient trifunctional electrocatalyst (2023)

A new coordination polymer for trifunctional electrocatalysis (ORR, OER, and HER) synthesized via Schiff base condensation and in situ self-assembly using triphenylamine and Co( ii )-terpyridine ligand.
Synthesis and Optical Properties of the C-8 Adduct of Benzo[<i>a</i>]pyrene and Deoxyguanosine (2005)

8-(Benzo[a]pyren-6-yl)-2′-deoxyguanosine (Bp-dG) was prepared via a palladium-catalyzed Suzuki-Miyaura-type cross-coupling reaction from the pinacol ester of 6-benzo[a]pyrenyl boronic acid and the corresponding brominated deoxyguanosine precursor. The absorption and steady-state fluorescence properties of Bp-dG were characterized and compared with that of 6-benzo[a]pyrene. The modified nucleoside Bp-dG exhibits an unexpected high stability towards nucleosidic hydrolysis even under irradiation with UV light.
Kinetic Resolution of the Racemic 2‐Hydroxyalkanoates Using the Enantioselective Mixed‐Anhydride Method with Pivalic Anhydride and a Chiral Acyl‐Transfer Catalyst (2009)

A variety of optically active 2-hydroxyalkanoates and the corresponding 2-acyloxyalkanoates are produced by the kinetic resolution of racemic 2-hydroxyalkanoates by using achiral 2,2-diarylacetic acid with hindered carboxylic anhydrides as the coupling reagents. The combined use of diphenylacetic acid, pivalic anhydride, and (+)-(R)-benzotetramisole ((R)-BTM) effectively produces (S)-2-hydroxyalkanoates and (R)-2-acyloxyalkanoates from the racemic 2-hydroxyalkanoates (s-values=47-202). This protocol directly provides the desired chiral 2-hydroxyalkanoate derivatives from achiral diarylacetic acid and racemic secondary alcohols that do not include the sec-phenethyl alcohol moiety by using the transacylation process to generate the mixed anhydrides from the acid components with bulky carboxylic anhydrides under the influence of the chiral acyl-transfer catalyst. The transition state that provides the desired (R)-2-acyloxyalkanoate from (R)-2-hydroxyalkanoate included in the racemic mixture is disclosed by DFT calculations, and the structural features of the transition form are also discussed.
Cloud radios with limited feedback (2014)

Cooperation in a cellular network is seen as a key technique in managing other cell interference to observe a gain in achievable rate. In this paper, we present the achievable rates for a cloud radio network using a zero forcing (ZF) equalizer with dirty paper precoding (DPC). We show that when complete channel state information is available at the cloud, rates close to those achievable with total interference cancellation can be achieved. With mean capacity gains, of up to 200% over the conventional cellular network in the downlink, this precoding scheme shows great promise for implementation in a cloud radio network. To simplify the analysis, we use a stochastic geometric framework based on Poisson point processes instead of the traditional grid based cellular network model. We study the impact of limiting the channel state information on the achievable rate. Bounds are developed on the achievable rate with limited feedback. These bounds are shown to be tight while permitting analytical tractability. Specifically, we show that with a limited feedback of about 5-6 channel states from each user, we obtain significant gain compared to conventional systems.
Engineering selectivity of <i>Cutibacterium acnes</i> phages by epigenetic imprinting (2021)

Abstract Cutibacterium acnes (C. acnes) is a gram-positive bacterium and a member of the human skin microbiome. Despite being the most abundant skin commensal, certain members have been associated with common inflammatory disorders such as acne vulgaris . The availability of the complete genome sequences from various C. acnes clades have enabled the identification of putative methyltransferases, some of them potentially belonging to restriction-modification (R-M) systems which protect the host of invading DNA. However, little is known on whether these systems are functional in the different C. acnes strains. To investigate the activity of these putative R-M and their relevance in host protective mechanisms, we analyzed the methylome of seven representative C. acnes strains by Oxford Nanopore Technologies (ONT) sequencing. We detected the presence of a 6-methyladenine modification at a defined DNA consensus sequence in strain KPA171202 and recombinant expression of this R-M system confirmed its methylation activity. Additionally, a R-M knockout mutant verified the loss of methylation properties of the strain. We studied the potential of one C. acnes bacteriophage (PAD20) in killing various C. acnes strains and linked an increase in its specificity to phage DNA methylation acquired upon infection of a methylation competent strain. We demonstrate a therapeutic application of this mechanism where phages propagated in R-M deficient strains selectively kill R-M deficient acne-prone clades while probiotic ones remain resistant to phage infection. Graphical abstract
Transmission performance of MC-CDMA signals in hybrid fiber-radio systems (2002)

An analysis is reported for the evaluation of the down-link transmission performance of multiple carrier (MC)-CDMA system, in hybrid fiber-radio access network, for broadband signals distribution. The nonlinear effects due to optical link give rise to severe constraints in the design of such MC-CDMA systems. In particular, it has been shown as nonlinear distortions cause significant performance degradation, because the receiver is no more able to achieve correctly the separation of the signals due to the lost of orthogonality among code words.
Digital Signal Processing in Spatially Multiplexed Coherent Communications (2012)

Based on recent experimental results for spatially multiplexed transmission, we analyze the impulse response matrix of few-mode fiber links that support the propagation of LP01 and LP11 modes over up to 1,200-km. We characterize the channel’s modal delay spread and mode-dependent loss.
Effects of finite aspect ratio on wind turbine airfoil measurements (2016)

Wind turbines partly operate in stalled conditions within their operational cycle. To simulate these conditions, it is also necessary to obtain 2-D airfoil data in terms of lift and drag coefficients at high angles of attack. Such data has been obtained previously, but often at low aspect ratios and only barely past the stall point, where strong wall boundary layer influence is expected. In this study, the influence of the wall boundary layer on 2D airfoil data, especially in the post stall domain, is investigated. Here, a wind turbine airfoil is tested at different angles of attack and with two aspect ratios of AR = 1 and AR = 2. The tests are conducted in a wind tunnel that is pressurized up to 150 bar in order to achieve a constant Reynolds number of Rec = 3 ∙ 106, despite the variable chord length.
A Novel Pseudopodial Component of the Dendritic Cell Anti-Fungal Response: The Fungipod (2010)

Fungal pathologies are seen in immunocompromised and healthy humans. C-type lectins expressed on immature dendritic cells (DC) recognize fungi. We report a novel dorsal pseudopodial protrusion, the "fungipod", formed by DC after contact with yeast cell walls. These structures have a convoluted cell-proximal end and a smooth distal end. They persist for hours, exhibit noticeable growth and total 13.7+/-5.6 microm long and 1.8+/-0.67 microm wide at the contact. Fungipods contain clathrin and an actin core surrounded by a sheath of cortactin. The actin cytoskeleton, but not microtubules, is required for fungipod integrity and growth. An apparent rearward flow (225+/-55 nm/second) exists from the zymosan contact site into the distal fungipod. The phagocytic receptor Dectin-1 is not required for fungipod formation, but CD206 (Mannose Receptor) is the generative receptor for these protrusions. The human pathogen Candida parapsilosis induces DC fungipod formation strongly, but the response is species specific since the related fungal pathogens Candida tropicalis and Candida albicans induce very few and no fungipods, respectively. Our findings show that fungipods are dynamic actin-driven cellular structures involved in fungal recognition by DC. They may promote yeast particle phagocytosis by DC and are a specific response to large (i.e., 5 microm) particulate ligands. Our work also highlights the importance of this novel protrusive structure to innate immune recognition of medically significant Candida yeasts in a species specific fashion.
Elevated FMR1-mRNA and lowered FMRP – A double-hit mechanism for psychiatric features in men with FMR1 premutations (2020)

Fragile X syndrome (FXS) is caused by a full mutation of the FMR1 gene (>200 CGG repeats and subsequent methylation), such that there is little or no FMR1 protein (FMRP) produced, leading to intellectual disability (ID). Individuals with the premutation allele (55-200 CGG repeats, generally unmethylated) have elevated FMR1 mRNA levels, a consequence of enhanced transcription, resulting in neuronal toxicity and a spectrum of premutation-associated disorders, including the neurodegenerative disorder fragile X-associated tremor/ataxia syndrome (FXTAS). Here we described 14 patients who had both lowered FMRP and elevated FMR1 mRNA levels, representing dual mechanisms of clinical involvement, which may combine features of both FXS and FXTAS. In addition, the majority of these cases show psychiatric symptoms, including bipolar disorder, and/or psychotic features, which are rarely seen in those with just FXS.
Anisotropic x-ray absorption effects in the optical luminescence yield of ZnO nanostructures (2006)

The authors have found that the directionality of the orbital populated following core-level x-ray absorption of a hexagonal nanostructure has a strong influence on the resulting optical luminescence yield spectra. For ZnO, there is an enhancement of the band gap exciton luminescence following O 1s to 2pz relative to 2px,y excitation. The defect luminescence O 1s excitation spectrum also shows sensitivity to the nature of the defect (surface or bulk).
ChemInform Abstract: Alkene Chemoselectivity in Ruthenium‐Catalyzed Z‐Selective Olefin Metathesis. (2013)

Abstract This method yields E,Z‐dienes from dienes and terminal alkenes or internal Z‐alkenes with high chemoselectivity (with regard to the diene substrate) and complete stereoselectivity.
Crystal Structure of LSD1 in Complex with 4-[5-(Piperidin-4-ylmethoxy)-2-(p-tolyl)pyridin-3-yl]benzonitrile (2018)

Because lysine-specific demethylase 1 (LSD1) regulates the maintenance of cancer stem cell properties, small-molecule inhibitors of LSD1 are expected to be useful for the treatment of several cancers. Reversible inhibitors of LSD1 with submicromolar inhibitory potency have recently been reported, but their exact binding modes are poorly understood. In this study, we synthesized a recently reported reversible inhibitor, 4-[5-(piperidin-4-ylmethoxy)-2-(<i>p</i>-tolyl)pyridin-3-yl]benzonitrile, which bears a 4-piperidinylmethoxy group, a 4-methylphenyl group, and a 4-cyanophenyl group on a pyridine ring, and determined the crystal structure of LSD1 in complex with this inhibitor at 2.96 Å. We observed strong electron density for the compound, showing that its cyano group forms a hydrogen bond with Lys661, which is a critical residue in the lysine demethylation reaction located deep in the catalytic center of LSD1. The piperidine ring interacts with the side chains of Asp555 and Asn540 in two conformations, and the 4-methylphenyl group is bound in a hydrophobic pocket in the catalytic center. Our elucidation of the binding mode of this compound can be expected to facilitate the rational design of more-potent reversible LSD1 inhibitors.
In vitro activity of sorafenib against imatinib- and sunitinib-resistant kinase mutations associated with drug-resistant GI stromal tumors (2009)

10500 Background: Most gastrointestinal stromal tumors (GISTs) harbor mutant KIT or platelet-derived growth factor receptor alpha (PDGFRA) kinases, which are targets of imatinib (front-line therapy) or sunitinib (second-line therapy). Resistance to imatinib (IM) or sunitinib (SU) is commonly associated with the acquisition of secondary kinase mutations. In phase II studies, sorafenib (SOR), which targets KIT, PDGFRs, and several other kinases, has demonstrated efficacy in GIST patients after failure of IM and SU. We evaluated the in vitro activity of SOR against IM and/or SU resistant kinases. Methods: Kinase mutants were biochemically profiled for SOR, SU, and IM sensitivity by measuring inhibition of kinase phosphorylation after drug treatment in mutant-expressing CHO cells. We also tested the biochemical and cellular activity of SOR and IM against GIST cells derived from IM-resistant tumor clones. Results: SOR had superior potency to IM against IM-resistant KIT secondary mutations involving the ATP binding pocket (V654A, T670I) and the activation loop (D816H, D820A/G, N822K, Y823D). SOR and SU had similar potency against IM-resistant KIT secondary mutations involving the ATP binding pocket. In contrast, SOR had markedly increased potency, compared to SU, against IM-resistant KIT activation loop mutations. Both SOR and SU were more potent than IM against the isolated KIT exon 9 mutation. To confirm these observations in a GIST cellular context, we tested the relative potency of IM and SU against two previously described IM-resistant GIST cell lines (GIST430: exon 11 + V654A, GIST48: exon 11 + D820A). SOR was significantly more potent than IM against KIT in these cell lines. This also correlated with enhanced inhibition of downstream signaling pathways and cellular proliferation. Conclusions: SOR has superior in vitro potency compared with IM or SU against a panel of GIST-relevant mutant kinases. Notably, SOR, unlike SU, is active against most IM-resistant secondary mutations involving the KIT activation loop. Based on these results, we hypothesize that SOR might have superior clinical activity to SU in the setting of imatinib-resistant GIST and should be further evaluated for clinical efficacy in the second-line setting. [Table: see text]
Stabilization of a high-order harmonic generation seeded extreme ultraviolet free electron laser by time-synchronization control with electro-optic sampling (2015)

A fully coherent free electron laser (FEL) seeded with a higher-order harmonic (HH) pulse from high-order harmonic generation (HHG) is successfully operated for a sufficiently prolonged time in pilot user experiments by using a timing drift feedback. For HHG-seeded FELs, the seeding laser pulses have to be synchronized with electron bunches. Despite seeded FELs being non-chaotic light sources in principle, external laser-seeded FELs are often unstable in practice because of a timing jitter and a drift between the seeding laser pulses and the accelerated electron bunches. Accordingly, we constructed a relative arrival-timing monitor based on non-invasive electro-optic sampling (EOS). The EOS monitor made uninterrupted shot-to-shot monitoring possible even during the seeded FEL operation. The EOS system was then used for arrival-timing feedback with an adjustability of 100 fs for continual operation of the HHG-seeded FEL. Using the EOS-based beam drift controlling system, the HHG-seeded FEL was operated over half a day with an effective hit rate of 20%–30%. The output pulse energy was $20~{\rm\mu}\text{J}$ at the 61.2 nm wavelength. Towards seeded FELs in the water window region, we investigated our upgrade plan to seed high-power FELs with HH photon energy of 30–100 eV and lase at shorter wavelengths of up to 2 nm through high-gain harmonic generation (HGHG) at the energy-upgraded SPring-8 Compact SASE Source (SCSS) accelerator. We studied a benefit as well as the feasibility of the next HHG-seeded FEL machine with single-stage HGHG with tunability of a lasing wavelength.
Noise Control Engineering Education: Recommendations from the 2019 TQA Workshop (2021)

This paper summarizes recommendations about noise control engineering education made in a special session on noise control engineering education at NOISE-CON 2019 in San Diego and during an National Academy of Engineering (NAE)-hosted workshop under the auspices of the Technology of Quieter America (TQA) program. Speakers in both the special session and at the workshop represented industry, academe, and government emphasizing the need for more noise control engineers, the expertise required, and the areas in which they are needed. The ensuing discussions, summarized in two published reports, also point to the new technologies that affect noise control engineering education.