gebhart/patrepeval huggingface dataset:
Lipid membrane permeability of modified c[D‐Pen2, D‐pen5]enkephalin peptides (1996)

Permeability coefficients of a series of analogues of a potent opioid peptide, c[D-Pen2, D-Pen5]enkephalin, were measured in a model membrane system. The analogues included hydrophobic amino acid substitutions on position 3. Liposomes of a mixed composition consisting of zwitterionic lipids and cholesterol served as the model membranes. The obtained permeability coefficients range between 0.38 x 10(-12) and 2.9 x 10(-12) cm/s. These data were correlated with the hydrophobicity scale of Nozaki and Tanford (J. Biol. Chem. 246, 1971, 2211-2217) (correlation coefficient = 0.9933) and with determinations of lipid order perturbation by differential scanning calorimetry (correlation coefficient = -0.9779). The reasonably good correlation obtained within the family of analogues substituted on position 3 (Gly, Ala, Leu, Phe) indicates that changes in permeabilities are primarily related to increases in the partition coefficient of the peptide. However, Phe residue added on the N-terminal end of the peptide (position 0) does not appear to follow the observed trend, showing stronger lipid perturbation and lower permeability compared to the Phe3 analog. This observation demonstrates that each class of peptide modifications requires a new basis of permeability analysis and predictions.
Faculty Opinions recommendation of Nova regulates brain-specific splicing to shape the synapse. (2005)

Alternative RNA splicing greatly increases proteome diversity and may thereby contribute to tissue-specific functions. We carried out genome-wide quantitative analysis of alternative splicing using a custom Affymetrix microarray to assess the role of the neuronal splicing factor Nova in the brain. We used a stringent algorithm to identify 591 exons that were differentially spliced in the brain relative to immune tissues, and 6.6% of these showed major splicing defects in the neocortex of Nova2-/- mice. We tested 49 exons with the largest predicted Nova-dependent splicing changes and validated all 49 by RT-PCR. We analyzed the encoded proteins and found that all those with defined brain functions acted in the synapse (34 of 40, including neurotransmitter receptors, cation channels, adhesion and scaffold proteins) or in axon guidance (8 of 40). Moreover, of the 35 proteins with known interaction partners, 74% (26) interact with each other. Validating a large set of Nova RNA targets has led us to identify a multi-tiered network in which Nova regulates the exon content of RNAs encoding proteins that interact in the synapse. PMID: 16041372
Purification and characterization of the indole‐3‐glycerolphosphate synthase/anthranilate synthase complex of Saccharomyces cerevisiae (1985)

The indole-3-glycerolphosphate synthase/anthranilate synthase complex from Saccharomyces cerevisiae was purified to apparent homogeneity. The native complex with Mr approximately equal to 130 000 consists of two different subunits, the TRP2 gene product with Mr = 64 000 and the TRP3 gene product with Mr = 58 000. The larger polypeptide was identified as anthranilate synthase and is active in vitro with ammonia as cosubstrate without need of complex formation. The smaller polypeptide carries both glutamine amidotransferase activity and indole-3-glycerolphosphate synthase activity. Various steady-state kinetic parameters as well as the amino acid composition of the two polypeptides were determined.
Automatic operation of a high-precision Wheatstone bridge (1974)

A novel logic circuit which has been successfully applied to secure automatic operation of a high precision Wheatstone bridge is described. The method relies on the fact that the installation determines the instant of equilibrium of the resistance of a platinum wire subjected to a constant heat flux, thus giving highly accurate pairs of values of wire temperature and time. The logic circuit starts and stops six electronic counters in the right sequence and unbalances the bridge by a predetermined resistance after each equilibrium. The latter instant provides the signal to stop one preselected counter.
Photochemical DNA Activation (2007)

A new photocaged nucleoside was synthesized and incorporated into DNA with the use of standard synthesis conditions. This approach enabled the disruption of specific H-bonds and allowed for the analysis of their contribution to the activity of a DNAzyme. Brief irradiation with nonphotodamaging UV light led to rapid decaging and almost quantitative restoration of DNAzyme activity. The developed strategy has the potential to find widespread application in the light-induced regulation of oligonucleotide function.
DNA damage response at telomeres boosts the transcription of SARS-CoV-2 receptor ACE2 during aging (2021)

Abstract The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is known to be more common in the elderly, who show also more severe symptoms and a higher risk of hospitalization and death. Here we show that the expression of the Angiotensin Converting Enzyme 2 (ACE2), the SARS-CoV2 cell receptor, increases during aging in mouse and human lungs, and following telomere shortening or dysfunction in mammalian cells and in mouse models. This increase is regulated at the transcription level, and Ace2 promoter activity is DNA damage response (DDR)-dependent. Indeed, ATM inhibition or the selective inhibition of telomeric DDR, through the use of antisense oligonucleotides, prevents Ace2 upregulation following telomere damage, in cultured cells and in mice. We propose that during aging telomeric shortening, by triggering DDR activation, causes the upregulation of ACE2, the SARS-CoV2 cell receptor, thus making the elderly likely more susceptible to the infection.
An Open Vocabulary OCR System with Hybrid Word-Subword Language Models (2017)

The accuracy of a typical state-of-the-art optical character recognition (OCR) system benefits greatly from using a language model (LM). However, a conventional LM has a limited vocabulary, resulting in out-of-vocabulary (OOV) words that cannot be recognized by the OCR system. In this paper, we present an open vocabulary OCR system based on a hybrid LM. The vocabulary of the hybrid LM consists of both words and subwords. OOV words can be generated by combinations of subwords. A refined hybrid LM training scheme is applied by interpolating a standard hybrid LM, a word-based LM and a subword-based LM. An efficient word combination method is performed by modeling optional space symbols in a decoding network. The overall system deals with OOV words in a general, data-driven and language-independent way. We conduct experiments on an English handwriting OCR task. Evaluations on three testing sets demonstrate that the OCR system with the proposed method achieves a word error rate of 33.4% on an OOV-only testing set, yet without degrading the recognition accuracies on the other two testing sets mainly consisting of in-vocabulary words.
High efficient terahertz emission from InN surfaces (2007)

Abstract Terahertz radiation was measured from InN and compared to p‐InAs excited by femtosecond optical pulses at 1060 and 800 nm. At 800 nm, atomically smooth InN with low background electron concentration exhibit higher THz emission than the highly effective material p‐InAs. The higher THz emission efficiency of InN is caused by the absences of any intervalley scattering, which in the case of InAs increases the effective mass of the photo generated electrons and, thus, reduces the Dember field, which is responsible for THz emission. Consequently, InN is a promising material for THz emission; however, further improvement of the material quality (surface roughness and carrier concentration) is needed. (© 2007 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Synthesis and Biological Validation of a Harmine-Based, Central Nervous System (CNS)-Avoidant, Selective, Human β-Cell Regenerative Dual-Specificity Tyrosine Phosphorylation-Regulated Kinase A (DYRK1A) Inhibitor (2020)

Recently, our group identified that harmine is able to induce β-cell proliferation both in vitro and in vivo, mediated via the DYRK1A-NFAT pathway. Since, harmine suffers from a lack of selectivity, both against other kinases and CNS off-targets, we therefore sought to expand structure-activity relationships for harmine's DYRK1A activity, to enhance selectivity for off-targets while retaining human β-cell proliferation activity. We carried out optimization of the 9-<i>N</i>-position of harmine to synthesize 29 harmine-based analogs. Several novel inhibitors showed excellent DYRK1A inhibition and human β-cell proliferation capability. An optimized DYRK1A inhibitor, <b>2-2c</b>, was identified as a novel, efficacious in vivo lead candidate. <b>2-2c</b> also demonstrates improved selectivity for kinases and CNS off-targets, as well as in vivo efficacy for β-cell proliferation and regeneration at lower doses than harmine. Collectively, these findings demonstrate that <b>2-2c</b> is a much improved in vivo lead candidate as compared to harmine for the treatment of diabetes.
Studies of the source and mask optimization for 20nm node in the active layer (2012)

As semiconductor process technology moves to smaller dimension, RET (resolution enhancement technology) becomes more and more important, especially in low k1 processes. From 28nm node to 20nm node, the k1 becomes smaller with smaller dimension and pitch because exposure tool can provide larger NA (numerical aperture) or smaller exposure wavelength. SMO (source mask optimization) is a RET solution for low k1 process and provide better lithographic common process window in single exposure technology. Base on our studies of aerial image simulation and real wafer experiments on 20nm node, SMO could provide a better solution for 20nm node with 1.35 NA and 193nm exposure wavelength than the other RET sources (Quasar, C-Quad., Dipole). In the first step, the concerned patterns are important for the optimization because the main purpose of SMO is to obtain better performance in those. Through SMO iteration, we can find out a better source for our design rule and concerned patterns (like SRAM, and Small Island patterns). Then, we evaluate whether the simulation results can provide enough accuracy from real wafer data. Base on this study, we can develop a suitable SMO process for 20nm node. In this paper, we will show the optical theory, simulation result and wafer performance of SMO technology.
Wrapping TV Interface for Watching Multiple Programs Efficiently (2007)

We developed a TV browser user-interface called "wrapping interface" with clip and paste manners for watching multiple programs efficiently. We studied operations based on the concept of the wrapping interface and developed several prototypes, and we discussed additional ideas for enhancing the wrapping interface.
Breaking the $\epsilon$-Soundness Bound of the Linearity Test over GF(2) (2010)

For Boolean functions that are $\epsilon$-far from the set of linear functions, we study the lower bound on the rejection probability (denoted by $\textsc{rej}(\epsilon)$) of the linearity test suggested by Blum, Luby, and Rubinfeld [J. Comput. System Sci., 47 (1993), pp. 549–595]. This problem is arguably the most fundamental and extensively studied problem in property testing of Boolean functions. The previously best bounds for $\textsc{rej}(\epsilon)$ were obtained by Bellare et al. [IEEE Trans. Inform. Theory, 42 (1996), pp. 1781–1795]. They used Fourier analysis to show that $\textsc{rej}(\epsilon)\geq\epsilon$ for every $0\leq\epsilon\leq1/2$. They also conjectured that this bound might not be tight for $\epsilon$'s which are close to $1/2$. In this paper we show that this indeed is the case. Specifically, we improve the lower bound of $\textsc{rej}(\epsilon)\geq\epsilon$ by an additive constant that depends only on $\epsilon$: $\textsc{rej}(\epsilon)\geq\epsilon+\min\{1376\epsilon^{3}(1-2\epsilon)^{12},\frac{1}{4}\epsilon(1-2\epsilon)^{4}\}$, for every $0\leq\epsilon\leq1/2$. Our analysis is based on a relationship between $\textsc{rej}(\epsilon)$ and the weight distribution of a coset code of the Hadamard code. We use both Fourier analysis and coding theory tools to estimate this weight distribution.
Unit normalization of multinomials over Gaussian integers (2010)

Polynomials over the Gaussian integers Z[ i ] are a unique factorization domain, and the units in Z[ i ] are 1, -1, i and -- i . To implement the advantageous uniqueness, we might have to factor one of these units out of some multinomial factors to make all of the factors unit normal. Not doing so can lead to unnecessarily complicated results, disastrous unrecognized division by 0, and lost opportunities to obtain closed-form integrals, sums, limits, equation solutions, etc. For example, the default simplification of at least two major computer algebra systems don't recognize that the linear factors in the numerator and denominator of the following ratio are proportional, hence do not simplify the ratio to 1: -- i ((1 + i ) z + i ) / (1 -- i ) z + 1 →1. Unlike polynomials over the integers or rational numbers, the literature doesn't appear to address unit normalization over the Gaussian integers. Therefore this note proposes two alternative definitions. They are easy to implement, execute quickly, and can't greatly increase the bulk of an expression. Consequently they are good candidates for inclusion in the default simplification of every computer algebra system.
Noninvasive Assessment of Aqueous Humor Turnover in the Mouse Eye (2003)

Monitoring decay of fluorescence provides a noninvasive index of aqueous humor dynamics in the mouse eye that facilitates study of ocular hypotensive drugs and mouse models of glaucoma. Coupled with knowledge of IOP, it permits semiquantitative conclusions about the relative roles of aqueous humor inflow and outflow in conditions with altered IOP. Based on this approach, dimethylamiloride appears to lower mouse IOP primarily by enhancing outflow of aqueous humor.
SIGHInt: Special Interest Group for Human-Computer Integration (2021)

Human-Computer Integration (HInt) is a growing paradigm within HCI which seeks to understand how humans can, and already are, merging with computational machines. HInt’s recent inception and evolution has seen much discussion in a variety of symposiums, workshops, and publications for HCI. This has enabled a democratized and decentralised emergence of its core concepts. While this has allowed for rapid growth in our understanding of HInt, there is some discrepancy in how the proponents of this movement might describe its principles, motivations, definitions, and ultimate goals, with many offshoot concepts of HInt beginning to emerge. SIGHint aims to provide a platform to facilitate high level discussion and collation of information between researchers and designers seeking to learn from and contribute to the development of Human-Computer Integration. It is our intention that through this SIG we may better understand how new and emerging, diverging ideas, and perspectives within Human-Computer Integration relate to each other, ultimately facilitating a mapping of the paradigm and a synthesis of its concepts.
Serologic Evidence forCryptococcus neoformansInfection in Early Childhood (2001)

Our findings provide both indirect and direct evidence of C neoformans infection in immunocompetent children. Our results indicate that C neoformans infects a majority of children living in the Bronx after 2 years old. These results are consistent with several observations: the ubiquitous nature of C neoformans in the environment, including its association with pigeon excreta; the large number of pigeons in urban areas; and the increased likelihood of environmental exposure for children once they have learned to walk. The signs and symptoms associated with C neoformans infection in immunocompetent children remained to be determined. Primary pulmonary cryptococcosis may be asymptomatic or produce symptoms confused with viral infections and, therefore, not recognized as a fungal infection. Our results suggest that the low incidence of symptomatic cryptococcal disease in children with AIDS is not a result of lack of exposure to C neoformans. These findings have important implications for C neoformans pathogenesis and the development of vaccine strategies.
Immunodetection of Estrogen Receptor and 52,000-Dalton Protein in Fine Needle Aspirates of Breast Cancer Tumors<xref ref-type="fn" rid="FN2">2</xref><xref ref-type="fn" rid="FN3">3</xref> (1987)

The double immunohistochemical detection of estrogen receptor (ER) and the estrogen-regulated 52,000-dalton protein (52kDa-P) was performed on 35 fine needle aspirates of primary breast cancers. The nuclear ER, stained brown, was differentiated from the 52kDa-P, stained in red, in the cytoplasm of the same cells. The significant correlation obtained between the percentages of positive aspirated cells and the cytosolic concentrations of these two markers showed the validity of semiquantitative detection in fine needle aspirates, which appeared to be more representative of the content of these markers in tumors than was the detection in a single tissue section. Tumor heterogeneity also was defined by this double immunostaining, since among the tumors positive for both ER and 52kDa-P (18 of 35 cases), a heterogeneous group of 12 tumors contained the markers in two distinct cell populations, whereas a more homogeneous group of 6 tumors contained double-stained cells. The first information provided by this study is that the 52kDa-P is not correlated with the ER. This absence of correlation is in accordance with other studies and indicates that the 52kDa-P is associated with tumor proliferation and possibly invasion, rather than with hormone responsiveness or differentiation. The feasibility and validity of double immunostaining of these two markers in human breast cancer aspirates should stimulate larger studies--with clinical follow-up of the patients--aimed at establishing the clinical usefulness of this presurgical test.
Optimization of medium with perfusion microbioreactors for high density CHO cell cultures at very low renewal rate aided by design of experiments (2023)

A novel approach of design of experiment (DoE) is developed for the optimization of key substrates of the culture medium, amino acids, and sugars, by utilizing perfusion microbioreactors with 2 mL working volume, operated in high cell density continuous mode, to explore the design space. A mixture DoE based on a simplex-centroid is proposed to test multiple medium blends in parallel perfusion runs, where the amino acids concentrations are selected based on the culture behavior in presence of different amino acid mixtures, and using targeted specific consumption rates. An optimized medium is identified with models predicting the culture parameters and product quality attributes (G0 and G1 level N-glycans) as a function of the medium composition. It is then validated in runs performed in perfusion microbioreactor in comparison with stirred-tank bioreactors equipped with alternating tangential flow filtration (ATF) or with tangential flow filtration (TFF) for cell separation, showing overall a similar process performance and N-glycosylation profile of the produced antibody. These results demonstrate that the present development strategy generates a perfusion medium with optimized performance for stable Chinese hamster ovary (CHO) cell cultures operated with very high cell densities of 60 × 10<sup>6</sup> and 120 × 10<sup>6</sup> cells/mL and a low cell-specific perfusion rate of 17 pL/cell/day, which is among the lowest reported and is in line with the framework recently published by the industry.
Employing a 2D surface grating to improve light out coupling of a substrate emitting organic LED (2007)

We present simulation and experimental results to achieve increased light extraction of a substrate emitting OLED. We present a comparison between a grating surface on the OLED and an array of microlenses at the interface between substrate and air. This experimentally gives -in both cases- a relative improvement of approx. 30 %. We also demonstrate the concept of a RC<sup>2</sup>LED, applied to an OLED. The RC<sup>2</sup>LED is composed by adding a high, low and high index layers between ITO and glass, i.e. the interface between organic layers and glass. These extra layers create a cavity which numerically gives a relative improvement of over 60% at the resonance wavelength of the cavity over a wavelength range of 50-100 nm. The influence of an array of micro lenses in addition to the RC<sup>2</sup> layers is also investigated in this paper.
Supplementary Table S1 from <i>Nedd9</i> Restrains Autophagy to Limit Growth of Early Stage Non–Small Cell Lung Cancer (2023)

&lt;p&gt;Antibodies used in study&lt;/p&gt;
Positive streamer discharges along insulating surfaces (2001)

By measuring the currents associated with the streamer discharge along silicone rubber surfaces, parameters of streamer propagation such as the minimum field of streamer crossing, the field of stable streamer propagation, the mean velocity and the streamer charge distribution have been analyzed and compared to the streamer discharge in air alone. Clear differences were observed in the measured currents for the individual surfaces at low background fields (285 kV/m). For higher fields the streamer crosses the gap almost independently of the surface type. The minimum streamer field was found to be slightly increased compared to air. The field of stable streamer propagation also was higher than in air. It is /spl sim/ 570 kV/m, larger than that of the streamer discharge in air (/spl sim/ 500), under the same conditions. The streamer speed was found slightly increased in the presence of the silicone rubber surface and the distinction between the individual surfaces was modest. A discussion on possible mechanisms for the observed differences in the streamer speed and currents with and without the insulator surfaces is presented. The net positive charge of the streamer along an insulating surface seems to be distributed along the streamer channel rather than localized in the front part of the channel as the case for the streamer in air.
A Nanoparticle Based Sp17 Peptide Vaccine Exposes New Immuno-Dominant and Species Cross-reactive B Cell Epitopes (2015)

Sperm protein antigen 17 (Sp17), expressed in primary as well as in metastatic lesions in >83% of patients with ovarian cancer, is a promising ovarian cancer vaccine candidate. Herein we describe the formulation of nanoparticle based vaccines based on human Sp17 (hSp17) sequence derived peptides, and map the immuno-dominant T cell and antibody epitopes induced using such formulations. The primary T and B cell immuno-dominant region within Sp17 was found to be the same when using biocompatible nanoparticle carriers or the conventional "mix-in" pro-inflammatory adjuvant CpG, both mapping to amino acids (aa) 111-142. However, delivery of hSp17111-142 as a nanoparticle conjugate promoted a number of new properties, changing the dominant antibody isotype induced from IgG2a to IgG1 and the fine specificity of the B cell epitopes within hSp17111-142, from an immuno-dominant region 134-142 aa for CpG, to region 121-138 aa for nanoparticles. Associated with this change in specificity was a substantial increase in antibody cross-reactivity between mouse and human Sp17. These results indicate conjugation of antigen to nanoparticles can have major effects on fine antigen specificity, which surprisingly could be beneficially used to increase the cross-reactivity of antibody responses.