gebhart/patrepeval huggingface dataset:
Abstract 4396: Conjugation site modulates the stability and biological activity of antibody drug conjugates (2010)

Abstract Antibody drug conjugates (ADCs) are attractive targeted chemo-therapeutic molecules as they combine ideal properties of both antibodies and cytotoxic drugs by targeting potent cytotoxic drugs to the antigen-expressing tumor cells, thereby enhancing their anti-tumor activity. The successful ADC development for a given target antigen depends on optimization of antibody selection, linker stability, cytotoxic drug potency and mode of linker-drug conjugation to the antibody. Recently, we have developed antibodies with cysteine substitutions (THIOMABs) at sites where the engineered cysteines are available for conjugation but do not perturb immunoglobulin folding and assembly or alter antigen binding and effector functions (Junutula, et al., Nature Biotech., 26, 925-932, 2008). These THIOMABs can then be derivatized through the engineered cysteine thiol group to obtain ADCs with uniform stoichiometry (∼2 drugs per antibody). Studies with multiple antibodies against different antigens have shown that THIOMAB drug conjugates (TDCs) are as efficacious as conventional conjugates in xenograft models and are tolerated at higher doses in relevant preclinical models. To further understand improved therapeutic activity and in vivo metabolism of TDCs, we have engineered TDCs with drug attachment at different parts of the antibody (light chain-Fab, heavy chain-Fab and heavy chain-Fc). TDCs produced by THIOMAB technology provided an unique advantage over conventional ADCs to answer several unresolved questions in ADC therapeutics due to their homogeneity and site-specific conjugation to cytotoxic drugs. We will discuss novel findings that were observed with these TDC varaints and the influence of conjugation site in modulating stability and biological activity of antibody drug conjugates. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4396.
Live Respiratory Syncytial Virus Attenuated by M2-2 Deletion and Stabilized Temperature Sensitivity Mutation 1030s Is a Promising Vaccine Candidate in Children (2019)

LID/ΔM2-2/1030s had excellent infectivity without evidence of genetic instability, induced durable immunity, and primed for anamnestic antibody responses, making it an attractive candidate for further evaluation.
CALIBRATION OF THE QESTRAL MODEL FOR THE PREDICTION OF SPATIAL QUALITY (2023)

The QESTRAL model is a perceptual model that aims to predict changes to spatial quality of service (SQoS) between the soundfield reproduced by a reference system and that of an impaired version of the reference system. To calibrate the model subjective data collected from listening tests is required. The QESTRAL model is designed to be format independent and therefore it relies on acoustical measurements of the reproduced soundfield derived using probe signals (or test signals). The measurements are used to create a series of perceptually motivated metrics, which are then fitted to the subjective data using a statistical model. This paper has two parts. The first part describes the implementation and results of a listening experiment designed to investigate changes to spatial quality. The second part, presents results from a calibration and forecasts prediction power (via cross-validation) of the QESTRAL model.
Single particle tracking through highly scattering media with multiplexed two-photon excitation (2015)

3D single-particle tracking (SPT) has been a pivotal tool to furthering our understanding of dynamic cellular processes in complex biological systems, with a molecular localization accuracy (10-100 nm) often better than the diffraction limit of light. However, current SPT techniques utilize either CCDs or a confocal detection scheme which not only suffer from poor temporal resolution but also limit tracking to a depth less than one scattering mean free path in the sample (typically <15μm). In this report we highlight our novel design for a spatiotemporally multiplexed two-photon microscope which is able to reach sub-diffraction-limit tracking accuracy and sub-millisecond temporal resolution, but with a dramatically extended SPT range of up to 200 μm through dense cell samples. We have validated our microscope by tracking (1) fluorescent nanoparticles in a prescribed motion inside gelatin gel (with 1% intralipid) and (2) labeled single EGFR complexes inside skin cancer spheroids (at least 8 layers of cells thick) for ~10 minutes. Furthermore we discuss future capabilities of our multiplexed two-photon microscope design, specifically to the extension of (1) simultaneous multicolor tracking (i.e. spatiotemporal co-localization analysis) and (2) FRET studies (i.e. lifetime analysis). The high resolution, high depth penetration, and multicolor features of this microscope make it well poised to study a variety of molecular scale dynamics in the cell, especially related to cellular trafficking studies with in vitro tumor models and in vivo.
Block Size Optimization in Deduplication Systems (2009)

Data deduplication is a popular dictionary based compression method in storage archival and backup. The deduplication efficiency improves for smaller chunk sizes, however the files become highly fragmented requiring many disk accesses during reconstruction or chattiness in a client-server architecture. Within the sequence of chunks that an object (file) is decomposed into, sub-sequences of adjacent chunks tend to repeat. We exploit this insight to optimize the chunk sizes by joining repeated sub-sequences of small chunks into new super chunks with the constraint to achieve practically the same matching performance. We employ suffix arrays to find these repeating sub-sequences and to determine a new encoding that covers the original sequence. With super chunks we significantly reduce fragmentation, improving reconstruction time and the overall deduplication ratio by lowering the amount of metadata. As a result, fewer chunks are used to represent a file, reducing the number of disk accesses needed to reconstruct the file and requiring fewer entries in the chunk dictionary and fewer hashes to encode a file. To encode a sequence of chunks we proved two facts: (1) any subsequence that repeats is part of some super chunk (su- permaximal in Figure 1) - therefore the dictionary contains just supermaximals and non-repeats, and (2) maximals are the only repeats not covered (overlapped) by the containing supermaximals - so once we discover the maximals with the suffix array, and encode them, there is no need for maintaining auxiliary data structures like bit masks, to guarantee the coverage (encoding) of the entire object. Our experimental evaluation (Figure 2) yields a reduction in fragmentation between 89%-97% and a reduction of dictionary metadata (number of entries) between 80%-97%, without increasing the total amount of storage required for unique chunks.
Antineoplastic agents. 190. Isolation and structure of the cyclodepsipeptide dolastatin 14 (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAntineoplastic agents. 190. Isolation and structure of the cyclodepsipeptide dolastatin 14George R. Pettit, Yoshiaki Kamano, Cherry L. Herald, Claude Dufresne, Robert B. Bates, Jean M. Schmidt, Ronald L. Cerny, and Haruhisa KizuCite this: J. Org. Chem. 1990, 55, 10, 2989–2990Publication Date (Print):May 1, 1990Publication History Published online1 May 2002Published inissue 1 May 1990https://pubs.acs.org/doi/10.1021/jo00297a001https://doi.org/10.1021/jo00297a001research-articleACS PublicationsRequest reuse permissionsArticle Views204Altmetric-Citations51LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Demonstration of single crystal growth via solid-solid transformation of a glass (2016)

Many advanced technologies have relied on the availability of single crystals of appropriate material such as silicon for microelectronics or superalloys for turbine blades. Similarly, many promising materials could unleash their full potential if they were available in a single crystal form. However, the current methods are unsuitable for growing single crystals of these oftentimes incongruently melting, unstable or metastable materials. Here we demonstrate a strategy to overcome this hurdle by avoiding the gaseous or liquid phase, and directly converting glass into a single crystal. Specifically, Sb2S3 single crystals are grown in Sb-S-I glasses as an example of this approach. In this first unambiguous demonstration of an all-solid-state glass → crystal transformation, extraneous nucleation is avoided relative to crystal growth via spatially localized laser heating and inclusion of a suitable glass former in the composition. The ability to fabricate patterned single-crystal architecture on a glass surface is demonstrated, providing a new class of micro-structured substrate for low cost epitaxial growth, active planar devices, etc.
Orthopedic rehabilitation using the "Rutgers ankle" interface. (2000)

A novel ankle rehabilitation device is being developed for home use, allowing remote monitoring by therapists. The system will allow patients to perform a variety of exercises while interacting with a virtual environment (VE). These game-like VEs created with WorldToolKit run on a host PC that controls the movement and output forces of the device via an RS232 connection. Patients will develop strength, flexibility, coordination, and balance as they interact with the VEs. The device will also perform diagnostic functions, measuring the ankle's range of motion, force exertion capabilities and coordination. The host PC transparently records patient progress for remote evaluation by therapists via our existing telerehabilitation system. The "Rutgers Ankle" Orthopedic Rehabilitation Interface uses double-acting pneumatic cylinders, linear potentiometers, and a 6 degree-of-freedom (DOF) force sensor. The controller contains a Pentium single-board computer and pneumatic control valves. Based on the Stewart platform, the device can move and supply forces and torques in 6 DOFs. A proof-of-concept trial conducted at the University of Medicine and Dentistry of New Jersey (UMDNJ) provided therapist and patient feedback. The system measured the range of motion and maximum force output of a group of four patients (male and female). Future medical trials are required to establish clinical efficacy in rehabilitation.
Identification of Threshold Functions and Synthesis of Threshold Networks (2011)

This paper presents a new and efficient heuristic procedure for determining whether or not a given Boolean function is a threshold function, when the Boolean function is given in the form of a decision diagram. The decision diagram based method is significantly different from earlier methods that are based on solving linear inequalities in Boolean variables that derived from truth tables. This method's success depends on the ordering of the variables in the binary decision diagram (BDD). An alternative data structure, and one that is more compact than a BDD, called a max literal factor tree (MLFT) is introduced. An MLFT is a particular type of factoring tree and was found to be more efficient than a BDD for identifying threshold functions. The threshold identification procedure is applied to the MCNC benchmark circuits to synthesize threshold gate networks.
New LP-derived features for speaker identification (1994)

A new set of features is introduced that has been found to improve the performance of automatic speaker identification systems, The new set of features is referred to as the adaptive component weighting (ACW) cepstral coefficients. The new features emphasize the formant structure of the speech spectrum while attenuating the broad-bandwidth spectral components. The attenuated components correspond to the variations in spectral tilt of transmission and recording environment, and other characteristics that are irrelevant to speaker identification. The resulting ACW spectrum introduces zeros into the usual all-pole linear prediction (LP) spectrum. This is equivalent to applying a finite impulse response (FIR) filter that normalizes the narrow-band modes of the spectrum. Unlike existing fixed cepstral weighting schemes, the ACW cepstrum provides an adaptively weighted version of the LP cepstrum. The adaptation results in deemphasizing the irrelevant variations of the LP cepstral coefficients on a frame-by-frame basis. The ACW features are evaluated for text-independent speaker identification and are shown to yield improved performance.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A highly efficient fire‐retardant nanomaterial based on carbon nanotubes and magnesium hydroxide (2012)

SUMMARY Hybrid buckypapers (HBP) were developed and showed potential as efficient fire‐retardant materials by implementing multiple fire retardance mechanisms. The fabrication of HBP was performed using multi‐walled carbon nanotubes (MWCNTs) and magnesium hydroxide (Mg(OH) 2 ) nanoparticles. The Mg(OH) 2 nanoparticles were well dispersed throughout the CNTs network, as revealed by scanning electron microscopy and Energy Dispersive X‐ray spectroscopy. Thermogravimetric analysis and differential scanning calorimetry both confirmed the decomposition of magnesium hydroxide in the HBPs and heat absorption under elevated temperatures. Our initial results indicated that when used as a skin layer, the HBP has the potential to significantly improve the fire‐retardant properties of epoxy carbon fiber composites. Copyright © 2012 John Wiley & Sons, Ltd.
SAW Analysis of the MgxZn1-xO/SiO2/Si System (2003)

Magnesium zinc oxide (MgxZn1-xO) is a new piezoelectric material formed by alloying ZnO and MgO. In this study, the SAW velocity dispersion and electro-mechanical coupling coefficients (K 2 )i n the MgxZn1-xO (x=0-30%)/SiO2/Si system are analyzed using the transfer matrix method. Si is chosen as the substrate for potential integration of SAW devices with the main stream integrated circuits technology. The use of different Mg content in MgxZn1-xO films leads to change in piezoelectric properties. The SAW characteristics of the system can be further tailored by varying the thickness ratio between the MgxZn1-xO and SiO2 layers. The effect of different MgxZn1-x Ot o SiO2 thickness ratios on SAW propagation in the multilayer structure is investigated. Four possible multilayer SAW device configurations, including IDT/MgxZn1-xO/SiO2/Si, MgxZn1-xO/ IDT/ SiO2 /S i, IDT/ MgxZn1-xO/ metal ground plane/ SiO2/ Si, and metal ground plane/ MgxZn1-xO/ IDT/ SiO2/ Si, are studied. It is found that at the high frequency range, with each 10% increase of the Mg content in the MgxZn1-xO, SAW velocity increases by 5~8%, whereas K 2 decreases by around 30%. With same IDT configuration, VSAW decreases as SiO 2 layer thickens. However, as MgxZn1-xO thickness- frequency products hf reach high values, the SAW energy for the base wave mode is trapped in the MgxZn1-xO layer and the thickness of SiO2 no longer affects the SAW propagation. The multilayer configurations also play an important role. It is found that the MgxZn1-xO/ IDT/ SiO2 /S i configuration with MgxZn1-xO: SiO2=2:1 yields the highest coupling coefficient (x=0) and the highest SAW velocity (x=0.3). The current study indicates that using MgxZn1-xO-based multilayer structures will provide flexibility in SAW device design as well as the ability to tailor SAW properties.
Immunoprecipitation of Native Botulinum Neurotoxin Complexes from Clostridium botulinum Subtype A Strains (2014)

Botulinum neurotoxins (BoNTs) naturally exist as components of protein complexes containing nontoxic proteins. The nontoxic proteins impart stability of BoNTs in the gastrointestinal tract and during purification and handling. The two primary neurotoxin complexes (TCs) are (i) TC1, consisting of BoNT, nontoxin-nonhemagglutinin (NTNH), and hemagglutinins (HAs), and (ii) TC2, consisting of BoNT and NTNH (and possibly OrfX proteins). In this study, BoNT/A subtypes A1, A2, A3, and A5 were examined for the compositions of their TCs in culture extracts using immunoprecipitation (IP). IP analyses showed that BoNT/A1 and BoNT/A5 form TC1s, while BoNT/A2 and BoNT/A3 form TC2s. A Clostridium botulinum host strain expressing recombinant BoNT/A4 (normally present as a TC2) from an extrachromosomal plasmid formed a TC1 with complexing proteins from the host strain, indicating that the HAs and NTNH encoded on the chromosome associated with the plasmid-encoded BoNT/A4. Strain NCTC 2916 (A1/silent B1), which carries both an ha silent bont/b cluster and an orfX bont/a1 cluster, was also examined. IP analysis revealed that NCTC 2916 formed only a TC2 containing BoNT/A1 and its associated NTNH. No association between BoNT/A1 and the nontoxic proteins from the silent bont/b cluster was detected, although the HAs were expressed as determined by Western blotting analysis. Additionally, NTNH and HAs from the silent bont/b cluster did not form a complex in NCTC 2916. The stabilities of the two types of TC differed at various pHs and with addition of KCl and NaCl. TC1 complexes were more stable than TC2 complexes. Mouse serum stabilized TC2, while TC1 was unaffected.
Characterization of the promoter for the human P-selectin gene. (1993)

P-selectin, an adhesion receptor for leukocytes, is synthesized selectively by megakaryocytes and endothelial cells. We have cloned the 5'-flanking region of the human P-selectin gene and conducted a preliminary analysis of its features. As determined by primer extension, RNase protection, and anchored polymerase chain reaction cloning, there were multiple transcriptional initiation sites from -95 to -25 nucleotides relative to the start of protein-coding sequence. Transfection of bovine aortic endothelial cells with serially truncated segments of the 5'-flanking region linked to luciferase indicated that the sequence from -249 to -13 was sufficient to promote high level gene expression. Deletions to -197, -147, and -128 gradually reduced expression to basal levels, and further deletion to -100 abolished expression. The sequence from -309 to -13 supported only basal luciferase expression in COS-7, 293, or HeLa cells. Putative regulatory elements in the short 5'-flanking sequence included a CACCC sequence, two inverted repeats similar to binding sites for the ETS and NF-kappa B/rel families, a GATA motif, and a sequence related to the GT-IIC element of the SV40 enhancer. The GATA element was functional, as it bound recombinant GATA-2, and mutations in the core sequence impaired both nuclear protein binding and gene expression. These data suggest that the P-selectin gene is regulated by a combination of cis elements and their cognate transcription factors.
Probing allelochemical biosynthesis in sorghum root hairs (2008)

Allelopathic interaction between plants is thought to involve the release of phytotoxic allelochemicals by one species, thus inhibiting the growth of neighboring species in competition for limited resources. Sorgoleone represents one of the more potent allelochemicals characterized to date, and its prolific production in root hair cells of Sorghum spp. has made the investigation of its biosynthetic pathway ideally-suited for functional genomics investigations. Through the use of a recently-released EST data set generated from isolated Sorghum bicolor root hair cells, significant inroads have been made toward the identification of genes and the corresponding enzymes involved in the biosynthesis of this compound in root hairs. Here we provide additional information concerning our recent report on the identification of a 5-n-alk(en) ylresorcinol utilizing O-methyltransferase, as well as other key enzymes likely to participate in the biosynthesis of this important allelochemical.
Algorithms and architectures for low power spike detection and alignment (2006)

We introduce algorithms and architectures for automatic spike detection and alignment that are designed for low power. Some of the algorithms are based on principal component analysis (PCA). Others employ a novel integral transform analysis and achieve 99% of the precision of a PCA detector, while requiring only 0.05% of the computational complexity. The algorithms execute autonomously, but require off-line training and setting of computational parameters. We employ pre-recorded neuronal signals to evaluate the accuracy of the proposed algorithms and architectures: the recorded data are processed by a standard PCA spike detection and alignment software algorithm, as well as by the several hardware algorithms, and the outcomes are compared.
New array codes for multiple phased burst correction (1993)

An optimal family of array codes over GF(q) for correcting multiple phased burst errors and erasures, where each phased burst corresponds to an erroneous or erased column in a code array, is introduced. As for erasures, these array codes have an efficient decoding algorithm which avoids multiplications (or divisions) over extension fields, replacing these operations with cyclic shifts of vectors over GF(q). The erasure decoding algorithm can be adapted easily to handle single column errors as well. The codes are characterized geometrically by means of parity constraints along certain diagonal lines in each code array, thus generalizing a previously known construction for the special case of two erasures. Algebraically, they can be interpreted as Reed-Solomon codes. When q is primitive in GF(q), the resulting codes become (conventional) Reed-Solomon codes of length P over GF(q/sup p-1/), in which case the new erasure decoding technique can be incorporated into the Berlekamp-Massey algorithm, yielding a faster way to compute the values of any prescribed number of errors.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Association of a Marker of <i>N</i>-Acetylglucosamine With Progressive Multiple Sclerosis and Neurodegeneration (2021)

This study suggests that deficiency of GlcNAc plus its stereoisomers (HexNAc) may be a biomarker for PMS. Previous preclinical, human genetic, and ex vivo human mechanistic studies revealed that N-glycan branching and/or GlcNAc may reduce proinflammatory responses, promote myelin repair, and decrease neurodegeneration. Combined, the data suggest that GlcNAc deficiency may be associated with progressive disease and neurodegeneration in patients with MS.