gebhart/patrepeval huggingface dataset:
Facile repurposing of peptide–MHC-restricted antibodies for cancer immunotherapy (2023)

Monoclonal antibodies (Abs) that recognize major histocompatability complex (MHC)-presented tumor antigens in a manner similar to T cell receptors (TCRs) have great potential as cancer immunotherapeutics. However, isolation of 'TCR-mimic' (TCRm) Abs is laborious because Abs have not evolved the structurally nuanced peptide-MHC restriction of αβ-TCRs. Here, we present a strategy for rapid isolation of highly peptide-specific and 'MHC-restricted' Abs by re-engineering preselected Abs that engage peptide-MHC in a manner structurally similar to that of conventional αβ-TCRs. We created structure-based libraries focused on the peptide-interacting residues of TCRm Ab complementarity-determining region (CDR) loops, and rapidly generated MHC-restricted Abs to both mouse and human tumor antigens that specifically killed target cells when formatted as IgG, bispecific T cell engager (BiTE) and chimeric antigen receptor-T (CAR-T). Crystallographic analysis of one selected pMHC-restricted Ab revealed highly peptide-specific recognition, validating the engineering strategy. This approach can yield tumor antigen-specific antibodies in several weeks, potentially enabling rapid clinical translation.
Cell identification performance based on hierarchical synchronization channels in dense small cell environment (2013)

In order to cope with the dramatic growth in the amount of data traffic, future radio access networks may consist of a large number of small cells that are densely deployed. In this paper, we focus on the identification of densely deployed small cells based on hierarchical synchronization channels specified in the Long Term Evolution (LTE) standard. The contribution of this paper is that the cell identification performance based on hierarchical synchronization channels and the problem of cell identification in a dense deployment scenario are clarified. Simulation results show that a set of user equipment (UE) applying the LTE cell identification algorithm can identify at least one small cell even in a dense deployment scenario; however, the UE can only identify a few small cells that are close to it. Furthermore, if we assume a synchronized network, miss-identification sometimes occurs due to pilot signal interference even though the received signal power of the small cell is sufficiently high. Based on the results of cell identification, we also clarify the relationship among the cell density, cell identification interval, UE speed, and quality of the connection. Initial evaluation results show that medium or high-speed UEs should employ a short cell identification interval to avoid degradation in the connection link quality; however, such UEs may suffer from higher battery consumption due to the frequent cell identification.
Single-molecule electron diffraction imaging with charge replacement (2008)

We investigate the possibility of non-destructive electron diffraction imaging of a single molecule to determine its structure. The molecular specimen will be held on a free-standing sheet of graphene. Due to the high conductivity of graphene, electrons lost by ionization would be rapidly replaced, enabling repeated nondestructive interrogation. Limits of resolution, maximum particle size and required electron flux are assessed.
The cobalt corrole catalyzed hydrogen evolution reaction: surprising electronic effects and characterization of key reaction intermediates (2014)

A surprising effect of halide substituents on reduction potentials and catalytic activity of halogenated cobalt corroles has been deduced by experimental and computational methods; the proton-activating cobalt(I) and the cobalt(II) corrole that is formed in the step during which hydrogen is formed are characterized by NMR spectroscopy.
Syntheses and X-ray characterization of metal complexes with the pentadentate thiosemicarbazone ligand bis(4-N-methylthiosemicarbazone)-2,6-diacetylpyridine. The first pentacoordinate lead(ii) complex with a pentagonal geometry (2004)

In this paper we describe the electrochemical synthesis and characterization of new neutral manganese, iron, cobalt, nickel, copper, zinc, cadmium and lead complexes with the ligand bis(4-N-methylthiosemicarbazone)-2,6-diacetylpyridine, H4DAPTsz-Me. X-Ray structures of [Mn(H2DAPTsz-Me)(EtOH)2] 1, [Pb(H2DAPTsz-Me)] 3 and [Zn(H2DAPTsz-Me)]2.EtOH.2H2O 4, were also determined. In these complexes the ligand behaves as bis-deprotonated and SNNNS pentadentate. In the manganese complex the metal is heptacoordinated, in a distorted pentagonal-bipyramidal environment, with the N3S2 donor set of the ligand in the pentagonal girdle and two solvent molecules occupying the axial positions. In the lead complex 3 the metal is pentacoordinated, bound exclusively to the five donor atoms of the ligand, as a consequence of the existence of "inert pair effect". The bishelical zinc complex 4 shows each zinc atom with different coordination geometry, one octahedrally six-coordinate while the other is distorted tetrahedrally four-coordinate.
Optimized collectives using a DMA on a parallel computer (2023)

Optimizing collective operations using direct memory access controller on a parallel computer, in one aspect, may comprise establishing a byte counter associated with a direct memory access controller for each submessage in a message. The byte counter includes at least a base address of memory and a byte count associated with a submessage. A byte counter associated with a submessage is monitored to determine whether at least a block of data of the submessage has been received. The block of data has a predetermined size, for example, a number of bytes. The block is processed when the block has been fully received, for example, when the byte count indicates all bytes of the block have been received. The monitoring and processing may continue for all blocks in all submessages in the message.
MPPC technique for gate etch process monitoring using CD-SEM images and its validity verification (2004)

The effectiveness of multiple parameter profile characterization (MPPC) as a three-dimensional measurement technique for etched gates is examined by comparison of shape indices with device performance. The MPPC method derives shape indices from top-down, critical-dimension scanning electron microscopy (CD-SEM) images to characterize the sidewall angle and footing roundness of the gate, which are considered to be the structural features that have a great effect on device performance. The capabilities of the proposed method are evaluated through experiments using processed gate wafers etched under different conditions, comparing the shape indices with the cross-sectional profiles obtained by atomic force microscopy. The relationship between the MPPC indices and threshold voltage is also investigated, confirming that variations in sidewall angle and footing roundness have several times the impact on threshold voltage as line width variation. This study confirms the importance of three-dimensional measurement of gate profiles for process monitoring through the use of a method such as MPPC.
Therapeutic Drug Monitoring of Anti-TNFα Inhibitors: A Matter of Cut-Off Ranges (2023)

Therapeutic drug monitoring (TDM) is a useful tool for optimising the use of anti-TNFα inhibitors in patients with inflammatory bowel diseases (IBDs). Recently, point-of-care methods for the quantification of drug levels and anti-drug antibodies (ADAs) have been developed to overcome the limitations of conventional enzyme-linked immunoabsorbent assays (ELISAs). Here, we evaluated the performance, interchangeability, and agreement between an automated ELISA-based immunoassay (CHORUS Promonitor) and the lateral flow assay (RIDA<sup>®</sup>QUICK) for the quantification of infliximab (IFX, <i>n</i> = 65) and adalimumab (ADM, <i>n</i> = 58) plasma levels in IBD patients. Thirty-two samples for IFX and twenty-three samples for ADM that tested positively for the presence of ADAs were also used. Overall, data analysis showed a good agreement of ADM trough concentrations (R<sup>2</sup> = 0.75) between the two assays as well as for ADA measurement (K > 0.8). However, IFX levels highlighted a weak correlation (R<sup>2</sup> = 0.58) between the two kits, with the RIDA<sup>®</sup>QUICK assay overestimating IFX plasma values by 30% when compared to the CHORUS Promonitor kit. Results from this study show that the two assays are not quantitatively and qualitatively interchangeable due to substantial discrepancies in some results. Accordingly, the same assay should be used for the longitudinal follow-up of IBD patients.
Variable-angle directional emissometer for moderate-temperature emissivity measurements (2008)

We have developed a system to measure the directional thermal emission from a surface, and in turn, calculate its emissivity. This approach avoids inaccuracies sometimes encountered with the traditional method for calculating emissivity, which relies upon subtracting the measured total reflectivity and total transmissivity from unity. Typical total reflectivity measurements suffer from an inability to detect backscattered light, and may not be accurate for high angles of incidence. Our design allows us to vary the measurement angle (&theta;) from near-normal to ~80&deg;, and can accommodate samples as small as 7 mm on a side by controlling the sample interrogation area. The sample mount is open-backed to eliminate shine-through, can be heated up to 200 &deg;C, and is kept under vacuum to avoid oxidizing the sample. A cold shield reduces the background noise and stray signals reflected off the sample. We describe the strengths, weaknesses, trade-offs, and limitations of our system design, data analysis methods, the measurement process, and present the results of our validation of this Variable-Angle Directional Emissometer.
Systems biology surveillance decrypts pathological transcriptome remodeling (2015)

Diagnostic surveillance, through an algorithm that integrates pluripotent stem cell transcriptomes with advanced high throughput assays and computational bioinformatics, revealed collective gene expression network changes that underlie differential phenotype development. Stem cell transcriptomes provide a deep collective molecular index that reflects ad hoc robustness of the pluripotent gene network. Remodeling events such as monogenic lesions provide a background by which high priority candidate disease effectors and regulators can be identified, demonstrated here by a molecular profiling algorithm that decrypts pluripotent wild type versus disrupted genomes.
Most of rare missense alleles in humans are deleterious: implications for evolution of \ncomplex disease and association studies (2006)

The accumulation of mildly deleterious missense mutations in individual human genomes has been proposed to be a genetic basis for complex diseases. The plausibility of this hypothesis depends on quantitative estimates of the prevalence of mildly deleterious de novo mutations and polymorphic variants in humans and on the intensity of selective pressure against them. We combined analysis of mutations causing human Mendelian diseases, human-chimpanzee divergence and systematic data on human SNPs and found that about 20 percent of new missense mutations in humans result in a loss of function, while about 27 percent are effectively neutral. Thus, more than half of new missense mutations have mildly deleterious effects. These mutations give rise to many low frequency deleterious allelic variants in the human population as evident from a new dataset of 37 genes sequenced in over 1,500 individual human chromosomes. Surprisingly, up to 70 percent of low frequency missense alleles are mildly deleterious and associated with a heterozygous fitness loss in the range 0.001-0.003. Thus, the low allele frequency of an amino acid variant can by itself serve as a predictor of its functional significance. Several recent studies have reported a significant excess of rare missense variants in disease populations compared to controls in candidate genes or pathways. These studies would be unlikely to work if most rare variants were neutral or if rare variants were not a significant contributor to the genetic component of phenotypic inheritance. Our results provide a justification for these types of candidate gene (pathway) association studies and imply that mutation-selection balance may be a feasible mechanism for evolution of some common diseases.
Influence of processing conditions on performance and stability in polycrystalline thin-film CdTe-based solar cells (1999)

The influence of processing conditions on the performance of polycrystalline thin-film CdTe-based solar cells and the relationship to device stability are addressed. Specifically, processing conditions with respect to the window layer, post-CdTe deposition treatments, and contacting treatments are examined. The use of high resistivity interlayers between the transparent conductive oxide and the CdS allows open circuit voltage to be maintained as the CdS thickness is reduced. CdS-CdTe interdiffusion is reduced by either use of a short 600 °C anneal prior to CdCl2 vapor treatment or by use of CdTe1−xSx alloy absorber layers. Finally, the effects of CdTe1−xSx surface modification and Cu reaction on device current-voltage behavior are presented.
The Effect of a Powered Drive on Pushing and Pulling Forces When Maneuvering Bariatric Hospital Beds (2015)

Powered drives designed to provide assistance moving hospital beds are commercially available but no research has evaluated whether they reduce push and pull forces. This study measured hand forces of 10 caregivers when maneuvering a manual and powered bariatric hospital bed in activities designed to simulate transporting a hospital patient. Compared to the manual bed, powered drive significantly reduced the peak push force required to initiate movement (238N manual, 119N powered) and peak pull force required to stop (155N manual, 8N powered). Powered drive significantly reduced the integral of hand force when maneuvering in tight spaces (847N manual, 557N powered), and was associated with lower subjective ratings of exertion for all tasks. However, powered drive did not affect the force required to sustain movement during straight-line pushing. Bariatric hospital beds with powered drive may reduce the risk of caregiver injury or reduce the number of caregivers needed for transport tasks.
Stretchable and transparent electrodes based on in-plane structures (2015)

Stretchable electronics has attracted great interest with compelling potential applications that require reliable operation under mechanical deformation. Achieving stretchability in devices, however, requires a deeper understanding of nanoscale materials and mechanics beyond the success of flexible electronics. In this regard, tremendous research efforts have been dedicated toward developing stretchable electrodes, which are one of the most important building blocks for stretchable electronics. Stretchable transparent thin-film electrodes, which retain their electrical conductivity and optical transparency under mechanical deformation, are particularly important for the favourable application of stretchable devices. This minireview summarizes recent advances in stretchable transparent thin-film electrodes, especially employing strategies based on in-plane structures. Various approaches using metal nanomaterials, carbon nanomaterials, and their hybrids are described in terms of preparation processes and their optoelectronic/mechanical properties. Some challenges and perspectives for further advances in stretchable transparent electrodes are also discussed.
Securing the communication of medical information using local biometric authentication and commercial wireless links (2010)

Medical information is extremely sensitive in nature - a compromise, such as eavesdropping or tampering by a malicious third party, may result in identity theft, incorrect diagnosis and treatment, and even death. Therefore, it is important to secure the transfer of medical information from the patient to the recording system. We consider a portable, wireless device transferring medical information to a remote server. We decompose this problem into two sub-problems and propose security solutions to each of them: (1) to secure the link between the patient and the portable device, and (2) to secure the link between the portable device and the network. Thus we push the limits of the network security to the edge by authenticating the user using their biometric information; authenticating the device to the network at the physical layer; and strengthening the security of the wireless link with a key exchange mechanism. The proposed authentication methods can be used for recording the readings of medical data in a central database and for accessing medical records in various settings.
Solution structure of the general transcription factor 2I domain in mouse TFII‐I protein (2007)

The general transcription factor TFII-I, with the corresponding gene name GTF2I, is an unusual transcriptional regulator that associates with both basal and signal-induced transcription factors. TFII-I consists of six GTF2I repeat domains, called I-repeats R1-R6. The structure and function of the GTF2I domain are not clearly understood, even though it contains a helix-loop-helix motif, which is considered to be the protein-protein interaction area, based on biochemical analyses. Here, we report the solution structure of the fifth repeat of the six GTF2I repeat domains from murine TFII-I, which was determined by heteronuclear multidimensional NMR spectroscopy (PDB code 1Q60). The three-dimensional structure of the GTF2I domain is classified as a new fold, consisting of four helices (residues 8-24, 34-39, 63-71, and 83-91), two antiparallel beta strands (residues 44-47 and 77-80), and a well-defined loop containing two beta-turns between sheet 1 and helix 3. All of the repeats probably have similar folds to that of repeat 5, because the conserved residues in the GTF2I repeat domains are assembled on the hydrophobic core, turns, and secondary structure elements, as revealed by a comparison of the sequences of the first through the sixth GTF2I repeats in TFII-I.
An Improved Gramian-based Interaction Measure for Time-Delay Systems (2020)

In this paper, a modified Gramian based control configuration selection (CCS) method for linear multi-input multi-output (MIMO) plants with time delays in input-output channels is proposed. In contrast to the typical approach of approximating the delayed system, the time delay is directly integrated in the method by using the finite-time H2 norm for the time- delay system (TDS). The methodology is based on an explicit formula for computing the finite-time H2 norm for stable SISO systems. Gramian-based CCS methods are either insensitive to time delays or favor channels with large delays, while the proposed method suggests configuration which are more reasonable. A numerical examples is used to discuss and benchmark the method. It is concluded that the proposed methods provides adequate configuration suggestions and circumvents a well-known shortcoming.
Passivation of photonic nanostructures for crystalline silicon solar cells (2014)

We report on the optical and electrical performances of periodic photonic nanostructures, prepared by nanoimprint lithography (NIL) and two different etching routes, plasma, and wet chemical etching. Optically, these periodic nanostructures offer a lower integrated reflectance compared with the industrial state-of-the-art random pyramid texturing. However, electrically, they are known to be more challenging for solar cell integration. We propose the use of wet chemical etching for fabricating inverted nanopyramids as a way to minimize the surface recombination velocities and maintain a conventional cell integration flow. In contrast to the broadly used plasma etching for nanopatterning, the wet chemically etched nanopatterning results in low surface recombination velocities, comparable with the state-of-the-art random pyramid texturing. Applied to 40-µm thick epitaxially grown crystalline silicon foils bonded to a glass carrier superstrate, the periodic-inverted nanopyramids show carrier lifetimes comparable with the non-textured reference foils (τeff = 250 µs). We estimate a maximum effective surface recombination velocity of ~8 cm/s at the patterned surface, which is comparable with the state-of-the-art values for crystalline silicon solar cells. Copyright © 2014 John Wiley & Sons, Ltd.
The Role of Genetics in Susceptibility to Diabetic Retinopathy (2009)

International Ophthalmology Clinics: Spring 2009 - Volume 49 - Issue 2 - p 35-52 doi: 10.1097/IIO.0b013e31819fd5d7
Functional magnetic resonance imaging and lung function tests in cystic fibrosis (2017)

Cystic fibrosis (CF) is characterized by chronic respiratory infections and functional impairment of the lung. Lung function tests such as nitrogen multiple breath washout (N2-MBW), are sensitive in detecting ventilation inhomogeneity, but cannot determine its exact origin. Novel magnetic resonance imaging (MRI) methods such as matrix pencil decomposition MRI can visualize functional changes in the lung without the administration of contrast agents and the need for breathing maneuvers. We examined the correlation between novel functional MRI and lung function tests in patients with CF. Forty patients with CF (mean age 11.7 years, range 6–18) underwent MRI and lung function tests on the same day. Functional MRI provided semi-quantitative measures of the perfusion (RQ) and ventilation (RFV) impairment as percentages of the affected lung volume. Morphological MRI was evaluated using a CF-specific score. N2-MBW provided information about global (lung clearance index, LCI) ventilation inhomogeneity. MRI detected functional impairment in all patients with CF: RFV ranged from 19% to 38% and RQ ranged from 16% to 35%. RFV and RQ were strongly correlated with LCI (r=0.76, p&lt;0.001; r=0.85, p&lt;0.001, respectively), as well as total morphology scores and sub-scores. Non-invasive functional MRI is a promising method to detect and visualize perfusion and ventilation impairment in CF without the need of contrast agents or breath holding maneuvers. These results suggest a promising role for functional MRI as a diagnostic tool in monitoring patients with CF.
LBL Assembled Laminates with Hierarchical Organization from Nano- to Microscale: High-Toughness Nanomaterials and Deformation Imaging (2009)

Layer-by-layer assembly (LBL) can generate unique materials with high degrees of nanoscale organization and excellent mechanical, electrical, and optical properties. The typical nanometer scale thicknesses restrict their utility to thin films and coatings. Preparation of macroscale nanocomposites will indicate a paradigm change in the practice of LBL, materials manufacturing, and multiscale organization of nanocomponents. Such materials were made in this study via consolidation of individual LBL sheets from polyurethane. Substantial enhancement of mechanical properties after consolidation was observed. The resulting laminates are homogeneous, transparent, and highly ductile and display nearly 3x higher strength and toughness than their components. Hierarchically organized composites combining structural features from 1 to 1 000 000 nm at six different levels of dimensionality with a high degree of structural control at every level can be obtained. The functionality of the resulting fluorescent sandwiches of different colors makes possible mechanical deformation imaging with submicrometer resolution in real time and 3D capabilities.