gebhart/patrepeval huggingface dataset:
Adaptive Nanoparticle Platforms for High Throughput Expansion and Detection of Antigen-Specific T cells (2020)

T cells are critical players in disease; yet, their antigen-specificity has been difficult to identify, as current techniques are limited in terms of sensitivity, throughput, or ease of use. To address these challenges, we increased the throughput and translatability of magnetic nanoparticle-based artificial antigen presenting cells (aAPCs) to enrich and expand (E+E) murine or human antigen-specific T cells. We streamlined enrichment, expansion, and aAPC production processes by enriching CD8+ T cells directly from unpurified immune cells, increasing parallel processing capacity of aAPCs in a 96-well plate format, and designing an adaptive aAPC that enables multiplexed aAPC construction for E+E and detection. We applied these adaptive platforms to process and detect CD8+ T cells specific for rare cancer neoantigens, commensal bacterial cross-reactive epitopes, and human viral and melanoma antigens. These innovations dramatically increase the multiplexing ability and decrease the barrier to adopt for investigating antigen-specific T cell responses.
ChemInform Abstract: Comparative Analysis of Diastereoselection Levels Attainable During Controlled Exo and Endo Addition of Chiral Cyclopentenyl Organometallics to Optically Pure and Racemic 1‐Vinylnorbornan‐2‐ones. (1990)

Abstract The levels of diastereoselection attainable during the addition of the cyclopentenyl organometallics (II) and (VII) to the norbornanones (I) and (VI) are tested.
High Energy Density and Stable Three‐Dimensionally Structured Se‐Loaded Bicontinuous Porous Carbon Battery Electrodes (2021)

3D‐structured Se‐loaded bicontinuous porous carbon (BPC) electrodes are fabricated through colloidal templating of BPC followed by pulsed‐voltage Se electrodeposition. The resultant electrodes are found to deliver a specific capacity of 665 mAh g −1 at a rate of 0.1 C, near the theoretical value for Se. When a vinylene carbonate (VC) containing electrolyte is utilized, the capacity fade over 500 cycles at 1 C rate is as small as a few percent. Impedance measurements and physical characterization of cycled electrodes indicate the exceptionally stable cycling performance is possibly due to VC resulting in the formation of a stable solid electrolyte interface (SEI) during cycling. Along with the cycling stability, the rate performance of the 3D Se/BPC electrodes is also good. Due to the bicontinuous structure of carbonaceous current collector at rates as high as 5 C, the deliverable capacity is about 300 mAh g −1 .
Characterization of field emission cathodes with different forms of diamond coatings (1999)

The emission of different diamond coatings on silicon field emitter arrays were investigated: chemical vapor deposition diamond, high pressure and high temperature synthetic diamond, and shock-synthesized nanodiamond. Practical emission characteristics such as: emission threshold, maximum current, current stability, and reproducibility were tested. The effects of surface modification, the size of diamond crystallites, and hydrogen plasma treatments were also studied.
Arthroscopic Trillat Procedure: A Guided Technique (2020)

The Trillat procedure is a surgical treatment for recurrent anterior shoulder instability in the setting of significant or irreparable rotator cuff tears in elderly patients. The procedure comprises an inferior closing wedge partial osteotomy of the coracoid process with fixation to the glenoid neck. This results in a lowered and medialized coracoid process that acts as a bone block and the conjoint tendon is brought closer to the glenohumeral joint, thus closing the subcoracoid space, which blocks humeral dislocation. We describe an arthroscopic step-by-step guided Trillat technique that is simple, efficient, and reproducible, while minimizing risk in the extra-articular subcoracoid space. Our technique does not require the release of the pectoralis minor tendon from the coracoid process, which reduces the risk of damaging the brachial plexus. We use a tight-rope fixation construct that allows progressive transfer of the coracoid process, limiting fracture risk and the risk of overtightening of the subscapularis muscle. Because there is a trend for more complex procedures being performed arthroscopically, it is important to develop and simplify operative techniques, aiding surgeons in achieving reproducible and reliable patient outcomes.
Microfiber Nonwovens as Potential Membranes (2018)

This article provides an overview of the membrane bioreactor technology where nonwovens can be applied as an alternative medium for separation. The main objective is to identify the nonwoven characteristics leading to higher removal efficiency, higher flux, and lower fouling behavior. The general limitations associated with common nonwoven separation media are related to the large pore and wide pore size distributions. Consequently, due to their large pore network, nonwovens often behave as a depth filter structure. Common nonwovens having large fibers cannot replace microfiltration membranes yet. Further refinements of these structures are necessary for developing a suitable replacement.
Regioselective Carbon–Carbon Bond Formation in Proteins with Palladium Catalysis; New Protein Chemistry by Organometallic Chemistry (2005)

Palladium-catalyzed reactions have contributed to the advancement of many areas of organic chemistry, in particular, the synthesis of organic compounds such as natural products and polymeric materials. In this study, we have used a Mizoroki-Heck reaction for site-specific carbon-carbon bond formation in the Ras protein. This was performed by the following two steps: 1) the His6-fused Ras protein containing 4-iodo-L-phenylalanine at position 32 (iF32-Ras-His) was prepared by genetic engineering and 2) the aryl iodide group on the iF32-Ras-His was coupled with vinylated biotin in the presence of a palladium catalyst. The biotinylation was confirmed by Western blotting and liquid chromatography-mass spectrometry (LC-MS). The regioselectivity of the Mizoroki-Heck reaction was furthermore confirmed by LC-MS/MS analysis. However, in addition to the biotinylated product (bF32-Ras-His), a dehalogenated product (F32-Ras-His) was detected by LC-MS/MS. This dehalogenation resulted from the undesired termination of the Mizoroki-Heck reaction due to steric and electrostatic hindrance around residue 32. The biotinylated Ras showed binding activity for the Ras-binding domain as its downstream target, Raf-1, with no sign of decomposition. This study is the first report of an application of organometallic chemistry in protein chemistry.
High Speed/Low Dose Analytical Electron Microscopy with Machine Learning and Multi-Objective Dynamic Sampling (2018)

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Differential impact of transdiagnostic, dimensional psychopathology on multiple scales of functional connectivity (2021)

Abstract Introduction Dimensional psychopathology strives to associate different domains of cognitive dysfunction with brain circuitry. Connectivity patterns as measured by functional magnetic resonance imaging (fMRI) exist at multiple scales, with global networks of connectivity composed of microscale interactions between individual nodes. It remains unclear how separate dimensions of psychopathology might differentially impact these different scales of organization. Methods Patients experiencing anxious misery symptomology (depression, anxiety and trauma; n = 192) were assessed for symptomology and received resting-state fMRI scans. Three modeling approaches (seed-based correlation analysis [SCA], support vector regression [SVR] and Brain Basis Set Modeling [BSS]), each relying on increasingly dense representations of functional connectivity patterns, were used to associate connectivity patterns with six different dimensions of psychopathology: anxiety sensitivity, anxious arousal, rumination, anhedonia, insomnia and negative affect. Importantly, a full 50 patients were held-out in a testing dataset, leaving 142 patients as training data. Results Different symptom dimensions were best modeled by different scales of brain connectivity: anhedonia and anxiety sensitivity were best modeled with single connections (SCA), insomnia and anxious arousal by mesoscale patterns (SVR) and negative affect and ruminative thought by broad, cortex-spanning patterns (BBS). Dysfunction within the default mode network was implicated in all symptom dimensions that were best modeled by multivariate models. Conclusion These results suggest that symptom dimensions differ in the degree to which they impact different scales of brain organization. In addition to advancing our basic understanding of transdiagnostic psychopathology, this has implications for the translation of basic research paradigms to human disorders.
Telomere length associates with chronological age and mortality across racially diverse pulmonary fibrosis cohorts (2023)

Pulmonary fibrosis (PF) is characterized by profound scarring and poor survival. We investigated the association of leukocyte telomere length (LTL) with chronological age and mortality across racially diverse PF cohorts. LTL measurements among participants with PF stratified by race/ethnicity were assessed in relation to age and all-cause mortality, and compared to controls. Generalized linear models were used to evaluate the age-LTL relationship, Cox proportional hazards models were used for hazard ratio estimation, and the Cochran-Armitage test was used to assess quartiles of LTL. Standardized LTL shortened with increasing chronological age; this association in controls was strengthened in PF (R = -0.28; P < 0.0001). In PF, age- and sex-adjusted LTL below the median consistently predicted worse mortality across all racial groups (White, HR = 2.21, 95% CI = 1.79-2.72; Black, HR = 2.22, 95% CI = 1.05-4.66; Hispanic, HR = 3.40, 95% CI = 1.88-6.14; and Asian, HR = 2.11, 95% CI = 0.55-8.23). LTL associates uniformly with chronological age and is a biomarker predictive of mortality in PF across racial groups.
Design and implementation of position sensorless starting control in industrial drives with output filter and transformer for oil/pump applications (2017)

This paper proposes a position sensorless control scheme for an induction and permanent magnetic motor drive with output filter and transformer. The proposed method provides sufficient starting torque with controlled drive/motor current. In addition, transformer saturation is addressed. The sensorless starting scheme presented in this paper has been implemented in a commercial drive for deep well applications.
Cationic Cellulose Nanocrystals for Flocculation of Microalgae: Effect of Degree of Substitution and Crystallinity (2019)

Flocculation could offer a low-cost and straightforward solution to harvest microalgae in an economic and energy-efficient way. Cationically modified cellulose nanocrystals (CNCs) have been proposed as an alternative to biopolymer-based flocculants such as chitosan. The aim of this study was to fine-tune the cationic modification of CNCs for use as flocculants for harvesting the freshwater microalgae Chlorella vulgaris. CNCs were functionalized with two cationic groups, pyridinium (PYR) or methylimidazolium (MIM), and the degree of substitution (DS) was varied by controlling reaction conditions (stoichiometry, reaction time, and temperature). The DS ranged from 0.08 to 0.34 for PYR modifications and from 0.10 to 0.29 for MIM modifications. All cationic CNCs achieved flocculation efficiencies of >95% at optimal dosage. The required dose to induce flocculation decreased with increasing DS and did not differ between the PYR and MIM modified CNCs. The relation between DS and the flocculant dose points to the importance of electrostatic interactions in the flocculation mechanism. To check the advantages of a rigid flocculant compared to a flexible flocculant, we compared flocculation between rigid cationic CNCs and the flexible molecular polymer chitosan. While CNCs required a slightly higher dose by weight compared to chitosan, CNCs required a lower dose than chitosan when expressed per number of cationic charges added. Moreover, overdosing resulted in dispersion restabilization when chitosan was used but not when cationic CNCs were used, pointing to a different mechanism of flocculation between rigid cationic CNCs and the molecular polymer chitosan. Opposed to flexible flocculants, CNCs cannot reorient all their charges toward the microalgal cell. This results in patches of positive charges onto the surface. Because of the rigidity of CNCs, we propose an electrostatic patch mechanism as the mechanism of flocculation for CNC-based flocculants.
Patterning of Self-assembled Thin Films Using Vacuum Ultraviolet Irradiation Through Anodic Porous Alumina Mask (2007)

Abstract The high-throughput patterning of self-assembled monolayer (SAM) on Au substrates could be achieved by vacuum ultraviolet (VUV: λ=172 nm) irradiation through an anodic porous alumina mask. The fluorescence image of the patterned SAM indicated the formation of a hole array on the submicron scale identical to that in the alumina mask.
High-Speed Control of Lightwave Amplitude, Phase, and Frequency by Use of Electrooptic Effect (2007)

High-speed control of lightwave using electrooptic (EO) effect is investigated in this paper. Agile optical frequency shift can be achieved by optical single-sideband (SSB) and frequency-shift-keying (FSK) modulators, where high-speed optical phase-shift-keying (PSK) signals can also be generated by using FSK/SSB modulators. We also describe ultrahigh extinction ratio optical intensity modulation (IM) technique for two-tone lightwave signals with high spurious suppression, which is useful for photonic microwave and millimeter-wave generation. In addition, we investigated high-order optical sideband generation techniques: quadruple dual-sideband suppressed carrier (QDSB-SC) modulation and reciprocating optical modulation (ROM). Sub-tetrahertz signals can be obtained from lightwaves with high-order sidebands
Clostridial Neurotoxins (2001)

Introduction General considerations The disease Characteristics and epidemiology of the organisms Genetic organization of toxin genes The organization of the toxin genes Strains carrying more than one toxin gene Localization of the genes Involvement of transposons Regulatory control of toxin gene expression CntR is a transcription factor Gene transcription in gene loci structures I and II Transcription of other botulinum genetic loci Transcription of the neurotoxin genes Gene transfer in neurotoxinogenic clostridia Conjugative transposons Introduction of autonomous cloning vehicles CNT structure and function Protein architecture Associated complex proteins Sequence homologies Crystal structures L chains Binding domains HN domains CNT mechanism of action The “SNARE” proteins The “SNARE motif” Substrate interaction Therapeutic development “The molecular scalpel” Clinical indications Engineered toxin fragments Future prospects
Performance Analysis of Underlay Cognitive Radio Systems: Estimation-Throughput Tradeoff (2015)

In this letter, we study the performance of cognitive Underlay Systems (USs) that employ power control mechanism at the Secondary Transmitter (ST). Existing baseline models considered for the performance analysis either assume the knowledge of involved channels at the ST or retrieve this information by means of a feedback channel, however, such situations hardly exist in practice. Motivated by this fact, we propose a novel approach that incorporates the estimation of the involved channels at the ST, in order to characterize the performance of USs under realistic scenarios. Moreover, we apply an outage constraint that captures the impact of imperfect channel knowledge, particularly on the interference power received at the primary receiver. Besides this, we employ a transmit power constraint at the ST to determine an operating regime for the US. Finally, we analyze an interesting tradeoff between the estimation time and the secondary throughput allowing an optimized performance of the US.
Airport radar monitoring of wake vortex in all weather conditions (2010)

To assess maturity and capability of X-band radars to monitor wake roll-ups in all weather conditions, Radar data were collected on airports, near runway at ORLY airport and just under its ILS Interception Area. Additional trials took place on Paris-CDG Airport to benchmark Lidar & Radar Technologies. Continuous Detection, characterization and profiling capabilities of wake vortices, up to a range of 2000 m, have been proved in clear air and rainy weather. Recorded data have been correlated with electromagnetic and fluid mechanical models of Wake Turbulences for better and more accurate understanding of roll-ups radar cross section (RCS) and Doppler signature. X-band Radar has been proved to be a full-fledged alternative, which can make a significant contribution to a wake vortex alert system, but to achieve as much reliability as possible, collaborative Electro-optical & electromagnetic sensors solution is envisaged encapsulated in a Wake Vortex Advisory System. These sensors could be used to permanently monitor wake turbulence on runways.
Alloyed junction Ge Esaki diodes on Si substrates realised by aspect ratio trapping technique (2008)

A Ge Esaki diode is demonstrated on Si atop a coalesced epitaxial layer of Ge grown through narrow openings in SiO2 that are used to trap threading dislocations from the lattice mismatch. Spin-on doping was used to form the n-type junction and a controlled alloyed reaction of Al and Ge forms the p-type junction. At an alloy temperature of 580°C for 1 s, the Ge-on-Si diodes were found to have a peak-to-valley current ratio of 1.1 with a peak current density of 4.1 kA/cm2.
67 Cancer aneuploidy is associated with a distinct tumor immune microenvironment and impacts outcomes to immune checkpoint inhibition in nonsquamous non-small cell lung cancer (2021)

<h3>Background</h3> Cancer aneuploidy, an unbalanced number of chromosomes, is associated with somatic mutation rate, expression of proliferative genes, and altered immune signaling. Whether aneuploidy correlates with a distinct tumor immunophenotype or impacts clinical outcomes to immune checkpoint inhibitors (ICIs) in NSCLC is unclear. <h3>Methods</h3> Among nonsquamous NSCLCs which underwent targeted next-generation sequencing, we retrospectively quantified aneuploidy using the fraction of chromosomal arm alterations (FAA), defined as the number of aneuploid chromosome arms divided by the number of chromosome arms assessed. An unbiased recursive partitioning algorithm was used to investigate an FAA level which best discriminated responders from non-responders to ICIs. Multiplexed immunofluorescence to quantify CD8, FOXP3, and PD-1-positive cell counts, as well as PD-L1 expression was performed on a separate cohort of nonsquamous NSCLCs to determine differences in tumor immune cells subsets according to FAA levels. <h3>Results</h3> Among 1426 nonsquamous NSCLCs identified, FAA increased along with the increase of pathologic stage, and was highest among tumors harboring EGFR mutations and RET fusions, and lowest among those with KRAS, BRAF, and MET mutations. FAA inversely correlated with PD-L1 expression levels, and positively correlated with tumor mutational burden (TMB) (figure 1A-D). Among 281 NSCLCs treated with ICIs, the median FAA was significantly lower among patients with a partial response to ICI compared to those with stable or progressive disease (0.11 vs 0.21, P=0.006). A fractional aneuploidy level of 0.06 (representing the lowest quartile of FAA) was identified as an optimal cutpoint to discriminate responders from non-responders to ICI. Compared to pts with an FAA &gt;0.06 (N=212), pts with FAA ≤0.06 (N=69) had a significantly higher ORR (42.0% vs 19.3%, P&lt;0.001), longer median progression-free survival (mPFS 6.8 vs 3.2 months, HR: 0.64, P=0.004), and longer median overall survival (mOS 24.8 vs 13.8 months, HR: 0.65, P=0.012) with ICIs (figure 2). After adjusting for performance status, PD-L1 expression, TMB, and line of treatment, FAA retained a significant association with improved PFS (HR: 0.66, P=0.018) and OS (HR: 0.66, P=0.041) to immunotherapy. FAA had no impact on clinical outcomes among pts who received first-line platinum doublet chemotherapy without ICI (figure 3). Among 239 nonsquamous NSCLCs profiled by multiplex immunofluorescence, cancers with a low FAA (≤25th percentile) were significantly enriched in CD8+ T cells and had a higher CD8+ to FOXP3+ ratio compared to those with high FAA (&gt;25th percentile) (figure 4). <h3>Conclusions</h3> Nonsquamous NSCLCs with low aneuploidy have a distinct immune microenvironment and more favorable outcomes to ICIs.
Distributed Bragg reflector structures based on PT-symmetric coupling with lowest possible lasing threshold (2013)

A new approach towards the design of optimized distributed Bragg reflector (DBR) structures is proposed by taking advantage of recent developments related to the concept of parity-time (PT) in optics. This approach is based on using unidirectional gratings that provide coupling between co-propagating modes. Such couplers with PT symmetric gratings can provide co-directional mode coupling occurring only in one direction. This specific coupling property is achieved through a combined contribution of superimposed index and gain/loss modulations with same grating periodicity, but shifted with respect to one another by a quarter periods. Based on the transfer matrix approach, the transmission and reflection properties of the structure are modeled. One of the unique characteristics of the structure is very low lasing threshold. Such low threshold can be achieved by 100% reflectivity of the both Bragg grating mirrors, and by releasing the amplified signal in one single direction through a PT symmetric grating assisted co-directional coupler. Besides the lasing applications, the proposed structure can be implemented as an optical memory unit of replicating any input optical waveform.
Digital subband filtering predistorter architecture for wireless transmitters (2005)

In this paper, a new architecture for baseband digital predistortion dedicated to wide-band transmissions is presented. The proposed predistorter consists of a cascade of a static lookup-table-based predistorter and a subband filtering block. The subband filtering technique is used to improve the correction bandwidth limitation of conventional architectures. The cases of four- and eight-subband decomposition were considered and compared to the case where the full-band signal is processed. This revealed that the subband processing results in a better sensitivity and an independent tuning ability of the predistorter at each subband. In addition, it was shown that, in the proposed predistorter, the computational complexity and the required processing speed are reduced proportionally to the number of subbands. Moreover, in an adaptive digital predistortion context, a quicker convergence can be achieved. Experimental validation of the subband-based predistortion concept was successfully carried on a 100-W peak envelop power lateral double diffused metal-oxide semiconductor power amplifier.