gebhart/patrepeval huggingface dataset:
Streptavidin-Coated Au Nanoparticles Coupled with Biotinylated Antibody-Based Bifunctional Linkers as Plasmon-Enhanced Immunobiosensors (2020)

The localized surface plasmon resonance (LSPR) effect of aggregating gold nanoparticles (AuNPs) has facilitated the development of colorimetric biosensors that can potentially be employed on site. We have developed an effective strategy to enhance the LSPR color-change signal by decoupling target detection and signal generation steps during immunobiosensing. The biosensor consists of streptavidin-coated AuNPs coupled with biotinylated antibacteria antibody as bifunctional linkers (BLs). While a BL can function both as an immunoreactor to bind to the target and as a cross-linker to aggregate AuNPs, its cross-linking function is largely limited when it binds with the target. We investigated the effect of number density (Dn) of AuNPs on the LSPR signal enhancement and the attendant improvement in detection sensitivity and rapidity of our biosensor by changing the particle size (5 to 50 nm diameter) when holding the absorbance of the AuNPs solution constant (Abs = 0.4 at 10× dilution). The performance enhancement of the biosensor was demonstrated by detecting a model target, streptavidin, and two bacteria, Escherichia coli and Legionella pneumophila. The results show that when Abs is held constant, the systems with lower Dn but larger particles perform better. Therefore, our visual biosensing system can be suitably composed to maximize the limit of detection and rapidity.
β-Arrestin-1 mediates glucagon-like peptide-1 signaling to insulin secretion in cultured pancreatic β cells (2008)

Glucagon-like peptide-1 (GLP-1) is a polypeptide hormone secreted from enteroendocrine L cells and potentiates glucose-dependent insulin secretion in pancreatic beta cells. Recently the GLP-1 receptor (GLP-1 R) has been a focus for new anti-diabetic therapy with the introduction of GLP-1 analogues and DPP-IV inhibitors, and this has stimulated additional interest in the mechanisms of GLP-1 signaling. Here we identify a mechanism for GLP-1 action, showing that the scaffold protein beta-arrestin-1 mediates the effects of GLP-1 to stimulate cAMP production and insulin secretion in beta cells. Using a coimmunoprecipitation technique, we also found a physical association between the GLP-1 R and beta-arrestin-1 in cultured INS-1 pancreatic beta cells. beta-Arrestin-1 knockdown broadly attenuated GLP-1 signaling, causing decreased ERK and CREB activation and IRS-2 expression as well as reduced cAMP levels and impaired insulin secretion. However, beta-arrestin-1 knockdown did not affect GLP-1 R surface expression and ligand-induced GLP-1 R internalization/desensitization. Taken together, these studies indicate that beta-arrestin-1 plays a role in GLP-1 signaling leading to insulin secretion, defining a previously undescribed mechanism for GLP-1 action.
A Low-Complexity Probabilistic Amplitude Shaping With Short Linear Block Codes (2021)

We propose a new probabilistic amplitude shaping (PAS) scheme based on short linear block codes. In the proposed system, the capacity-approaching signal distribution is generated in the process of decoding linear block codes for a given information bit sequence. We associate the design problem of shaping codes with the classical covering problem, suggesting the use of good covering codes for shaping. From simulation results, it is demonstrated that by selecting <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">perfect</i> binary codes as our shaping codes, the proposed scheme offers a shaping gain of around 0.3–1.0 dB. By comparing with the enumerative sphere shaping (ESS) of the same block length, we verify that the proposed scheme achieves significantly lower storage complexity and computational complexity at the receiver even with comparable block error rate performance.
Structural Observation of the Primary Isomerization in Vision with Femtosecond-Stimulated Raman (2005)

The primary event that initiates vision is the light-induced 11-cis to all-trans isomerization of retinal in the visual pigment rhodopsin. Despite decades of study with the traditional tools of chemical reaction dynamics, both the timing and nature of the atomic motions that lead to photoproduct production remain unknown. We used femtosecond-stimulated Raman spectroscopy to obtain time-resolved vibrational spectra of the molecular structures formed along the reaction coordinate. The spectral evolution of the vibrational features from 200 femtoseconds to 1 picosecond after photon absorption reveals the temporal sequencing of the geometric changes in the retinal backbone that activate this receptor.
157-nm pellicles: polymer design for transparency and lifetime (2002)

The introduction of 157 nm as the next optical lithography wavelength has created a need for new soft (polymeric) or hard (quartz) pellicle materials. Pellicles should be&amp;gt; 98 % transparent to incident 157 nm light and, ideally, sufficiently resistant to photochemical damage to remain useful for an exposure lifetime of 7.5 kJ/cm2. The transparency specification has been met. We have developed families of experimental Teflon™AF (TAFx) polymers with&amp;gt; 98 % transparency which can be spin coated and lifted as micron-scale, unsupported membranes. Still higher transparencies should be possible once optimization of intrinsic (composition, end groups, impurities, molecular weight) and extrinsic (oxygen, absorbed hydrocarbons, contaminants) factors are completed. The measured transparencies of actual pellicle films, however, are affected by many factors other than absorption. Film thickness must be precisely controlled so as to allow operation at the fringe maxima for the lithographic wavelength. Roughness and thickness uniformity are also critical. An important part of our program has thus been learning how to spin membranes from the solvents that dissolve our pellicle candidates. Meeting the durability specification at 157 nm remains a major concern. The 157 nm radiation durability lifetime of a polymer is determined by two fundamental properties: the fraction of 157 nm radiation absorbed and the fraction (quantum efficiency) of this absorbed radiation that results in photochemical darkening. Originally it was assumed that lifetime
Gait and Stair Function in Total and Resurfacing Hip Arthroplasty: A Pilot Study (2009)

Standard total hip arthroplasty (THA) is the established surgical treatment for patients older than 65 years with progressive osteoarthritis but survivorship curves wane in patients younger than 50. Resurfacing hip arthroplasty (RHA) is an alternative for younger, active patients reportedly providing superior range of motion. Quantitative investigation of functional recovery following arthroplasty may elucidate limitations that aid in device selection. Although limited long-term kinematic data are available, the early rate of recovery and gait compensations are not well described. This information may aid in refining rehabilitation protocols based on limitations specific to the implant. We presumed hip motion and forces for subjects receiving RHA are more similar to age-matched controls during physically demanding tasks, such as stair negotiation, at early time points than those for THA. In a pilot study, we quantified walking and stair negotiation preoperatively and 3 months postoperatively for seven patients with RHA (mean age, 49 years), seven patients with standard THA (mean age, 52 years), and seven age-matched control subjects (mean age, 56 years). Although both treatment groups demonstrated trends toward functional recovery, the RHA group had greater improvements in hip extension and abduction moment indicating typical loading of the hip. Further investigation is needed to determine if differences persist long term or are clinically meaningful.
Longitudinal sampling and aliasing in spiral CT (1999)

Although analyses of in-plane aliasing have been done for conventional computed tomography (CT) images, longitudinal aliasing in spiral CT has not been properly investigated. We propose a mathematical model of the three-dimensional (3-D) sampling scheme in spiral CT and analyze its effects on longitudinal aliasing. We investigated longitudinal aliasing as a function of the helical-interpolation algorithm, pitch, and reconstruction interval using CT simulations and actual phantom scans. Our model predicts, and we verified, that for a radially uniform object at the isocenter, the spiral sampling scheme results in spatially varying cancellation of the aliased spectral islands which, in turn, results in spatially varying longitudinal aliasing. The aliasing is minimal at the scanner isocenter, but worsens with distance from it and rapidly becomes significant. Our results agree with published results observed at the isocenter of the scanner and further provide new insight into the aliasing conditions at off-isocenter locations with respect to the pitch, interpolation algorithm, and reconstruction interval. We conclude that longitudinal aliasing at off-isocenter locations can be significant, and that its magnitude and effects cannot be predicted by measurements made only at the scanner isocenter.
Three dimensional two-photon imaging of neuronal activity in freely moving mice using a miniature fiber coupled microscope with active axial-scanning (2018)

Abstract We present a miniature head mounted two-photon fiber-coupled microscope (2P-FCM) for neuronal imaging with active axial focusing enabled using a miniature electrowetting lens. Full three-dimensional two-photon imaging of GCaMP6s showing individual neuron activity in multiple focal planes was achieved in a freely-moving mouse. Two-color simultaneous imaging of GFP and tdTomato fluorescence is also demonstrated. Additionally, dynamic control of the axial scanning of the electrowetting lens allows tilting of the focal plane enabling cells in multiple focal planes to be imaged simultaneously. Two-photon imaging allows increased penetration depth in tissue yielding a working distance of 450 μm with an additional 180 μm of active axial focusing. The objective NA is 0.45 with a lateral resolution of 1.8 μm, an axial resolution of 10 μm, and a field-of-view of 240 μm diameter. The 2P-FCM has a weight of only ∼2.5 g and is capable of repeatable and stable head-attachment. The 2P-FCM with dynamic axial scanning provides a new capability to record from functionally distinct neuronal layers, opening new opportunities in neuroscience research.
Role for SUR2A ED Domain in Allosteric Coupling within the KATP Channel Complex (2008)

Allosteric regulation of heteromultimeric ATP-sensitive potassium (K(ATP)) channels is unique among protein systems as it implies transmission of ligand-induced structural adaptation at the regulatory SUR subunit, a member of ATP-binding cassette ABCC family, to the distinct pore-forming K+ (Kir6.x) channel module. Cooperative interaction between nucleotide binding domains (NBDs) of SUR is a prerequisite for K(ATP) channel gating, yet pathways of allosteric intersubunit communication remain uncertain. Here, we analyzed the role of the ED domain, a stretch of 15 negatively charged aspartate/glutamate amino acid residues (948-962) of the SUR2A isoform, in the regulation of cardiac K(ATP) channels. Disruption of the ED domain impeded cooperative NBDs interaction and interrupted the regulation of K(ATP) channel complexes by MgADP, potassium channel openers, and sulfonylurea drugs. Thus, the ED domain is a structural component of the allosteric pathway within the K(ATP) channel complex integrating transduction of diverse nucleotide-dependent states in the regulatory SUR subunit to the open/closed states of the K+-conducting channel pore.
Somatic hypermutation of antibody genes: a hot spot warms up (1998)

In the course of an immune response, antibodies undergo affinity maturation in order to increase their efficiency in neutralizing foreign invaders. Affinity maturation occurs by the introduction of multiple point mutations in the variable region gene that encodes the antigen binding site. This somatic hypermutation is restricted to immunoglobulin genes and occurs at very high rates. The precise molecular basis of this process remains obscure. However, recent studies using a variety of in vivo and in vitro systems have revealed important regulatory regions, base motifs that are preferred targets of mutation and evidence that transcription may play an active role in hypermutation.
Selection-Bias-Corrected Visualization via Dynamic Reweighting (2020)

The collection and visual analysis of large-scale data from complex systems, such as electronic health records or clickstream data, has become increasingly common across a wide range of industries. This type of retrospective visual analysis, however, is prone to a variety of selection bias effects, especially for high-dimensional data where only a subset of dimensions is visualized at any given time. The risk of selection bias is even higher when analysts dynamically apply filters or perform grouping operations during ad hoc analyses. These bias effects threaten the validity and generalizability of insights discovered during visual analysis as the basis for decision making. Past work has focused on bias transparency, helping users understand when selection bias may have occurred. However, countering the effects of selection bias via bias mitigation is typically left for the user to accomplish as a separate process. Dynamic reweighting (DR) is a novel computational approach to selection bias mitigation that helps users craft bias-corrected visualizations. This paper describes the DR workflow, introduces key DR visualization designs, and presents statistical methods that support the DR process. Use cases from the medical domain, as well as findings from domain expert user interviews, are also reported.
Novel mechanisms to inhibit HIV reservoir seeding using Jak inhibitors (2017)

Despite advances in the treatment of HIV infection with ART, elucidating strategies to overcome HIV persistence, including blockade of viral reservoir establishment, maintenance, and expansion, remains a challenge. T cell homeostasis is a major driver of HIV persistence. Cytokines involved in regulating homeostasis of memory T cells, the major hub of the HIV reservoir, trigger the Jak-STAT pathway. We evaluated the ability of tofacitinib and ruxolitinib, two FDA-approved Jak inhibitors, to block seeding and maintenance of the HIV reservoir in vitro. We provide direct demonstration for involvement of the Jak-STAT pathway in HIV persistence in vivo, ex vivo, and in vitro; pSTAT5 strongly correlates with increased levels of integrated viral DNA in vivo, and in vitro Jak inhibitors reduce the frequency of CD4+ T cells harboring integrated HIV DNA. We show that Jak inhibitors block viral production from infected cells, inhibit γ-C receptor cytokine (IL-15)-induced viral reactivation from latent stores thereby preventing transmission of infectious particles to bystander activated T cells. These results show that dysregulation of the Jak-STAT pathway is associated with viral persistence in vivo, and that Jak inhibitors target key events downstream of γ-C cytokine (IL-2, IL-7 and IL-15) ligation to their receptors, impacting the magnitude of the HIV reservoir in all memory CD4 T cell subsets in vitro and ex vivo. Jak inhibitors represent a therapeutic modality to prevent key events of T cell activation that regulate HIV persistence and together, specific, potent blockade of these events may be integrated to future curative strategies.
Training and assessment of laparoscopic skills. (2004)

Laparoscopic surgery is gaining popularity among the surgical community. While its prevalence expands, the need for reliable training and assessment tools is becoming increasingly important. Laparoscopic skills are not an innate behavior, nor can they be easily mimicked, and can only be acquired through hands-on training. A consensus exists among physicians that establishment and evaluation of technical skill in surgical training programs are inadequate and in need of improvement. A validated, reliable bench model that could train and assess could be standardized and provide numerous benefits including determination of which medical students should consider a career in surgery, valuable feedback to residents, a tracking mechanism of resident performance, a possible certification and recertification tool, and to allow for interinstitutional comparison. To this end, several potentially successful bench models testing dexterity, hand-eye coordination, and depth perception have been developed. A few models have been proven to be both valid and reliable indicators of technical skill. Although the future remains uncertain, enough groundwork has been laid to begin incorporating technical skill training and assessment into surgical training programs.
CHAPTER 1. Catalytic Conversion of Biomass in Ionic Liquids (2014)

Lignocellulosic biomass, an alternative and sustainable energy source for the future, can be used as a feedstock for bioconversion into fermentable sugars or other value-added chemicals. The ability of ionic liquids to dissolve lignocellulosic materials provides new opportunities for the utilization of this renewable resource. In this chapter, the catalytic conversion of cellulose, lignin, hemicellulose, and raw lignocellulosic biomass in the presence of ionic liquids to sugars or other value-added chemicals, such as furfural and 5-hydroxymethylfurfural, is reviewed. Mineral acids, solid acids, metal salts, and acidic ionic liquids are efficient catalysts for the conversion of lignocelluloses in ionic liquids. This conversion process can be carried out under mild conditions, which enables the energy-efficient and cost-effective conversion of biomass to biofuels and platform chemicals. However, several challenges in this area need to be addressed and some of these are considered at the end of this chapter.
A Potent Inhibitor of the Cystic Fibrosis Transmembrane Conductance Regulator Blocks Disease and Morbidity Due to Toxigenic Vibrio cholerae (2022)

<i>Vibrio cholerae</i> uses cholera toxin (CT) to cause cholera, a severe diarrheal disease in humans that can lead to death within hours of the onset of symptoms. The catalytic activity of CT in target epithelial cells increases cellular levels of 3',5'-cyclic AMP (cAMP), leading to the activation of the cystic fibrosis transmembrane conductance regulator (CFTR), an apical ion channel that transports chloride out of epithelial cells, resulting in an electrolyte imbalance in the intestinal lumen and massive water loss. Here we report that when administered perorally, benzopyrimido-pyrrolo-oxazinedione, (R)-BPO-27), a potent small molecule inhibitor of CFTR, blocked disease symptoms in a mouse model for acute diarrhea caused by toxigenic <i>V. cholerae</i>. We show that both (R)-BPO-27 and its racemic mixture, (R/S)-BPO-27, are able to protect mice from CT-dependent diarrheal disease and death. Furthermore, we show that, consistent with the ability of the compound to block the secretory diarrhea induced by CT, BPO-27 has a measurable effect on suppressing the gut replication and survival of <i>V. cholerae</i>, including a 2010 isolate from Haiti that is representative of the most predominant 'variant strains' that are causing epidemic and pandemic cholera worldwide. Our results suggest that BPO-27 should advance to human Phase I studies that could further address its safety and efficacy as therapeutic or preventative drug intervention for diarrheal syndromes, including cholera, that are mediated by CFTR channel activation.
Pulmonary Valve Replacement With Small Intestine Submucosa-Extracellular Matrix in a Porcine Model (2016)

The SIS-ECM valved conduit implanted into a piglet demonstrated cellular infiltration with vascular remodeling and an increase in diameter. Conduit stenosis was a result of slower rates of size increase than native tissue. Suboptimal leaflet performance requires design modifications.
Adaptive wavelet transforms via lifting (2002)

This paper develops two new adaptive wavelet transforms based on the lifting scheme. The lifting construction exploits a spatial-domain, prediction-error interpretation of the wavelet transform and provides a powerful framework for designing customized transforms. We use the lifting construction to adaptively tune a wavelet transform to a desired signal by optimizing data-based prediction error criteria. The performances of the new transforms are compared to existing wavelet transforms, and applications to signal denoising are investigated.
Identification of the Rem-responsive element of mouse mammary tumor virus (2008)

Mouse mammary tumor virus (MMTV) has previously been shown to encode a functional homolog of the human immunodeficiency virus-1 (HIV-1) nuclear export protein Rev, termed Rem. Here, we show that deletion of the rem gene from a MMTV molecular clone interfered with the nucleo-cytoplasmic transport of genomic length viral mRNA and resulted in a loss of viral capsid (Gag) protein production. Interestingly, nuclear export of single-spliced env mRNA was only moderately affected, suggesting that this transcript is, at least to some extent, transported via a distinct, Rem-independent export mechanism. To identify and characterize a cis-acting RNA element required for Rem responsiveness (RmRE), extensive computational and functional analyses were performed. By these means a region of 490 nt corresponding to positions nt 8517-nt 9006 in the MMTV reference strain was identified as RmRE. Deletion of this fragment, which spans the env-U3 junction region, abolished Gag expression. Furthermore, insertion of this sequence into a heterologous HIV-1-based reporter construct restored, in the presence of Rem, HIV-1 Gag expression to levels determined for the Rev/RRE export system. These results clearly demonstrate that the identified region, whose geometry resembles that of other retroviral-responsive elements, is capable to functionally substitute, in the presence of Rem, for Rev/RRE and thus provide unequivocal evidence that MMTV is a complex retrovirus.
Synthesis of proteoglycan 4 by chondrocyte subpopulations in cartilage explants, monolayer cultures, and resurfaced cartilage cultures (2004)

The results described here indicate that the phenotype of PRG4 secretion by chondrocytes in culture is generally maintained, in that PRG4 is expressed to a much greater degree by chondrocytes from the superficial zone than by those from the middle and deep zones. The marked up-regulation of PRG4 synthesis by ascorbic acid may have implications for cartilage homeostasis and prevention of osteoarthritic disease. Transplanting specialized cells that secrete PRG4 to a surface may impart functional lubrication and be generally applicable to many tissues in the body.
Design and global optimization of high-efficiency solar thermal systems with tungsten cermets (2011)

Solar thermal, thermoelectric, and thermophotovoltaic (TPV) systems have high maximum theoretical efficiencies; experimental systems fall short because of losses by selective solar absorbers and TPV selective emitters. To improve these critical components, we study a class of materials known as cermets. While our approach is completely general, the most promising cermet candidate combines nanoparticles of silica and tungsten. We find that 4-layer silica-tungsten cermet selective solar absorbers can achieve thermal transfer efficiencies of 84.3% at 400 K, and 75.59% at 1000 K, exceeding comparable literature values. Three layer silica-tungsten cermets can also be used as selective emitters for InGaAsSb-based thermophotovoltaic systems, with projected overall system energy conversion efficiencies of 10.66% at 1000 K using realistic design parameters. The marginal benefit of adding more than 4 cermet layers is small (less than 0.26%, relative).