gebhart/patrepeval huggingface dataset:
Real-time delay-multiply-and-sum beamforming with coherence factor for in vivo clinical photoacoustic imaging of humans (2019)

In the clinical photoacoustic (PA) imaging, ultrasound (US) array transducers are typically used to provide B-mode images in real-time. To form a B-mode image, delay-and-sum (DAS) beamforming algorithm is the most commonly used algorithm because of its ease of implementation. However, this algorithm suffers from low image resolution and low contrast drawbacks. To address this issue, delay-multiply-and-sum (DMAS) beamforming algorithm has been developed to provide enhanced image quality with higher contrast, and narrower main lobe compared but has limitations on the imaging speed for clinical applications. In this paper, we present an enhanced real-time DMAS algorithm with modified coherence factor (CF) for clinical PA imaging of humans <i>in vivo</i>. Our algorithm improves the lateral resolution and signal-to-noise ratio (SNR) of original DMAS beamformer by suppressing the background noise and side lobes using the coherence of received signals. We optimized the computations of the proposed DMAS with CF (DMAS-CF) to achieve real-time frame rate imaging on a graphics processing unit (GPU). To evaluate the proposed algorithm, we implemented DAS and DMAS with/without CF on a clinical US/PA imaging system and quantitatively assessed their processing speed and image quality. The processing time to reconstruct one B-mode image using DAS, DAS with CF (DAS-CF), DMAS, and DMAS-CF algorithms was 7.5, 7.6, 11.1, and 11.3 ms, respectively, all achieving the real-time imaging frame rate. In terms of the image quality, the proposed DMAS-CF algorithm improved the lateral resolution and SNR by 55.4% and 93.6 dB, respectively, compared to the DAS algorithm in the phantom imaging experiments. We believe the proposed DMAS-CF algorithm and its real-time implementation contributes significantly to the improvement of imaging quality of clinical US/PA imaging system.
Molecular and genetic characterization of GABPI3 (1994)

This report outlines three observations relating to GABPI3 , a polypeptide constituent of the heterotetrameric transcription factor GABP. Evidence is presented showing that the mouse genome encodes two highly related GABPI3 polypeptides, designated GABPI31-1 and GABPI32-1. Genomic and eDNA copies of the newly defined Gabpb2 gene were cloned and characterized, providing the conceptually translated amino acid sequence of GABPI32-1. The genes encoding these two proteins, as well as GABPc~, were mapped to three unlinked chromosomal loci. Although physically unlinked, the patterns of expression of the three genes were strikingly concordant. Finally, the molecular basis of GABPI3 dimerization was resolved. Carboxy-terminal regions of the two GABPI3 polypeptides, which mediate dimerization, bear highly related primary amino acid sequences. Both sequences are free of oL-helix destabilizing residues and, when displayed on idealized c~-helical projections, reveal marked amphipathy. Two observations indicate that these regions adopt an a-helical conformation and intertwine as coiled-coils. First, the dimer-forming region of GABPI32-1 can functionally replace the leucine zipper of a bZIP transcription factor. Second, a synthetic peptide corresponding to this region shows distinctive helical properties when examined by circular dichroism spectroscopy. Finally, evidence is presented showing that GABPI31-1 and GABPI32-1 can heterodimerize through this carboxy-terminal domain, but neither protein can heterodimerize via the dimer-forming region of the bZIP protein C/EBPI3.
The global distribution and diversity of protein vaccine candidate antigens in the highly virulent Streptococcus pnuemoniae serotype 1 (2017)

Serotype 1 is one of the most common causes of pneumococcal disease worldwide. Pneumococcal protein vaccines are currently being developed as an alternate intervention strategy to pneumococcal conjugate vaccines. Pre-requisites for an efficacious pneumococcal protein vaccine are universal presence and minimal variation of the target antigen in the pneumococcal population, and the capability to induce a robust human immune response. We used in silico analysis to assess the prevalence of seven protein vaccine candidates (CbpA, PcpA, PhtD, PspA, SP0148, SP1912, SP2108) among 445 serotype 1 pneumococci from 26 different countries, across four continents. CbpA (76%), PspA (68%), PhtD (28%), PcpA (11%) were not universally encoded in the study population, and would not provide full coverage against serotype 1. PcpA was widely present in the European (82%), but not in the African (2%) population. A multi-valent vaccine incorporating CbpA, PcpA, PhtD and PspA was predicted to provide coverage against 86% of the global population. SP0148, SP1912 and SP2108 were universally encoded and we further assessed their predicted amino acid, antigenic and structural variation. Multiple allelic variants of these proteins were identified, different allelic variants dominated in different continents; the observed variation was predicted to impact the antigenicity and structure of two SP0148 variants, one SP1912 variant and four SP2108 variants, however these variants were each only present in a small fraction of the global population (<2%). The vast majority of the observed variation was predicted to have no impact on the efficaciousness of a protein vaccine incorporating a single variant of SP0148, SP1912 and/or SP2108 from S. pneumoniae TIGR4. Our findings emphasise the importance of taking geographic differences into account when designing global vaccine interventions and support the continued development of SP0148, SP1912 and SP2108 as protein vaccine candidates against this important pneumococcal serotype.
Accelerating Wavepackets (2015)

We review the recent progress on accelerating wavepackets, highlighting ideas common to many wave systems ranging from self-bending beams of Maxwell's equations and self-accelerating Dirac fermions to deep underwater ultrasonic beams propagating on curved trajectories.
Spatial and temporal characterization of 60 GHz indoor channels (2002)

This paper presents measurement results and models for 60 GHz channels. Multipath components were resolved in time by using a sliding correlator with 10 ns resolution, and in space by sweeping a directional antenna with 70 half power azimuthal beamwidth around the azimuth. Power delay profiles (PDPs) and power angle profiles (PAPs) were measured in various indoor and short-range outdoor environments. Detailed multipath structure was retrieved from PDPs and PAPs, and compared with site-specific environments. Results show an excellent correlation between the propagation environments and the multipath channel structures. The measurement results confirm that the majority of the multipath components can be determined from image based ray tracing techniques for LOS applications. For NLOS propagation through walls, the metallic structure of composite walls must be considered for propagation predictions. From the recorded PDPs and PAPs, received signal power and statistical parameters of angle-of-arrival (AOA) and time-of-arrival (TOA) were also calculated.
Molecular Rotations, Multiscale Order, Hyperuniformity, and Signatures of Metastability during the Compression/Decompression Cycles of Amorphous Ices (2023)

We model, via large-scale molecular dynamics simulations, the isothermal compression of low-density amorphous ice (LDA) to generate high-density amorphous ice (HDA) and the corresponding decompression extending to negative pressures to recover the low-density amorphous phase (LDA<sub><i>HDA</i></sub>). Both LDA and HDA are nearly hyperuniform and are characterized by a dynamical HBN, showing that amorphous ices are nonstatic materials and implying that nearly hyperuniformity can be accommodated in dynamical networks. In correspondence with both the LDA-to-HDA and the HDA-to-LDA<sub><i>HDA</i></sub> phase transitions, the (partial) activation of rotational degrees of freedom activates a cascade effect that induces a drastic change in the connectivity and a pervasive reorganization of the HBN topology which, ultimately, break the samples' hyperuniform character. Key to this effect is the rapid rate at which changes occur, and not their magnitude. The inspection of structural properties from the short- to the long-range shows that signatures of metastability are present at all length-scales, hence providing further solid evidence in support of the liquid-liquid critical point scenario. LDA and LDA<sub><i>HDA</i></sub> differ in terms of HBN and structural properties, implying that they are distinct low-density glasses. Our work unveils the role of molecular rotations in the phase transitions between amorphous ices and shows how the unfreezing of rotational degrees of freedom generates a cascade effect that propagates over multiple length-scales. Our findings greatly improve our basic understanding of water and amorphous ices and can potentially impact the field of molecular network-forming materials at large.
The anti‐inflammatory effect of celecoxib does not prevent liver fibrosis in bile duct‐ligated rats (2008)

The present study provides morphological and molecular biological evidences for the role of celecoxib in cholestatic liver fibrosis. Celecoxib protects against hepatic inflammation in the early stage of BDL rats, but does not have an effect on liver fibrosis.
ChemInform Abstract: New Building Blocks for Efficient and Highly Diastereoselective Polyol Production. Synthesis and Utility of (R′,R′,S,S) and (S′,S′,R,R)‐2,3‐Butane Diacetal Protected Butane Tetrol Derivatives. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Spectroscopy of Single CdSe Nanocrystallites (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Adsorption of BSA (Bovine Serum Albuminum) and lysozyme on poly(vinyl acetate) particles (2016)

Poly(vinyl acetate) (PVAc) particles find many uses in the biomedical field, including the use as particle embolizers. Particularly, embolizing particles can combine physical and chemical effects when they are doped with pharmaceuticals. For this reason, the adsorption of bovine serum albuminum (BSA) and lysozyme (used as model biomolecules) on PVAc particles produced through suspension polymerization is studied in the present manuscript in a broad range of pH values. It is shown that significant amounts of BSA and lysozyme can be adsorbed onto PVAc particles in the vicinities of the isoelectric point of the biomolecules (0.65mg of BSA and 1.0mg of lysozyme per g of PVAc), allowing for production of chemoembolizers through adsorption. Particularly, it is shown that lysozyme still presents residual activity after the adsorption process, which can constitute very important characteristic for real biomedical applications.
Fast structural responses of gap junction membrane domains to AB5 toxins (2013)

Gap junctions (GJs) represent connexin-rich membrane domains that connect interiors of adjoining cells in mammalian tissues. How fast GJs can respond to bacterial pathogens has not been known previously. Using Bessel beam plane illumination and confocal spinning disk microscopy, we found fast (~500 ms) formation of connexin-depleted regions (CDRs) inside GJ plaques between cells exposed to AB5 toxins. CDR formation appears as a fast redistribution of connexin channels within GJ plaques with minor changes in outline or geometry. CDR formation does not depend on membrane trafficking or submembrane cytoskeleton and has no effect on GJ conductance. However, CDR responses depend on membrane lipids, can be modified by cholesterol-clustering agents and extracellular K(+) ion concentration, and influence cAMP signaling. The CDR response of GJ plaques to bacterial toxins is a phenomenon observed for all tested connexin isoforms. Through signaling, the CDR response may enable cells to sense exposure to AB5 toxins. CDR formation may reflect lipid-phase separation events in the biological membrane of the GJ plaque, leading to increased connexin packing and lipid reorganization. Our data demonstrate very fast dynamics (in the millisecond-to-second range) within GJ plaques, which previously were considered to be relatively stable, long-lived structures.
Rosai–Dorfman Disease (Sinus Histiocytosis with Massive Lymphadenopathy) of the Pancreas: Third Reported Occurrence (2012)

Sinus histiocytosis with massive lymphadenopathy (SHML) was first described in 1969 by Rosai and Dorfman [1]. It is a rare inflammatory disorder with key clinicopathological characteristics such as emperipolesis and positive immunostaining for S-100 protein [2] and CD68. Rosai–Dorfman disease (RDD) is primarily manifested in the lymph nodes, yet extranodal disease has been reported in as many as half of patients [3]. Such cases affect primarily the head and neck, upper respiratory tract, and central nervous system, although the disease has been found in almost every organ system. The gastrointestinal tract is rarely involved, and only two cases of primary involvement of the pancreas have been previously described [4, 5].
Automatic Partitioning of Parallel Loops for Cache-Coherent Multiprocessors (1993)

This paper presents a theoretical framework for automatically partitioning parallel loops to minimize cache coherency traffic on shared-memory multiprocessors. While several previous papers have looked at hyperplane partitioning of iteration spaces to reduce communication traffic, the problem of deriving the optimal tiling parameters for minimal communication in loops with general affine index expressions and multiple arrays has remained open. Our paper solves this open problem by presenting a method for deriving an optimal hyperparallelepiped tiling of iteration spaces for minimal communication in multiprocessors with caches. We show that the same theoretical framework can also be used to determine optimal tiling parameters for data and loop partitioning in distributed memory multiprocessors without caches. Like previous papers, our framework uses matrices to represent iteration and data space mappings and the notion of uniformly intersecting references to capture temporal locality in array references. We introduce the notion of data footprints to estimate the communication traffic between processors and use lattice theory to compute precisely the size of data footprints. We have implemented a subset of this framework in a compiler for the Alewife machine.
Preliminary characterization of mucin from effusions of cleft palate patients (1993)

Middle ear effusions from children undergoing myringotomy were classified into three groups-cleft palate, thick (mucoid), and thin (serous). Mucin was purified from each of the three groups using CsCI equilibrium density gradient centrifugation. Analysis of the cleft palate mucin on Sepharose CL-2B showed it was excluded and therefore of large molecular weight. It could be broken down into smaller glycopeptide units by proteolysis and these glycopeptides had, based on elution position, a larger hydrodynamic size than those from the thick mucin. Intrinsic viscosity measurements demonstrated that the intact mucins could be ranked in order of molecular space occupancy; cleft palate > thick > thin. Amino acid analysis showed the cleft palate mucin to have an amino acid composition similar to other mucins, with serine, threonine, and proline constituting 41% by weight of the protein core. Thiol analysis gave evidence of a possible difference in polymerization between the three mucins, in that thin (the smallest mucin) contained the lowest number of thiols. This preliminary analysis of cleft palate mucin suggests a mucin with larger glycopeptide units forming an intact mucin of larger hydrodynamic size than either thick or thin middle ear mucins from anatomically normal children.
MF59 adjuvant: the best insurance against influenza strain diversity (2011)

MF59 is a well-established, safe and potent vaccine adjuvant that has been licensed for more than 13 years for use in an influenza vaccine focused on elderly subjects (Fluad®), Novartis, Cambridge, MA, USA). Recently, MF59 was shown to be safe in a seasonal influenza vaccine for young children and was able to increase vaccine efficacy from 43 to 89%. A key and consistent feature of MF59 is the ability of the emulsion to induce fast priming of influenza antigen-specific CD4(+) T-cell responses, to induce strong and long-lasting memory T- and B-cell responses and to broaden the immune response beyond the influenza strains actually included in the vaccine. The enhanced breadth of response is valuable in the seasonal setting, but is particularly valuable in a (pre-) pandemic setting, when it is difficult to predict which strain will emerge to cause the pandemic. We have shown that the ability of MF59 to increase the breadth of immune response against influenza vaccines is mainly due to the spreading of the repertoire of the B-cell epitopes recognized on the hemagglutinin and neuraminidase of the influenza virus.
Observation of Hydrogenated Silicon Clusters Si6Hxwith Controlled Hydrogen Content on Si (111)-(7×7) Surfaces (2003)

We studied how Si6Hx clusters behave on Si (111)-(7×7) surfaces depending on hydrogen content x by scanning tunneling microscopy. The Si6Hx+ ions were synthesized in an ion trap and deposited onto the (7×7) surfaces with an impact kinetic energy of 3 eV, i.e., 0.5 eV/Si atom, without decomposition. Deposited Si6H10–13 clusters favorably adsorbed on faulted halves of the (7×7) surfaces while Si6H0–5 clusters were randomly distributed. A clear difference of the electronic structure between Si6H0–5 and Si6H10–13 clusters was found in the tunneling spectra of the clusters.
F44 Alloy Characterization and Identification Using the Rubbing Technique with Micro X-ray Fluorescence (2005)

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Advancing EUV lithography optics (Conference Presentation) (2019)

The optical train is a key element of each lithography scanner. The single patterning resolution limit of a scanner is determined by the characteristics and performance of its imaging system consisting of illumination and projection optics. The most relevant performance parameters of the illumination system are the maximum achievable setting flexibility, off-axis imaging capability (sigma) and pupil fill ratio (PFR). The key drivers of the projection optics are numerical aperture (NA), aberration level, and stray light. In this paper, we present an overview of the current EUVL generation and the optical system, designed to improve resolution limit, contrast and overlay performance within the scanner. The projection optics features a NA of 0.33 with significantly reduced aberration levels. These key scanner parameters have been substantially reduced to improve overlay and image contrast supporting volume production. While double patterning is a possible extension with the current generation of EUVL tools, there is still a strong desire to print smaller chip patterns directly. Therefore a next generation of EUV called “High-NA EUV” is already in preparation. This tool generation with an optical system -ZEISS Starlith®5000- will have a NA of 0.55 and a resolution of 8nm for direct printing of these finest features. Achieving 8nm resolution means tighter specifications for the wavefront. Therefore, extreme aspheres with improved accuracy of the mirror surface are needed that pose next to the large size of the mirrors and the anamorphic design another challenge to the optics manufacturing. To build these systems a completely new production infrastructure is needed which is under installation in parallel with the product design and technology development. In this paper the current progress of the development will be shown.
Thompson’s Hack (2018)

Ken Thompson is a famous computer scientist with many accomplishments, but we are interested in him primarily for what he did to teach the world about the problem of trust in software systems. Among his achievements, Thompson was one of the inventors of an operating system named Unix that has been very popular and influential. In 1983 that work won him the Turing Award, often described as the “Nobel Prize of computer science.” That might not seem very relevant to our story, but here's where things get interesting.
Doing Remote Controlled Studies with Humans: Tales from the COVID Trenches (2021)

How should empirical researchers conduct controlled, remote “lab” studies in the uncontrolled, noisy conditions of each participant's own home? Volatility in participant home environments, hardware, internet connection, and surrounding distractions takes the “controlled” out of controlled studies. This paper recounts our in-the-trenches mitigations for designing and conducting two complex controlled studies under COVID, in which participants, from home, interactively localized faults in an AI system. The studies with our COVID-era mitigations in 5 categories-Privacy/Security, Data Collection, Control, Technology Issues, Payment-ultimately produced crisp results beyond what we thought possible under such uncontrolled circumstances.
Privacy-Preserving Reinforcement Learning Beyond Expectation (2022)

Cyber and cyber-physical systems equipped with machine learning algorithms such as autonomous cars share environments with humans. In such a setting, it is important to align system (or agent) behaviors with the preferences of one or more human users. We consider the case when an agent has to learn behaviors in an unknown environment. Our goal is to capture two defining characteristics of humans: i) a tendency to assess and quantify risk, and ii) a desire to keep decision making hidden from external parties. We incorporate cumulative prospect theory (CPT) into the objective of a reinforcement learning (RL) problem for the former. For the latter, we use differential privacy. We design an algorithm to enable an RL agent to learn policies to maximize a CPT-based objective in a privacy-preserving manner and establish guarantees on the privacy of value functions learned by the algorithm when rewards are sufficiently close. This is accomplished through adding a calibrated noise using a Gaussian process mechanism at each step. Through empirical evaluations, we highlight a privacy-utility tradeoff and demonstrate that the RL agent is able to learn behaviors that are aligned with that of a human user in the same environment in a privacy-preserving manner