gebhart/patrepeval huggingface dataset:
Angular compounding for physically informed training of speckle suppression algorithms (2023)

Optical coherence tomography (OCT) reveals microstructure of biological tissue by measuring the pathlength difference of backscattered light at micron-scale resolution and millimeter-scale depth of penetration. Speckle grains, with a size corresponding to the spatial resolution of the OCT system, complicate the identification of tissue morphology and obscure subtle differences in tissue scattering properties. There is a need for a physics-based approach to generate standardized ground truth for OCT speckle suppression processing algorithms. Here we demonstrate an angular compounding system using sample tilting in combination with a model-based affine transformations to generate physically derived speckle suppressed ground truth data.
Spike vs nucleocapsid SARS-CoV-2 antigen detection: application in nasopharyngeal swab specimens (2021)

Abstract Public health experts emphasize the need for quick, point-of-care SARS-CoV-2 detection as an effective strategy for controlling virus spread. To this end, many “antigen” detection devices were developed and commercialized. These devices are mostly based on detecting SARS-CoV-2’s nucleocapsid protein. Recently, alerts issued by both the FDA and the CDC raised concerns regarding the devices’ tendency to exhibit false positive results. In this work we developed a novel alternative spike-based antigen assay, comprised of four high-affinity, specific monoclonal antibodies, directed against different epitopes on the spike’s S1 subunit. The assay’s performance was evaluated for COVID-19 detection from nasopharyngeal swabs, compared to an in-house nucleocapsid-based assay, composed of antibodies directed against the nucleocapsid. Detection of COVID-19 was carried out in a cohort of 284 qRT-PCR positive and negative nasopharyngeal swab samples. The time resolved fluorescence (TRF) ELISA spike-assay displayed very high specificity (99%) accompanied with a somewhat lower sensitivity (66% for Ct&lt;25), compared to the nucleocapsid ELISA assay which was more sensitive (85% for Ct&lt;25) while less specific (87% specificity). Despite being out-performed by qRT-PCR, we suggest that there is room for such tests in the clinical setting, as cheap and rapid pre-screening tools. Our results further suggest that when applying antigen detection, one must consider its intended application (sensitivity vs specificity), taking into consideration that the nucleocapsid might not be the optimal target. In this regard, we propose that a combination of both antigens might contribute to the validity of the results. Abstract Figure Graphic abstract Schematic representation of sample collection and analysis. The figure was created using BioRender.com
Accurate 2D soft segmentation of medical image via SoftGAN network. (2020)

Accurate 2D lung nodules segmentation from medical Computed Tomography (CT) images is crucial in medical applications. Most current approaches cannot achieve precise segmentation results that preserving both rich edge details description and smooth transition representations between image regions due to the tininess, complexities, and irregularities of lung nodule shapes. To address this issue, we propose a novel Cascaded Generative Adversarial Network (CasGAN) to cope with CT images super-resolution and segmentation tasks, in which the semantic soft segmentation form on precise lesion representation is introduced for the first time according to our knowledge, and lesion edges can be retained accurately after our segmentation that can promote rapid acquisition of high-quality large-scale annotation data based on RECIST weak supervision information. Extensive experiments validate that our CasGAN outperforms the state-of-the-art methods greatly in segmentation quality, which is also robust on the application of medical images beyond lung nodules. Besides, we provide a challenging lung nodules soft segmentation dataset of medical CT images for further studies.
Specialized proresolving mediators (SPMs) inhibit human B‐cell IgE production (2015)

Specialized proresolving mediators (SPMs) constitute a recently recognized class of bioactive molecules thatpromote the resolution of inflammation. We recently reported that the SPMs resolvin D1 (RvD1) and 17-hydroxydocosahexaenoic acid (17-HDHA) promote the differentiation of IgG-secreting B cells and enhance antibody-mediated immune responses. However, there is an important knowledge gap regarding whether or not SPMs regulate human B-cell IgE production, which is the key effector in diseases such as asthma and allergy. Therefore, we investigated whether a panel of diverse SPMs influences B-cell IgE production. An important finding was that 17-HDHA and RvD1 inhibit IgE production by human B cells and suppress the differentiation of naïve B cells into IgE-secreting cells by specifically blocking epsilon germline transcript. This effect is specific to human IgE, as the SPMs do not inhibit production of IgM and IgG and did not suppress other IL-4-upregulated genes. 17-HDHA and RvD1 act by stabilizing the transcriptional repressor B-cell lymphoma 6, which competes with STAT6 for binding at the epsilon germline transcript promoter. Overall, these new findings demonstrate that certain SPMs inhibit the differentiation of IgE-producing B cells, without being broadly immune suppressive, representing a novel class of potential therapeutics for IgE-driven diseases such as asthma and allergy.
Electronic Bisection of a Single-Wall Carbon Nanotube by Controlled Chemisorption (2007)

Conversion of two diametrically opposed atomic rows on a carbon nanotube to sp(3) hybridization produces two identical weakly coupled one-dimensional electronic systems within a single robust covalently bonded package: a biribbon. Arm-chair tubes, when so divided, acquire a pair of narrow spin-polarized bands at the Fermi energy; interaction across the sp(3) dividers produces a tunable band splitting in the THz range. For semiconducting tubes, the eigenvalues of the low-energy electronic states are surprisingly unaffected by the bifurcation; however, the tubes' response functions to external electric fields are dramatically altered. These modified tubes could be produced by uniaxial compression transverse to the tube axis followed by site-selective chemisorption.
The Clinical Representativeness of Couple Therapy Outcome Research (2007)

The clinical representativeness of outcome studies is defined as the generalizability of recruitment processes, assessment/diagnostic procedures, treatment protocols, and therapeutic results from research settings to naturalistic treatment settings. The main goal of the present study was to examine the clinical representativeness of couple therapy in outcome studies. The data set was formed by 50 published clinical trials, including 34 couple therapy outcome studies for marital distress (CTMD) and 16 couple therapy outcome studies for comorbid relational and mental disorders (CTMD + C). The present findings showed that, overall, the clinical representativeness of couple therapy outcome studies is only fair (i.e., the mean global score is slightly lower than the midpoint of the rating scale used to assess representativeness). CTMD + C studies fared better than CTMD studies on many dimensions of clinical relevance. Studies in which pretherapy training was less intensive (for CTMD studies only), treatment was less structured, and therapists were more experienced showed larger effect sizes than those in which such was not the case.
Sa1777 Ex Vivo Activation of Triggering Receptor Expressed on Myeloid Cells 1 Enhances the Production of PRO-Inflammatory Cytokines by Inflammatory Bowel Disease Mucosa (2013)

BACKGROUND AND AIMS. Intestinal macrophages play a central role in the pathogenesis of inflammatory bowel disease (IBD). The phenotype of mucosal macrophages changes dramatically at the site of inflammation, where high numbers of CD33+CD68+ macrophages overexpress toll-like receptors, CD14 and triggering receptor expressed on myeloid cells 1 (TREM-1). TREM-1 is expressed on the surface of neutrophils and macrophages and contributes to the amplification of inflammatory responses by enhancing degranulation and secretion of pro-inflammatory mediators. After comparing the percentage of TREM-1-expressing macrophages in IBD versus control mucosa, we explored the ex vivo effects of an activating anti-TREM-1 antibody on the intestinal immune response in IBD. METHODS. Lamina propria mononuclear cells (LPMCs) were isolated from the inflamed colon of 11 IBD patients (5 ulcerative colitis and 6 Crohn's disease), and from normal colon of 8 control subjects, and the expression of CD68, CD33 and TREM-1 was analysed by flow cytometry. TREM1 mRNA expression in CD33+ LPMCs was evaluated by qRT-PCR. IBD biopsies from inflamed mucosa were cultured ex vivo with an activating anti-TREM-1 antibody or its control isotype, and the production of pro-inflammatory cytokines, namely interleukin (IL)1beta, IL-6 and IL-8, was determined by ELISA. RESULTS. The percentage of mucosal CD33+CD68+ macrophages was significantly (p,0.05) higher both in Crohn's disease and ulcerative colitis (17%±1.4 and 15%±7.6, respectively) in comparison to control subjects (6.0%±1.0). TREM-1 expression by mucosal macrophages was significantly (p,0.05) higher both in ulcerative colitis and in Crohn's disease (6.4%±0.2 and 4.4%±0.6) than in control subjects (0.8%±0.1). TREM-1 transcripts were significantly (p,0.05) higher in CD33+ LPMCs from inflamed IBD compared to control subjects. TREM-1 activation significantly (p,0.01) increased IL-1beta, IL-6 and IL-8 production by IBD biopsies cultured ex vivo. CONCLUSIONS. TREM-1 is overexpressed on macrophages infiltrating inflamed IBD mucosa, and its activation amplifies the production of pro-inflammatory cytokines. Further studies using chromatin immunoprecipitation assays are underway in order to establish whether TREM-1 overexpression in IBD may derive from epigenetic changes.
The Founding of The China Quarterly (1995)

In the beginning was Soviet Survey , published in London by the Paris-based Congress for Cultural Freedom (CCF). The Hundred Flowers episode sparked a special issue, the communes a special supplement. The editors of Soviet Survey persuaded Paris HQ that China had become interesting enough to merit its own journal. I had contributed to the Soviet Survey Hundred Flowers issue and in 1958 the CCF had commissioned me to prepare a documentary volume on the theme (The Hundred Flowers Campaign and the Chinese Intellectuals in the United States). In early 1959, Walter Laqueur, then Soviet Survey's principal editor, asked me to edit a new journal on China.
A Residual Chlorine Removal Method to Allow Drinking Water Monitoring by Biological Early Warning Systems (2005)

Abstract : Aquatic biomonitors can provide continuous, real-time monitoring for toxicity in source water supplies, but they cannot be used to directly monitor chlorinated drinking waters because of aquatic organism sensitivity to residual chlorine. The threshold for a toxicity alarm by a biomonitor using bluegills (Lepomis macrochirus) was between 0.015 and 0.066 mg/L total residual chlorine (TRC). A portable dechlorinator that injected 6 mg/L sodium bisulfite into water containing 1.5 to 2.0 mg/L TRC was effective in removing TRC-related toxicity during a nine month evaluation at a water treatment plant. Three biomonitor alarms that occurred were not caused by dechlorinator malfunctions. In one-hour laboratory exposures to sodium bisulfite alone, the biomonitor did not respond until concentrations exceeded 48 mg/L. This study demonstrated the feasibility of using a biomonitor in conjunction with a portable dechlorinator for continuous monitoring of chlorinated drinking waters. Future studies should evaluate dechlorinator suitability in waters with total organic carbon levels exceeding 2 mg/L or that have been disinfected with chloramines.
Bispecific Molecules Directed to the Fc Receptor for IgA (FcαRI, CD89) and Tumor Antigens Efficiently Promote Cell-Mediated Cytotoxicity of Tumor Targets in Whole Blood (1998)

Abstract The FcR for IgA (FcαRI, CD89) is primarily expressed on cytotoxic immune effector cells. By chemically cross-linking F(ab′) fragments of the FcR for IgA (FcαRI)-specific mAb (A77) with tumor Ag-specific mAb (anti-HER2/neu and anti-epidermal growth factor receptor), we have developed bispecific molecules (BSM) that simultaneously bind to respective tumor Ags and FcαRI-expressing effector cells in whole blood. These BSM mediated up to 55% of specific lysis of appropriate tumor Ag-expressing target cells (from a variety of tumors) with purified polymorphonuclear leukocytes, monocytes, or whole blood effector cells without preactivation with exogenous cytokines. To our knowledge, this is the first demonstration of Ab-dependent cell-mediated cytotoxic activity via FcαRI in whole blood. Also, monocyte-derived macrophages mediated phagocytosis of HER2/neu-expressing tumor cells (&amp;gt;95% tumor cell loss). These BSM-mediated cytotoxic activities were completely inhibited by F(ab′)2 of A77, demonstrating the specific role of FcαRI as a trigger molecule. Furthermore, the binding of these BSM to monocytes or polymorphonuclear leukocytes in whole blood did not induce modulation of FcαRI in the absence of the target Ag. Therefore, immune effector cells may be “armed” with FcαRI-directed BSM in whole blood. These FcαRI-directed BSM may offer new treatment options for various malignancies and other disease conditions.
Studies of osmotic diarrhea induced in normal subjects by ingestion of polyethylene glycol and lactulose. (1989)

The purpose of these studies was to gain insight into the pathophysiology of pure osmotic diarrhea and the osmotic diarrhea caused by carbohydrate malabsorption. Diarrhea was induced in normal volunteers by ingestion of polyethylene glycol (PEG), which is nonabsorbable, not metabolized by colonic bacteria, and carries no electrical charge. In PEG-induced diarrhea, (a) stool weight was directly correlated with the total mass of PEG ingested; (b) PEG contributed 40-60% of the osmolality of the fecal fluid, the remainder being contributed by other solutes either of dietary, endogenous, or bacterial origin; and (c) fecal sodium, potassium, and chloride were avidly conserved by the intestine, in spite of stool water losses exceeding 1,200 g/d. Diarrhea was also induced in normal subjects by ingestion of lactulose, a disaccharide that is not absorbed by the small intestine but is metabolized by colonic bacteria. In lactulose-induced diarrhea, (a) a maximum of approximate 80 g/d of lactulose was metabolized by colonic bacteria to noncarbohydrate moieties such as organic acids; (b) the organic acids were partially absorbed in the colon; (c) unabsorbed organic acids obligated the accumulation of inorganic cations (Na greater than Ca greater than K greater than Mg) in the diarrheal fluid; (d) diarrhea associated with low doses of lactulose was mainly due to unabsorbed organic acids and associated cations, whereas with larger doses of lactulose unmetabolized carbohydrates also played a major role; and (e) the net effect of bacterial metabolism of lactulose and partial absorption of organic acids on stool water output was done dependent. With low or moderate doses of lactulose, stool water losses were reduced by as much as 600 g/d (compared with equimolar osmotic loads of PEG); with large dose, the increment in osmotically active solutes within the lumen exceeded the increment of the ingested osmotic load, and the severity of diarrhea was augmented.
Monocarbamates, Derived from (S)-2-(Dibenzylamino)butane-1,4-diol, and the Influence of the Second O-Protecting Group on the Regioselectivity of Deprotonation - Application to the Synthesis of the Boletus Toxin (2S,4S)-γ-Hydroxy-norvaline (1998)

stereoselective lithiation - chiral aminodiols - directed lithiation - chiral carbanion - (-)-sparteine
Analysis and fabrication of high-contrast InGaAsP/InP Mach-Zehnder modulators for use at 1.55 μm wavelength (2002)

Summary form only given. A multiple quantum well InGaAsP-InP Mach-Zehnder (MZ) interferometer with a high-contrast ratio of >40 dB, and a low voltage-length product of 1.8 V-mm, is demonstrated and analyzed. Using the Lanczos-Helmhortz beam propagation method (LHBPM), we find that the linear and quadratic electrooptic coefficients for lnGaAsP quantum wells.
MULTITURN SPIRAL TIME-OF-FLIGHT MASS ANALYZER BASED ON CYLINDRICAL SECTOR FIELDS AND PERIODIC LENSES (2018)

This paper describes an online realtime data acquisition system.The design utilizes ARM singleboard computers that bring very low power requirements, portability and lightweightness.We have implemented a unified approach to acquire, transfer and store the measurements.The approach takes advantages of SeedLink protocol to establish online realtime data flows between the components of the system.Communication over IPv4 rely on secure virtual private networks.The system features remote management of data logger and all connected devices.For purposes of testing and technology showcase we've implemented support for a range of variometer-type magnetometers.
Structural and strain anisotropies of N-polar GaN epilayers on offcut sapphire substrates (2016)

The dependence of the structure and strain upon the crystal direction (anisotropies) of N-polar GaN films grown on offcut c-plane sapphire substrates was examined by varying the degree of substrate offcut and the V/III ratio. On offcut substrates, the broadening of GaN (0002¯) rocking curves was found to depend upon the x-ray incidence azimuth, whereby the maxima and minima of the broadening, respectively, occurred parallel and perpendicular to the offcut direction. In contrast, no such structural anisotropies were observed for samples grown on the on-axis substrates. Mosaic tilt was suggested as the determining factor for the structural anisotropy, which was further aided by the different island coalescence rates in the two orthogonal directions during the initial nucleation stage. In addition, the off-axis samples exhibited larger in-plane strains occurring in the direction perpendicular to the substrate offcut than in other directions, which was significantly different from the uniform in-plane strain found in the on-axis sample. The in-plane strain anisotropy was attributed to preferential strain relaxation along the substrate offcut direction via the formation of geometrical partial misfit dislocations along the orthogonal direction. Moreover, the structural (strain) anisotropy decreased (increased) as the substrate offcut increased, and both anisotropies were affected only marginally by the V/III ratio.
Practical implementation of successive interference cancellation in DS/CDMA systems (2002)

This paper addresses the practical implementation of successive interference cancellation (SIC) for DS/CDMA systems. The practical aspects of such an implementation are discussed and an FPGA-based detector employing SIC are presented. An important aspect is the integration of power control and interference cancellation which has several benefits.
Influence of atrial fibrillation on efficacy and safety of omecamtiv mecarbil in heart failure: the GALACTIC-HF trial (2022)

Patients in AFF at baseline were less likely to benefit from omecamtiv mecarbil than patients without AFF, although the attenuation of the treatment effect was disproportionally concentrated in patients with AFF who were also receiving digoxin.Clinical Trial Registration: NCT02929329.
Computational Principles of Mobile Robotics (2010)

This textbook for advanced undergraduates and graduate students emphasizes algorithms for a range of strategies for locomotion, sensing, and reasoning. It concentrates on wheeled and legged mobile robots but discusses a variety of other propulsion systems. This edition includes advances in robotics and intelligent machines over the ten years prior to publication, including significant coverage of SLAM (simultaneous localization and mapping) and multi-robot systems. It includes additional mathematical background and an extensive list of sample problems. Various mathematical techniques that were assumed in the first edition are now briefly introduced in appendices at the end of the text to make the book more self-contained. Researchers as well as students in the field of mobile robotics will appreciate this comprehensive treatment of state-of-the-art methods and key technologies.
Frustrated Lewis Pair Chelation as a Vehicle for Low‐Temperature Semiconductor Element and Polymer Deposition (2020)

The stabilization of silicon(II) and germanium(II) dihydrides by an intramolecular Frustrated Lewis Pair (FLP) ligand, PB, <sup>i</sup> Pr<sub>2</sub> P(C<sub>6</sub> H<sub>4</sub> )BCy<sub>2</sub> (Cy=cyclohexyl) is reported. The resulting hydride complexes [PB{SiH<sub>2</sub> }] and [PB{GeH<sub>2</sub> }] are indefinitely stable at room temperature, yet can deposit films of silicon and germanium, respectively, upon mild thermolysis in solution. Hallmarks of this work include: 1) the ability to recycle the FLP phosphine-borane ligand (PB) after element deposition, and 2) the single-source precursor [PB{SiH<sub>2</sub> }] deposits Si films at a record low temperature from solution (110 °C). The dialkylsilicon(II) adduct [PB{SiMe<sub>2</sub> }] was also prepared, and shown to release poly(dimethylsilane) [SiMe<sub>2</sub> ]<sub>n</sub> upon heating. Overall, this study introduces a "closed loop" deposition strategy for semiconductors that steers materials science away from the use of harsh reagents or high temperatures.
On the Temporal Structure of Events (1997)

The temporal interpretation of events is crucial to many applications of natural language understanding. Interpreting events as described in individual utterances and discourse requires both semantic and pragmatic processing. We develop representations for events that reflect the internal structure of different situation types. We propose semantic constraints through which the representations of different events can be related based on their tense, aspect, and situation type. Our approach uses semantic information to a greater extent than previous approaches, and thereby generates constraints that restrict the ultimate pragmatic interpretations. We develop our approach on the notorious when-clauses, and show how it may be used for understanding events in discourse. 1 Introduction Temporal reference is the problem of (a) inferring the internal structure of events as described in natural language, and (b) determining how events relate to one another. Determining the temporal reference...
Mapping the immunogenic landscape of near-native HIV-1 envelope trimers in non-human primates (2020)

The induction of broad and potent immunity by vaccines is the key focus of research efforts aimed at protecting against HIV-1 infection. Soluble native-like HIV-1 envelope glycoproteins have shown promise as vaccine candidates as they can induce potent autologous neutralizing responses in rabbits and non-human primates. In this study, monoclonal antibodies were isolated and characterized from rhesus macaques immunized with the BG505 SOSIP.664 trimer to better understand vaccine-induced antibody responses. Our studies reveal a diverse landscape of antibodies recognizing immunodominant strain-specific epitopes and non-neutralizing neo-epitopes. Additionally, we isolated a subset of mAbs against an epitope cluster at the gp120-gp41 interface that recognize the highly conserved fusion peptide and the glycan at position 88 and have characteristics akin to several human-derived broadly neutralizing antibodies.