gebhart/patrepeval huggingface dataset:
Removing per‐ and polyfluoroalkyl substances from groundwaters using activated carbon and ion exchange resin packed columns (2020)

Abstract Human exposure to per‐ and polyfluoroalkyl substances (PFAS) in drinking water is of growing concern as a result of increasing reports of occurrence and potential regulation. Adsorption of PFAS by granular activated carbon (GAC) or ion exchange (IX) resin is a suitable treatment technique. However, few studies compare PFAS removal in continuous flow GAC or IX adsorption systems using real drinking water sources. In this study, rapid small‐scale column tests (RSSCTs) were used to investigate the effects of PFAS type and chain length on adsorption by GAC and IX resin for six groundwaters used as drinking water supplies. Seven PFAS substances with chain lengths of C4–C9 were detected in the groundwaters with the sum of their concentrations (ΣPFAS) ranging from 156 to 7,044 ng/L. Adsorption capacities ( q ΣPFAS ) were calculated to compare the removal capacity among different sorbents and q ΣPFAS values ranged from 10.3 to 228 ng PFAS/mg sorbent after about 100,000 bed volumes treated. Coal‐based GACs had higher adsorption capacity compared with coconutshell‐based GAC, which was likely due to higher mesopore and macropore volumes. IX resins performed better than GAC in removing PFAS, but they were not effective in treating short‐chain perfluorocarboxylic acids (PFCAs). Perfluorosulfonic acids (PFSAs) broke through later than PFCAs with the same chain length. Within PFSA or PFCA classes, shorter‐chain PFAS species always broke through before longer‐chain PFAS. Statistical analysis demonstrated that PFAS with higher hydrophobicity and molecular weight are more amenable to GAC adsorption. Empirical models were developed and predicted PFAS breakthrough. By quantifying PFAS selectivity and removal efficiency, this work provides benchmark data for commercially available treatment technologies and guidance toward specific PFAS classes for which new treatment technologies may be most beneficial.
Time-resolved two-dimensional profiles of electron density and temperature of laser-produced tin plasmas for extreme-ultraviolet lithography light sources (2017)

Time-resolved two-dimensional (2D) profiles of electron density (n <sub>e</sub>) and electron temperature (T <sub>e</sub>) of extreme ultraviolet (EUV) lithography light source plasmas were obtained from the ion components of collective Thomson scattering (CTS) spectra. The highest EUV conversion efficiency (CE) of 4% from double pulse lasers irradiating a Sn droplet was obtained by changing their delay time. The 2D-CTS results clarified that for the highest CE condition, a hollow-like density profile was formed, i.e., the high density region existed not on the central axis but in a part with a certain radius. The 2D profile of the in-band EUV emissivity (η<sub>EUV</sub>) was theoretically calculated using the CTS results and atomic model (Hullac code), which reproduced a directly measured EUV image reasonably well. The CTS results strongly indicated the necessity of optimizing 2D plasma profiles to improve the CE in the future.
Spacetime stereo and its applications (2005)

A long-standing challenge in computer vision is to recover 3D shapes from images, especially when the shapes change over time. Among the numerous existing shape acquisition methods, very few are able to accurately measure time-varying shapes at both high spatial and temporal resolution. Furthermore, some previous methods have strict assumptions on surface color and texture and do not work robustly for complex object shapes. In this dissertation, we address these limitations and present a new approach, spacetime stereo, for dynamic shape acquisition. 
Spacetime stereo formulates stereo matching as a 3D window warping problem in video volumes. This new formulation incorporates the temporal variations of image pixels as a cue for better shape reconstruction, and is a general framework for different variants of triangulation-based shape reconstruction methods, namely, passive stereo, active stereo, one-shot structured light, and multi-shot structured light. Under this framework, we develop algorithms that accurately reconstruct deforming objects at high spatial and temporal resolution. Spacetime stereo is also effective for a class of natural scenes, such as waving trees and flowing water, which have repetitive textures and chaotic behaviors and are challenging for existing stereo algorithms. 
To demonstrate an application of spacetime stereo, we build a dynamic face capture system that consists of off-the-shelf cameras, projectors, and computers. We also propose a new template fitting and tracking method that computes a sequence of 3D face meshes with vertex-to-vertex correspondence by combining shape and optical flow estimation. The resulting system is able to continuously (20Hz) capture high resolution (about 20K points) facial motion simultaneously from multiple viewpoints without the need to paint markers on the face. Finally, we develop data-driven facial animation tools that take advantage of the captured 3D face sequence. These tools enable untrained users to produce realistic facial expressions and animations.
MYD88 mutated and wild-type Waldenström’s Macroglobulinemia: characterization of chromosome 6q gene losses and their mutual exclusivity with mutations in CXCR4 (2018)

Waldenstrom’s Macroglobulinemia (WM) is a lymphoplasmacytic lymphoma characterized by bone marrow (BM) infiltration of immunoglobulin M (IgM)-secreting lymphoplasmacytic cells.[1][1] Activating mutations in MYD88 are present in 93-97% of WM and 50-70% of IgM monoclonal gammopathy of undetermined
ChemInform Abstract: Total Synthesis of Rutamycin B (I), a Macrolide Antibiotic from Streptomyces aureofaciens. (2001)

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.
Streamlined Yeast Colorimetric Reporter Activity Assays Using Scanners and Plate Readers (2000)

Two-hybrid systems have become favored tools for detection and analysis of protein interactions because of their low cost and ease of use compared to biochemical or biophysical interaction technologies. It is possible to augment the utility of two-hybrid systems and derivative systems such as dual-bait two-hybrid systems by adapting strategies that speed the analysis of the relative strength of a series of protein-protein associations. This report describes two simple techniques that employ either a flatbed scanner or a plate reader to quantitate the activity of colorimetric reporters such as LacZ or GusA commonly used in two-hybrid approaches.
Supplementary Figure S5 from The PSMA-targeting Half-life Extended BiTE Therapy AMG 160 has Potent Antitumor Activity in Preclinical Models of Metastatic Castration-resistant Prostate Cancer (2023)

&lt;p&gt;Figure S5. AMG 160 engages NHP PSMA and CD3 in vitro.&lt;/p&gt;
Avoiding leaching of silica supported metallocenes in slurry phase ethylene homopolymerization (2017)

Leaching of (<italic>n</italic>-BuCp)<sub>2</sub>ZrCl<sub>2</sub>/MAO catalyst from silica supports has been studied in slurry phase ethylene homopolymerisation by changing i) the polymerization protocol, ii) aluminum alkyl scavengers and iii) by adding butylated hydroxytoluene (BHT-H) along with aluminum alkyl scavengers.
Electrodynamics study of plasmonic bonding and antibonding forces in a bisphere (2008)

Light excitation of surface plasmons in metallic nanoparticle clusters can induce huge forces. We study such forces by using an electrodynamics approach, which fully incorporates the retardation effect. As two particles approach each other, the single-particle plasmons hybridize and split into attractive bonding modes and repulsive antibonding modes, which eventually evolve into an attractive band and a repulsive band. At an intensity of about $0.05\text{ }\text{W}/\ensuremath{\mu}{\text{m}}^{2}$, the force can reach nano-Newtons and, hence, can dominate over other relevant interactions.
ALD Barrier Deposition on Porous Low-k Dielectric Materials for Interconnects (2011)

To achieve very low permittivity values, advanced generations of low-k dielectrics for interconnects have a porous structure. Precursor penetration during metal barrier deposition by atomic layer deposition needs to be avoided not to degrade the low-k material properties. In this paper, we compare various options to seal a highly porous low-k material with a k-value of 2.0 against penetration during TaN ALD. This includes the exploration of a higher deposition temperature, the use of additional sealing layers, and the introduction of a short PVD Ta flash exposure prior to ALD. Depending on the technique used, pore penetration can be quasi completely avoided.
Two step synthesis of ultrathin transition metal tellurides (2022)

Transition metal tellurides (TMTs) are an exciting group of two-dimensional materials with a wide variety of polytypes and properties. Here, we demonstrate a simple and versatile two-step method for producing MoTe2, WTe2, and PtTe2 films via tellurization of thin metals at temperatures between 400 and 700 °C. Across this temperature range, monoclinic 1T′ phase of MoTe2, orthorhombic Td phase of WTe2, and hexagonal 2H phase of PtTe2 were formed. Based on x-ray diffraction and Raman analysis, temperatures greater than 600 °C were found to produce the best quality MoTe2 and WTe2. In contrast, lower temperatures (400 °C) were preferred for PtTe2, which becomes discontinuous and eventually decomposes above 650 °C. The presence of H2 in the tellurization process was critical to facilitate the formation of H2Te, which is known to be more reactive than Te vapor. In the absence of H2, neither MoTe2 nor WTe2 formed, and although PtTe2 was formed under pure N2, the crystal quality was significantly reduced. Temperature-dependent resistivity (ρ) measurements were performed on the best quality TMT films revealing all films to be highly conductive. MoTe2 showed metallic behavior up to 205 K where it underwent a phase transition from the semimetallic Td to semiconducting 1T′ phase. WTe2 exhibited a consistent semiconducting behavior with a small positive increase in ρ with decreasing temperature, and PtTe2 showed a metallic dependence from 10 K up to room temperature. Spectroscopic ellipsometry for TMT films provides complex optical constants n and k from ultraviolet to infrared.
Viral Serologic Test in Sudden Sensorineural Hearing Loss and Acute Peripheral Facial Paralysis：Is It Always Necessary? (2008)

Background and Objectives：Sudden sensorineural hearing loss (SSNHL) and acute peripheral facial paralysis (APFP) are common otologic diseases related to viral infections. In this study, we investigated the clinical necessity of viral serologic tests in the diagnosis of SSNHL and APFP. Subjects and Method：A retrospective study was carried out for 348 patients with SSNHL, 121 patients of Bell’s palsy (BP) and 37 patients of Ramsay Hunt syndrome (RHS). The serologic tests for IgM and IgG titers of herpes simplex virus (HSV) and varicella zoster virus (VZV) using enzyme-linked immunosorbent assay were performed within 10 days after onset in all patients. Clinical manifestations, abnormalities on MRI and prognosis were compared in relation to the results of viral serologic tests. Mean duration between the onset and the serologic tests was 4.6±2.9 days. The prognosis was determined using pure tone audiometry and House-Brackmann grading system after 6 months. Results：The positivity of VZV IgM and titer of VZV IgG in RHS were significantly higher than those in the others (p .05). Conclusion：The serologic tests for IgM and IgG titers of HSV and VZV performed once in the acute stage are unlikely to provide additional information for the prognosis of SSNHL or APFP, but they might be helpful in the differential diagnosis process of APFP. (Korean J Otorhinolaryngol-Head Neck Surg 2008;51:1088-92)
Desiccating Stress Decreases Apical Corneal Epithelial Cell Size-Modulation by the Metalloproteinase Inhibitor Doxycycline (2008)

Desiccating stress decreases apical corneal epithelial cell area, increases apical cell density, and promotes epithelial cell loss. Treatment with the metalloproteinase inhibitor doxycycline during desiccating stress preserves cell area and apical cell density and prevents EDE-induced corneal epithelial cell loss. These findings suggest that metalloproteinases mediate apical corneal epithelial loss during desiccating stress.
Spiking Neural Networks Based on OxRAM Synapses for Real-Time Unsupervised Spike Sorting (2016)

In this paper, we present an alternative approach to perform spike sorting of complex brain signals based on spiking neural networks (SNN). The proposed architecture is suitable for hardware implementation by using resistive random access memory (RRAM) technology for the implementation of synapses whose low latency (<1μs) enables real-time spike sorting. This offers promising advantages to conventional spike sorting techniques for brain-computer interfaces (BCI) and neural prosthesis applications. Moreover, the ultra-low power consumption of the RRAM synapses of the spiking neural network (nW range) may enable the design of autonomous implantable devices for rehabilitation purposes. We demonstrate an original methodology to use Oxide based RRAM (OxRAM) as easy to program and low energy (<75 pJ) synapses. Synaptic weights are modulated through the application of an online learning strategy inspired by biological Spike Timing Dependent Plasticity. Real spiking data have been recorded both intra- and extracellularly from an <i>in-vitro</i> preparation of the Crayfish sensory-motor system and used for validation of the proposed OxRAM based SNN. This artificial SNN is able to identify, learn, recognize and distinguish between different spike shapes in the input signal with a recognition rate about 90% without any supervision.
Transmission of integrin β7 transmembrane domain topology enables gut lymphoid tissue development (2018)

Integrin activation regulates adhesion, extracellular matrix assembly, and cell migration, thereby playing an indispensable role in development and in many pathological processes. A proline mutation in the central integrin β3 transmembrane domain (TMD) creates a flexible kink that uncouples the topology of the inner half of the TMD from the outer half. In this study, using leukocyte integrin α4β7, which enables development of gut-associated lymphoid tissue (GALT), we examined the biological effect of such a proline mutation and report that it impairs agonist-induced talin-mediated activation of integrin α4β7, thereby inhibiting rolling lymphocyte arrest, a key step in transmigration. Furthermore, the α4β7(L721P) mutation blocks lymphocyte homing to and development of the GALT. These studies show that impairing the ability of an integrin β TMD to transmit talin-induced TMD topology inhibits agonist-induced physiological integrin activation and biological function in development.
Ultrafast time resolved studies of the photochemistry of acyl and sulfonyl azides (2012)

A graphical abstract is available for this content
A long-acting C-natriuretic peptide for achondroplasia (2022)

The C-natriuretic peptide (CNP) analog vosoritide has recently been approved for treatment of achondroplasia in children. However, the regimen requires daily subcutaneous injections in pediatric patients over multiple years. The present work sought to develop a long-acting CNP that would provide efficacy equal to or greater than that of vosoritide but require less frequent injections. We used a technology for half-life extension, whereby a drug is attached to tetra-polyethylene glycol hydrogels (tetra-PEG) by β-eliminative linkers that cleave at predetermined rates. These hydrogels-fabricated as uniform ∼60-μm microspheres-are injected subcutaneously, where they serve as a stationary depot to slowly release the drug into the systemic circulation. We prepared a highly active, stable CNP analog-[Gln<sup>6,14</sup>]CNP-38-composed of the 38 C-terminal amino acids of human CNP-53 containing Asn to Gln substitutions to preclude degradative deamidation. Two microsphere [Gln<sup>6,14</sup>]CNP-38 conjugates were prepared, with release rates designed to allow once-weekly and once-monthly administration. After subcutaneous injection of the conjugates in mice, [Gln<sup>6,14</sup>]CNP-38 was slowly released into the systemic circulation and showed biphasic elimination pharmacokinetics with terminal half-lives of ∼200 and ∼600 h. Both preparations increased growth of mice comparable to or exceeding that produced by daily vosoritide. Simulations of the pharmacokinetics in humans indicated that plasma [Gln<sup>6,14</sup>]CNP-38 levels should be maintained within a therapeutic window over weekly, biweekly, and likely, monthly dosing intervals. Compared with vosoritide, which requires ∼30 injections per month, microsphere [Gln<sup>6,14</sup>]CNP-38 conjugates-especially the biweekly and monthly dosing-could provide an alternative that would be well accepted by physicians, patients, and patient caregivers.
Incidence and Seroprevalence of Avian Influenza in a Cohort of Backyard Poultry Growers, Egypt, August 2015–March 2019 (2020)

Currently enzootic avian influenza H5N1, H9N2, and H5N8 viruses were introduced into poultry in Egypt in 2006, 2011, and 2016, respectively. Infections with H5N1 and H9N2 were reported among poultry-exposed humans. We followed 2,402 persons from households raising backyard poultry from 5 villages in Egypt during August 2015-March 2019. We collected demographic, exposure, and health condition data and annual serum samples from each participant and obtained swab samples from participants reporting influenza-like illness symptoms. We performed serologic and molecular analyses and detected 4 cases of infection with H5N1 and 3 cases with H9N2. We detected very low seroprevalence of H5N1 antibodies and no H5N8 antibodies among the cohort; up to 11% had H9 antibodies. None of the exposure, health status, or demographic variables were related to being seropositive. Our findings indicate that avian influenza remains a public health risk in Eqypt, but infections may go undetected because of their mild or asymptomatic nature.
Learning from Collective Intelligence in Groups (2012)

Collective intelligence, which aggregates the shared information from large crowds, is often negatively impacted by unreliable information sources with the low quality data. This becomes a barrier to the effective use of collective intelligence in a variety of applications. In order to address this issue, we propose a probabilistic model to jointly assess the reliability of sources and find the true data. We observe that different sources are often not independent of each other. Instead, sources are prone to be mutually influenced, which makes them dependent when sharing information with each other. High dependency between sources makes collective intelligence vulnerable to the overuse of redundant (and possibly incorrect) information from the dependent sources. Thus, we reveal the latent group structure among dependent sources, and aggregate the information at the group level rather than from individual sources directly. This can prevent the collective intelligence from being inappropriately dominated by dependent sources. We will also explicitly reveal the reliability of groups, and minimize the negative impacts of unreliable groups. Experimental results on real-world data sets show the effectiveness of the proposed approach with respect to existing algorithms.
Retrieval and on-the-fly alignment of sequence fragments from the HIV database (2001)

The MPAlign (Multiple Pairwise Alignment) web interface is a collection of Perl scripts that retrieves sequences from the Los Alamos HIV sequence database based on a number of search parameters. All sequences were pairwise-aligned to a model sequence using the Hidden Markov Model-based program HMMER. The HMMER model is general enough to accommodate virtually all HIV-1 sequences stored in the database. To create a multiple sequence alignment, gaps were inserted into the sequences during retrieval, so that they are aligned to one another. Retrieving and aligning the almost 560 gp120 sequences (approximately>1500 nt) stored in the database is at least 1500 times faster than a similar Clustal alignment.
Magnetic resonance imaging in multiple sclerosis: Decreased signal in thalamus and putamen (1987)

High-field strength (1.5 Tesla) magnetic resonance imaging in 15 patients with multiple and extensive white-matter lesions and clinically definite multiple sclerosis delineated a previously undescribed finding of abnormally decreased signal intensity on T2-weighted images in the thalamus and putamen. The decreased signal intensity (preferential decreased T2 relaxation time) is most likely to be related to abnormally increased iron accumulation causing local magnetic field heterogeneities.
Innate Invariant NKT Cell Recognition of HIV-1–Infected Dendritic Cells Is an Early Detection Mechanism Targeted by Viral Immune Evasion (2016)

Invariant NKT (iNKT) cells are innate-like T cells that respond rapidly with a broad range of effector functions upon recognition of glycolipid Ags presented by CD1d. HIV-1 carries Nef- and Vpu-dependent mechanisms to interfere with CD1d surface expression, indirectly suggesting a role for iNKT cells in control of HIV-1 infection. In this study, we investigated whether iNKT cells can participate in the innate cell-mediated immune response to HIV-1. Infection of dendritic cells (DCs) with Nef- and Vpu-deficient HIV-1 induced upregulation of CD1d in a TLR7-dependent manner. Infection of DCs caused modulation of enzymes in the sphingolipid pathway and enhanced expression of the endogenous glucosylceramide Ag. Importantly, iNKT cells responded specifically to rare DCs productively infected with Nef- and Vpu-defective HIV-1. Transmitted founder viral isolates differed in their CD1d downregulation capacity, suggesting that diverse strains may be differentially successful in inhibiting this pathway. Furthermore, both iNKT cells and DCs expressing CD1d and HIV receptors resided in the female genital mucosa, a site where HIV-1 transmission occurs. Taken together, these findings suggest that innate iNKT cell sensing of HIV-1 infection in DCs is an early immune detection mechanism, which is independent of priming and adaptive recognition of viral Ag, and is actively targeted by Nef- and Vpu-dependent viral immune evasion mechanisms.
Transvalencin A, a Thiazolidine Zinc Complex Antibiotic Produced by a Clinical Isolate of Nocardia transvalensis: II.Structure Elucidation (2004)

A novel antifungal antibiotic, transvalencin A, is produced by Nocardia transvalensis IFM 10065 isolated from a patient with actinomycotic mycetoma in Japan. The antibiotic structure was elucidated using NMR, mass spectrometric investigations, and X-ray crystallographic analysis. Transvalencin A is a 1:1 complex of a zinc and an organic acid with a phenolic substituent. Transvalencin A is comprised of o-substituted p-chlorophenol, tetrasubstituted oxazoline, disubstituted thiazolyl-N-methylthiazolidine and monosubstituted N-methylthiazolidine.