gebhart/patrepeval huggingface dataset:
Separation and concentration of bacteria with immobilized antibody fragments (1995)

New methods to quantitatively remove bacteria from food and water samples are required to meet modern safety standards. The recent development of techniques to make Fab/Fv/scFv fragments in bacteria has provided the opportunity to exploit antibodies as specialized chemicals for affinity removal technologies. Single-chain fragments against Pseudomonas aeruginosa have been expressed in Escherichia coli, purified via a fused poly-histidine tail and immobilized upon polystyrene beads. The resulting immunoaffinity columns have been shown to effectively remove greater than 90% of an applied 10 million bacteria after a single passage through the column. Column material in the absence of single-chain retained less than 10% of the bacteria. Pseudomonas were also removed from milk, mixed bacterial cultures and when present at low cell densities.
MEMS based color-VGA micro-projector system (2010)

This paper presents a complete portable laser-based projection system using twofold of one dimensional magnetic actuated MEMS linear scanning micro-mirrors. Dedicated high speed electronics was developed to drive the MEMS, detect the mirror scanning position at any time and synchronize the two mirrors and the laser pulsation. The achieved projection system head is 4.5 cm3 and is able to project colorful static images and videos (50 fps) with projection size of 50 cm diagonal at 50 cm distance with VGA (640×480 px) resolution.
COSIN (2008)

We develop a content-based audio COver Song IdeNtification (COSIN) system to detect/group cover songs.The COSIN takes music audio content as input and performs similarity searching to locate variants of the input (i.e., cover versions). Identified cover songs are returned in the rank order according to their similarity to the input.The COSIN also incorporates a set of tools to evaluate retrieval performance so researchers can explore different retrieval schemes and parameters (e.g. recall, precision).The COSIN utilizes a suite of techniques to detect cover songs including: Pitch + Dynamic Programming (DP), Chroma + DP, and Semantic Feature Summarization (SFS) + Hash-Based Approximate Matching (HBAM). Demonstration system shows that COSIN is a very potential music content retrieval tool. Running some music retrieval schemes on COSIN platform, recent experiments with SFS + LSH Variants demonstrate a nicely balanced efficiency (search speed) v. performance (search accuracy) tradeoff.
Molecular Basis of Valine-Citrulline-PABC Linker Instability in Site-Specific ADCs and Its Mitigation by Linker Design (2016)

The degree of stability of antibody-drug linkers in systemic circulation, and the rate of their intracellular processing within target cancer cells are among the key factors determining the efficacy of antibody-drug conjugates (ADC) in vivo Previous studies demonstrated the susceptibility of cleavable linkers, as well as auristatin-based payloads, to enzymatic cleavage in rodent plasma. Here, we identify Carboxylesterase 1C as the enzyme responsible for the extracellular hydrolysis of valine-citrulline-p-aminocarbamate (VC-PABC)-based linkers in mouse plasma. We further show that the activity of Carboxylesterase 1C towards VC-PABC-based linkers, and consequently the stability of ADCs in mouse plasma, can be effectively modulated by small chemical modifications to the linker. While the introduced modifications can protect the VC-PABC-based linkers from extracellular cleavage, they do not significantly alter the intracellular linker processing by the lysosomal protease Cathepsin B. The distinct substrate preference of the serum Carboxylesterase 1C offers the opportunity to modulate the extracellular stability of cleavable ADCs without diminishing the intracellular payload release required for ADC efficacy. Mol Cancer Ther; 15(5); 958-70. ©2016 AACR.
A RELIABLE MULTI-KILOGRAM PREPARATION OF 4-PHENYLURAZOLE (2004)

(2004). A RELIABLE MULTI-KILOGRAM PREPARATION OF 4-PHENYLURAZOLE. Organic Preparations and Procedures International: Vol. 36, No. 5, pp. 469-472.
Utilization of paramagnetic relaxation enhancements for structural analysis of actin-binding proteins in complex with actin (2016)

Actin cytoskeleton dynamics are controlled by various actin binding proteins (ABPs) that modulate the polymerization of the monomeric G-actin and the depolymerization of filamentous F-actin. Although revealing the structures of the actin/ABP complexes is crucial to understand how the ABPs regulate actin dynamics, the X-ray crystallography and cryoEM methods are inadequate to apply for the ABPs that interact with G- or F-actin with lower affinity or multiple binding modes. In this study, we aimed to establish the alternative method to build a structural model of G-actin/ABP complexes, utilizing the paramagnetic relaxation enhancement (PRE) experiments. Thymosin β4 (Tβ4) was used as a test case for validation, since its structure in complex with G-actin was reported recently. Recombinantly expressed G-actin, containing a cysteine mutation, was conjugated with a nitroxyl spin label at the specific site. Based on the intensity ratio of the <sup>1</sup>H-<sup>15</sup>N HSQC spectra of Tβ4 in the complex with G-actin in the paramagnetic and diamagnetic states, the distances between the amide groups of Tβ4 and the spin label of G-actin were estimated. Using the PRE-derived distance constraints, we were able to compute a well-converged docking structure of the G-actin/Tβ4 complex that shows great accordance with the reference structure.
The Common Case Transactional Behavior of Multithreaded Programs (2006)

Transactional memory (TM) provides an easy-to-use and high-performance parallel programming model for the upcoming chip-multiprocessor systems. Several researchers have proposed alternative hardware and software TM implementations. However, the lack of transaction-based programs makes it difficult to understand the merits of each proposal and to tune future TM implementations to the common case behavior of real application. This work addresses this problem by analyzing the common case transactional behavior for 35 multithreaded programs from a wide range of application domains. We identify transactions within the source code by mapping existing primitives for parallelism and synchronization management to transaction boundaries. The analysis covers basic characteristics such as transaction length, distribution of read-set and write-set size, and the frequency of nesting and I/O operations. The measured characteristics provide key insights into the design of efficient TM systems for both non-blocking synchronization and speculative parallelization.
A Highly Selective Synthesis of 1,1′-Bi-2-naphthol by Oxidative Coupling of Naphthol on Mesoporous Fe,Cu/MCM-41 Aluminosilicates (1999)

The oxidative coupling of 2-naphtol to 2,2′-dihydroxy-1,1′-binaphthyl (binaphthol) by air or oxygen has been carried out in the presence of Cu2+- and Fe3+-doped MCM-41 aluminosilicate as catalyst. Fe-exchanged MCM-41 was found to be a very efficient catalyst; excellent mass balances (> 95%) with almost total conversion and selectivity to binaphthol were achieved. The same reaction has also been carried out on Cu2+– and Fe3+–Y zeolites. Taking into account the relative dimensions of binaphthol and the catalyst pores, molecular modeling predicts that binaphthol can be accommodated inside the zeolite Y supercages (1.3 nm), but it cannot diffuse outside the zeolite cavities through the smaller pore apertures (0.74 nm). This prediction has been confirmed by dissolving a Y zeolite after the reaction, whereby unextractable binaphthol entrapped within the cavities was recovered. Variable amounts of two secondary by-products have also been detected, and their structure assigned to (2,8′);(8,2′)-dioxo-1,1′-binaphthyl and bisnaphthofuran based on analytical and spectroscopic data. Their percentage is particularly high when alumina-supported CuSO4 is used as the catalyst.
Experimental study of flow mechanics in a hollow-fiber membrane module for plasma separation. (1992)

Flow characteristics that control the performance of a hollow-fiber membrane module are investigated experimentally. The test fluid used is pure water, and the velocity at the entrance and at the exit of the bundle of fibers, the pressure loss and the transmembrane pressure are measured. It becomes clear that Hagen-Poiseuille’s law is almost applicable to the flow in respective fibers and that Darcy’s law is applicable to permeation through the membrane. In addition, impulse response tests are carried out and some information concerning dead space in the shell side and stagnation of liquid in an entrance cap is obtained. On the basis of the results, a simple model concerning the flow mechanism in the module is proposed and is confirmed to be appropriate.
Effect of gonadotropin‐inhibitory hormone on luteinizing hormone secretion in humans (2017)

Gonadotropin-inhibitory hormone decreased LH secretion in postmenopausal women in this first-in-human study. Kisspeptin-stimulated LH secretion in men was not inhibited during concomitant administration of GnIH.
Segmentation of Images Using Level Set Analysis. (2002)

We propose an image segmentation technique using level set analysis. Image level set is the binary decomposition of a gray level image. Connected components in the level set, less than a pre-defined size are removed from the level set. Based on level set topology an exposed connected component is defined in the level set. These exposed connected components are merged based on a proximity value derived between the neighboring components. This proximity measure is a function of intensity difference and the shared boundary length between image regions described by the connected components present in the level set. The result obtained using the proposed method is shown and compared with a similar process along with the accuracy measure of the segmentation.
Intracavity fiber array beam combining (2005)

In this paper we present results of an analysis of a method of effectively combining the output of a fiber array into a single beam by using a laser cavity in stable configuration. To couple the individual channels, our approach uses the nature of the high index modes with their spatial pattern resembling a combination of the sub-beams. The structure of such modes allows for very efficient matching (up to 97%) of the individual channels of the fiber array to an intra-cavity field distribution. As the high index mode has a spherical wavefront with &pi;-phase shift between the nearest sub-beams this allows use of a simple phase corrector to form a diffraction limited output beam. In the configuration under analysis, the intra-cavity power per individual channel of the array is low enough to avoid damaging the fiber while the total output power is the sum of the power of all the channels. This paper describes the characteristics of the proposed fiber array beam coupling, in particular, the selection and stabilization of the chosen operating mode without losses in oscillation efficiency.
Supplementary Figure 3 from Sensitive Detection of Minimal Residual Disease in Patients Treated for Early-Stage Breast Cancer (2023)

&lt;p&gt;Overview schematic of MRD assay. MRD assay workflow from characterizing a primary tumor to determining if a blood draw contains evidence of residual disease.&lt;/p&gt;
A simple gold nanoparticle-mediated immobilization method to fabricate highly homogeneous DNA microarrays having higher capacities than those prepared by using conventional techniques (2008)

A simple, highly efficient immobilization method to fabricate DNA microarrays, that utilizes gold nanoparticles as the mediator, has been developed. The fabrication method begins with electrostatic attachment of amine-modified DNA to gold nanoparticles. The resulting gold-DNA complexes are immobilized on conventional amine or aldehyde functionalized glass slides. By employing gold nanoparticles as the immobilization mediator, implementation of this procedure yields highly homogeneous microarrays that have higher binding capacities than those produced by conventional methods. This outcome is due to the increased three-dimensional immobilization surface provided by the gold nanoparticles as well as the intrinsic effects of gold on emission properties. This novel immobilization strategy gives microarrays that produce more intense hybridization signals for the complementary DNA. Furthermore, the silver enhancement technique, made possible only in the case of immobilized gold nanoparticles on the microarrays, enables simple monitoring of the integrity of the immobilized DNA probe.
New Decision Making Criterion for Multiobjective Optimization Problems (2017)

This work presents a new decision making criterion for analysis of multiobjective optimization problems, based on the evaluation of the optimum solutions in the Pareto set. This new technique allows for discrimination among the solutions that constitute the Pareto set, so that a single alternative (the least sensitive one) is selected for real implementation. In order to do that, the effects of process uncertainties on the variable responses are analyzed individually, with the help of the process model, and used to compute a sensitivity index. The proposed technique was applied to three distinct problems, and the obtained results showed that the method is able to discriminate the solutions successfully, allowing for appropriate selection of the best candidates for real implementation among the many candidates in the Pareto set.
Supplementary Methods from Oncolytic Vaccinia Virus Disrupts Tumor-Associated Vasculature in Humans (2023)

&lt;p&gt;Supplementary Methods PDF file - 44K, GLP toxicology study, In vivo imaging and mouse immunohistochemical analyses&lt;/p&gt;
Pharmacodynamic Studies of Gefitinib in Tumor Biopsy Specimens From Patients With Advanced Gastric Carcinoma (2006)

Gefitinib reached the tumors at concentrations sufficient to inhibit EGFR activation in advanced gastric carcinoma patients, although this did not translate into clinical benefit. Overall, intratumoral phosphorylation of MAPK and Akt was not significantly inhibited by gefitinib. However, the finding that decreases in pAkt correlated with enhanced apoptosis deserves further exploration.
Multimodal X-ray imaging of nanocontainer-treated macrophages and calcium distribution in the perilacunar bone matrix (2020)

Studies of biological systems typically require the application of several complementary methods able to yield statistically-relevant results at a unique level of sensitivity. Combined X-ray fluorescence and ptychography offer excellent elemental and structural imaging contrasts at the nanoscale. They enable a robust correlation of elemental distributions with respect to the cellular morphology. Here we extend the applicability of the two modalities to higher X-ray excitation energies, permitting iron mapping. Using a long-range scanning setup, we applied the method to two vital biomedical cases. We quantified the iron distributions in a population of macrophages treated with Mycobacterium-tuberculosis-targeting iron-oxide nanocontainers. Our work allowed to visualize the internalization of the nanocontainer agglomerates in the cytosol. From the iron areal mass maps, we obtained a distribution of antibiotic load per agglomerate and an average areal concentration of nanocontainers in the agglomerates. In the second application we mapped the calcium content in a human bone matrix in close proximity to osteocyte lacunae (perilacunar matrix). A concurrently acquired ptychographic image was used to remove the mass-thickness effect from the raw calcium map. The resulting ptychography-enhanced calcium distribution allowed then to observe a locally lower degree of mineralization of the perilacunar matrix.
Development of a highly automated and multiplexed targeted proteome pipeline and assay for 112 rat brain synaptic proteins (2014)

We present a comprehensive workflow for large scale (>1000 transitions/run) label-free LC-MRM proteome assays. Innovations include automated MRM transition selection, intelligent retention time scheduling that improves S/N by twofold, and automatic peak modeling. Improvements to data analysis include a novel Q/C metric, normalized group area ratio, MLR normalization, weighted regression analysis, and data dissemination through the Yale protein expression database. As a proof of principle we developed a robust 90 min LC-MRM assay for mouse/rat postsynaptic density fractions which resulted in the routine quantification of 337 peptides from 112 proteins based on 15 observations per protein. Parallel analyses with stable isotope dilution peptide standards (SIS), demonstrate very high correlation in retention time (1.0) and protein fold change (0.94) between the label-free and SIS analyses. Overall, our method achieved a technical CV of 11.4% with >97.5% of the 1697 transitions being quantified without user intervention, resulting in a highly efficient, robust, and single injection LC-MRM assay.
Total Synthesis and Biological Evaluation of the Glycosylated Macrocyclic Antibiotic Mangrolide A (2018)

The macrocyclic antibiotic mangrolide A has been described to exhibit potent activity against a number of clinically important Gram-negative pathogens. Reported is the first enantioselective total synthesis of mangrolide A and derivatives. Salient features of this synthesis include a highly convergent macrocycle preparation, stereoselective synthesis of the disaccharide moiety, and two β-selective glycosylations. The synthesis of mangrolide A and its analogues enabled the re-examination of its activity against bacterial pathogens, and only minimal activity was observed.
A highly virulent variant of HIV-1 circulating in the Netherlands (2022)

We discovered a highly virulent variant of subtype-B HIV-1 in the Netherlands. One hundred nine individuals with this variant had a 0.54 to 0.74 log<sub>10</sub> increase (i.e., a ~3.5-fold to 5.5-fold increase) in viral load compared with, and exhibited CD4 cell decline twice as fast as, 6604 individuals with other subtype-B strains. Without treatment, advanced HIV-CD4 cell counts below 350 cells per cubic millimeter, with long-term clinical consequences-is expected to be reached, on average, 9 months after diagnosis for individuals in their thirties with this variant. Age, sex, suspected mode of transmission, and place of birth for the aforementioned 109 individuals were typical for HIV-positive people in the Netherlands, which suggests that the increased virulence is attributable to the viral strain. Genetic sequence analysis suggests that this variant arose in the 1990s from de novo mutation, not recombination, with increased transmissibility and an unfamiliar molecular mechanism of virulence.
ChemInform Abstract: Chemoenzymatic Preparation of the Novel Antifolate Thymidylate Synthase Inhibitor N‐(4‐{N‐[(6S)‐2‐Methyl‐4‐oxo‐3,4,7,8‐tetrahydro‐6H‐cyclopenta [g]quinazolin‐6‐yl]‐N‐(prop‐2‐ynyl)amino}benzoyl)‐L‐glutamic Acid (Ia) and Its Glutamyl Cleavage Product (Ib). (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.
Zinc therapy of Wilson's disease: Two views (1986)

After initial promotion of copper excretion with D-penicillamine, the effect of oral zinc sulphate (3×150 mg/day, loading dose; 3×100 mg/day, maintenance dose) in two children with clinically stable Wilson's disease was evaluated after completion of three years' treatment. The course, judged by clinical, biochemical, and histological parameters was satisfactory in both. The urinary copper concentration reverted to less than 1.26 μmol/24 hours; and the serum copper concentration decreased further during zinc sulphate treatment. In one child the rise in 24 hour urinary copper excretion observed after a challenge dose of D-penicillamine (±20 mg/kg) remained constant throughout the period of observation while the liver copper content fell from 1460 μg/g dry weight to 890 μg/g dry weight. In the other patient, however, the liver copper content as well as the 24 hour urinary copper excretion increased after D-penicillamine challenge during the third year of treatment. We conclude that zinc sulphate is a low toxic and well tolerated alternative for D-penicillamine. The dosage depends, however, on individual factors not yet well understood, and we recommend restriction of its use to patients who do not tolerate D-penicillamine well. We suggest monitoring of treatment with yearly D-penicillamine challenge and a liver biopsy if liver function deteriorates.
Coverage Evaluation for 5G Reduced Capability New Radio (NR-RedCap) (2021)

The fifth-generation (5G) wireless technology is primarily designed to address a wide range of use cases categorized into the enhanced mobile broadband (eMBB), ultra-reliable and low latency communication (URLLC), and massive machine-type communication (mMTC). Nevertheless, there are a few other use cases that are in-between these main use cases such as industrial wireless sensor networks, video surveillance, or wearables. In order to efficiently serve such use cases, in Release 17, the 3rd generation partnership project (3GPP) introduced the reduced capability NR devices (NR-RedCap) with lower cost and complexity, smaller form factor, and longer battery life compared to regular NR devices. However, one key potential consequence of device cost and complexity reduction is coverage loss. In this paper, we provide a comprehensive evaluation of NR RedCap coverage for different physical channels and initial access messages to identify the channels/messages that are potentially coverage limiting for RedCap UEs. We perform the coverage evaluations for RedCap UEs operating in three different scenarios, namely Rural, Urban and Indoor with carrier frequencies 0.7 GHz, 2.6 GHz and 28 GHz, respectively. Our results confirm that for all the considered scenarios, the amounts of required coverage recovery for RedCap channels are either less than 1 dB or can be compensated by considering smaller data rate targets for RedCap use cases.
Study of the decay mode D0→K−K−K+π+ (2003)

Using data from the FOCUS (E831) experiment at Fermilab, we present a new measurement of the branching ratio for the Cabibbo-favored decay mode D0→K−K−K+π+. From a sample of 143±19 fully reconstructed D0→K−K−K+π+ events, we measure Γ(D0→K−K−K+π+)/Γ(D0→K−π−π+π+)=0.00257±0.00034(stat.)±0.00024(syst.). A coherent amplitude analysis has been performed to determine the resonant substructure of this decay mode. This analysis reveals a dominant contribution from φ and K∗0(892) states.