gebhart/patrepeval huggingface dataset:
Fully Automated Microinjection System for <i>Xenopus laevis</i> Oocytes with Integrated Sorting and Collection (2011)

Microinjection is the most flexible transfection method in terms of choice of reagents to inject into cells. But this method lacks the high throughput to compete with less flexible methods like chemical- or viral-based approaches. Various approaches have been pursued to increase the throughput by automating the microinjection process. However, these approaches focused solely on the microinjection itself and disregarded the tasks before and after the injection, which also belong to the critical time path of the whole process, that is, sorting out viable cells from a cell suspension, placing the cell for injection, and collecting the cell after the injection. In the approach with our XenoFactor, we demonstrate a system capable of running the whole process automatically. By optimizing the XenoFactor for Xenopus laevis oocytes, we could demonstrate the successful automated injection. Starting from a suspension with a mixture of defolliculated oocytes at different stages and quality levels, the manual approach requires 1 day in total for the preparation of 400 microinjected oocytes. The XenoFactor takes only 4h for the same amount and delivers injected oocytes of reproducible quality and without the fatigue symptoms experienced during the manual approach.
A rapid chemiluminescent method for quanititation of human DNA (1992)

A sensitive and simple method for the quantitation of human DNA is described. This method is based on probe hybridization to a human alpha satellite locus, D17Z1. The biotinylated probe is hybridized to sample DNA immobilized on nylon membrane. The subsequent binding of streptavidin-horseradish peroxidase to the bound probe allows for chemiluminescent detection using a luminol-based reagent and X-ray film. Less than 150 pg of human DNA can easily be detected with a 15 minute exposure. The entire procedure can be performed in 1.5 hours. Microgram quantities of nonhuman DNA have been tested and the results indicate very high specificity for human DNA. The data on film can be scanned into a computer and a commercially available program can be used to create a standard curve where DNA quantity is plotted against the mean density of each slot blot signal. The methods described can also be applied to the very sensitive determination of quantity and quality (size) of DNA on Southern blots. The high sensitivity of this quantitation method requires the consumption of only a fraction of sample for analysis. Determination of DNA quantity is necessary for RFLP and many PCR-based tests where optimal results are obtained only with a relatively narrow range of DNA quantities. The specificity of this quantitation method for human DNA will be useful for the analysis of samples that may also contain bacterial or other non-human DNA, for example forensic evidence samples, ancient DNA samples, or clinical samples.
Inverted-V chirped phased arrays of gain-guided GaAs/GaAlAs diode lasers (1984)

Inverted-V chirped arrays of multiple quantum well GaAs/GaAlAs lasers were grown by molecular beam epitaxy. These arrays consisted of seven gain-guided lasers whose stripe widths decreased, from the central laser to the outermost ones, symmetrically. This structure makes it possible to discriminate against the higher order array supermodes, which results in diffraction limited beams with a single lobe directed perpendicular to the laser facet. Single lobed far-field patterns, 3°–4° wide, were obtained from inverted-V chirped arrays operated up to 1.5Ith. The supermode structure of these arrays was identified by studying their spectrally resolved near fields.
High-Order Coaxial Bandpass Filters With Multiple Levels of Transfer Function Tunability (2020)

This letter reports on high-order coaxial-resonator-based bandpass filters (BPFs) with multiple levels of transfer function tunability, namely center frequency (f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">cen</sub> ), bandwidth (BW), and intrinsic switching off. They are based on cascaded multi-resonant cells, each exhibiting one pole and two transmission zeros (TZs), and in-line resonators. The proposed concept allows for high-order quasi-elliptic responses without cross couplings that can be reconfigured by only tuning the resonators' f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">cen</sub> . Low-cost integration using 3-D printed cavities and varactor-based PCB tuners is also shown. For proof-of-concept validation purposes, a five-pole/four-TZ BPF with f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">cen</sub> tuning 1.3-1.77 GHz (1.4:1), BW tuning: 62-217 MHz (3.5:1), and an intrinsic switching-off state with >35 dB of isolation was manufactured and measured.
ChemInform Abstract: FORTIMICIN B CYCLIC CARBAMATES (1982)

Abstract Durch Basen‐katalysierte Cyclisierungen von Alkoxycarbonylaminogruppen und Hydroxylgruppen am Cyclitring werden die schwieriger zugänglichen monocyclischen Carbamate und ein Bis‐carbamat von Fortimicin B (I) hergestellt.
Structure-Based Design and Synthesis of 1,3-Oxazinan-2-one Inhibitors of 11β-Hydroxysteroid Dehydrogenase Type 1 (2011)

Structure based design led directly to 1,3-oxazinan-2-one 9a with an IC(50) of 42 nM against 11β-HSD1 in vitro. Optimization of 9a for improved in vitro enzymatic and cellular potency afforded 25f with IC(50) values of 0.8 nM for the enzyme and 2.5 nM in adipocytes. In addition, 25f has 94% oral bioavailability in rat and >1000× selectivity over 11β-HSD2. In mice, 25f was distributed to the target tissues, liver, and adipose, and in cynomolgus monkeys a 10 mg/kg oral dose reduced cortisol production by 85% following a cortisone challenge.
Molecular building blocks approach to the assembly of zeolite-like metal–organic frameworks (ZMOFs) with extra-large cavities (2006)

Two novel porous anionic zeolite-like metal-organic frameworks, rho-ZMOF and sod-ZMOF, have been synthesized by metal-ligand-directed assembly of rigid and directional tetrahedral building units, InN4 synthesized in situ, and doubly deprotonated bis(bidentate) imidazoledicarboxylic acid ligands (HImDC) in the presence of different structure directing agents (SDAs).
ChemInform Abstract: DESCARBOXYLYSERGIC ACID (9,10‐DIHYDRO‐6‐METHYLERGOLINE) (1974)

Abstract Aus 3‐Indol‐propionsäure (I) ist nach bekannten Verfahren der Tetracyclus (IIa) zugänglich, der bei der elektrolytischen Reduktion lediglich unter Reduktion der Doppelbindung zu (III) reagiert.
Hydrogel Bioink Reinforcement for Additive Manufacturing: A Focused Review of Emerging Strategies (2019)

Bioprinting is an emerging approach for fabricating cell-laden 3D scaffolds via robotic deposition of cells and biomaterials into custom shapes and patterns to replicate complex tissue architectures. Bioprinting uses hydrogel solutions called bioinks as both cell carriers and structural components, requiring bioinks to be highly printable while providing a robust and cell-friendly microenvironment. Unfortunately, conventional hydrogel bioinks have not been able to meet these requirements and are mechanically weak due to their heterogeneously crosslinked networks and lack of energy dissipation mechanisms. Advanced bioink designs using various methods of dissipating mechanical energy are aimed at developing next-generation cellularized 3D scaffolds to mimic anatomical size, tissue architecture, and tissue-specific functions. These next-generation bioinks need to have high print fidelity and should provide a biocompatible microenvironment along with improved mechanical properties. To design these advanced bioink formulations, it is important to understand the structure-property-function relationships of hydrogel networks. By specifically leveraging biophysical and biochemical characteristics of hydrogel networks, high performance bioinks can be designed to control and direct cell functions. In this review article, current and emerging approaches in hydrogel design and bioink reinforcement techniques are critically evaluated. This bottom-up perspective provides a materials-centric approach to bioink design for 3D bioprinting.
A Novel Triterpenoid Isolated from the Root Bark of Ailanthus excelsa Roxb (Tree of Heaven), AECHL-1 as a Potential Anti-Cancer Agent (2009)

The present data demonstrate the activity of a triterpenoid AECHL-1 which possess a broad spectrum of activity against cancer cells. We propose here that AECHL-1 is a futuristic anti-cancer drug whose therapeutic potential needs to be widely explored for chemotherapy against cancer.
Low-Complexity Transcoding of JPEG Images With Near-Optimal Quality Using a Predictive Quality Factor and Scaling Parameters (2009)

A common transcoding operation consists of reducing the file size of a JPEG image to meet bandwidth or device constraints. This can be achieved by reducing its quality factor (QF) or reducing its resolution, or both. In this paper, using the Structural SIMilarity (SSIM) index as the quality metric, we present a system capable of estimating the QF and scaling parameters to achieve optimal quality while meeting a device's constraints. We then propose a novel low-complexity JPEG transcoding system which delivers near-optimal quality. The system is capable of predicting the best combination of QF and scaling parameters for a wide range of device constraints and viewing conditions. Although its computational complexity is an order of magnitude smaller than the system providing optimal quality, the proposed system yields quality results very similar to those of the optimal system.
Bacterial infection induces nitric oxide synthase in human neutrophils. (1997)

The identification of human inflammatory cells that express inducible nitric oxide synthase and the clarification of the role of inducible nitric oxide synthase in human infectious or inflammatory processes have been elusive. In neutrophil-enriched fractions from urine, we demonstrate a 43-fold increase in nitric oxide synthase activity in patients with urinary tract infections compared with that in neutrophil-enriched fractions from noninfected controls. Partially purified inducible nitric oxide synthase is primarily membrane associated, calcium independent, and inhibited by arginine analogues with a rank order consistent with that of purified human inducible nitric oxide synthase. Molecular, biochemical, and immunocytochemical evidence unequivocally identifies inducible nitric oxide synthase as the major nitric oxide synthase isoform found in neutrophils isolated from urine during urinary tract infections. Elevated inducible nitric oxide synthase activity and elevated nitric oxide synthase protein measured in patients with urinary tract infections and treated with antibiotics does not decrease until 6-10 d of antibiotic treatment. The extended elevation of neutrophil inducible nitric oxide synthase during urinary tract infections may have both antimicrobial and proinflammatory functions.
Terahertz antennas with silicon micromachined front-end (2014)

Increasingly, terahertz systems are being used for multi-pixel receivers for different applications from mapping the star-forming regions of galaxies to stand-off radar imaging. Since microstrip patch antennas are too lossy and corrugated horn antenna arrays are difficult to machine at terahertz frequencies, suitable antenna array designs have been one of the key area of research for this field. Moreover, silicon micromachined waveguide housing for front-end integration is becoming very popular for multi-pixel terahertz instruments. This paper describes multi-pixel terahertz instruments with silicon-micromachined front-end and discusses design challenges for integrating terahertz antennas with such systems.
ChemInform Abstract: Synthesis and Chemistry of Perfluoro‐2‐iodo‐2‐methylalkanes. (1988)

Abstract Starting with the perfluoroalkenes (I), the perfluoro‐tert‐alkyl iodides (II) are prepared using two different methods.
Sequence Detection Algorithms for Dynamic Spectrum Access Networks (2010)

Spectrum sensing is a critical function for enabling dynamic spectrum access (DSA) in wireless networks that utilize cognitive radio (CR). In DSA networks, unlicensed secondary users can gain access to a licensed spectrum band as long as they do not interfere with primary users. Spectrum sensing is subject to errors in the form of false alarms and missed detections. False alarms cause spectrum under-use by secondary users, and missed detections cause interference to primary users. Although existing research has demonstrated the utility of a Markov chain for modeling the spectrum access pattern of primary users over time, little effort has been directed toward spectrum sensing based upon such models. In this paper, we develop soft-input sequence detection algorithms of Markov sources in noise for spectrum sensing in DSA networks. We assign different Bayesian cost factors for missed detections and false alarms, and we show that a suitably modified Forward-Backward sequence detection algorithm is optimal in minimizing the detection risk. Along the way, we observe new fundamental limitations that we call "Risk Floor" and "Limiting ROC" for energy detection and coherent detection due to the PU's spectrum access pattern.
Cyclotetrabenzoin: Facile Synthesis of a Shape‐Persistent Molecular Square and Its Assembly into Hydrogen‐Bonded Nanotubes (2015)

Abstract Cyanide‐catalyzed benzoin condensation of terephthaldehyde produces a cyclic tetramer, which we propose to name cyclotetrabenzoin. Cyclotetrabenzoin is a square‐shaped macrocycle ornamented with four α‐hydroxyketone functionalities pointing away from the central cavity, the dimensions of which are 6.9×6.9 Å. In the solid state, these functional groups extensively hydrogen bond, resulting in a microporous three‐dimensional organic framework with one‐dimensional nanotube channels. This material exhibits permanent—albeit low‐porosity, with a Langmuir surface area of 52 m 2 g −1 . Cyclotetrabenzoin’s easy and inexpensive synthesis and purification may inspire the creation of other shape‐persistent macrocycles and porous molecular crystals by benzoin condensation.
Synthesis, Crystal Structure, and Molecular Modeling of a Layered Manganese(II) Phosphate: Mn<sub>3</sub>(PO<sub>4</sub>)<sub>4</sub>×2 (H<sub>3</sub>NCH<sub>2</sub>CH<sub>2</sub>)<sub>3</sub>N×6 (H<sub>2</sub>O). (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Innovative nano-layered solid sorbents for CO<sub>2</sub>capture (2010)

Nano-layered sorbents for CO(2) capture, for the first time, were developed using layer-by-layer nanoassembly. A CO(2)-adsorbing polymer and a strong polyelectrolyte were alternately immobilized within porous particles. The developed sorbents had fast CO(2) adsorption and desorption properties and their CO(2) capture capacity increased with increasing nano-layers of the CO(2)-adsorbing polymer.
Botrocetin (venom coagglutinin): reaction with a broad spectrum of multimeric forms of factor VIII macromolecular complex. (1983)

Botrocetin, originally called venom coagglutinin, is a Bothrops factor that causes aggregation of blood platelets in the presence of the von Willebrand component of the factor VIII macromolecular complex. The complex consists of a series of multimers with a molecular weight of about 1-20 x 10(6). Ristocetin, another agent that causes platelet aggregation dependent on von Willebrand factor, reacts with only the higher molecular weight multimers. We report on the reactivity of botrocetin in relation to the multimeric structure of the factor VIII complex. Several plasmas or plasma fractions with abnormal distribution of the multimeric sizes were examined, including variant von Willebrand disease type IIA with lack of the higher molecular weight forms, commercial antihemophilic factor concentrates with a preponderance of lower molecular weight forms, cryoprecipitate-free plasma containing mainly the smaller multimers, and a chromatographic fraction of plasma containing only the highest molecular weight polymers. Factor VIII-related antigen content was adjusted to 25-100%. All of the preparations lacking the high molecular weight forms caused prompt platelet aggregation with botrocetin, but none of them caused aggregation in the ristocetin test made isochronal with the botrocetin test. The very high molecular weight polymers were equally effective with botrocetin and ristocetin. These findings indicate that the Bothrops factor is reactive with a broad spectrum of high to low molecular weight forms of the factor VIII complex, suggesting that bioassays of von Willebrand factor with botrocetin should correlate better with immunoassays for factor VIII-related antigen and could reflect better the full platelet-aggregating function of the complex than do ristocetin determinations.
Complex Host Cell Responses to Antisense Suppression of <i>ACHE</i> Gene Expression (2001)

3'-End-capped, 20-mer antisense oligodeoxynucleotides (AS-ODN) protected with 2'-O-methyl (Me) or phosphorothioate (PS) substitutions were targeted to acetylcholinesterase (AChE) mRNA and studied in PC12 cells. Me-modified AS-ODN suppressed AChE activity up to 50% at concentrations of 0.02-100 nM. PS-ODN was effective at 1-100 nM. Both AS-ODN displayed progressively decreased efficacy above 10 nM. In situ hybridization and confocal microscopy demonstrated dose-dependent decreases, then increases, in AChE mRNA. Moreover, labeling at nuclear foci suggested facilitated transcription or stabilization of AChE mRNA or both under AS-ODN. Intracellular concentrations of biotinylated oligonucleotide equaled those of target mRNA at extracellular concentrations of 0.02 nM yet increased only 6-fold at 1 microM ODN. Above 50 nM, sequence-independent swelling of cellular, but not nuclear, volume was observed. Our findings demonstrate suppressed AChE expression using extremely low concentrations of AS-ODN and attribute reduced efficacy at higher concentrations to complex host cell feedback responses.
Mask‐free Localized Grafting of Organic Polymers at the Micrometer or Submicrometer Scale on Composite Conductors or Semiconductor Substrates (2004)

Abstract This work presents a new one‐step process enabling the mask‐free localized functionalization by organic polymers of the conducting or semiconducting parts of composite surfaces at the micrometer and submicrometer scale. The functionalization is carried out via cathodic electrografting of suitable precursors of composite cathodes, which gives an insulating polymer film strongly grafted to selected parts of the composite electrodes and guarantees that the resolution is that of the pre‐existing pattern, even when the whole surface is dipped into the reaction medium. The presumed mechanism is based on a regioselective extraction of electrons from the composite surface according to its apparent local work function in solution.
Expression studies of the core+1 protein of the hepatitis C virus 1a in mammalian cells (2007)

Recent studies have suggested the existence of a novel protein of hepatitis C virus (HCV) encoded by an ORF overlapping the core gene in the +1 frame (core+1 ORF). Two alternative translation mechanisms have been proposed for expression of the core+1 ORF of HCV-1a in cultured cells; a frameshift mechanism within codons 8-11, yielding a protein known as core+1/F, and/or translation initiation from internal codons in the core+1 ORF, yielding a shorter protein known as core+1/S. To date, the main evidence for the expression of this protein in vivo has been the specific humoral and cellular immune responses against the protein in HCV-infected patients, inasmuch as its detection in biopsies or the HCV infectious system remains elusive. In this study, we characterized the expression properties of the HCV-1a core+1 protein in mammalian cells in order to identify conditions that facilitate its detection. We showed that core+1/S is a very unstable protein, and that expression of the core protein in addition to proteosome activity can downregulate its intracellular levels. Also, we showed that in the Huh-7/T7 cytoplasmic expression system the core+1 ORF from the HCV-1 isolate supports the synthesis of both the core+1/S and core+1/F proteins. Finally, immunofluorescence and subcellular fractionation analyses indicated that core+1/S and core+1/F are cytoplasmic proteins with partial endoplasmic reticulum distribution in interphase cells, whereas in dividing cells they also localize to the microtubules of the mitotic spindle.
Leveraging mmWave Imaging and Communications for Simultaneous Localization and Mapping (2019)

In this work, we propose a novel approach for high accuracy user localization by merging tools from both millimeter wave (mmWave) imaging and communications. The key idea of the proposed solution is to leverage mmWave imaging to construct a high-resolution 3D image of the line-of-sight (LOS) and non-line-of-sight (NLOS) objects in the environment at one antenna array. Then, uplink pilot signaling with the user is used to estimate the angle-of-arrival and time-of-arrival of the dominant channel paths. By projecting the AoA and ToA information on the 3D mmWave images of the environment, the proposed solution can locate the user with a sub-centimeter accuracy. This approach has several gains. First, it allows accurate simultaneous localization and mapping (SLAM) from a single standpoint, i.e., using only one antenna array. Second, it does not require any prior knowledge of the surrounding environment. Third, it can locate NLOS users, even if their signals experience more than one reflection and without requiring an antenna array at the user. The approach is evaluated using a hardware setup and its ability to provide sub-centimeter localization accuracy is shown.
Fate of artificial sweeteners through wastewater treatment plants and water treatment processes (2018)

Five full-scale wastewater treatment plants (WWTPs) in China using typical biodegradation processes (SBR, oxidation ditch, A2/O) were selected to assess the removal of four popular artificial sweeteners (ASs). All four ASs (acesulfame (ACE), sucralose (SUC), cyclamate (CYC) and saccharin (SAC)) were detected, ranging from 0.43 to 27.34μg/L in the influent. Higher concentrations of ASs were measured in winter. ACE could be partly removed by 7.11-50.76% through biodegradation and especially through the denitrifying process. The A2/O process was the most efficient at biodegrading ASs. Adsorption (by granular activated carbon (GAC) and magnetic resin) and ultraviolet radiation-based advanced oxidation processes (UV/AOPs) were evaluated to remove ASs in laboratory-scale tests. The amounts of resin adsorbed were 3.33-18.51 times more than those of GAC except for SUC. The adsorption ability of resin decreased in the order of SAC > ACE > CYC > SUC in accordance with the pKa. Degradation of ASs followed pseudo-first-order kinetics in UV/H2O2 and UV/PDS. When applied to the secondary effluent, ASs could be degraded from 30.87 to 99.93% using UV/PDS in 30 minutes and UV/PDS was more efficient and economic.