gebhart/patrepeval huggingface dataset:
Interpreting holographic molecular binding assays with effective medium theory (2020)

Holographic molecular binding assays use holographic video microscopy to directly detect molecules binding to the surfaces of micrometer-scale colloidal beads by monitoring associated changes in the beads' light-scattering properties. Holograms of individual spheres are analyzed by fitting to a generative model based on the Lorenz-Mie theory of light scattering. Each fit yields an estimate of a probe bead's diameter and refractive index with sufficient precision to watch a population of beads grow as molecules bind. Rather than modeling the molecular-scale coating, however, these fits use effective medium theory, treating the coated sphere as if it were homogeneous. This effective-sphere analysis is rapid and numerically robust and so is useful for practical implementations of label-free immunoassays. Here, we assess how measured effective-sphere properties reflect the actual properties of molecular-scale coatings by modeling coated spheres with the discrete-dipole approximation and analyzing their holograms with the effective-sphere model.
Ion Separations Based on Spontaneously Arising Streaming Potentials in Rotating Isoporous Membranes (2022)

Highly selective ion separations are vital for producing pure salts, and membrane-based separations are promising alternatives to conventional ion-separation techniques. Our previous work demonstrated that simple pressure-driven flow through negatively charged isoporous membranes can separate Li<sup>+</sup> and K<sup>+</sup> with selectivities as high as 70 in dilute solutions. The separation mechanism relies on spontaneously arising streaming potentials that induce electromigration, which opposes advection and separates cations based on differences in their electrophoretic mobilities. Although the separation technique is simple, this work shows that high selectivities are possible only with careful consideration of experimental conditions including transmembrane pressure, solution ionic strength, the K<sup>+</sup>/Li<sup>+</sup> ratio in the feed, and the extent of concentration polarization. Separations conducted with a rotating membrane show Li<sup>+</sup>/K<sup>+</sup> selectivities as high as 150 with a 1000 rpm membrane rotation rate, but the selectivity decreases to 1.3 at 95 rpm. These results demonstrate the benefits and necessity of quantitative control of concentration polarization in highly selective separations. Increases in solution ionic strength or the K<sup>+</sup>/Li<sup>+</sup> feed ratio can also decrease selectivities more than an order of magnitude.
Extracorporeal Membrane Oxygenation to Aid Cardiopulmonary Resuscitation in Infants and Children (2007)

ECMO used to support CPR rescued one third of patients in whom death was otherwise certain. Patient diagnosis, absence of severe metabolic acidosis before ECMO support, and uncomplicated ECMO course were associated with improved survival.
Proteomic Profiling for Cardiovascular Biomarker Discovery in Orthostatic Hypotension (2018)

Orthostatic hypotension (OH) has been linked with higher incidence of cardiovascular disease, but little is known about the mechanisms behind this association. We aimed to identify cardiovascular disease biomarkers associated with OH through a proteomic profiling approach. Seven hundred seventy-eight patients with unexplained syncope or orthostatic intolerance underwent head-up tilt test and supine blood samples. Of these, 220 met diagnostic criteria of OH, and 179 demonstrated normal hemodynamic response during head-up tilt test. Blood samples were analyzed by antibody-based Proximity Extension Assay technique simultaneously measuring 92 cardiovascular disease-related human protein biomarkers. The discovery algorithm was a sequential 2-step process of biomarker signature identification by supervised, multivariate, principal component analysis and verification by univariate ANOVA with Bonferroni correction. Patients with OH were older (67 versus 60 years; <i>P</i><0.001) and more likely to be women (48% versus 41%; <i>P</i>>0.001) but did not differ from OH-negative patients in medical history. Principal component analysis identified MMP-7 (matrix metalloproteinase-7), TM (thrombomodulin), MB (myoglobin), TIM-1 (T-cell immunoglobulin and mucin domain-1), CASP-8 (caspase-8), CXCL-1 (C-X-C motif chemokine-1), Dkk-1 (dickkopf-related protein-1), lectin-like LOX-1 (oxidized low-density lipoprotein receptor-1), PlGF (placenta growth factor), PAR-1 (proteinase-activated receptor-1), and MCP-1 (monocyte chemotactic protein-1) as the most robust proteomic signature for OH. From this proteomic feature selection, MMP-7 and TIM-1 met Bonferroni-adjusted significance criteria in univariate and multivariate regression analyses. Proteomic profiling in OH reveals a biomarker signature of atherothrombosis and inflammation. Circulating levels of MMP-7 and TIM-1 are independently associated with OH and may be involved in cardiovascular disease promotion.
Ion implantation of sputtered Y-Ba-Cu-O films (1989)

Thin films of Y-Ba-Cu-O were deposited by rf magnetron sputtering from a single stoichiometric target and then altered in composition by ion implantation. Under optimum deposition conditions the films are deficient in Ba and Cu. Ion implantation of Cu was performed using a metal-vapor vacuum-arc source having high current and a broad energy spectrum for good depth distribution. Composition was determined by Rutherford backscattering spectrometry. The zero-resistance temperature was greatly increased after implantation and reannealing. This method could be used to write superconducting patterns on insulating material.
Chemistry of polynuclear metal complexes with bridging carbene or carbyne ligands. Part 86. Aikylidyne(carbaborane)molybdenum–gold, –rhodium and –iron complexes; crystal structure of [NEt4][MoFe2(µ3-CC6H4Me-4)(µ-σ : σ′ : η5C2B9H7Me2)(CO)8] (1989)

The alkylidyne–molybdenum complex [NEt4][Mo(CC6H4Me-4)(CO){P(OMe)3}(η5-C2B9H9Me2)] has been prepared, and used to prepare compounds with bonds between molybdenum and gold, rhodium, and iron. Reactions of the molybdenum compound with [AuCl(PPh3)],[Rh(cod)(PPh3)2][PF6](cod = cyclo-octa-1,5-diene), and [Fe2(CO)9] afford, respectively, the complexes [MoAu(µ-CC6H4Me-4)(CO){P(OMe)3}(PPh3)(η5-C2B9H9Me2)], [MoRh(µ-CC6H4Me-4)(µ-CO){P(OMe)3}(PPh3)2(η5-C2B9H9Me2)], and [NEt4][MoFe2(µ3-CC6H4Me-4)(µ-σ : σ′ : η5-C2B9H7Me2)(CO)8]. The structure of the latter has been established by X-ray diffraction. There are two crystallographically independent anions with their associated cations in the asymmetric unit but with overall very similar geometries. In the anions a triangle of metal atoms is symmetrically capped on one side by the alkylidyne ligand. On the other side of the triangle the molybdenum atom is η5-ligated by the C2B9cage, but two boron atoms in the pentagonal face are σ bonded to the two iron atoms. The molybdenum carries two carbonyl groups and each of the iron atoms is bonded by three of these ligands. The reaction between [Fe2(CO)9] and [NEt4][Mo(CC6H4Me-4)(CO){P(OMe)3}(η5-C2B9H9Me2)] also affords the novel mononuclear molybdenum compound [NEt4][Mo{σ,η5-CH (C6H4Me-4)C2B9H8Me2}(CO)3]. Protonation (HBF4·Et2O) of CO-saturated CH2Cl2solutions of the latter gives the neutral complex [Mo(CO)4{η5-C2B9H8(CH2C6H4Me-4)Me2}]. Protonation in the presence of an excess of PMe3 gives a mixture of the two compounds [Mo(CO)3(L){η5-C2B9H8(CH2C6H4Me-4)Me2}](L = PMe3 or CO). The n.m.r. data (1H, 13C-{1H},11B-{1H}, and 31P-(1H}) for the new compounds are reported and discussed.
Ubiquity and Diversity of Human-Associated Demodex Mites (2014)

Demodex mites are a group of hair follicle and sebaceous gland-dwelling species. The species of these mites found on humans are arguably the animals with which we have the most intimate interactions. Yet, their prevalence and diversity have been poorly explored. Here we use a new molecular method to assess the occurrence of Demodex mites on humans. In addition, we use the 18S rRNA gene (18S rDNA) to assess the genetic diversity and evolutionary history of Demodex lineages. Within our samples, 100% of people over 18 years of age appear to host at least one Demodex species, suggesting that Demodex mites may be universal associates of adult humans. A phylogenetic analysis of 18S rDNA reveals intraspecific structure within one of the two named human-associated Demodex species, D. brevis. The D. brevis clade is geographically structured, suggesting that new lineages are likely to be discovered as humans from additional geographic regions are sampled.
10-GHz, 13-ps erbium fiber laser employing soliton pulse shortening (1996)

An actively mode-locked single-polarization erbium fiber laser modulated at 10 GHz utilizes intracavity soliton formation to produce 1.3-ps pulses, well below the Kuizenga-Siegman limit, without passive mode locking. The observed degree of pulse shortening agrees with the predictions of recently developed soliton laser models. The pulse dropout ratio was measured to be less than 10(-12), and the rms amplitude and phase jitter are less than 1.1% and 0.16 ps, respectively.
Protein-directed synthesis of pH-responsive red fluorescent copper nanoclusters and their applications in cellular imaging and catalysis (2013)

The development of functional copper nanoclusters (Cu NCs) is becoming increasingly widespread in consumer technologies due to their applications in cellular imaging and catalysis. Herein, we report a simple protein-directed synthesis of stable, water-soluble and fluorescent Cu NCs, using BSA as the stabilising agent. Meanwhile, in this study, hydrazine hydrate (N₂H₄·2H₂O) was used as the reducing agent. N₂H₄·2H₂O was a mild reducing agent suggesting that all processes could be operated at room temperature. The as-prepared Cu NCs showed red fluorescence with a peaking center at 620 nm (quantum yield 4.1%). The fluorescence of the as-prepared BSA-Cu NCs was responsive to pH in that the intensity of fluorescence increased rapidly by decreasing the pH from 12 to 6. Besides, with an arresting set of features including water-dispersibility, red fluorescence, good biocompatibility, surface-bioactivity and small size, the resultant BSA-Cu NCs could be used as probes for cellular imaging and catalysis. In this study, CAL-27 cells and the reaction of oxidation of styrene are used as models to achieve fluorescence imaging and elucidate the catalytic activity of the as-prepared BSA-Cu NCs.
Translational approach to neurodegenerative diseases: A small peptide derived from neuronal cell cycle kinase (Cdk5) prevents neurodegeneration (2017)

Aim: Tissue plasminogen activator (t-PA) is the only FDA approved drug for acute ischemic stroke, but its use is limited with the therapeutic time window within 4.5 hours and hemorrhagic transformation (HT). We aim to test the hypothesis that peroxynitrite (ONOO-), a representative of reactive nitrogen species, could be a critical therapeutic target for preventing delayed thrombolytic HT and improving outcome in ischemic stroke. We tested whether peroxynitrite decomposition catalyst (PDC) could prevent such complication. Furthermore, we investigated that baicalin, a natural antioxidant, could scavenge ONOO- and prevent HT in ischemic stroke animal model with delayed t-PA treatment. Methods: Male Sprague-Dawley (SD) rats were subjected to middle cerebral artery occlusion (MCAO) with t-PA (10 mg/kg) or t-PA plus FeTMPyP (3 mg/kg, a representative PDC) or baicalin (10, 25, 50 mg/kg) at MCAO for 2 or 5 h and reperfusion for 22 or 19 h, respectively. HT was assessed with hemoglobin assay. Neurological deficit was evaluated with Modified Neurological Severity Score (mNSS). Peroxynitrite was examined by detecting 3-nitrotyrosine (3-NT) and our newly developed high selective ONOO- fluorescent probe. The expression and activity of MMP-9/MMP-2 were assessed by Western blotting and gelatin zymography. Results: T-PA infusion at 2 h after cerebral ischemia did not induce HT but attenuated neurological deficit, whereas at 5 h significantly induced HT and worsened neurological outcome. Co-treatment of FeTMPyP revealed to prevent HT and improve neurological functions. Early t-PA infusion at 2 h inhibited iNOS activity, ONOO- production, MMP-9/MMP-2 expression and activity, whereas delayed t-PA infusion at 5 h up-regulated iNOS activity, increased 3-NT formation, and down-regulated MMP-9/MMP-2 expression and activity. Co-treatment of FeTMPyP revised those changes in the ischemic brain with delayed t-PA infusion 5 h. Meanwhile, Baicalin revealed strong ONOO--scavenging activity and protected the neuronal cells from ONOO--induced neurotoxicity, reduced infarct size and attenuated apoptotic cell death and HT. Conclusion: Peroxynitrite could be a critical therapeutic target for preventing hemorrhagic transformation and improving neurological outcome in ischemic brains with delayed t-PA treatment.
Kerstersia gyiorum gen. nov., sp. nov., a novel Alcaligenes faecalis-like organism isolated from human clinical samples, and reclassification of Alcaligenes denitrificans Ruger and Tan 1983 as Achromobacter denitrificans comb. nov. (2003)

A polyphasic taxonomic study was performed on nine isolates recovered from various human clinical samples. Phenotypically, these isolates resembled Alcaligenes faecalis. Whole-cell protein analysis distinguished two different species, and this was confirmed by DNA-DNA hybridizations. Cellular fatty acid analysis and 16S rDNA sequence analysis indicated that these isolates were related to the genera Alcaligenes, Bordetella, Achromobacter and Pigmentiphaga and belonged to the family Alcaligenaceae. On the basis of the results of this study, the organisms were classified in a novel genus, Kerstersia gen. nov. This genus comprises one species, Kerstersia gyiorum sp. nov. (type strain LMG 5906(T)=API 184-2-84(T)=CCUG 47000(T)), and several unnamed isolates. The DNA G+C content of members of the genus Kerstersia is between 61.5 and 62.9 mol%. On the basis of previously published DNA-DNA hybridization results and data from chemotaxonomic studies, it is proposed that Alcaligenes denitrificans Rüger and Tan 1983 be reclassified as Achromobacter denitrificans comb. nov.
A Concise and Scalable Strategy for the Total Synthesis of Dictyodendrin B Based on Sequential CH Functionalization (2015)

Abstract A sequential CH functionalization strategy for the synthesis of the marine alkaloid dictyodendrin B is reported. Our synthesis begins from commercially available 4‐bromoindole and involves six direct functionalizations around the heteroarene core as part of a gram‐scale strategy towards the natural product.
Synthesis and Applications of Chemical Probes for HumanO6-Alkylguanine-DNA Alkyltransferase (2001)

Novel affinity labels for human O6-alkylguanine-DNA alkyltransferase (hAGT), leading to specific biotinylation of this DNA repair protein (see schematic picture), have been synthesized and characterized. These chemical probes can be used for the specific detection of active hAGT. In addition, a system based on these probes and the display of active hAGT on phage λ has been introduced, which can be applied for the directed molecular evolution of hAGT by using in vitro selection. Supporting information for this article is available on the WWW under http://www.chembiochem.com or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Characterization and properties of polyphthalamide/polyamide blends and polyphthalamide/polyamide/polyolefin blends (1996)

Abstract Polyphthalamide(PPA)/polyamide(PA) blends were analyzed to determine the effect of PA addition to PPA on melting point, glass transition temperature, dynamic modulus, and heat distortion temperature. Results indicate that the choice of PPA and the choice of PA for the blend systems affects not only the above properties but also the miscibility of the blend systems. In general, PA addition to PPA lowers the melting point and glass transition, which potentially makes these blend materials easier to process. Also, the PPA/PA blends were observed to have dynamic modulus curves with transitions shifted to lower temperatures and crystalline plateaus shifted to lower modulus. PPA/PA/polyolefin(PP) systems were investigated to determine if a useful balance of properties could be obtained, even though the blend components would have to be processed at unusually high processing temperatures (in excess of 320°C). Morphological characterization indicates that small dispersed domains of PP are obtained. The modifiers utilized in these systems were either found at the interface of the PP domain or dispersed within the PP domain. The properties of PPA/PA/PP blends indicates that these systems are ductile and have a good balance of strength, stiffness, impact, and thermal performance.
Gel permeation chromatography. Calibration of columns for imperfect resolution (1976)

Abstract A computer simulation of gel permeation chromatographic (GPC) fractionation of polymers was performed on the basis of Tung's phenomenological theory taking account of the limited resolution of GPC columns. Particularly an attempt was made to examine the effect of the limited resolution on a GPC unit which has a permeability limit and a distorted log (molecular weight) versus elution volume calibration. The results were compared with the performance of an actual GPC unit. A simple method of calibrating the column resolution was proposed: The method consists of analyzing apparent average molecular weight values (those directly calculated from chromatograms without any corrections) of a series of standard samples of known and preferably narrow molecular weight distributions.
Lignin catalytic hydroconversion towards valuable products (2013)

International @ RAFFINAGE+BJF:DLA:CGE
Comparison of properties of electrical test structures patterned in BESOI and SIMOX films for CD reference-material applications (1998)

The National Institute of Standards and Technology (NIST) is exploring the feasibility of using artifacts fabricated on silicon-on-insulator (SOI) materials to quantify methods divergence, for critical dimension (CD) metrology applications. Test structures, patterned on two types of (110) SOI materials, SIMOX (Separation by IMplantation of OXygen) and BESOI (Bonded-and-Etched-back Silicon-on-Insulator), have been compared. In this paper, we describe results of electrical critical dimension (ECD) measurements and the relative performance of the test structures fabricated on the two SOI materials.
Teaching Study Skills (1994)

Examines how the study skills module can effectively assist the teacher when covering a wide range of courses. Also discusses how students, using study skills, can analyse their progress and identify strengths and weaknesses by self‐assessment. Suggests “mapping out” as a means of assessing course stages to enable students to monitor their progress.
<p>Enhancement of Simvastatin ex vivo Permeation from Mucoadhesive Buccal Films Loaded with Dual Drug Release Carriers</p> (2020)

Mucoadhesive buccal films containing SMV IC and drug MM can be used to improve drug bioavailability; however, additional pharmacokinetic and pharmacodynamic studies are required.
Preliminary analysis of force-torque measurements for robot-assisted fracture surgery (2015)

Our group at Bristol Robotics Laboratory has been working on a new robotic system for fracture surgery that has been previously reported [1]. The robotic system is being developed for distal femur fractures and features a robot that manipulates the small fracture fragments through small percutaneous incisions and a robot that re-aligns the long bones. The robots controller design relies on accurate and bounded force and position parameters for which we require real surgical data. This paper reports preliminary findings of forces and torques applied during bone and soft tissue manipulation in typical orthopaedic surgery procedures. Using customised orthopaedic surgical tools we have collected data from a range of orthopaedic surgical procedures at Bristol Royal Infirmary, UK. Maximum forces and torques encountered during fracture manipulation which involved proximal femur and soft tissue distraction around it and reduction of neck of femur fractures have been recorded and further analysed in conjunction with accompanying image recordings. Using this data we are establishing a set of technical requirements for creating safe and dynamically stable minimally invasive robot-assisted fracture surgery (RAFS) systems.
Minimizing Labeling Cost for Nuclei Instance Segmentation and Classification with Cross-domain Images and Weak Labels (2021)

Nucleus instance segmentation and classification in histopathological images is an essential prerequisite in pathology diagnosis/prognosis. However, nucleus annotations (e.g., segmentation and labeling) require domain experts, and annotating nuclei at pixel-level is time-consuming and labor-intensive. Moreover, nuclei from different cancer types vary in shapes and appearances. These inter-cancer variations require careful annotations for specific cancer types. Therefore, to minimize the labeling cost, we propose a novel application that considers each cancer type as an individual domain and apply domain adaptation techniques to improve the segmentation/classification performance among different cancer types. Unlike the previous studies that focus on unsupervised or weakly-supervised domain adaptation independently, we would like to discover what kinds of labeling can achieve the most cost-effective domain adaptation performance in nucleus instance segmentation and classification. Specifically, we propose a unified framework that is applicable to different level annotations: no annotations, image-level, and point-level annotations. Cyclic adaptation with pseudo labels and adversarial discriminator are utilized for unsupervised domain alignment. Image-level or point-level annotations are additionally adopted to supervise the nucleus classification and refine the pseudo labels. Experiments demonstrate the effectiveness and efficacy of the proposed framework (jointly using unsupervised and weakly supervised learning) on adapting the segmentation and classification model from one cancer type to 18 other cancer types.
ChemInform Abstract: Synthesis and Activity of 6‐Substituted Purine Linker Amino Acid Immunostimulants. (1997)

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.
Polymerisation and related reactions involving nucleophilic aromatic substitution. Part 3. Mathematical models of the polycondensation reactions of halogenobenzophenones (1988)

Linear free energy relations have been used to calculate rate coefficients for the stages in the polycondensation reaction of the potassium salt of 4-fluoro-4′-hydroxybenzophenone and for the polycondensation reactions of 4,4′-difluorobenzophenone with the dipotassium salt of 4,4′-dihydroxybenzophenone and the dipotassium salt of hydroquinone. These rate coefficients have been used in a kinetic model of the polycondensations to calculate how the concentrations of the individual molecular species formed vary with time. The kinetic model is used to show that the molecular composition of the solutions, when considered as a function of the percentage reaction, should be relatively insensitive to the initial monomer concentration and to medium effects provided that all of the species concerned are fully soluble.