gebhart/patrepeval huggingface dataset:
What is a “DNA-Compatible” Reaction? (2016)

DNA-encoded synthesis can generate vastly diverse screening libraries of arbitrarily complex molecules as long as chemical reaction conditions do not compromise DNA's informational integrity, a fundamental constraint that "DNA-compatible" reaction development does not presently address. We devised DNA-encoded reaction rehearsal, an integrated analysis of reaction yield and impact on DNA, to acquire these key missing data. Magnetic DNA-functionalized sensor beads quantitatively report the % DNA template molecules remaining viable for PCR amplification after exposure to test reaction conditions. Analysis of solid-phase bond forming (e.g., Suzuki-Miyaura cross-coupling, reductive amination) and deprotection reactions (e.g., allyl esters, silyl ethers) guided the definition and optimization of DNA-compatible reaction conditions (>90% yield, >30% viable DNA molecules), most notably in cases that involved known (H(+), Pd) and more obscure (Δ, DMF) hazards to DNA integrity. The data provide an empirical yet mechanistically consistent and predictive framework for designing successful DNA-encoded reaction sequences for combinatorial library synthesis.
Teaching Research of Electric Design Automatization (2007)

This article mainly researches the mistakes students often make in studing Electric Design Automatization and Teaching Method which teachers should pay attention to in teaching.
Chitosan-Modified Stable Colloidal Gold Nanostars for the Photothermolysis of Cancer Cells (2013)

The preparation and properties of plasmonic gold nanostars (Au NSs) modified with a biopolymer chitosan are reported. The colloidal stability of Au NSs at the physiological pH of 7.5 and their performance in the photothermolysis of cancer cells in vitro were compared with those of gold nanorods (Au NRs). The optical characteristics of chitosan-modified Au NSs dispersed in a medium with pH = 7.5 had higher stability than those of chitosan-capped NRs because of the slower aggregation of NSs. At pH = 7.5, the chitosan-modified Au NRs formed aggregates with highly nonuniform sizes. On the other hand, Au NSs formed small chain-like clusters, in which individual NSs were connected to one another, preferably via association of branches with central cores. It is possible that the difference in areal charge density at these parts of NSs is responsible for their preferred association. Flow cytometry analysis showed the relatively nonequivalent distribution of the chitosan-capped Au NRs across the cell line compared with that of Au NSs because of the fast and nonuniform aggregation of NRs. An in-vitro photothermolysis experiment on J5 cancer cells showed that energy fluences of 23 and 33 mJ/cm2 are necessary to cause complete death of J5 cells incubated with 4 μg/mL chitosan-capped Au NSs and NRs, respectively. When chitosan was used as a surface-capping agent, the Au NSs exhibited higher colloidal stability at the physiological pH than the NRs and lower energy fluence necessary for cell photothermolysis because of more uniform cellular uptake.
Humidity‐Insensitive Tissue Oxygen Tension Sensing for Wearable Devices† (2019)

Quantification of tissue oxygen partial pressure (pO<sub>2</sub> ) at the skin surface is crucial for diagnostic applications in burns, reconstructive surgeries, diabetic ulcers, etc. Further, current advances in wearable and communications technologies have widened the use of transcutaneous oxygen monitors (TCOM) for home care or even enhance athletic performance. For TCOM technology to find widespread use, devices must function reliably yet independently of changes in environmental conditions, humidity in particular. To this end, we have explored the incorporation of an oxygen-sensing metalloporphyrin within different host matrix materials of different compositions with the goal of overcoming the humidity sensitivity of previously explored oxygen-sensing materials. We developed a tetraethyl orthosilicate (TEOS)-based, highly breathable, oxygen-sensing metalloporphyrin polymer film which responds to changes in oxygenation independent of humidity.
A Dynamic Load-Balanced Hashing Scheme for Networking Applications (2008)

Network applications often require large data storage resources, fast queries, and frequent updates. Hash tables support these operations with low costs, yet they cannot provide worst-case guarantees because of hash collisions. Also, the widely used, low-cost Dynamic Random Access Memory (DRAM) cannot suitably accommodate hash tables because DRAMs provide full bandwidth only if accessed in bursts, whereas hash tables require random access. In this paper, we propose a hash co-processor to support hash tables on DRAMs. The co-processor provides a load-balancing method to reduce the impact of hash collisions on the worst-case behavior by moving multiple keys within the hash table in constant time. This leads to a balanced distribution of keys in the hash table despite the collisions. Furthermore, the coprocessor guarantees the full DRAM bandwidth is always utilized by defining all fundamental hash table operations, namely insert, query, and delete, in terms of burst accesses. In the worst case, the query, delete, and insert operations take one, two, and three burst accesses, respectively. The proposed architecture reduces hash overflows by 35% compared to a naive hash table and for each key uses 6.42 bits of on-chip memory.
Isolation and characterization of adociavirin, a novel HIV‐inhibitory protein from the sponge Adocia sp.1 (1998)

Aqueous extracts of the New Zealand sponge Adocia sp. (Haplosclerida) displayed potent anticytopathic activity in CEM-SS cells infected with HIV-1. Protein fractions of the extract bound both to the viral coat protein gp120 and to the cellular receptor CD4, but not to other tested proteins. The purified active protein, named adociavirin, was characterized by isoelectric focusing, amino acid analysis, MALDI-TOF mass spectrometry and N-terminal sequencing. Adociavirin, a disulfide-linked homodimer with a native molecular weight of 37 kDa, was active against diverse strains and isolates of HIV-1, as well as HIV-2, with EC50 values ranging from 0.4 nM to > 400 nM. The anti-HIV potency of adociavirin appears dependent on host cell type, with macrophage cultures being the most sensitive and peripheral blood lymphocytes the most resistant.
ChemInform Abstract: 13C NMR Quantitative Spectrometric Data—Activity Relationship (QSDAR) Models of Steroids Binding the Aromatase Enzyme. (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.
Carbon Capture, Utilization, & Storage (CCUS) in Achieving a Net Zero Emissions Future - System Cost of Replacement Energy (SCoRE): A Tool for Assessing Technology Substitution Pathways to Decarbonization (2023)

This presentation outlines the SCoRE tool, which can be used to identify the least-cost technology substitution pathway to meeting a decarbonization target within an operating region of the United States. The presentation showcases results from an application of the tool in the ERCOT operating region.
Targeting PIM2 by JP11646 results in significant antitumor effects in solid tumors (2022)

Proviral integration of Moloney virus 2 (PIM2) is a pro‑survival factor of cancer cells and a possible therapeutic target in hematological malignancies. However, the attempts at inhibiting PIM2 have yielded underwhelming results in early clinical trials on hematological malignancies. Recently, a novel pan‑PIM inhibitor, JP11646, was developed. The present study examined the utility of targeting PIM2 in multiple solid cancers and investigated the antitumor efficacy and the mechanisms of action of JP11646. When PIM2 expression was compared between normal and cancer tissues in publicly available datasets, PIM2 was found to be overexpressed in several types of solid cancers. PIM2 ectopic overexpression promoted tumor growth in <i>in vivo</i> xenograft breast cancer mouse models. The pan‑PIM inhibitor, JP11646, suppressed <i>in vitro</i> cancer cell proliferation in a concentration‑dependent manner in multiple types of cancers; a similar result was observed with siRNA‑mediated PIM2 knockdown, as well as an increased in cell apoptosis. By contrast, another pan‑PIM inhibitor, AZD1208, suppressed the expression of downstream PIM2 targets, but not PIM2 protein expression, corresponding to no apoptosis induction. As a mechanism of PIM2 protein degradation, it was found that the proteasome inhibitor, bortezomib, reversed the apoptosis induced by JP11646, suggesting that PIM2 degradation by JP11646 is proteasome‑dependent. JP11646 exhibited significant anticancer efficacy with minimal toxicities at the examined doses and schedules in multiple <i>in vivo</i> mice xenograft solid cancer models. On the whole, the present study demonstrates that PIM2 promotes cancer progression in solid tumors. JP11646 induces apoptosis at least partly by PIM2 protein degradation and suppresses cancer cell proliferation <i>in vitro</i> and <i>in vivo</i>. JP11646 may thus be a possible treatment strategy for multiple types of solid cancers.
Clinical and Biological Applications of ECL (2004)

The application of electrochemiluminescence (ECL) to the detection of biologically important analytes has seen substantial success, as measured by the widespread use of the technology in basic research, in environmental and industrial testing, and in clinical laboratory analyzers. Initial interest in the technique was spurred by the ability of ECL measurements to detect analytes in extremely low concentrations, though other favorable attributes such as insensitivity to matrix effects and a high dynamic range have contributed to ECL’s acceptance as a robust detection methodology. The flexibility of the technique permits the probing of nearly any type of molecular interaction. ECL-based assays have been developed to detect proteins, nucleic acids, and small molecules and to probe ligand-receptor interactions and enzyme activity. The commercial availability of ECL reagents and instruments has also played a large part in fueling interest in the technique. Relatively inexpensive commercial instrumentation and ECL labels with linker groups that are easily attached to biomolecules have allowed researchers to quickly and easily develop numerous assay formats for a variety of applications. Fields that currently use ECL in the detection of biological analytes include clinical diagnostics, food and water testing, biowarfare agent detection, and basic research within both academia and industry.
Genetic Identity and Biological Phenotype of a Transmitted/Founder Virus Representative of Nonpathogenic Simian Immunodeficiency Virus Infection in African Green Monkeys (2010)

Understanding the lack of disease progression in nonpathogenic simian immunodeficiency virus (SIV) infections is essential for deciphering the immunopathogenesis of human AIDS. Yet, in vivo studies have been hampered by a paucity of infectious molecular clones (IMCs) of SIV suitable to dissect the viral and host factors responsible for the nonpathogenic phenotype. Here, we describe the identification, cloning, and biological analysis of the first transmitted/founder (T/F) virus representing a nonpathogenic SIV infection. Blood was collected at peak viremia from an acutely infected sabaeus monkey (Chlorocebus sabaeus) inoculated intravenously with an African green monkey SIV (SIVagm) strain (Sab92018) that had never been propagated in vitro. To generate IMCs, we first used conventional (bulk) PCR to amplify full-length viral genomes from peripheral blood mononuclear cell (PBMC) DNA. Although this yielded two intact SIVagmSab genomes, biological characterization revealed that both were replication defective. We then performed single-genome amplification (SGA) to generate partially overlapping 5' (n = 10) and 3' (n = 13) half genomes from plasma viral RNA. Analysis of these amplicons revealed clusters of nearly identical viral sequences representing the progeny of T/F viruses. Synthesis of the consensus sequence of one of these generated an IMC (Sab92018ivTF) that produced infectious CCR5-tropic virions and replicated to high titers in Molt-4 clone 8 cells and African green monkey PBMCs. Sab92018ivTF also initiated productive infection in sabaeus monkeys and faithfully recapitulated the replication kinetics and nonpathogenic phenotype of the parental Sab92018 strain. These results thus extend the T/F virus concept to nonpathogenic SIV infections and provide an important new tool to define viral determinants of disease nonprogression.
Large Area Fabrication of Moth-Eye Antireflection Structures Using Self-Assembled Nanoparticles in Combination with Nanoimprinting (2010)

A moth-eye structure, which suppresses the reflection on a surface, was fabricated on the entire surface of a large silicon wafer by the formation of a self-assembled particle monolayer as a dry-etch mask formed by our embedded particle monolayer (EPM) method. We optimized the shape of moth-eye structures by optical calculation and improved the fabrication procedure to allow formation over a large area. As a result, we succeeded in fabricating a moth-eye structure on the entire surface of a 12-in. silicon wafer and the surface reflectance was reduced to less than 0.8% in the visible light range. A large nickel mold, which is able to transfer the pattern to an 8-in. display, could be formed using the 12-in. silicon substrate as a master. A moth-eye film was fabricated by UV nanoimprinting using the nickel mold and the high antireflection performance was confirmed. The fabrication cost of the moth-eye structure over a large area would be markedly reduced by the use of the self-assembly technique in combination with nanoimprinting.
Development of a Wireless Surface Acoustic Wave Methane Sensor Using an MOF as a Sensing Layer for Natural Gas Pipelines (2021)

Presented by NETL at 235th ECS Meeting, 05/19
Comparison of lipopolysaccharides composition of two different strains of Helicobacter pylori (2017)

The composition analysis of H. pylori LPS, revealed differences in sugars and fatty acids composition between a mouse adapted strain SS1 and G27. This knowledge provides a novel way to dissect out their importance in host-pathogen interaction in further studies.
Analysis of the physical and microbiocidal characteristics of an emerging and innovative UV disinfection technology (2021)

Introduction Surface disinfection is one of the key points to reduce the risk of transmission both in healthcare and other public spaces. A novel UV-chip disinfection technology is presented. Technological, photonic and microbiocidal characteristics are evaluated taking as reference an ultraviolet-C (UV-C) LED source of equivalent radiant power. Methods The UV chip has a circular radiating surface with a diameter of 1.3 cm, emitting UV cold light at about 5 mW and driven current of about 80 µA. Four bacterial strains were used to conduct the microbiological tests at 4°C and 60°C to evaluate the bactericidal performance of the two technologies under the same operating conditions. Results Spectral differences were found between the UV-C LED and the chip, with an emission curve strictly around 280 nm and a broader band centred around 264 nm, respectively. Between-technology microbiological inactivation levels were comparable, achieving total abatement (99.999%) in 8 min at 7.5 cm. Discussion The UV chip exhibits unique properties that make it applicable in some specific contexts, where UV-C LEDs present the most critical issues. Besides, it is portable and exhibits a broad spectrum of UV wavelengths with a peak where the maximum microbiocidal efficacy occurs. Important issues to be addressed to improve this technology are the high voltage management and the too low energy efficiency. Conclusion This cold emission technology is virtually unaffected by changes in ambient temperature and is particularly useful in short-distance applications. Recent developments in technology are moving towards a progressive increase in the chip’s radiant power.
Definition and Identification of an Improved Preisach Model for Magnetic Hysteresis Based on the KP operator (2022)

The Preisach approach is widely employed for modeling magnetic hysteresis. However, it is characterized by high complexity. When computational burden is critical, it can be discretized, but it yields to an inherently discontinuous output. To overcome this problem, the present paper applies the Krasnosel’skii-Pokrovskii operator to derive a discretized Preisach-like model for magnetic hysteresis having continuous input-output relationship. The proposed formulation allows exploiting the anti-symmetrical behavior of magnetic materials to further reduce complexity. The identification procedure, based on constrained optimization, is characterized by robustness and moderate computational cost. Experimental results show the high accuracy achieved in predicting the flux density waveforms.
The Coupled Atom Transistor: A first realization with shallow donors implanted in a FDSOI silicon nanowire (2013)

Following the recent development of Single Atom Transistors [1,2], we realized the first Coupled Atom Transistor in a small silicon nanowire MOSFET. Three independent gates control two donors connected in series between the source and the drain in a small volume of silicon. The devices, either implanted with Phosphorus (10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">24</sup> m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> ) or Arsenic atoms, are fabricated with SOI technology on 200 and 300 mm wafers [3]. We observe resonant transport through two donors in series, and spectroscopy of a single donor state can be performed. We further demonstrate charge pumping and coherent electron exchange between the two donors involving Landau-Zener transitions.
Carbon Dioxide Insufflation During Endoscopic Pancreatic Function Test Does Not Significantly Change Duodenal Juice Bicarbonate Concentration (2016)

Introduction: Compared with air, the use of carbon dioxide (CO2) insufflation during endoscopic procedures results in reduced post-procedure discomfort and improved patient satisfaction. The secretinstimulated endoscopic pancreatic function test (ePFT) uses peak bicarbonate (HCO3) levels < 80 mEq/L as a cut-off for the diagnosis of chronic pancreatitis. The impact of CO2 insufflation on bicarbonate levels of endoscopically collected duodenal aspirates is largely unknown. Aim: To compare pancreatic fluid HCO3 concentration obtained with use of air and CO2 insufflation. Methods: Twenty-two patients underwent ePFT during the study period. Using air insufflation, duodenal fluid was collected at 30, 35, 40 and 45-minutes after secretin administration per our standard institutional ePFT protocol. CO2 insufflation was then initiated and a 50-minute duodenal fluid sample was collected. Bicarbonate concentrations were measured in all fluid samples using a clinical chemistry autoanalyzer. For each patient the predicted (air) 50-minute HCO3 was calculated using linear regression analysis based on HCO3 measurements from earlier time points, and predicted values were compared with the measured (CO2) 50-minute HCO3. Results: Nine of 22 patients (41%) had an abnormal ePFT with peak HCO3 levels less than 80 mEq/L. Although there was substantial intra-subject variability in HCO3 concentrations measured between 30 and 45 minutes (pooled standard deviation = 6.8), the mean slope of the 30-45 minute HCO3 concentrations was 0.34, implying little aggregate change over time. The mean difference between observed and predicted 50 minute HCO3 was -1.7 ± 17.0 mEq/L. Overall there was no significant difference between observed (CO2) and predicted (air) 50-minute HCO3 values (Figure 1, p = 0.64). Two out of the nine patients with an abnormal test using air-insufflation (peak HCO3 levels of 72 and 69 mEq/L) would have been reclassified as ‘normal’ based on 50-minute HCO3 levels of 84 and 87 mEq/L obtained under CO2 insufflation.Figure 1Conclusion: Endoscopic CO2-insufflation does not appear to significantly alter measured HCO3 concentration of duodenal aspirates during ePFT. There is substantial intra-subject variability in measured HCO3 levels over time.
Design and Structure–Function Characterization of 3D Printed Synthetic Porous Biomaterials for Tissue Engineering (2017)

3D printing is now adopted for use in a variety of industries and functions. In biomedical engineering, 3D printing has prevailed over more traditional manufacturing methods in tissue engineering due to its high degree of control over both macro- and microarchitecture of porous tissue scaffolds. However, with the improved flexibility in design come new challenges in characterizing the structure-function relationships between various architectures and both mechanical and biological properties in an assortment of clinical applications. Presently, the field of tissue engineering lacks a comprehensive body of literature that is capable of drawing meaningful relationships between the designed structure and resulting function of 3D printed porous biomaterial scaffolds. This work first discusses the role of design on 3D printed porous scaffold function and then reviews characterization of these structure-function relationships for 3D printed synthetic metallic, polymeric, and ceramic biomaterials.
Semantic word embedding neural network language models for automatic speech recognition (2016)

Semantic word embeddings have become increasingly important in natural language processing tasks over the last few years. This popularity is due to their ability to easily capture rich semantic information through a distributed representation and the availability of fast and scalable algorithms for learning them from large text corpora. State-of-the-art neural network language models (NNLMs) used in automatic speech recognition (ASR) and natural language processing also learn word embeddings optimized to model local N-gram dependencies given training text but are not optimized to capture semantic information. We hypothesize that semantic word embeddings provide diverse information compared to the word embeddings learned by NNLMs. We propose novel feedforward NNLM architectures that incorporate semantic word embeddings. We apply the resulting NNLMs to ASR on broadcast news and show improvements in both perplexity and word error rate.