gebhart/patrepeval huggingface dataset:
Diastereoselective Aldol Reaction of α-Bromo Ketones with Aliphatic Aldehydes by Using Titanium(II) Chloride and Copper (1999)

Abstract Highly diastereoselective aldol reaction of α-bromo ketones with aliphatic aldehydes was successfully carried out by using titanium(II) chloride and copper in dichloromethane at low temperature. Similarly, Reformatsky-type reaction of α-bromo thioester with aliphatic aldehydes was promoted under mild conditions to afford β-hydroxy thioesters in good to moderate yields.
The neuronal ceroid lipofuscinosis Cln8 gene expression is developmentally regulated in mouse brain and up-regulated in the hippocampal kindling model of epilepsy (2005)

Expression of Cln8 in the developing and mature brain suggests roles for Cln8 in maturation, differentiation and supporting the survival of different neuronal populations. The relevance of Cln8 up-regulation in hippocampal neurons of kindled mice should be further explored.
Optics in computers, servers, and data centers (2012)

Based on well-known laws of physics, a lower bound on the energy-per-bit required for transmitting information using a photonic channel is established. The analysis includes the energy required to convert information from the electronic to the photonic domain and back. We investigate links that employ a directly modulated laser as well as links that employ an external modulator. It is shown that the power dissipation of the channel also imposes a bound on the maximum bandwidth density for a photonic link. Keeping this in mind, opportunities for optics in computing systems are discussed, especially from a systems perspective.
Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays (2006)

Recent reports indicate that copy number variations (CNVs) within the human genome contribute to nucleotide diversity to a larger extent than single nucleotide polymorphisms (SNPs). In addition, the contribution of CNVs to human disease susceptibility may be greater than previously expected, although a complete understanding of the phenotypic consequences of CNVs is incomplete. We have recently reported a comprehensive view of CNVs among 270 HapMap samples using high-density SNP genotyping arrays and BAC array CGH. In this report, we describe a novel algorithm using Affymetrix GeneChip Human Mapping 500K Early Access (500K EA) arrays that identified 1203 CNVs ranging in size from 960 bp to 3.4 Mb. The algorithm consists of three steps: (1) Intensity pre-processing to improve the resolution between pairwise comparisons by directly estimating the allele-specific affinity as well as to reduce signal noise by incorporating probe and target sequence characteristics via an improved version of the Genomic Imbalance Map (GIM) algorithm; (2) CNV extraction using an adapted SW-ARRAY procedure to automatically and robustly detect candidate CNV regions; and (3) copy number inference in which all pairwise comparisons are summarized to more precisely define CNV boundaries and accurately estimate CNV copy number. Independent testing of a subset of CNVs by quantitative PCR and mass spectrometry demonstrated a >90% verification rate. The use of high-resolution oligonucleotide arrays relative to other methods may allow more precise boundary information to be extracted, thereby enabling a more accurate analysis of the relationship between CNVs and other genomic features.
Radioiodination of extravesicular surface constituents to study the biocorona, cell trafficking and storage stability of extracellular vesicles (2021)

The EV biocorona affects EV mediated biological processes in health and disease. Acquiring knowledge of the EV biocorona composition, dynamics, stability and structure not only informs the diagnostic and therapeutic translation of EVs but also aids in designing biomimetic nanomaterials for drug delivery.
B. subtilis Ribosomal Proteins: Structural Homology and Post-Translational Modifications (2009)

Ribosomal proteins of the model gram-positive bacterium B. subtilis 168 were extensively characterized in a proteomic study. Mass spectra of the 52 proteins expected to be constitutive components of the 70S ribosome were recorded. Peptide MS/MS analysis with an average sequence coverage of 85% supported the identification of these proteins and facilitated the unambiguous assignment of post-translational modifications, including the methylation of S7, L11, and L16 and the N-terminal acetylation of S9. In addition, the high degree of structural homology between B. subtilis and other eubacterial ribosomal proteins was demonstrated through chemical labeling with S-methylthioacetimidate. One striking difference from previous characterizations of bacterial ribosomal proteins is that dozens of protein masses were found to be in error and not easily accounted for by post-translational modifications. This, in turn, led us to discover an inordinate number of sequencing errors in the reference genome of B. subtilis 168. We have found that these errors have been corrected in a recently revised version of the genome.
Enthalpy–Entropy Compensation Effect in Hydrogen Storage Materials: Striking Example of Alkali Silanides MSiH3 (M = K, Rb, Cs) (2014)

Safe storage of hydrogen is a key issue for development of the hydrogen economy. Solid-state hydrogen storage through reversible formation of hydrides is one of the most promising methods. Herein reports for the very first time a combined experimental and theoretical study of the hydrogen absorption–desorption of MSi Zintl phases (M = K, Rb, and Cs). Upon direct hydrogenation of the MSi phases at 100 °C, the α-MSiH3 silanides (4.3, 2.6, and 1.85 wt % H2 for M = K, Rb, and Cs, respectively) are formed and the corresponding alloys are reobtained upon desorption. Besides the full resolution of the crystal structures of the α-MSiH3 silanides and their low-temperature β-phases, by neutron powder diffraction, we show an enthalpy–entropy compensation effect for the MSi/α-MSiH3 equilibrium: a simultaneous linear increase in the enthalpy (more stable silanide) and entropy change (more localized H atoms in the crystal structure) for the larger cation (Cs+). Through this phenomenon, a desorption temperature of ca. 410 K is obtained at 0.1 MPa hydrogen equilibrium pressure for all three systems. Indeed, this study shows for the first time that the alkali silanides form a new family of complex hydrides that can be considered as promising materials for reversible hydrogen storage near ambient conditions in the solid state.
Understanding the Oxygen Reduction Reaction Activity and Oxidative Stability of Pt Supported on Nb‐Doped TiO2 (2019)

Abstract Invited for this month′s cover are the groups of Prof. Vijay Ramani at Washington University in St. Louis and Prof. Plamen Atanassov at the University of New Mexico (presently the University of California, Irvine). The image represents a fuel cell‐powered car with a highly durable and active catalyst. The Full Paper itself is available at 10.1002/cssc.201900499 .
The Role of Yes-Associated Protein (YAP) in Regulating Programmed Death-Ligand 1 (PD-L1) in Thoracic Cancer (2018)

The programmed death-ligand 1(PD-L1)/PD-1 pathway is an immunological checkpoint in cancer cells. The binding of PD-L1 and PD-1 promotes T-cell tolerance and helps tumor cells escape from host immunity. Immunotherapy targeting the PD-L1/PD-1 axis has been developed as an anti-cancer therapy and used in treating advanced human non-small cell lung cancer (NSCLC) and malignant pleural mesothelioma (MPM). Yes-associated protein (YAP) is a key mediator of the Hippo/YAP signaling pathway, and plays important roles in promoting cancer development, drug resistance and metastasis in human NSCLC and MPM. YAP has been suggested as a new therapeutic target in NSCLC and MPM. The role of YAP in regulating tumor immunity such as PD-L1 expression has just begun to be explored, and the correlation between YAP-induced tumorigenesis and host anti-tumor immune responses is not well known. Here, we review recent studies investigating the correlation between YAP and PD-L1 and demonstrating the mechanism by which YAP regulates PD-L1 expression in human NSCLC and MPM. Future work should focus on the interactions between Hippo/YAP signaling pathways and the immune checkpoint PD-L1/PD-1 pathway. The development of new synergistic drugs for immune checkpoint PD-L1/PD-1 blockade in NSCLC and MPM is warranted.
High-Temperature Conductivity Measurements of Magnesium-Ion-Conducting Solid Oxide Mg0.5−x(Zr1−xNbx)2(PO4)3(x= 0.15) Using Mg Metal Electrodes (2017)

Conductivity of a Mg2+-ion-conducting solid oxide Mg0.5−x(Zr1−xNbx)2(PO4)3 (x = 0.15) was measured with non-blocking Mg metal electrodes at 350°C in vacuum. The oxidation of Mg electrodes was suppressed by preventing their exposure to air throughout the deposition and measurements. The observed conductivity agreed with conductivities measured by ac impedance spectroscopy with blocking Pt electrodes. The transport number of Mg2+ ions derived from the conductivities measured with Mg electrodes by dc polarization method and ac impedance spectroscopy was ∼1. These observations evidenced that this compound is a pure Mg2+-ion conductor and stable in contact with Mg.
Methods for Monitoring of the Anti‐Angiogenic Activity of Agents in Patients: Novel Trial Design (2006)

This chapter contains sections titled: Introduction Tumour micro-environmental factors Possible mechanisms of acquired resistance to anti-angiogenic drugs Standard chemotherapy versus angiogenesis inhibitors Monitoring clinical trials Tumour dormancy and tumour progression Tumour markers Microvessel density Surrogate endpoints Molecular imaging New insights into trial design Concluding remarks References
Analysis of data quality issues in real-world industrial data (2013)

&#x0D; &#x0D; &#x0D; In large industries usage of advanced technological methods and modern equipment comes with the problem of storing, interpreting and analyzing huge amount of information. Handling information becomes more complicated and important at the same time. So, data quality is one of major challenges considering a rapid growth of information, fragmentation of information systems, incorrect data formatting and other issues. The aim of this paper is to describe industrial data processing and analytics on the real- world use case. The most crucial data quality issues are described, examined and classified in terms of Data Quality Dimensions. Factual industrial information supports and illustrates each encountered data deficiency. In addition, we describe methods for elimination data quality issues and data analysis techniques, which are applied after cleaning data procedure. In addition, an approach to address data quality problems in large-scale industrial datasets is proposed. This techniques and methods comprise several well-known techniques, which come from both worlds of mathematical logic and also statistics, improving data quality procedure and cleaning results.&#x0D; &#x0D; &#x0D;
First Synthetic Method for the Preparation of 6-Unsubstituted-2,3-dihydro-1,3-oxazin-4-ones (1996)

The first synthetic pathway to synthesize 6-unsubstituted-2,3-dihydro-1,3-oxazin-4-ones is described. The α-formylation of the starting amide and the cyclization of the α-formylamide with a desired aldehyde under acidic conditions gave compounds 5a−h (R = nPr, iPr, cPr, cHex, Ph, CH2Ph, nHex, and R1 = H, Me). This strategy was used with little modification for the preparation of new monocyclic organic nitrates such as 2a−c (2a (R = Ph, R1 = H, and R2 = H), 2b (R = Ph, R1 = H, and R2 = Me), and 2c (R = H, R1 = Ph, and R2 = H).
What Process Algebra Proofs Use Instead of Invariance (2016)

Working on [110] got me thinking about how process-algebraic proofs work. This draft note describes my preliminary thoughts about what those proofs use instead of invariance. I never developed this far enough to know if it’s right.
Feasibility of Desorption Electrospray Ionization Mass Spectrometry for Diagnosis of Oral Tongue Squamous Cell Carcinoma (2017)

RationaleDesorption electrospray ionization mass spectrometry (DESI-MS) has demonstrated utility in differentiating tumor from adjacent normal tissue in both urologic and neurosurgical specimens. We sought to evaluate if this technique had similar accuracy in differentiating oral tongue squamous cell carcinoma (SCC) from adjacent normal epithelium due to current issues with late diagnosis of SCC in advanced stages.MethodsFresh frozen samples of SCC and adjacent normal tissue were obtained by surgical resection. Resections were analyzed using DESI-MS sometimes by a blinded technologist. Normative spectra were obtained for separate regions containing SCC or adjacent normal epithelium. Principal Component Analysis and Linear Discriminant Analysis (PCA-LDA) of spectra were used to predict SCC versus normal tongue epithelium. Predictions were compared with pathology to assess accuracy in differentiating oral SCC from adjacent normal tissue.ResultsInitial PCA score and loading plots showed clear separation of SCC and normal epithelial tissue using DESI-MS. PCA-LDA resulted in accuracy rates of 95% for SCC versus normal and 93% for SCC, adjacent normal and normal. Additional samples were blindly analyzed with PCA-LDA pixel-by-pixel predicted classifications as SCC or normal tongue epithelial tissue and compared against histopathology. The m/z 700-900 prediction model showed a 91% accuracy rate.ConclusionsDESI-MS accurately differentiated oral SCC from adjacent normal epithelium. Classification of all typical tissue types and pixel predictions with additional classifications should increase confidence in the validation model.
Improving the Voltage Modulation Depth of Radiofrequency Produced by Nonlinear Transmission Lines Using a Shock Wave Configuration (2020)

Low power nonlinear transmission lines - LPNLTL using varactor diode as a nonlinear element has been studied to produce RF signals to be used in communication systems, radars, satellites, biomedical and military applications <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> . Nowadays Nonlinear Transmission Lines - NLTL has been studied to generate waves on ultrahigh-frequency in the terahertz range <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , The frequency, voltage modulation depth - VMD, power, and number of oscillations are the main parameters to be analyzed for the design of these devices. In this work, we propose a new configuration to improve the VMD using more than one LPNLTL connected to a load, named as shock wave configuration. The simulation was made by using the LT-Spice software. The results with a single line produced an RF signal with a frequency of the order of 36.4 MHz, VMD near to 9.4 V, and the number of oscillations equal to 8. In the simulation using a shock wave configuration with six lines, the VMD increased to 13.7 V, which means 45.7% higher than VMD produced with a single line. The oscillation peaks remained unchanged under the shock wave configuration and the frequency has a little increase going of the 36.4 MHz (single line) to 40 MHz, which means 9.9% higher using shock wave configuration. A MOSFET amplifier was used to increase the RF signal produced by the shock wave configuration, reaching a VMD of the order of 80 V. This technique shows that VMD is increased when RF is produced by an LPNLTL using the shock wave configuration, which can widen the cover range of the signal.
Correlation of Trace Silicone Contamination Analyses on Epoxy Composites Using X-ray Photoelectron Spectroscopy (XPS) and Laser-Induced Breakdown Spectroscopy (LIBS) (2018)

Surface treatment and surface characterization techniques are critical to ensure that adherends are chemically activated and free of contaminants before adhesive bonding. Silicone contamination from mold release agents and other sources can interfere with interfacial bonding, decreasing the durability and performance of bonded composite structures. It is necessary to have tools and methods that can be used in a production environment to reliably detect low levels of contaminants in a rapid, simple, and cost-effective manner to improve bond reliability. In this work, surface characterization of carbon fiber reinforced polymer (CFRP) composites with epoxy matrix was performed using laser-induced breakdown spectroscopy (LIBS), and the results were compared with those obtained from X-ray photoelectron spectroscopy (XPS). Laser-induced breakdown spectroscopy offers many advantages over XPS in terms of ease of use, sample preparation, and real-time results. The objective of the comparison was to study the sensitivity of LIBS and to investigate the quantification of the surface species measured by LIBS. Another objective was to assess the reliability of each technique for surface contaminant characterization. The as-processed CFRP panels had trace surface silicone contamination from the fabrication process, the source of which was not investigated. The composites were laser treated at select average laser power levels, resulting in varying levels of contamination reduction. The Si atomic percentage measurements using XPS were conducted on both control and laser-ablated surfaces. The results showed an excellent correlation in Si concentration between the two techniques.
Interactions in milk suggest a physiological role for β-lactoglobulin (2019)

Abstract β-Lactoglobulin is the most abundant protein in the whey fraction of ruminant milks, yet is absent in human milk. It has been studied intensively due to its impact on the processing and allergenic properties of ruminant milk products. However, the physiological function of β-lactoglobulin remains unclear. Sedimentation velocity experiments have identified new interactions between fluorescently-labelled β-lactoglobulin and other components in milk. Co-elution experiments support that these β-lactoglobulin interactions occur naturally in milk and provide evidence that the interacting partners are immunoglobulins, while further sedimentation velocity experiments confirm that an interaction occurs between these molecules. Ruminants (e.g. cows and goats) are born without circulating immunoglobulins, which they must obtain from their mothers’ milk, whilst humans obtain immunoglobulins both through milk and during gestation via the placenta. We propose that β-lactoglobulin serves to protect immunoglobulins within ruminant milk during digestion, ensuring their efficient transfer from mother to offspring. Statement of Significance β-Lactoglobulin is an abundant protein in the whey fraction of ruminant milks (e.g. cow and goat milk), yet it is completely absent in human milk. While this protein has been extensively studied, due to its impact on the processing and allergenic properties of milk, its physiological function remains unclear. We fluorescently labelled β-lactoglobulin to monitor its interactions with other milk components within its physiological environment, milk. Under these near physiological conditions β-lactoglobulin is capable of interacting with several classes of immunoglobulins. Immunoglobulins are susceptible to digestion, but are required to confer immunity from the mother to the offspring. We propose that β-lactoglobulin serves to protect immunoglobulins within ruminant milk during digestion, ensuring their efficient transfer from mother to offspring.
Enhancement and Bandwidth Compression of Noisy Speech. (1979)

Over the past several years there has been considerable attention focused on the problem of enhancement and bandwidth compression of speech degraded by additive background noise. This interest is motivated by several factors including a broad set of important applications, the apparent lack of robustness in current speech-compression systems and the development of several potentially promising and practical solutions. One objective of this paper is to provide an overview of the variety of techniques that have been proposed for enhancement and bandwidth compression of speech degraded by additive background noise. A second objective is to suggest a unifying framework in terms of which the relationships between these systems is more visible and which hopefully provides a structure which will suggest fruitful directions for further research.
Sequences essential for transposition at the termini of IS50. (1983)

The DNA sequences found repeated in opposite orientation at the ends of insertion (IS) elements are thought to contain sites at which transposase proteins act during transposition. Many elements have repeats of at least 15 base pairs (bp). Those of IS50 are quite short, however: just 8 of the first 9 bp. Functional tests had indicated that one end of IS50 is more effective in transposition than the other end and suggested that at least one of the recognition sites of IS50 extends beyond the common 8/9 bp. To determine the lengths of recognition sites of IS50 we mutagenized IS50 in vitro and tested the transposition proficiency of the resulting mutants. Our results show that the recognition sites at each end of IS50 are about 19 bp long. These findings suggest models for the evolution of IS elements from simpler immobile gene complexes.
Advanced Devices for Safer Freight Train Switching Operations (2010)

Freight train switching operations involve significant manual operations creating a safety hazard for the train crew and resulting in numerous injuries and fatalities every year. There is a need to develop, test, and deploy advanced devices that enable automation and improve the safety and efficiency of freight train switching operations. With that goal in mind, the Federal Railroad Administration has funded multiple projects aimed at developing these advanced devices. This paper presents three advanced devices — Remote Controlled Cut Lever, Remote Controlled Angle Cock, and Hand Brake Release Sensor — that will bring the industry one step closer to safer, more efficient and automated freight train switching operations. These devices were tested extensively in a laboratory and in a rail-yard environment and work is under way for testing these devices in a mainline operation.
Impaired Pancreatic Polypeptide Secretion in Chronic Pancreatitis* (1978)

In patients with chronic pancreatitis, the plasma pancreatic polypeptide (PP) response to insulininduced hypoglycemia is impaired, although basal levels are within the normal range. Somatostatin lowers the PP response in normal people and in patients with chronic pancreatitis. The PP response may be a useful index of pancreatic function.