gebhart/patrepeval huggingface dataset:
The Discovery-Oriented Approach to Organic Chemistry. 2. Selectivity in Alcohol Oxidation. An Exercise in 1H NMR Spectroscopy for Sophomore Organic Laboratories (1999)

We have developed a simple oxidation experiment that presents the student with a puzzle and is a good exercise in 1H NMR spectroscopy. The experiment, which illustrates the important concept of selectivity in organic synthesis, involves selective oxidation of a mixture of 1-heptanol and 2-heptanol using commercial swimming pool chlorine. 1H NMR analysis of the product mixture allows the student to determine the selectivity exhibited by the reagent.
Peptidyl-prolyl cis–trans isomerase Pin1 in ageing, cancer and Alzheimer disease (2011)

Phosphorylation of proteins on serine or threonine residues preceding proline is a key signalling mechanism in diverse physiological and pathological processes. Pin1 (peptidyl-prolyl cis-trans isomerase) is the only enzyme known that can isomerise specific Ser/Thr-Pro peptide bonds after phosphorylation and regulate their conformational changes with high efficiency. These Pin1-catalysed conformational changes can have profound effects on phosphorylation signalling by regulating a spectrum of target activities. Interestingly, Pin1 deregulation is implicated in a number of diseases, notably ageing and age-related diseases, including cancer and Alzheimer disease. Pin1 is overexpressed in most human cancers; it activates numerous oncogenes or growth enhancers and also inactivates a large number of tumour suppressors or growth inhibitors. By contrast, ablation of Pin1 prevents cancer, but eventually leads to premature ageing and neurodegeneration. Consistent with its neuroprotective role, Pin1 has been shown to be inactivated in neurons of patients with Alzheimer disease. Therefore, Pin1-mediated phosphorylation-dependent prolyl isomerisation represents a unique signalling mechanism that has a pivotal role in the development of human diseases, and might offer an attractive new diagnostic and therapeutic target.
Hole and Interface Traps in Mg-doped Al<sub>0.1</sub>Ga<sub>0.9</sub>N/GaN Grown by Metalorganic Chemical Vapor Deposition (2002)

Deep level traps in Mg-doped Al0.1Ga0.9N/undoped GaN heterostructures grown by metalorganic vapor deposition with different Cp2Mg molar flow rates are studied by deep level transient spectroscopy (DLTS). Two distinct hole traps were observed, one with an activation energy of 0.18 eV (AD1) and the other with an activation energy of 0.88 eV (AD2) above the valence band maximum. From an analysis of the voltage dependence of DLTS spectra, the AD1 trap is associated with a defect in the Al0.1Ga0.9N/GaN interface based on the Poole–Frenkel model to interpret the enhancement of the thermal emission rate due to potential barrier lowering. The DLTS peak intensity of the AD2 trap steadily decreases with decreasing the Cp2Mg molar flow rate. It appears that the AD2 hole trap is strongly related to Mg-related deep levels, which contribute to the strong blue emission observed by photoluminescence measurements.
The promotional role of Mn in CO2 hydrogenation over Rh-based catalysts from a surface organometallic chemistry approach (2023)

Rh-based catalysts modified by transition metals have been intensely studied for CO2 hydrogenation due to their high activity. However, understanding the role of promoters at the molecular-level remains challenging due to the ill-defined structure of heterogeneous catalysts. Here, we constructed well-defined RhMn@SiO2 and Rh@SiO2 model catalysts via surface organometallic chemistry combined with thermolytic molecular precursors (SOMC/TMP) approach to rationalize the promotional effect of Mn in CO2 hydrogenation. We found that the addition of Mn shifts the products from almost pure CH4 to a mixture of methane and oxygenates (CO, CH3OH, and CH3CH2OH) upon going from Rh@SiO2 to RhMn@SiO2. In situ X-ray absorption spectroscopy (XAS) confirms that the MnII is atomically dispersed in the vicinity of metallic Rh nanoparticles, and enables to induce the oxidation of Rh to form Mn-O-Rh interface under reaction conditions. The formed interface is key to maintain Rh+ site to promote the formation of CO, CH3OH and CH3CH2OH.
Charge control of blockade of Cooper pair tunneling in highly disordered TiN nanowires in an inductive environment (2019)

A central problem in understanding the superconductor-insulator transition in disordered superconductors is that the properties of grains and intergrain medium cannot be independently studied. Here we demonstrate an approach to the study of strongly disordered superconducting films by relying on the stochastic nature of the disorder probed by electrostatic gating in a restricted geometry. Charge tuning and magnetotransport measurements in quasihomogeneous TiN nanowires embedded in a superinductor environment allow us to classify different devices and distinguish between spontaneously formed Coulomb islands (with typical blockade voltage in the mV range) and homogeneous wires showing behavior indicative of coherent quantum phase slips (with significantly smaller blockade voltage).
An Operationally Simple and Mild Oxidative Homocoupling of Aryl Boronic Esters To Access Conformationally Constrained Macrocycles (2017)

Constrained macrocyclic scaffolds are recognized as challenging synthetic motifs with few general macrocyclization methods capable of accessing these types of systems. Although palladium catalyzed oxidative homocoupling of aryl boronic acids and esters to biphenyls has been recognized as a common byproduct in Suzuki-Miyaura cross-couplings for decades, this reactivity has not been leveraged for the synthesis of challenging molecules. Here we report an oxidative boronic ester homocoupling reaction as a mild method for the synthesis of strained and conformationally restricted macrocycles. Higher yields and better efficiencies are observed for intramolecular diboronic ester homocouplings when directly compared to the analogous intramolecular Suzuki-Miyaura cross-couplings or reductive Yamamoto homocouplings. Substrates included strained polyphenylene macrocycles, strained cycloalkynes, and a key macrocyclic intermediate toward the synthesis of acerogenin A. Notably, this oxidative homocoupling reaction is performed at room temperature, open to atmosphere, and without the need to rigorously exclude water, thus representing an operationally simple alternative to traditional cross-coupling macrocyclizations. The mechanism of the reaction was investigated indicating that 1-5 nm palladium nanoparticles may serve as the active catalyst.
Method to produce water-soluble sugars from biomass using solvents containing lactones (2023)

A process to produce an aqueous solution of carbohydrates that contains C6-sugar-containing oligomers, C6 sugar monomers, C5-sugar-containing oligomers, C5 sugar monomers, or any combination thereof is presented. The process includes the steps of reacting biomass or a biomass-derived reactant with a solvent system including a lactone and water, and an acid catalyst. The reaction yields a product mixture containing water-soluble C6-sugar-containing oligomers, C6-sugar monomers, C5-sugar-containing oligomers, C5-sugar monomers, or any combination thereof. A solute is added to the product mixture to cause partitioning of the product mixture into an aqueous layer containing the carbohydrates and a substantially immiscible organic layer containing the lactone.
Use of a Modified Tryptophanase Promoter to Direct High‐Level Expression of Foreign Proteins in <i>E. coli</i> (1996)

We have modified the tryptophanase promoter (PtnaA) for use as a temperature-independent promoter for the production of recombinant proteins. Although any protein will have a temperature range in which its expression is optimal, we find the tryptophanase promoter functions at all physiologically relevant temperatures (20 degrees C to 42 degrees C). Induction at temperatures below 37 degrees C avoids eliciting the heat-shock response and may favor the production of protein in the soluble state. A short segment of the E. coli tnaA promoter containing the catabolite gene activator protein (CAP) binding site but no tryptophan-responsive elements was used to direct synthesis of various proteins. Conditions for high cell density fermentation and induction control were developed. Expression was induced by depletion of glucose and was maximal when an alternative nonrepressing carbon source was supplied. Expression of certain proteins was tightly controlled; however, pre-induction expression was observed with other reporter genes. The tnaC leader portion of the tnaA promoter was found to reduce pre-induction expression in the presence of glucose, although maximal expression was observed only in the absence of this region. The effect of temperature on expression of several recombinant proteins was investigated. Although some proteins were produced only in inclusion bodies as insoluble material, the production of one protein in soluble form was clearly temperature dependent.
The crystal structure of ICAM-2, its comparison to other integrin-binding proteins (1996)

MACROMOLECULESand pmified.Tm values of each mutant were determined by circular dichroism (CD) spectra.The change ofTm value (6Tm) from native BstHU was +3.1 °C(T13A), +1.7°C(T33L), -2.0°C(E34D), and -4.0°C(K38N) respectively.Each mutant was crystallized for X-ray structure analysis.The crystallization conditions of each mutant were 40% MPD, 80m.M phosphate(pH 8.0), and protein concentration was 25mg/ml.E34D mutant was crystallized as above condition plus 6% dioxane.X-ray expeliments were clone for Tl3A mutant, and this crystal diffracts at least 2.5A.Cell parameters are a=65.5 b=37.3 c=65.5 and 8=114.5 (that is isomorphous to native B.st HU crystal), and overall merging-R was 3.8%.Structure determination was clone by a molecular replacement.For model structure, we used the coordinates of native B.stHU.Refinement of this mutant structure was clone with X-plor and cur~ rent R-factor is 20%.We discuss the difference of thermal stability between native and mutant based on the structure.
Hybrid Neural Network Augmented Physics-based Models for Nonlinear Filtering (2022)

In this paper we present a hybrid neural network augmented physics-based modeling (APBM) framework for Bayesian nonlinear latent space estimation. The proposed APBM strategy allows for model adaptation when new operation conditions come into play or the physics-based model is insufficient (or incomplete) to properly describe the latent phenomenon. One advantage of the APBMs and our estimation procedure is the capability of maintaining the physical interpretability of estimated states. Furthermore, we propose a constraint filtering approach to control the neural network contributions to the overall model. We also exploit assumed density filtering techniques and cubature integration rules to present a flexible estimation strategy that can easily deal with nonlinear models and high-dimensional latent spaces. Finally, we demonstrate the efficacy of our methodology by leveraging a target tracking scenario with nonlinear and incomplete measurement and acceleration models, respectively.
Auto-calibration for a planar epicardial wire robot (2015)

Gene therapies have emerged as a promising treatment for congestive heart failure, yet they lack a method for minimally invasive, uniform delivery. To address this need we developed Cerberus, a minimally invasive parallel wire robot for cardiac interventions. Prior work on controlling the movement of Cerberus required accurate knowledge of device geometry. In order to determine the geometry of the device <i>in vivo</i>, this paper presents work on developing an auto-calibration procedure to measure the geometry of the robot using force sensors to move injector. The presented auto-calibration routine is able to identify the shape of the device to within 0.5 mm and 0.9°.
Table S3 from Therapeutically Increasing MHC-I Expression Potentiates Immune Checkpoint Blockade (2023)

&lt;p&gt;Traf3-knockout signature derived from RNA-seq&lt;/p&gt;
Fine-tuned LSTM-Based Model for Efficient Honeypot-Based Network Intrusion Detection System in Smart Grid Networks (2022)

Honeypot is considered a powerful complement to the Network Intrusion Detection System (NIDS) in smart grid (SG) systems, which minimizes the workload of NIDSs while providing access to information about the attacker's actions. This assists in further tracing the attack surface and, in return, enables the NIDSs to prevent such behaviors. Machine learning (ML) has recently attracted considerable attention in the SG security domain as a stringent technique for designing and implementing algorithms to predict security threats. However, large data sets collected by honeypots require more effort for faster response, real-time processing, and decision-making, especially for limited resources SG's devices. Thus, this paper proposes an approach to address this challenge, including feature extraction, oversampling and weak label combinations. We demonstrate that all classic ML algorithms cannot maintain the desired performance level when reducing the number of selected features (i.e., using only 25% of the features). As a result, we resort to the Deep Learning approach and propose an LSTM-based model that outperforms the state-of-the-art in terms of accuracy, precision, recall, and f1-score. We conduct extensive simulations using a realistic dataset that includes large log files. The proposed approach can employ just 25% of the features from each collected network packet while attaining 99.8% testing accuracy with a 13% improvement compared to the benchmarks.
Structures of 1-hydrophenanthroimidazoles: building blocks in the synthesis of expanded-ring bis(imidazoles) (2009)

The structures of 1H-phenanthro[9,10-d]imidazole, C15H10N2, (I), and 3,6-dibromo-1H-phenanthro[9,10-d]imidazole hemihydrate, C15H8Br2N(2).0.5H2O, (II), contain hydrogen-bonded polymeric chains linked by columns of pi-pi stacked essentially planar phenanthroimidazole monomers. In the structure of (I), the asymmetric unit consists of two independent molecules, denoted (Ia) and (Ib), of 1H-phenanthro[9,10-d]imidazole. Alternating molecules of (Ia) and (Ib), canted by 79.07 (3) degrees, form hydrogen-bonded zigzag polymer chains along the a-cell direction. The chains are linked by pi-pi stacking of molecules of (Ia) and (Ib) along the b-cell direction. In the structure of (II), the asymmetric unit consists of two independent molecules of 3,6-dibromo-1H-phenanthro[9,10-d]imidazole, denoted (IIa) and (IIb), along with a molecule of water. Alternating molecules of (IIa), (IIb) and water form hydrogen-bonded polymer chains along the [110] direction. The donor-acceptor distances in these N(imine)...H-O(water)...H-N(amine) hydrogen bonds are the shortest thus far reported for imidazole amine and imine hydrogen-bond interactions with water. Centrosymmetrically related molecules of (IIa) and (IIb) alternate in columns along the a-cell direction and are canted by 48.27 (3) degrees. The present study provides the first examples of structurally characterized 1H-phenanthroimidazoles.
Update of the list of QPS‐recommended biological agents intentionally added to food or feed as notified to EFSA 12: suitability of taxonomic units notified to EFSA until March 2020 (2020)

The qualified presumption of safety (QPS) was developed to provide a generic safety evaluation for biological agents to support EFSA's Scientific Panels. It is based on an assessment of the taxonomic identity, the body of knowledge, safety concerns and antimicrobial resistance. Safety concerns identified for a taxonomic unit (TU) are where possible to be confirmed at strain or product level, reflected by 'qualifications'. No new information was found that would change the previously recommended QPS TUs of the 39 microorganisms notified to EFSA between October 2019 and March 2020, 33 were excluded, including five filamentous fungi, five <i>Escherichia coli</i>, two <i>Enterococcus faecium</i>, two <i>Streptomyces</i> spp. and 19 TUs already evaluated. Six TUs were evaluated. <i>Akkermansia muciniphila</i> was not recommended for QPS status due to safety concerns. <i>Clostridium butyricum</i> was not recommended because some strains contain pathogenicity factors. This TU was excluded for further QPS evaluation. <i>Galdieria sulphuraria</i> and <i>Pseudomonas chlororaphis</i> were also rejected due to a lack of body of knowledge. The QPS status of <i>Corynebacterium ammoniagenes</i> (with the qualification 'for production purposes only') and of <i>Komagataella pastoris</i> (with the qualification 'for enzyme production') was confirmed. In relation to the taxonomic revision of the <i>Lactobacillus</i> genus, previously designated <i>Lactobacillus</i> species will be reassigned to the new species and both the old and new names will be retained in the QPS list.
High Levels of Genomic Aberrations in Serous Ovarian Cancers Are Associated with Better Survival (2013)

Genomic instability and copy number alterations in cancer are generally associated with poor prognosis; however, recent studies have suggested that extreme levels of genomic aberrations may be beneficial for the survival outcome for patients with specific tumour types. We investigated the extent of genomic instability in predominantly high-grade serous ovarian cancers (SOC) using two independent datasets, generated in Norway (n = 74) and Australia (n = 70), respectively. Genomic instability was quantified by the Total Aberration Index (TAI), a measure of the abundance and genomic size of copy number changes in a tumour. In the Norwegian cohort, patients with TAI above the median revealed significantly prolonged overall survival (p,0.001) and progression-free survival (p,0.05). In the Australian cohort, patients with above median TAI showed prolonged overall survival (p,0.05) and moderately, but not significantly, prolonged progression-free survival. Results were confirmed by univariate and multivariate Cox regression analyses with TAI as a continuous variable. Our results provide further evidence supporting an association between high level of genomic instability and prolonged survival of high-grade SOC patients, possibly as disturbed genome integrity may lead to increased sensitivity to chemotherapeutic agents.
Bone Mineral Density in Young Women With Primary Ovarian Insufficiency: Results of a Three-Year Randomized Controlled Trial of Physiological Transdermal Estradiol and Testosterone Replacement (2014)

Long-term physiological transdermal estradiol replacement in combination with oral medroxyprogesterone acetate restores mean femoral neck BMD to normal in young women with spontaneous 46,XX primary ovarian insufficiency. However, the addition of physiological transdermal T replacement did not provide additional benefit.
Velocities before, during, and after drilling (1999)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 1999Velocities before, during, and after drillingAuthors: David C. BartelDavid C. BartelChevron North America Exploration and Production Co.https://doi.org/10.1190/1.1820858 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1820858FiguresReferencesRelatedDetailsCited ByTime to depth conversion and uncertainty assessment using average velocity modelingDavid C. Bartel, Mark Busby, Jeff Nealon, and Joerg Zaske6 October 2006Piecewise Occam inversion for smoothing time‐depth information from checkshots and VSPsDavid C. Bartel and Scott Neal3 January 2005 SEG Technical Program Expanded Abstracts 1999ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 1999 Pages: 2061 publication data© 1999 Copyright © 1999 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished: 04 Jan 2005 CITATION INFORMATION David C. Bartel, (1999), "Velocities before, during, and after drilling," SEG Technical Program Expanded Abstracts : 168-171. https://doi.org/10.1190/1.1820858 Plain-Language Summary PDF DownloadLoading ...
CMET-05. ASSOCIATION BETWEEN TUMOR LOCATION AND TOXICITY OUTCOMES AFTER STEREOTACTIC RADIOSURGERY FOR BRAIN METASTASES (2018)

The toxicities associated with stereotactic radiosurgery (SRS) are important factors when considering treatment options and supportive management for patients with brain metastases. We assessed the association between brain metastasis location and rates of toxicity after SRS. We conducted a retrospective single-institution review of 170 patients treated with SRS for brain metastases from 2008–2016 with median follow-up of 8.6 months. Typical SRS doses were 18-20Gy in 1 fraction (lesions <2cm), 18-21Gy in 3 fractions (lesions 2-3cm), and 25-30Gy in 5 fractions (lesions > 3cm). Toxicity measures evaluated included radiation necrosis, seizure, and dexamethasone requirement. A total of 221 lesions were treated among frontal (29%), cerebellar (23%), parietal (16%), temporal (15%), occipital (14%), and other (brainstem, thalamus, basal ganglia) (4%) regions. The rate of SRS-related radionecrosis was 4% for all patients and significantly correlated with metastasis volume (increasing from 1% to 7% for lesions ≤1cm3 to > 3cm3) and prior whole brain radiotherapy (WBRT) but not with metastasis location or prior resection on multi-variable analysis (P<0.05). Post-SRS seizure occurred in 9% of all patients but was significantly higher after SRS to primary motor cortex and sensory cortex lesions, associated with 50% and 33% seizure rates, respectively (P<0.05). Of patients who initially presented with seizure and were on anti-epileptic medication during SRS, 62% had no further seizures, while 38% did have post-SRS seizures, nearly all with motor cortex lesions. Only 5% of patients had new-onset seizure after SRS, related to lesion hemorrhage or motor cortex location. Dexamethasone use > 3 months post-SRS was higher for motor strip lesions. Brain metastasis location in the primary motor cortex was associated with higher rates of post-SRS seizure, including new-onset seizures and breakthrough seizures on anti-epileptic medication during SRS. Rates of radionecrosis were associated with lesion volume and prior WBRT but not with metastasis location.
Losing a Grip on the Notion of β-Cell Specificity for Immune Responses in Type 1 Diabetes: Can We Handle the Truth? (2014)

You can’t handle the truth!— Jack Nicholson, A Few Good Men 

Research utilizing human pancreata to define a role for the immune response in the pathogenesis of what we now term type 1 diabetes (T1D) has come a long way since 1902 when Schmidt, a German pathologist, noted a small cellular peri-islet infiltrate upon microscopic evaluation of the pancreas obtained from a 10-year-old child with diabetes (1). Efforts by Shields Warren in the 1920s drew attention to the relationship between this infiltrate and the age of diabetes onset (2), while the term “insulitis” was not coined until 1940 by the famous liver pathologist Hanns von Meyenburg (3). Subsequent work led by Gepts (4), LeCompte (5), Foulis (6), and others in ensuing decades (7,8) taught us much regarding this inflammatory lesion. We gained insight into its relative infrequency in older individuals diagnosed with the disease, the association with reduction in β-cell mass, identification of “pseudo-atrophic” islets (i.e., islets devoid of insulin-containing cells), the preferential targeting of insulitis for β-cells containing insulin, upregulation of class I MHC, and many other seminal findings. Taken collectively, these efforts not only formed an “intellectual cornerstone” upon which much of the research enterprise in T1D over the last 40 years has been built but also led to the oft-cited notion that T1D results from an autoimmune destruction of the insulin-secreting pancreatic β-cells.

As a community of researchers, we built our models regarding the natural history of T1D around this …