gebhart/patrepeval huggingface dataset:
Supplemental Figure 1 from Identification of Anti-CA125 Antibody Responses in Ovarian Cancer Patients by a Novel Deep Sequence–Coupled Biopanning Platform (2023)

&lt;p&gt;OvCa and normal plasma reactivity to DISGTNTSRA by ELISA.&lt;/p&gt;
Practical linear models for large-scale one-class collaborative filtering (2016)

Collaborative filtering has emerged as the de facto approach to personalized recommendation problems. However, a scenario that has proven difficult in practice is the one-class collaborative filtering case (OC-CF), where one has examples of items that a user prefers, but no examples of items they do not prefer. In such cases, it is desirable to have recommendation algorithms that are personalized, learning-based, and highly scalable. Existing linear recommenders for OC-CF achieve good performance in benchmarking tasks, but they involve solving a large number of a regression subproblems, limiting their applicability to large-scale problems. We show that it is possible to scale up linear recommenders to big data by learning an OCCF model in a randomized low-dimensional embedding of the user-item interaction matrix. Our algorithm, Linear-FLow, achieves state-of-the-art performance in a comprehensive set of experiments on standard benchmarks as well as real data.
GS9.6 - Characterization of a Selective, Zero Power Sensor for Distributed Sensing of H2 in Energy Applications (2018)

The use of hydrogen as an energy source is increasing rapidly. There are safety concerns wherever H2 is made, used, and transported [pipelines and tanks] for both vehicle and stationary applications. Mobile and localized detectors are needed to meet safety codes and to enable a smooth rollout of H2 as an energy alternative. One impediment is a sensor that simultaneously has the combined features of small size, low cost for easy deployment in large numbers, low power to simplify fixed and mobile applications, and high performance including sensitivity, selectivity, fast response, stability and long lifetime. A new novel printed electrocatalytic amperometric gas sensor or AGS [1] with a circuit for monitoring H2 in air has been fabricated and evaluated for low level leak detection [0-1000 ppm H2 in air] and safety levels [alarms at 0.5%, 2.5%, and 4% in air]. The new H2 sensor is designed for manufacture [DFM] [PE] and is made on a template the size of an 8 wafer to enable volume low cost manufacture by leveraging PE and semiconductor fab infrastructure.
Effect of Molecular Therapeutics on Liver Regeneration in a Murine Model (2008)

Purpose Unresectable metastatic colorectal cancer (CRC) can be rendered resectable with systemic chemotherapy in approximately 20% of cases. Most patients with metastatic CRC receive chemotherapy with the addition of targeted therapy with anti–vascular endothelial growth factor (VEGF) or anti–epidermal growth factor receptor (EGFR) antibodies. We sought to determine whether anti-VEGF receptor (VEGFR) or anti-EGFR therapy would impair liver regeneration after partial hepatectomy (PH) in mice. Materials and Methods Mice underwent either 66% PH or sham laparotomy. In the first experiment, mice in the PH group were randomly assigned to receive daily intraperitoneal injections of monoclonal antibodies (MoABs) to murine VEGFR-2 or nonspecific MoABs (control). In the second experiment, mice in the PH group were randomly assigned to receive intraperitoneal injections of antimurine EGFR or nonspecific (control) MoABs. In both experiments, therapy was initiated the day before surgery and continued until the mice were killed on day 5. Livers were collected and processed. Results Anti–VEGFR-2 therapy slightly impaired liver regeneration and hepatic cell proliferation compared with control. Hematoxylin and eosin staining showed no differences in liver morphology. CD105 staining showed decreased levels of activated endothelium in livers in the VEGFR-2 MoAB group. VEGFR-2 MoAB therapy decreased the levels of the cell cycle regulators cyclin D1 and cyclin D3 and the regenerative cytokine interleukin-6. Anti-EGFR therapy had no effect on liver regeneration or cellular proliferation. Conclusion Anti–VEGFR-2 therapy slightly impaired liver regeneration in this murine model, whereas anti-EGFR therapy had no effect on liver regeneration.
Discovery of 2-Phenylquinolines with Broad-Spectrum Anti-coronavirus Activity (2022)

A selection of compounds from a proprietary library, based on chemical diversity and various biological activities, was evaluated as potential inhibitors of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in a phenotypic-based screening assay. A compound based on a 2-phenylquinoline scaffold emerged as the most promising hit, with EC<sub>50</sub> and CC<sub>50</sub> values of 6 and 18 μM, respectively. The subsequent selection of additional analogues, along with the synthesis of ad hoc derivatives, led to compounds that maintained low μM activity as inhibitors of SARS-CoV-2 replication and lacked cytotoxicity at 100 μM. In addition, the most promising congeners also show pronounced antiviral activity against the human coronaviruses HCoV-229E and HCoV-OC43, with EC<sub>50</sub> values ranging from 0.2 to 9.4 μM. The presence of a 6,7-dimethoxytetrahydroisoquinoline group at the C-4 position of the 2-phenylquinoline core gave compound <b>6g</b> that showed potent activity against SARS-CoV-2 helicase (nsp13), a highly conserved enzyme, highlighting a potentiality against emerging HCoVs outbreaks.
Characterization of a liposomal copper(II)-quercetin formulation suitable for parenteral use (2019)

Quercetin (3,3',4',5,7-pentahydroxyflavone) is a naturally derived flavonoid that is commonly found in fruits and vegetables. There is mounting evidence to suggest that quercetin has potential anticancer effects and appears to interact synergistically when used in combination with approved chemotherapeutic agents such as irinotecan and cisplatin. Unfortunately, quercetin has shown limited clinical utility, partly due to low bioavailability related to its poor aqueous solutions (< 10 μg/mL). In this study, liposomal formulations of quercetin were developed by exploiting quercetin's ability to bind copper. Quercetin powder was added directly to pre-formed copper-containing liposomes (2-distearoyl-sn-glycero-3-phosphocholine (DSPC) and cholesterol (CHOL) (55:45 M ratio)). As a function of time and temperature, the formation of copper-quercetin was measured. Using this methodology, a final quercetin-to-lipid (mol:mol) ratio of 0.2 was achievable and solutions containing quercetin at concentrations of > 5 mg/mL were attained, representing at least a > 100-fold increase in apparent solubility. The resulting formulation was suitable for intravenous dosing with no overt toxicities when administered at doses of 50 mg/kg in mice. Pharmacokinetic studies demonstrated that the copper-quercetin formulations had an AUC<sub>0-24H</sub> of 8382.1 μg h/mL when administered to mice at 50 mg/kg. These studies suggested that quercetin (not copper-quercetin) dissociates from the liposomes after administration. The resulting formulation is suitable for further development and also serves as a proof-of-concept for formulating other flavonoids and flavonoid-like compounds. Given that quercetin exhibits an IC<sub>50</sub> of >10 μM when tested against cancer cell lines, we believe that the utility of this novel quercetin formulation for cancer indications will ultimately be as a component of a combination product.
Severe Community-acquired Pneumonia Due toStaphylococcus aureus, 2003–04 Influenza Season (2006)

During the 2003-04 influenza season, 17 cases of Staphylococcus aureus community-acquired pneumonia (CAP) were reported from 9 states; 15 (88%) were associated with methicillin-resistant S. aureus (MRSA). The median age of patients was 21 years; 5 (29%) had underlying diseases, and 4 (24%) had risk factors for MRSA. Twelve (71%) had laboratory evidence of influenza virus infection. All but 1 patient, who died on arrival, were hospitalized. Death occurred in 5 (4 with MRSA). S. aureus isolates were available from 13 (76%) patients (11 MRSA). Toxin genes were detected in all isolates; 11 (85%) had only genes for Panton-Valentine leukocidin. All isolates had community-associated pulsed-field gel electrophoresis patterns; all MRSA isolates had the staphylococcal cassette chromosome mec type IVa. In communities with a high prevalence of MRSA, empiric therapy of severe CAP during periods of high influenza activity should include consideration for MRSA.
Total synthesis of (±)-sesbanimide A and B (1992)

The total synthesis of sesbanimide A (1) and B (2) is reported which features (a) the reaction of cyclopentadiene with glyoxylic acid leading to the useful bicyclic lactone building block 3 and (b) the use of 2.5 mol dm–3 lithium perchlorate in diethyl ether to promote the conjugate addition of 1-methoxy-1-(tert-butyldimethylsiloxy)ethene to unsaturated lactone 11.
A Boronic Acid Catalyzed Route to Imidazoles. Synthesis of LFA-1 Antagonists (2011)

Reported is the synthesis of 1H-­imidazo[1,2-a]imidazole-2-ones 2 via the boronic acid catalyzed cyclodehydration of 1 in the presence of trimethylorthoformate. Investigation of this procedure demonstrated the necessity of the acetal functionality present in 1 for effective product formation. Furthermore, bulkier acetals (such as diethyl acetal) proved less efficacious in the transformation. Control reactions conducted demonstrated that the cyclic urea 4 is not an intermediate in the reaction as it fails to progress to the desired product under the optimized conditions. In addition, the reaction is reported to be highly scalable (>1 kg), although only limited substrate scope was examined.
Exchange Interactions Between Chromium Ions in Ruby (1965)

Twenty-eight of the 100 or so sharp lines observed in relatively concentrated ruby (∼0.5%) are assigned to exchange-coupled pairs of chromium ions in two different relative positions. It is shown that the splitting of the 4A2 ground state of the Cr3+ ion is described by an isotropic exchange interaction in both cases, but that the splitting of the R levels (2E in an octahedral approximation to the crystal field) cannot be described so simply, probably because of the crystal field distortion due to the substitution of a Cr3+ ion for a nearby Al3+ ion. Values for the coupling parameters in the lower states are deduced, the criteria for the assignment discussed, and the pairs tentatively identified.
Active and Tuneable Metallic Nanoslit Lenses (2013)

In diffractive optics, typical feature sizes are on the order of the wavelength—around 1 μm for visible and near-infrared light. Although nanometer-scale features do not diffract optical waves, nanosized structures could enable us to design novel diffractive optical devices. Plasmonics and metamaterials are the two ways to couple light into nanoscale. This chapter talks about planar plasmonic diffractive focusing devices that consist of arrays of nanoslits milled in gold films. It gives a brief overview on the experimental characterization and full-wave numerical simulations of light propagation in the fabricated prototypes. Next, it shows that the focusing properties of nanoslit lenses can be externally tuned by filling the slits with index-changing materials such as a liquid crystal (LC) material. The chapter also discusses hyperbolic metamaterials (HMMs)-assisted nanoslit devices for subwavelength focusing. A case study on active HMM dispersions is discussed.
Isoquinoline Antimicrobial Agent: Activity against Intracellular Bacteria and Effect on Global Bacterial Proteome (2022)

A new class of alkynyl isoquinoline antibacterial compounds, synthesized via Sonogashira coupling, with strong bactericidal activity against a plethora of Gram-positive bacteria including methicillin- and vancomycin-resistant <i>Staphylococcus aureus (S. aureus)</i> strains is presented. HSN584 and HSN739, representative compounds in this class, reduce methicillin-resistant <i>S. aureus</i> (MRSA) load in macrophages, whilst vancomycin, a drug of choice for MRSA infections, was unable to clear intracellular MRSA. Additionally, both HSN584 and HSN739 exhibited a low propensity to develop resistance. We utilized comparative global proteomics and macromolecule biosynthesis assays to gain insight into the alkynyl isoquinoline mechanism of action. Our preliminary data show that HSN584 perturb <i>S. aureus</i> cell wall and nucleic acid biosynthesis. The alkynyl isoquinoline moiety is a new scaffold for the development of potent antibacterial agents against fatal multidrug-resistant Gram-positive bacteria.
Modeling and optimization method for thermal THz sensing with MOS transistors (2014)

In the pursuit of an uncooled THz sensor, we address the specific modeling and optimization method for micro-machined transistors for the implementation of antenna-coupled MOSFET bolometers. We discuss the degrees of freedom for maximizing the device's SNR, outlining also the trade-offs in relation to the requirements of an integrated read-out circuit. The methodology was applied to novel antenna-coupled THz sensors manufactured in a 0.18-μm SOI CMOS process. The theoretical results are supported by the measurements of these devices.
The c-myc oncogene is translocated to the involved chromosome 12 in mouse plasmacytoma. (1985)

Although it is known that the c-myc oncogene is rearranged in a head-to-head fashion with the immunoglobulin heavy chain locus in mouse plasmacytomas, it has not been clear whether the c-myc oncogene is translocated to the heavy chain locus on mouse chromosome 12 or whether the heavy chain locus is translocated to the c-myc locus on mouse chromosome 15. To determine which of these two possibilities is correct, we hybridized Chinese hamster fibroblasts with J558 mouse plasmacytoma cells that carry a reciprocal chromosome translocation between chromosomes 12 and 15, and we examined the segregating hybrids for the presence of the normal and rearranged mouse c-myc genes, for the presence of different regions of the mouse heavy chain locus, and for the presence of genes located on mouse chromosomes 12 and 15. The results of this analysis indicate that, as in human Burkitt lymphomas with the 8;14 chromosome translocation, the c-myc gene is translocated to the heavy chain locus in mouse plasmacytomas. Thus the orientation of the heavy chain locus on mouse chromosome 12 and of the c-myc gene on mouse chromosome 15 is the same as the orientation of the homologous loci in man.
High-precision Kicking Force Control using Joint Torque Feedback of Leg Robot with Bi-articular Muscle (2018)

It is important for realization of dynamic walking to generate kicking force in the direction connecting the waist position and the foot tip in the kicking out period. The leg robot with bi-articular muscle in this study can generate kicking force of this direction using one motor simulating the bi-articular muscle. In order to realize dynamic walking in the robot of this study, it is necessary to control exact kicking force within 0.2 seconds. Also, it is necessary for the joint torque to respond to the command value at 30rad/sec. Therefore, joint torque was controlled so as to satisfy 30rad/sec using bi-articular muscle and indirectly controlled kicking force. As a result, in the steady state, high-precise kicking force control with an error of 6% from the command value could be realized.
Translucent Answer Predictions in Multi-Hop Reading Comprehension (2020)

Research on the task of Reading Comprehension style Question Answering (RCQA) has gained momentum in recent years due to the emergence of human annotated datasets and associated leaderboards, for example CoQA, HotpotQA, SQuAD, TriviaQA, etc. While state-of-the-art has advanced considerably, there is still ample opportunity to advance it further on some important variants of the RCQA task. In this paper, we propose a novel deep neural architecture, called TAP (Translucent Answer Prediction), to identify answers and evidence (in the form of supporting facts) in an RCQA task requiring multi-hop reasoning. TAP comprises two loosely coupled networks – Local and Global Interaction eXtractor (LoGIX) and Answer Predictor (AP). LoGIX predicts supporting facts, whereas AP consumes these predicted supporting facts to predict the answer span. The novel design of LoGIX is inspired by two key design desiderata – local context and global interaction– that we identified by analyzing examples of multi-hop RCQA task. The loose coupling between LoGIX and the AP reveals the set of sentences used by the AP in predicting an answer. Therefore, answer predictions of TAP can be interpreted in a translucent manner. TAP offers state-of-the-art performance on the HotpotQA (Yang et al. 2018) dataset – an apt dataset for multi-hop RCQA task – as it occupies Rank-1 on its leaderboard (https://hotpotqa.github.io/) at the time of submission.
Data from MicroRNA-31 Predicts the Presence of Lymph Node Metastases and Survival in Patients with Lung Adenocarcinoma (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; We conducted genome-wide miRNA-sequencing (miRNA-seq) in primary cancer tissue from patients of lung adenocarcinoma to identify markers for the presence of lymph node metastasis.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Markers for lymph node metastasis identified by sequencing were validated in a separate cohort using quantitative PCR. After additional validation in the The Cancer Genome Atlas (TCGA) dataset, functional characterization studies were conducted &lt;i&gt;in vitro&lt;/i&gt;.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; MiR-31 was upregulated in lung adenocarcinoma tissues from patients with lymph node metastases compared with those without lymph node metastases. We confirmed miR-31 to be upregulated in lymph node-positive patients in a separate patient cohort (&lt;i&gt;P&lt;/i&gt; = 0.009, &lt;i&gt;t&lt;/i&gt; test), and to be expressed at higher levels in adenocarcinoma tissue than in matched normal adjacent lung tissues (&lt;i&gt;P&lt;/i&gt; &lt; 0.0001, paired &lt;i&gt;t&lt;/i&gt; test). MiR-31 was then validated as a marker for lymph node metastasis in an external validation cohort of 233 lung adenocarcinoma cases of the TCGA (&lt;i&gt;P&lt;/i&gt; = 0.031, &lt;i&gt;t&lt;/i&gt; test). &lt;i&gt;In vitro&lt;/i&gt; functional assays showed that miR-31 increases cell migration, invasion, and proliferation in an ERK1/2 signaling-dependent manner. Notably, miR-31 was a significant predictor of survival in a multivariate cox regression model even when controlling for cancer staging. Exploratory &lt;i&gt;in silico&lt;/i&gt; analysis showed that low expression of miR-31 is associated with excellent survival for T&lt;sub&gt;2&lt;/sub&gt;N&lt;sub&gt;0&lt;/sub&gt; patients.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; We applied miRNA-seq to study microRNomes in lung adenocarcinoma tissue samples for the first time and potentially identified a miRNA predicting the presence of lymph node metastasis and survival outcomes in patients of lung adenocarcinoma. &lt;i&gt;Clin Cancer Res; 19(19); 5423–33. ©2013 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Legacy Technology Reemergence: The Case of the Vinyl Record (2020)

This paper studies the vinyl records as a cultural icon that “refuses to die” in order to enhance the existing theory about legacy technology and how instead of disappearing, got redefined by its enthusiasts, remerged and created a sustained market growth. After the appearance of CDs and Mp3s, Vinyl Records reached the lowest level of sales from their existence but in 2008 vinyl records managed to gain market share again and year by year became again an equal competitor of the other music formats. This research reveals the processes that vinyl records have gone through in order to reemerge. Furthermore, all the factors that contributed to vinyl records resurgence are analytically discussed and analysed. The vinyl record is being analysed as a cultural icon and a legacy technology and how it managed to reemerge in the digital era. Vinyl records’ enthusiasts' community following the lead of the community’s influencers increased the sales by 300% in a year redefining the meaning of vinyl records and generating word-of-mouth and online and offline mentions about vinyl records. This caused the increase in demand for vinyl records which are considered to have an alternative value rather than functionality.
Radical CC Bond Formation by Photoinduced Electron Transfer Addition of α‐Silyl Carbamates to Acceptor‐Substituted Alkenes (1995)

α-Silyl carbamates are suitable precursors for carbon radicals. The silyl group is cleaved by photosensitized oxidative fragmentation, and the resulting radicals can add to alkenes. Equation (a) shows one example. A = acceptor, Tms = trimethylsilyl.
Characteristics and the Model of Resistive Random Access Memory Switching of the Ti/TiO2 Resistive Material Depending on the Thickness of Ti (2011)

The effects of the reactive Ti layer on the resistive switching characteristics of TiN/Ti/TiO 2 /TiN resistive random access memory (ReRAM) are investigated. Nitridation at the top region of Ti during reactive sputtering of the TiN layer and oxygen gettering of Ti from TiO 2 make the TiON/TiO 2- x interface. It results in TiO 2 with a higher concentration of oxygen vacancies during metal alloy annealing, resulting in the low-initial-resistance state. This leads to a stable bipolar switching after the first set process. A larger thickness of Ti decreases resistance value in the high-resistance state, which enables the adjustment of on/off resistance ratio.
Chapter 12. β-Lactoglobulin Aggregates from Heating with Charged Cosolutes: Formation, Characterization and Foaming (2007)

Foamed products are gaining more importance in the food industry because of their smooth and light texture. Food foams can be stabilized by emulsifiers and fats, but proteins are the most commonly used foaming agents. Globular proteins (e.g., whey proteins) exhibit good foaming properties, but in or...
Continuous Flow Synthesis of 2-Imidazolidinone from Ethylenediamine Carbamate in Ethylenediamine Solvent over the CeO2 Catalyst: Insights into Catalysis and Deactivation (2023)

Synthesis of 2-imidazolidinone (EU) from ethylenediamine carbamate (EDA-CA), which was produced via chemical absorption of CO2 in ethylenediamine (EDA), with a fixed-bed flow reactor was performed using CeO2 and EDA as a heterogeneous catalyst and reaction solvent, respectively. In the previously reported batch system for the same reaction, the yield of EU was low (62%) due to its sequential reaction with EDA into N,N′-bis(2-aminoethyl)urea (LU) with 38% yield in the liquid phase under the optimized reaction conditions at 413 K. In stark contrast, the flow reaction enabled the highly selective and high-yielding production of EU (94% yield) under the optimized reaction conditions at 363 K. This difference in the selectivity of EU originated from the lower ratio of the amount of EDA to that of the CeO2 catalyst in the current flow reaction system compared to the previous batch system. The highly crystallized CeO2 surface bearing both acid and base sites was found to be responsible for its high catalytic performance. The combination of the kinetics, density functional theory calculations, and adsorption experiments demonstrated that EDA-CA is preferentially adsorbed onto the surface of CeO2 even in the presence of an excess amount of EDA, which is used as a solvent, to be activated and transformed into EU. The solid-state 13C magic angle spinning/cross polarization nuclear magnetic resonance spectroscopy revealed that the CeO2 catalyst was deactivated gradually in a long-term reaction operation due to the formation and deposition of polyurea-like organic compounds on the catalyst surface.