gebhart/patrepeval huggingface dataset:
The effect of oxygen on the three‐component radical photoinitiator system: Methylene blue, N‐methyldiethanolamine, and diphenyliodonium chloride (2000)

In this article, we extend our mechanistic study of the three-component radical photoinitiator system, consisting of methylene blue (MB), N-methyldiethanolamine, and diphenyliodonium chloride, by investigating the influence of oxygen on the rate of the consumption of MB dye. The mechanism involves electron transfer/proton transfer from the amine to the dye as the primary photochemical reaction. Oxygen quenches the triplet state of the dye, leading to retardation of the reaction. We used time-resolved steady-state fluorescence monitoring to observe the MB concentration in situ in both a constant oxygen environment and a sealed reactor as the dye is consumed via photoreaction. In the sealed reactor, we observed a retardation period (attributed to the presence of oxygen) followed by rapid exponential decay of the MB fluorescence after the oxygen was depleted. On the basis of the impact of the amine and iodonium concentrations on the fluorescence intensity and the duration of the retardation period, our proposed mechanism includes an oxygen-scavenging pathway, in which the tertiary amine radicals formed in the primary photochemical process consume the oxygen via a cyclic reaction mechanism. The iodonium salt is an electron acceptor, acting to reoxidize the neutral dye radical back to its original state and allowing it to reenter the primary photochemical process. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 3336–3346, 2000
Ally: A Smartphone-based Physical Activity Intervention (2017)

No behavior has an impact on human health as great as physical activity (PA). We therefore developed Ally, a smartphone-based 6-week PA intervention. Ally seeks to exploit the ubiquity and sensing capabilities of mobile phones to adapt the provision of PA interventions to the context of the user. In this research we investigate the following research questions: (1) What are effective components of Ally, a mHealth physical activity intervention? and (2) Can mobile sensor data predict opportune moments for interventions?
Putative Clinical Potential of ERBB2 Amplification Assessment by ddPCR in FFPE-DNA and cfDNA of Gastroesophageal Adenocarcinoma Patients (2022)

Anti-HER2 monoclonal antibody trastuzumab improves the survival of those patients with advanced gastroesophageal adenocarcinoma (GEA) exhibiting HER2/ERBB2 overexpression/amplification. The current gold standard methods used to diagnose the HER2 status in GEA are immunohistochemistry (IHC) and silver or fluorescence in situ hybridization (SISH or FISH). However, they do not permit spatial and temporal tumor monitoring, nor do they overcome intra-cancer heterogeneity. Droplet digital PCR (ddPCR) was used to implement the assessment of HER2 status in formalin-fixed paraffin-embedded (FFPE) tumor DNA from a retrospective cohort (86 patients) and in cell-free DNA (cfDNA) samples from a prospective cohort (28 patients). In comparison to IHC/SISH, ddPCR assay revealed ERBB2 amplification in a larger patient fraction, including HER2 2+ and 0–1+ of the retrospective cohort (45.3% vs. 15.1%). In addition, a considerable number of HER2 2+ and 0–1+ prospective patients who were negative in FFPE by both IHC/SISH and ddPCR, showed ERBB2 amplification in the cfDNA collected just before surgery. cfDNA analysis in a few longitudinal cases revealed an increasing ERBB2 trend at progression. In conclusion, ddPCR in liquid biopsy may improve the detection rate of HER2 positive patients, preventing those patients who could benefit from targeted therapy from being incorrectly excluded.
Competition-level code generation with AlphaCode (2022)

Programming is a powerful and ubiquitous problem-solving tool. Systems that can assist programmers or even generate programs themselves could make programming more productive and accessible. Recent transformer-based neural network models show impressive code generation abilities yet still perform poorly on more complex tasks requiring problem-solving skills, such as competitive programming problems. Here, we introduce AlphaCode, a system for code generation that achieved an average ranking in the top 54.3% in simulated evaluations on recent programming competitions on the Codeforces platform. AlphaCode solves problems by generating millions of diverse programs using specially trained transformer-based networks and then filtering and clustering those programs to a maximum of just 10 submissions. This result marks the first time an artificial intelligence system has performed competitively in programming competitions.
Raman Spectroscopy of Laminated Polymer Films by Integrated Optical Techniques (1981)

Abstract Raman spectra have been observed from two adjacent thin polymer films and the interfacial region. This has been made possible by the application of integrated optical techniques to Raman spectroscopy. The observed Raman spectra have their strongest intensity contributions from regions near the optical field intensity maxima, which can occur in either film or at the interface. Both the optical intensity and the scattering volume are increased significantly and Raman spectra with good signal-to-noise ratios can be obtained. The method will be briefly illustrated and spectra for a thin film of poly(styrene) on a film of polyvinyl alcohol) will be shown for various (modes) optical profiles.
Biotechnology Provides New Tools for Plant Breeding (2002)

Author(s): Suslow, Trevor V; Thomas, Bruce R; Bradford, Kent J | Abstract: Recombinant DNA is still a relatively new technology. This publication gives a basic introduction to how it works and how it's being used in plant breeding.
Energy-dependent relaxation time in quaternary amorphous oxide semiconductors probed by gated Hall effect measurements (2017)

Despite the success of exploiting the properties of amorphous oxide semiconductors for device applications, the charge transport in these materials is still not clearly understood. The observation of a definite Hall voltage suggests that electron transport in the conduction band is free-electron-like. However, the temperature dependence of the Hall and field-effect mobilities cannot be explained using a simple bandlike model. Here, we perform gated Hall effect measurements in field-effect transistors, which allow us to make two independent estimates of the charge carrier concentration and determine the Hall factor providing information on the energy dependence of the relaxation time. We demonstrate that the Hall factor in a range of sputtered and solution-processed quaternary amorphous oxides, such as a-InGaZnO, is close to two, while in ternary oxides, such as InZnO, it is near unity. This suggests that quaternary elements like Ga act as strong ionized impurity scattering centers in these materials.
A Patient-Specific Single Equivalent Dipole Model (2022)

Sophisticated models for the electrocardiographic inverse problem are available, but their reliance on imaging data and large numbers of electrodes limit their use. Simple models such as the single equivalent dipole model (SEDM) therefore remain relevant. We developed a probabilistic approach to the equivalent unbounded uniform single dipole problem and developed a natural extension to the bounded nonuniform case that relies on a patientspecific statistical inference of the propagation mechanism between the location of the dipole and the electrode locations. The two models were tested on data simulated with a detailed heart-torso model with four different activation sequences and three different sets of tissue characteristics. We observed a throughout enhancement of the ability to reconstruct the ECG of the patient-specific model when compared to the uniform unbounded dipole model.
Harmonic modelocking at up to 440GHz repetition rates in InGaAs-InAlGaAs quantum well lasers (1998)

The InGaAs-InAlGaAs quaternary quantum well material system forms an alternative to the conventional InGaAsP based diode lasers for use in 1.3µm and 1.55µm fibre optic systems. Larger conduction band offsets and a greater thermal stability compared to the InGaAsP system makes InAlGaAs material attractive for both high speed modulators [1] and room temperature high power lasers. In this paper we present the first demonstration to our knowledge of monolithic modelocking action from InGaAs-InAlGaAs laser diodes.
Controlling the Outcome of the Toll-Like Receptor Signaling Pathways (2012)

The Toll-Like Receptors (TLRs) are proteins involved in the immune system that increase cytokine levels when triggered. While cytokines coordinate the response to infection, they appear to be detrimental to the host when reaching too high levels. Several studies have shown that the deletion of specific TLRs was beneficial for the host, as cytokine levels were decreased consequently. It is not clear, however, how targeting other components of the TLR pathways can improve the responses to infections. We applied the concept of Minimal Cut Sets (MCS) to the ihsTLR v1.0 model of the TLR pathways to determine sets of reactions whose knockouts disrupt these pathways. We decomposed the TLR network into 34 modules and determined signatures for each MCS, i.e. the list of targeted modules. We uncovered 2,669 MCS organized in 68 signatures. Very few MCS targeted directly the TLRs, indicating that they may not be efficient targets for controlling these pathways. We mapped the species of the TLR network to genes in human and mouse, and determined more than 10,000 Essential Gene Sets (EGS). Each EGS provides genes whose deletion suppresses the network's outputs.
White Paper: Challenges and Considerations for the Creation of a Large Labelled Repository of Online Videos with Questionable Content (2021)

This white paper presents a summary of the discussions regarding critical considerations to develop an extensive repository of online videos annotated with labels indicating questionable content. The main discussion points include: 1) the type of appropriate labels that will result in a valuable repository for the larger AI community; 2) how to design the collection and annotation process, as well as the distribution of the corpus to maximize its potential impact; and, 3) what actions we can take to reduce risk of trauma to annotators.
Brainstem pathology in DYT1 primary torsion dystonia (2004)

DYT1 dystonia is a severe form of young-onset dystonia caused by a mutation in the gene that encodes for the protein torsinA, which is thought to play a role in protein transport and degradation. We describe, for the first time to our knowledge, perinuclear inclusion bodies in the midbrain reticular formation and periaqueductal gray in four clinically documented and genetically confirmed DYT1 patients but not in controls. The inclusions were located within cholinergic and other neurons in the pedunculopontine nucleus, cuneiform nucleus, and griseum centrale mesencephali and stained positively for ubiquitin, torsinA, and the nuclear envelope protein lamin A/C. No evidence of inclusion body formation was detected in the substantia nigra pars compacta, striatum, hippocampus, or selected regions of the cerebral cortex. We also noted tau/ubiquitin-immunoreactive aggregates in pigmented neurons of the substantia nigra pars compacta and locus coeruleus in all four DYT1 dystonia cases, but not in controls. This study supports the notion that DYT1 dystonia is associated with impaired protein handling and the nuclear envelope. The role of the pedunculopontine and cuneiform nuclei, and related brainstem brainstem structures, in mediating motor activity and controlling muscle tone suggests that alterations in these structures could underlie the pathophysiology of DYT1 dystonia [corrected]
S-MMICs: Sub-mm-Wave Transistors and Integrated Circuits (2008)

Abstract : Transistor and power amplifier IC technology was developed under UCSB tbr the DARPA SWIFT program. SWIFT seeks to develop sub-mm-wave transistors and ICs to support 340 GHz-band imaging and radar systems. By program end, HBT power-gain cutoff frequencies were increased to 880 GHz, simultaneous with a 5 V breakdown voltage. HBT layer structure designs and process flows, and initial 340 GHz power amplifier designs developed at UCSB were transferred to Teledyne Scientific. Teledyne Scientific then fabricated both transistors and ICs under the financial support of a separate DARPA program; results at TSC include a 2 mW power amplifier at 340 GHz. Device technology development at UCSB included a number of significant accomplishments supporting the future development of sub-mm-wave transistors and integrated circuits, including all-dry-etched processes for reliable formation of ~128 nm feature size transistor emitters and ultra low resistivity contacts for the emitter and base contacts. These several features are critical in enabling transistor bandwidths to extend to the low THz regime.
Mitochondrial matrix chaperone and c-myc inhibition causes enhanced lethality in glioblastoma (2017)

Malignant gliomas display high levels of the transcription factor c-myc and organize a tumor specific chaperone network within mitochondria. Here, we show that c-myc along with mitochondrial chaperone inhibition displays massive tumor cell death. Inhibition of mitochondrial matrix chaperones and c-myc was established by utilizing genetic as well as pharmacological approaches. Bromodomain and extraterminal (BET) family protein inhibitors, JQ1 and OTX015, were used for c-myc inhibition. Gamitrinib was applied to interfere with mitochondrial matrix chaperones. A xenograft model was used to determine the in vivo efficacy. Combined inhibition of c-myc and mitochondrial matrix chaperones led to a synergistic reduction of cellular proliferation (CI values less than 1) in established glioblastoma, patient-derived xenograft and stem cell-like glioma cultures. The combinatorial treatment of BET inhibitors and Gamitrinib elicited massive apoptosis induction with dissipation of mitochondrial membrane potential and activation of caspases. Mechanistically, BET-inhibitors and Gamitrinib mediated a pronounced integrated stress response with a PERK-dependent up regulation of ATF4 and subsequent modulation of Bcl-2 family of proteins with down-regulation of Mcl-1 and its interacting partner, Usp9X, and an increase in pro-apoptotic Noxa. Blocking ATF4 by siRNA attenuated Gamitrinib/BET inhibitor mediated increase of Noxa. Knockdown of Noxa and Bak protected from the combinatorial treatment. Finally, the combination treatment of Gamitrinib and OTX015 led to a significantly stronger reduction of tumor growth as compared to single treatments in a xenograft model of human glioma without induction of toxicity. Thus, Gamitrinib in combination with BET-inhibitors should be considered for the development for clinical application.
Young‐onset colorectal cancer in the Asia–Pacific region (2016)

hen O'Connell and colleagues published their systematic review of young-onset colorectal cancer (CRC) in 2004, 1 defined as CRC in a person no older than 40 years of age, there had only been one study in the AsiaePacific region. 2 Several reports have subsequently raised concerns about an increasing incidence of young-onset CRC in this region. If the number of patients is indeed rising, should we respond to this epidemiological problem with new measures? Strong evidence suggests that the incidence of young-onset CRC is increasing in the United States and Europe, in contrast to a declining incidence in older people. Most of this evidence comes from population-based analyses of data from the SEER (Surveillance, Epidemiology and End Results) registries. 3 In this issue of the MJA, investigators from New South Wales suggest that, at least at present, the incidence of young-onset CRC is not increasing here. Different trends in the incidence of young-onset CRC were reported by two earlier population-based studies in Australia. The most likely explanations for the disparity in the results of these studies involve differences in the study periods and baseline incidence of young-onset CRC. For the rest of the AsiaePacific region, only two population-based studies have reported trends for young-onset CRC. An analysis of data from the Hong Kong Cancer registry did not find an increase in the incidence of young-onset CRC during 1983e2006. he second study, analysing data from the Korean cancer registry, similarly found no increase during 1999e2009 in the overall incidence of young-onset CRC relative to older patients, although the incidence of rectal cancer in the younger age group increased.
Selective inhibition of caspases in skeletal muscle reverses the apoptotic synaptic degeneration in slow-channel myasthenic syndrome (2013)

Slow-channel syndrome (SCS) is a congenital myasthenic disorder caused by point mutations in subunits of skeletal muscle acetylcholine receptor leading to Ca(2+) overload and degeneration of the postsynaptic membrane, nuclei and mitochondria of the neuromuscular junction (NMJ). In both SCS muscle biopsies and transgenic mouse models for SCS (mSCS), the endplate regions are shrunken, and there is evidence of DNA damage in the subsynaptic region. Activated caspase-9, -3 and -7 are intensely co-localized at the NMJ, and the Ca(2+)-activated protease, calpain, and the atypical cyclin-dependent kinase (Cdk5) are overactivated in mSCS. Thus, the true mediator(s) of the disease process is not clear. Here, we demonstrate that selective inhibition of effector caspases, caspase-3 and -7, or initiator caspase, caspase-9, in limb muscle in vivo by localized expression of recombinant inhibitor proteins dramatically decreases subsynaptic DNA damage, increases endplate area and improves ultrastructural abnormalities in SCS transgenic mice. Calpain and Cdk5 are not affected by this treatment. On the other hand, inhibition of Cdk5 by expression of a dominant-negative form of Cdk5 has no effect on the degeneration. Together with previous studies, these results indicate that focal activation of caspase activity at the NMJ is the principal pathological process responsible for the synaptic apoptosis in SCS. Thus, treatments that reduce muscle caspase activity are likely to be of benefit for SCS patients.
Analysis of a Microwave Crossbar Mixer (1980)

A theory for analyzing microwave mixers with any number of diodes is briefly described. In this theory diodes have nonlinear conductance and nonlinear capacitance. Any linear embedding network is allowed. The theory has been utilized to analyze a crossbar mixer configuration. Some computed results are given and discussed.
Prominent Expression of β-defensins 2 and 3 in Vaginal Epithelial Cells of Healthy Fertile Women (2005)

Prominent Expression of β-defensins 2 and 3 in Vaginal Epithelial Cells of Healthy Fertile Women
Multi-omic profiles of human non-alcoholic fatty liver disease tissue highlight heterogenic phenotypes (2015)

Non-alcoholic fatty liver disease (NAFLD) is a consequence of sedentary life style and high fat diets with an estimated prevalence of about 30% in western countries. It is associated with insulin resistance, obesity, glucose intolerance and drug toxicity. Additionally, polymorphisms within, e.g., APOC3, PNPLA3, NCAN, TM6SF2 and PPP1R3B, correlate with NAFLD. Several studies have already investigated later stages of the disease. This study explores the early steatosis stage of NAFLD with the aim of identifying molecular mechanisms underlying the etiology of NAFLD. We analyzed liver biopsies and serum samples from patients with high- and low-grade steatosis (also pre-disease states) employing transcriptomics, ELISA-based serum protein analyses and metabolomics. Here, we provide a detailed description of the various related datasets produced in the course of this study. These datasets may help other researchers find new clues for the etiology of NAFLD and the mechanisms underlying its progression to more severe disease states.
Atlas of the clinical genetics of human dilated cardiomyopathy (2014)

This is to our knowledge, the first study that comprehensively investigated the genetics of DCM in a large-scale cohort and across a broad gene panel of the known DCM genes. Our results underline the high analytical quality and feasibility of Next-Generation Sequencing in clinical genetic diagnostics and provide a sound database of the genetic causes of DCM.
Silicon microdisk-based full adders for optical computing (2018)

Due to the projected saturation of Moore's law, as well as the drastically increasing trend of bandwidth with lower power consumption, silicon photonics has emerged as one of the most promising alternatives that has attracted a lasting interest due to the accessibility and maturity of ultra-compact passive and active integrated photonic components. In this Letter, we demonstrate a ripple-carry electro-optic 2-bit full adder using microdisks, which replaces the core part of an electrical full adder by optical counterparts and uses light to carry signals from one bit to the next with high bandwidth and low power consumption per bit. All control signals of the operands are applied simultaneously within each clock cycle. Thus, the severe latency issue that accumulates as the size of the full adder increases can be circumvented, allowing for an improvement in computing speed and a reduction in power consumption. This approach paves the way for future high-speed optical computing systems in the post-Moore's law era.
ChemInform Abstract: FRAGMENTATION OF BICYCLO(4.4.1)UNDECAN-11-ONES (1983)

Aus den beiden ungesättigten bicyclischen Ketonen (I) bzw. (IV) werden die gesättigten Verbindungen (IIa) bzw. (Va) erhalten, die über die Alkohole (IIb) bzw. (Vb) und die Mesylate (IIc) bzw. (Vc) zu den isomeren Hydroxymethyl-cyclodecenen (III) bzw. (VI) gespalten werden.
Replication, reconfiguration, and the Argus mail repository (1986)

The Argus Distributed Mail Repository is being implemented to gain experience with a sizable distributed application, to experiment with techniques for building distributed applications that are highly available and scalable, and to evaluate the programming language Argus when used for such applications.This note briefly describes Argus, the goals for the distributed repository, the project's status, and experience to date with the system.
Multimodal imaging of the human temporal bone: A comparison of CT and optical scanning techniques (2003)

A collaborative effort between Washington University in St. Louis and Spencer Technologies in Seattle, WA has been undertaken to create a multimodal 3D reconstruction of the human cochlea and vestibular system. The goal of this project is to improve the accuracy of in vivo CT reconstructions of implanted cochleae, and to expand the knowledge of high-resolution anatomical detail provided by orthogonal-plane optical sectioning (OPFOS). At WUSL, computed tomography (CT) images of the cochlea are used to determine the position of cochlear implant electrodes relative to target auditory neurons. The cochlear implant position is determined using pre- and post-operative CT scans. The CT volumes are cross-registered to align the semicircular canals and internal auditory canal, which have a unique configuration in 3-D space. The head of a human body donor was scanned with a clinical CT device, after which the temporal bones were removed, fixed in formalin and trimmed prior to scanning with a laboratory Micro CT scanner. Following CT, the temporal bones were sent to the OPFOS Imaging Lab at Spencer Technologies for a further analysis. 3-D reconstructions of CT and OPFOS imaging modalities were compared, and results are presented. [Work supported by NIDCD Grants R44-03623-5 and R01-00581-13.]
Autoencoding Density-Based Anomaly Detection for Signal Integrity Applications (2018)

This paper presents a machine learning-based framework for anomaly detection (AD) in signal integrity applications. The proposed approach employs autoencoders and density-based AD techniques to detect anomalies and is validated on a digital counter circuit.