gebhart/patrepeval huggingface dataset:
cDNA Sequences Reveal mRNAs for Two Gα Signal Transducing Proteins from Larval Cilia (1991)

In planktonic larvae of the gastropod mollusk, Haliotis rufescens (red abalone), settlement behavior and subsequent metamorphosis are controlled by two convergent chemosensory pathways that report unique peptide and amino acid signals from the environment. The integration of signals from these two sensory pathways provides for variable amplification, or fine-tuning, of larval responsiveness to the inducers of settlement and metamorphosis. These pathways may be analogous to the neuronal and molecular mechanisms of facilitation and longterm potentiation characterized in other (adult) molluscan systems. Recently, the chemosensory receptors and signal transducers apparently belonging to the regulatory pathway (including a G protein and protein kinase C) have been identified in cilia purified from H. rufescens larvae. These elements retain their sequential receptor-dependent regulation in the isolated cilia in vitro. As a first step toward the molecular genetic dissection of the receptors, transducers, and the mechanisms of their control of settlement behavior and metamorphosis, we present evidence that the cilia purified from these larvae contain polyadenylated mRNA corresponding to unique signal transducers. Purification of this mRNA, enzymatic synthesis of the corresponding cDNAs, amplification by the polymerase chain reaction, cloning, and sequence analysis reveal that the ciliary mRNA includes sequences that apparently code for two G{alpha} signal transducing proteins. One of these is highly homologous to members of the Gq family, recently shown in other systems to control the activity of phospholipase C; the other is more closely related to Gi and Go. These results extend the tractability of the Haliotis system to analyses of cDNA and protein sequences of chemosensory elements from isolated cilia. This is the first time that mRNA has been purified from isolated cilia, and the corresponding cDNA synthesized and characterized.
The effect of patterning options on embedded memory cells in logic technologies at iN10 and iN7 (2017)

Static Random Access Memory (SRAM) cells are used together with logic standard cells as the benchmark to develop the process flow for new logic technologies. In order to achieve successful integration of Spin-Transfer Torque Magnetic Random Access Memory (STT-MRAM) as area efficient higher level embedded cache, it also needs to be included as a benchmark. The simple cell structure of STT-MRAM brings extra patterning challenges to achieve high density. The two memory types are compared in terms of minimum area and critical design rules in both the iN10 and iN7 node, with an extra focus on patterning options in iN7. Both the use of Self-Aligned Quadruple Patterning (SAQP) mandrel and spacer engineering, as well as multi-level via’s are explored. These patterning options result in large area gains for the STT-MRAM cell and moreover determine which cell variant is the smallest.
Author response: Three-dimensional growth of breast cancer cells potentiates the anti-tumor effects of unacylated ghrelin and AZP-531 (2020)

3D culture of breast cancer in biologically relevant ECM potentiates the growth-inhibitory effects of unacylated ghrelin and AZP-531, and clinical response may be predictable based on a MAPK gene signature.
All Wet Photoresist Strip by Solvent Aerosol Spray (2009)

The introduction of metal gates and high-k dielectrics in FEOL and porous ULK dielectrics in BEOL presents severe issues [1] and leads to the requirement of new chemistries and processes. A major challenge in cleaning is the removal of photoresist (PR) in both FEOL and BEOL. In current semiconductor device fabrication flow, the photoresist strip process in FEOL is mostly achieved by applying a sequence of plasma ashing followed by a wet-clean step with sulfuric-peroxide mixture (SPM). But in general, ashing leads to strong oxidation or etching of silicon substrate. Hence, several approaches for ashless PR strip have been reported, such as hot SPM [2] and the combination of a pre-treatment using high velocity CO2 aerosol [3].
Bump’em: an Open-Source, Bump-Emulation System for Studying Human Balance and Gait (2020)

Fall-related injury is a significant health problem on a global scale and is expected to grow with the aging population. Laboratory-based perturbation systems have the capability of simulating various modes of fall-inducing perturbations in a repeatable way. These systems enable fundamental research on human gait and balance and facilitate the development of devices to assist human balance. We present a robotic, rope-driven system capable of rendering bumps and force-fields at a person's pelvis in any direction in the transverse plane with forces up to 200 N, and a 90% rise time of as little as 44 ms, which is faster than a human's ability to sense and respond to the force. These capabilities enable experiments that require stabilizing or destabilizing subjects as they stand or walk on a treadmill. To facilitate use by researchers from all backgrounds, we designed both a configuration with simpler open-loop force control, and another with higher-performance, closed-loop force control. Both configurations are modular, and the open-loop system is made entirely from 3D-printed and catalog components. The design files and assembly instructions for both are freely available in an online repository.
Proteolytic cleavage of phospholipase C–γ1 during apoptosis in Molt–4 cells (2000)

Apoptosis is a cell suicide mechanism that requires the activation of cellular death proteases for its induction. We examined whether the progress of apoptosis involves cleavage of phospholipase C-gamma1 (PLC-gamma1), which plays a pivotal role in mitogenic signaling pathway. Pretreatment of T leukemic Molt-4 cells with PLC inhibitors such as U-73122 or ET-18-OCH(3) potentiated etoposide-induced apoptosis in these cells. PLC-gamma1 was fragmented when Molt-4 cells were treated with several apoptotic stimuli such as etoposide, ceramides, and tumor necrosis factor alpha. Cleavage of PLC-gamma1 was blocked by overexpression of Bcl-2 and by specific inhibitors of caspases such as Z-DEVD-CH(2)F and YVAD-cmk. Purified caspase-3 and caspase-7, group II caspases, cleaved PLC-gamma1 in vitro and generated a cleavage product of the same size as that observed in vivo, suggesting that PLC-gamma1 is cleaved by group II caspases in vivo. From point mutagenesis studies, Ala-Glu-Pro-Asp(770) was identified to be a cleavage site within PLC-gamma1. Epidermal growth factor receptor (EGFR) -induced tyrosine phosphorylation of PLC-gamma1 resulted in resistance to cleavage by caspase-3 in vitro. Furthermore, cleaved PLC-gamma1 could not be tyrosine-phosphorylated by EGFR in vitro. In addition, tyrosine-phosphorylated PLC-gamma1 was not significantly cleaved during etoposide-induced apoptosis in Molt-4 cells. This suggests that the growth factor-induced tyrosine phosphorylation may suppress apoptosis-induced fragmentation of PLC-gamma1. We provide evidence for the biochemical relationship between PLC-gamma1-mediated signal pathway and apoptotic signal pathway, indicating that the defect of PLC-gamma1-mediated signaling pathway can facilitate an apoptotic progression.
City of enterprise : perspectives on Auckland business history (2006)

From its earliest days, the city of Auckland thrived on business; it quickly became, and still remains, the commercial and financial capital of the country. This important book, City of Enterprise, sets Auckland's business history in the wider context of national economic growth, and includes cutting-edge studies on aspects of that history. Written by leading scholars, chapters cover the stock and station agent industry, Maori enterprise, maritime history, leading companies, the timber trade, newspapers and accounting. This handsome book is part of a larger project to reinvigorate the research, teaching and dissemination of business history. It vividly demonstrates the insights, as well as the lively interest this type of history, too long neglected, can provide.
Microelectromechanical Systems Oscillator with an 80 MHz Resonator Utilizing Torsional-to-Transverse Vibration Conversion (2015)

This paper describes the oscillation for a novel silicon microelectromechanical systems (MEMS) resonator which utilizes the torsional-to-transverse vibration conversion with quarter-wavelength torsional support beams. A fabricated 0.1-µm-gap resonator was measured with a laser-Doppler (LD) vibrometer to have a resonant frequency of 78.518 MHz and the Q-factor of 8.5 × 103 in vacuum. The electrical characteristic evaluated with a network analyzer for the resonator showed the electrical transmission (S21) and the phase shift of -42.7 dB and 12 degrees, respectively. Such a large insertion loss and small phase shift shows the need of compensation circuit to achieve the oscillation. We fabricate oscillation circuits and evaluate each component: i) In order to increase the phase shift, a C0 compensation technique is used to cancel feedthrough current in the resonator. This compensation technique has provided the increase of the phase shift, 70 degrees; ii) A voltage follower circuit is adapted to convert the resonator impedance, alleviating mismatch loss and thus providing the increase in the transmission of the signal up to -17.4 dB; iii) An inverter amplifier is used to amplify this signal. With a loop of these circuits with the resonator, the oscillation utilizing the torsional-to-transverse vibration conversion has successfully been achieved for the first time. The measured phase noise of the oscillator at 1 kHz offset from the carrier has been -101 dBc/Hz.
Phase I study of domatinostat (4SC‐202), a class I histone deacetylase inhibitor in patients with advanced hematological malignancies (2018)

Administration of domatinostat was safe, well tolerated with signs of antitumor activity. Four hundred milligram TDD in a 200 mg BID schedule (14 + 7) is the recommended phase II dose for monotherapy.
Probabilistic Programming with CuPPL (2020)

Probabilistic Programming Languages (PPLs) are a powerful tool in machine learning, allowing highly expressive generative models to be expressed succinctly. They couple complex inference algorithms, implemented by the language, with an expressive modelling language that allows a user to implement any computable function as the generative model. Such languages are usually implemented on top of existing high level programming languages and do not make use of hardware accelerators. PPLs that do make use of accelerators exist, but restrict the expressivity of the language in order to do so. In this paper, we present a language and toolchain that generates highly efficient code for both CPUs and GPUs. The language is functional in style, and the tool chain is built on top of LLVM. Our implementation uses de-limited continuations on CPU to perform inference, and custom CUDA codes on GPU. We obtain significant speed ups across a suite of PPL workloads, compared to other state of the art approaches on CPU. Furthermore, our compiler can also generate efficient code that runs on CUDA GPUs.
Exposure–Response Analyses for Upadacitinib Efficacy and Safety in the Crohn's Disease CELEST Study and Bridging to the Extended‐Release Formulation (2019)

Upadacitinib plasma concentrations, efficacy, and safety data from 216 subjects with moderate-to-severe active Crohn's disease (CD) from the 16-week induction period of the CELEST study were analyzed to characterize upadacitinib exposure-response relationships in CD. Subjects in CELEST received either placebo or upadacitinib (3, 6, 12, 24 mg b.i.d. or 24 mg q.d.). Exposure-response models were developed and utilized to simulate efficacy of induction doses of the immediate-release (IR) and extended-release (ER) formulations. Upadacitinib exposures associated with 18-24 mg b.i.d. (IR formulation) or 45-60 mg q.d. (ER formulation) are estimated to have greater efficacy during 12-week induction in patients with CD compared with lower doses. No exposure-response relations were observed with decreases in hemoglobin or lymphocytes at week 16 or with herpes zoster infections, pneumonia, or serious infections during 16 weeks of treatment in this study. These analyses informed the selection of upadacitinib induction dose for phase III studies in CD.
Search for Higgs and Z boson decays to J/ψ or Y pairs in the four-muon final state in proton-proton collisions at s=13TeV (2019)

A search for decays of the Higgs and Z boson to pairs of J/ψ or Y(nS) (n = 1, 2, 3) mesons, with their subsequent decay to μ+μ− pairs, is presented. The analysis uses data from proton-proton collisions at s=13TeV, collected with the CMS detector at the LHC in 2017 and corresponding to an integrated luminosity of 37.5fb−1. While an observation of such a decay with this sample would indicate the presence of physics beyond the standard model, no significant excess is observed. Upper limits at 95% confidence level are placed on the branching fractions of these decays. In the J/ψ pair channel, the limits are 1.8×10−3 and 2.2×10−6 for the Higgs and Z boson, respectively, while in the combined Y(nS) pair channel, the limits are 1.4×10−3 and 1.5×10−6, respectively, when the mesons from the Higgs and Z boson decay are assumed to be unpolarized. When fully longitudinal and transverse polarizations are considered the limits reduce by about 22–29% and increase by about 10–13%, respectively.
Material Design and Development of High-Ductility Composite Reinforced with Short Random Polyvinyl Alcohol Fiber (1998)

Peer Reviewed
Dielectrophoretic (DEP) separation of live/dead cells on a glass slide functionalized with interdigitated 3D silicon ring microelectrodes (2014)

This paper describes a microfluidic device which offers a dielectrophoretic solution to cell sorting via interdigitated 3D silicon (Si) electrodes on a transparent glass substrate. The Si electrodes with a self-aligned array of lateral rings were fabricated through a single mask process on an anodically bonded Si-glass wafer. The device has been characterized for separation of live/dead human colorectal carcinoma cells at select flow rates and voltages. The live cell capture and dead cell removal efficiencies both reached 90% at an AC activation of 5V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">p</sub> 450kHz applied against a flow rate up to 0.25ml/hr. The device disclosed here, with successful demonstration of continuous live/dead cell separation, offers great potential as a bioparticle sorting front-end module for a lab-on-a chip system.
Analysis of AtZDP substrate specificity (2008)

DNA bases can be modified by endogenous agents (e.g. oxidized by products of respiration and photosynthesis or methylated by gene silencing processes) as well as by environmental agents (e.g. oxidized by UV light). In the process of removing modified bases, a 3’-phosphate group is sometimes left in the resulting gap, and has to be removed since it blocks the incorporation of a new nucleotide by DNA polymerase. The aim of this thesis was the characterization of AtZDP, a plant enzyme with a DNA 3’-phosphatase activity.By homologous modeling, the existence of four domains was predicted in AtZDP, three independent zinc-finger and one DNA 3’-phosphatase domains. AtZDP was found to be localized in the nucleus by bimolecular fluorescence complementation. Western blotting analysis showed that the enzyme was ubiquitously expressed in plant tissues.AtZDP was found in a 600,000 molecular-weight protein complex by gel chromatography and glycerol gradient sedimentation centrifugation. The fractions containing AtZDP in the complex displayed 3’-DNA phosphatase activity as shown by desphosphorylation of a DNA oligonucleotide with a 3’-phosphate terminus. Also fractions of the gel chromatography corresponding to lower molecular weight showed 3’-DNA phosphatase activity, but antibodies against AtZDP did not recognize this fraction inferring that in plants, at least another protein with similar activity exists.In mammals, polynucleotide kinase, an enzyme with the same activity phosphatase activity as AtZDP, is involved in single-strand and double-strand repair pathways. To elucidate if AtZDP could be part of similar pathways, different double strand and single-strand oligonucleotides with 3’-phosphate termini were separately incubated with AtZDP. All substrates were dephosphorylated by AtZDP, assuming that this enzyme could potentially be involved in double-strand DNA repair. A double-strand oligonucleotide containing a one-bp gap with a 3’-phosphate terminus was repaired by a leaf protein extract. The activities of a 3’-DNA phosphatase, a flap 5’ to 3’ endonuclease-like, a DNA polymerase and a DNA ligase were observed. The presence of these enzymes revealed that these damages are in plants predominantly repaired by long-patch base excision repair.
The Adsorption of Major Tear Film Lipids In Vitro to Various Silicone Hydrogels over Time (2008)

In vitro lipid adsorption varied greatly depending on the lens material for both polar and nonpolar lipids. Overall, there was less in vitro adsorption of lipid to the lotrafilcon A and B polymers than for any of the other silicone hydrogel polymers tested. The quantity of lipid adsorption by lotrafilcon polymers was similar to "conventional" hydrogel lenses.
Pattern environment impact on wafer of metal layers with high-NA process on advanced node (2014)

In the High NA process, pattern environment will become very aggressive because of scattering effect. Especially on metal layers, maybe it will cause pattern bridge when the pattern density is varied. We need to find out the root cause and have a good solution to minimize the wafer CD difference that comes from environmental effect (pattern density). In this paper, we analyze the root cause by checking the pattern density influence on mask CD and wafer printing CD. We design different pattern density layout to measure the mask CD error, use AIMS (Aerial Image Measurement System) to measure the aerial image CD and print wafer to check the real result. Then, we try to add some assistant feature (pattern density balance) and use simulation tool to simulate whether this method can have improvement.
Characterization of the Aquaporin-9 Inhibitor RG100204 In Vitro and in db/db Mice (2022)

Aquaporin-9 (AQP9) is a facilitator of glycerol and other small neutral solute transmembrane diffusion. Identification of specific inhibitors for aquaporin family proteins has been difficult, due to high sequence similarity between the 13 human isoforms, and due to the limited channel surface areas that permit inhibitor binding. The few AQP9 inhibitor molecules described to date were not suitable for in vivo experiments. We now describe the characterization of a new small molecule AQP9 inhibitor, RG100204 in cell-based calcein-quenching assays, and by stopped-flow light-scattering recordings of AQP9 permeability in proteoliposomes. Moreover, we investigated the effects of RG100204 on glycerol metabolism in mice. In cell-based assays, RG100204 blocked AQP9 water permeability and glycerol permeability with similar, high potency (~5 × 10<sup>-8</sup> M). AQP9 channel blocking by RG100204 was confirmed in proteoliposomes. After oral gavage of <i>db/db</i> mice with RG100204, a dose-dependent elevation of plasma glycerol was observed. A blood glucose-lowering effect was not statistically significant. These experiments establish RG100204 as a direct blocker of the AQP9 channel, and suggest its use as an experimental tool for in vivo experiments on AQP9 function.
Definition of cis-Regulatory Elements of the Mouse Interleukin-5 Gene Promoter (1995)

We have previously reported that the promoter region of the mouse interleukin-5 (IL-5) gene, extending from a nucleotide position about -1,200 to +33 relative to the transcription initiation site, can mediate transcriptional stimulation by phorbol 12-myristate 13-acetate and dibutyryl cAMP (Bt2cAMP) in mouse thymoma EL-4 cells. Here, we describe identification of four cis-regulatory elements necessary for full activity of the IL-5 promoter, using deletion and mutation analyses. We designated these elements as IL-5A (-948 approximately -933), IL-5P (-117 approximately -92), IL-5C (-74 approximately -56), and IL-5CLE0 (-55 approximately -38). We found that IL-5P bears homology to the binding site for the nuclear factor of activated T cells (NF-AT) and interacted with protein factors in nuclear extracts prepared from EL-4 cells stimulated with phorbol 12-myristate 13-acetate and Bt2cAMP (designated NFIL-5P). NFIL-5P complex was inhibited in the presence of an excess NF-AT and AP1 oligonucleotides and super-shifted by antisera raised against NF-ATp, c-Fos, and c-Jun. It thus seems likely that an NF-AT-related factor is involved in the regulation of IL-5 gene transcription.
Bandwidth-Scalable Digital Predistortion of Active Phased Array Using Transfer Learning Neural Network (2023)

This paper proposes a transfer learning neural network (TLNN) approach for digital predistortion (DPD) of mm-Wave active phased arrays (APA) operated under variable signal bandwidth regimes. Compared with the conventional artificial neural network (ANN) method, the proposed approach can achieve similar linearization performance with much lower computational complexity by transferring part of a trained model from one bandwidth to another bandwidth. In the recently introduced 5G, the increased signal bandwidth triggers considerable memory effects in the APA. Moreover, dealing with different signal bandwidths typically requires a time-consuming recalculation of the predistorter parameters. In this paper, the authors propose to have those challenges solved by using a DPD model based on the transfer learning method. The proposed approach was validated with over-the-air (OTA) measurements on an APA excited with signals of varying bandwidth, namely from 20 MHz to 100 MHz. Experimental results show a significant reduction in the training time while ensuring good linearization performance. With the applied TLNN DPD, an 8.5 dB improvement of adjacent channel leakage ratio (ACLR) and 8.6 % points improvement of error vector magnitude (EVM) is achieved. Under the variable bandwidth regime, the complexity of the DPD model in terms of the number of multiplications is reduced from 199168 to 160. The proposed TLNN DPD proved to be robust concerning variation in the bandwidth of the APA excitation signal.
Zero-field quantum tunneling relaxation of the molecular spin in Fe 8 observed by 57 Fe Mössbauer spectrometry (2014)

International audience
Work-in-Progress: SuperNAS: Fast Multi-Objective SuperNet Architecture Search for Semantic Segmentation (2022)

We present SuperNAS, a fast multi-objective neural architecture search framework for semantic segmentation. SuperNAS subsamples the structure and pre-trained parameters of DeepLabV3+, without fine-tuning, dramatically reducing training time during search. To further reduce candidate evaluation time, we use a subset of the validation dataset during search. Only the final, Pareto-dominant, candidates are ultimately fine-tuned using the complete training set. We evaluate SuperNAS by searching for models that effectively trade accuracy and computational cost on the PASCAL VOC 2012 dataset. SuperNAS finds competitive designs quickly, e.g., taking just 0.5 GPU days to discover a DeepLabV3+ variant that reduces FLOPs and parameters by 10% and 20% respectively, for less than 3% increased error.
Postharvest interventions, key for improvement of food systems : Exploring the impact of postharvest interventions on increasing food availability, stability and income generation in developing economies (2020)

cities & migration" (KB-35-002-001 / 2282700540). The aim is to develop a tool to assess