gebhart/patrepeval huggingface dataset:
562. Modification of TCR Specificity by TALEN and CRISPR (2015)

Adoptive T-cell transfer of T-cells with transgenic high avidity T-cell receptors (TCR) holds a lot of promise as therapeutic approach, however comprising certain challenges. Endogenous and transferred TCR-chains compete for surface expression and may pair inappropriately, potentially leading to autoimmunity. Designer nucleases like transcription activator-like effector nucleases (TALEN) and RNA-guided nucleases of the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated (Cas) system introduce specific DNA double strand breaks (DSB) at their target sites. This ability can be exploited for targeted genome editing. DSB repair through non-homologous end joining (NHEJ) can result in permanent gene knockout. Alternatively, if a homology-containing donor template is provided, transgenes can be inserted into the specific target locus by homology directed repair (HDR). In order to disrupt endogenous TCR expression, we assembled seven TALEN monomers and two guide RNAs targeting the constant regions of the TCR α-chain (TRAC) and the TCR β-chain (TRBC1 and TRBC2), respectively. Here we show the specific DSB induction by TALEN and CRISPR-Cas nucleases at their target sites, examined in K562 and T-cells using Cel1-assay and deep sequencing. Compared to nucleofection of TALEN-expressing plasmids, electroporation of mRNA considerably improved TCR knockout efficiency in primary T-cells. Using TRAC-TALEN and TRBC-TALEN mRNA, surface CD3 expression was successfully eliminated in about 75% and 60% of T-cells, respectively. The nuclease specificity was examined by identifying integrase-deficient lentiviral vector (IDLV)-marked DSB using LAM-PCR and deep sequencing. Although clustered IDLV integration sites were detected at the TALEN and CRISPR target sites, we did not detect any off-target activity, indicating high specificity. Additionally, K562 cells were nucleofected with TALEN-expressing plasmids and a donor template containing a GFP expression cassette flanked by 800bp homologous sequences to the TRAC locus. Thereby we were able to verify targeted gene addition through HDR of TALEN-mediated DSB in about 10% of treated cells. TALEN and CRISPR that show high efficiency and specificity to their target sequence will be used for generating T-cells with high avidity TCR.
Co^2+:YSGG saturable absorber Q switch for infrared erbium lasers (1995)

Passive Q switching of Er:glass (1.53 microm) with a new, robust, solid-state saturable absorber, Co(2+):Y(3)Sc(2)Ga(3)O(12), has been demonstrated. Q-switched pulses of 20 ns and 4 mJ of energy were obtained. An absorption cross section of 5 x 10(-20) cm(2) was measured. Preliminary results for a Co(2+):Y(3)Al(5)O(12) saturable absorber Q switch are also discussed.
The Challenge for Antibacterial Drugs Against Multidrug-Resistant Bacteria: Antibacterial Drugs without Causing Resistance (2019)

抗菌薬は病原菌による感染症の治療になくてはならない薬剤であるが，各抗菌薬に対する多剤耐性細菌の出現に加え，近年，腸内細菌叢（マイクロビオーム）に及ぼす2次的な健康被害（免疫疾患など）が報告されている．これらの欠点を克服した次世代型抗菌薬の一つとして，病原菌の情報伝達（two-component signal transduction: TCS）を標的にしたヒスチジンキナーゼ阻害剤の開発が期待されている．本稿では，ヒスチジンキナーゼ阻害剤の開発の現状と重要性を解説する．
Wisent: Robust downstream communication and storage for computational RFIDs (2016)

Computational RFID (CRFID) devices are emerging platforms that can enable perennial computation and sensing by eliminating the need for batteries. Although much research has been devoted to improving upstream (CRFID to RFID reader) communication rates, the opposite direction has so far been neglected, presumably due to the difficulty of guaranteeing fast and error-free transfer amidst frequent power interruptions of CRFID. With growing interest in the market where CRFIDs are forever-embedded in many structures, it is necessary for this void to be filled. Therefore, we propose Wisent — a robust downstream communication protocol for CRFIDs that operates on top of the legacy UHF RFID communication protocol: EPC C1G2. The novelty of Wisent is its ability to adaptively change the frame length sent by the reader, based on the length throttling mechanism, to minimize the transfer times at varying channel conditions. We present an implementation of Wisent for the WISP 5 and an off-the-shelf RFID reader. Our experiments show that Wisent allows transfer up to 16 times faster than a baseline, non-adaptive shortest frame case, i.e. single word length, at sub-meter distance. As a case study, we show how Wisent enables wireless CRFID reprogramming, demonstrating the world's first wirelessly reprogrammable (software defined) CRFID.
Wearable Games - An Approach for Defining Design Principles (2006)

This paper describes the efforts on designing games for wearable computing technology taken by the 23 students of the project PEnG Physical Environment Games. Creating wearable game concepts we are faced with a lack of good design principles and therefore found out that some of our concepts are not very playable. Finding out where our concepts failed will result in knowledge about what rules a good design principle for wearable games must follow.
Targeting Therapeutic Liabilities Engendered by <i>PIK3R1</i> Mutations for Cancer Treatment (2016)

The regulatory subunit of PI3K, p85α (encoded by PIK3R1), binds, stabilizes and inhibits the PI3K p110 catalytic subunit. Functional characterization of PIK3R1 mutations has identified not only hypomorphs with reduced inhibition of p110, but also hypomorphs and dominant negative mutants that disrupt a novel regulatory role of p85α on PTEN or neomorphs that activate unexpected signaling pathways. The diverse phenotypic spectrum of these PIK3R1 driver mutations underscores the need for different treatment strategies targeting tumors harboring these mutations. This article describes the functional consequences of the spectrum of PIK3R1 driver mutations and therapeutic liabilities they may engender.
Modeling Silicon Photonics in Distributed Computing Systems: from the Device to the Rack (2014)

SiP interconnects are envisioned for large scale distributed computing platforms. In such applications, optical systems involving millions of devices have to be modeled. We review key model transformation methods that allow scalable modeling.
A Comparative Assessment of Two Techniques for Modal Identification From Power System Measurements (2008)

Power system oscillatory behavior can be analyzed in terms of modes, expressed as exponentially modulated sinusoids, exhibited in signals measured on the system. These signals are driven by the behavior of a large, nonlinear, time-variant system. In this paper, two modal identification methods are examined comparatively: Prony analysis and a method based on the Hilbert transform. Considerable structural differences exist between the two methods. Prony analysis yields modes which are directly expressed as exponentially modulated sinusoids, whereas the Hilbert method provides a more general solution. Synthetic and measured signals are used in the comparison. Some general conclusions are drawn from the analysis of several signals, including two sets of measured field data.
Threshold Current Reduction and Output Power Enhancement with Magnetic Field in Sub-Monolayer InAs Quantum Dot VCSELs (2007)

The characteristics of a InAs/GaAs self-organized quantum dot (QD) vertical cavity surface-emitting laser (VCSEL) with both non-magnetic and ferromagnetic (FM) contacts under an externally-applied magnetic field in the Faraday geometry is investigated. Considerable enhancement in output light intensity and threshold current reduction when the magnetic field is in the out-of-plane direction is observed. In contrast, little or no change is observed for an in-plane magnetic field.
Discovery and in Vivo Evaluation of Macrocyclic Mcl-1 Inhibitors Featuring an α-Hydroxy Phenylacetic Acid Pharmacophore or Bioisostere (2019)

Overexpression of the antiapoptotic protein Mcl-1 provides a survival advantage to some cancer cells, making inhibition of this protein an attractive therapeutic target for the treatment of certain types of tumors. Herein, we report our efforts toward the identification of a novel series of macrocyclic Mcl-1 inhibitors featuring an α-hydroxy phenylacetic acid pharmacophore or bioisostere. This work led to the discovery of 1, a potent Mcl-1 inhibitor (IC50 = 19 nM in an OPM-2 cell viability assay) with good pharmacokinetic properties and excellent in vivo efficacy in an OPM-2 multiple myeloma xenograft model.
Electroabsorption spectroscopy on tris-(8-hydroxyquinoline) aluminum-based light emitting diodes (1999)

We determined the electric-field distribution in organic light emitting diode LED structures fabricated with 4,4′-bis [N-(1-naphthyl)-N-phenylamino]-biphenyl (α-NPD) as hole-transport material and tris-(8-hydroxyquinoline) aluminum (Alq) as electron-transport and emissive material. The electric-field distribution was obtained from an investigation of the linear and the nonlinear Stark effect of the materials when employed in organic LEDs using electroabsorption spectroscopy. We measured the electric-field distribution as a function of the applied voltage in the forward and in the reverse direction. Whilst the average electric fields in the α-NPD and the Alq layers are equal in the reverse direction, the field in the Alq layer is considerably larger than that in the α-NPD layer in the forward direction, and the factor by which these fields differ changes with increasing voltage, in particular in the vicinity of the turn-on voltage. We discuss the electric-field distribution in terms of the charge injection and charge transport in devices as well as the possibility of charge accumulation at the α-NPD/Alq interface.
Fibre-optic measurement of strain and shape on a helicopter rotor blade during a ground run: 1. Measurement of strain (2022)

Abstract Optical fibre strain and shape measurement sensors were deployed on a 5-m long rotor blade during a full-speed (rotation rate 6.6 Hz) helicopter ground run, with real-time data wirelessly streamed from rotor hub-mounted sensor interrogators. In Part 1 of a 2-part paper series, the strain sensing capabilities of the two optical fibre-based sensing techniques, optical fibre Bragg grating (FBG) and fibre segment interferometry (FSI), are compared, while Part 2 (Kissinger et al 2022 Smart Mater. Struct. accepted) specifically investigates the blade shape measurement based on the FSI approach. In part 1, the rotor hub-mounted instrumentation is described, and data on the dynamics of the blade obtained from a sequence of controlled pilot inputs are analysed both in the time and spectral domains. It is shown that this can provide insights into the aeroelastic properties of the blade. Noise standard deviations of 0.2 n <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:mi>ϵ</mml:mi> </mml:math> / <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:msqrt> <mml:mtext>Hz</mml:mtext> </mml:msqrt> </mml:math> and 30 n <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:mi>ϵ</mml:mi> </mml:math> / <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:msqrt> <mml:mtext>Hz</mml:mtext> </mml:msqrt> </mml:math> for the FSI and FBG-based sensing approaches, respectively, were observed over a strain range of 3500 µϵ .
Patient‐reported outcomes in a phase 2 study comparing atezolizumab alone or with bevacizumab vs sunitinib in previously untreated metastatic renal cell carcinoma (2020)

PROs suggested that atezolizumab alone or with bevacizumab maintained daily function compared with sunitinib. Notably, symptoms were least severe with atezolizumab alone vs sunitinib (IMmotion150; ClinicalTrials.gov Identifier: NCT01984242).
Impact of contralateral and ipsilateral reference tissue selection on self-referencing differential spectroscopy for breast cancer detection (2011)

We previously developed a self-referencing differential spectroscopic (SRDS) method to detect lesions by identifying a spectroscopic biomarker of breast cancer, i.e., the specific tumor component (STC). The SRDS method is based on the assumption of the exclusive presence of this spectroscopic biomaker in malignant disease. Although clinical results using this method have already been published, the dependence of the STC spectra on the choice of reference tissue has not yet been addressed. In this study, we explore the impact of the selection of the reference region size and location on the STC spectrum in 10 subjects with malignant breast tumors. Referencing from both contralateral and ipsilateral sides was performed. Regardless of the referencing, we are able to obtain consistent high contrast images of malignant lesions using the STC with less than 13% deviation. These results suggest that the STC measurements are independent of any type, location, and amount of normal breast tissue used for referencing. This confirms the initial assumption of the SRDS analysis, that there are specific tumor components in cancer that do not exist in normal tissue. This also indicates that bilateral measurements are not required for lesion identification using the STC method.
Gastroenterologist perceptions of faecal microbiota transplantation (2015)

AIM: To explore gastroenterologist perceptions towards and experience with faecal microbiota transplantation(FMT).METHODS: A questionnaire survey consisting of 17 questions was created to assess gastroenterologists’ attitude towards and experience with FMT. This was anonymously distributed in hard copy format amongst attendees at gastroenterology meetings in Australia between October 2013 and April 2014. Basic descriptive statistical analyses were performed.RESULTS: Fifty-two clinicians participated. Twenty one percent had previously referred patients for FMT,8% more than once. Ninety percent would refer patients with Clostridium difficile infection(CDI) for FMT if easily available,37% for ulcerative colitis,13% for Crohn’s disease and 6% for irritable bowel syndrome. Six percent would not refer any indication,including recurrent CDI. Eighty-six percent would enroll patients in FMT clinical trials. Thirty-seven percent considered the optimal mode of FMT administration transcolonoscopic,17% nasoduodenal,13% enema and 8% oral capsule. The greatest concerns regarding FMT were: 42% lack of evidence,12% infection risk,10% non infectious adverse effects/lack of safety data,10% aesthetic,10% lack of efficacy,4% disease exacerbation,and 2% inappropriate use; 6% had no concerns. Seventy seven percent believed there is a lack of accessibility while 52% had an interest in learning how to provide FMT. Only 6% offered FMT at their institution.CONCLUSION: Despite general enthusiasm,most gastroenterologists have limited experience with,or access to,FMT. The greatest concerns were lack of supportive evidence and safety issues. However a significant proportion would refer indications other than CDI for FMT despite insufficient evidence. These data provide guidance on where education and training are required.
Three-Dimensional Reconstruction of Porous LSCF Cathodes (2007)

In this initial study the electrochemically active region of a (LSCF) cathode was reconstructed in three dimensions using a focused ion beam/scanning electron microscope. The reconstructed volume totaled from the free air surface to the dense yttria-stabilized zirconia electrolyte interface. Various microstructural properties were measured, including overall porosity, closed porosity, graded porosity, surface area, tortuosity, triple-phase boundary length, and pore size. Electrochemical impedance spectroscopy data was correlated to microstructure.
Determination of Gentamicin Released from Orthopedic Carrier System by a Novel HPLC Method (2011)

A new, fast high-performance liquid chromatograpic-UV method has been developed and validated for quantitative analysis of gentamicin carrier samples drawn in drug release studies. The samples of the calibration curve were prepared in physiological salt solution, which were applied as dissolution medium for the drugs. The calibration curve is in the range of 1-100 µg/mL. The mobile phase consisted of methanol-water-acetate buffer (0.02 M ammonium acetate solution, adjusted with cc. ammonia to pH = 9), a reverse phase, Zorbax Rx-C-18 2.1 × 150 mm, 5 µm column has been used. Validation procedure of this newly developed method is carried out. Linearity, specificity, intra- and inter-day precision and accuracy, robustness, limits of detection, and quantitation are investigated.
Multi-function reconfigurable microwave component based on a switchable FET circuit (2013)

A three-port multi-function reconfigurable microwave component based on a switchable FET circuit is proposed and demonstrated. The component consists of the interconnection of three common-gate anti-parallel FET circuits. It can be reconfigured by FET biasing control voltages to provide different microwave functions, including attenuation, isolation, M-pole N-Throw switching, power combination, and power division. The proposed concept can be generalized to an N-port network, allowing very reconfigurable for software defined radio (SDR) wireless communication systems.
Influence of Aerosol Delivered BCG Vaccination on Immunological and Disease Parameters Following SARS-CoV-2 Challenge in Rhesus Macaques (2022)

The tuberculosis vaccine, Bacille Calmette-Guerin (BCG), also affords protection against non-tuberculous diseases attributable to heterologous immune mechanisms such as trained innate immunity, activation of non-conventional T-cells, and cross-reactive adaptive immunity. Aerosol vaccine delivery can target immune responses toward the primary site of infection for a respiratory pathogen. Therefore, we hypothesised that aerosol delivery of BCG would enhance cross-protective action against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection and be a deployable intervention against coronavirus disease 2019 (COVID-19). Immune parameters were monitored in vaccinated and unvaccinated rhesus macaques for 28 days following aerosol BCG vaccination. High-dose SARS-CoV-2 challenge was applied by intranasal and intrabronchial instillation and animals culled 6-8 days later for assessment of viral, disease, and immunological parameters. Mycobacteria-specific cell-mediated immune responses were detected following aerosol BCG vaccination, but SARS-CoV-2-specific cellular- and antibody-mediated immunity was only measured following challenge. Early secretion of cytokine and chemokine markers associated with the innate cellular and adaptive antiviral immune response was detected following SARS-CoV-2 challenge in vaccinated animals, at concentrations that exceeded titres measured in unvaccinated macaques. Classical CD14+ monocytes and Vδ2 γδ T-cells quantified by whole-blood immunophenotyping increased rapidly in vaccinated animals following SARS-CoV-2 challenge, indicating a priming of innate immune cells and non-conventional T-cell populations. However, viral RNA quantified in nasal and pharyngeal swabs, bronchoalveolar lavage (BAL), and tissue samples collected at necropsy was equivalent in vaccinated and unvaccinated animals, and in-life CT imaging and histopathology scoring applied to pulmonary tissue sections indicated that the disease induced by SARS-CoV-2 challenge was comparable between vaccinated and unvaccinated groups. Hence, aerosol BCG vaccination did not induce, or enhance the induction of, SARS-CoV-2 cross-reactive adaptive cellular or humoral immunity, although an influence of BCG vaccination on the subsequent immune response to SARS-CoV-2 challenge was apparent in immune signatures indicative of trained innate immune mechanisms and primed unconventional T-cell populations. Nevertheless, aerosol BCG vaccination did not enhance the initial clearance of virus, nor reduce the occurrence of early disease pathology after high dose SARS-CoV-2 challenge. However, the heterologous immune mechanisms primed by BCG vaccination could contribute to the moderation of COVID-19 disease severity in more susceptible species following natural infection.
Creativity support for computational literature (2009)

The creativity support community has a long history of providing valuable tools to artists and designers. Similarly, creative digital media practice has proven a valuable pedagogical strategy for teaching core computational ideas. Neither strain of research has focused on the domain of literary art however, instead targeting visual, and aural media almost exclusively.
To address this situation, this thesis presents a software toolkit created specifically to support creativity in computational literature. Two primary hypotheses direct the bulk of the research presented: first, that it is possible to implement effective creativity support tools for literary art given current resource constraints; and second, that such tools, in addition to facilitating new forms of literary creativity, provide unique opportunities for computer science education.
Designed both for practicing artists and for pedagogy, the research presented directly addresses impediments to participation in the field for a diverse range of users and provides an end-to-end solution for courses attempting to engage the creative faculties of computer science students, and to introduce a wider demographic—from writers, to digital artists, to media and literary theorists—to procedural literacy and computational thinking.
The tools and strategies presented have been implemented, deployed, and iteratively refined in real-world contexts over the past three years. In addition to their use in large-scale projects by contemporary artists, they have provided effective support for multiple iterations of 'Programming for Digital Art & Literature', a successful inter-disciplinary computer science course taught by the author. 
Taken together, this thesis provides a novel set of tools for a new domain, and demonstrates their real-world efficacy in providing both creativity and pedagogical support for a diverse and emerging population of users.
Base‐catalyzed derivatization methodology for FA analysis. Application to milk fat and celery seed lipid TAG (2002)

In this paper, an alternative base-catalyzed methodology for the facile derivatization in mild conditions of lipid TAG prior to FA analysis is proposed. Reagents were prepared by proton exchange between potassium tert-butoxide and either ethanol, n-propanol, n-butanol, or 2-methoxyethanol and used for the synthesis, at 40 degrees C for 15 min, of the corresponding derivatives, which were directly analyzed by GC. This methodology can be used on a routine basis and has been applied to standard and complex natural lipid samples. Tripalmitin was used to determine optimal reaction conditions; and bovine milk fat, containing C4 to C22 acids, and celery (Apium graveolens) seed oil, characterized by a high level of petroselinic acid, were comparatively analyzed as their ethyl, n-propyl, n-butyl, and 2-methoxyethyl esters.