gebhart/patrepeval huggingface dataset:
Stochastic theory of molecular radiative transport (1995)

The radiative transport (or radiative migration) of electronic excitation energy in a molecular ensemble is analyzed from a stochastic point of view. This approach yields results considerably more general than those of previous treatments, where successive hops are (implicitly) assumed to be uncorrelated, while they constitute in fact a Markov process. The time evolution of the fluorescence intensity emitted by the molecular ensemble, in response to excitation by an external beam of linearly polarized and essentially monochromatic light is obtained. In contrast to the previous treatments, only known parameters are required. The time evolution of the fluorescence anisotropy is also obtained for the first time.
Using a Linear Sectioned Bus And a Communication Processor to Reduce Energy Costs in Synchronous On-Chip Communication (2007)

The sectioned bus is an energy-optimal architecture for system-on-chip (SoC) communication, where we save energy by consequently switching off unused bus sections on a cycle-by-cycle basis. The communication processor is a paradigm for the control of such a bus by means of software. Synchronous communication takes place within the tiles of a SoC in the deep sub-micron technology domain. We explore design alternatives for a linear software-controlled sectioned bus while building the hardware model of a single-instruction-issue processor, and run, in simulation, a media benchmark on it. We determine the energy cost of controlling this bus, compare it with the energy gain obtained from the sectioning, and find it favorable. The control cost is only 5% of the bus transport energy, leaving us with a gain by segmentation of 81%. We demonstrate the feasibility of the control of a low-power synchronous communication system by the processor. Starting out from this case study at the low-end to medium range of network complexity, we consider the implications of growing complexity that will arise from using multiple sectioned buses on multiple-issue computers (VLIWs). We find that control of linear bus topologies of medium-level complexity is now well understood. Further work is needed at the high-end of non-linear topologies.
Modeling and Characterization of a Pull-in Free MEMS Microphone (2020)

In this study, we examine the feasibility of designing a MEMS microphone employing a levitation based electrode configuration. This electrode scheme enables capacitive MEMS sensors that could work for large bias voltages without pull-in failure. Our experiments and simulations indicate that it is possible to create robust sensors properly working at high DC voltages, which is not feasible for most of the conventional parallel plate electrode-based-microscale devices. In addition, the use of larger bias voltages will improve signal-to-noise ratios in MEMS sensors because it increases the signal relative to the noise in read-out circuits. This study presents the design, fabrication, and testing of a capacitive microphone, which is made of approximately 2 μm thick highly-doped polysilicon as a diaphragm. It has approximately 1 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> surface area and incorporates interdigitated sensing electrodes on three of its sides. Right underneath these moving electrodes, there are fixed fingers being held at the same voltage potential as the moving electrodes and separated from them with a 2 μm thick air gap. The electronic output is obtained using a charge amplifier. Measured results obtained on three different microphone chips using bias voltages up to 200 volts indicate that pull-in failure is completely avoided. The sensitivity of this initial design was measured to be 16.1 mV/Pa at 200 V bias voltage, and the bandwidth was from 100 Hz to 4.9 kHz.
Abstract LB223: Intratumoral administration of modified vaccinia Ankara expressing a tumor associated antigen and the costimulatory molecules IL-12 and 4-1BBL induces potent systemic long-term immune responses against murine tumors (2023)

Abstract In the last decade, immunotherapy has revolutionized cancer treatment. However, the lack of potent therapy-induced immune responses against solid tumors due to the immune-suppressive tumor microenvironment (TME) is still a major drawback. One approach to reprogram TME is virotherapy, which can target tumors via destruction of infected tumor cells as well as activating immune cell populations in the TME. A versatile and safe tool for virotherapy is modified vaccinia virus Ankara (MVA), which has already been approved by the FDA as a non-replicating vaccine against smallpox and monkeypox and is also in clinical trials against other infectious diseases and cancer. In the current study, we deciphered the anti-tumorigenic effect of a novel MVA vector encoding a tumor associated antigen (TAA) and the costimulatory molecules IL-12 and 4-1BBL, called MVA-TAA-4-1BBL-IL12. We could show that repetitive intratumoral (IT) injection of MVA-TAA-4-1BBL-IL12 resulted in strong tumor growth control, shrinkage and/or complete elimination of tumors and induction of tumor-specific CD8 T cell response. Furthermore, MVA-TAA-4-1BBL-IL12 treatment promoted a systemic anti-tumor immune response not only against the treated tumor but also untreated, distant tumors. Importantly, local virotherapy also resulted in the generation of tumor-specific memory response, which protected mice against local recurrence after rechallenge. As a conclusion, our findings show that MVA-TAA-4-1BBL-IL12 IT treatment induces an effective anti-tumorigenic immune response in different solid tumor models, which gives rise to long-term protection against cancer recurrence. Citation Format: Cigdem Atay Langbein, Raphael Giessel, Mahmad Ismail Housni, Kerstin Lämmermann, Barbara Bathke, André Riedl, Jürgen Hausmann, Markus Kalla, Paul Chaplin, Hubertus Hochrein, José Medina-Echeverz, Maria Hinterberger. Intratumoral administration of modified vaccinia Ankara expressing a tumor associated antigen and the costimulatory molecules IL-12 and 4-1BBL induces potent systemic long-term immune responses against murine tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB223.
Back-gated SOI technology: power-adaptive logic and non-volatile memory using identical processing (2004)

A back-gated scalable silicon-on-insulator (SOI) technology that provides a non-volatile memory, logic with adaptive power-performance trade-off and buried interconnectivity is reported. The back-gate approach has the following characteristics: (1) a logic transistor whose threshold voltage modulation allows adaptive power control of digital and analog circuits, (2) a non-volatile memory where the read-transistor scaling is decoupled from storage constraints, (3) good SOI thickness control, (4) speed degradation due to alignment tolerances lower than 16%, (5) a new analog design approach to achieve adaptive low voltage operation within digital constraints.
cAb-Rep: A Database of Curated Antibody Repertoires for Exploring Antibody Diversity and Predicting Antibody Prevalence (2019)

The diversity of B cell receptors provides a basis for recognizing numerous pathogens. Antibody repertoire sequencing has revealed relationships between B cell receptor sequences, their diversity, and their function in infection, vaccination, and disease. However, many repertoire datasets have been deposited without annotation or quality control, limiting their utility. To accelerate investigations of B cell immunoglobulin sequence repertoires and to facilitate development of algorithms for their analysis, we constructed a comprehensive public database of curated human B cell immunoglobulin sequence repertoires, cAb-Rep (https://cab-rep.c2b2.columbia.edu), which currently includes 306 immunoglobulin repertoires from 121 human donors, who were healthy, vaccinated, or had autoimmune disease. The database contains a total of 267.9 million V(D)J heavy chain and 72.9 million VJ light chain transcripts. These transcripts are full-length or near full-length, have been annotated with gene origin, antibody isotype, somatic hypermutations, and other biological characteristics, and are stored in FASTA format to facilitate their direct use by most current repertoire-analysis programs. We describe a website to search cAb-Rep for similar antibodies along with methods for analysis of the prevalence of antibodies with specific genetic signatures, for estimation of reproducibility of somatic hypermutation patterns of interest, and for delineating frequencies of somatically introduced <i>N</i>-glycosylation. cAb-Rep should be useful for investigating attributes of B cell sequence repertoires, for understanding characteristics of affinity maturation, and for identifying potential barriers to the elicitation of effective neutralizing antibodies in infection or by vaccination.
Task switching performance reveals heterogeneity amongst patients with mild cognitive impairment. (2010)

This study demonstrates that variability in performance on measures of task-switching can highlight important heterogeneity in the MCI population.
Detection ofIn VivoDynamic 3-D Motion Patterns in the Wrist Joint (2008)

We present a method for measurement dynamic in vivo carpal motion patterns. The method consists of a 4-D rotational X-ray (RX) with improved image quality and image processing for accurate detection in vivo wrist motion measurements. Dynamic 3-D imaging yields a number of volume reconstructions of the wrist at different phases of its cyclic motion. Next, the carpal reconstructions are registered to their static acquired and segmented counterpart in all phases. With this information, the relation between the applied motion and carpal kinematic behavior is acquired, i.e., the motion patterns. We investigated the precision of the image acquisition and processing and tested it on three healthy subjects. The precision of the image acquisition and image processing is in the range of submillimeters and subdegrees, respectively, which is better than existing systems and sufficient for clinical investigations. Reproducibility measurements show some more deviation ( > 1 degrees). This method was tested on four human volunteers and agrees for the greater part with previously done invasive and nondynamic measurements. In vivo motion pattern measurement with 4-D-RX imaging and processing is accurate and noninvasive. The motion patterns can reveal disorders that could not have been detected in either video fluoroscopy, computed tomography, or MRI.
Anisotropy of the electron effective mass in rutile SnO2 determined by infrared ellipsometry (2013)

Abstract Generalized infrared spectroscopic ellipsometry (GIRSE) was applied to Sb‐doped rutile SnO 2 (101) films grown by plasma‐assisted molecular beam epitaxy (PAMBE). Coupled longitudinal‐optical (LO) phonon–plasmon (LPP) modes for the two principal polarization directions of the optically anisotropic SnO 2 were identified and their frequencies were determined as a function of electron concentrations obtained by Hall effect measurements. The analysis of these modes yielded very accurate values for the plasma frequencies and finally the anisotropy of the electron effective masses as a function of carrier density. Comparison to Hall effect electron concentrations yielded a non‐parabolicity of the conduction band.
Leveraging artificial intelligence to predict ERG gene fusion status in prostate cancer (2022)

A deep learning-based model can successfully predict ERG rearrangement status in the majority of prostatic adenocarcinomas utilizing only H&E-stained digital slides. Such an artificial intelligence-based model can eliminate the need for using extra tumor tissue to perform ancillary studies in order to assess for ERG gene rearrangement in prostatic adenocarcinoma.
Novel liquid-liquid extraction and self-emulsion methods for simplified isolation of extra-virgin olive oil phenolics with emphasis on (-)-oleocanthal and its oral anti-breast cancer activity (2019)

Epidemiological and clinical studies compellingly documented the ability of Mediterranean diet rich in extra-virgin olive oil (EVOO) to reduce breast and colon cancers incidence, cardiovascular diseases, and aging cognitive functions decline. (-)-Oleocanthal (OC) and other EVOO phenolics gain progressive research attention due to their documented biological effects against cancer, inflammations, and Alzheimer's disease. There is no simple, reliable, and cost-effective isolation protocol for EVOO phenolics, which hinder their therapeutic applications. This study develops novel methods to isolate OC and other EVOO phenolics. This includes the use of ultra-freezing to eliminate most EVOO fats and the successful water capacity to efficiently extract OC and EVOO phenolics as self-emulsified nano-emulsion. Subsequent resin entrapment and size exclusion chromatography afforded individual EVOO phenolics in high purity. OC in vitro and in vivo oral anti-breast cancer (BC) activities validated its lead candidacy. Effective isolation of EVOO phenolics provided in this study will facilitate future preclinical and clinical investigations and stimulate the therapeutic development of these important bioactive natural products.
Breast Cancer Index Is a Predictive Biomarker of Treatment Benefit and Outcome from Extended Tamoxifen Therapy: Final Analysis of the Trans-aTTom Study (2022)

Novel findings demonstrate that BCI (H/I) significantly predicts benefit from extended tamoxifen in HR+ N+ patients with HER2- disease. Moreover, BCI (H/I) demonstrates significant treatment to biomarker interaction across survival outcomes.
Structural Basis of Antibody Conformation and Stability Modulation by Framework Somatic Hypermutation (2022)

Accumulation of somatic hypermutation (SHM) is the primary mechanism to enhance the binding affinity of antibodies to antigens <i>in vivo</i>. However, the structural basis of the effects of many SHMs remains elusive. Here, we integrated atomistic molecular dynamics (MD) simulation and data mining to build a high-throughput structural bioinformatics pipeline to study the effects of individual and combination SHMs on antibody conformation, flexibility, stability, and affinity. By applying this pipeline, we characterized a common mechanism of modulation of heavy-light pairing orientation by frequent SHMs at framework positions 39<sub>H</sub>, 91<sub>H</sub>, 38<sub>L</sub>, and 87<sub>L</sub> through disruption of a conserved hydrogen-bond network. Q39L<sub>H</sub> alone and in combination with light chain framework 4 (FWR4<sub>L</sub>) insertions further modulated the elbow angle between variable and constant domains of many antibodies, resulting in improved binding affinity for a subset of anti-HIV-1 antibodies. Q39L<sub>H</sub> also alleviated aggregation induced by FWR4<sub>L</sub> insertion, suggesting remote epistasis between these SHMs. Altogether, this study provides tools and insights for understanding antibody affinity maturation and for engineering functionally improved antibodies.
New evidence of a mitochondrial genetic background paradox: Impact of the J haplogroup on the A3243G mutation (2008)

Thus, our study supports the existence of mutational hotspot on mtDNA and a "haplogroup J paradox," a haplogroup that may increase the expression of mtDNA pathogenic mutations, but also be beneficial in certain environmental contexts.
Decreased expression of transmembrane TNFR2 in lung leukocytes subpopulations of patients with non-fibrotic hypersensitivity pneumonitis compared with the fibrotic disease (2020)

Hypersensitivity pneumonitis (HP) is an interstitial lung disease, characterized by lung inflammation (non-fibrotic HP) that may often progresses to fibrosis (Fibrotic HP). The tumor necrosis factor (TNF) and its receptors (TNFR1 and TNFR2) can be found as soluble (sol) and transmembrane (tm) forms, playing pro-inflammatory functions but also has been related to immune regulatory functions. Bronchioalveolar lavage from fibrotic and non-fibrotic HP patients was obtained, and immune cells were characterized by flow cytometry, whereas soluble proteins were analyzed by ELISA. Compare to fibrotic HP patients, HP patients with non-fibrotic disease have accumulation of pro-inflammatory CD3+ myeloid cells, cell subpopulations that have decreased tmTNFR2 expression, and low frequency of regulatory-T cells. Whereas solTNF, solTNFR2, and IL-8 are increased. These findings suggest that the TNF pathway may explain, at least partially, the differences between both HP clinical forms. The evaluation of the TNF family molecules may help to develop new therapeutic approaches.
Characterization of the interaction between the influenza A virus polymerase subunit PB1 and the host nuclear import factor Ran-binding protein 5 (2011)

The influenza A virus RNA polymerase is a heterotrimer that transcribes and replicates the viral genome in the cell nucleus. Newly synthesized RNA polymerase subunits must therefore be imported into the nucleus during an infection. While various models have been proposed for this process, the consensus is that the polymerase basic protein PB1 and polymerase acidic protein PA subunits form a dimer in the cytoplasm and are transported into the nucleus by the beta-importin Ran-binding protein 5 (RanBP5), with the PB2 subunit imported separately to complete the trimeric complex. In this study, we characterized the interaction of PB1 with RanBP5 further and assessed its importance for viral growth. In particular, we found that the N-terminal region of PB1 mediates its binding to RanBP5 and that basic residues in a nuclear localization signal are required for RanBP5 binding. Mutating these basic residues to alanines does not prevent PB1 forming a dimer with PA, but does reduce RanBP5 binding. RanBP5-binding mutations reduce, though do not entirely prevent, the nuclear accumulation of PB1. Furthermore, mutations affecting RanBP5 binding are incompatible with or severely attenuate viral growth, providing further support for a key role for RanBP5 in the influenza A virus life cycle.
Evaluation of Quantitative IFN-γ Response for Risk Stratification of Active Tuberculosis Suspects (2009)

Higher quantitative IFN-gamma results were associated with active tuberculosis, and added clinical value to a prediction model incorporating conventional risk factors. Although this benefit may be attenuated within highly experienced centers, the predictive accuracy of quantitative IFN-gamma levels should be evaluated in other settings.
CARAVAN: Providing Location Privacy for VANET (2005)

Abstract — In vehicular ad hoc networks (VANET), it is possible to locate and track a vehicle based on its transmissions, during communication with other vehicles or the road-side infrastructure. This type of tracking leads to threats on the location privacy of the vehicle’s user. In this paper, we study the problem of providing location privacy in VANET by allowing vehicles to prevent tracking of their broadcast communications. We first, identify the unique characteristics of VANET that must be considered when designing suitable location privacy solutions. Based on these observations, we propose a location privacy scheme called CARAVAN, and evaluate the privacy enhancement achieved under some existing standard constraints of VANET applications, and in the presence of a global adversary. I.
Evaluation of throughput employing hybrid ARQ packet combining in forward link OFCDM broadband wireless access (2003)

The paper presents the throughput performance when employing hybrid automatic repeat request packet combining, i.e., Chase combining and incremental redundancy, in forward-link orthogonal frequency and code division multiplexing (OFCDM) broadband packet wireless access achieving a peak throughput above 100 Mbps. Simulation results elucidate that the achievable throughput at the average received signal energy per symbol-to-background noise power spectrum density ratio (E/sub s//N/sub 0/) of 4 dB and 10 dB, employing incremental redundancy, is increased by approximately 50% and 70% in a 12-path exponentially decayed fading channel compared to that using Chase combining for QPSK and 16QAM data modulation, respectively. However, we show that despite the superiority of incremental redundancy to Chase combining in the achievable throughput for the respective modulation and coding schemes (MCSs), the total throughput when employing incremental redundancy associated with a near optimum MCS set in an actual adaptive modulation and coding (AMC) operation becomes almost identical to that using Chase combining in a low maximum Doppler frequency, f/sub D/, channel. Finally, we show that incremental redundancy coupled with a higher channel coding rate is still more effective than Chase combining in improving the throughput for a high f/sub D/ channel owing to its large coding gain.
Reactivity of co-ordinated ligands. Part XVIII. Cationic ruthenium(II) and osmium(II) complexes by electrophilic attack on a π-allyl ligand (1974)

Monocationic ruthenium(II) and osmium(II) complexes containing labile acetonitrile ligands have been prepared by electrophilic attack on a π-allyl ligand in M (diene)(π-allyl), species (M = Ru or OS, diene = norbornadiene or cyclo-octa-1,5-diene). The acetonitrile ligands may be replaced by Group VA chelating ligands. The allyl ligand in the monocationic species is also attacked by electrophiles to yield dicationic complexes. The stereospecific exchange of acetonitrile ligands in the cationic species is described. N.m.r. data, including a reinterpretation of those for the Ru(diene)(π-allyl)2 species, are presented and discussed.
Redox-responsive release of self-healing agent for anticorrosion (2013)

The use of self-healing (SH) materials is a promising approach to hinder corrosion. Extrinsic SH materials based on nanocapsules are good candidates because they can be embedded in coatings without impacting negatively on their structures. Conducting polymers are applied in various fields due to their high electrical conductivity, g ood thermal and environmental stabilities [1]. Polyaniline (PANI) is one of the most popular conducting polymers. It has three different oxidation states (Figure 1): the fully reduced leucoemeraldine (y=1), the fully oxidized pernigraniline (y=0), and the half-oxidized emeraldine (y=0.5). Therefore, PANI can also exhibit redox-responsive properties upon electro- or chemical stimuli based on which it has been studied for anticorrosion in metal system [2, 3]. In the present study, we proposed a class of self-healing materials structure based on PANI nanocapsules prepared via miniemulsion polymerization and studied their release behavior upon oxidation or reduction. It was found that the PANI capsules exhibited a release of self-healing agent when reduced by reducing agent. This responsive release behavior after reduction may be due to the chemical structure and morphology change which were investigated by fourier transform infrared spectroscopy (FTIR), ultraviolet–visible spectroscopy (UV-Vis) and scanning electron microscopy (SEM). These conductive nanocontainers are therefore promising for self-healing of corroded metals.