gebhart/patrepeval huggingface dataset:
Towards Better Confidence Estimation for Neural Models (2019)

In this work we focus on confidence modeling for neural network based text classification and sequence to sequence models in the context of Natural Language Understanding (NLU) tasks. For most applications, the confidence of a neural network model in it's output is computed as a function of the posterior probability, determined via a softmax layer. In this work, we show that such scores can be poorly calibrated [1]. We propose new ensemble and gradient based features that predict model uncertainty and confidence. We evaluate the impact of these features through a gradient boosted decision tree (GBDT) framework to produce calibrated confidence scores. We demonstrate that the performance of our proposed approach surpasses the baseline across multiple tasks. Moreover, we show that this method produces confidence scores which are better suited for Out-Of-Distribution(OOD) classification when compared to the baseline.
Volumetric assessment of mediastinal lymphoma masses in Hodgkin lymphoma (2019)

The large mediastinal mass (LMM) at initial staging represents a risk factor in Hodgkin lymphoma (HL) and is measured by X-ray. Depending on location of the LMM, different results can occur regardless of the initial lymphoma volume. To assess this risk factor more accurately, we evaluated the method of volumetry in 77 patients of HD13/14 study of the German Hodgkin Study Group. Furthermore, volume calculations based on three or only one diameter, were performed to simplify volume assessment. Inter-rater reliability was good for all methods. The 3-diameter measurement produced larger volumes than volumetric assessment with an intraclass correlation coefficient (ICC) of 0.93, which could be improved to 0.95 by multiplying volumes with a correction factor of 0.86. The 1-dimensional measurement strongly overestimated the volume with an ICC of 0.7. In conclusion, the simplified volume estimation based on 3 largest diameters provides a reliable concept for the staging of HL patients.
Stress Pathway Activation Induces Phosphorylation of Retinoid X Receptor (2000)

Cellular stresses inhibit retinoid signaling, but the molecular basis for this phenomenon has not been revealed. Here, we present evidence that retinoid X receptor (RXR) is a substrate for both mitogen-activated protein kinase kinase-4 (MKK4/SEK1) and its downstream mediator c-Jun N-terminal kinase (JNK). MKK4/SEK1 and JNK recognized distinct features on RXR in the DE and AB regions, respectively. Phosphorylation by MKK4/SEK1 had profound effects on the biochemical properties of RXR, inhibiting the expression of genes activated by RXR-retinoic acid receptor complexes. Tyr-249 in the RXR DE region was required for the inhibitory effect of MKK4/SEK1. These effects were significantly reduced in MKK4/SEK1-null cells, indicating that MKK4/SEK1 is required for the suppression of retinoid signaling by stress. Findings presented here demonstrate that MKK4/SEK1 can directly modulate transcription by phosphorylating RXR, a novel MKK4/SEK1 substrate.
Cloning and Characterization of a Hybridoma Secreting a 4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK)-Specific Monoclonal Antibody and Recombinant F(ab) (2013)

Smokeless tobacco products have been associated with increased risks of oro-pharyngeal cancers, due in part to the presence of tobacco-specific nitrosamines (TSNAs) such as 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK). These potent carcinogens are formed during tobacco curing and as a result of direct nitrosation reactions that occur in the oral cavity. In the current work we describe the isolation and characterization of a hybridoma secreting a high-affinity, NNK-specific monoclonal antibody. A structurally-related benzoyl derivative was synthesized to facilitate coupling to NNK-carrier proteins, which were characterized for the presence of the N-nitroso group using the Griess reaction, and used to immunize BALB/c mice. Splenocytes from mice bearing NNK-specific antibodies were used to create hybridomas. Out of four, one was selected for subcloning and characterization. Approximately 99% of the monoclonal antibodies from this clone were competitively displaced from plate-bound NNKB conjugates in the presence of free NNK. The affinity of the monoclonal antibody to the NNKB conjugates was Kd = 2.93 nM as determined by surface plasmon resonance. Free nicotine was a poor competitor for the NNKB binding site. The heavy and light chain antibody F(ab) fragments were cloned, sequenced and inserted in tandem into an expression vector, with an FMDV Furin 2A cleavage site between them. Expression in HEK 293 cells revealed a functional F(ab) with similar binding features to that of the parent hybridoma. This study lays the groundwork for synthesizing transgenic tobacco that expresses carcinogen-sequestration properties, thereby rendering it less harmful to consumers.
Autoantibodies to glutamic acid decarboxylase and phenotypic features associated with early insulin treatment in individuals with adult‐onset diabetes mellitus (1998)

We investigated the association of serum antibodies to glutamic acid decarboxylase (GADab) with early start of insulin treatment (≤ 1 year from diagnosis, or ≤ 2 years from diagnosis) using data from a representative sample of 374 adult-onset insulin-treated individuals from the Tasmanian Diabetes Register. Furthermore, we examined whether this association was stronger than the phenotypic characteristics (age at diagnosis, sex, family history of diabetes, level of obesity, duration of diabetes) often used for diabetes classification. In this cohort, 35.9 % of males and 38.5 % of females were GADab positive. Within the first year from diagnosis, 78.4 % of GADab positive people compared to 44.0 % of GADab negative people (p < 0.001) had started insulin treatment. Univariate associations with insulin treatment ≤ 1 year from diagnosis included GADab positivity, no family history of diabetes, lower BMI for men, and GADab positivity and lower BMI for women. In multivariate models, significant associations with insulin treatment ≤ 1 year from diagnosis included a family history of diabetes (OR = 0.47, 95 % CI = 0.23–0.95) and GADab positivity (OR = 2.19, 95 % CI = 1.01–4.73) for men, but only GADab positivity (OR = 7.53, 95 % CI = 3.09–18.30) for women. Age at diagnosis was not associated with insulin treatment ≤ 1 year or ≤ 2 years from diagnosis for either sex. These findings indicate that a positive GADab test result is strongly associated with start of insulin treatment within 1 or 2 years from diagnosis, more so than characteristics such as level of obesity and age at diagnosis. © 1998 John Wiley & Sons, Ltd.
Characterization of the mid-IR image quality at Gemini South (2010)

To help the prospective observer take full advantage of the mid-IR capability of Gemini South, we characterize a key aspect of the mid-IR performance of the 8-meter telescope at Gemini-S, namely, the appearance and stability of its delivered mid-IR image profiles, with the goal of demonstrating that it can be used with a level of precision not used before. About 2000 images obtained with T-ReCS (a facility mid-IR camera at Gemini-S) between late 2003 and early 2009 were used for our image quality analysis. All targets are flux standards and recorded at one or more of the four bands Si-2 (8.74 &mu;m), N (10.36 &mu;m), Si-5 (11.66 &mu;m), and Qa (18.3 &mu;m). A non-linear least squares fitting of three profile models (Lorentzian, Gaussian, and Moffat) was performed on each image, and key parameters such as FWHM, ellipticity, position angle and Strehl-ratio were measured from the fitted profile. We find that the long-time-scale image quality is quite stable in terms of profile width or ellipticity, though short-time-scale variation is evident. We also examined the correlation between image quality and many ambient parameters and confirmed the interdependence between the image quality in the Qa band and the ambient humidity. The ellipticity of the profile was analyzed statistically as well. The average profiles for different filters can be used as important references in the future when a high-quality profile reference is not available during an observation.
Enantioselective Total Synthesis of (−)‐Euxanmodin B: An Axially Chiral Natural Product with an Anthraquinone–Xanthone Composite Structure (2011)

The first total synthesis of (−)-euxanmodin B is described. An axially chiral, enantiomerically pure biphenyl, available by enzymatic desymmetrization of σ-symmetric biaryl diacetate, was used as the key chiral biaryl building block. Two annulation reactions allowed the construction of the xanthone–anthraquinone composite structure with full stereochemical control. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
A Tumor of the Uterine Cervix with a Complex Histology in a Peutz–Jeghers Syndrome Patient with Genomic Deletion of the STK11 Exon 1 Region (2014)

Patients with Peutz-Jeghers syndrome (PJS) have a risk of complicating malignant tumors, including cancer of the uterine cervix. Mutations in the STK11 gene have been identified as being responsible for PJS. However, the genotype-phenotype correlation in PJS is poorly understood, especially with respect to malignant tumors. Here, we report a detailed analysis of a case of a cervical tumor in a PJS patient showing a large genomic deletion in exon 1 of STK11 without human papillomavirus infection. Histological examination revealed a complex histology consisting of three components: lobular endocervical gland hyperplasia (LEGH), minimal deviation adenocarcinoma (MDA) and mucinous adenocarcinoma. Immunohistochemistry for STK11 was positive in the LEGH and MDA components, while that of the mucinous adenocarcinoma stained very faintly. These findings support a close relationship among LEGH, MDA and mucinous adenocarcinoma and imply that inactivation of STK11 may occur during progression from MDA to mucinous adenocarcinoma.
Radio Positioning and Tracking of High-Speed Devices in 5G NR Networks: System Concept and Performance (2019)

This paper addresses high-efficiency radio positioning and tracking of high-speed objects in emerging fifth generation (5G) new radio (NR) networks. Methods and system concept are described, building on network side reference signal measurements and data fusion and tracking. Also realistic performance results are provided and analyzed, in the context of mmWave NR deployment for high-speed trains at 30 GHz carrier frequency. It is shown that below 3 m positioning accuracy can be achieved with 95% availability, which fits in the positioning performance requirements for traffic monitoring and control, as specified by the 3rd generation partnership project (3GPP). Moreover, the given positioning performance can be achieved without assuming clock synchronization between the baseband units (BBUs) at the network side. In fact, the proposed approach enables sub-nanosecond estimation accuracy of network clock offsets, which benefits various radio resource management (RRM) functionalities of the network for increased spectral efficiency.
Analytical description of STED microscopy performance (2010)

Stimulated emission depletion (STED) resolves fluorescent features that are closer than the far-field optical diffraction limit by applying a spatially modulated light field keeping all but one of these features dark consecutively. For estimating the efficiency of transient fluorophore darkening, we developed analytical equations considering the spatio-temporal intensity profile of the STED beam. These equations provide a quick analysis and optimization of the resolution and contrast to be gained under various conditions, such as continuous wave or pulsed STED beams having different pulse durations. Particular emphasis is placed on fluorescence fluctuation methods such as correlation spectroscopy (FCS) using STED.
Probing polypeptide GalNAc-transferase isoform substrate specificities by in vitro analysis (2014)

N-acetylgalactosaminyltransferase (GalNAc)-type (mucin-type) O-glycosylation is an abundant and highly diverse modification of proteins. This type of O-glycosylation is initiated in the Golgi by a large family of up to 20 homologous polypeptide GalNAc-T isoenzymes that transfer GalNAc to Ser, Thr and possibly Tyr residues. These GalNAc residues are then further elongated by a large set of glycosyltransferases to build a variety of complex O-glycan structures. What determines O-glycan site occupancy is still poorly understood, although it is clear that the substrate specificities of individual isoenzymes and the repertoire of GalNAc-Ts in cells are key parameters. The GalNAc-T isoenzymes are differentially expressed in cells and tissues in principle allowing cells to produce unique O-glycoproteomes dependent on the specific subset of isoforms present. In vitro analysis of acceptor peptide substrate specificities using recombinant expressed GalNAc-Ts has been the method of choice for probing activities of individual isoforms, but these studies have been hampered by biological validation of actual O-glycosylation sites in proteins and number of substrate testable. Here, we present a systematic analysis of the activity of 10 human GalNAc-T isoenzymes with 195 peptide substrates covering known O-glycosylation sites and provide a comprehensive dataset for evaluating isoform-specific contributions to the O-glycoproteome.
Synthesis of Monolayer Hexagonal Boron Nitride on Cu Foil Using Chemical Vapor Deposition (2011)

Hexagonal boron nitride (h-BN) is very attractive for many applications, particularly, as protective coating, dielectric layer/substrate, transparent membrane, or deep ultraviolet emitter. In this work, we carried out a detailed investigation of h-BN synthesis on Cu substrate using chemical vapor deposition (CVD) with two heating zones under low pressure (LP). Previous atmospheric pressure (AP) CVD syntheses were only able to obtain few layer h-BN without a good control on the number of layers. In contrast, under LPCVD growth, monolayer h-BN was synthesized and time-dependent growth was investigated. It was also observed that the morphology of the Cu surface affects the location and density of the h-BN nucleation. Ammonia borane is used as a BN precursor, which is easily accessible and more stable under ambient conditions than borazine. The h-BN films are characterized by atomic force microscopy, transmission electron microscopy, and electron energy loss spectroscopy analyses. Our results suggest that the growth here occurs via surface-mediated growth, which is similar to graphene growth on Cu under low pressure. These atomically thin layers are particularly attractive for use as atomic membranes or dielectric layers/substrates for graphene devices.
Simulation and Measurement of High-Beta Plasma in a Magnetic Nozzle (2007)

Peer Reviewed
Heck Cross-Coupling for Synthesizing Metal-Complexing Monomers (2006)

New polymerizable ligands for complexing metal ions have been synthesized. The polymerizable ligands were made by Heck cross-coupling of aromatic bromides with high pressure ethylene gas under mild conditions at room temperature. The vinyl substituted ligands were prepared in good yields and characterized by GC-MS, FT-NMR, FT-IR and microanalysis.
Ophthalmic manifestations of Allgrove syndrome: report of a case (2001)

A male patient with the ocular manifestations of Allgrove or triple-A syndrome is described. The need for early diagnosis based on alacrima, anisocoria and optic atrophy of this potentially fatal condition is stressed.
How Does Cell-Free Massive MIMO Support Multiple Federated Learning Groups? (2021)

Federated learning (FL) has been considered as a promising learning framework for future machine learning systems due to its privacy preservation and communication efficiency. In beyond-5G/6G systems, it is likely to have multiple FL groups with different learning purposes. This scenario leads to a question: How does a wireless network support multiple FL groups? As an answer, we first propose to use a cell-free massive multiple-input multiple-output (MIMO) network to guarantee the stable operation of multiple FL processes by letting the iterations of these FL processes be executed together within a large-scale coherence time. We then develop a novel scheme that asynchronously executes the iterations of FL processes under multicasting downlink and conventional uplink transmission protocols. Finally, we propose a simple/low-complexity resource allocation algorithm which optimally chooses the power and computation resources to minimize the execution time of each iteration of each FL process.
W-Band Vector Signal Generation via Optical Millimeter-wave Generation and Direct Modulation of NBUTC-PD (2009)

The generation of optical millimeter-wave with frequency 8-tupling is experimentally demonstrated. 625-Mb/sec QPSK data transmission at 105-GHz (W-band) is achieved for the first time using the millimeter-wave generation technique and direct modulation of a NBUTC-PD.
Psikharpax: An autonomous and adaptive artificial rat (2014)

The Psikharpax project aims at endowing a robot with a sensori-motor equipment and a neural control architecture that will afford some of the capacities of autonomy and adaptation that are exhibited by real rats. The paper summarizes the current state of achievement of the project. It successively describes the robot’s future sensors and actuators, and several biomimetic models of the anatomy and physiology of structures in the rat’s brain, like the hippocampus and the basal ganglia, that have already been put at work on various robots and that make navigation and action selection possible. Preliminary results on the implementation of learning mechanisms in these structures are also presented. I.
Nested Sparse Bayesian Learning for block-sparse signals with intra-block correlation (2014)

In this work, we address the recovery of block sparse vectors with intra-block correlation, i.e., the recovery of vectors in which the correlated nonzero entries are constrained to lie in a few clusters, from noisy underdetermined linear measurements. Among Bayesian sparse recovery techniques, the cluster Sparse Bayesian Learning (SBL) is an efficient tool for block-sparse vector recovery, with intrablock correlation. However, this technique uses a heuristic method to estimate the intra-block correlation. In this paper, we propose the Nested SBL (NSBL) algorithm, which we derive using a novel Bayesian formulation that facilitates the use of the monotonically convergent nested Expectation Maximization (EM) and a Kalman filtering based learning framework. Unlike the cluster-SBL algorithm, this formulation leads to closed-form EM updates for estimating the correlation coefficient. We demonstrate the efficacy of the proposed NSBL algorithm using Monte Carlo simulations.
A 1 to 20 GHz Silicon-Germanium Low-Noise Distributed Driver for RF Silicon Photonic Mach-Zehnder Modulators (2019)

This paper investigates co-design of a broadband RF low-noise driver for silicon photonic (SiP) Mach-Zehnder modulators (MZM). The frequency response of SiP modulators demonstrates significant spur-free dynamic range (SFDR) reduction in microwave bands due to a reduction in the linearity and noise figure of the modulator. A low-noise distributed driver circuit is proposed in a 0.13μm SiGe process for the SiP modulator. The driver consists of a broadband LNA, an active balun, and a high-voltage swing driver. The MZM is fabricated in a 65-nm Silicon Photonic (SiP) process. The RoF transmitter achieves a 1-20 GHz bandwidth and an SFDR of 109 dB·Hz <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2/3</sup> at 7 GHz and 11 GHz.
Aberrant gliogenesis and excitation in MEF2C autism patient hiPSC-neurons and cerebral organoids (2020)

Abstract MEF2C has been shown to be a critical transcription factor for neurodevelopment, whose loss-of-function mutation in humans results in MEF2C haploinsufficiency syndrome (MHS), a severe form of autism spectrum disorder (ASD)/intellectual disability (ID). Here, we use patient hiPSC-derived cerebrocortical neurons and cerebral organoids to characterize MHS deficits. Unexpectedly, we found an aberrant micro-RNA-mediated gliogenesis pathway that contributes to decreased neurogenesis. We also demonstrate network-level hyperexcitability in neurons, as evidenced by excessive synaptic and extrasynaptic activity contributing to excitatory/inhibitory (E/I) imbalance. Notably, the extrasynaptic NMDA receptor antagonist, NitroSynapsin, corrects this aberrant electrical activity associated with abnormal phenotypes. During neurodevelopment, MEF2C regulates many ASD-associated gene networks suggesting that our approach may lead to personalized therapy for multiple forms of ASD. One sentence summary Autism-like MEF2C +/- patient hiPSC models show miRNA-mediated overproduction of astrocytes and hyperactivity of neurons.
Remediation of Polycyclic Aromatic Hydrocarbon Compounds in Groundwater Using Poplar Trees (2005)

A seven-year study was conducted to assess the effectiveness of hybrid poplar trees to remediate polycyclic aromatic hydrocarbon (PAH) compounds in soil and groundwater at a creosote-contaminated site. A reduction in the areal extent of the PAH plume was observed in the upper half of the 2-m-thick saturated zone, and PAH concentration levels in the groundwater declined throughout the plume. PAH concentrations began to decline during the period between the third and fourth growing seasons, which coincided with the propagation of the tree roots to the water table region. Remediation was limited to naphthalene and several three-ring PAHs (acenaphthylene and acenaphthene). PAH concentrations in soil and aquifer sediment samples also declined over time; however, levels of four-ring PAHs persisted at the lower depths during the study period. The naphthalene to total PAH concentration ratio in the most contaminated groundwater decreased from >0.90 at the beginning of the second growing season to approximately 0.70 at the end the study. Remediation in the lower region of the saturated zone was limited bythe presence of a 0.3-m-thick layer of creosote present as a dense nonaqueous phase liquid (DNAPL). The nearly steady-state condition of the PAH concentrations observed during the last three years of the study suggests that the effectiveness of the phytoremediation system is limited by the rate of PAH dissolution from the DNAPL source.