gebhart/patrepeval huggingface dataset:
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 (< or = 1 year from diagnosis, or < 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 < or = 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 < or = 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 < or = 1 year or < 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.
EKF based on two FDE schemes for GNSS Vehicle Navigation (2021)

Due to the presence of outliers in GNSS measurements, a fault detection and exclusion module (FDE) is mandatory for applications such as vehicle navigation. In this paper, we propose a navigation processor with two different FDE. A first FDE based on the EKF innovation used when the convergence is ensured taking the benefit of the covariance matrix information. A second FDE with a standalone approach is used if the convergence is not ensured. Then, the performance of the proposed approach is evaluated with a large database of experiments.
Micromechanics Based Design for Pseudo Strain-Hardening in Cementitious Composites (1992)

Micromechanical model constructed on the basis of fracture mechanics and fiber bridging provides a means of selection of fiber, matrix and interface property combinations for which short random fiber reinforced cementitious composites will undergo pseudo strain-hardening when loaded beyond the elastic limit. This paper reviews the basic elements of the micromechanical model, and demonstrate with experimental results how pseudo strain-hardening has been achieved. Emphasis will be placed on the fact that fiber volume fraction is but one adjustable parameter in tailoring the material composition for pseudo strain-hardening. The role of other parameters, such as fiber aspect ratio, matrix toughness, and interfacial bond strength in controlling pseudo strain-hardening, are discussed.
Cloning and Functional Analysis of C. elegans 7B2 (1998)

The neuroendocrine protein 7B2 is a binding protein for the prohormone convertase 2 (PC2) and is required for the intracellular conversion of proPC2 to active PC2. Both full-length 7B2 and its carboxy-terminal 31-residue peptide (CT peptide) are capable of potent inhibition of PC2; the 7B2 protein thus regulates both the biosynthesis and the activity of PC2. Vertebrate 7B2s are highly conserved (92%-97% homology), and thus, species comparison has not been informative in assessing the crucial protein domains responsible for bioactivity. We here report the cloning of the Caenorhabditis elegans 7B2 protein. Although weakly conserved with the vertebrate sequences (23% similarity with mouse 7B2), C. elegans 7B2 contains the signature PPNPCP motif as well as a highly conserved heptapeptide within the CT peptide. In in vitro assays, C. elegans 7B2 possessed significant inhibitory activity against recombinant vertebrate PC2 (IC50 130 nM), and in two functional tests, the amino-terminal domain of C. elegans 7B2 facilitated the activation of proPC2. We conclude that despite low amino acid conservation overall, both functional domains within 7B2 have been conserved between the C. elegans and the vertebrate proteins.
Communicating the sum of sources over a network (2010)

We consider the network communication scenario, over directed acyclic networks with unit capacity edges in which a number of sources $s_i$ each holding independent unit-entropy information $X_i$ wish to communicate the sum $\sum{X_i}$ to a set of terminals $t_j$. We show that in the case in which there are only two sources or only two terminals, communication is possible if and only if each source terminal pair $s_i/t_j$ is connected by at least a single path. For the more general communication problem in which there are three sources and three terminals, we prove that a single path connecting the source terminal pairs does not suffice to communicate $\sum{X_i}$. We then present an efficient encoding scheme which enables the communication of $\sum{X_i}$ for the three sources, three terminals case, given that each source terminal pair is connected by {\em two} edge disjoint paths.
Combining speakers of multiple languages to improve quality of neural voices (2021)

In this work, we explore multiple architectures and training procedures for developing a multi-speaker and multi-lingual neural TTS system with the goals of a) improving the quality when the available data in the target language is limited and b) enabling cross-lingual synthesis. We report results from a large experiment using 30 speakers in 8 different languages across 15 different locales. The system is trained on the same amount of data per speaker. Compared to a single-speaker model, when the suggested system is fine tuned to a speaker, it produces significantly better quality in most of the cases while it only uses less than $40\%$ of the speaker's data used to build the single-speaker model. In cross-lingual synthesis, on average, the generated quality is within $80\%$ of native single-speaker models, in terms of Mean Opinion Score.
Libraries of cluster-assembled titania films for chemical sensing (2005)

We report the fabrication of libraries of nanostructured TiO2 films with a gradient in nanoparticle crystalline phase and dimensions. By supersonic cluster beam deposition it is possible to produce rutile nanoparticles with a diameter smaller than 10nm and to spread them into a co-deposited amorphous titania matrix. Upon thermal annealing rutile nanocrystals act as growth seeds of a film with a spatially controlled rutile/anatase ratio. Films with controlled crystalline phase variation have been deposited on micropatterned substrate to produce arrays of chemoresistive sensors of volatile organic compounds. Devices with different nanocrystalline structures and performances are obtained by a simple one-step thermal treatment after deposition.
Tracking Multiple Handball Players using Multi-Commodity Network Flow for Assessing Tactical Behavior (2013)

The aim of this work is to present an approach that can help to characterize teamsâ and playersâ tactical behavior using two techniques to aid handball coaches to assess tactical procedures when using spatial measures derived from players position data. Results suggest that it is possible to identify tactical spatial differences between fast-break and fast throw-off. The approach presented in this work may be useful to reduce the time spent in game analysis and to improve coachesâ assessment of tactical performance during the training sessions.
Structure of Active Sites of Fe-N-C Nano-Catalysts for Alkaline Exchange Membrane Fuel Cells (2018)

Platinum group metal-free (PGM-free) catalysts based on transition metal-nitrogen-carbon nanomaterials have been studied by a combination of ex situ and in situ synchrotron X-ray spectroscopy techniques; high-resolution Transmission Electron Microscope (TEM); Mößbauer spectroscopy combined with electrochemical methods and Density Functional Theory (DFT) modeling/theoretical approaches. The main objective of this study was to correlate the HO₂<sup>-</sup> generation with the chemical nature and surface availability of active sites in iron-nitrogen-carbon (Fe-N-C) catalysts derived by sacrificial support method (SSM). These nanomaterials present a carbonaceous matrix with nitrogen-doped sites and atomically dispersed and; in some cases; iron and nanoparticles embedded in the carbonaceous matrix. Fe-N-C oxygen reduction reaction electrocatalysts were synthesized by varying several synthetic parameters to obtain nanomaterials with different composition and morphology. Combining spectroscopy, microscopy and electrochemical reactivity allowed the building of structure-to-properties correlations which demonstrate the contributions of these moieties to the catalyst activity, and mechanistically assign the active sites to individual reaction steps. Associated with Fe-N<sub>x</sub> motive and the presence of Fe metallic particles in the electrocatalysts showed the clear differences in the variation of composition; processing and treatment conditions of SSM. From the results of material characterization; catalytic activity and theoretical studies; Fe metallic particles (coated with carbon) are main contributors into the HO₂<sup>-</sup> generation.
Inhibition of dopamine neurons prevents incentive value encoding of a reward cue: With revelations from deep phenotyping (2023)

Activity of dopamine neurons in the ventral tegmental area (VTA) during cue presentation is necessary for the development of a sign-tracking, but not a goal-tracking, conditioned response in a Pavlovian task. We capitalized on the temporal precision of optogenetics to pair cue presentation with inhibition of VTA dopamine neurons. A detailed behavioral analysis with DeepLabCut revealed that cue-directed behaviors do not emerge without VTA dopamine. Importantly, however, when optogenetic inhibition is lifted, cue-directed behaviors increase, and a sign-tracking response develops. These findings confirm the necessity of VTA dopamine during cue presentation to encode the incentive value of reward cues.
Progress in Intracoronary Optical Coherence Tomography (2010)

Understanding the etiology and evolution of the vulnerable coronary plaque is important for the early detection, treatment, and prevention of coronary artery disease. Intravascular optical coherence tomography (OCT) enables imaging of the coronary arteries <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">in vivo</i> with sufficient resolution to accurately differentiate arterial pathology, however, the clinical utility of this technology has been limited due to slow image acquisition rates. The development of high-speed Fourier-domain OCT techniques, including optical frequency-domain imaging, enables comprehensive microstructural imaging of long coronary artery segments. Other OCT advancements, including polarization sensitive OCT provide complementary birefringence information that is related to tissue composition. Together with new image processing, acquisition, and display techniques, these advances have enhanced the usability and utility of intracoronary OCT, bringing it closer to becoming a mainstream imaging modality in interventional cardiology.
Mesh/arc networking: an architecture for efficient survivable self-healing networks (2002)

This paper summarises the results of a study which compares two architectures for survivable self-healing transport networks. Mesh/ring and mesh/arc networks are compared in terms of equipment counts required to achieve fully survivability against single span failure. Heuristic design procedures are developed. The mesh/arc network architecture is shown to be superior in all cases studied. Two main contributions to survivable network design/planning have resulted from this study. The first is the use of the network nodal degree distribution to partition a network into core and access regions. The second is the use of span elimination techniques as a cost-reducing transformation for the access region of networks.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Astressin Analogues (Corticotropin-Releasing Factor Antagonists) with Extended Duration of Action in the Rat (1998)

In earlier reports we identified specific point substitutions (dPhe12,Nle21,38), cyclization strategies [in particular, introduction of lactam rings such as that of cyclo(Glu30,Lys33)], and deletions (residues 1−7) in the CRF molecule that led to agonists. We also noted that further deletions (residues 8−14) produced antagonists such as astressin {cyclo(30−33)[dPhe12,Nle21,38,Glu30, Lys33]hCRF(12-41)} (1). We hypothesized that the lactam ring promoted conformational stability to yield analogues with increased potency both in vitro and in vivo as compared to that of their linear counterparts. Additionally, we reported that cyclo(30−33)[dPhe12,Nle21,38, Glu30,dHis32,Lys33]hCRF(12-41) (3) and dicyclo(26−36,30−33)[Ac−Asp9,dPhe12,Nle21,38,Cys26, Glu30,Lys33,Cys36]hCRF(9-41) were ca. twice and 1/100 as potent as astressin, respectively, suggesting a putative turn that encompasses residues 30−33 (previous paper: Koerber et al. J. Med. Chem. 1998, 41). To increase the potency of 1 and/or 3 in vivo, we extended their chain length by one (5−8), two (9, 10), and three (11, 12) residues at the N-terminus and acetylated (6, 8, 10, 12). Of the compounds tested for duration of action (1, 3−6, 8), we found 6 and 8 to be slightly longer-acting than astressin or [dHis32]astressin, while their potencies in vitro were not significantly different from that of 3. Additionally, we introduced CαMe-leucine residues in lieu of leucine at positions 14, 15, 19, 27, and 37 in [dHis32]astressin. The analogue [CαMe-Leu27,dHis32]astressin (16) was more potent (although not statistically in all cases) than the other four analogues in vitro. While acetylation of the N-terminus of 16 (i.e., 18) or of [CαMe-Leu27]astressin (i.e., 19) did not have a significant effect on in vitro potency, elongation of the N-terminus by one or three residues in addition to acetylation resulted in cyclo(30−33)[dPhe12,Nle21,CαMe-Leu27,Glu30,dHis32,Lys33,Nle38]Ac-hCRF(11-41) (21), cyclo(30−33)[dPhe12,Nle21,CαMe-Leu27,Glu30,Lys33,Nle38]Ac-hCRF(9-41) (22), and cyclo(30−33)[dPhe12, Nle21,CαMe-Leu27,Glu30,dHis32,Lys33,Nle38]Ac-hCRF(9-41) (23) that were longer-acting than 6 and 8 (ca. 2 h inhibition of ACTH secretion at 25 μg/adrenalectomized rat). Analogues 22 and 23 were also more potent than astressin at reversing intracisternal CRF- and abdominal surgery-induced delay of gastric emptying in conscious rats.
Lysis of Human Immunodeficiency Virus Type 1 by a Specific Secreted Human Phospholipase A2 (2006)

Phospholipase A2 (PLA2) proteins affect cellular activation, signal transduction, and possibly innate immunity. A specific secretory PLA2, sPLA2-X, is shown here to neutralize human immunodeficiency virus type 1 (HIV-1) through degradation of the viral membrane. Catalytic function was required for antiviral activity, and the target cells of infection were unaffected. sPLA2-X potently reduced gene transfer of HIV-1 Env-pseudotyped lentivirus vectors and inhibited the replication of both CCR5- and CXCR4-tropic HIV-1 in human CD4+ T cells. Virions resistant to damage by antibody and complement were sensitive to lysis by sPLA2-X, suggesting a novel mechanism of antiviral surveillance independent of the acquired immune system.
ACCRUE—An Integral Index for Measuring Experimental Relevance in Support of Neutronic Model Validation (2021)

A key challenge for the introduction of any design changes, e.g., advanced fuel concepts, first-of-a-kind nuclear reactor designs, etc., is the cost of the associated experiments, which are required by law to validate the use of computer models for the various stages, starting from conceptual design, to deployment, licensing, operation, and safety. To achieve that, a criterion is needed to decide on whether a given experiment, past or planned, is relevant to the application of interest. This allows the analyst to select the best experiments for the given application leading to the highest measures of confidence for the computer model predictions. The state-of-the-art methods rely on the concept of similarity or representativity, which is a linear Gaussian-based inner-product metric measuring the angle—as weighted by a prior model parameters covariance matrix—between two gradients, one representing the application and the other a single validation experiment. This manuscript emphasizes the concept of experimental relevance which extends the basic similarity index to account for the value accrued from past experiments and the associated experimental uncertainties, both currently missing from the extant similarity methods. Accounting for multiple experiments is key to the overall experimental cost reduction by prescreening for redundant information from multiple equally-relevant experiments as measured by the basic similarity index. Accounting for experimental uncertainties is also important as it allows one to select between two different experimental setups, thus providing for a quantitative basis for sensor selection and optimization. The proposed metric is denoted by ACCRUE, short for Accumulative Correlation Coefficient for Relevance of Uncertainties in Experimental validation. Using a number of criticality experiments for highly enriched fast metal systems and low enriched thermal compound systems with accident tolerant fuel concept, the manuscript will compare the performance of the ACCRUE and basic similarity indices for prioritizing the relevance of a group of experiments to the given application.
Functional Organization of the Autotransporter Adhesin Involved in Diffuse Adherence (2007)

The Escherichia coli adhesin involved in diffuse adherence (AIDA-I) is a multifunctional autotransporter protein that mediates bacterial aggregation and biofilm formation, as well as adhesion and invasion of cultured epithelial cells. To elucidate the structure-function relationships of AIDA-I, we performed transposon-based linker scanning mutagenesis and constructed mutants with site-directed deletions. Twenty-nine different mutants with insertions that did not affect protein expression were obtained. Eleven mutants were deficient for one or two but not all of the functions associated with the expression of AIDA-I. Functional characterization of the transposon mutants and of an additional deletion mutant suggested that the N-terminal third of mature AIDA-I is involved in binding of this protein to cultured epithelial cells. The purified product of the putative domain could bind to cultured epithelial cells, confirming the importance of this region in adhesion. We also identified several different mutants in which invasion and adhesion were changed to different extents and two mutants in which autoaggregation and biofilm formation were also affected differently. These results suggest that although conceptually linked, adhesion and invasion, as well as autoaggregation and biofilm formation, are phenomena that may rely on distinct mechanisms when they are mediated by AIDA-I. This study sheds new light on the workings of a protein belonging to an emerging family of strikingly versatile virulence factors.
Mutation-based detection of molecular tumor margins in colorectal liver metastasis. (2010)

3610 Background: Defining adequate resection margins of liver metastasis especially after preoperative chemotherapy is based on empirically determined recommendations and random screening of macroscopic and microscopic tissue sections surrounding the liver metastasis. Mutations are highly specific for tumors and therefore can be used as a marker to accurately determine molecular tumor margins. Methods: In our study we evaluated 12 patients with metastatic colon cancer who underwent partial hepatectomy of 1-6 liver metastasis. Samples were obtained by 2-4 punch biopsies in different directions of surrounding liver tissue at 4, 8, 12 and 16 mm distance to the macroscopic tumor border. A total of 88 samples were analyzed. Tumor specific mutations including KRAS, PIK3CA, APC and TP53 were determined by sequencing tumor tissue. DNA was isolated from biopsies of surrounding liver tissue and analyzed by BEAMing, a highly sensitive PCR based method of mutation detection. Molecular results were correlated with microscopic tissue analysis and clinical data. Results: We were able to detect tumor DNA in surrounding liver tissue in 3 out of 12 patients with 4 samples positive at 4 mm and all samples negative at 8, 12 and 16 mm distance to the macroscopic tumor border with negative control samples. In average 1,047 mutant single stranded DNA fragments were found in 150,000 analyzed DNA fragments. 3 out of 10 patients with previous chemotherapy had positive molecular margins, whereas the 2 patients with naive liver tissue were tested negative for tumor DNA in their marginal zones. Conclusions: The measurement of tumor DNA in tissue is a highly sensitive molecular marker of tumor margins identifying consistently negative margins at > 0.4 cm distance to the macroscopic tumor border in all samples. Tumor DNA as a marker of molecular tumor margins could be helpful in determining accurate biological resection guidelines of liver metastasis and can help to understand the process of tumor reduction after preoperative chemotherapy. Author Disclosure Employment or Leadership Position Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Inostics Inostics Inostics
C−H Bond Functionalization via Hydride Transfer: Lewis Acid Catalyzed Alkylation Reactions by Direct Intramolecular Coupling of sp3 C−H Bonds and Reactive Alkenyl Oxocarbenium Intermediates (2008)

C-H bond functionalization enables strategically new approaches to the synthesis of complex organic molecules including biologically active compounds, research probes and functional organic materials. To address the shortcomings of transition metal catalyzed processes, we have developed a new approach to direct coupling of sp(3) C-H bonds and alkenes based on Lewis acid-promoted hydride transfer. Activation of alpha,beta-unsaturated aldehydes and ketones with Lewis acid triggers intramolecular hydride transfer, leading to a zwitterionic intermediate, which in turn undergoes ionic cyclization to afford the cyclic alkylation product. The scope of this method is expanded by the generation of alkenyl-oxocarbenium species as highly activated alkene intermediates capable of abstracting a hydride from unreactive carbon centers, including benzyl-, allyl-, and crotyl-ethers, as well as primary alkyl ethers, at room temperature. The alkenyl acetal and ketal substrates show dramatically faster rates of cyclization, as well as improved chemical yield and diastereoselectivity, compared to the corresponding carbonyl compounds. Furthermore, the use of boron trifluoride etherate as the Lewis acid and ethylene glycol as the organocatalyst provides a highly active catalytic system, presumably via the in situ formation of alkenyl-oxocarbenium intermediates, which eliminates the need for expensive transition metal Lewis acids or the preparation of ketal substrates. This binary catalytic system greatly improves the efficiency of the hydride transfer-initiated alkylation reactions.