gebhart/patrepeval huggingface dataset:
An Antibody-based Blood Test Utilizing a Panel of Biomarkers as a New Method for Improved Breast Cancer Diagnosis (2013)

In order to develop a new tool for diagnosis of breast cancer based on autoantibodies against a panel of biomarkers, a clinical trial including blood samples from 507 subjects was conducted. All subjects showed a breast abnormality on exam or breast imaging and final biopsy pathology of either breast cancer patients or healthy controls. Using an enzyme-linked immunosorbent assay, the samples were tested for autoantibodies against a predetermined number of biomarkers in various models that were used to determine a diagnosis, which was compared to the clinical status. Our new assay achieved a sensitivity of 95.2% [CI = 92.8-96.8%] at a fixed specificity of 49.5%. Receiver-operator characteristic curve analysis showed an area under the curve of 80.1% [CI = 72.6-87.6%]. These results suggest that a blood test which is based on models comprising several autoantibodies to specific biomarkers may be a new and novel tool for improving the diagnostic evaluation of breast cancer.
Preparation and Analysis of Oligonucleotides Containing the C4‘-Oxidized Abasic Site and Related Mechanistic Probes (2005)

The C4'-oxidized abasic site (C4-AP) is produced by a variety of DNA damaging agents. This alkali labile lesion can exist in up to four diastereomeric cyclic forms, in addition to the acyclic keto-aldehyde. Synthetic oligonucleotides containing the lesion were prepared from a stable photochemical precursor. Chemical integrity of the lesion containing oligonucleotides was probed using phosphodiesterase lability. Analysis of the 3',5'-phosphate diester of the monomeric lesion released from single diastereomers of photolabile precursors by 1H NMR indicates that isomerization of the hemiacetal and/or hemiketal is rapid. The syntheses and characterization of oligonucleotides containing configurationally stable analogues of C4-AP, which serve as mechanistic probes for deciphering the structural basis of the biochemical and biological effects of the C4'-oxidized abasic lesion, are also described.
Halogen bonding drives the self-assembly of piperazine cyclophanes into tubular structures (2009)

Halogen bonding with 1,4-diiodotetrafluorobenzene leads to the self-assembly of piperazine cyclophanes into well-defined tubular structures with solvent inclusion.
Expression of Two Soybean Vegetative Storage Protein Genes during Development and in Response to Water Deficit, Wounding, and Jasmonic Acid (1990)

Hugh S. Mason, John E. Mullet, Expression of Two Soybean Vegetative Storage Protein Genes during Development and in Response to Water Deficit, Wounding, and Jasmonic Acid, The Plant Cell, Vol. 2, No. 6 (Jun., 1990), pp. 569-579
Virtual Reality Environment for Simulating Tasks With a Myoelectric Prosthesis: An Assessment and Training Tool (2011)

Intuitively and efficiently controlling multiple degrees of freedom is a major hurdle in the field of upper limb prosthetics. A virtual reality myoelectric transhumeral prosthesis simulator has been developed for cost-effectively testing novel control algorithms and devices. The system acquires EMG commands and residual limb kinematics, simulates the prosthesis dynamics, and displays the combined residual limb and prosthesis movements in a virtual reality environment that includes force-based interactions with virtual objects. A virtual Box and Block Test is demonstrated. Three normally-limbed subjects performed the simulated test using a sequential and a synchronous control method. With the sequential method, subjects moved on average 6.7±1.9 blocks in 120 seconds, similar to the number of blocks transhumeral amputees are able to move with their physical prostheses during clinical evaluation. With the synchronous method, subjects moved 6.7±2.2 blocks. The virtual reality prosthesis simulator is thus a promising tool for developing and evaluating control methods, prototyping novel prostheses, and training amputees.
Synthesis, in vitro and in vivo antimalarial assessment of sulfide, sulfone and vinyl amide-substituted 1,2,4-trioxanes prepared via thiol-olefin co-oxygenation (TOCO) of allylic alcohols (2010)

Thiol-Olefin Co-Oxygenation (TOCO) methodology has been applied to the synthesis of a small library of weak base and polar 1,2,4-trioxanes. The 1,2,4-trioxane units synthesised exhibit remarkable stability as they survive base catalysed hydrolysis and mixed anhydride/amine coupling reactions. This unique stability feature has enabled a range of novel substitution patterns to be incorporated within the spiro 1,2,4-trioxane unit. Selected analogues express potent in vitro nM antimalarial activity, low cytotoxicity and oral activity in the Plasmodium berghei mouse model of malaria.
Involvement of 5-HT1A and 5-HT2A Receptors but Not α2-Adrenoceptors in the Acute Electrophysiological Effects of Cariprazine in the Rat Brain In Vivo (2018)

Cariprazine, an orally active and potent dopamine D<sub>3</sub>-preferring D<sub>3</sub>/D<sub>2</sub> receptor partial agonist, is approved to treat adults with schizophrenia (in the United States and Europe) and manic or mixed episodes associated with bipolar I disorder (in the United States). Cariprazine also displays partial agonism at serotonin [5-hydroxytryptamine (5-HT)] 5-HT<sub>1A</sub> receptors and antagonism at 5-HT<sub>2A</sub> and 5-HT<sub>2B</sub> receptors in vitro. The study objective was to determine whether cariprazine leads to functional alterations of monoamine systems in vivo via electrophysiological recordings from anesthetized rats. Dorsal raphe nucleus (DRN), locus coeruleus (LC), and hippocampus pyramidal neurons were recorded, and cariprazine was administered systemically or locally through iontophoresis. In the DRN, cariprazine completely inhibited the firing activity of 5-HT neurons, which was fully reversed by the 5-HT<sub>1A</sub> receptor antagonist, WAY100635. In the LC, cariprazine reversed the inhibitory effect of the preferential 5-HT<sub>2A</sub> receptor agonist, 2,5-dimethoxy-4-iodoamphetamine, on norepinephrine (NE) neurons (ED<sub>50</sub> = 66 <i>µ</i>g/kg) but did not block the inhibitory effect of the <i>α</i> <sub>2</sub>-adrenergic receptor agonist, clonidine. Cariprazine, iontophorized into the hippocampus, diminished pyramidal neuronal firing through activation of 5-HT<sub>1A</sub> receptors, while its concomitant administration did not dampen the suppressant effect of 5-HT. These results indicate that, in vivo, cariprazine acted as a 5-HT<sub>1A</sub> autoreceptor agonist in the DRN, a 5-HT<sub>2A</sub> receptor antagonist in modulating the firing activity of LC NE neurons, and a full agonist at 5-HT<sub>1A</sub> receptors mediating the electrophysiological effect of 5-HT on pyramidal neurons. The modulatory actions of cariprazine on these monoaminergic systems may contribute to its therapeutic effectiveness in patients with depressive episodes.
Robust linear spectral unmixing using outlier detection (2015)

This paper presents a Bayesian algorithm for linear spectral unmixing that accounts for outliers present in the data. The proposed model assumes that the pixel reflectances are linear mixtures of unknown endmembers, corrupted by an additional term modelling outliers and additive Gaussian noise. A Markov random field is considered for outlier detection based on the spatial and spectral structures of the anomalies. This allows outliers to be identified in particular regions and wavelengths of the data cube. A Bayesian algorithm is proposed to estimate the parameters involved in the model yielding a joint linear unmixing and outlier detection algorithm. Simulations conducted with synthetic data demonstrate the accuracy of the proposed unmixing and outlier detection strategy for the analysis of hyperspectral images.
&lt;title&gt;Localized lossless authentication watermark (LAW)&lt;/title&gt; (2003)

A novel framework is proposed for lossless authentication watermarking of images which allows authentication and recovery of original images without any distortions. This overcomes a significant limitation of traditional authentication watermarks that irreversibly alter image data in the process of watermarking and authenticate the watermarked image rather than the original. In particular, authenticity is verified before full reconstruction of the original image, whose integrity is inferred from the reversibility of the watermarking procedure. This reduces computational requirements in situations when either the verification step fails or the zero-distortion reconstruction is not required. A particular instantiation of the framework is implemented using a hierarchical authentication scheme and the lossless generalized-LSB data embedding mechanism. The resulting algorithm, called localized lossless authentication watermark (LAW), can localize tampered regions of the image; has a low embedding distortion, which can be removed entirely if necessary; and supports public/private key authentication and recovery options. The effectiveness of the framework and the instantiation is demonstrated through examples.
Towards an understanding of cell-specific functions of signal-dependent transcription factors (2013)

The ability to regulate gene expression in a cell-specific manner is a feature of many broadly expressed signal-dependent transcription factors (SDTFs), including nuclear hormone receptors and transcription factors that are activated by cell surface receptors for extracellular signals. As the most plastic cells of the hematopoietic system, macrophages are responsive to a wide spectrum of regulatory molecules and provide a robust model system for investigation of the basis for cell-specific transcriptional responses at a genome-wide level. Here, focusing on recent studies in macrophages, we review the evidence suggesting a model in which cell-specific actions of SDTFs are the consequence of priming functions of lineage determining transcription factors. We also discuss recent findings relating lineage-determining and SDTF activity to alterations in the epigenetic landscape as well as the production and function of enhancer RNAs. These findings have implications for the understanding of how natural genetic variation impacts cell-specific programs of gene expression and suggest new approaches for altering gene expression in vivo.
Evaluation of Anisotropic Filters for Diffusion Tensor Imaging (2006)

Diffusion tensor imaging (DTI) measures, such as fractional anisotropy (FA), and trace are very sensitive to noise contained in the acquired diffusion weighted images. Typical isotropic smoothing methods reduce the high spatial frequency image content and blur the image features. We hypothesized that the diffusion tensor would be an approximate anisotropic Gaussian filter function because the blur will tend to be oriented parallel to the white matter structures. Thus, we implemented and evaluated an anisotropic Gaussian kernel smoothing method based on the diffusion tensor for preserving diffusion tensor structural features while significantly reducing the noise. We compared the diffusion tensor anisotropic filtering with isotropic Gaussian filtering, and a Perona-Malik (PM) filtering algorithm, which was derived from the intensity gradients of diffusion weighted images. Human brain DTI data with high SNR was used as a gold standard for evaluation. Overall, the anisotropic filters performed similarly, with slightly better performance using the DT anisotropic filter across the whole brain.
Targeting new drugs with choline metabolism. (2012)

MILLIONS OF PEOPLE all over the world suffer from parasitic diseases, such as African sleeping sickness and Chagas’ disease, which, particularly in the less developed countries, lead to sickness, deformities and ultimately death. Additionally, with global warming there are growing concerns about the threat from insect-transmitted diseases increasing as vectors move into new areas, including southern Europe and the southern states of the US. Most of the conventional drug therapies that are currently used to treat these parasitic diseases have unknown drug targets. Thus, research is underway to build a deeper understanding of the differences between the parasitic metabolism and that of humans. At the University of St Andrews in Scotland a group of researchers is using multidisciplinary approaches, incorporating chemistry, biochemistry and molecular parasitology, to investigate phospholipid and glycolipid metabolism in the hopes of uncovering some of the parasite’s secrets.

Their ultimate aim is the discovery of new therapeutic agents for parasitic diseases. To achieve this they are focusing on uncovering the lipid metabolic pathways that are present in parasites. Dr Terry Smith, a Reader in the University’s Schools of Biology and Chemistry and the man in charge of this latest research, says that a biosynthetic step which is unique to the parasite, is often favoured as a drug therapy which targets this process, and is likely to have no effect on the patient. However, through their investigations they have demonstrated that the parasite is potentially vulnerable to drug intervention because of the metabolic route and steps that they are missing. “In other words, we can inhibit the only route by which parasites make their essential choline containing phospholipids, whereas we as humans have redundant routes or processes by which to make choline-containing phospholipids,” Smith adds.
Near-Optimal DAPSK Demodulation Using a PARAFAC Decomposition (2017)

Differential amplitude phase shift keying (DAPSK) is a promising modulation technique for use in high-mobility environments, as it does not require channel estimation. In this paper, a novel reduced complexity soft demodulator for high-order DAPSK constellations is proposed. The main idea relies on a two-step approximation of the sum-log demapper. In the first step, a parallel factor analysis (PARAFAC) decomposition is used to approximate log-likelihood ratios. Next, the basis functions obtained through the first step are approximated by piecewise-linear curves. Numerical optimization techniques are employed for the PARAFAC decomposition and its piecewise-linear approximation whose parameters are then stored in a lookup table. It has been verified through computer simulations that the proposed scheme clearly outperforms the scheme proposed in the paper “Reduced-complexity noncoherent soft-decision-aided DAPSK dispensing with channel estimation,” (IEEE Trans. Veh. Technol., vol. 62, pp. 2633-2643, 2013.), while also having lower computational cost. Moreover, it is shown that the performance of the exact sum-log demapper and the proposed demapper is very close for 2 × 4 and 4 × 16 DAPSK constellations.
The Bingel Monoadducts of La@C<sub>82</sub>: Synthesis, Characterization, and Electrochemistry (2006)

The reaction of La@C82 with diethyl bromomalonate in the presence of base (the Bingel reaction) generated five monoadducts which have been fully characterized. It was found that four of them (mono-A, -B, -C, and -D) are ESR-inactive, suggesting singly bonded regioisomers. In contrast, the fifth product (mono-E) is ESR-active, indicating that it possesses a cyclic moiety between the appended malonate group and the fullerene cage, analogous to conventional Bingel adducts. The differences in the molecular structures of mono-A, -B, -C, and -E result in varying thermal stabilities and electrochemical behavior. In particular, the singly bonded monoadducts undergo the retro-Bingel reaction either under thermal treatment or during electron transfer on the cyclic voltammetric timescale. However, mono-E shows remarkable thermal stability and perfect reversibility under the same experimental conditions.
SIESTA: Efficient Online Continual Learning with Sleep (2023)

In supervised continual learning, a deep neural network (DNN) is updated with an ever-growing data stream. Unlike the offline setting where data is shuffled, we cannot make any distributional assumptions about the data stream. Ideally, only one pass through the dataset is needed for computational efficiency. However, existing methods are inadequate and make many assumptions that cannot be made for real-world applications, while simultaneously failing to improve computational efficiency. In this paper, we propose a novel continual learning method, SIESTA based on wake/sleep framework for training, which is well aligned to the needs of on-device learning. The major goal of SIESTA is to advance compute efficient continual learning so that DNNs can be updated efficiently using far less time and energy. The principal innovations of SIESTA are: 1) rapid online updates using a rehearsal-free, backpropagation-free, and data-driven network update rule during its wake phase, and 2) expedited memory consolidation using a compute-restricted rehearsal policy during its sleep phase. For memory efficiency, SIESTA adapts latent rehearsal using memory indexing from REMIND. Compared to REMIND and prior arts, SIESTA is far more computationally efficient, enabling continual learning on ImageNet-1K in under 2 hours on a single GPU; moreover, in the augmentation-free setting it matches the performance of the offline learner, a milestone critical to driving adoption of continual learning in real-world applications.
Exploring Features For Localized Detection of Speech Recognition Errors (2013)

We address the problem of localized error detection in Automatic Speech Recognition (ASR) output to support the generation of tar-geted clarifications in spoken dialogue sys-tems. Localized error detection finds specific mis-recognized words in a user utterance. Tar-geted clarifications, in contrast with generic ‘please repeat/rephrase ’ clarifications, target a specific mis-recognized word in an utter-ance (Stoyanchev et al., 2012a) and require accurate detection of such words. We extend and modify work presented in (Stoyanchev et al., 2012b) by experimenting with a new set of features for predicting the likelihood of a local error in an ASR hypothesis on an un-sifted version of the original dataset. We im-prove over baseline results, where only ASR-generated features are used, by constructing optimal feature sets for utterance and word mis-recognition prediction. The f-measure for identifying incorrect utterances improves by 2.2 % and by 3.9 % for identifiying incorrect words. 1
Recent Advances in Carbon Nanotube-Based Enzymatic Fuel Cells (2014)

This review summarizes recent trends in the field of enzymatic fuel cells. Thanks to the high specificity of enzymes, biofuel cells can generate electrical energy by oxidation of a targeted fuel (sugars, alcohols, or hydrogen) at the anode and reduction of oxidants (O2, H2O2) at the cathode in complex media. The combination of carbon nanotubes (CNT), enzymes and redox mediators was widely exploited to develop biofuel cells since the electrons involved in the bio-electrocatalytic processes can be efficiently transferred from or to an external circuit. Original approaches to construct electron transfer based CNT-bioelectrodes and impressive biofuel cell performances are reported as well as biomedical applications.
1A1-C07 A Flexible Multi-degree of Freedom Surgical Tool Using Interference-Free Wire-Driven Joint (2008)

We have developed a new flexible medical instrument to enable surgical treatment in the deep and narrow internal operative field of patients. This instrument is equipped with a forceps on the tip of a flexible tube through a 3-DOF (degree-of-freedom) interference-free wire-driven joint developed for a surgical manipulator. This instrument is also equipped with a manual-operation interface to manipulate the forceps and the joint on the other end of the flexible tube. The forceps and the joint are linked with the manual-operation interface by a wire that is fed through the flexible tube. The opening angle of the forceps is 90 degrees, and 2-DOF bending angles of the joint are ±125.5 degrees and ±106.5 degrees by operation with the manual-operation interface. The reaction time from the start of operation to the opening movement of the forceps is 0.009 seconds, and reaction times from the start of operation to the 2-DOF bending movements of the joint are 0.017 seconds and 0.014 seconds.
Optimization of Wind Driven RO Plant for Brackish Water Desalination during Wind Speed Fluctuation with and without Battery (2021)

This work aimed to carry out an optimal investigation of the design and operation of a large capacity reverse osmosis (RO) desalination plant powered by wind energy. Different scenarios involving two design options, such as using storage tanks or batteries, and operation options, such as using variable or fixed feed pressure, were analyzed and optimized. In addition, another operation option, of using a fixed number of RO vessels or a varying number of active RO vessels, was also considered. It was found that an optimized plant using storage tanks can provide a less expensive water cost and a less complicated plant structure. Moreover, the use of a variable feed pressure can help in attenuating the disturbances incurred in the form of wind intermittency. Conversely, the use of fixed feed pressure and constantly supplied power per vessel can run the RO units smoothly, leading to a predictable production rate. However, this requires operating the plant on different active sets of vessels each hour, which mandates additional automatic control systems. The water cost when storage tanks are utilized can be as low as 7.42 $/m<sup>3</sup>, while it is around 19.7 $/m<sup>3</sup> when a battery is used.
Zur Fluiddynamik und zum Stoffübergang newtonscher und nichtnewtonscher Gemische auf Siebböden (1987)

Abstract In der chemischen, pharmazeutischen und petrochemischen Industrie sowie in der Nahrungsmittelindustrie finden Stoffaustauschvorgänge häufig in hochviskosen Medien statt, wobei zahlreich vorkommende Gemische jedoch ein nichtnewtonsches Verhalten aufweisen. Um die Kenntnis der Stoffaustauschvorgänge in newtonschen und nichtnewtonschen Gemischen zu verbessern, wurden systematische Versuche zur Fluiddynamik und zum Stoffübergang an einzelnen Siebböden durchgeführt. Aufgrund der bisher erzielten Ergebnisse durch Untersuchungen an mittel‐ bis hochviskosen newtonschen Gemischen konnten konkrete Angaben bezüglich der Auswahl der Betriebsparameter sowie der Siebbodengeometrie zur Erhöhung der Trennleistung von Bodenkolonnen gemacht werden. Gegenstand der Arbeit ist an Hand von Absorptionsversuchen von Luftsauerstoff in Wasser und in Carboxylmethylcellulose sowie Polyacrylamid‐Wasser‐Gemischen bei Variation der Betriebsparameter und der Siebbodengeometrie eine Untersuchung der Fragestellung, inwieweit sich die erzielten Ergebnisse auf niedrigviskose sowie nicht newtonsche Gemische übertragen lassen. Neben den Messungen wurden Korrelationen zur Berechnung des Stoffaustauschs in mittel‐ bis hochviskosen Gemischen auf Siebböden aufgestellt.