gebhart/patrepeval huggingface dataset:
The Piezo1 hypothesis of renal anemia (2022)

Erythropoietin deficiency is an extensively researched cause of renal anemia. The etiology and consequences of shortened red blood cell (RBC) life span in chronic kidney disease (CKD) are less well understood. Traversing capillaries requires RBC geometry changes, a process enabled by adaptions of the cytoskeleton. These changes are mediated by transient activation of the mechanosensory Piezo1 channel, resulting in calcium influx. Importantly, prolonged Piezo1 activation shortens RBC life span, presumably through activation of calcium-dependent intracellular pathways triggering RBC death. Two Piezo1-activating small molecules, Jedi1 and Jedi2, share remarkable structural similarities with 3-carboxy-4-methyl-5-propyl-2-furanpropanoic acid (CMPF), a uremic retention solute cleared by the healthy kidney. We hypothesize that in CKD the accumulation of CMPF leads to prolonged activation of Piezo1 (similar in effect to Jedi1 and Jedi2), thus reducing RBC life span. This hypothesis can be tested through bench experiments and, ultimately, by studying the effect of CMPF removal on renal anemia.
ChemInform Abstract: Targeting the Conformational Transitions of MDM2 and MDMX: Insights into Dissimilarities and Similarities of p53 Recognition. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Carbon-13 nuclear magnetic resonance in solid ammonium tartrate (1974)

Chemical shielding tensors have been determined for 13C in single crystals of ammonium D-tartrate using proton-enhanced NMR. The unit cell contains two molecules, and in some orientations eight lines are resolved from the eight magnetically inequivalent carbon nuclei. Details of the experimental approach, equipment, and analysis are provided, and results are presented for three determinations on two single crystals. These indicate a precision of ±2 ppm in the determination of the principal values and ±3° in the orientation of the principal axes for the carboxyl groups, with lower precision for the hydroxyl groups. The orientations of the principal axes of the tensors are related to the crystallographic (a, b, c*) axes by employing orientation data from x-ray precession work in this study. The most plausible assignment of the tensors to particular 13C nuclei in the unit cell indicates that the heaviest shielding for 13C in the carboxyl groups occurs when H0 is perpendicular to the carboxyl plane and the lightest shielding when H0 is in the carboxyl plane bisecting the C–O bonds. For the hydroxyl 13C, the heaviest shielding occurs with H0 roughly along the C–O bond. The average principal shielding values are, for the carboxyl 13C, σ11=−110.5, σ22=−61.7, σ33=21.6; and for the hydroxyl 13C, σ11=41.9, σ22=48.0, σ33=74.0 in parts per million (±2) relative to an external reference of liquid benzene. The effects of hydrogen bonding on the tensors are discussed briefly.
5G Technologies (2016)

There are many questions surrounding 5G’s key features, so in this chapter we will answer some important ones in an organized way to provide the most recent information on the progress of 5G.
Why is My Component and Connector Views Specification Unsatisfiable? (2017)

Component and connector (C&C) views specifications, with corresponding verification and synthesis techniques, have been recently suggested as a means for formal yet intuitive structural specification of component and connector models. One challenge for effective use of C&C views synthesis relates to the case where the specification is unsatisfiable. In this work we present an approach to deal with unsatisfiable C&C views specifications. First, we define a notion of a C&C views specification core, a locally minimal unsatisfiable subset of the views specification. Second, based on the core, we generate explicit, concrete, structured natural-language report, which explains the cause of unsatisfiability. Finally, we extend our work to support specifications with architecture styles, library components, and Boolean formulas beyond simple conjunctions. Our views core computation relies on a new translation to SAT, via Alloy, which is refined enough to allow the extraction of detailed explanations. We implemented our work and evaluated it using 12 synthetic and real-world C&C views specifications. The evaluation examines the cost of the core computation and its effectiveness in reducing the size of the specification.
Design and synthesis of aryl-piperidine derivatives as potent and selective PET tracers for cholesterol 24-hydroxylase (CH24H) (2022)

Cholesterol 24-hydroxylase (CH24H, CYP46A1) is a cytochrome P450 family enzyme that maintains the homeostasis of brain cholesterol. Soticlestat, a potent and selective CH24H inhibitor, is in development as a therapeutic agent for Dravet syndrome and Lennox-Gastaut syndrome. Herein, we report the discovery of aryl-piperidine derivatives as potent and selective CH24H positron emission tomography (PET) tracers which can be used for dose guidance of a clinical CH24H inhibitor and as a diagnostic tool for CH24H-related pathology. Starting from compound 1 (IC<sub>50</sub> = 16 nM, logD = 1.7), which was reported as a CH24H inhibitor with lower lipophilicity, a<sup>18</sup>F-labeling site (3-fluoroazetidine) was incorporated by structure-based drug design (SBDD) utilizing the co-crystal structure of a compound 1 analog. Subsequent optimization to adjust key parameters for PET tracers, such as potency, lipophilicity, brain penetration, and unbound plasma protein binding, enabled compounds 3f (IC<sub>50</sub> = 8.8 nM) and 3g (IC<sub>50</sub> = 8.7 nM) as PET imaging candidates. Selectivity of these compounds for CH24H was validated by a brain distribution study using CH24H-WT and KO mice. In non-human primate PET imaging, [<sup>18</sup>F]3f and [<sup>18</sup>F]3g showed similar regional uptake in the brain, indicating that these tracers were specific to the CH24H-expressed regions and validated the expression of CH24H in the living brain by different tracers.
An ADMM Based Framework for AutoML Pipeline Configuration (2019)

We study the AutoML problem of automatically configuring machine learning pipelines by jointly selecting algorithms and their appropriate hyper-parameters for all steps in supervised learning pipelines. This black-box (gradient-free) optimization with mixed integer &amp; continuous variables is a challenging problem. We propose a novel AutoML scheme by leveraging the alternating direction method of multipliers (ADMM). The proposed framework is able to (i) decompose the optimization problem into easier sub-problems that have a reduced number of variables and circumvent the challenge of mixed variable categories, and (ii) incorporate black-box constraints along-side the black-box optimization objective. We empirically evaluate the flexibility (in utilizing existing AutoML techniques), effectiveness (against open source AutoML toolkits),and unique capability (of executing AutoML with practically motivated black-box constraints) of our proposed scheme on a collection of binary classification data sets from UCI ML&amp; OpenML repositories. We observe that on an average our framework provides significant gains in comparison to other AutoML frameworks (Auto-sklearn &amp; TPOT), highlighting the practical advantages of this framework.
Design and Synthesis of Copper–Cobalt Catalysts for the Selective Conversion of Synthesis Gas to Ethanol and Higher Alcohols (2014)

Abstract Combining quantum‐mechanical simulations and synthesis tools allows the design of highly efficient CuCo/MoO x catalysts for the selective conversion of synthesis gas (CO+H 2 ) into ethanol and higher alcohols, which are of eminent interest for the production of platform chemicals from non‐petroleum feedstocks. Density functional theory calculations coupled to microkinetic models identify mixed Cu–Co alloy sites, at Co‐enriched surfaces, as ideal for the selective production of long‐chain alcohols. Accordingly, a versatile synthesis route is developed based on metal nanoparticle exsolution from a molybdate precursor compound whose crystalline structure isomorphically accommodates Cu 2+ and Co 2+ cations in a wide range of compositions. As revealed by energy‐dispersive X‐ray nanospectroscopy and temperature‐resolved X‐ray diffraction, superior mixing of Cu and Co species promotes formation of CuCo alloy nanocrystals after activation, leading to two orders of magnitude higher yield to high alcohols than a benchmark CuCoCr catalyst. Substantiating simulations, the yield to high alcohols is maximized in parallel to the CuCo alloy contribution, for Co‐rich surface compositions, for which Cu phase segregation is prevented.
Supplementary Figure 1 from Cyclophosphamide Induces Differentiation of Th17 Cells in Cancer Patients (2023)

Supplementary Figure 1 from Cyclophosphamide Induces Differentiation of Th17 Cells in Cancer Patients
Supplementary Table 1 from Tissue-Wide Expression Profiling Using cDNA Subtraction and Microarrays to Identify Tumor-Specific Genes (2023)

Supplementary Table 1 from Tissue-Wide Expression Profiling Using cDNA Subtraction and Microarrays to Identify Tumor-Specific Genes
Hysteresis and threshold voltage shift of pentacene thin-film transistors and inverters with Al2O3 gate dielectric (2007)

The pentacene organic thin-film transistors (OTFTs) with plasma-enhanced atomic-layer-deposited 150nm thick Al2O3 as a gate dielectric and the inverters comprised of these OTFTs have been fabricated. The hysteresis in transfer characteristics of the OTFTs depends on the scan range of negative gate voltage, regardless of drain voltage. Negative gate-bias stress leads to the progressive negative shift of threshold voltage. The hysteresis of D inverter is similar to that of E inverter, but the former has a wider swing range and a higher gain in comparison with the latter.
ChemInform Abstract: Synthesis of Arylpiperazines via Palladium‐Catalyzed Aromatic Amination Reactions of Bromoarenes with N‐tert‐Butoxycarbonylpiperazine. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
An International Laboratory for Systems and Computational Neuroscience (2017)

The neural basis of decision-making has been elusive and involves the coordinated activity of multiple brain structures. This NeuroView, by the International Brain Laboratory (IBL), discusses their efforts to develop a standardized mouse decision-making behavior, to make coordinated measurements of neural activity across the mouse brain, and to use theory and analyses to uncover the neural computations that support decision-making.
Separate measurement of conductive and pulsive components of leakage current of porcelain and polymeric materials for outdoor insulators (2002)

Leakage current and the resultant cumulative charge are important parameters to evaluate the insulation performance of polymeric insulating materials by the accelerated aging test. We define leakage current into conductive and pulsive components and measured them. For measurements of the pulsive component, we have developed a new computer aided discharge measurement system. Leakage current was measured separately with the change of electric field and conductivity of the salt fog so as to obtain the cumulative charge for porcelain as a reference sample. Measurement results indicate that this technique can quantitatively measure the pulsive component of the leakage current. We also investigated surface dryband formation of the sample.
Detection of telomerase activity in oral rinses from head and neck squamous cell carcinoma patients. (1996)

Telomerase is a ribonucleoprotein that maintains telomere length and whose activity is associated with escape from cellular senescence. Telomerase activity has been found in germline, immortalized, and malignant tumor cells. Using a modified PCR-based assay for telomerase activity, 26 of 35 (80%) primary, fresh, head and neck squamous cell cancer specimens and 3 of 6 head and neck squamous dysplastic lesions possessed telomerase activity. In addition, 14 of 44 (32%) oral rinses from a separate group of head and neck squamous cell cancer patients contained detectable telomerase activity, whereas 1 of 22 (5%) oral rinses from normal control patients exhibited telomerase activity. Telomerase activity in oral rinses was compared with corresponding activity in paired primary tumor samples for 19 cases: 7 of 19 demonstrated activity in both tumor and oral rinse, 2 of 19 lacked activity in both tumor and oral rinse, 10 of 19 tumors demonstrated activity that could not be detected in corresponding oral rinses, and there were no examples of positive oral rinses with corresponding negative tumors. Although currently limited in its sensitivity, analysis of telomerase activity in oral rinses represents a novel method to detect the presence of cancer cells shed in the upper aerodigestive tract.
A Self-Adaptive Artificial Intelligence Technique to Predict Oil Pressure Volume Temperature Properties (2018)

Reservoir fluid properties such as bubble point pressure (Pb) and gas solubility (Rs) play a vital role in reservoir management and reservoir simulation. In addition, they affect the design of the production system. Pb and Rs can be obtained from laboratory experiments by taking a sample at the wellhead or from the reservoir under downhole conditions. However, this process is time-consuming and very costly. To overcome these challenges, empirical correlations and artificial intelligence (AI) models can be applied to obtain these properties. The objective of this paper is to introduce new empirical correlations to estimate Pb and Rs based on three input parameters—reservoir temperature and oil and gas gravities. 760 data points were collected from different sources to build new AI models for Pb and Rs. The new empirical correlations were developed by integrating artificial neural network (ANN) with a modified self-adaptive differential evolution algorithm to introduce a hybrid self-adaptive artificial neural network (SaDE-ANN) model. The results obtained confirmed the accuracy of the developed SaDE-ANN models to predict the Pb and Rs of crude oils. This is the first technique that can be used to predict Rs and Pb based on three input parameters only. The developed empirical correlation for Pb predicts the Pb with a correlation coefficient (CC) of 0.99 and an average absolute percentage error (AAPE) of 6%. The same results were obtained for Rs, where the new empirical correlation predicts the Rs with a coefficient of determination (R2) of 0.99 and an AAPE of less than 6%. The developed technique will help reservoir and production engineers to better understand and manage reservoirs. No additional or special software is required to run the developed technique.
Dynamic changes in the osteoclast cytoskeleton in response to growth factors and cell attachment are controlled by β3 integrin (2003)

The beta3 integrin cytoplasmic domain, and specifically S752, is critical for integrin localization and osteoclast (OC) function. Because growth factors such as macrophage colony-stimulating factor and hepatocyte growth factor affect integrin activation and function via inside-out signaling, a process requiring the beta integrin cytoplasmic tail, we examined the effect of these growth factors on OC precursors. To this end, we retrovirally expressed various beta3 integrins with cytoplasmic tail mutations in beta3-deficient OC precursors. We find that S752 in the beta3 cytoplasmic tail is required for growth factor-induced integrin activation, cytoskeletal reorganization, and membrane protrusion, thereby affecting OC adhesion, migration, and bone resorption. The small GTPases Rho and Rac mediate cytoskeletal reorganization, and activation of each is defective in OC precursors lacking a functional beta3 subunit. Activation of the upstream mediators c-Src and c-Cbl is also dependent on beta3. Interestingly, although the FAK-related kinase Pyk2 interacts with c-Src and c-Cbl, its activation is not disrupted in the absence of functional beta3. Instead, its activation is dependent upon intracellular calcium, and on the beta2 integrin. Thus, the beta3 cytoplasmic domain is responsible for activation of specific intracellular signals leading to cytoskeletal reorganization critical for OC function.
SARS: Understanding the Virus and Development of Rational Therapy (2005)

In late 2002 a new disease, severe atypical respiratory syndrome (SARS), emerged in China. A hitherto unknown animal coronavirus (CoV) that had crossed the species barrier through close contact of humans with infected animals was identified as the etiological agent. It rapidly adapted to the new host and not only became readily transmissible between humans but also more pathogenic. Air travel spread it rapidly around the world and ultimately the virus infected 8096 people and caused 774 deaths in 26 countries on 5 continents. Aggressive quarantine measures successfully terminated the disease. Currently, there are no SARS cases recorded and most likely the virus no longer circulates in the human population. In this review we present an overview over SARS-Co virus biology, the disease and discuss strategies to develop antiviral drugs and vaccines.
A Performance Model for Memory Bandwidth Constrained Applications on Graphics Engines (2012)

Graphics engines are excellent execution platforms for high-throughput computations that exploit a large degree of available parallelism. The achieved performance is, however, highly dependent on the access patterns that the applicationimposes on the memory subsystem. Here, we propose an analytic model that helps improve the understanding of the performance of memory-limited kernels that employ randommemory access schemes, especially as impacted by cache andvarious configuration parameters that can be used to tunekernel execution, such as the number of blocks and the number of threads per block. The analytic model is first explored through the use of a synthetic micro-benchmark, which is then followed by an empirical validation using a pair of production applications used in computational biology.
The Relationship of Foot Shape and Sensitivity to Comfort of Shoe-Inserts (1998)

Abstract : Army personnel are generally very physically active individuals performing various different physical activities. The choice of appropriate footwear is essential for any physical activity and any specific individual. It is speculated that comfortable footwear will optimize an individual's performance and reduce the frequency of traumatic and overuse injuries. Although it is generally accepted that individuals with different foot and leg characteristics require subject specific functional footwear, this option is not readily available to army personnel. This is probably due to the fact that footwear requirements for specific foot and leg characteristics are not available. For example, if an individual has a high arched foot, do they require footwear with a high or low arch? To increase performance and decrease injuries it is necessary to determine which specific characteristics of the human foot or leg determine the reaction to different footwear and insert variables. Ultimately, this information should be used to prescribe appropriate footwear to specific individuals. This study is a first step in understanding this complex set of questions.
A New Way to Burn Fat (2006)

Acetyl-CoA carboxylase controls fat storage and utilization in adipose cells. An important regulator of this enzyme modulates its degradation and is a potential therapeutic target for treatment of insulin resistance and obesity.
P‐27: Adaptive Display Color Correction Based on Real‐time Viewing Angle Estimation (2004)

Abstract We propose a method for adaptive LCD color correction through manipulating the pixel values to be displayed based on automatically detected viewing angle. The viewing angle detection is achieved through gaze/eye/face detection and tracking in the image/video captured by a camera that is fixed on the display. The proposed approach does not require physical modifications to the LCD display.
Extrapolation of Ventricular Activation Times From Sparse Electroanatomical Data Using Graph Convolutional Neural Networks (2021)

Electroanatomic mapping is the gold standard for the assessment of ventricular tachycardia. Acquiring high resolution electroanatomic maps is technically challenging and may require interpolation methods to obtain dense measurements. These methods, however, cannot recover activation times in the entire biventricular domain. This work investigates the use of graph convolutional neural networks to estimate biventricular activation times from sparse measurements. Our method is trained on more than 15,000 synthetic examples of realistic ventricular depolarization patterns generated by a computational electrophysiology model. Using geometries sampled from a statistical shape model of biventricular anatomy, diverse wave dynamics are induced by randomly sampling scar and border zone distributions, locations of initial activation, and tissue conduction velocities. Once trained, the method accurately reconstructs biventricular activation times in left-out synthetic simulations with a mean absolute error of 3.9 ms ± 4.2 ms at a sampling density of one measurement sample per cm 2 . The total activation time is matched with a mean error of 1.4 ms ± 1.4 ms. A significant decrease in errors is observed in all heart zones with an increased number of samples. Without re-training, the network is further evaluated on two datasets: (1) an in-house dataset comprising four ischemic porcine hearts with dense endocardial activation maps; (2) the CRT-EPIGGY19 challenge data comprising endo- and epicardial measurements of 5 infarcted and 6 non-infarcted swines. In both setups the neural network recovers biventricular activation times with a mean absolute error of less than 10 ms even when providing only a subset of endocardial measurements as input. Furthermore, we present a simple approach to suggest new measurement locations in real-time based on the estimated uncertainty of the graph network predictions. The model-guided selection of measurement locations allows to reduce by 40% the number of measurements required in a random sampling strategy, while achieving the same prediction error. In all the tested scenarios, the proposed approach estimates biventricular activation times with comparable or better performance than a personalized computational model and significant runtime advantages.
The VMP multiprocessor: initial experience, refinements and performance evaluation (2003)

VMP is an experimental multiprocessor being developed at Stanford University, suitable for high-performance workstations and server machines. Its primary novelty lies in the use of software management of the per-processor caches and the design decisions in the cache and bus that make this approach feasible. The design and some uniprocessor trace-driven simulations indicating its performance have been reported previously. Initial experience with the VMP design, based on a running prototype as well as various refinements to the design, is presented. Performance evaluation is based both on measurement of actual execution as well as trace-driven simulation of multiprocessor executions from the Mach operating system.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Predicting the behavior of cellulose nanocrystal suspensions and expanding their use at high temperatures (2019)

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