gebhart/patrepeval huggingface dataset:
PEA-15 Inhibits Tumor Cell Invasion by Binding to Extracellular Signal-Regulated Kinase 1/2 (2007)

Phosphoprotein enriched in astrocytes of 15 kDa (PEA-15) binds to extracellular signal-regulated kinase 1 and 2 (ERK1/2) mitogen-activated protein (MAP) kinases to alter ERK1/2 cellular localization and target preferences and binds to adaptors in the extrinsic cell death pathway to block apoptosis. Here, we report that PEA-15 protein expression is inversely correlated with the invasive behavior of breast cancer in an immunohistochemical analysis of a breast cancer progression tissue microarray. Short hairpin RNA-mediated inhibition of PEA-15 expression increased the invasion of PEA-15-expressing tumor cells in vitro, suggesting a causative role for PEA-15 in the inhibition of invasion. This causative role was confirmed by the finding that the enforced expression of PEA-15 in invasive tumor cells reduced invasion. The effect of PEA-15 on tumor invasion is mediated by its interaction with ERK1/2 as shown by the following: (a) PEA-15 mutants that fail to bind ERK1/2 did not inhibit invasion; (b) overexpression of ERK1 or activated MAP/ERK kinase (MEK) reversed the inhibitory effect of PEA-15; (c) when an inhibitor of ERK1/2 activation reduced invasion, PEA-15 expression did not significantly reduce invasion further. Furthermore, we find that the effect of PEA-15 on invasion seems to relate to the nuclear localization of activated ERK1/2. PEA-15 inhibits invasion by keeping ERK out of the nucleus, as a PEA-15 mutant that cannot prevent ERK nuclear localization was not able to inhibit invasion. In addition, membrane-localized ERK1, which sequesters endogenous ERK1 to prevent its nuclear localization, also inhibited invasion. These results reveal that PEA-15 regulates cancer cell invasion via its ability to bind ERK1/2 and indicate that nuclear entry of ERK1/2 is important in tumor behavior.
Calbindin D28K Overexpression Protects Striatal Neurons From Transient Focal Cerebral Ischemia (2001)

We conclude that viral vector-mediated overexpression of CaBP leads to neuroprotection in this model of central nervous system injury. This is the first demonstration that CaBP overexpression protects neurons in a focal stroke model.
Supplementary Table 10 from Somatic Mosaic Chromosomal Alterations and Death of Cardiovascular Disease Causes among Cancer Survivors (2023)

&lt;p&gt;Supplementary Table 10: The effect of expanded mosaic chromosomal alterations on death of cardiovascular disease causes, coronary artery disease causes, from cancer, and any cause of death&lt;/p&gt;
Relationship of postsaccadic oscillation with the state of the pupil inside the iris and with cognitive processing (2019)

Recent studies using video-based eye tracking have presented accumulating evidence that postsaccadic oscillation defined in reference to the pupil center (PSOp) is larger than that to the iris center (PSOi). This indicates that the relative motion of the pupil reflects the viscoelasticity of the tissue of the iris. It is known that the pupil size controlled by the sphincter/dilator pupillae muscles reflects many aspects of cognition. A hypothesis derived from this fact is that cognitive tasks affect the properties of PSOp due to the change in the state of these muscles. To test this hypothesis, we conducted pro- and antisaccade tasks for human participants and adopted the recent physical model of PSO to evaluate the dynamic properties of PSOp/PSOi. The results showed the dependence of the elasticity coefficient of the PSOp on the antisaccade task, but this effect was not significant for the PSOi. This suggests that cognitive tasks such as antisaccade tasks affect elasticity of the muscle of the iris. We found that the trial-by-trial fluctuation in the presaccade absolute pupil size correlated with the elasticity coefficient of PSOp. We also found the task dependence of the viscosity coefficient and overshoot amount of PSOi, which probably reflects the dynamics of the entire eyeball movement. The difference in task dependence between PSOp and PSOi indicates that the separate measures of these two can be means to distinguish factors related to the oculomotor neural system from those related to the physiological states of the iris tissue.<b>NEW & NOTEWORTHY</b> The state of the eyeball varies dynamically moment by moment depending on underlying neural/cognitive processing. Combining simultaneous measurements of pupil-centric and iris-centric movements and a recent physical model of postsaccadic oscillation (PSO), we show that the pupil-centric PSO is sensitive to the type of saccade task, suggesting that the physical state of the iris muscles reflects the underlying cognitive processes.
A combined order selection and parameter estimation algorithm for undamped exponentials (2000)

We propose an approximate maximum likelihood parameter estimation algorithm, combined with a model order estimator for superimposed undamped exponentials in noise. The algorithm combines the robustness of Fourier-based estimators and the high-resolution capabilities of parametric methods. We use a combination of a Wald (1945) statistic and a MAP test for order selection and initialize an iterative maximum likelihood descent algorithm recursively based on estimates at higher candidate model orders. Experiments using simulated data and synthetic radar data demonstrate improved performance over MDL, MAP, and AIC in places of practical interest.
Verification of chip multiprocessor memory systems using a relaxed scoreboard (2008)

Verification of chip multiprocessor memory systems remains challenging. While formal methods have been used to validate protocols, simulation is still the dominant method used to validate memory system implementation. Having a memory scoreboard, a high-level model of the memory, greatly aids simulation based validation, but accurate score-boards are complex to create since often they depend not only on the memory and consistency model but also on its specific implementation. This paper describes a methodology of using a relaxed scoreboard, which greatly reduces the complexity of creating these memory models. The relaxed scoreboard tracks the operations of the system to maintain a set of values that could possibly be valid for each memory location. By allowing multiple possible values, the model used in the scoreboard is only loosely coupled with the specific design, which decouples the construction of the checker from the implementation, allowing the checker to be used early in the design and to be built up incrementally, and greatly reduces the scoreboard design effort. We demonstrate the use of the relaxed scoreboard in verifying RTL implementations of two different memory models, Transactional Coherency and Consistency (TCC) and Relaxed Consistency, for up to 32 processors. The resulting checker has a performance slowdown of 19% for checking Relaxed Consistency, and less than 30% for TCC, allowing it to be used in all simulation runs.
MUSCLE-DERIVED STEM CELLS PROMOTE PERIPHERAL NERVE AND SKELETAL MUSCLE REPAIR BUT GENERATE TUMORS IN A NICHE DEPENDENT MANNER (2002)

5cells) were transplanted into the gastrocnemius muscles of mdx (dystrophic) mice. Mice were sacrificed 2 weeks after transplantation, and the gastrocnemius muscles were harvested, frozen, and cryostat-sectioned. Neurogenic differentiation was examined by creating a Seven-millimeter sciatic nerve defects in SCID mice. Immediately thereafter, FN-MDSCs or phosphate buffered saline (PBS; control) was injected into the defects. Some of the mice from each group were sacrificed 6 weeks after transplantation, and the hind limbs, including the sciatic nerve and gastrocnemius muscles, were harvested, frozen, and cryostat-sectioned for further analysis. LacZ expression was revealed by histochemistry, and immunohistochemistry was used to colocalize donor cells and neuronal markers. The remaining mice were kept until later time points (up to 15 weeks) to check for possible tumor formation.
Thermal Design and Packaging of a Prototype Refrigeration Cooling System for CMOS-Based MCMs (2003)

Thermal design and packaging strategy of a prototype dual-loop vapor compression refrigeration cooling system, developed as a pilot model for thermal management of high performance CMOS based MCMs, is introduced in this paper. The cooling system was comprised of two separated refrigeration units providing low temperature cooling via a dual-path cooling module (evaporator) mounted on a CPU-MCM package. Cooling capacity for each refrigeration unit was controlled ranging from 250W to 2500W with a refrigerant evaporating temperature at −25 degree centigrade. The CPU-MCM mounted with the refrigeration cooling module was packaged on a system board assembly, together with other electronic devices. The assembly was accommodated into a dew-point control box where two dewpoint control units were operating in a redundancy to remove moisture and keep a dew temperature inside the box below −30 degree centigrade for completely preventing from condensation. Cooling redundancy was provided by both the refrigeration units and dual-path cooling module. The cooling module was redundant in that two sets of refrigerant passages were staggered within a thin copper plate, where each set was connected to a separated refrigeration unit. Apart from the robust system and steady operation, the configuration and operation mode also provided the cooling system a high power efficiency and much shortened starting time. Numerical simulations were also performed for investigating airflow and thermal characteristics, in a system board level inside the dew-point control box. Detailed predictions of airflow and temperature distributions were significantly helpful for improving and verifying practical system designs.
061 Metabolic alteration in hypertrophic cardiomyopathy (METAL-HCM Study): randomised double blinded placebo controlled trial of perhexiline therapy in patient with hypertrophic cardiomyopathy (2010)

<h3>Background</h3> Patients with hypertrophic cardiomyopathy (HCM) exhibit myocardial energetic impairment, but a causative role for this energy deficiency in the pathogenesis of HCM remains unproven. We hypothesised that the metabolic modulator, perhexiline would ameliorate myocardial energy deficiency and thereby improve diastolic function and exercise capacity. <h3>Methods</h3> Forty-six consecutive patients with symptomatic exercise limitation (peak oxygen consumption – peak VO2&lt;75% of predicted) due to non-obstructive HCM (mean age 55±0.26 years old) were randomised to perhexiline (n=25) or placebo (n=21). Myocardial PCr/ATP ratio, an established marker of cardiac energetic status, as measured by 31P magnetic resonance spectroscopy, LV diastolic filling (heart rate normalised time to peak filling, nTTPF) at rest and during exercise using radionuclide ventriculography, peak VO2, symptoms, quality of life and serum metabolites were assessed at baseline and at the end of the study (4.6±1.8 months). (ClinicalTrials.gov identifier, NCT00500552). <h3>Results</h3> Perhexiline improved myocardial PCr/ATP ratios (from 1.27±0.02 to 1.73±0.02; p=0.003) and normalised the abnormal prolongation of nTTPF between rest and exercise (δ nTTPF: +0.11±0.008 s vs −0.01±0.005; p=0.03). These changes were accompanied by improvement in peak VO2 (22.2±0.2 to 24.29±0.2 ml/kg/min; p=0.003) and symptoms (NYHA class by 0.8 units p&lt;0.001) (all p-values ANCOVA). <h3>Conclusion</h3> In symptomatic HCM, perhexiline, a modulator of substrate metabolism, ameliorates cardiac energetic impairment, corrects diastolic dysfunction and increases exercise capacity. This study supports the hypothesis that energy deficiency contributes to the pathogenesis and provides a rationale for further consideration of metabolic therapies in HCM.
Structure and Spectromagnetic Properties of the Superoxide Radical Adduct of the DMPO in Water: Elucidation by Theoretical Investigations (2010)

In the field of spin trapping chemistry, the design of more efficient radical traps can be assisted by the development of theoretical methods able to give a quantitative evaluation of the electron paramagnetic resonance (EPR) spectrum features of the spin-adduct radical, even before initiating the experimental work. The superoxide radical adduct of the 5,5-dimethyl-1-pyrroline-&lt;i&gt;N&lt;/i&gt;-oxide nitrone (DMPO−OOH) has been reported in a huge number of papers devoted to the study of the oxidative stress. Here, we present for the first time the theoretical study of DMPO−OOH in an explicit water solution, based on the combined QM/MM//MD protocol we recently proposed, featuring a full coupling between the solute and all the explicit water molecules. Our results show that the DMPO−OOH EPR spectrum, whose interpretation is still debated, can be explained in the light of two sites in chemical exchange, in agreement with the most recent experimental data. Moreover, we demonstrate that each site consists of an equilibrium between the two main 5-membered ring conformations of DMPO−OOH. We provide also an analysis of the solvent contribution to the hyperfine coupling constants (hcc’s) as well as an exhaustive study of the possible relationship between the hcc’s and the main structural characteristics of DMPO−OOH. Our QM/MM//MD protocol appears thus to be an accurate theoretical tool allowing the investigation of the magnetic properties of large nitroxide spin adducts in complex environments.
Biochemical and immunological characterization of rat spleen prostaglandin D synthetase. (1987)

Rat spleen prostaglandin D synthetase (Christ-Hazelhof, E., and Nugteren, D. H. (1979) Biochim. Biophys. Acta 572, 43-51) is very similar to rat brain prostaglandin D synthetase (Urade, Y., Fujimoto, N., and Hayaishi O. (1985) J. Biol. Chem. 260, 12410-12415) as judged by their pI (4.7-5.2), Mr (26,000-27,000), and self-inactivation during the isomerase reaction from prostaglandin H2 to prostaglandin D2. However, the amino acid compositions of these two enzymes were quite different. Furthermore, the spleen enzyme was associated with the glutathione S-transferase activity, differing from the brain enzyme. The synthetase and transferase activities of the spleen enzyme showed almost identical pH and glutathione dependencies, the optimum pH = 8.0 and Km for glutathione = 300 microM. The Km values for prostaglandin H2 and 1-chloro-2,4-dinitrobenzene (a substrate for the transferase) were about 200 microM and 5 mM, respectively. The synthetase activity was dose-dependently inhibited by 1-chloro-2,4-dinitrobenzene (IC50: approximately 5 mM) and more strongly by nonsubstrate ligands, such as bilirubin and indocyanine green (IC50: 150 and 2 microM, respectively). Both the synthetase and transferase activities of the purified enzyme dose-dependently decreased and showed identical immunotitration curves by incubation with antibody against this enzyme, but remained unchanged when treated with antibody against the brain enzyme. The antibody specific for the spleen enzyme absorbed almost all of the synthetase activity and about 10% of the transferase activity in the spleen, but not the transferase activity in the liver, heart, and testis. These results show that the two types of prostaglandin D synthetase are similar but different enzymes and that the spleen enzyme is a unique glutathione S-transferase differing from other isozymes and their subunits reported previously.
Snapshot molecular imaging using coded energy-sensitive detection (2013)

We demonstrate a technique for measuring the range-resolved coherent scatter form factors of different objects from a single snapshot. By illuminating the object with an x-ray pencil beam and placing a coded aperture in front of a linear array of energy-sensitive detector elements, we record the coherently scattered x-rays. This approach yields lateral, range, and momentum transfer resolutions of 1 mm, 5 mm, and 0.2 nm⁻¹, respectively, which is sufficient for the distinguishing a variety of solids and liquids. These results indicate a path toward real-time volumetric molecular imaging for non-destructive examination in a variety of applications, including medical diagnostics, quality inspection, and security detection.
Deep Probabilistic Programming Languages: A Qualitative Study (2018)

Deep probabilistic programming languages try to combine the advantages of deep learning with those of probabilistic programming languages. If successful, this would be a big step forward in machine learning and programming languages. Unfortunately, as of now, this new crop of languages is hard to use and understand. This paper addresses this problem directly by explaining deep probabilistic programming languages and indirectly by characterizing their current strengths and weaknesses.
Optimal entry point and trajectory for endoscopic third ventriculostomy: evaluation of 53 patients with volumetric imaging guidance (2012)

While the entry point may need to be modified from the ideal trajectory for other anatomical reasons, such as a trajectory through the motor cortex, in general, the authors found that the optimal entry point for ETV was more posterior than previously published and highly variable. Using image guidance or a customized trajectory based on analysis of a patient's own imaging is highly preferable to using an empirical ideal trajectory.
Regulation of testicular insulin-like growth factor-I in pubertal growth hormone-deficient male rats (1991)

GH plays a major role in pubertal growth, effects mainly mediated by stimulation of insulin-like growth factor-I (IGF-I) production by the liver. However, the role of GH in the regulation of pubertal onset, spermatogenesis and fertility is still under debate. GH and FSH have, in addition, been implicated in the regulation of IGF-I production by Sertoli cells in a number of studies, although conflicting results have been reported. The interpretation of studies using GH-deficient mutant mice has been complicated by the presence of additional defects in the hypothalamic-pituitary-gonadal axis of these animals. We have therefore used GH-deficient mutant male rats with no other documented hormonal deficiencies to study the effect of GH administration on somatic and testicular development, circulating and testicular IGF-I concentrations and testicular histology. Body weights in GH-deficient rats substituted with GH were not significantly different from untreated or GH-treated normal rats and were significantly higher than body weights in untreated dwarf rats. Similarly, circulating IGF-I concentrations in GH-treated GH-deficient rats were not significantly different from those in untreated or GH-treated normal rats but were significantly higher than circulating IGF-I concentrations in untreated dwarf rats. No differences in testicular IGF-I concentrations were observed in any of the groups studied. Testicular weights remained low in both untreated and GH-treated GH-deficient animals compared with control animals but spermatogenesis was qualitatively and quantitatively normal in all groups at the end of the observation period.(ABSTRACT TRUNCATED AT 250 WORDS)
Implementing SDL specifications using algebraic reduction techniques (1989)

Proposes a new strategy for automatic code synthesis without the drawbacks of simple translations schemes. Its prime advantage is that the performance of the generated code is insensitive to the way and degree of partitioning of its specifications. By eliminating the 'internal' interprocess communication, it also solves the problem of queue dimensioning. The main idea behind the proposed method is to map SDL onto some kind of process algebra. The problem with SDL is that it is a language and not an algebra: there is no way of telling whether two SDL expressions are equivalent, apart from their being textually identical. Since the semantics of SDL are formally defined (which happened only recently), one can argue that two SDL expressions are equivalent when they exhibit the same behaviour (whatever that may be) but one still lacks operators that can be applied to SDL expressions. By mapping SDL onto a true process algebra, one has the opportunity to apply transformations on a specification, working toward a more efficient implementation while preserving the overall behaviour, and to analyze the specified behaviour. >
A decision-process analysis of implicit coscheduling (2002)

This paper presents a theoretical framework based on Bayesian decision theory for analyzing recently reported results on implicit coscheduling of parallel applications on clusters of workstations. Using probabilistic modeling, We show that the approach presented can be applied for processes with arbitrary communication mixes. We also note that our approach can be used for deciding the additional spin times in the case of spin-yield. Finally, we present arguments for the use of a different notion of fairness than assumed by prior work.
Linac4 PIMS Construction and First Operation (2017)

Linac4, CERN's new H⁻ injector Linac uses PI-Mode Structures (PIMS) for the energy range between 10³ and 160 MeV. 180 copper elements for 12 PIMS cavities have been fabricated in a collaboration between CERN, NCBJ and FZJ from 2011 to 2016. The cavities have been assembled, RF tuned and validated at CERN. This paper reports on the results as well as the experience with construction, installation, RF conditioning and first operation with beam.
Combined multistep heterogeneous transition metal catalysis and aminocatalysis for asymmetric cascade reactions (2013)

Combined multistep heterogeneous transition metal catalysis and aminocatalysis for asymmetric cascade reactions
An SRAM-Based Multibit In-Memory Matrix-Vector Multiplier With a Precision That Scales Linearly in Area, Time, and Power (2020)

A novel interleaved switched-capacitor and SRAM-based multibit matrix-vector multiply-accumulate engine for in-memory computing is presented. Its operation principle is based on first converting an SRAM-stored n-bit weight into a proportional voltage using a pipeline D/A converter built from n+1 equally sized stages. A switched-capacitor stage then multiplies these voltages with an m-bit digital input activation. Finally, the output voltages that correspond to the different multiplication results are accumulated along one column by means of charge-sharing. With our proposed architecture, the required circuit area, computation time, and power consumption scale linearly versus the bit resolution of both the inputs and the weights. Analytical formulas are presented for the energy consumption in both capacitors and switches. Moreover, the impact of fabrication mismatch on analog computation accuracy is examined. The full system architecture is described, and the feasibility is demonstrated, via a full macroimplementation study in 14 nm, detailing area and energy consumption, as well as the overall latency. Finally, a specific design of a 128 × 2048 6 -bit weight and 6-bit input signed matrix-vector multiplication accelerator system in 14 nm is presented, which runs at 2.43 TOP/s at an efficiency of 16.94 TOP/s/W, while using the nominal supply voltage of 0.8 V. If the operands' precision is considered in the metric, then the efficiency becomes 609.7 TOP/s/W.