gebhart/patrepeval huggingface dataset:
Numerical Simulation of Local Blood Flow in the Carotid and Cerebral Arteries Under Altered Gravity (2005)

A computational fluid dynamics (CFD) approach was presented to model the blood flows in the carotid bifurcation and the brain arteries under altered gravity. Physical models required for CFD simulation were introduced including a model for arterial wall motion due to fluid-wall interactions, a shear thinning fluid model of blood, a vascular bed model for outflow boundary conditions, and a model for autoregulation mechanism. The three-dimensional unsteady incompressible Navier-Stokes equations coupled with these models were solved iteratively using the pseudocompressibility method and dual time stepping. Gravity source terms were added to the Navier-Stokes equations to take the effect of gravity into account. For the treatment of complex geometry, a chimera overset grid technique was adopted to obtain connectivity between arterial branches. For code validation, computed results were compared with experimental data for both steady-state and time-dependent flows. This computational approach was then applied to blood flows through a realistic carotid bifurcation and two Circle of Willis models, one using an idealized geometry and the other using an anatomical data set. A three-dimensional Circle of Willis configuration was reconstructed from subject-specific magnetic resonance images using an image segmentation method. Through the numerical simulation of blood flow in two model problems, namely, the carotid bifurcation and the brain arteries, it was observed that the altered gravity has considerable effects on arterial contraction/dilatation and consequent changes in flow conditions.
Synthesis of the Racemate of the Stereoisomer at C-6a of BE-40644, a Bioactive Metabolite of Actinoplanes sp. with a Sesquiterpene-substituted p-Benzoquinone Structure (2001)

BE-40644 is a tetracyclic metabolite of Actinoplanes sp. A 40644 possessing a sesquiterpene-substituted p-benzoquinone structure with cis-fused B/C ring stereochemistry that inhibits the human thioredoxin system as the well as the growth of several cancer cell lines. Its B/C trans-fused stereoisomer at C-6a was synthesized as a racemate starting from geranylacetone and 3,5-dihydroxybenzoic acid.
Preparation and characterization of surface plasmon resonance tunable gold and silver films (2002)

Precise control of thermal evaporation deposition parameters allows the reproducible production of silver and gold island films on glass substrates with tunable surface plasmon resonance wavelengths. Specific combinations of substrate temperature, deposition rate, and film thickness produce films exhibiting surface plasmon resonance wavelengths that can be adjusted from throughout the visible and into the near infrared regions of the electromagnetic spectrum. The effects of deposition parameters on surface plasmon resonance wavelengths are quantified using a so-called “design of experiment” analysis. The analysis produces reliable predictive models for producing Ag and Au films with predetermined surface plasmon resonance wavelengths.
Unstable atherosclerotic plaque. Pathophysiology and therapeutic guidelines. (1998)

Plaque disruption promoted by local inflammation and oxidative stress seem to be the triggering mechanisms of acute coronary syndromes. Oxidized low-density lipoproteins (LDL) play a key role in this inflammatory process. Within the inflammatory region, angiotensin-converting enzyme (ACE) accumulation has been described, leading to enhanced production of local angiotensin II which stimulates adhesion molecule expression and increases oxidative stress (leading to excessive degradation of EDNO). According to recent clinical trials, drugs like statins or ACE inhibitors seem promising and could stabilize the plaque, probably by attenuation of the inflammatory process. Finally, as thrombus formation also plays a role in these acute coronary syndromes, another approach may be the use of antithrombotic therapy.
Role of Surface Iron in Enhanced Activity for the Oxygen Reduction Reaction on a Pd<sub>3</sub>Fe(111) Single‐Crystal Alloy (2011)

Working together: Pd0.9Fe0.1–Pd3Fe(111) (see picture, Pd adatoms yellow, Fe purple, Pd blue-green, O red, H white) displays enhanced performance for the oxygen reduction reaction with five to eight times higher activity than Pd(111). The high catalytic activity may originate from a cooperative effect of a segregated Pd layer with its large tendency to remove surface O species by protonation and active Fe with its ability to dissociate O2. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Effect of nucleotide excision repair on <i>hprt</i> gene mutations in rodent cells exposed to DNA ethylating agents (1997)

The role of the nucleotide excision repair (NER) pathway in removal of DNA ethylation damage was investigated by means of hprt mutational spectra analysis in the NER-deficient Chinese hamster ovary cell line UV5, which lacks ERCC2/XPD, and in its parental cell line AA8. Both cell lines were exposed to ethyl methanesulfonate (EMS) or N-ethyl-N-nitrosourea (ENU). EMS gave a similar dose-dependent increase in hprt mutants in UV5 compared with AA8. In both cell lines EMS-induced mutations in the hprt coding region consisted almost exclusively of GC-->AT transitions, probably due to the direct miscoding lesion O6-ethylguanine. ENU, an agent that in addition to O6-ethylguanine also induces other O-alkylation products, was significantly more mutagenic in UV5 than in AA8. Mutational spectra analysis showed that the proportions of ENU-induced GC-->AT, AT-->TA and AT-->GC base pair changes were similar for both cell lines. ENU-induced DNA lesions that may be involved in GC-->AT transitions are O6-ethylguanine and O2-ethylcytosine, the latter being a chemically stable DNA lesion of which the miscoding properties and repair characteristics are largely unknown. ENU-induced AT-->TA transversions are probably caused by O2-ethylthymine, which mispairs with thymine. In AA8 thymines in ENU-induced AT-->TA transversions were exclusively located in the non-transcribed strand of the hprt gene, whereas in UV5 30% of these thymines were found in the transcribed strand. Together, these results indicate that O6-ethylguanine is a poor substrate for NER in rodent cells and that O2-ethylpyrimidines are preferentially removed from the transcribed strand of the hprt gene by NER.
Quality-fair HTTP adaptive streaming over LTE network (2014)

In HTTP adaptive streaming (HAS) applications multiple video clients sharing the same wireless channel may experience different video qualities as result of both different video content complexity and different channel conditions. This causes unfairness in the end-user video quality. In this paper, we propose a quality-fair adaptive streaming (QFAS) solution to deliver fair video quality to HAS clients competing for the same resources in an LTE cell. In the QFAS framework the share of radio resource is optimized according to video content characteristics and channel condition. The proposed solution is compared with other state-of-the-art strategies and numerical results in terms of SSIM quality metric shows that it significantly improves the quality fairness among heterogeneous HAS users.
Automatic Extrinsic Calibration of a Camera and a 3D LiDAR Using Line and Plane Correspondences (2018)

In this paper, we address the problem of extrinsic calibration of a camera and a 3D Light Detection and Ranging (LiDAR) sensor using a checkerboard. Unlike previous works which require at least three checkerboard poses, our algorithm reduces the minimal number of poses to one by combining 3D line and plane correspondences. Besides, we prove that parallel planar targets with parallel boundaries provide the same constraints in our algorithm. This allows us to place the checkerboard close to the LiDAR so that the laser points better approximate the target boundary without loss of generality. Moreover, we present an algorithm to estimate the similarity transformation between the LiDAR and the camera for the applications where only the correspondences between laser points and pixels are concerned. Using a similarity transformation can simplify the calibration process since the physical size of the checkerboard is not needed. Meanwhile, estimating the scale can yield a more accurate result due to the inevitable measurement errors of the checkerboard size and the LiDAR intrinsic scale factor that transforms the LiDAR measurement to the metric measurement. Our algorithm is validated through simulations and experiments. Compared to the plane-only algorithms, our algorithm can obtain more accurate result by fewer number of poses. This is beneficial to the large-scale commercial application.
Source and path recovery from vibration response monitoring (1987)

Thesis. (M.S.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 1987.
Repair Machinery of Symbiotic Photosynthesis as the Primary Target of Heat Stress for Reef-Building Corals (2004)

In a coral-algae symbiotic system, heat-dependent photoinhibition of photosystem II (PSII) leads to coral bleaching. When the reef-building coral Acropora digitifera was exposed to light, a moderate increase of temperature induced coral bleaching through photobleaching of algal pigments, but not through expulsion of symbiotic algae. Monitoring of PSII photoinhibition revealed that heat-dependent photoinhibition was ascribed to inhibition of the repair of photodamaged PSII, and heat susceptibility of the repair machinery varied among coral species. We conclude that the efficiency of the photosynthesis repair machinery determines the bleaching susceptibility of coral species under elevated seawater temperatures.
The Stimulation of Uterine Complement Component C3 Gene Expression by Antiestrogens (1990)

We have previously demonstrated that complement component C3 is regulated by estradiol in the rat uterus. The antiestrogens tamoxifen, LY117018, and LY156758 exert both agonist and antagonist effects on the immature rat uterus. In this study, these three antiestrogens also stimulated an increase in the synthesis and secretion of C3. The combination of LY117018 and estradiol did not increase C3 to a greater extent than LY117018 alone, which suggests a similar mechanism of regulation. The regulation may be transcriptional since both estradiol and tamoxifen increase the concentration of C3 mRNA. Results of in situ hybridization revealed that the increase in C3 mRNA occurred in the luminal epithelial cells. Although the induction by estradiol and the antiestrogens was similar in most aspects, the time course for tamoxifen-stimulated synthesis differed from estradiol in that the time required to achieve maximal concentrations of C3 was delayed by 12 h with tamoxifen. This pattern did not appear to be related to the time it took to convert tamoxifen to 4-hydroxytamoxifen since the C3 response for these antiestrogens were identical. The antiestrogen-stimulated increase in C3 synthesis and mRNA concentration was prevented by the co-administration of progesterone lending support to the hypothesis that the antiestrogens regulate C3 synthesis via a mechanism similar to estrogen.
Direct determination of grain-boundary and dislocation self-diffusion coefficients in silver from experiments in type-C kinetics (1992)

The use of an implanted, mass-separated carrier-free 105Ag radiotracer improves the sensitivity for measuring grain-boundary (GB) penetration profiles. In this way the GB self-diffusion coefficient DGB in silver was directly determined from experiments in type-C kinetics conditions. When multiplying the DGB values with a GB width δ=0.5 nm the results are in agreement with GB diffusivities P=δDGB measured in the same Ag material in the usual type-B kinetics experiments which were performed between 911 and 540 K and extrapolated to the low-temperature regime of type-C kinetics experiments (455–353 K). From the near-surface part of the type-C diffusion profiles the dislocation diffusion coefficient Dd was directly determined. These Dd values are compared with experiments of Turnbull and Hoffman [Acta Metall. 2, 419 (1954)] who applied the dislocation pipe model for a low-angle-tilt GB in silver. The good agreement confirms a dislocation core diameter of about 0.5 nm.
Execution Trace Analysis through Massive Sequence and Circular Bundle Views (2008)

Preprint of article published in: Journal of Systems and Software (Elsevier), 81 (12), 2008; doi:10.1016/j.jss.2008.02.068 An important part of many software maintenance tasks is to gain a sufficient level of understanding of the system at hand. The use of dynamic information to aid in this software understanding process is a common practice nowadays. A major issue in this context is scalability: due to the vast amounts of information, it is a very difficult task to successfully navigate through the dynamic data contained in execution traces without getting lost. In this paper, we propose the use of two novel trace visualization techniques based on the massive sequence and circular bundle view, which both reflect a strong emphasis on scalability. These techniques have been implemented in a tool called Extravis. By means of distinct usage scenarios that were conducted on three different software systems, we show how our approach is applicable in three typical program comprehension tasks: trace exploration, feature location, and top-down analysis with domain knowledge.
A 45,X sterile male with Yp disguised as 21p (2002)

An azoospermic male was found to have, by means of banding techniques, a 45,X karyotype including a monocentric chromosome 21 with an euchromatic short arm that looked similar to Yp. This rearranged chromosome was further characterized by FISH with a whole Y chromosome paint and the alphoid repeats DYZ3 and D13Z1/D21Z1; the former probe gave a positive signal onto such a peculiar arm without spreading into the long arm, whereas the alphoid repeats revealed an apparent compound centromere with Y- and 21-sequences. Therefore, an unbalanced Y;21 whole arm translocation was concluded and the karyotype written as 45,X.ish der(Y;21)(p10;q10)(wcpY+,DYZ3+,D13Z1/D21Z1+). This patient represents the first case of a Y;21 translocation in an apparent 45,X male, constitutes the fifth instance of a 45,X sterile male, and conforms to previously established karyotype-phenotype correlations.
Major Molecular Markers in Pancreatic Ductal Adenocarcinoma and Their Roles in Screening, Diagnosis, Prognosis, and Treatment (2011)

Pancreatic cancer is notorious for its late presentation, early and aggressive local invasion, metastatic potential, and poor outcome. It presents at a clinically advanced stage that precludes the possibility of surgical resection in most cases and shows constitutive resistance to chemotherapy and radiotherapy in others. As a result, mortality from this disease parallels its incidence rates.Recent breakthroughs in the molecular biology of pancreatic cancer have assisted in translational research, giving hope for individualized therapy and better disease management. Molecular biology tools are guiding early diagnosis, the assessment of prognosis, and isolation of novel, more effective therapeutic targets.This review discusses the signature mutations of pancreatic cancer, implications of these mutations to pancreatic cancer biology, their linked pathways, and recent advances in their understanding as biomarkers as diagnostic, prognostic, and therapeutic tools in dealing with this disease.
All-fiber wavelength- and mode-selective coupler for optical interconnections (2002)

We experimentally demonstrate a new wavelength- and mode-selective coupler utilizing intermodal coupling between a standard single-mode fiber (SMF) and a hollow optical fiber (HOF). The fabricated device routes optical signals such that a 1.3-microm signal is directed to the HOF port, adiabatically converting the LP(01) mode into a ring-shaped mode, which can be further connected to a gigabit ethernet link, reducing the differential mode-dispersion penalty. Optical signals near 1.5microm , meanwhile, stay in the LP(01) mode of the SMF arm for further connection to conventional wavelength-division multiplexing links based on erbium-doped fiber amplifiers. The performance of the device is characterized in terms of insertion loss, channel isolation, and mode-conversion efficiency.
A String Constraint Solver for Detecting Web Application Vulnerability. (2010)

Given the bytecode of a software system, is it possible to automatically generate attack signatures that reveal its vulnerabilities? A natural solution would be symbolically executing the target system and constructing constraints for matching path conditions and attack patterns. Clearly, the constraint solving technique is the key to the above research. This paper presents Simple Linear String Equation (SISE), a formalism for specifying constraints on strings. SISE uses finite state transducers to precisely model various regular replacement operations, which makes it applicable for analyzing text processing programs such as web applications. We present a recursive algorithm that computes the solution pool of a SISE. Given the solution pool, a concrete variable solution can be generated. The algorithm is implemented in a Java constraint solver called SUSHI, which is applied to security analysis of web applications. 1
Retracted: Predictive Validity of a Medication Adherence Measure in an Outpatient Setting (2008)

This study examines the psychometric properties and tests the concurrent and predictive validity of a structured, self-reported medication adherence measure in patients with hypertension. The authors also assessed various psychosocial determinants of adherence, such as knowledge, social support, satisfaction with care, and complexity of the medical regimen. A total of 1367 patients participated in the study; mean age was 52.5 years, 40.8% were male, 76.5% were black, 50.8% graduated from high school, 26% were married, and 54.1% had income <$5,000. The 8-item medication adherence scale was reliable (alpha=.83) and significantly associated with blood pressure control (P<.05). Using a cutpoint of <6, the sensitivity of the measure to identify patients with poor blood pressure control was estimated to be 93%, and the specificity was 53%. The medication adherence measure proved to be reliable, with good concurrent and predictive validity in primarily low-income, minority patients with hypertension and might function as a screening tool in outpatient settings with other patient groups.
A 131 GHz push-push VCO in 90-nm CMOS technology (2005)

A 131 GHz cross-coupled push-push voltage controlled oscillator (VCO) is realized in 90-nm CMOS technology. It can be tuned from 129.8 to 132 GHz, with an estimated phase noise of -108.4 dBc/Hz at 10 MHz offset. The oscillator provides a push-push output power of -15.2 dBm and a fundamental output power of +0.33 dBm, under core current of 20 mA from a 1-V supply voltage. Maximum push-push and fundamental output powers are -11.4 dBm and +2.1 dBm, respectively. To the authors' knowledge, this is the highest frequency CMOS VCO ever reported.
A survey of DNA motif finding algorithms (2007)

Despite considerable efforts to date, DNA motif finding remains a complex challenge for biologists and computer scientists. Researchers have taken many different approaches in developing motif discovery tools and the progress made in this area of research is very encouraging. Performance comparison of different motif finding tools and identification of the best tools have proven to be a difficult task because tools are designed based on algorithms and motif models that are diverse and complex and our incomplete understanding of the biology of regulatory mechanism does not always provide adequate evaluation of underlying algorithms over motif models.
Optimal Blade System Design of a New Concept VTOL Vehicle Uusing the Departmental Computing Grid System (2005)

The blade system of a new concept VTOL vehicle is designed utilizing high performance and Grid computing technologies. The VTOL vehicle called cyclocopter employs a cycloidal propulsion system to generate the propulsion and lift for VTOL maneuver. The structural design and weight minimization of the composite blade system are critically related to the efficiency of whole cyclocopter system. The structural design is carried out using a hybrid genetic algorithm-based optimization framework on the Departmental Computing Grid(DCG) system, an aggregation of cluster resources installed in the Aerospace department of Seoul National University. High-fidelity simulation is conducted using our parallel finite element code (IPSAP) which employs the domain-wise parallel multifrontal solver, a direct solution method characterized by the solution robustness and the predictability of running time. The optimization results and computational aspects are displayed emphasizing the potential of the high performance Grid computing technology utilized for high-fidelity simulation based aerospace system design.
Discrete element simulation and experimental study of powder spreading process in additive manufacturing (2016)

Powders used in additive manufacturing (AM) are spread onto a compact layer of particles for sintering and this process is repeated layer by layer to form the final products. Spreading of rod-shaped particles in realistic AM settings is simulated using the discrete element method (DEM) to investigate the effects of particle shape and operating conditions on the bed quality, characterised by its surface roughness and solid volume fraction. It is discovered that larger particle aspect ratios, A r , or higher spreader translational velocities result in a lower bed quality, i.e. a larger surface roughness and a smaller volume fraction. The surface roughness increases monotonically with A r . However, the volume fraction exhibits a maximum at A r = 1.5 for randomly packed powder beds that are formed by the roller type spreaders moving at low translational velocities. It is also found that a roller outperforms a blade spreader in terms of the quality of the prepared bed at the same operating conditions. The micro-structural analysis of the beds also shows particle alignment in response to the induced flow, which is qualitatively confirmed by a set of purposelydesigned experiments. In addition, a shape segregation is documented for powders with mixed aspect ratios (A r ) such that particles with larger A r tend to accumulate on the upper layers of the bed.
Enhanced Waterflood for Middle East Carbonate Cores — Impact of Injection Water Composition (2011)

Abstract Carbonate coreflood experiments have demonstrated the potential for Advanced Ion Management (AIMSM) to significantly increase oil recovery compared to waterflood using formation water. AIMSM involves adding and/or removing ions from the injection water to improve waterflood performance. AIMSM further improves current state-of-the-art processes through the addition of certain salts and/or the softening of water. Simulations have accurately matched the experiments, providing a tool to assess field-scale recovery and supporting the premise that the increased recovery is due to a change in wettability. This study shows that a relatively inexpensive and straightforward modification of injection water composition can significantly increase oil recovery.