gebhart/patrepeval huggingface dataset:
Typing of Candida krusei clinical isolates by restriction endonuclease analysis and hybridization with CkF1,2 DNA probe (1994)

The use of restriction endonuclease analysis and Southern hybridization with our new CkF1,2 DNA probe, cold labeled with peroxidase, for the typing of Candida krusei isolates has been investigated. Fifty-five clinical samples isolated from forty-five patients hospitalized in eight centers, one environmental strain, and two reference strains were evaluated. Patterns were analyzed by a computer-assisted method and compared by numerical analysis. Clearer and less ambiguous patterns were obtained by restriction with endonuclease HinfI. It generated 9 to 14 (average, 11) well-separated fragments in the range of 6.5 to 2.0 kb. Both their numbers and sizes varied greatly among the strains studied. The CkF1,2 probe hybridized with one to seven fragments of HinfI patterns. A total of 48 distinct types were distinguished among the 58 strains studied. HinfI and CkF1,2 patterns showed similarities of less than 83 and 75% for unrelated strains and more than 91 and 100% for related strains, respectively. The methods showed 100% typeability, 98% reproducibility, and a discriminatory power of 1. C. krusei isolates from each patient were distinct, whether from one hospital or from different hospitals. Multiple isolates from the same patient were identical, both over time and at different anatomic sites. An endogenous origin is suggested for the colonizing and infecting isolates among the 45 patients. The CkF1,2 probe enhanced discrimination of the strains and provided a definitive comparison for strain identity. Genetic linkages between isolates were assessed at the subspecies level, and 12 clusters were delineated. A typing scheme is proposed for epidemiological studies of C. krusei.
Mitochondrial DNA and Disease (1995)

The mitochondrial encephalomyopathies are a diverse group of disorders that result from the structural, biochemical, or genetic derangement of mitochondria.1 Since mitochondrial dysfunction can affect virtually all organ systems (Figure 1), physicians in many specialties see patients with mitochondrial diseases. Despite a bewildering array of clinical manifestations (Table 1 and Table 2) and variations in the mode of onset, course, and progression of disease, many mitochondrial disorders share prominent systemic effects (Table 2) that contribute to their morbidity.Our understanding of the role of mitochondrial DNA in certain diseases has evolved rapidly since 1988, when the first mutations in mitochondrial DNA were . . .
Radiation-Force Assisted Targeting Facilitates Ultrasonic Molecular Imaging (2004)

Ultrasonic molecular imaging employs contrast agents, such as microbubbles, nanoparticles, or liposomes, coated with ligands specific for receptors expressed on cells at sites of angiogenesis, inflammation, or thrombus. Concentration of these highly echogenic contrast agents at a target site enhances the ultrasound signal received from that site, promoting ultrasonic detection and analysis of disease states. In this article, we show that acoustic radiation force can be used to displace targeted contrast agents to a vessel wall, greatly increasing the number of agents binding to available surface receptors. We provide a theoretical evaluation of the magnitude of acoustic radiation force and show that it is possible to displace micron-sized agents physiologically relevant distances. Following this, we show in a series of experiments that acoustic radiation force can enhance the binding of targeted agents: The number of biotinylated microbubbles adherent to a synthetic vessel coated with avidin increases as much as 20-fold when acoustic radiation force is applied; the adhesion of contrast agents targeted to alpha(v)beta3 expressed on human umbilical vein endothelial cells increases 27-fold within a mimetic vessel when radiation force is applied; and finally, the image signal-to-noise ratio in a phantom vessel increases up to 25 dB using a combination of radiation force and a targeted contrast agent, over use of a targeted contrast agent alone.
Maturation of 17 beta-estradiol binding protein in the hypothalamus and anterior pituitary of male rats. (1978)

Levels of estrogen binding proteins in the cytosol of hypothalamic and pituitary tissue of male rats at different ages were estimated. Two classes of estrogen binding sites were detected in 13 and 20 days old animals. The number of high affinity estrogen binding sites (K = ca. 2 x 10(-10) mol) of the hypothalamus was slightly larger in 13 days old animals, then decreased to constant levels at the age of 20 days and no changes were observed thereafter. Levels of low affinity binding sites of the hypothalamus (K = ca. 5 x 10(-9) mol) decreased with age and were no longer detectable in 30 days old animals. Similarly, a decrease of low affinity estrogen binding sites with age was recorded for pituitary cytosol samples and this class of receptor sites was no longer observable in 30 days old male rat. At 13 days high levels of high affinity 17 beta-estradiol binding protein was registered and minimal numbers of binding sites were found at 20, 30 and 40 days. Thereafter, the levels remained constant until 100 days and were similar to values observed in the 13 days old male animals. Apparent affinity constants of two classes of binding sites in hypothalamus and pituitary were similar...
A motion planning processor on reconfigurable hardware (2006)

Motion planning algorithms enable us to find feasible paths for moving objects. These algorithms utilize feasibility checks to differentiate valid paths from invalid ones. Unfortunately, the computationally expensive nature of such checks reduces the effectiveness of motion planning algorithms. However, by using hardware acceleration to speed up the feasibility checks, we can greatly enhance the performance of the motion planning algorithms. Of course, such acceleration is not limited to feasibility checks; other components of motion planning algorithms can also be accelerated using specially designed hardware. A field programmable gate array (FPGA) is a great platform to support such an acceleration. An FPGA is a collection of digital gates which can be reprogrammed at run time, i.e., it can be used as a CPU that reconfigures itself for a given task. In this paper, we study the feasibility of an FPGA based motion planning processor and evaluate its performance. In order to leverage its highly parallel nature and its modular structure, our processor utilizes the probabilistic roadmap method at its core. The modularity enables us to replace the feasibility criteria with other ones. The reconfigurability lets us run our processor in different roles, such as a motion planning co-processor, an autonomous motion planning processor or dedicated collision detection chip. Our experiments show that such a processor is not only feasible but also can greatly increase the performance of current algorithms
Tsunami study from underwater landslides in the Gulf of Naples - Southern Tyrrhenian Sea, Italy: importance of the landslides directionality in 3D numerical modeling (2023)

In this study, we propose a 3D numerical modeling of tsunami waves generated by an underwater landslide. The simulated gravity instabilities are located in the Gulf of Naples. The availability of a detailed bathymetric map both with a good knowledge of the local geology allowed us to obtain reliable simulation results. Submarine landslides in the Gulf of Naples can be considered a potential tsunami hazard for the following reason: some dated landslides in the Gulf of Naples, suggest that triggering conditions for these landslides are connected to the seismicity of the area. There are many geological evidences of tsunami events in Gulf of Naples. In fact, several papers describe the effects induced by geological events on the tsunami origin. GEOWAVE numerical model was employed to simulate tsunami generation and propagation. Model results revealed that this probable landslide tsunami is capable of generating high waves and considerable run-ups along the coasts of countries near the landslide zone. A further important role in this study is determined by the directionality of the landslide which strongly influences the tsunami energy.
Revisiting Graduate Student Training to Address Agricultural and Environmental Societal Challenges (2017)

Core Ideas Society is faced with daunting environmental and agricultural challenges. There is a pressing need for multidisciplinary teams of collaborative scientists. Novel graduate educational models may be needed to train students to address grand challenges. An example of illustrating the model through microbiome science of plants and soil is presented. Society and the higher education system are faced with daunting challenges associated with supplying food, energy, and water to a growing population while maintaining environmental quality and preserving natural resources. Too often, the higher education system does not facilitate collaborative immersion required to foster concerted multidisciplinary efforts needed to address societal grand challenges. In this commentary, we present an innovative model of cohort education, which equips graduate students with core skills and enables collaborative dissertation research among students. In addition, we provide an example of a program aimed at understanding the plant–soil microbiome, a critical research area that may yield significant advances in plant health and productivity.
Electrochemical and Structural Studies of Petroleum Coke in Carbonate‐Based Electrolytes (1995)

The behavior of petroleum coke (Conoco) was examined in a propylene carbonate/ethylene carbonate/dimethylcarbonate (1/1/3 volume) mixture with as the lithium salt. The thermodynamics and the kinetics of the lithium intercalation/deintercalation processes in the carbon matrix were investigated by galvanostatic curves and by cyclic voltammetry. X‐ray measurements were also done.
Concurrent MCL1 and JUN amplification in pseudomyxoma peritonei: a comprehensive genetic profiling and survival analysis (2013)

Pseudomyxoma peritonei (PMP) is a rare abdominal malignancy. We hypothesized that next-generation exomic sequencing would identify recurrent mutations that may have prognostic or therapeutic implications. Ten patients were selected on the basis of availability of tissue and adequate follow-up. They were treated at our institution between September 2002 and August 2004. Using next-generation exomic sequencing, we tested for mutations in 236 cancer-related genes in formalin-fixed paraffin-embedded slides. MCL1 amplification was additionally tested with immunohistochemical staining. Detectable mutations were found in 8 patients (80%). Seven patients harbored a KRAS mutation, most commonly involving codon 12. Four GNAS mutations (R201H/R201C substitutions) were also detected. MCL1 and JUN were concurrently amplified in three patients. One patient with MCL1 and JUN amplification had concurrent amplification of MYC and NFKBIA. ZNF703 was amplified in one patient. Patients with MCL1 amplification were also found to express MCL1 with immunohistochemistry, but MCL1 expression was also detected in some patients without amplification. To our knowledge, we are the first to report MCL1 and JUN coamplification in PMP. Expression of MCL1 may not be completely dependent on amplification. The prognostic and therapeutic implications of these recurrent mutational events are the subject of ongoing investigation.
Image compression based on the Karhunen-Loeve color transform with Inverse Pyramid decomposition (2011)

In this paper is presented one new approach for efficient still image compression based on the Karhunen-Loeve color transform and the Inverse Pyramid decomposition. In result of the strong decorrelation between the color components after the transform, the image is successfully restored with retained image quality despite the significant reduction of the coefficients, used to compose the pyramidal representation. The presented approach permits flexible selection of the transform coefficients, together with corresponding quantization of their values. In result, it offers the ability to select a sequence of sets of coefficients, which produce restored images of consecutive increasing quality. The software implementation of the method in C++ confirmed its efficiency. A generalized part of the experimental results are presented in this paper together with corresponding conclusions.
Personalized structural biology reveals the molecular mechanisms underlying heterogeneous epileptic phenotypes caused by de novo KCNC2 variants (2022)

Whole-exome sequencing (WES) in the clinic has identified several rare monogenic developmental and epileptic encephalopathies (DEE) caused by ion channel variants. However, WES often fails to provide actionable insight for rare diseases, such as DEEs, due to the challenges of interpreting variants of unknown significance (VUS). Here, we describe a "personalized structural biology" (PSB) approach that leverages recent innovations in the analysis of protein 3D structures to address this challenge. We illustrate this approach in an Undiagnosed Diseases Network (UDN) individual with DEE symptoms and a <i>de novo</i> VUS in <i>KCNC2</i> (p.V469L), the Kv3.2 voltage-gated potassium channel. A nearby <i>KCNC2</i> variant (p.V471L) was recently suggested to cause DEE-like phenotypes. Computational structural modeling suggests that both affect protein function. However, despite their proximity, the p.V469L variant is likely to sterically block the channel pore, while the p.V471L variant is likely to stabilize the open state. Biochemical and electrophysiological analyses demonstrate heterogeneous loss-of-function and gain-of-function effects, as well as differential response to 4-aminopyridine treatment. Molecular dynamics simulations illustrate that the pore of the p.V469L variant is more constricted, increasing the energetic barrier for K<sup>+</sup> permeation, whereas the p.V471L variant stabilizes the open conformation. Our results implicate variants in <i>KCNC2</i> as causative for DEE and guide the interpretation of a UDN individual. They further delineate the molecular basis for the heterogeneous clinical phenotypes resulting from two proximal pathogenic variants. This demonstrates how the PSB approach can provide an analytical framework for individualized hypothesis-driven interpretation of protein-coding VUS.
ROBUST SOUND LOCALIZATION USING SMALL NUMBER OF MICROPHONES (2005)

In this paper, robust sound localization is proposed for systems with spatially distributed microphones fewer than 4, the minimum required criteria for 3D sound localization in the literature, in an effort to address the robustness issues of microphone failures. It is shown that, for three- and two-microphone systems, two and four samples of the Interaural Time Difference (ITD) measurements are required respectively. In a one-microphone system, five samples of the Interaural Intensity Difference (IID) measurement should be used instead. These investigations are important because if one microphone fails, the remaining system can still function to locate the sound source without significant impact on the localization system. In addition, our investigation also shows that a 3-microphone system can estimate the azimuth and elevation simultaneously, which usually requires 4 microphones in the literature. Simulation and experimental results are presented to illustrate the performance of a three-microphone system. Results show that the system can locate the sound source with satisfactory accuracy.
Experiments on adaptive antenna array diversity transceiver for base station application in W-CDMA mobile radio (2002)

This paper presents a configuration including a pilot symbol-assisted (PSA) adaptive antenna array diversity (AAAD) receiver/transmitter for base station (BS) applications in W-CDMA mobile radio, and performance results based on laboratory and field experiments. In our scheme, the receiver antenna weights are adaptively controlled by minimizing the generated mean squared error (MSE) after RAKE combining. This results in an improvement in the average signal-to-interference power ratio (SIR) for each user and is accomplished by directing beam nulls toward the interference. Transmitter antenna weights are generated by modifying the generated receiver antenna weights: RF circuitry calibration and carrier frequency calibration. The experimental results using the implemented four-antenna PSA-AAAD transceiver show that it is effective in decreasing severe multiple access interference (MAI) from high rate users and is more effective than using a space diversity receiver with the same number of antennas in the W-CDMA reverse/forward links.
Understanding and Preventing Tacit Collusion among Telecommunication Operators (2009)

International audience
Serum Interleukin 9 Levels Are Increased in Patients with Systemic Sclerosis: Association with Lower Frequency and Severity of Pulmonary Fibrosis (2011)

Serum IL-9 level was increased in patients with SSc, and was associated with lower frequency and severity of pulmonary fibrosis in SSc. IL-9 could be a protective factor against the development of pulmonary fibrosis in this disease, and as such would be a possible therapeutic target.
Magnetic-field requirements for an active-control flap on a rotorcraft (1996)

In this paper, we describe a nonlinear constitutive relation for magnetostrictive materials that includes coupling between temperature, applied loads, and magnetic field strengths. The model is used to predict the magnetic field requirements for actuating a control flap to reduce the vibrational loads in a rotorcraft system. This prediction is based on the force/displacement requirements presently available in the literature for a particular flap. Results indicate that reasonable changes in the ambient temperature and centrifugal forces generated by the rotating blade strongly influence magnetic field requirements.
The hydrodynamic structure of unstable cellular detonations (2007)

The study analyses the cellular reaction zone structure of unstable methane–oxygen detonations, which are characterized by large hydrodynamic fluctuations and unreacted pockets with a fine structure. Complementary series of experiments and numerical simulations are presented, which illustrate the important role of hydrodynamic instabilities and diffusive phenomena in dictating the global reaction rate in detonations. The quantitative comparison between experiment and numerics also permits identification of the current limitations of numerical simulations in capturing these effects. Simulations are also performed for parameters corresponding to weakly unstable cellular detonations, which are used for comparison and validation. The numerical and experimental results are used to guide the formulation of a stochastic steady one-dimensional representation for such detonation waves. The numerically obtained flow fields were Favre-averaged in time and space. The resulting one-dimensional profiles for the mean values and fluctuations reveal the two important length scales, the first being associated with the chemical exothermicity and the second (the ‘hydrodynamic thickness’) with the slower dissipation of the hydrodynamic fluctuations, which govern the location of the average sonic surface. This second length scale is found to be much longer than that predicted by one-dimensional reaction zone calculations.
A Billion Open Interfaces for Eve and Mallory : MitM, DoS, and Tracking Attacks on iOS and macOS Through Apple Wireless Direct Link (2019)

Apple Wireless Direct Link (AWDL) is a key protocol in Apple's ecosystem used by over one billion iOS and macOS devices for device-to-device communications. AWDL is a proprietary extension of the IEEE 802.11 (Wi-Fi) standard and integrates with Bluetooth Low Energy (BLE) for providing services such as Apple AirDrop. We conduct the first security and privacy analysis of AWDL and its integration with BLE. We uncover several security and privacy vulnerabilities ranging from design flaws to implementation bugs leading to a man-in-the-middle (MitM) attack enabling stealthy modification of files transmitted via AirDrop, denial-of-service (DoS) attacks preventing communication, privacy leaks that enable user identification and long-term tracking undermining MAC address randomization, and DoS attacks enabling targeted or simultaneous crashing of all neighboring devices. The flaws span across AirDrop's BLE discovery mechanism, AWDL synchronization, UI design, and Wi-Fi driver implementation. Our analysis is based on a combination of reverse engineering of protocols and code supported by analyzing patents. We provide proof-of-concept implementations and demonstrate that the attacks can be mounted using a low-cost ($20) micro:bit device and an off-the-shelf Wi-Fi card. We propose practical and effective countermeasures. While Apple was able to issue a fix for a DoS attack vulnerability after our responsible disclosure, the other security and privacy vulnerabilities require the redesign of some of their services.
Tumor-Associated Macrophages Enhance Tumor Hypoxia and Aerobic Glycolysis (2019)

Tumor hypoxia and aerobic glycolysis are well-known resistance factors for anticancer therapies. Here, we demonstrate that tumor-associated macrophages (TAM) enhance tumor hypoxia and aerobic glycolysis in mice subcutaneous tumors and in patients with non-small cell lung cancer (NSCLC). We found a strong correlation between CD68 TAM immunostaining and PET <sup>18</sup>fluoro-deoxyglucose (FDG) uptake in 98 matched tumors of patients with NSCLC. We also observed a significant correlation between <i>CD68</i> and glycolytic gene signatures in 513 patients with NSCLC from The Cancer Genome Atlas database. TAM secreted TNFα to promote tumor cell glycolysis, whereas increased AMP-activated protein kinase and peroxisome proliferator-activated receptor gamma coactivator 1-alpha in TAM facilitated tumor hypoxia. Depletion of TAM by clodronate was sufficient to abrogate aerobic glycolysis and tumor hypoxia, thereby improving tumor response to anticancer therapies. TAM depletion led to a significant increase in programmed death-ligand 1 (PD-L1) expression in aerobic cancer cells as well as T-cell infiltration in tumors, resulting in antitumor efficacy by PD-L1 antibodies, which were otherwise completely ineffective. These data suggest that TAM can significantly alter tumor metabolism, further complicating tumor response to anticancer therapies, including immunotherapy. SIGNIFICANCE: These findings show that tumor-associated macrophages can significantly modulate tumor metabolism, hindering the efficacy of anticancer therapies, including anti-PD-L1 immunotherapy.