gebhart/patrepeval huggingface dataset:
Glycolysis is the primary bioenergetic pathway for cell motility and cytoskeletal remodeling in human prostate and breast cancer cells (2014)

The ability of a cancer cell to detach from the primary tumor and move to distant sites is fundamental to a lethal cancer phenotype. Metabolic transformations are associated with highly motile aggressive cellular phenotypes in tumor progression. Here, we report that cancer cell motility requires increased utilization of the glycolytic pathway. Mesenchymal cancer cells exhibited higher aerobic glycolysis compared to epithelial cancer cells while no significant change was observed in mitochondrial ATP production rate. Higher glycolysis was associated with increased rates of cytoskeletal remodeling, greater cell traction forces and faster cell migration, all of which were blocked by inhibition of glycolysis, but not by inhibition of mitochondrial ATP synthesis. Thus, our results demonstrate that cancer cell motility and cytoskeleton rearrangement is energetically dependent on aerobic glycolysis and not oxidative phosphorylation. Mitochondrial derived ATP is insufficient to compensate for inhibition of the glycolytic pathway with regard to cellular motility and CSK rearrangement, implying that localization of ATP derived from glycolytic enzymes near sites of active CSK rearrangement is more important for cell motility than total cellular ATP production rate. These results extend our understanding of cancer cell metabolism, potentially providing a target metabolic pathway associated with aggressive disease.
Step Response Analysis of MEMS Electro-Thermal Gas Sensors of Differing Geometry (2016)

MEMS gas sensors have the advantage of low power operation, fast response time, and have attracted a lot of interest because of their potential low cost. There is a need for monitoring of changes in the environment, in particular for carbon dioxide and methane. These gases can be detected using electro-thermal method based upon thermal conductivity changes. MEMS based micro-TCD which are ultra-low power, requiring less than 6 uJ per measurement and have a response time 100uS or less [1]. Because of their rapid response time they are also very suitable for MEMS-GC systems [2]. We have investigated different modes of pulsed operation for these sensors using constant current, constant resistance, constant power and constant energy. The detection of helium and hydrogen in nitrogen indicated a low level of detection less than 500ppm or better. A comparison of thermal time constants and resistance response for micro-thermal conductivity sensors with different aspect ratio, surface area to volume, operated at constant power density or at similar average temperatures will be discussed. Fitting a model based upon kinetic theory of gases to temperature dependent sensor response of gas mixtures has potential for evaluation of multi component mixtures. References [1]A. Mahdavifar, M. Findlay, J. R. Stetter, P. J. Hesketh, “Transient thermal response of micro-thermal conductivity detector for the identification of gas mixtures: An ultra-fast and low power method,” Nature Microsystems and Nanooengineering Vol. 1 , pg. 15025 (2015). [2] A. Mahdavifar , M. Navaei , P. J. Hesketh , J. D. Dimandja , J. R. Stetter , G. McMurray, “Implementation of a polysilicon micro electro-thermal detector in gas chromatography system with applications in portable environmental monitoring,” Journal of Solid State Science and Technology, Vol. 4, No. 10, pp. S1-S5 (2015).
Off-axis scatterer filters for improved aberration measurements (2004)

Successful adaptive imaging requires accurate measurements of the aberration profile across the array surface. A spatial filter is proposed in this work to obtain more accurate aberration measurements by suppressing wavefronts from off-axis scatterers. Application of these filters to the RF signals of the individual elements rejects wavefronts arriving from angles other than the look direction and results in an increase in element-to-element correlation. Off-axis scatterer filtering reduced the amount of residual error after phase correction by up to 36% on a 1 /spl times/ 192 array and as much as 21% for a 8 /spl times/ 96 array. Contrast measurements show that lesion contrast can increase up to 18% with this method.
Accurate IoT Based Slope Instability Sensing System for Landslide Detection (2022)

Landslides are one of the prominent natural disasters in India that account for an estimated property loss of 66 million USD and the fatality of 200 lives in the Himalayan region and the Western Ghats every year. The present systems for monitoring, detecting and early warning of these landslides are based upon radar satellite interferometry, laser scanning or LIDAR, high-resolution imaging via satellites and wireless geophysical sensor networks. All the above systems are either too expensive for large area deployment or less accurate or lack real-time characteristics required for landslide detection. Above all different types of landslides like rainfall induced landslides, earthquake induced landslides, creep landslides, shallow landslides and deep seated landslides pose several challenges in monitoring and detection such as (a) time duration for event detection (swift to long duration) (b) localizing the slip surface depth for event detection (c) recurrence of the precursor triggering events (d) extent of durability of sensor system (e) uncertainty in spatial coverage of the event. To address the above challenges, this paper proposes the design and development of a wireless integrated landslide monitoring system. To enhance the reliability of this system, a low-cost slope instability sensing sensor was also integrated to this Landslide Early Warning System. This sensor’s design, development, testing and calibration is the primary focus of this paper. Further,the paper also discusses about the real-world deployment of this system to monitor one of the thickly populated landslide-prone area in Sikkim, North Eastern Himalayas.
Fine-grained access control of personal data (2012)

The immensity and variety of personal information (e.g., profile, photo, and microblog) on social sites require access control policies tailored to individuals' privacy needs. Today such policies are still mainly specified manually by ordinary users, which is usually coarse-grained, tedious, and error-prone. This paper presents the design, implementation, and evaluation of an automated access control policy specification tool, XACCESS, that helps non-expert users effectively specify who should have access to which part of their data. A series of key features distinguish XACCESS from prior work: 1) it adopts a role-based access control model (instead of the conventional rule-based paradigm) to capture the implicit privacy/interest preference of social site users; 2) it employs a novel hybrid mining method to extract a set of semantically interpretable, functional "social roles", from both static network structures and dynamic historical activities; 3) based on the identified social roles, confidentiality setting of personal data, and (optional and possibly inconsistent) predefined user-permission assignments, it recommends a set of high-quality privacy settings; 4) it allows user feedback in every phase of the process to further improve the quality of the suggested privacy policies. A comprehensive experimental evaluation is conducted over real social network and user study data to validate the efficacy of XACCESS.
CERAPP: Collaborative Estrogen Receptor Activity Prediction Project (2020)

BACKGROUND: Humans are exposed to thousands of man-made chemicals in the environment. Some chemicals mimic natural endocrine hormones and, thus, have the potential to be endocrine disruptors. Most of these chemicals have never been tested for their ability to interact with the estrogen receptor (ER). Risk assessors need tools to prioritize chemicals for evaluation in costly in vivo tests, for instance, within the U.S. EPA Endocrine Disruptor Screening Program. OBJECTIVES: We describe a large-scale modeling project called CERAPP (Collaborative Estrogen Receptor Activity Prediction Project) and demonstrate the efficacy of using predictive computational models trained on high-throughput screening data to evaluate thousands of chemicals for ER-related activity and prioritize them for further testing. METHODS: CERAPP combined multiple models developed in collaboration with 17 groups in the United States and Europe to predict ER activity of a common set of 32,464 chemical structures. Quantitative structure-activity relationship models and docking approaches were employed, mostly using a common training set of 1,677 chemical structures provided by the U.S. EPA, to build a total of 40 categorical and 8 continuous models for binding, agonist, and antagonist ER activity. All predictions were evaluated on a set of 7,522 chemicals curated from the literature. To overcome the limitations of single models, a consensus was built by weighting models on scores based on their evaluated accuracies. RESULTS: Individual model scores ranged from 0.69 to 0.85, showing high prediction reliabilities. Out of the 32,464 chemicals, the consensus model predicted 4,001 chemicals (12.3%) as high priority actives and 6,742 potential actives (20.8%) to be considered for further testing. CONCLUSION: This project demonstrated the possibility to screen large libraries of chemicals using a consensus of different in silico approaches. This concept will be applied in future projects related to other end points. CITATION: Mansouri K, Abdelaziz A, Rybacka A, Roncaglioni A, Tropsha A, Varnek A, Zakharov A, Worth A, Richard AM, Grulke CM, Trisciuzzi D, Fourches D, Horvath D, Benfenati E, Muratov E, Wedebye EB, Grisoni F, Mangiatordi GF, Incisivo GM, Hong H, Ng HW, Tetko IV, Balabin I, Kancherla J, Shen J, Burton J, Nicklaus M, Cassotti M, Nikolov NG, Nicolotti O, Andersson PL, Zang Q, Politi R, Beger RD, Todeschini R, Huang R, Farag S, Rosenberg SA, Slavov S, Hu X, Judson RS. 2016. CERAPP: Collaborative Estrogen Receptor Activity Prediction Project. Environ Health Perspect 124:1023-1033; http://dx.doi.org/10.1289/ehp.1510267.
Subcortical atrophy and cognition (2012)

Six years postdiagnosis, almost all subcortical structures were affected by MS, especially in men. Cognition was most severely affected in male patients. Thalamic volume, sex, and education best predicted average cognition. These results underline the relevance of specific subcortical structures to cognition, as well as the relevance of (sex-specific) atrophy in MS.
Sound Field Reproduction using the Lasso (2010)

Reproducing a sampled sound field using an array of loudspeakers is a problem with well-appreciated applications to acoustics and ultrasound treatment. Loudspeaker signal design has traditionally relied on (possibly regularized) least-squares (LS) criteria. In many cases however, the desired sound field can be reproduced using only a few loudspeakers, which are sparsely distributed in space. To exploit this feature, the fresh look advocated here permeates benefits from advances in variable selection and compressive sampling to sound field synthesis by formulating a sparse linear regression problem that is solved using the least-absolute shrinkage and selection operator (Lasso). An efficient implementation of the Lasso for the problem at hand is developed based on a coordinate descent iteration. Analysis and simulations demonstrate that Lasso-based sound field reproduction yields better performance than LS especially at high frequencies and for reproduction of under-sampled sound fields. In addition, Lasso-based synthesis enables judicious placement of loudspeaker arrays.
A physical-space approach for the probability hypothesis density and cardinalized probability hypothesis density filters (2006)

The probability hypothesis density (PHD) filter, an automatically track-managed multi-target tracker, is attracting increasing but cautious attention. Its derivation is elegant and mathematical, and thus of course many engineers fear it; perhaps that is currently limiting the number of researchers working on the subject. In this paper, we explore a physical-space approach - a bin model - which leads us to arrive the same filter equations as the PHD. Unlike the original derivation of the PHD filter, the concepts used are the familiar ones of conditional probability. The original PHD suffers from a "target-death" problem in which even a single missed detection can lead to the apparent disappearance of a target. To obviate this, PHD originator Mahler has recently developed a new "cardinalized" version of PHD (CPHD). We are able to extend our physical-space derivation to the CPHD case as well. We stress that the original derivations are mathematically correct, and need no embellishment from us; our contribution here is to offer an alternative derivation, one that we find appealing.
Low Specific Contact Resistivity Measurements using a New Test Structure and its Reduction to 10−9 ohm-cm2 in p-type SiGe/Metal Contacts using Flash Lamp Annealing (2019)

Reduction of the contact resistance at source/drain and metal electrodes is one of the key challenges in the fabrication of high performance CMOS devices. In recent years, several studies have addressed the issue of minimizing the specific contact resistivity (ρ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> ) [1] - [5] . Quite low values of ρ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> in the sub-10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-9</sup> ohm-cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> region have been reported for advanced technologies.
DOPAMINE (2022)

In this paper, we investigate how Joint Communication And Sensing (JCAS) can be used to improve the Inertial Measurement Unit (IMU)-based tracking accuracy of eXtended Reality (XR) Head-Mounted Displays (HMDs). Such tracking is used when optical and InfraRed (IR) tracking is lost, and its lack of accuracy can lead to disruption of the user experience. In particular, we analyze the impact of using doppler-based speed estimation to aid the accelerometer-based position estimation, and Angle of Arrival (AoA) estimation to aid the gyroscope-based orientation estimation. Although less accurate than IMUs for short times in fact, the JCAS based methods require one fewer integration step, making the tracking more sustainable over time. Based on the proposed model, we conclude that at least in the case of the position estimate, introducing JCAS can make long lasting optical/IR tracking losses more sustainable.
Activation of group I metabotropic glutamate receptors produces a direct excitation and disinhibition of GABAergic projection neurons in the substantia nigra pars reticulata (2001)

A pathological increase in excitatory glutamatergic input to substantia nigra pars reticulata (SNr) from the subthalamic nucleus (STN) is believed to play a key role in the pathophysiology of Parkinson's disease. We present an analysis of the physiological roles that group I metabotropic glutamate receptors (mGluRs) play in regulating SNr functions. Immunocytochemical analysis at the light and electron microscopic levels reveal that both mGuR1a and mGluR5 are localized postsynaptically in the SNr. Consistent with this, activation of group I mGluRs depolarizes SNr GABAergic neurons. Interestingly, although both group I mGluRs (mGluR1 and mGluR5) are expressed in these neurons, the effect is mediated solely by mGluR1. Light presynaptic staining for mGluR1a and mGluR5 was also observed in some terminals forming symmetric synapses and in small unmyelinated axons. Consistent with this, activation of presynaptic mGluR1a and mGluR5 decreases inhibitory transmission in the SNr. The combination of direct excitatory effects and disinhibition induced by activation of group I mGluRs could lead to a large excitation of SNr projection neurons. This suggests that group I mGluRs are likely to play an important role in the powerful excitatory control that the STN exerts on basal ganglia output neurons.
Proteolytic fragments of the nicotinic acetylcholine receptor identified by mass spectrometry: implications for receptor topography (1989)

A triple-state quadrupole or a tandem quadrupole Fourier-transform mass spectrometer was used to detect and sequence the peptides released by proteolytic cleavage of the acetylcholine receptor (AcChR) from Torpedo californica electroplax. Fragments in mass range up to 3479 daltons were characterized on the above instrumentation and used to determine proteolytically accessible sites on the receptor. These data were consistent with the cleavage points determined for membrane-bound fragments of the same AcChR samples using gas-phase microsequencing. Each subunit of the receptor is readily cleaved near the C-terminus in the region between the proposed transmembrane hydrophobic alpha-helices MIII and MIV. This region includes the putative regulatory phosphorylation sites and the amphipathic alpha-helix. Cleavage is also observed in the N-terminal domain, but occurs much more slowly than in the C-terminal region. No cleavage was detected in the middle third of the receptor, which includes the proposed transmembrane alpha-helices MI and MII. An evaluation of these data in terms of the transmembrane topography of the AcChR peptides is consistent with a synaptic or extracellular disposition for the region between MIII and MIV.
Monolithic integrated InP distributed bragg reflector (DBR) lasers on (001) silicon (2015)

Silicon Photonics more and more is considered as a competitive platform for building complex photonic ICs, applicable in various fields, but the lack of a practical on-chip integrated compact, high-yield and electricallydriven laser source remains a major bottleneck. Due to its indirect bandgap, silicon itself is a poor light emitter. Therefore, new materials such as Germanium, III-V compounds and rare earth doped nanocrystals are being investigated and laser operation from hybrid III-V lasers 1, monolithic Germanium lasers 2 and monolithic IIIV nanowire lasers 3 has been demonstrated. While III-V provides generally better performance, realizing monolithically integrated in-plane lasers that can be integrated with other waveguide circuits remains extremely challenging. In this paper, using a selective area growth technique originally developed for realizing nextgeneration ultrafast electronic transistors, we demonstrate a room temperature operating monolithic integrated inplain InP DBR laser grown on a standard 300mm (001)-silicon substrate. Conventional approaches for growing III-V compounds on silicon require a micrometers-thick buffer to cope with the large lattice mismatch and thermal expansion coefficient difference between silicon and III-Vs. In our work, InP waveguides were selectively grown inside narrow trenches defined by a Shallow-Trench-Isolation (STI) method 4 and V-groove etching. The transmission electron microscope (TEM) image shown in Fig. 1a shows that the InP-material is of high crystalline quality except for the 20nm buffer layer located at the InP-Si interface. Following the epitaxy, we defined first order Bragg gratings (165 nm period, 60 nm etching depth, and 50% Duty Cycle) on top of the diamond-shape InP-waveguides using electron beam lithography (EBL) and plasma etching. Next, the silicon substrate beneath the InP was removed using a selective dry etch process to prevent leakage of the optical field (Fig. 1b). For characterization, 7 ns pump pulses from a 532 nm Nd:YAG nanosecond pulsed laser are delivered to the sample in a uniform rectangular area covering a single cavity. After being scattered by the second order grating located at one end of the DBR laser, the laser emissions is collected by a 50x, 0.65 numerical aperture (NA) objective and measured through a 1⁄4 m monochromator. The single mode spectrum in Fig. 1c and the S-shaped light-light curve convincingly show the devices exhibit indeed laser operation. Efficiencies of more than 5% and high reproducibility of these results over multiple devices and multiple wafers has been demonstrated. The top-down integration process, high yield and high controllability together with the in-plane laser configuration, thin buffer layer and selective area process make this device highly promising as a source for future photonic ICs.
Emergence of Pork Carnitas as a Cause of Foodborne Disease Outbreaks in Chicago (2004)

Carnitas are fried chunks of pork frequently served in Mexican-origin households, food service establishments, and social gatherings. During 1995-2002, carnitas emerged as the most frequently implicated vehicle of transmission in foodborne disease outbreaks in Chicago. Five (6%) of 90 foodborne disease outbreaks investigated and reported in Chicago during this period were linked to carnitas, and they accounted for 108 illnesses and 11 hospitalizations. The etiologic agent in four outbreaks was Salmonella, and these outbreaks accounted for 29% of the 14 Salmonella-associated foodborne disease outbreaks in Chicago during this period. Unsafe food handling practices that occurred after cooking were identified as contributing to multiple carnitas-associated outbreaks. Local health departments that serve significant Mexican-origin populations should be aware of carnitas as a potential source of foodborne disease, particularly salmonellosis.
A touch-and-go lipid wrapping technique in microfluidic channels for rapid fabrication of multifunctional envelope-type gene delivery nanodevices (2011)

Multifunctional envelope-type gene delivery nanodevices (MENDs) are promising non-viral vectors for gene therapy. Though MENDs remain strong in prolonged exposure to blood circulation, have low immunogenic response, and are suitable for gene targeting, their fabrication requires labor-intensive processes. In this work, a novel approach has been developed for rapid fabrication of MENDs by a touch-and-go lipid wrapping technique in a polydimethylsiloxane (PDMS)/glass microfluidic device. The MEND was fabricated on a glass substrate by introduction of a condensed plasmid DNA core into microfluidic channels that have multiple lipid bilayer films. The principle of the MEND fabrication in the microfluidic channels is based on electrostatic interaction between the condensed plasmid DNA cores and the coated lipid bilayer films. The constructed MEND was collected off-chip and characterized by dynamic light scattering. The MEND was constructed within 5 min with a narrow size distribution centered around 200 nm diameter particles. The size of the MEND showed strong dependence on flow velocity of the condensed plasmid DNA core in the microfluidic channels, and thus, could be controlled to provide the optimal size for medical applications. This approach was also proved possible for fabrication of a MEND in multiple channels at the same time. This on-chip fabrication of the MEND was very simple, rapid, convenient, and cost-effective compared with conventional methods. Our results strongly indicated that MENDs fabricated with our microfluidic device have a good potential for medical use. Moreover, MENDs fabricated by this microfluidic device have a great potential for clinical use because the devices are autoclavable and all the fabrication steps can be completed inside closed microfluidic channels without any external contamination.
<title>Stark anomalous dispersion optical filter for doubled Nd:YLF lasers</title> (1994)

The Stark anomalous dispersion optical filter is a wide-frequency-tunable ultra-narrow bandwidth optical filter. The first theoretical investigation of this filter, which matched wavelength with doubled Nd:YLF lasers for deepspace laser communications, is reported. The results show that the filter may provide about 86% transmission, 1.6 GHz bandwidth, 3 GHz noise equivalent bandwidth, and wide frequency tuning range.