gebhart/patrepeval huggingface dataset:
Polyoma virus middle T antigen: relationship to cell membranes and apparent lack of ATP-binding activity. (1982)

Middle T antigen of polyoma virus is associated principally with the plasma membrane. Comparison of the trypsin sensitivity of middle T in intact cells and "inside out" membrane preparations showed that middle T is oriented towards the inside of the cell. This was confirmed by labeling of middle T in permeabilized cells, but not in intact cells, using [gamma-32P]ATP. Middle T molecules active in the in vitro kinase reaction could be differentiated from the bulk (metabolically labeled) middle T based on resistance to trypsin treatment. The active fraction also behaved differently from the bulk when cell frameworks were prepared with Triton-containing buffers; whereas the bulk middle T was evenly distributed in the soluble and cell framework fractions, the kinase-active forms were largely associated with the framework. Middle T molecules labeled in vivo with 32PO4 were found largely in the framework fraction, like the molecules that show kinase activity in vitro. Experiments with ATP affinity reagents 8-azido-ATP and 2,3-dialdehyde ATP have failed to label the middle T antigen. However, 2,3-dialdehyde ATP could be used to inhibit the kinase reaction. This raises the question of whether middle T antigen possesses intrinsic kinase activity or, rather, associates with a cellular tyrosine kinase.
Identification of novel biomarker as citrullinated inter-alpha-trypsin inhibitor heavy chain 4, specifically increased in sera with experimental and rheumatoid arthritis (2018)

Our results suggest that serum citrullinated ITIH4 was specifically increased in patients with RA and could be a novel biomarker for assessing disease activity in patients with RA.
Resolving visual-tactual incongruity depends on sensory reliability (2005)

The visuomotor system recalibrates when visual and motor maps are in conflict, bringing the maps back into correspondence. For recalibration to occur, a conflict has to be detected. Here we investigate the effect of signal reliability on the rate of recalibration. In a first study we showed that the rate of recalibration in a one-dimensional visually guided pointing task depends on the uncertainty of the feedback: faster recalibration with less uncertainty. We further also examined two-dimensional recalibration and how the specific form of visual feedback affects it. Subjects pointed with an unseen hand to a brief visual target. Visual feedback was given indicating where the point landed. We introduced a constant incongruity between pointing (tactual) and feedback (visual) location and examined the changes in pointing as the subject recalibrated. With this task we asked whether differential vertical and horizontal uncertainty in the visual feedback affects recalibration rate differentially, or whether rate is determined by the total uncertainty. We also varied feedback uncertainty in two ways. (1) We blurred the visual feedback, thereby reducing its localizability; in this condition, uncertainty could be determined on-line from one feedback stimulus. (2) We introduced random trial-by-trial perturbations in the feedback; in this condition, uncertainty had to be learned over time. In both cases, the distributions determining the vertical and horizontal uncertainties were 2D Gaussians. Recalibration profiles (changes over time in the point location relative to the visual feedback) changed only in response to changes in localizability. Recalibration was slowest in the direction of greatest uncertainty when uncertainty was due to blur, but rate was unaffected by trial-by-trial variation. This means that subjects do not estimate uncertainty over time in order to adjust reaching. Rather, they adjust trial by trial based mostly on feedback from the previous trial.
Modeling and visualizing geo-sensitive queries based on user clicks (2008)

The number of search queries that are associated with geographical locations, either explicitly or implicitly, has been quadrupled in recent years. For such geo-sensitive queries, the ability to accurately infer users' geographical preference greatly enhances their search experience. By mining past user clicks and constructing a geographical click probability distribution model, we address two important issues in spatial Web search: how do we determine whether a search query is geo-sensitive, and how do we detect, disambiguate, and visualize the associated geographical location(s). We present our empirical study on a large-scale dataset with about 9,000 unique queries randomly drawn from the logs of a popular commercial search engine Yahoo! Search, and about 430 million user clicks on 1.6M unique Web pages over an eight-month period. Our classification method achieved recall of 0.98 and precision of 0.75 in identifying geo-sensitive search queries. We also present our preliminary findings in using geographical click probability distributions to cluster search results for queries with geographical ambiguities.
Passively Mode-Locked Pulse Generation at 40 GHz Repetition Rate by Semiconductor Lasers with Distributed Bragg Reflector for Oscillating Mode Control (2003)

Passively mode-locked pulse generations at a 40 GHz repetition rate were demonstrated without using any saturable absorbers. In a conventional dispersive Fabry-Perot cavity with the length corresponding to a mode-locking frequency of lower tens GHz, the phase differences between longitudinal modes become large and cause the out-of-phase mode-locking. In the present work, the gain section was restricted to a half-length of the cavity, then the phase differences were suppressed, and mode-locked pulse generations were achieved. A distributed Bragg reflector (DBR) was implemented in the cavity as an oscillating mode selector. The obtained pulses were almost transform-limited. A typical time-bandwidth product of 0.45 was obtained for a DBR length of 291 µm. By varying the DBR current, the center wavelength of mode-locked pulses was changed over 5 nm. Time-bandwidth products for pulses generated from lasers with various coupling lengths of DBR are also investigated experimentally.
Graph Cut Algorithms in Vision, Graphics and Machine Learning (2004)

This integrative paper studies graph-cut and network flow algorithms on graphs and compares its applications towards solving diverse problems in Computer Vision, Computer Graphics and Machine Learning. The following three papers form the core of this comparative study. An Experimental Comparison of Min-Cut/Max-Flow Algorithms for Energy Minimization in Vision by Boykov et.al.[1] Graph Cut Textures: Image and Video Synthesis using Graph Cuts’ by Kwatra et. al. [4] Semi Supervised Learning using Randomized Mincuts by Blum et.al. [5]
NOVEL VIEW TELEPRESENCE WITH HIGH-SCALABILITY USING MULTI-CASTED OMNI-DIRECTIONAL VIDEOS (2007)

The advent of high-speed network and high performance PCs has prompted research on networked telepresence, which allows a user to see virtualized real scenes in remote places. View-dependent representation, which provides a user with arbitrary view images using an HMD or an immersive display, is especially effective in creating a rich telepresence. The goal of our work is to realize a networked novel view telepresence system which enables multiple users to control the viewpoint and view-direction independently by virtualizing real dynamic environments. In this paper, we describe a novel view generation method from multiple omni-directional images captured at different positions. We mainly describe our prototype system with highscalability which enables multiple users to use the system simultaneously and some experiments with the system. The novel view telepresence system constructs a virtualized environment from real live videos. The live videos are transferred to multiple users by using multi-cast protocol without increasing network traffic. The system synthesizes a view image for each user with a varying viewpoint and view-direction measured by a magnetic sensor attached to an HMD and presents the generated view on the HMD. Our system can generate the user’s view image in real-time by giving correspondences among omni-directional images and estimating camera intrinsic and extrinsic parameters in advance.
Leber’s Hereditary Optic Neuropathy Mutations in Korean Patients with Multiple Sclerosis (2001)

Several different mitochondrial DNA (mtDNA) sites for mutations of Leber's hereditary optic neuropathy (LHON) have been reported to be present in patients with multiple sclerosis (MS). To further study this association of LHON and MS in the Korean population, we tested 20 MS patients for the presence of mtDNA mutations at nucleotide (nt) 11778 in all 20 patients, and at nt 14484, nt 3460 and nt 15257 in 15, 12 and 12 patients, respectively. However, none of the MS patients exhibited any pathogenic LHON mtDNA mutations. In conclusion, we found no evidence for any association between MS and the LHON mutation in the Korean population.
A Braille Recognition System by the Mobile Phone with Embedded Camera (2007)

It has been suggested that blind and visually impaired people may have difficulty reading Braille that is widely set in the public place according to barrier free policy of the government. This paper describes a new system that recognizes Braille characters from a photo taken by a mobile phone with embedded camera. The photo is dealt with by a Java program developed by "DoJa I-appli tool kit " to supply a real time reply.
Fast and Accurate Array Calibration Using a Synthetic Array Approach (2011)

A new method for the calibration of arrays is presented that allows the simultaneous calibration of <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</i> array elements. It comprises the measurement of the array output signal at <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">M</i> phase settings applied to the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</i> elements involved in the calibration. These <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">M</i> phase settings correspond to a linear phase taper that is unique for each of the involved elements and reveals therefore <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</i> different phase tapers. The complex <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">M</i> measurements of the array signal are thought to be the excitation coefficients of a synthetic <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">M</i> -element linear phased array. The array factor of this synthetic <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">M</i> -element array comprises a superposition of <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</i> +1 array factors all pointing with their main beam into different directions. By converting this superposition of <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</i> +1 array factors into a set of <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</i> +1 simultaneous linear equations, the signals of the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</i> individual elements to be calibrated including the combined signal contribution of the static elements, can be solved by standard matrix inversion techniques. Computer simulations are presented to demonstrate the capabilities of the new calibration method.
Surfactant and a mixture of surfactant and nanoparticles to stabilize CO2/brine foam, control gas mobility, and enhance oil recovery (2019)

Abstract Injecting carbon dioxide into oil reservoirs has the potential to serve as an enhanced oil recovery (EOR) technique, mitigating climate change by storing CO 2 underground. Despite the successful achievements reported of CO 2 to enhance oil recovery, mobility control is one of the major challenges faced by CO 2 injection projects. The objective of this work is to investigate the potential of using surfactant and a mixture of surfactant and nanoparticles to generate foam to reduce gas mobility and enhance oil recovery. A newly developed anionic surfactant and a mixture of the surfactant and surface-modified silica nanoparticles were used to assess the ability of generating a stable foam at harsh reservoir conditions: sc-CO 2 and high temperature. Dynamic foam tests and coreflood experiments were conducted to evaluate foam stability and strength. To measure the mobility of injected fluids in sandstone rocks, the foam was generated by co-injection of sc-CO 2 and surfactant, as well as a mixture of surfactant and nanoparticles at 90% quality. The coreflood experiments were conducted using non-fractured and fractured sandstone cores at 1550 psi and 50 °C. The use of surfactant and mixture was able to generate foam in porous media and reduce the CO 2 mobility. The mobility reduction factor (MRF) for both cases was about 3.5 times higher than that of injecting CO 2 and brine at the same conditions. The coreflood experiments in non-fractured sandstone rocks showed that both surfactant and a mixture of surfactant and nanoparticles were able to enhance oil recovery. The baseline experiment in the absence of surfactant resulted in a total recovery of 71.50% of the original oil in place. However, the use of surfactant was able to bring oil recovery to 76% of the OOIP. The addition of nanoparticles to surfactant, though, resulted in higher oil recovery, 80% of the OOIP. In fractured rocks, oil recoveries during secondary production mechanisms for the mixture, the surfactant alone, and sc-CO 2 alone were 12.62, 8.41, and 7.21% of the OOIP, respectively. Huge amount of oil remains underground following the primary and secondary oil production schemes. CO 2 has been widely used to enhance oil recovery. However, its high mobility might result in unfavorable and unsuccessful projects. The use of specially designed surfactants and the synergistic effect of surfactant and nanoparticles may provide a solution to stabilize CO 2 /brine foam at harsh reservoir conditions and, therefore, reduce the gas mobility and, consequently, enhance oil recovery.
Transgenes Delivered by Lentiviral Vector are Suppressed in Human Embryonic Stem Cells in A Promoter-Dependent Manner (2007)

Lentiviruses have been increasingly used for genetic modification of human cells including embryonic stem (ES) cells. Using four ubiquitous promoters--cytomegalovirus (CMV), cytomegalovirus immediate-early enhancer/chicken beta-actin hybrid (CAG), phosphoglycerate kinase (PGK), and human elongation factor-1alpha (EF1alpha)--in a lentiviral vector to drive the expression of the enhanced green fluorescent protein (EGFP) gene in human ES cells and mouse ES cells, we determined the extent of EGFP suppression by assessing the percentage of cells that were transduced with the EGFP gene but did not fluoresce green. A much higher level of transgene suppression was observed in human ES cells as compared to mouse ES cells. The suppression was also highly promoter dependent, leading to inactivation of more than 95% of the EGFP genes under the CMV or CAG promoter while only 55% under the PGK promoter. No promoter-dependent suppression was observed in transient transfection of human ES cells. Thus, the common phenomenon of poor transgene expression in human ES cells may be caused mainly by suppression of the transgene right after transduction and integration. Cautions should be taken to choose the optimal promoter when lentiviruses are used for genetic modification of human ES cells.
Humans With Traumatic Brain Injuries Show Place-Learning Deficits in Computer-Generated Virtual Space (2000)

Spatial learning and memory has been linked to the hippocampus and temporal lobes and though these areas are often damaged in traumatic brain injury (TBI), spatial learning deficits after TBI have not received much attention. In the present study, a virtual environment was used to challenge people with TBI to solve a task comparable to the Morris water maze, which in turn has been shown to be highly sensitive to hippocampal and frontal lobe dysfunction in laboratory animals. A regular computer monitor was used to present 12 participants with TBI and 12 age- and sex-matched comparison participants with a computer-generated, three-dimensional "virtual arena maze," consisting of a large round arena within a very large square room. Participants were required to learn the place of an invisible target on the floor of the room based solely on distal cues on the walls of the room. Eight of the 12 participants with moderate to severe TBI showed substantial place-learning deficits in comparison to the uninjured participants. Performance in the virtual environment correlated with self-reported frequency of wayfinding problems in everyday life and with scores on a test of episodic memory, the Rivermead Behavioural Memory Task. These data confirm that deficits in spatial learning and memory follow TBI, and suggest that the virtual arena maze may provide a new method for objectively assessing them.
MnTBAP, a synthetic metalloporphyrin, inhibits production of tumor necrosis factor-Î± in lipopolysaccharide-stimulated RAW 264.7 macrophages cells via inhibiting oxidative stress-mediating p38 and SAPK/JNK signaling (2007)

Antioxidants are able to inhibit inflammatory gene expression in response to lipopolysaccharide via down-regulating generation of intracellular reactive oxygen species (ROS) as second messengers. The effect of manganese (III) tetrakis (4-benzoic acid) porphyrin (MnTBAP), a synthetic metalloporphyrin with antioxidant activity, on tumor necrosis factor (TNF)-alpha production in lipopolysaccharide-stimulated RAW 264.7 macrophage cells was examined. MnTBAP prevented the generation of intracellular ROS in lipopolysaccharide-stimulated RAW 264.7 cells and further inhibited lipopolysaccharide-induced TNF-alpha production. MnTBAP exclusively prevented the phosphorylation of p38 mitogen-activated protein kinase (MAPK) and stress-activated protein kinase (SAPK/JNK) whereas it did not affect the phosphorylation and activation of nuclear factor-kappaB and extracellular signal regulated kinase 1/2. MnTBAP was suggested to inhibit lipopolysaccharide-induced TNF-alpha production by the prevention of intracellular ROS generation and subsequent inactivation of p38 MAPK and SAPK/JNK.
A Convenient Method for the Preparation of 1‐(<i>tert</i>‐Butyloxycarbonyl) pyrroles (1984)

Attachment of the Boc group to pyrrole nitrogen can now be achieved by a universally applicable method. Preparation of the N-Boc derivatives 1 from the corresponding pyrroles has been accomplished with Boc2O in presence of the strong acylating catalyst 4-dimethylaminopyridine in CH3CN or CH2Cl2 at room temperature. A wide variety of substituents R1—R4 can be used.
Problem-Based Learning Using Mobile Devices (2006)

Small handheld devices such as PDAs and smart phones become more and more popular. Thus, we are seeing a growing number of projects using mobile devices for educational purposes. Due to the limitations of screen size, CPU performance, and memory size, software development for mobile devices is challenging. More critical argument is about the lack of pedagogic and didactic concepts on the usage of mobile devices in education. In this paper, we present a system using mobile devices which supports research experiences for students in a laboratory context. The system allows students to efficiently monitor and control their scientific experiments at anytime, from anywhere. We describe several usage scenarios in the area of nanoscience studies, where the remote control of microscopes is mandatory. We present our system architecture and describe the implementation based on open-source software.
Thermokinetic actuation for batch assembly of microscale hinged structures (2003)

This paper reports on surface micromachined hinged structure assembly using thermokinetic forces in the molecular flow regime. Ultrasonic vibration energy is used to reduce the static friction making the thermokinetic force comparatively significant. The thermokinetic force, resulting from the more energetic gas molecules emanating from the heated substrate, increases with pressure and substrate temperature in the molecular flow regime. The transition from viscous to molecular regime occurs as the molecular mean-free-path approximately equals the flap length, making the pressure threshold for thermokinetic flap actuation size dependent. In addition to the experimental results, one-dimensional (1-D) and two-dimensional (2-D) force models are presented. Examples of assembled structures are shown and assembly jig suitable for automated MEMS batch assembly is demonstrated.
Skeptical of Skeptics (1991)

Skepticism permeates our profession. It is ingrained during medical training and reinforced by professional experience. Who among us has not repeatedly seen claims for fourth-generation drugs with no side effects, new operations that yield glowing results with minimal complications, or the latest infallible, high-tech diagnostic procedure... only to discover months or years later that these claims missed the truth by miles. Small wonder most of us are skeptics. To be skeptical is to be detached, rational, and objective. Skepticism is widely perceived as the prudent, conservative way to deal with ambiguous situations—times when even experts are confounded. Healthy skepticism is the in attitude for intelligent, discriminating physicians. But healthy for whom? Four years ago I was diagnosed as having chronic fatigue syndrome (CFS). The experience has given me a new perspective of my profession, one that is not always flattering. In one early report, the average CFS patient had previously
Mental Health: A Report of the Surgeon General (1999)

The past century has witnessed extraordinary progress in our improvement of the public health through medical sciencea nd ambitious, often innovative, approachest o health care services.P revious Surgeons General reports have saluted our gains while continuing to set ever higher benchmarks for the public health. Through much of this era of great challenge and greater achievement, however, concerns regarding mental illness and mental health too often were relegated to the rear of our national consciousness. Tragic and devastating disorders such as schizophrenia, depression and bipolar disorder, Alzheimer’s disease, the mental and behavioral disorders suffered by children, and a range of other mental disorders affect nearly one in five Americans in any year, yet continue too frequently to be spoken of in whispers and shame. Fortunately, leaders in the mental health field-fiercely dedicated advocates, scientists, government officials, and consumers-have been insistent that mental health flow in the mainstream of health. I agree and issue this report in that spirit. This report makes evident that the neuroscience of mental health-a term that encompasses studies extending from molecular events to psychological, behavioral, and societal phenomena-has emerged as one of the most exciting arenas of scientific activity and human inquiry. We recognize that the brain is the integrator of thought, emotion, behavior, and health. Indeed, one of the foremost contributions of contemporary mental health research is the extent to which it has mended the destructive split between “mental’ and “physical” health.
Regression — Yet Another Clustering Method (2001)

The paper contains description of a new clustering methodology that partitions data set into clusters, such that regression indetermination coefficient for data from each cluster is minimized. A clustering algorithm that realizes this methodology with genetic programming approaches, as well as, some experimental results are presented. The application of the algorithm for planning cellular telephone networks is discussed.