gebhart/patrepeval huggingface dataset:
Dissecting Sholl Analysis into Its Functional Components (2019)

Sholl analysis has been an important technique in dendritic anatomy for more than 60 years. The Sholl intersection profile is obtained by counting the number of dendritic branches at a given distance from the soma and is a key measure of dendritic complexity; it has applications from evaluating the changes in structure induced by pathologies to estimating the expected number of anatomical synaptic contacts. We find that the Sholl intersection profiles of most neurons can be reproduced from three basic, functional measures: the domain spanned by the dendritic arbor, the total length of the dendrite, and the angular distribution of how far dendritic segments deviate from a direct path to the soma (i.e., the root angle distribution). The first two measures are determined by axon location and hence microcircuit structure; the third arises from optimal wiring and represents a branching statistic estimating the need for conduction speed in a neuron.
Overall survival in patients with metastatic melanoma (2015)

Among patients diagnosed with unresectable metastatic melanoma from 2004 to 2009, patients at later stages had lower median overall survival and higher mortality rates than patients at earlier stages. Limitations of this analysis include the lack of information on disease progression, therapies used, and genetic factors.
Proximal First Metatarsal Opening Wedge Osteotomy with a Low Profile Plate (2009)

We believe PMOW osteotomy was near ideal in terms of reliable, predictable correction and healing. Length of the first metatarsal was maintained and patients ambulated safely in a CAM walking boot immediately after surgery. We believe a first web space release may result in hallux varus and increased distal metatarsal articular angle (DMAA) was associated with hallux valgus recurrence.
Characterization of the 5'-flanking region of the rat protein kinase C gamma gene. (1990)

The 5'-flanking region of protein kinase C (PKC) gamma gene was identified from a rat liver genomic library in a bacteriophage lambda Charon 4A. A 3.6-kilobase (kb) genomic fragment containing the 5'-flanking region, first exon, and first intron was isolated and sequenced. The transcriptional initiation site, identified by S1 mapping and primer extension, was located 243 base pairs upstream from the translational initiation site. Promoter activity of a DNA segment spanning the 5'-flanking region was demonstrated by both in vitro transcription using HeLa cell nuclear extracts and chloramphenicol acetyltransferase assay by transfection of 293 cells with a PKC gamma-CAT fusion construct. Chloramphenicol acetyltransferase assay revealed that a fragment of about 0.16 kb from the transcriptional initiation site was sufficient for promoter activity in these cells, and the construct containing up to 1.6 kb from the cap site was expressed at a similar level. This promoter-active fragment contains several regions similar to defined transcriptional elements in other mammalian promoters, such as those for stimulatory protein 1 (Sp1), activator proteins 1 and 2 (AP1, AP2), c-myc, cAMP regulatory element-binding protein (CREB), and enhancer core (EnhC). Investigation of the genomic structure of PKC gamma gene may lead to the identification of cis-elements controlling tissue-specific and developmental stage-specific expression of PKC gamma.
On water repellency (2005)

Water-repellency is a property of some materials, either natural or synthetic, which makes water hardly stick to them: drops roll very easily off these solids, and bounce back upon impacting them. Here we discuss recent advances in this field, which has been particularly lively in recent years. We first examine the physical causes for this effect. Then we discuss the loss of adherence of the drops in such a state, and stress their remarkable dynamic behaviour. We finally suggest several remaining challenges in the field.
Distributed memory compiler design for sparse problems (1995)

This paper addresses the issue of compiling concurrent loop nests in the presence of complicated array references and irregularly distributed arrays. Arrays accessed within loops may contain accesses that make it impossible to precisely determine the reference pattern at compile time. This paper proposes a run time support mechanism that is used effectively by a compiler to generate efficient code in these situations. The compiler accepts as input a Fortran 77 program enhanced with specifications for distributing data, and outputs a message passing program that runs on the nodes of a distributed memory machine. The runtime support for the compiler consists of a library of primitives designed to support irregular patterns of distributed array accesses and irregularly distributed array partitions. A variety of performance results on the Intel iPSC/860 are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Design of Nonlinear Dynamic Systems Using Surrogate Models of Derivative Functions (2013)

Optimization of nonlinear (or linear state-dependent) dynamic systems often requires system simulation. In many cases the associated state derivative evaluations are computationally expensive, resulting in simulations that are significantly slower than real-time. This makes the use of optimization techniques in the design of such systems impractical. Optimization of these systems is particularly challenging in cases where control and physical systems are designed simultaneously. In this article, an efficient two-loop method, based on surrogate modeling, is proposed for solving dynamic system design problems with computationally expensive derivative functions. A surrogate model is constructed for only the derivative function instead of the complete system analysis, as is the case in previous studies. This approach addresses the most expensive element of system analysis (i.e., the derivative function), while limiting surrogate model complexity. Simulation is performed based on the surrogate derivative functions, preserving the nature of the dynamic system, and improving estimation accuracy. The inner loop solves the system optimization problem for a given derivative function surrogate model, and the outer loop updates the surrogate model based on optimization results. This solution approach presents unique challenges. For example, the surrogate model approximates derivative functions that depend on both design and state variables. As a result, the method must not only ensure accuracy of the surrogate model near the optimal design point in the design space, but also the accuracy of the model in the state space near the state trajectory that corresponds to the optimal design. This method is demonstrated using two simple design examples, followed by a wind turbine design problem. In the last example, system dynamics are modeled using a linear state-dependent model where updating the system matrix based on state and design variable changes is computationally expensive.
Monitoring a bioprocess for ethanol production using FT-MIR and FT-Raman spectroscopy (2001)

The application of Fourier transform mid-infrared (FT-MIR) spectroscopy and Fourier transform Raman (FT-Raman) spectroscopy for process and quality control of fermentative production of ethanol was investigated. FT-MIR and FT-Raman spectroscopy along with multivariate techniques were used to determine simultaneously glucose, ethanol, and optical cell density of Saccharomyces cerevisiae during ethanol fermentation. Spectroscopic measurement of glucose and ethanol were compared and validated with the high-performance liquid chromatography (HPLC) method. Spectral wave number regions were selected for partial least-squares (PLS) regression and principal component regression (PCR) and calibration models for glucose, ethanol, and optical cell density were developed for culture samples. Correlation coefficient (R(2)) value for the prediction for glucose and ethanol was more than 0.9 using various calibration methods. The standard error of prediction for the PLS first-derivative calibration models for glucose, ethanol, and optical cell density were 1.938 g/l, 1.150 g/l, and 0.507, respectively. Prediction errors were high with FT-Raman because the Raman scattering of the cultures was weak. Results indicated that FT-MIR spectroscopy could be used for rapid detection of glucose, ethanol, and optical cell density in S. cerevisiae culture during ethanol fermentation.
Deep ultraviolet enhanced wet chemical etching of gallium nitride (1998)

We report a study of the ultraviolet (UV) irradiation effects on the wet chemical etching of unintentionally doped n-type gallium nitride (GaN) layers grown on sapphire substrates. When illuminated with a 253.7 nm mercury line source, etching of GaN is found to take place in aqueous phosphorus acid (H3PO4) and potassium hydroxide (KOH) solutions of pH values ranging from −1 to 2 and 11 to 15, respectively. Formation of gallium oxide is observed on GaN when illuminated in dilute H3PO4 and KOH solutions. These results are attributed to a two-step reaction process upon which the UV irradiation is shown to enhance the oxidative dissolution of GaN.
Potentiation of Glucose Uptake in 3T3-L1 Adipocytes by PPARγ Agonists Is Maintained in Cells Expressing a PPARγ Dominant-Negative Mutant: Evidence for Selectivity in the Downstream Responses to PPARγ Activation (2001)

Pharmacological agonists for the nuclear receptor PPAR gamma enhance glucose disposal in a variety of insulin-resistant states in humans and animals. The precise mechanisms whereby activation of PPAR gamma leads to increased glucose uptake in metabolically active cells remain to be determined. Notably, certain novel, synthetic PPAR gamma ligands appear to antagonize thiazolidinedione-induced adipogenesis yet stimulate cellular glucose uptake. We have explored the molecular mechanisms underlying the enhancement of glucose uptake produced by PPAR gamma agonists in 3T3-L1 adipocytes. Rosiglitazone treatment for 48 h significantly increased basal and insulin-stimulated glucose uptake and markedly increased the cellular expression of GLUT1 but not GLUT4. Rosiglitazone increased plasma membrane levels of GLUT1, but not GLUT4, both basally and after insulin stimulation. Surprisingly, adenoviral expression of a dominant-negative mutant PPAR gamma, which was demonstrated to strongly inhibit adipogenesis, completely failed to inhibit rosiglitazone-stimulated glucose uptake. Similar findings were obtained with the non-thiazolidinedione PPAR gamma agonists, GW1929 and GW7845. The insensitivity of PPAR gamma agonist-stimulated glucose uptake to expression of a dominant-negative mutant, compared with the latter's marked inhibitory effects on preadipocyte differentiation, suggests that, as is the case for other nuclear receptors, the precise molecular mechanisms linking PPAR gamma activation to downstream events may differ depending on the nature of the biological response. The growing evidence that the effects of PPAR gamma on adipogenesis and glucose uptake can be dissociated may have important implications for the development of improved antidiabetic drug treatments.
Surface Measurement and Analysis of Drillstring Vibrations While Drilling (1993)

Abstract Drillstring vibrations while drilling cause premature drillstring component and bit failure, and represent a waste of drilling energy. To increase drilling efficiency, drillstring vibrations are monitored and analyzed and the optimum drilling parameters and practices are determined as a well is drilled. This results in a reduction in the frequency of drillstring failures and the amount of time spent tipping and/or fishing, and an increase in both bit life and drilling rate. This paper presents vibration signatures and analyses selected from over 15,000 hours of vibration data obtained using a surface vibration measurement sub. The case histories demonstrate the surface detection of drillstring resonance, BHA (Bottom Hole Assembly) lateral vibrations, PDC (fixed cutter) bit whirl, shock sub closure, torsional string oscillations, premature bit bearing failure and impending stuck pipe.
Implementation of multiple pagesize support in HP-UX (1998)

To reduce performance degradation from Translation Lookaside Buffer (TLB) misses without significant increase in TLB size, most modern processors implement TLBs that support multiple pagesizes. For example, Hewlett-Packard&amp;apos;s PA-8000 processor allows 8 hardware pagesizes, in multiples of four, ranging from 4 Kbytes to 64 Mbytes. In implementing multiple pagesize support in HP-UX, wechose to create large pages at page-fault service time. Wehave a buddy system allocator that provides interfaces for allocating and freeing multiple pagesizes. We maintain the Virtual Memory (VM) data structures such as the pagetable entry, virtual page frame descriptor, and physical page frame descriptor based on the smallest pagesize, and represent a large pagesize as a collection of these base pagesize structures. In our implementation, VM operations on a large pagesize such as 16KB are carried out by looping over the 4KB-based constituent VM data structures. Our system offers significant application perfor...
Anti-trap protection for an intelligent smart car door system (2012)

A majority of driver assistance systems focuses on assisting the driver when the car is in motion. There is relatively less, to almost no work on assistance systems when the car is stationary. The focus of this paper is on such a system and describes the design and realization of a novel, camera-based anti-trap protection system for smart car doors. Our system uses a single omnidirectional camera that is integrated in each inner door of a vehicle, and detects obstacles such as fingers, hands or legs at the A and B-pillar, door sill and car door without any contact. This is an enhancement to currently available systems that require an active contact between obstacles and sensors in the door area for the detection of trapping. The paper also proposes a scheme for re-calibrating the camera position that may change due to vibrations during the life-time of the car door. Experiments on a fully realized car door prototype show that the proposed schemes prevent trapping by robustly detecting obstacles such as small fingers or hands in critical door regions, and output results in real-time. The latter is important when door users slam the car door. A first study with 20 test users showed that our system strongly supports the door users to prevent trapping.
Least-squares methods for the extraction of surface currents from CODAR crossed-loop data: Application at ARSLOE (1983)

Least-squares methods are demonstrated that extract surface current radial velocities from first-order Coastal Ocean Dynamics Applications Radar (CODAR) sea-echo Doppler spectra for the compact crossed-loop/monopole antenna system. Based on the known physics of first-order sea scatter at HF, these techniques, implemented as software, are objective and automatic in that they: a) determine from the sea-echo phase and amplitude correction factors for the antenna elements; b) separate the first-order spectrum from the surrounding continuum for arbitrarily varying current conditions; c) using statistical hypothesis testing, select and use either a single or dual-angle model for radial current patterns, whichever best fits the data; d) calculate angles associated with given radial velocities; e) combine the data into a polar-coordinate map of radial velocity versus position; and f) calculate radial velocity uncertainties at each point on the map. In addition, as interpretive aids, two methods are evaluated and compared that provide total current vectors from single-site CODAR data, along with their uncertainties: model fitting and the application of the equation of continuity. It is shown how these methods can be applied to the older, CODAR 4-element antenna system, however, the following advantages of the crossed-loop/monopole system are discussed: it is physically more compact; analysis procedures are more efficient; resulting current velocities are more accurate, because there are no side-lobe problems; and finally, it also gives the ocean wave-height directional spectrum. These methods are tested and optimized against data taken during the Atlantic Remote Sensing Land Ocean Experiment (ARSLOE) storm (October 23-27, 1980), when surface currents varied in speed between 0-50 cm/s and over nearly 300° in angle. Current velocities were measured to a range of 36 km from the radar. Standard deviations in angle are typically 1°-3°; these translate to 2-3 cm/s rms radial velocity uncertainties over most of the coverage area, with decreased accuracy in angular sectors nearest the coast. Total current velocity vectors in strips parallel to shore obtained from model fitting have typical speed and angle uncertainties of 4 cm/s and 12°, respectively. Of the several formulations for the equation of continuity evaluated here, the best gave uncertainties of 5 cm/s, 12° at the closest range cells; these values increase rapidly with range to exceed 20 cm/s, 30° for distances greater than 20 km. The surface currents were observed to follow the wind throughout most of the storm at ARSLOE, but the current was almost always more closely parallel to the shore than the wind. An interesting exception occurred when the onshore storm wind that had prevailed for two days ceased; there was a rush of surface current directly offshore as the storm-surge sea level dropped. The surface current speed measured by CODAR in the upper meter of the ocean was, on the average, 2.1 percent of the windspeed.
Recipient‐induced transfer of the symbiotic plasmid pRL1JI in <i>Rhizobium leguminosarum</i> bv. <i>viciae</i> is regulated by a quorum‐sensing relay (2003)

Analysis of the regulation of plasmid transfer genes on the symbiotic plasmid pRL1JI in Rhizobium leguminosarum bv. viciae has revealed a novel regulatory relay that is specifically poised to detect an N-acyl-homoserine lactone (AHL) made by different cells (potential recipients of pRL1JI). Adjacent to the traI-trbBCDEJKLFGHI plasmid transfer operon on pRL1JI are two regulatory genes, bisR and traR, which encode LuxR-type quorum-sensing regulators required for conjugation. Potential recipients of pRL1JI induce the traI-trb operon and plasmid transfer via a quorum-sensing relay involving BisR, TraR and the traI-trb operon in donor cells. BisR induces expression of traR in response to N-(3-hydroxy-7-cis-tetradecenoyl)-l-homoserine lactone (3-OH-C14:1-HSL), which is produced by CinI in potential recipient strains. In donor strains (carrying pRL1JI), BisR represses the expression of the chromosomal gene cinI; this repression results in a very low level of formation of 3-OH-C14:1-HSL and hence relatively low levels of expression of traR and the traI-trb operon in strains carrying pRL1JI. However, if 3-OH-C14:1-HSL from potential recipients is present, then traR and plasmid transfer are induced. The induction of traR occurs at very low concentrations of 3-OH-C14:1-HSL (around 1 nm). TraR then induces the traI-trb operon in a quorum-sensing dependent manner in re-sponse to the TraI-made AHLs, N-(3-oxo-octanoyl)-l-homoserine lactone and N-(octanoyl)-l-homoserine lactone. The resulting autoinduction results in high levels of expression of the traI-trb operon. Premature expression of the traI-trb operon is reduced by TraM, which probably titres out TraR preventing expression of traI when there are low levels of traR expression. Expression of traR in stationary phase cells is limited by feedback inhibition mediated by TraI-made AHLs.
Protective effects of the glutamate antagonist MK-801 on pyrithiamine- induced lesions and amino acid changes in rat brain (1990)

An acute bout of pyrithiamine-induced thiamine deficiency (PTD) produces pathologic lesions within thalamus, mammillary body, and periventricular regions of rat brain. The biological bases for these pathologic changes and their selective distribution within the brain are unclear. The type of tissue damage observed within the thalamus of PTD rats closely resembles that observed following anoxic-ischemic insults and suggests the involvement of excitotoxic amino acids in its pathogenesis. The effects of the N-methyl-D-aspartate receptor antagonist MK-801 (3 mg/kg, i. p.) on brain lesions and amino acid changes have been assessed in rats killed during the late acute stages of PTD. A marked loss of neurons within midline intralaminar nuclei and the posterior nuclear group of the thalamus were observed in the early acute stage of PTD treatment. In the late acute stage, these changes were present throughout the entire thalamus and extended caudally to the periacqueductal gray and mesencephalic tegmentum. Hemorrhagic lesions were observed only in the late acute group and were the primary lesion within the mammillary body and medial and lateral geniculates. No pathologic changes were observed in hippocampus, amygdala, and cortex. MK-801 administered during the late stages resulted in a marked attenuation of necrotic damage to thalamus and periacqueductal gray and a reduction in the number and size of hemorrhagic lesions. Significant reductions of aspartate and glutamate and increases of glycine were observed in 5 regions of thalamus, the hippocampus, hypothalamus, and mammillary bodies of both the early and late acute PTD groups. Levels of GABA and taurine in caudal areas were significantly elevated in the early acute stage but were unchanged from controls in the late acute group. These amino acid changes were reduced in the MK-801 treated late acute group. These observations suggest that NMDA receptors are involved the pathogenesis of PTD-induced brain lesions and that nuclei of the intralaminar and posterior nuclear groups are most vulnerable to PTD effects.
A novel inspection and annealing procedure to rejuvenate phase change memory from cycling-induced degradations for storage class memory applications (2014)

A novel Cycle Alarm Point (CAP) inspection is proposed to monitor PCM cycling degradation. The degradation appears in two stages - (1) right shift of R-I during moderate cycling degradation, and (2) left shift of R-I when cycling damage is severe. We further propose an In-Situ-Self-Anneal (ISSA) procedure, such that once a CAP signal is detected, the annealing procedure is issued to rejuvenate the cells. We demonstrate, for the first time, PCM cycling degradation can be recovered repeatedly. This opens a new window to extend PCM endurance and reliability for storage class memory (SCM) applications.
Fast recovery radiation enhanced diffusion (RED) diode: Palladium versus platinum (2009)

Modern power switches require the complementary diodes which are robust at the turn-off of ever higher currents at higher di/dts and supply voltages. A new technology to increase the ruggedness of free-wheeling and clamping diodes, which is based on the radiation enhanced diffusion (RED) of palladium, has been recently developed. In this work, the RED technology of palladium is confronted with that of the platinum. Silicon P-i-N diodes (V br = 2500 V, Area = 2 cm2, positive bevel, press pack contact) were subjected to the RED of Pd and Pt in the temperature range between 500 and 800 0C to locally control the carrier lifetime and doping profile, if possible. The devices are compared in static (leakage, voltage drop) and dynamic parameters (unclamped low inductance reverse recovery). The RED of Pd is shown to create a low doped P-layer that postpones the dynamic avalanche towards higher line voltages and increases the static breakdown voltage. Platinum does not provide this feature and the lifetime reduction is smaller. While the dynamic parameters of the palladium RED diodes are greatly improved, those of the Pt have much higher maximal recovery current and poor SOA. In spite of the qualitatively similar electronic properties of the Pt and Pd deep levels, the accumulation of Pt in the region with radiation defects is found to differ quantitatively during the RED process in the temperature range 500–650 0C. The RED of Pt is therefore evaluated as unsuitable for the local lifetime control using the existing RED process.