gebhart/patrepeval huggingface dataset:
Using Rule-Based Machine Learning for Candidate Disease Gene Prioritization and Sample Classification of Cancer Gene Expression Data (2012)

Microarray data analysis has been shown to provide an effective tool for studying cancer and genetic diseases. Although classical machine learning techniques have successfully been applied to find informative genes and to predict class labels for new samples, common restrictions of microarray analysis such as small sample sizes, a large attribute space and high noise levels still limit its scientific and clinical applications. Increasing the interpretability of prediction models while retaining a high accuracy would help to exploit the information content in microarray data more effectively. For this purpose, we evaluate our rule-based evolutionary machine learning systems, BioHEL and GAssist, on three public microarray cancer datasets, obtaining simple rule-based models for sample classification. A comparison with other benchmark microarray sample classifiers based on three diverse feature selection algorithms suggests that these evolutionary learning techniques can compete with state-of-the-art methods like support vector machines. The obtained models reach accuracies above 90% in two-level external cross-validation, with the added value of facilitating interpretation by using only combinations of simple if-then-else rules. As a further benefit, a literature mining analysis reveals that prioritizations of informative genes extracted from BioHEL's classification rule sets can outperform gene rankings obtained from a conventional ensemble feature selection in terms of the pointwise mutual information between relevant disease terms and the standardized names of top-ranked genes.
Statistical Performance Analysis of an Interframe Encoder for Broadcast Television Signals (1981)

This paper desribes an objective evaluation for coding performance of an interframe encoder (NETEC-22H). Also described is the coding performance improvement by an adaptive bit sharing multiplexer (ABS-MUX) in which transmission bit rate is dynamically allocated to several channels. Measurements made for actual broadcast TV programs over a time of 36 h show that an SNR of higher than 50 dB unweighted is obtained by this coding equipment for 99 percent of the time for broadcast TV programs at the transmission bit rate of 30 Mbits/s and for 93 percent of the time at 20 Mbits/s. The residual 1 percent at 30 Mbits/s or 7 percent at 20 Mbits/s is transmitted with a slightly lower SNR. The picture quality difference between the 20 and 30 Mbit/s transmission is about 6 dB in SNR on the average. It is also shown that a three-channel ABS-MUX (20 Mbits/s per channel on the average) reduces probability of coarse quantization by a factor of 5-10 compared with the fixed bit rate transmission at 20 Mbits/s.
Computer Simulation of Milling Ball Motion in Mechanical Alloying (<I>Overview</I>) (1995)

A model simulation of milling-ball motion during mechanical alloying done by the author’s group was reviewed. The Kelvin’s dashpot-spring model and the discrete element method were employed in the simulation. One, two and three dimensional milling-ball motions for three types of ball milling; vibratory, tumbling and planetary ball milling, were studied. The simulation formalism was first given, which takes into account the translational and rotational motion and three types of forces; visco-elastic, frictional and gravitational force. The whole motion of the milling balls was traced contact by contact. The simulation provided for each of the milling types the ball motion trajectories, impact velocities and frequencies of the balls, as well as the energy consumption during mechanical alloying. The results of the simulation were supported by the experimental observation.
Rocker shoe as walking aid in multiple sclerosis. (1981)

Evaluation of rocker shoes as a walking aid for multiple sclerosis patients included a mechanical analysis of the shoes, establishment of clinical criteria for appropriate patient selection, and laboratory gait measurements of patients with and without rocker shoes. Patient fitting demonstrated that the most significant measurement, the roll point, must be about 2cm proximal to the 1st metatarsal head. A snug fit as well as the addition of a heel strap was required to hold the shoe on the foot so its mechanical assistance was consistent. Rocker shoes were effective only in patients who still retained the ability to walk independently; retention of adequate hip and calf strength proved critical. Basic gait deficit was plantar flexion less than 15 degree while standing, leading to knee hypertension and forward trunk leaning, inadequate knee flexion and toe drag in swing, general awkwardness and fatigue. Gait improvement with the rocker shoes varied with clinical classification. Normal velocity and stride characteristic in rocker shoes were accompanied by a marked decrease in net energy cost. A mean saving of 150% of normal energy was gained with rocker shoes.
( In , Ga ) N ∕ Ga N microcavities with double dielectric mirrors fabricated by selective removal of an (Al,In)N sacrificial layer (2007)

Comparable microcavities with 3λ∕2 (∼240nm) active regions containing distributed (In,Ga)N quantum wells, grown on GaN substrates and bounded by two dielectric mirrors, have been fabricated by two different routes: one using laser lift-off to process structures grown on GaN-on-sapphire templates and the second using freestanding GaN substrates, which are initially processed by mechanical thinning. Both exploit the properties of an Al0.83In0.17N layer, lattice matched to the GaN substrate and spacer layers. In both cases cavity quality factors &gt;400 are demonstrated by measurements of the cavity-filtered room-temperature excitonic emission near 410nm.
CAATT/Enhancer-binding Proteins α and δ Interact with NKX2-1 to Synergistically Activate Mouse Secretoglobin 3A2 Gene Expression (2008)

Secretoglobin (SCGB) 3A2 is a small molecular weight secreted protein predominantly expressed in lung airways. We previously demonstrated that the expression of SCGB3A2 is regulated by homeodomain transcription factor NKX2-1. Here we show that CCAAT/enhancer-binding proteins, C/EBPalpha and C/EBPdelta, regulate mouse Scgb3a2 gene transcription in vivo and in vitro by binding to specific sites located in the Scgb3a2 promoter and the activity is synergistically enhanced through cooperative interaction with NKX2-1. Six C/EBP binding sites lie within 500 bp of the Scgb3a2 gene promoter, of which two sites, located at -44 to -54 bp and -192 to -201 bp, appear to be critical for the synergistic activation of Scgb3a2 gene transcription with NKX2-1. All three transcription factors, C/EBPalpha, C/EBPdelta, and NKX2-1, are expressed in the epithelial cells of airways, particularly the bronchus, where high expression of SCGB3A2 is found. The expression of these transcription factors markedly increases toward the end of gestation, which coincides with the marked increase of SCGB3A2, suggesting the importance of C/EBPalpha and C/EBPdelta, and their synergistic interaction with NKX2-1 in mouse Scgb3a2 gene transcription and lung development.
Multiscale Macromolecular Simulation: Role of Evolving Ensembles (2012)

Multiscale analysis provides an algorithm for the efficient simulation of macromolecular assemblies. This algorithm involves the coevolution of a quasiequilibrium probability density of atomic configurations and the Langevin dynamics of spatial coarse-grained variables denoted order parameters (OPs) characterizing nanoscale system features. In practice, implementation of the probability density involves the generation of constant OP ensembles of atomic configurations. Such ensembles are used to construct thermal forces and diffusion factors that mediate the stochastic OP dynamics. Generation of all-atom ensembles at every Langevin time step is computationally expensive. Here, multiscale computation for macromolecular systems is made more efficient by a method that self-consistently folds in ensembles of all-atom configurations constructed in an earlier step, history, of the Langevin evolution. This procedure accounts for the temporal evolution of these ensembles, accurately providing thermal forces and diffusions. It is shown that efficiency and accuracy of the OP-based simulations is increased via the integration of this historical information. Accuracy improves with the square root of the number of historical timesteps included in the calculation. As a result, CPU usage can be decreased by a factor of 3-8 without loss of accuracy. The algorithm is implemented into our existing force-field based multiscale simulation platform and demonstrated via the structural dynamics of viral capsomers.
Millimeter-Wave Multifunction Multiport Interferometric Receiver for Future Wireless Systems (2017)

In this paper, a receiver architecture is presented which is capable of handling angle-of-arrival (AOA) detection as well as data communication. The architecture of the proposed multifunction receiver is based on the multiport interferometer technique, and it integrates two previously reported six-port-based system functions that were realized as two distinct six-port receivers (SPRs). This unification of two SPRs is mainly achieved through a new configuration of RF/local oscillator (LO) signals at input ports, a new phase processing of the input signals within a structured eight-port passive network and a complementary postprocessing of the signals at the output of detectors. Using two RF input ports and two LO input ports that are switched in two consecutive time slots, the proposed multiport-based receiver (MPR) can estimate the AOA with a simple signal-processing algorithm. The plurality of the RF input ports can cause self-interference for the received communication signals. Therefore, a phasing network within the proposed eight-port wave correlator is devised such that the incoming quadrature modulated RF carriers are demodulated in an orthogonal manner at four output ports. It is found that receiving communication signal from a nonzero AOA makes imbalance between demodulated components. To this end, the proposed MPR can first find the angular position of the other unit and then recover the demodulation components through data fusion and postprocessing. The mathematical model for the developed MPR is derived along with the development of an appropriate calibration technique, and its principal functionality is theoretically analyzed. In addition, a transceiver architecture based on this MPR is implemented, and prototyped for operation around 77 GHz. The techniques for hybrid millimeter-wave system integration are explained in this paper. The proposed concept is proven and concluded with satisfactory measurements for both functions. This unified multifunction MPR can find applications in the future vehicle-to-vehicle radios and joint radar-communication systems.
Bone morphogenic protein signalling suppresses differentiation of pluripotent cells by maintaining expression of E-Cadherin (2013)

Bone morphogenic protein (BMP) signalling contributes towards maintenance of pluripotency and favours mesodermal over neural fates upon differentiation, but the mechanisms by which BMP controls differentiation are not well understood. We report that BMP regulates differentiation by blocking downregulation of Cdh1, an event that accompanies the earliest stages of neural and mesodermal differentiation. We find that loss of Cdh1 is a limiting requirement for differentiation of pluripotent cells, and that experimental suppression of Cdh1 activity rescues the BMP-imposed block to differentiation. We further show that BMP acts prior to and independently of Cdh1 to prime pluripotent cells for mesoderm differentiation, thus helping to reinforce the block to neural differentiation. We conclude that differentiation depends not only on exposure to appropriate extrinsic cues but also on morphogenetic events that control receptivity to those differentiation cues, and we explain how a key pluripotency signal, BMP, feeds into this control mechanism. DOI: http://dx.doi.org/10.7554/eLife.01197.001.
The use of hamstring tendons for anterior cruciate ligament reconstruction. Technique and results. (1993)

We feel that some of the current prejudice against use of hamstring tendon grafts for ACL reconstruction has not been justified if one critically reviews the literature. In this article, we have tried to provide the reader with our current indications, present our current surgical technique, and review some of the outcome studies involving use of the hamstring tendons for ACL reconstruction. We also feel that some of the poor results of hamstring tendon ACL reconstructions previously reported resulted from the use of inadequate strength grafts (single-stranded grafts) and lack of rigid fixation on both ends of the graft (usually secondary to inadequate graft length). We feel that the technique described in this article addresses both of these issues. It is our clinical impression that, in appropriately selected patients, this technique produces stability and functional outcome similar to that obtained with patellar tendon grafts but results in less postoperative pain, a quicker return of quadriceps muscle function, and less donor site morbidity.
Clonality and Prognostic Implications of <i>p53</i> and Epidermal Growth Factor Receptor Somatic Aberrations in Multiple Primary Lung Cancers (2007)

Our results suggest that analysis of somatic alterations in p53 and EGFR can significantly improve the clonality assessment and impact management of multiple primary lung cancer patients.
Efficacy of Artilysin Art-175 against Resistant and Persistent Acinetobacter baumannii (2016)

Bacteriophage-encoded endolysins have shown promise as a novel class of antibacterials with a unique mode of action, i.e., peptidoglycan degradation. However, Gram-negative pathogens are generally not susceptible due to their protective outer membrane. Artilysins overcome this barrier. Artilysins are optimized, engineered fusions of selected endolysins with specific outer membrane-destabilizing peptides. Artilysin Art-175 comprises a modified variant of endolysin KZ144 with an N-terminal fusion to SMAP-29. Previously, we have shown the high susceptibility of Pseudomonas aeruginosa to Art-175. Here, we report that Art-175 is highly bactericidal against stationary-phase cells of multidrug-resistant Acinetobacter baumannii, even resulting in a complete elimination of large inocula (≥10(8) CFU/ml). Besides actively dividing cells, Art-175 also kills persisters. Instantaneous killing of A. baumannii upon contact with Art-175 could be visualized after immobilization of the bacteria in a microfluidic flow cell. Effective killing of a cell takes place through osmotic lysis after peptidoglycan degradation. The killing rate is enhanced by the addition of 0.5 mM EDTA. No development of resistance to Art-175 under selection pressure and no cross-resistance with existing resistance mechanisms could be observed. In conclusion, Art-175 represents a highly active Artilysin against both A. baumannii and P. aeruginosa, two of the most life-threatening pathogens of the order Pseudomonadales.
High-flux thin-film nanofibrous composite ultrafiltration membranes containing cellulose barrier layer (2010)

A novel class of thin-film nanofibrous composite (TFNC) membrane consisting of a cellulose barrier layer, a nanofibrous mid-layer scaffold, and a melt-blown non-woven substrate was successfully fabricated and tested as an ultrafiltration (UF) filter to separate an emulsified oil and water mixture, a model bilge water for on-board ship bilge water purification. Two ionic liquids: 1-butyl-3-methylimidazolium chloride and 1-ethyl-3-methylimidazolium acetate, were chosen as the solvent to dissolve cellulose under mild conditions. The regenerated cellulose barrier layer exhibited less crystallinity (determined by wide-angle X-ray diffraction, WAXD) than the original cotton linter pulps, but good thermal stability (determined by thermal gravimetric analysis, TGA). The morphology, water permeation, and mechanical stability of the chosen TFNC membranes were thoroughly investigated. The results indicated that the polyacrylonitrile (PAN) nanofibrous scaffold was partially imbedded in the cellulose barrier layer, which enhanced the mechanical strength of the top barrier layer. The permeation flux of the cellulose-based TFNC membrane was significantly higher (e.g. 10×) than comparable commercial UF membranes (PAN10 and PAN400, Sepro) with similar rejection ratios for separation of oil/water emulsions. The molecular weight cut-off (MWCO) of TFNC membranes with cellulose barrier layer was evaluated using dextran feed solutions. The rejection was found to be higher than 90% with a dextran molecular weight of 2 000 KDa, implying that the nominal pore size of the membrane was less than ∼50 nm. High permeation flux was also observed in the filtration of an emulsified oil/water mixture as well as of a sodium alginate aqueous solution, while high rejection ratio (above 99.5%) was maintained after prolonged operation. A variation of the barrier layer thickness could dramatically affect the permeation flux and the rejection ratio of the TFNC membranes, while different sources of cellulose, ionic liquids, and non-woven supports did not. As ionic liquids can be recycled and reused without obvious decomposition, the chosen method also demonstrates a benign pathway to fabricate the cellulose barrier layer for other types of membranes.
Preface to this edition (2016)

David Armstrong's What is a Law of Nature? is a beautiful book. It offers its readers an exciting philosophical problem at the busy intersection of metaphysics, epistemology, and the philosophy of science – namely, what makes certain facts constitute matters of natural law? How do laws of nature (such as, according to current science, the fact that electric charge is conserved) differ from accidents (such as, in Reichenbach's example from Elements of Symbolic Logic, the fact that all solid gold cubes are smaller than one cubic mile)? In virtue of what is the former a law of nature whereas the latter is a coincidence – a ‘historical accident on the cosmic scale’ (Kneale, ‘Natural Laws and Contrary-to-Fact Conditionals’)? I am one of the many students who, after reading Armstrong's magisterial book, was firmly in the grip of this problem. It has never let go.
<i>In Situ</i> Identification of Semen Stains on Common Substrates via Raman Spectroscopy,, (2015)

The spectroscopic identification of body fluids in situ is a major objective in forensic science. This approach offers the confirmatory, nondestructive, rapid, and on-scene identification of various body fluids. Although Raman spectroscopy has shown tremendous promise toward this goal in prior proof-of-concept experiments, a significant challenge which still remains is substrate interference. Here, an approach for detecting semen stains in situ on various substrates using Raman spectroscopy is explored. Simulated semen evidence was prepared on skin, glass, and various fabrics. Raman data were accumulated from stains without any pretreatment using a common confocal mapping spectrometer using 785 nm laser excitation. The results demonstrate that the spectroscopic interferences encountered by substrates can be reduced and eliminated using a combination of existing subtraction techniques and chemometric models. Heterogeneous substrates proved most challenging, however, automatic subtraction treatment, and location of fluid hotspots was able to elucidate a clear spectroscopic signature of semen in every instance.
Adipose Tissue Interleukin‐18 mRNA and Plasma Interleukin‐18: Effect of Obesity and Exercise (2007)

Abstract Objectives: Obesity and a physically inactive lifestyle are associated with increased risk of developing insulin resistance. The hypothesis that obesity is associated with increased adipose tissue (AT) interleukin (IL)‐18 mRNA expression and that AT IL‐18 mRNA expression is related to insulin resistance was tested. Furthermore, we speculated that acute exercise and exercise training would regulate AT IL‐18 mRNA expression. Research Methods and Procedures: Non‐obese subjects with BMI < 30 kg/m 2 (women: n = 18; men; n = 11) and obese subjects with BMI >30 kg/m 2 (women: n = 6; men: n = 7) participated in the study. Blood samples and abdominal subcutaneous AT biopsies were obtained at rest, immediately after an acute exercise bout, and at 2 hours or 10 hours of recovery. After 8 weeks of exercise training of the obese group, sampling was repeated 48 hours after the last training session. Results: AT IL‐18 mRNA content and plasma IL‐18 concentration were higher ( p < 0.05) in the obese group than in the non‐obese group. AT IL‐18 mRNA content and plasma IL‐18 concentration was positively correlated ( p < 0.05) with insulin resistance. While acute exercise did not affect IL‐18 mRNA expression at the studied time‐points, exercise training reduced AT IL‐18 mRNA content by 20% in both sexes. Discussion: Because obesity and insulin resistance were associated with elevated AT IL‐18 mRNA and plasma IL‐18 levels, the training‐induced lowering of AT IL‐18 mRNA content may contribute to the beneficial effects of regular physical activity with improved insulin sensitivity.
Integration of clock skew and register delays into a retiming algorithm (2002)

The clock frequency of a synchronous circuit can be increased by retiming, an operation of temporally and physically relocating the registers. A new approach to the retiming process is presented which enables one to consider the effects on optimal retiming of electrical issues such as variable clock distribution delays and different register delays due to variable loads and cell instances. The algorithm provides increased accuracy in determining the maximum clock frequency and also eliminates any race conditions. Depending on the nature of the synchronous circuit, retiming using this algorithms may also provide an increase in system operating clock frequency.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Frequency agile bandstop filter (FABSF) (2008)

The frequency agile bandstop filter (FABSF) is an RF system component that functions as a frequency agile tunable notch filter capable of rejecting the low-level noise in presence of a high-level signal such as the out-of-band noise at the output of a high-power amplifier. The FABSF finds application in a frequency agile duplexer (FAD) system architecture to be implemented in the RF front-end of frequency division duplex (FDD) radio.
Observation of Liquid Crystals in Heavy Petroleum Fractions (2010)

In this work, we report for the first time the observation of naturally occurring discotic liquid-crystalline domains of ca. 100 μm in diameter in unreacted heavy fractions of petroleum. Precipitated solids from several bitumen and heavy oil samples exhibited the characteristic optical patterns of liquid crystals when observed under cross-polarized light. Samples included asphaltenes precipitated from Athabasca and Cold Lake bitumen (Canada), Maya heavy crude oil (Mexico), and Safaniya crude oil (Saudi Arabia) and a maltene fraction of Athabasca bitumen. The liquid-crystal domains appeared in asphaltene solids at ∼330 K in a nitrogen atmosphere and disappeared at ∼430 K. Upon cooling and subsequent reheating, the domains did not reappear. Liquid-crystal domains also appeared and then disappeared in the presence of toluene vapor at room temperature. Because the liquid crystals exhibit both thermotropic and lyotropic behavior, they are amphotropic. While amphotropic liquid crystals are known to arise in biological systems, the specific attributes of the liquid-crystal structures observed here are the first reported occurrence of such behavior in nature. The presence of liquid crystals in petroleum solids enriches our understanding of the complex phase and interfacial behavior of these materials and may provide new opportunities for partitioning petroleum.