gebhart/patrepeval huggingface dataset:
Machine Learning-Based Configuration Parameter Tuning on Hadoop System (2015)

Apache Hadoop system is a software framework with the capability to process large-scale datasets across a cluster of distributed machines using MapReduce programming model. However, there are two main challenges for system administrators to manage the Hadoop system, (1) system administrators are difficult to tune the parameters appropriately since the behaviors and characteristics of large-scale distributed systems are too complicated, (2) there are dozens of configuration parameters affecting the system performance which makes the configuration parameters tuning task becomes troublesome. In this paper, we focus on optimizing the Hadoop MapReduce job performance by tuning configuration parameters, and then we propose an analytical method to help system administrators choose approximately optimal configuration parameters depending on the characteristics of each application. Our approach has two key phases: prediction and optimization phase. The prediction phase is to estimate the performance of a MapReduce job, whereas the optimization phase is to search the approximately optimal configuration parameters strategically by invoking the predictor repeatedly. In our evaluation results, our work can help system administrators to improve the performance about 2X to 8X better than traditional methods.
Quantitative differential interference contrast microscopy based on structured-aperture interference (2008)

We report a quantitative differential interference contrast (DIC) microscope based on a structured-aperture (SA) wavefront sensor. Unlike a conventional DIC microscope, the SA-DIC microscope can separate the amplitude and the phase gradient information of the image wavefront, and form quantitative intensity and DIC images of the sample with good resolution; our prototype achieved resolution ∼2 μm. Furthermore, due to the nonpolarization nature of the microscope, we were able to image birefringent samples without artifacts.
An On-Line Engine Roughness Measurement Technique (1984)

&lt;div class="htmlview paragraph"&gt;Engine roughness may be characterized by nonuniform torque production among the cylinders of a multicylinder reciprocating internal combustion engine. This paper presents a technique for the on-line measurement of engine roughness based on fluctuations in engine crankshaft speed resulting from variations in torque production from cylinder to cylinder. The resulting roughness measure is suitable for use in a variety of engine control or diagnostic applications. The use of engine crankshaft speed information as the basis for the roughness measurement technique eliminates the need for any additional hardware beyond that found on conventional microprocessor-based engine control systems.&lt;/div&gt;
Estimated risk of transmission of the West Nile virus through blood transfusion in the US, 2002 (2003)

Estimates of the mean risk of WNV transmission by transfusion ranged from 1.46 to 12.33 per 10,000 donations for six high-incidence metropolitan areas during the 2002 epidemic. Because the risk was highly geographically and temporally variable, computation of geographically localized estimates is recommended. The derived approximating formula for the mean risk performed well for the estimates given.
Acquisition of Pseudonoise Signals by Recursion-Aided Sequential Estimation (1977)

An improved method of acquisition of pseudonoise signals (RARASE) is described and analyzed. This method is an outgrowth of the RASE method, rapid acquisition by sequential estimation. In the new method, the known recursion relation of the PN signal is used to determine if a short estimate of the state of the received PN signal is probably correct and if, consequently, an attempt should be made to track with that estimate. A high proportion of the incorrect initial state estimates can be discarded with relatively simple logic. Analyses are provided for a range of implementations from the simplest, a single 3-input modulo-2 gate, to multiple logic gates and for both a simple in-lock detector and a sequential detector. Significant improvement in acquisition time is shown for long PN signals and for the signal-to-noise range of -13 dB to +3 dB. Acquisition time reduction by a factor of 7.5 is calculated for a PN signal of length <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2^{15}-1</tex> bits compared to the sequential estimation (RASE) method using a simple in-lock detector. Reduction by factors of 1.5 to 3.5 is calculated using the sequential detector.
Infrared-Detectable Group Senses Changes in Charge Density on the Nickel Center in Hydrogenase from Chromatium vinosum (1995)

Fourier transform infrared studies of nickel hydrogenase from Chromatium vinosum reveal the presence of a set of three absorption bands in the 2100-1900 cm-1 spectral region. These bands, which do not arise from carbon monoxide, have line widths and intensities rivaling those of a band arising from the carbon monoxide stretching frequency (v(CO)) in the Ni(II).CO species of this enzyme [Bagley, K. A., Van Garderen, C. J., Chen, M., Duin, E. C., Albracht, S. P. J., & Woodruff, W. H. (1994) Biochemistry 33, 9229-9236]. The positions of each of these three infrared absorption bands respond in a consistent way to changes in the formal redox state of the nickel center and to the photodissociation of hydrogen bound to the nickel. Up to eight different states of the nickel center have been produced, depending on the redox state and/or the activity state of the enzyme and the presence of carbon monoxide. In seven of these states, the three IR absorption bands in the set have unique frequency positions. It is concluded that the set is due to intrinsic, non-protein groups in the enzyme, whose identities are presently unknown, and that these groups are situated very close to the nickel center and sense the charge density at the Ni site.
Automated detection of oestrus and mastitis in dairy cows (2000)

Detection models for oestrus and mastitis in dairy cows were developed, based on sensors for milk yield, milk temperature, electrical conductivity of milk, cow's activity and concentrate intake, and on combined processing of the sensor data. The detection model generated alerts for cows, that need the farmer's attention, because of a possible case of oestrus or mastitis. A first detection model for cows, milked twice a day, was based on time series models for the sensor variables, where the parameters were fitted on-line for each cow after each milking by a Kalman filter. This model was tested during two years on two experimental farms, and under field conditions on four farms during several years. A second detection model, for cows milked in an automatic milking system (AMS), was based on a generalisation of the first model. Two data sets (one small, one large) were used for testing. The results of both models for oestrus detection were good, for mastitis varying. Fuzzy logic was used for the classification of mastitis and oestrus alerts with both detection models, to reduce the number of false positive alerts. Input for the fuzzy logic model were alerts from the detection models and additional information. The number of false positive alerts decreased considerably, while keeping the number of detected cases at the same level. The models make automated detection possible in practice.
Optical performance of top-down fabricated InGaN/GaN nanorod light emitting diode arrays (2011)

Vertically aligned InGaN/GaN nanorod light emitting diode (LED) arrays were created from planar LED structures using a new top-down fabrication technique consisting of a plasma etch followed by an anisotropic wet etch. The wet etch results in straight, smooth, well-faceted nanorods with controllable diameters and removes the plasma etch damage. 94% of the nanorod LEDs are dislocation-free and a reduced quantum confined Stark effect is observed due to reduced piezoelectric fields. Despite these advantages, the IQE of the nanorod LEDs measured by photoluminescence is comparable to the planar LED, perhaps due to inefficient thermal transport and enhanced nonradiative surface recombination.
Expression of microRNAs and protein‐coding genes associated with perineural invasion in prostate cancer (2008)

Although preliminary, our findings suggest that alterations in microRNA expression, mitochondrial function, and cell metabolism occur at the transition from a noninvasive prostate tumor to a tumor with PNI.
Plasma levels of the chemokines monocyte chemotactic proteins-1 and -2 are elevated in human sepsis (1995)

Because of their effects on monocytes, monocyte chemotactic proteins-1 and -2 (MCP-1 and MCP-2) may participate in the pathophysiology of sepsis. We measured circulating MCP-1 and MCP-2 levels in 42 septic patients having positive local or blood cultures. MCP-1 and MCP-2 levels were elevated in 24 (57%) and 25 (59%) of 42 septic patients, respectively, compared with healthy volunteers. Both patients with gram-positive and gram-negative infections had elevated MCP-1 plasma levels (P = .0001) and P < .0001), respectively; Mann-Whitney-U test), whereas patients with gram-positive infection, but not those with gram-negative infection, had increased MCP-2 plasma levels (P= .0182). No relative differences in MCP-1 and MCP-2 plasma levels were observed between several subgroups of patients (sepsis v septic shock; survivors v nonsurvivors), although levels of MCP-1 were the highest in patients with the more severe forms of sepsis, ie, those with shock or a lethal outcome. Serial observations showed that MCP-1 and MCP-2 plasma levels remained elevated for at least 48 hours. MCP-1 correlated weakly with interleukin-8 and MCP-2, the correlations for which were most pronounced in patients with septic shock. MCP-2 correlated with interleukin-8, and surprisingly, with the complement activation product C3a; these correlations further improved when analyzing patients with septic shock or when applying gram-positive infections. Thus, our results not only show increased MCP-1 and MCP-2 levels in patients with sepsis, but also suggest that the synthesis and release of MCP-1 and MCP-2 in sepsis are differently regulated in part.
Human chitinases and chitinase-like proteins as indicators for inflammation and cancer. (2007)

Human Glyco_18 domain-containing proteins constitute a family of chitinases and chitinase-like proteins. Chitotriosidase and AMCase are true enzymes which hydrolyse chitin and have a C-terminal chitin-binding domain. YKL-40, YKL-39, SI-CLP and murine YM1/2 proteins possess solely Glyco_18 domain and do not have the hydrolytic activity. The major sources of Glyco_18 containing proteins are macrophages, neutrophils, epithelial cells, chondrocytes, synovial cells, and cancer cells. Both macrophages and neutrophils use the regulated secretory mechanism for the release of Glyco_18 containing proteins. Glyco_18 containing proteins are established biomarkers for human diseases. Chitotriosidase is overproduced by lipid-laden macrophages and is a major marker for the inherited lysosomal storage Gaucher disease. AMCase and murine lectin YM1 are upregulated in Th2-environment, and enzymatic activity of AMCase contributes to asthma pathogenesis. YKL proteins act as soluble mediators for the cell proliferation and migration, and are also involved in rheumatoid arthritis, inflammatory bowel disease, hepatic fibrosis and cirrhosis. Chitotriosidase and YKL-40 reflect the macrophage activation in atherosclerotic plaques. Serum level of YKL-40 is a diagnostic and prognostic marker for numerous types of solid tumors. YKL-39 is a marker for the activation of chondrocytes and the progression of the osteoarthritis in human. Recently identified SI-CLP is upregulated by Th2 cytokine IL-4 as well as by glucocorticoids. This unique feature of SI-CLP makes it an attractive candidate for the examination of individual sensitivity of patients to glucocorticoid treatment and prediction of side effects of glucocorticoid therapy. Human chitinases and chitinase-like proteins are found in tissues and circulation, and can be detected by non-invasive technologies.
Nanocrystals and quantum dots formed by high-dose ion implantation (1996)

Ion implantation and thermal annealing have been used to produce a wide range of nanocrystals and quantum dots in amorphous (SiO{sub 2}) and crystalline (Al{sub 2}O{sub 3}) matrices. Nanocrystals of metals (Au), elemental semiconductors (Si and Ge), and even compound semiconductors (SiGe, CdSe, CdS) have been produced. In amorphous matrices, the nanocrystals are randomly oriented, but in crystalline matrices they are three dimensionally aligned. Evidence for photoluminescence and quantum confinement effects are presented.
NUTSS: A SIP based approach to UDP and TCP connectivity (2004)

The communications establishment capability of the Session Initiation Protocol is being expanded by the IETF to include establishing network layer connectivity for UDP for a range of scenarios, including where hosts are behind NAT boxes, and host are running IPv6. So far, this work has been limited to UDP because of the assumed impossibility of establishing TCP connections through NAT, and because of the difficulty of predicting port assignments on certain common types of NATs. This paper reports on preliminary success in establishing TCP connections through NAT, and on port prediction. In so doing, we suggest that it may be appropriate for SIP to take a broader architectural role in P2P network layer connectivity for both IPv4 and IPv6.
Music Therapy and Elective Mutism: A Case Discussion (1990)

This paper describes individual music therapy sessions with a 20-year-old man with specific communication difficulties manifested as inappropriate behaviour and elective mutism in his daily life. It shows how music therapy was a particularly relevant treatment in the context of the Unit where he was being helped. It illustrates firstly how aspects of play can be embraced in the therapeutic relationship, and secondly how problems can be worked through in the experience of both musical and non-musical interaction. The therapist uses a psychodynamic viewpoint in her understanding and interpretation of the sessions.
Postsurgical Surveillance of Colon Cancer (1998)

OBJECTIVE: This study is the first to examine the relative and absolute costs of physician examination, carcinoembryonic antigen (CEA) assessment, chest x-ray, and colonoscopy in detecting recurrent disease in patients who have undergone surgical resection for primary colon carcinoma. METHODS: Of the 1356 Eastern Cooperative Oncology Group patients in Intergroup Protocol 0089 who underwent surgical resection for Dukes' B2 and C colon carcinoma, 421 patients who developed recurrent disease were reviewed. Follow-up testing was performed according to protocol guidelines, with the cost of each test equal to 1995 Medicare reimbursement. Follow-up was defined as the time to recurrence for the 421 patients in whom disease recurred (mean 18.6 months) or up to 5 years for the additional 930 patients in whom disease did not recur (mean 38.6 months). Patients were divided into three categories: nonrecurrent, recurrent but not resectable, and recurrent but resectable with curative intent. The estimated mean cost of each test in detecting group 3 (recurrent but resectable) patients was calculated. RESULTS: Of the 421 patients who developed recurrent disease, 96 underwent surgical resection of their disease with curative intent (group 3). For group 3 patients, the first indication of recurrent disease was CEA testing (30), chest x-ray (12), colonoscopy (14), and other (40). Of the 40 "other" patients, 24 presented with symptoms. Routine physician examination, however, failed to identify a single resectable recurrence, and the total cost for physician examination was $418,615. The detection rate for CEA testing was 2.2%, the total cost was $170,880, and the cost per recurrence was $5,696. The detection rate for chest x-ray was 0.9%, the total cost was $120,934, and the cost per recurrence was $10,078. The detection rate of colonoscopy was 1%, the total cost was $641,344, and the cost per recurrence was $45,810. CONCLUSIONS: CEA measurement was the most cost-effective test in detecting potentially curable recurrent disease. Physician visits were useful only in the evaluation of symptoms; a routine physician examination had no added benefit.
Spin-Polarized Current Induced Torque in Magnetic Tunnel Junctions (2005)

We present tight-binding calculations of the spin torque in non-collinear magnetic tunnel junctions based on the non-equilibrium Green functions approach. We have calculated the spin torque via the effective local magnetic moment approach and the divergence of the spin current. We show that both methods are equivalent, i.e. the absorption of the spin current at the interface is equivalent to the exchange interaction between the electron spins and the local magnetization. The transverse components of the spin torque parallel and perpendicular to the interface oscillate with different phase and decay in the ferromagnetic layer (FM) as a function of the distance from the interface. The period of oscillations is inversely proportional to the difference between the Fermi-momentum of the majority and minority electrons. The phase difference between the two transverse components of the spin torque is due to the precession of the electron spins around the exchange field in the FM layer. In absence of applied bias and for a relatively thin barrier the perpendicular component of the spin torque to the interface is non-zero due to the exchange coupling between the FM layers across the barrier.
Incremental density approximation and kernel-based Bayesian filtering for object tracking (2004)

Statistical density estimation techniques are used in many computer vision applications such as object tracking, background subtraction, motion estimation and segmentation. The particle filter (condensation) algorithm provides a general framework for estimating the probability density functions (pdf) of general non-linear and non-Gaussian systems. However, since this algorithm is based on a Monte Carlo approach, where the density is represented by a set of random samples, the number of samples is problematic, especially for high dimensional problems. In this paper, we propose an alternative to the classical particle filter in which the underlying pdf is represented with a semi-parametric method based on a mode finding algorithm using mean-shift. A mode propagation technique is designed for this new representation for tracking applications. A quasi-random sampling method in the measurement stage is used to improve performance, and sequential density approximation for the measurements distribution is performed for efficient computation. We apply our algorithm to a high dimensional color-based tracking problem, and demonstrate its performance by showing competitive results with other trackers.
The nonessentiality of essential genes in yeast provides therapeutic insights into a human disease (2016)

Essential genes refer to those whose null mutation leads to lethality or sterility. Theoretical reasoning and empirical data both suggest that the fatal effect of inactivating an essential gene can be attributed to either the loss of indispensable core cellular function (Type I), or the gain of fatal side effects after losing dispensable periphery function (Type II). In principle, inactivation of Type I essential genes can be rescued only by re-gain of the core functions, whereas inactivation of Type II essential genes could be rescued by a further loss of function of another gene to eliminate the otherwise fatal side effects. Because such loss-of-function rescuing mutations may occur spontaneously, Type II essential genes may become nonessential in a few individuals of a large population. Motivated by this reasoning, we here carried out a systematic screening for Type II essentiality in the yeast Saccharomyces cerevisiae Large-scale whole-genome sequencing of essentiality-reversing mutants reveals 14 cases whereby the inactivation of an essential gene is rescued by loss-of-function mutations on another gene. In particular, the essential gene encoding the enzyme adenylosuccinate lyase (ADSL) is shown to be Type II, suggesting a loss-of-function therapeutic strategy for the human disorder ADSL deficiency. A proof-of-principle test of this strategy in the nematode Caenorhabditis elegans shows promising results.
Effects of in vivo administration of anti-CD3 monoclonal antibody on T cell function in mice. II. In vivo activation of T cells. (1989)

Anti-CD3 mAb are known to be both immunosuppressive and mitogenic to T cells in vitro. However, only immunosuppression has been observed after in vivo administration of these mAb. The present study demonstrates that T cell activation does occur after in vivo administration of anti-CD3 mAb to mice, evidenced by increased IL-2R expression on T cells, CSF secretion, and extra-medullary hematopoiesis in the spleen. These effects required multivalent cross-linking of the mAb, since F(ab')2 fragments failed to induce them. However, the F(ab')2 fragments did induce modulation of CD3/TCR from the surface of T cells, demonstrating that TCR modulation is not sufficient to induce activation. In addition, interaction of the TCR with either intact or F(ab')2 fragments of the mAb led to increased expression of CD8 in vivo, suggesting that the F(ab')2 fragments of anti-CD3 mAb might be capable of inducing a T cell to undergo some, but not all, of the changes involved in reaching a fully activated state. Further study of the activating effects of anti-CD3 mAb might increase the understanding of the mechanisms of in vivo T cell activation and might also be exploited clinically to stimulate T cell function in immunocompromised states and to enhance hematopoiesis in myelodysplastic disorders.
Biosynthesis of heparin/heparan sulphate: mechanism of epimerization of glucuronyl C-5 (2000)

In the biosynthesis of heparin and heparan sulphate, D-glucuronic acid residues are converted into L-iduronic acid (IdoA) units by C-5 epimerization, at the polymer level. The reaction catalysed by the epimerase occurs by reversible abstraction and readdition of a proton at C-5 of target hexuronic acid residues, through a carbanion intermediate, with or without an inversion of configuration at C-5 [Prihar, Campbell, Feingold, Jacobsson, Jensen, Lindahl and Rodén (1980) Biochemistry 19, 495-500]. Incubation of chemically N-sulphated capsular polysaccharide from Escherichia coli K5 ([4GlcAβ1-4GlcNSO3α1-]n), or of O-desulphated heparin (predominantly [4IdoAα1-4GlcNSO3α1-]n) with purified C-5 epimerase from bovine liver, resulted in the interconversion of glucuronic acid and IdoA residues, which reached equilibrium (30-40% IdoA/total hexuronic acid) after approx. 1 h of incubation. Similar incubations performed in the presence of 3H2O resulted in progressive labelling at C-5 of the target hexuronic acid units of either substrate polysaccharide. Contrary to chemical D-gluco/L-ido equilibrium, established within 1 h of incubation, the accumulation of 3H label continued for at least 6 h. This isotope effect suggests that the second stage of the reaction, i.e. the re-addition of a proton to the carbanion intermediate, is the rate-limiting step of the overall process. Analysis of the 5-3H-labelled polysaccharide products showed that the 3H was approximately equally distributed between glucuronic acid and IdoA units, irrespective of incubation time (from 15 min to 72 h) and of the relative proportions of the two epimers in the substrate. This finding points to a catalytic mechanism in which the abstraction and re-addition of C-5 protons are effected by two polyprotic bases, presumably lysine residues. Previous experiments relating to the biosynthesis of dermatan sulphate were similarly interpreted in terms of a two-base epimerization mechanism but differed from the present findings by implicating one monoprotic and one polyprotic base function [Hannesson, Hagner-McWhirter, Tiedemann, Lindahl and Malmström (1996) Biochem. J. 313, 589-596].