gebhart/patrepeval huggingface dataset:
Bootstrapping Lasso Estimators (2011)

Abstract In this article, we consider bootstrapping the Lasso estimator of the regression parameter in a multiple linear regression model. It is known that the standard bootstrap method fails to be consistent. Here, we propose a modified bootstrap method, and show that it provides valid approximation to the distribution of the Lasso estimator, for all possible values of the unknown regression parameter vector, including the case where some of the components are zero. Further, we establish consistency of the modified bootstrap method for estimating the asymptotic bias and variance of the Lasso estimator. We also show that the residual bootstrap can be used to consistently estimate the distribution and variance of the adaptive Lasso estimator. Using the former result, we formulate a novel data-based method for choosing the optimal penalizing parameter for the Lasso using the modified bootstrap. A numerical study is performed to investigate the finite sample performance of the modified bootstrap. The methodology proposed in the article is illustrated with a real data example. Keywords: : Bootstrap variance estimationPenalized regressionRegularizationShrinkage
New Fixed-Off-Time PWM modulator provides constant frequency operation in boost PFC pre-regulators (2008)

The objective of this paper is to describe a new fixed-off-time (FOT) PWM modulator and its application in boost PFC pre-regulators. The uniqueness of this new modulator, suitable for integration in a control IC, is that it provides the OFF-time modulated with the instantaneous line voltage in such a way that the resulting switching frequency is constant and not dependent on the rms input voltage or on the output load as long as the boost stage operates in continuous conduction mode (CCM).
Dynamic cerebral autoregulation and beat to beat blood pressure control are impaired in acute ischaemic stroke. (2002)

Dynamic cerebral autoregulation, as assessed using spontaneous transient pressor and depressor BP stimuli, is globally impaired after acute ischaemic stroke and may prove to be an important factor in predicting outcome.
Blood Transcriptional Profiling Reveals Immunological Signatures of Distinct States of Infection of Humans with Leishmania infantum (2016)

Visceral leishmaniasis (VL) can be lethal if untreated; however, the majority of human infections with the etiological agents are asymptomatic. Using Illumina Bead Chip microarray technology, we investigated the patterns of gene expression in blood of active VL patients, asymptomatic infected individuals, patients under remission of VL and controls. Computational analyses based on differential gene expression, gene set enrichment, weighted gene co-expression networks and cell deconvolution generated data demonstrating discriminative transcriptional signatures. VL patients exhibited transcriptional profiles associated with pathways and gene modules reflecting activation of T lymphocytes via MHC class I and type I interferon signaling, as well as an overall down regulation of pathways and gene modules related to myeloid cells, mainly due to differences in the relative proportions of monocytes and neutrophils. Patients under remission of VL presented heterogeneous transcriptional profiles associated with activation of T lymphocytes via MHC class I, type I interferon signaling and cell cycle and, importantly, transcriptional activity correlated with activation of Notch signaling pathway and gene modules that reflected increased proportions of B cells after treatment of disease. Asymptomatic and uninfected individuals presented similar gene expression profiles, nevertheless, asymptomatic individuals exhibited particularities which suggest an efficient regulation of lymphocyte activation and a strong association with a type I interferon response. Of note, we validated a set of target genes by RT-qPCR and demonstrate the robustness of expression data acquired by microarray analysis. In conclusion, this study profiles the immune response during distinct states of infection of humans with Leishmania infantum with a novel strategy that indicates the molecular pathways that contribute to the progression of the disease, while also providing insights into transcriptional activity that can drive protective mechanisms.
Reduced Risk of Upper Gastrointestinal Ulcer Complications With Celecoxib, A Novel Cox-2 Inhibitor (2000)

The incidence of UGI ulcer complications associated with celecoxib was 8-fold lower than with nonspecific NSAIDs. The incidence of ulcer complications observed in celecoxib-treated patients was similar to that in patients receiving placebo in the RCTs, and to that in non-NSAID users reported in the literature.
Antigenic comparison of Canadian and US isolates of porcine reproductive and respiratory syndrome virus using monoclonal antibodies to the nucleocapsid protein. (1995)

Fifteen Canadian field isolates of porcine reproductive and respiratory syndrome (PRRS) virus from Quebec and Ontario were compared with 5 US PRRS virus (PRRSV) isolates and with the European Lelystad isolate using monoclonal antibodies (MAbs) SDOW17, EP147, and VO17 directed to the 15-kDa nucleocapsid protein of PRRSV. All Canadian and US isolates tested by indirect immunofluorescence were recognized by the 3 MAbs, and individual titers of MAbs towards Canadian and US PRRSV isolates were similar as well. In contrast, the Lelystad virus isolate reacted only with the SDOW17 MAb and showed no reactivity with either EP147 or VO17. The reactivity pattern with these MAbs suggests that the Canadian isolates of PRRSV tested are antigenically similar to US isolates of PRRSV, and that these North American isolates share highly conserved epitopes on the 15-kDa nucleocapsid protein that clearly differentiate them from the European Lelystad virus isolate.
Effect of terrains on the volatiles of Cabernet Sauvignon wines grown in Loess Plateau region of China (2012)

Volatile compounds of young Cabernet Sauvignon wines from the flat and slope lands grown in Loess Plateau region (China) were investigated in this research. Among the volatile compounds analyzed by headspace solid phase microextraction (HS-SPME) with gas chromatography-mass spectrometry (GC-MS), a total of 43 and 45 volatile compounds were identified and quantified in the flat and slope lands wines, respectively. In the volatiles detected, higher alcohols formed the most abundant group in the aroma components of two wines, followed by esters and fatty acids. According to their odor active values (OAVs) and relative odor contribution (ROC), the aromatic profiles for two wines were similar, showing only quantitative but not qualitative differences. Ethyl octanoate, ethyl hexanoate and isoamyl acetate were found to jointly contribute to 98.8 and 99.2% of the global aroma of the flat and slope wines, respectively. These odorants are associated with “fruity’’ and ‘‘ripe fruit’’ odor descriptors. Wine from flat land with higher OAVs of ethyl octanoate and isoamyl acetate seems to have more intense fruity aromas (pineapple, pear and banana), with floral notes. Keywords: Cabernet Sauvignon wines, volatiles, terrains, Loess Plateau region, headspace solid phase microextraction (HS-SPME), gas chromatography-mass spectrometry (GC-MS)
Scandium in aluminium alloys (2005)

A considerable part of the available literature on scandium in aluminium alloys is reviewed. Experimental data and assessments of the binary Al–Sc phase diagram, a wide range of ternary Al–Sc–X phase diagrams and a few higher order phase diagrams are accounted for, with emphasis on the aluminium rich part of the diagrams. The phase which is in equilibrium with Al, Al3Sc, can form by several different mechanisms, all of which are described. The precipitation kinetics of Al3Sc in binary Al–Sc alloys are discussed, and an overview of the reported influences of ternary alloying elements on the precipitation of Al3Sc is given. The Al3Sc phase particles can serve as a grain refiner in the Al melt, a dispersoid for controlling the grain structure of the alloy and a strengthening precipitate. Several examples of these three effects are mentioned, both in binary Al–Sc alloys, and in more complex alloys. The reported effects of Sc on the precipitation behaviour in Al–Cu, Al–Mg–Si, Al–Zn–Mg and Al–Li alloys are also revised. A brief account of the effects of Sc additions on the corrosion behaviour of Al and Al-alloys is given. Finally, some views on the current and future use of Sc-containing Al alloys are given.
Enrichment medium for the isolation of Bordetella (1977)

The development of a specimen collection and transport medium outfit for the rapid laboratory diagnosis of whoping cough is described. The transport medium consisted of a semisolid agar containing charcoal, cephalexin, and defibrinated horse blood. It was also found to be an excellent enrichment medium for the selective isolation of Bordetella pertussis and B. parapertussis from scantily populated specimens. The investigation of 3,237 specimens that yielded 1,419 positive isolates of Bordetella, including 86 B. parapertussis, during a 20-month period is presented. A total of 3,076 specimens were processed in the laboratory by using the enrichment medium in addition to the routine procedure. Of these specimens, 757 were submitted in our medium, from which 137 (18%) were positive. Of the 567 specimens received in Amies transport medium, 290 (51%) positive cultures were obtained by the enrichment method only and not by primary culture.
Stable and intense blue-green emission in porous silicon achieved by amine immersion and rapid thermal oxidation (1997)

Porous silicon treated by amine immersion and then rapid thermal oxidation results in a photoluminescence peak shift from ∼650 nm (red light) to a stable and intense ∼520 nm blue-green light. The amine immersion may catalyze a process during rapid thermal oxidation that both reduces the sizes of Si cores and more effectively saturates the dangling bonds on the inner surfaces of the porous silicon.
Controlling Synaptic Input Patterns In Vitro by Dynamic Photo Stimulation (2005)

Recent experimental and theoretical work indicates that both the intensity and the temporal structure of synaptic activity strongly modulate the integrative properties of single neurons in the intact brain. However, studying these effects experimentally is complicated by the fact that, in experimental systems, network activity is either absent, as in the acute slice preparation, or difficult to monitor and to control, as in in vivo recordings. Here, we present a new implementation of neurotransmitter uncaging in acute brain slices that uses functional projections to generate tightly controlled, spatio-temporally structured synaptic input patterns in individual neurons. For that, a set of presynaptic neurons is activated in a precisely timed sequence through focal photolytic release of caged glutamate with the help of a fast laser scanning system. Integration of synaptic inputs can be studied in postsynaptic neurons that are not directly stimulated with the laser, but receive input from the targeted neurons through intact axonal projections. Our new approach of dynamic photo stimulation employs functional synapses, accounts for their spatial distribution on the dendrites, and thus allows study of the integrative properties of single neurons with physiologically realistic input. Data obtained with our new technique suggest that, not only the neuronal spike generator, but also synaptic transmission and dendritic integration in neocortical pyramidal cells, can be highly reliable.
An ultrasensitive electrochemical immunosensor for determination of estradiol using coralloid Cu<sub>2</sub>S nanostructures as labels (2014)

Ultrasensitive electrochemical immunoassay based on coralloid Cu<sub>2</sub>S nanostructure for determination of estradiol.
The humoral antibacterial response of <i>Drosophila</i> (1993)

Drosophila, like other insects, responds to the injection of bacteria by the rapid and transient synthesis of a battery of potent antibacterial peptides. Only a few of these peptides have been fully characterized to date. We review our recent data on the control of the expression of a gene encoding one of the induced peptides, i.e. diptericin. Our data highlight the role of proximal cis-regulatory motifs similar to regulatory elements binding NF-kappa B and NF-IL6 in promoters of some immune genes of mammals. We argue that the Drosophila host defense is homologous to the mammalian acute phase response.
The distributed information search component (Disco) and the World Wide Web (1997)

The Distributed Information Search COmponent (DISCO) is a prototype heterogeneous distributed database that accesses underlying data sources. The DISCO prototype currently focuses on three central research problems in the context of these systems. First, since the capabilities of each data source is different, transforming queries into subqueries on data source is difficult. We call this problem the weak data source problem. Second, since each data source performs operations in a generally unique way, the cost for performing an operation may vary radically from one wrapper to another. We call this problem the radical cost problem. Finally, existing systems behave rudely when attempting to access an unavailable data source. We call this problem the ungraceful failure problem.
The Fault Diagnosis Research of Gearbox Based on Hilbert-Huang Transform (2011)

The signal processing based on Hilbert-Huang transform is very suitable for nonlinear and non stationary process, it can extract gear fault features effectively. In this paper we aim at the engineering need of gearbox real-time monitoring and fault diagnosis, expanding a study of JZQ250 Gear Box. We use Hilbert-Huang transform to measure gear vibration signal processing, and use the obtained instantaneous frequency Hilbert marginal spectrum as the fault feature of the gearbox fault diagnosis. Tests showed that, the marginal spectrum based on Hilbert-Huang transform can get the characteristics of fault signal frequency of the gearbox, thus it can identify the type of gearbox fault effectively and achieve early fault prediction. The characteristics of instantaneous frequency can describe the corresponding fault type better. It has a good prospect in the field of gearbox fault diagnosis.
Rapid, in Situ Synthesis of High Capacity Battery Anodes through High Temperature Radiation-Based Thermal Shock (2016)

High capacity battery electrodes require nanosized components to avoid pulverization associated with volume changes during the charge-discharge process. Additionally, these nanosized electrodes need an electronically conductive matrix to facilitate electron transport. Here, for the first time, we report a rapid thermal shock process using high-temperature radiative heating to fabricate a conductive reduced graphene oxide (RGO) composite with silicon nanoparticles. Silicon (Si) particles on the order of a few micrometers are initially embedded in the RGO host and in situ transformed into 10-15 nm nanoparticles in less than a minute through radiative heating. The as-prepared composites of ultrafine Si nanoparticles embedded in a RGO matrix show great performance as a Li-ion battery (LIB) anode. The in situ nanoparticle synthesis method can also be adopted for other high capacity battery anode materials including tin (Sn) and aluminum (Al). This method for synthesizing high capacity anodes in a RGO matrix can be envisioned for roll-to-roll nanomanufacturing due to the ease and scalability of this high-temperature radiative heating process.
A microfluidic chip with a U-shaped microstructure array for multicellular spheroid formation, culturing and analysis (2014)

Multicellular spheroids (MCS), formed by self-assembly of single cells, are commonly used as a three-dimensional cell culture model to bridge the gap between in vitro monolayer culture and in vivo tissues. However, current methods for MCS generation and analysis still suffer drawbacks such as being labor-intensive and of poor controllability, and are not suitable for high-throughput applications. This study demonstrates a novel microfluidic chip to facilitate MCS formation, culturing and analysis. The chip contains an array of U-shaped microstructures fabricated by photopolymerizing the poly(ethylene glycol) diacrylate hydrogel through defining the ultraviolet light exposure pattern with a photomask. The geometry of the U-shaped microstructures allowed trapping cells into the pocket through the actions of fluid flow and the force of gravity. The hydrogel is non-adherent for cells, promoting the formation of MCS. Its permselective property also facilitates exchange of nutrients and waste for MCS, while providing protection of MCS from shearing stress during the medium perfusion. Heterotypic MCS can be formed easily by manipulating the cell trapping steps. Subsequent drug susceptibility analysis and long-term culture could also be achieved within the same chip. This MCS formation and culture platform can be used as a micro-scale bioreactor and applied in many cell biology and drug testing studies.
Kinematic synthesis of adjustable robotic mechanisms. (1993)

Conventional hard automation, such as a linkage-based or a cam-driven system, provides high speed capability, and repeatability but not the flexibility required in many industrial applications. The conventional mechanisms, that are typically single-degree-of-freedom systems, are being increasingly replaced by multi-degree-of-freedom multi- actuators driven by logic controllers. Although this new trend in sophistication provides greatly enhanced flexibility, there are many instances where the flexibility needs are exaggerated and the associated complexity is unnecessary. Traditional mechanism-based hard automation, on the other hand, can neither fulfill multi-task requirements nor are cost-effective mainly due to lack of methods and tools to design-in flexibility. This dissertation attempts to bridge this technological gap by developing Adjustable Robotic Mechanisms (ARMs) or "programmable mechanisms" as a middle ground between high speed hard automation and expensive serial jointed-arm robots. This research introduces the concept of adjustable robotic mechanisms towards cost-effective manufacturing automation. A generalized analytical synthesis technique has been developed to support the computational design of ARMs that lays the theoretical foundation for synthesis of adjustable mechanisms. The synthesis method developed in this dissertation, called generalized adjustable dyad and triad synthesis, advances the well-known Burmester theory in kinematics to a new level. While this method provides planar solutions, a novel patented scheme is utilized for converting prescribed three-dimensional motion specifications into sets of planar projections. This provides an analytical and a computational tool for designing adjustable mechanisms that satisfy multiple sets of three-dimensional motion specifications. Several design issues were addressed; including adjustable parameter identification, branching defect, and mechanical errors. An efficient mathematical scheme for identification of adjustable member was also developed. The analytical synthesis techniques developed in this dissertation were successfully implemented in a graphic-intensive user-friendly computer program. A physical prototype of a general purpose adjustable robotic mechanism has been constructed to serve as a proof-of-concept model.
Inverse Polymerase Chain Reaction (PCR) (2019)

The standard polymerase chain reaction (PCR) is used to amplify a segment of DNA that lies between two inward-pointing primers. In contrast, inverse PCR (also known as inverted or inside-out PCR) is used to amplify DNA sequences that flank one end of a known DNA sequence and for which no primers are available. Inverse PCR DNA involves digestion by a restriction enzyme of a preparation of DNA containing the known sequence and its flanking region. The individual restriction fragments (many thousands in the case of total mammalian genomic DNA) are converted into circles by intramolecular ligation, and the circularized DNA is then used as a template in PCR. The unknown sequence is amplified by two primers that bind specifically to the known sequence and point in opposite directions. The product of the amplification reaction is a linear DNA fragment containing a single site for the restriction enzyme originally used to digest the DNA. This site marks the junction between the previously cloned sequence and the flanking sequences. The size of the amplified fragment depends on the distribution of restriction sites within known and flanking DNA sequences.
Deep learning for magnification independent breast cancer histopathology image classification (2016)

Microscopic analysis of breast tissues is necessary for a definitive diagnosis of breast cancer which is the most common cancer among women. Pathology examination requires time consuming scanning through tissue images under different magnification levels to find clinical assessment clues to produce correct diagnoses. Advances in digital imaging techniques offers assessment of pathology images using computer vision and machine learning methods which could automate some of the tasks in the diagnostic pathology workflow. Such automation could be beneficial to obtain fast and precise quantification, reduce observer variability, and increase objectivity. In this work, we propose to classify breast cancer histopathology images independent of their magnifications using convolutional neural networks (CNNs). We propose two different architectures; single task CNN is used to predict malignancy and multi-task CNN is used to predict both malignancy and image magnification level simultaneously. Evaluations and comparisons with previous results are carried out on BreaKHis dataset. Experimental results show that our magnification independent CNN approach improved the performance of magnification specific model. Our results in this limited set of training data are comparable with previous state-of-the-art results obtained by hand-crafted features. However, unlike previous methods, our approach has potential to directly benefit from additional training data, and such additional data could be captured with same or different magnification levels than previous data.
Host F1 Mice Pretreated With Granulocyte Colony-Stimulating Factor Accept Parental Bone Marrow Grafts in Hybrid Resistance System (1997)

In the setting of hybrid resistance, parental C57BL/6 bone marrow (BM) grafts are vigorously rejected by lethally irradiated (C57BL/6xDBA/2) F1 mice. However, F1 mice pretreated by continuous administration of granulocyte colony-stimulating factor (G-CSF) with a miniosmotic pump before BM grafting developed day-8 splenic colonies of donor origin. This inhibitory effect on rejection was reversible because F1 mice regained the capacity to reject parental BM when the pump ceased functioning. The appearance of only a small number of colonies with the administration of G-CSF soon after BM grafting suggested the importance in producing this inhibitory effect of pre-exposure of host mice to G-CSF. Because G-CSF administration with a syngeneic combination did not influence the number of colonies, an altered distribution of grafted precursors was unlikely. The absence of a reduction in the number of NK1.1-positive cells in G-CSF-treated mice suggested functional impairment of natural killer cells, major effectors in hybrid resistance, but further study is necessary to elucidate the mechanism underlying this phenomenon. However, our results indicate the importance of G-CSF as a regulator in a certain type of immune response and raise the possibility of clinical application in transplantation medicine.