gebhart/patrepeval huggingface dataset:
Cluster analysis with batch effect (2015)

Clustering, as a fundamental process in data science, is frequently used in preliminary data analysis. Batch effects are a powerful source of variation that can come from many sources in data collection, and influence data. We propose a method to simultaneously remove batch effects and perform cluster analysis. We see a batch effect as a fixed value added on to each batch, and do not make assumptions about the distribution of batch effects. We represent the data using a Gaussian mixture model, and use the EM algorithm to estimate the cluster means, the cluster covariance matrices, and the batch effects, and give predictions on which cluster each observation belongs to via their posterior probability. We also give two tests to identify the presence of batch effects in the data. Gap statistics are used to determine the number of clusters that should be used. We compare our method via simulation studies with a standard K-means method and K-means with the batch effects removed prior to analysis. Out simulations studies our method has better prediction results than both of these approaches. Our method does not assume the batch effects following any particular distribution, and works on data that have larger batch effects, as well as an interaction between clusters and batches.
Analysis of saccharification in Brachypodium distachyon stems under mild conditions of hydrolysis (2008)

Results presented here indicate that under mild conditions cellulose and hemicellulose are hydrolysed to differing extents, with hemicellulose hydrolysis predominating. We anticipate that the sub-optimal conditions for hydrolysis identified here will provide a sensitive assay to detect variations in saccharification among Brachypodium plants, providing a useful analytical tool for identifying plants with alterations in this trait.
Enzymatic Transformation of Morphine by Hydroxysteroid Dehydrogenase from <i>Pseudomonas testosteroni</i> (1975)

Eznyme preparations from Pseudomonas testosteroni containing alpha- and beta- hydroxysteroid dehydrogenases catalyzed the oxidation of morphine and codeine by nicotinamide adenine dinucleotide. Morphine was converted in relatively low yield into 14-hydroxymorphinone probably via morphinone as an intermediate. Codeine was converted to codeinone and 14-hydroxycodeinone. Only the conversions at the 6-position were carred out by the hydroxysteroid dehydrogenase. Hydroxylation at the 14-position did occur spontaneously (or enzymatically with a contaminating enzyme) ater oxidation at the 6-position.
Storage of apheresis platelet concentrates after manual replacement of >95% of plasma with <scp>PAS</scp> 5 (2014)

The 7-day in vitro storage parameters investigated were comparable between >95% PAS 5 and 100% plasma platelets derived from both Amicus and Trima plateletpheresis devices, with the exception that lactose dehydrogenase release rate and pH were significantly higher in PAS 5 units.
Shadow removal using Retinex theory (2011)

Shadows in images always cause problems to computer visual tasks, so how to remove shadow is an important topic of image processing. In this paper, we propose a new shadow removal method based on Retinex theory. We firstly use the gradient edge detection combined with 1-D illumination invariant image to detect the shadow area, then remove the shadow with Retinex algorithm, finally adjust the brightness of the shadow area. By transforming the RGB image into HSV space, we compute the average brightness of the non-shadow area in original image and shadow-free image, adjust the brightness of the image to coordinate with the original image. The experiment results show that our method can provide a good effect in shadow images.
Acoustic bubble traps (1999)

A small, oscillating bubble in a liquid can be trapped in the antinode of an acoustic standing wave field. Bubble stability is required for the study of single-bubble sonoluminescence (SBSL). The properties of the acoustic resonator are essential for the stable trapping of sonoluminescing bubbles. Its acoustic modes were measured by means of holographic interferometry and hydrophones. Flasks of different geometries (spherical, cylindrical, rectangular, ovoid) were investigated as well as different acoustic modes. Higher harmonic modes were used to trap several single, stable sonoluminescencent bubbles within one acoustic resonator (few bubble sonoluminescence, FBSL). This opens up the possibility to study bubble–bubble interactions (secondary Bjerknes forces).
Regulation by complement C3a and C5a anaphylatoxins of cytokine production in human umbilical vein endothelial cells (2003)

C3a and C5a anaphylatoxins are cytokine-like polypeptides generated during complement (C) system activation and released at the inflammatory site. They exert several biological activities through binding to the G-protein-coupled receptors C3aR and C5aR, respectively. Cloning and Northern blot experiments have indicated that both receptors are expressed by myeloid as well as nonmyeloid cells (e.g., endothelial and epithelial cells). To better understand the roles of C anaphylatoxins during inflammation, we investigated their effects on the expression of cytokine and chemokine genes by cultured human umbilical cord endothelial cells (HUVEC). HUVEC constitutively expressed both anaphylatoxin receptors, and addition of physiological concentrations of C3a or C5a (nM range) caused a strong up-regulation of IL-8, IL-1beta, and RANTES mRNA in a time- and dose-dependent manner. Conversely, a decrease in IL-6 mRNA was observed, but only with C5a stimulation. These variations in mRNA levels were inhibited by pretreatment with anti-C5aR and anti-C3aR antibodies as well as pertussis toxin, indicating that G-proteins are involved in anaphylatoxin-activated signal transduction pathways. Finally, we showed that C3a and C5a both strongly activate downstream MAP kinase signaling pathways (p44 and p42 Erk kinases).
Targeting histone methyltransferase EZH2 as cancer treatment (2014)

It is widely accepted that epigenetic alterations are associated with different stages of tumour formation and progression in many cancers. Therefore, epigenetic abnormalities in cancers are emerging as important biomarkers and may have therapeutic potential. The polycomb repressive complex 2 (PRC2) is a key epigenetic regulator that catalyses trimethylation of lysine 27 on histone H3 (H3K27me3) via the histone methyltransferase, EZH2, which confers stemness and regulates differentiation during embryonic development. Given these roles of EZH2 and H3K27me3, plastic and dynamic features of cancer cells, especially cancer stem cells (CSCs), may be closely associated with this epigenetic mechanism. In addition, recent sequencing technology revealed that there are many recurrent mutations in polycomb-related genes, including EZH2, in different types of cancers. Therefore, researchers focused on targeting EZH2 as a novel cancer treatment and identified small compounds that inhibit EZH2 activity. Some of them are now under clinical trial in B-cell lymphoma. However, the underlying mechanisms by which PRC2 precisely regulate epigenetic alterations at certain genomic loci under different cellular conditions remain unclear. In this review, I focus on the recent advancements in EZH2 research, especially its dynamic regulation of epigenetic alterations in tumour cells, including the CSC population, and discuss perspectives and challenges for cancer treatment in the near future.
Effects of Various Timings and Concentrations of Inhaled Nitric Oxide in Lung Ischemia–Reperfusion (1997)

Experimental studies reveal that inhaled nitric oxide (NO) can prevent, worsen, or have no effect on lung injury in the setting of ischemia-reperfusion (I-R). We tested the hypothesis that these disparate effects could be related to differences in the timing of administration and/or concentration of inhaled NO during I-R. Isolated rat lungs were subjected to 1-h periods of ischemia followed by 1-h periods of blood reperfusion. We investigated the effects of NO (30 ppm) given during ischemia, NO (30 or 80 ppm) begun immediately at reperfusion, or NO (30 ppm) given 15 min after the beginning of reperfusion, on total pulmonary vascular resistance (PVR), the coefficient of filtration (Kfc), the lung wet/dry weight ratio (W/D) of lung tissue, and lung myeloperoxidase activity (MPO). A control group did not receive NO. NO given during ischemia had no effect on Kfc or MPO, but decreased PVR. NO (30 ppm) during reperfusion (early or delayed) decreased PVR, W/D, Kfc and MPO. NO at 80 ppm decreased PVR and MPO but not W/D or Kfc. In conclusion, NO at 30 ppm, given immediately or in a delayed fashion during reperfusion, attenuates I-R-induced lung injury. NO at 30 ppm given during ischemia or at 80 ppm during reperfusion is not protective.
Control of blood flow to the gravid uterus of domestic livestock species (1995)

Uterine blood flow during pregnancy is controlled by two distinct phenomena: phasic contractility and tone. Phasic contractility, which mediates short-term contractions, functions through catecholamine activation of alpha 1-adrenergic receptors (AR), leading to hydrolysis of phosphatidylinositol 4, 5-bisphosphate (PIP2) to inositol triphosphate (IP3) and diacylglycerol (DAG). The phasic contractions proceed as IP3 stimulates the release of intracellular calcium stores that activate the calmodulin pathway, causing myosin filaments to slide past actin filaments; however, the contraction is quickly terminated via a reduction in free cytosolic calcium. A tonic contraction is initiated when the DAG generated during PIP2 hydrolysis binds to and activates protein kinase C (PKC) in the presence of increased cytosolic calcium, leading to shortening of the actin filaments. Concomitantly, stimulation of alpha 2-AR increases extracellular calcium uptake via the potential-sensitive channels (PSC), which potentiates activity of the membrane-bound PKC-DAG complexes, thus maintaining the degree of tonic contractility. Progesterone maintains the phasic contractility of uterine arterial smooth muscle throughout pregnancy by increasing alpha 1-AR numbers. Estrogens decrease uterine arterial tone (i.e., increase arterial diameter and flow) via their conversion to catechol estrogens by peroxidase in uterine lymphatic fluid. Catechol estrogens directly inhibit calcium uptake through PSC, resulting in a reduced activity of membrane-bound PKC-DAG complexes.
Development of 5006 Full-Length CDNAs in Barley: A Tool for Accessing Cereal Genomics Resources (2009)

A collection of 5006 full-length (FL) cDNA sequences was developed in barley. Fifteen mRNA samples from various organs and treatments were pooled to develop a cDNA library using the CAP trapper method. More than 60% of the clones were confirmed to have complete coding sequences, based on comparison with rice amino acid and UniProt sequences. Blastn homologies (E<1E-5) to rice genes and Arabidopsis genes were 89 and 47%, respectively. Of the 5028 possible amino acid sequences derived from the 5006 FLcDNAs, 4032 (80.2%) were classified into 1678 GreenPhyl multigenic families. There were 555 cDNAs showing low homology to both rice and Arabidopsis. Gene ontology annotation by InterProScan indicated that many of these cDNAs (71%) have no known molecular functions and may be unique to barley. The cDNAs showed high homology to Barley 1 GeneChip oligo probes (81%) and the wheat gene index (84%). The high homology between FLcDNAs (27%) and mapped barley expressed sequence tag enabled assigning linkage map positions to 151-233 FLcDNAs on each of the seven barley chromosomes. These comprehensive barley FLcDNAs provide strong platform to connect pre-existing genomic and genetic resources and accelerate gene identification and genome analysis in barley and related species. Sequence data from this article have been deposited with the DDBJ/EMBL/GenBank Data Libraries under accession nos AK248134-AK253139. The online database with annotation is available at http://www.shigen.nig.ac.jp/barley/.
Multi-scenario use case based demonstration of Buildings Cybersecurity Framework webtool (2017)

The purpose of this paper is to demonstrate the cybersecurity and software capabilities of Buildings Cybersecurity Framework (BCF) webtool. The webtool is designed based on BCF document and existing NIST standards. Its capabilities and features are depicted through a building use-case with four different investment scenarios geared towards improving the cybersecurity posture of the building. BCF webtool also facilitates implementation of the goals outlined in Presidential Executive Order (EO) on Strengthening the Cybersecurity of Federal Networks and Critical Infrastructure (May 2017. In realization of the EO goals, BCF includes five core elements: Identify, Protect, Detect, Respond, and Recover, to help determine various policy and process level vulnerabilities and provide mitigation strategies. With the BCF webtool, an organization can perform a cybersecurity self-assessment; determine the current cybersecurity posture; define investment based goals to achieve a target state; connect the cybersecurity posture with business processes, functions, and continuity; and finally, develop plans to answer critical organizational cybersecurity questions. In this paper, the webtool and its core capabilities are depicted by performing an extensive comparative assessment over four different scenarios.
Maximum-likelihood estimation of normalisation factors for PET (2002)

In this work an iterative ML technique is developed to normalise acquired PET data. We proposed a model for component-based correction featuring geometric, crystal efficiency and block timing factors. The algorithm is tested against the conventional fan-sum method and with a non-ML iterative technique on both simulated and acquired data. The results show that the iterative methods are superior to the conventional fan-sum technique. Furthermore the new method provides an improved normalisation over the previously published iterative technique when low statistics acquisitions are used.
Model and application of a binaural 360° sound localization system (2002)

We introduce a biologically inspired sound localization system, based on an open two-microphone configuration. Its purpose is to perform a robust, 360-degree detection of objects, in particular humans, in the horizontal plane. In our approach, we consider neurophysiological findings to discuss the biological plausibility of the coding and extraction of spatial features, but also meet the demands and constraints of a practical application in the field of human-robot interaction. We process interaural time differences for the left/right detection and spectrum-based features to discriminate between, in front and behind. Tests in real environments are used to demonstrate the function and the application of the system. We briefly touch the point of handling different acoustic room characteristics and give reasons why the proposed model can show advantages over conventional correlation methods.
A near-field scanning microwave microscope based on a superconducting resonator for low power measurements (2013)

We report on the design and performance of a cryogenic (300 mK) near-field scanning microwave microscope. It uses a microwave resonator as the near-field sensor, operating at a frequency of 6 GHz and microwave probing amplitudes down to 100 μV, approaching low enough photon population (N ∼ 1000) of the resonator such that coherent quantum manipulation becomes feasible. The resonator is made out of a miniaturized distributed fractal superconducting circuit that is integrated with the probing tip, micromachined to be compact enough such that it can be mounted directly on a quartz tuning-fork, and used for parallel operation as an atomic force microscope (AFM). The resonator is magnetically coupled to a transmission line for readout, and to achieve enhanced sensitivity we employ a Pound-Drever-Hall measurement scheme to lock to the resonance frequency. We achieve a well localized near-field around the tip such that the microwave resolution is comparable to the AFM resolution, and a capacitive sensitivity down to 6.4 × 10(-20) F/Hz, limited by mechanical noise. We believe that the results presented here are a significant step towards probing quantum systems at the nanoscale using near-field scanning microwave microscopy.
High-throughput trace melamine analysis in complex mixtures (2008)

Ambient ionization using a low-temperature plasma (LTP) probe combined with tandem mass spectrometry (MS/MS) allows detection and quantitation of melamine in milk powder, whole milk and other products at levels down to low ppb in analysis times of a few tens of seconds.
Structural and electrical properties of low pressure metalorganic chemical vapor deposition grown Eu2O3 films on Si(100) (2006)

Structural and electrical properties of Eu2O3 films grown on Si(100) in 500–600°C temperature range by low pressure metalorganic chemical vapor deposition are reported. As-grown films also possess the impurity Eu1−xO phase, which has been removed upon annealing in O2 ambient. Film’s morphology comprises uniform spherical mounds (40–60nm). Electrical properties of the films, as examined by capacitance-voltage measurements, exhibit fixed oxide charges in the range of −1.5×1011to−6.0×1010cm−2 and dielectric constant in the range of 8–23. Annealing has resulted in drastic improvement of their electrical properties. Effect of oxygen nonstoichiometry on the film’s property is briefly discussed.
A RATIONAL STRIP THEORY OF SHIP MOTIONS: PART I. (1969)

The exact ideal_fluid boundary-value problem is formulated for a ship forced to heave and pitch sinusoidally in otherwise calm water. This problem is then simplified by applying three restrictions: 1) the body must be slender; 2) the motions must be small in amplitude compared with ship beam or draft; 3) the frequency of oscillation, w , must be high, viz., w= O(e-1/2), where e is the slenderness parameter. The hydrodynamic problem is then recast as a singular perturbation problem which is solved to order de2 by the method of matched asymptotic expansions. ( d is a motion_amplitude parameter.) Formulas are derived for the hydrodynamic heave force and pitch moment, from which added-mass and damping coefficients can be easily obtained. The latter are similar but not identical to those used in several other versions of "strip theory;" in particular, the forward_speed effects have the symmetry required by the theorem of Timman and Newman, a result which has not been realized in previous versions of strip theory. In order to calculate the coefficients by the formulas derived, it is necessary to solve numerically a set of boundary-value problems in two dimensions, namely, the problem of a cylinder oscillating vertically in the free surface. At least two practical procedures are available to this purpose.
All-Digital Adaptive Module for Automatic Background IIP2 Calibration in CMOS Downconverters With Fast Convergence (2013)

An all-digital adaptive module for input-referred second-order intercept point (IIP2) calibration in CMOS downconverters is proposed. The proposed automatic background calibration scheme utilizes a modified least-mean-square algorithm with a variable update step to achieve fast convergence. An easily acquired and highly second-order-intermodulation-distortion-correlated reference input is used with delay estimation/optimization to improve the convergence efficiency and reduce the implementation complexity. The proposed all-digital adaptive module is implemented on a field-programmable gate array to calibrate the IIP2 of a 2.62-GHz downconverter fabricated in a 0.18-μm CMOS process. With the proposed automatic background IIP2 calibration, the measured IIP2 of the CMOS downconverter is improved by 21 dB from 62 to 83 dBm, while the IIP2 calibration converges in less than 0.1 ms with a 10-MHz clock, ten times faster than the conventional adaptive algorithm.
<i>Hypertension</i> —Update 2005 (2005)

W e greatly appreciate the privilege of serving as editors of Hypertension, the premier journal in its field. We are also grateful to you, the readers, authors, editorial board members, and reviewers, for your support of the journal and for your excellent scientific contributions, the primary reasons for the continued success of Hypertension.
A Possible Role of Water in the Protein Folding Process (2011)

The thermal folding of hydrated lysozyme has been investigated by means of the high resolution nuclear magnetic resonance (NMR) technique. The proton NMR signal belonging to the biomolecule hydration water (hydration level h = 0.3) was analyzed with the aim to explore the protein structural changes as well as to verify if water plays a role in this biological basic phenomenon. In such a way, we studied the proton chemical shift and the "apparent spin-spin relaxation time" for which water molecules assume the role of system probes in a situation in which the limited hydration of a solid-globular lyophilized protein sample (covering on average the first hydration shell) enables data interpretation devoid of complications arising from bulk water. The study was performed by means of proper temperature changes, different warming and cooling cycles, that starting from the protein in the native state explore the reversible and the irreversible phases of the denaturation. The obtained results confirm that water as a "local probe" follows accurately all the protein behaviors, detailing properly its structural and dynamical changes in this transition, from native to denatured. Since the water chemical shift, as proposed by commonly accepted theoretical and MD simulations findings, is linked to the hydrogen bond (HB) interactions, the obtained data suggest that the denaturation process is related to the average number of bonds in which the water molecules are involved.
High-performance liquid chromatography for small-scale studies of drug stability (1994)

The fundamentals of high-performance liquid chromatography (HPLC), as applied in small-scale studies of drug stability, are presented. Chromatography is the separation of a complex mixture into its individual compounds through partitioning between a mobile phase and a stationary phase. A high-performance liquid chromatograph consists of mobile-phase reservoirs, pumps, a mixer to mix the solvents, a valve into which the sample is injected, a guard column, a column containing the stationary phase, a detector, and a recorder. Once compounds have been separated in the column, they pass into the detector, where an electronic signal corresponding to the amount of compound present is recorded as a peak in a chromatogram. The most common detection method is ultraviolet and visible light spectroscopy. Key concepts in HPLC theory are retention time, the time from injection of the sample to detection of a peak; capacity factor, a measure of retention corrected for the elution of an unretained compound; resolution, a measure of how well two peaks are separated; the selectivity of the method; efficiency, or resolving power; and the degree of symmetry of the peaks produced. Most HPLC separations are performed in the reverse-phase mode, which involves a nonpolar stationary phase and a largely polar mobile phase. Other modes are normal phase, ion exchange, and size exclusion. Before a drug stability study is carried out, an HPLC method must be developed that suits the needs of the proposed experiment. A thorough literature search is essential. Literature procedures serve as useful starting points but may require a great deal of manipulation. After the HPLC separation has been performed, it is necessary to validate the method used. It must be proved that the method is stability indicating, that the chromatographic standards were properly prepared, that the standard curve is acceptable, and that the method is both precise and accurate. Pharmacists who ensure that reliable, reproducible HPLC methods are used throughout studies of drug stability will obtain sound data that may be of great value in pharmacy practice.