gebhart/patrepeval huggingface dataset:
MALD/I TOF PSD and CID (2004)

Part I of this thesis describes details of MS/MS experiments conducted on a TOFMS instrument and begins with an optimization of the CID conditions for poly(ethylene glycol) (PEG). Optimum conditions were found using lithium cation, helium collision gas, and a gas pressure that attenuated the parent-ion signal to between 25-50%. With these conditions, the use of PEG as a mass calibrant for PSD and CID was investigated, using a design of experiments to investigate the sources of variability related to precision and accuracy. There is a mass dependence with respect to precision within segments; however, the variability for a particular ion was not statistically significant for any of the variables tested. The variability associated with mass accuracy was demonstrated to be plate-position dependent, and most accurate results were obtained when the calibrant and analyte were close together on the sample plate. Several instrument-operating parameters were optimized, resulting in improvements to overall product-ion resolution and mass accuracy. Testing with different classes of polymers, as well as peptide examples, demonstrated that the PEG calibration method is robust for a variety of analyte types. Part II of the thesis focused on furthering the understanding of two types of discrimination observed in the MALD/I TOF analysis of synthetic polymers: 1) molecular weight distribution, and 2) polymer structure. Molecular weight discrimination was investigated with a series of narrow PMMA reference standards that demonstrated the importance of comparing the distribution, rather than simply average MW values, which also demonstrated limitations of the dynamic range of the detection system on the MALD/I TOF instrument. HPLC conditions were developed to relate the solubility of the matrix and analyte, demonstrating the importance of relative solubility in MALD/I sample preparation. The roles of salt-to-analyte and matrix-to-analyte ratios were investigated for polymers, which further demonstrated the importance of having good compatibility of matrix, analyte, and cationization reagent (i.e., solubility). The importance of solubility was exemplified with the development of conditions to analyze PET samples by MALD/I. Initial investigations of supporting analytical techniques were shown to have the potential to provide information to support the investigation of the role of solubility.
Current Issues in Plant Cryopreservation (2012)

Anja Kaczmarczyk1,2, Bryn Funnekotter1,2, Akshay Menon1,2, Pui Ye Phang1,2, Arwa Al-Hanbali1,2, Eric Bunn2,3 and Ricardo L. Mancera1 1Curtin Health Innovation Research Institute, Western Australian Biomedical Research Institute, Curtin University, Perth 2Botanic Gardens and Parks Authority, Fraser Avenue, West Perth 3School of Plant Biology, Faculty of Natural and Agricultural Sciences, University of Western Australia Australia
Solubility of Tadalafil in Pharmaceutical Solvent Mixtures at 298.2K (2014)

The experimental solubility of tadalafil in binary mixtures of ethanol (EtOH) + water, propylene glycol (PG) + water, polyethylene glycol 200 (PEG 200) + water, polyethylene glycol 400 (PEG 400) + water, and ternary mixtures of PEG 200 + PG + EtOH at 298.2 K were assessed. The experimental data were fitted to the Jouyban–Acree model. The mean percent deviations (MPD) of the back-calculated solubilities for EtOH + water, PG +water, PEG 200 + water, PEG 400 + water, and PEG 200 + PG + EtOH mixtures were 7.4%, 11.3%, 14.0%, 18.5%, and 5.6%, respectively and the overall MPD was 11.0%.
A Potent Cell Death Activity Associated with Transient High Level Expression of BCL-2 (1998)

The BCL-2 proto-oncogene contains unusually long untranslated 5' and 3' sequences. Deletion of the sequences flanking the BCL-2 open reading frame dramatically increases the level of protein expression. Transient high level BCL-2 protein expression mediated by plasmid transfection or by infection with recombinant adenovirus results in potent apoptosis of several cell lines. Detailed mutational (deletion and add-back) analysis reveals that both 5'- and 3'-flanking sequences contribute to the negative modulation of protein expression from the BCL-2 open reading frame. It appears that these sequences exert the negative regulatory effect in an orientation-dependent manner. Analysis of BCL-2 RNA levels indicate that elevated levels of mRNA may be the primary cause of elevated levels of protein expression. Apoptosis induced by adenovirus vectors expressing elevated levels of BCL-2 can be readily inhibited by the caspase inhibitor z-VAD-fmk, suggesting that high levels of BCL-2 expression induce apoptosis via the caspase cascade. Mutational analysis of BCL-2 indicates that its pro-apoptotic activity is separable from its anti-apoptosis activity. Our results raise the possibility that oncogenic conversion of BCL-2 may require somatic mutations in the pro-apoptotic activity, in addition to other activating mutations that result in enhanced expression. Consistent with this hypothesis, a somatic mutation of BCL-2 observed in multiple human tumors results in reduced apoptosis activity.
Detection of koi herpes virus (KHV) genome in apparently healthy fish (2009)

Koi herpesvirus (KHV) induces a lethal disease in species belonging to Cyprinus carpio, covering common carp and koi or fancy carp. To date, other cyprinid fish species kept together with KHV infected carp or koi, such as goldfish (Carassius auratus) or grass carp (Ctenopharyngodon idella) had never shown any sign of KHV infection. Unexplainable outbreaks of KHV infection in common carp or koi led to the suspicion that more disease influencing factors exist, than so far explained. In challenge experiments and by natural routes of infection, it has been demonstrated that naive carp or koi can be infected by the following mechanisms; exposure to water from severe KHV diseased fish, co-habitation with KHV infected carp, by infection or immersion with cell supernatant of KHV infected cultures. Experiments were conducted to determine if apparently healthy koi (carriers/survivors) or non-Cyprinus carpio species stocked with KHV infected carp could become infected. The study proved that these species were able to transfer KHV to naive carp. As a result scientists suspected that some ornamental fish species could act as reservoirs of KHV infection. In this study goldfish, grass carp, blue back ide (Leuciscus idus) and Ancistrus sp. were screened with routinely used diagnostic methods such as virus isolation in cell cultures and PCR and found to be KHV negative. This suggested that these fish species could not be infected by KHV. However, when using a more sensitive nested PCR, KHV DNA was detected from some of these fish. As confirmative methods sequence analysis of the nested PCR products and in-situ hybridization with different KHV probes were used. This study showed that the following cyprinid species; goldfish, grass carp and ide, and also non-cyprinid specides Ancistrus sp. may act as a carrier of KHV.
Scalable Iterative Classification for Sanitizing Large-Scale Datasets (2016)

Cheap ubiquitous computing enables the collection of massive amounts of personal data in a wide variety of domains. Many organizations aim to share such data while obscuring features that could disclose personally identifiable information. Much of this data exhibits weak structure (e.g., text), such that machine learning approaches have been developed to detect and remove identifiers from it. While learning is never perfect, and relying on such approaches to sanitize data can leak sensitive information, a small risk is often acceptable. Our goal is to balance the value of published data and the risk of an adversary discovering leaked identifiers. We model data sanitization as a game between 1) a publisher who chooses a set of classifiers to apply to data and publishes only instances predicted as non-sensitive and 2) an attacker who combines machine learning and manual inspection to uncover leaked identifying information. We introduce a fast iterative greedy algorithm for the publisher that ensures a low utility for a resource-limited adversary. Moreover, using five text data sets we illustrate that our algorithm leaves virtually no automatically identifiable sensitive instances for a state-of-the-art learning algorithm, while sharing over 93% of the original data, and completes after at most 5 iterations.
Self-Rated Aversion to Taste Qualities and the PROP Taster Phenotype Associate with Alcoholic Beverage Intake and Preference (2021)

Consumers often identify “taste” as an important factor when selecting alcoholic beverages. Although it is assumed that reduced alcohol consumption in PROP super-tasters is due to a greater dislike of the nominally aversive sensations that they experience more intensely (e.g., bitterness) when compared to PROP non-tasters, this question has not been specifically asked to them. Therefore, we examined consumers’ self-reported aversion towards specific sensory attributes (bitter, hot/burn, dry, sour, sweet, carbonation) for four alcoholic beverage types (white wine, red wine, beer, spirits) using a convenience sample of U.S. wine consumers (n = 925). Participants rated 18 statements describing different combinations of sensory attributes and alcoholic beverages on a 5-point Likert scale (e.g., Beer tastes too bitter for me). Individuals who tended to agree more strongly with the statements (i.e., they were more averse; p(F) &lt; 0.05) tended to (i) consume less of all beverage types, (ii) consume a higher proportion of white wine (p(r) &lt; 0.05), and (iii) were more likely to be female or PROP super-tasters. The results suggest that self-reported aversion to specific sensory attributes is associated with not only lower overall intake of alcoholic beverages, but also a shift in the relative proportions of beverage type consumed; a key finding for studies investigating how taste perception impacts alcohol consumption.
Predicting Billboard Success Using Data-Mining in P2P Networks (2009)

Peer to Peer networks are the leading cause for music piracy but also used for music sampling prior to purchase. In this paper we investigate the relations between music file sharing and sales (both physical and digital) using large Peer-to-Peer query database information. We compare file sharing information on songs to their popularity on the Billboard Hot 100 and the Billboard Digital Songs charts, and show that popularity trends of songs on the Billboard have very strong correlation (0.88-0.89) to their popularity on a Peer-to-Peer network. We then show how this correlation can be utilized by common data mining algorithms to predict a song's success in the Billboard in advance, using Peer-to-Peer information.
Advanced voltage control of induction generator using rotor field-oriented control (2005)

This paper describes a simple control structure and power conditioning system for indirect vector controlled standalone induction generator (IG) used to operate under variable speeds and different load types. The required reactive power for the IG system is supplied by means of a capacitor bank and a voltage-source PWM converter. Using a capacitor bank to transfer the reactive power to the IG under the rated speed and no-load conditions starts the IG operation and reduces the PWM converter size. The vector control structures for the variable speed IG power conditioning system compensating for changes in the electrical loads with considering the magnetizing curve of the IG is developed to regulate the DC link and AC output voltages. This proposed scheme can be used efficiently for variable speed, wind energy conversion system. The experimental and simulated performance results of an IG power conditioning system at various speeds and loads are given and show that this system are capable of good AC and DC output voltage regulation.
Small-Molecule Inhibitors of Histone Acetyltransferase Activity:  Identification and Biological Properties (2006)

Starting from a yeast phenotypic screening performed on 21 compounds, we described the identification of two small molecules (9 and 18) able to significantly reduce the S. cerevisiae cell growth, thus miming the effect of GCN5 deletion mutant. Tested on a GCN5-dependent gene transcription assay, compounds 9 and 18 gave a high reduction of the reporter activity. In S. cerevisiae histone H3 terminal tails assay, the H3 acetylation levels were highly reduced by treatment with 0.6-1 mM 9, while 18 was effective only at 1.5 mM. In human leukemia U937 cell line, at 1 mM 9 and 18 showed effects on cell cycle (arrest in G1 phase, 9), apoptosis (9), and granulocytic differentiation (18). When tested on U937 cell nuclear extracts to evaluate their histone acetyltransferase (HAT) inhibitory action, both compounds were able to reduce the enzyme activity when used at 500 microM. Another quinoline, compound 22, was synthesized with the aim to improve the activity observed with 9 and 18. Tested in the HAT assay, 22 was able to reduce the HAT catalytic action at 50 and 25 microM, thereby being comparable to anacardic acid, curcumin, and MB-3 used as references. Finally, in U937 cells, compounds 9 and 18 used at 2.5 mM were able to reduce the extent of the acetylation levels of histone H3 (9) and alpha-tubulin (9 and 18). In the same assay, 22 at lower concentration (100 microM) showed the same hypoacetylating effects with both histone and non-histone substrates.
Equivalence Study of a Dental Anatomy Computer‐Assisted Learning Program (2004)

Tooth Morphology is a computer-assisted learning program designed to teach the anatomy of the adult dentition. The purpose of this study was to test whether Tooth Morphology could teach dental anatomy to first-year dental students as well as the traditional lecture. A randomized controlled trial was performed with forty-five first-year dental students. The students were randomly assigned to either the Tooth Morphology group (n=23), which used the computer-assisted learning program and did not attend lecture, or the lecture group (n=22), which attended the traditional lecture and did not use Tooth Morphology. The Tooth Morphology group had a final exam average of 90.0 (standard deviation=5.2), and the lecture group had a final exam average of 90.9 (sd=5.3). Analysis showed that the two groups' scores were statistically equivalent (p<0.05), with a priori equivalence bounds around the difference between the groups set at +/-5 points. It was concluded that Tooth Morphology taught the anatomy of the adult dentition as well as traditional lecture, as measured by exams. Based on the results of this study and student feedback, Tooth Morphology, in combination with interactive class meetings, has replaced the traditional dental anatomy lectures.
Identification of the phosphorylation sites of clathrin light chain LCb. (1988)

Clathrin light chains, LCa and LCb, are products of two closely related genes whose mRNAs undergo differential splicing to result in at least four different light chain isoforms. The physiological significance of clathrin light chain diversity remains unclear. To date, the only evidence for a functional distinction of LCa and LCb is the preferential phosphorylation of LCb, which takes place at serine residues and is mediated by coated vesicle-associated casein kinase II. As a first step toward determining the function of light chain diversity, we have mapped the in vitro phosphorylation sites on LCb. We use [32P]ATP to phosphorylate LCb within coated vesicles, followed by sequencing of 32P-labeled chymotryptic peptides thereof, to identify serine residues at positions 11 and 13 as the phosphorylation sites. We find that phosphorylation of LCb within coated vesicles can be inhibited by four monoclonal antibodies specific for different epitopes of the clathrin light chains.
Flavin Reductase P:  Structure of a Dimeric Enzyme That Reduces Flavin, (1996)

We report the structure of an NADPH:FMN oxidoreductase (flavin reductase P) that is involved in bioluminescence by providing reduced FMN to luciferase. The 1.8 A crystal structure of flavin reductase P from Vibrio harveyi was solved by multiple isomorphous replacement and reveals that the enzyme is a unique dimer of interlocking subunits, with 9352 A2 of surface area buried in the dimer interface. Each subunit comprises two domains. The first domain consists of a four-stranded antiparallel beta-sheet flanked by helices on either side. The second domain reaches out from one subunit and embraces the other subunit and is responsible for interlocking the two subunits. Our structure explains why flavin reductase P is specific for FMN as cofactor. FMN is recognized and tightly bound by a network of 16 hydrogen bonds, while steric considerations prevent the binding of FAD. A flexible loop containing a Lys and an Arg could account for the NADPH specificity. The structure reveals information about several aspects of the catalytic mechanism. For example, we show that the first step in catalysis, which is hydride transfer from C4 of NADPH to cofactor FMN, involves addition to the re face of the FMN, probably at the N5 position. The limited accessibility of the FMN binding pocket and the extensive FMN-protein hydrogen bond network are consistent with the observed ping-pong bisubstrate--biproduct reaction kinetics. Finally, we propose a model for how flavin reductase P might shuttle electrons between NADPH and luciferase.
Deep Learning-enabled Spatial Phase Unwrapping for 3D Measurement (2022)

In terms of 3D imaging speed and system cost, the single-camera system projecting single-frequency patterns is the ideal option among all proposed Fringe Projection Profilometry (FPP) systems. This system necessitates a robust spatial phase unwrapping (SPU) algorithm. However, robust SPU remains a challenge in complex scenes. Quality-guided SPU algorithms need more efficient ways to identify the unreliable points in phase maps before unwrapping. End-to-end deep learning SPU methods face generality and interpretability problems. This paper proposes a hybrid method combining deep learning and traditional path-following for robust SPU in FPP. This hybrid SPU scheme demonstrates better robustness than traditional quality-guided SPU methods, better interpretability than end-to-end deep learning scheme, and generality on unseen data. Experiments on the real dataset of multiple illumination conditions and multiple FPP systems differing in image resolution, the number of fringes, fringe direction, and optics wavelength verify the effectiveness of the proposed method.
Feature Extraction and Generation of Robot Writing Motion Using Encoder-Decoder Based Deep Neural Network (2020)

Recent improvement of control technologies allows robots to precisely follow given commands. Robots will be able to expand their executable tasks by saving the motion data that humans demonstrated beforehand. However, it is difficult to deal with the saved motion data when the number of the data increases. In this paper, we focus on writing task and propose an encoder-decoder based neural network for generating time series of motion as a framework for giving motion command directly to the robot. Motions of the robots can be represented as time series data of position data, which contains features of the motions. We can get low dimensional expression of the motion data that is called latent variables by training the network using the saved motion data. We can deal with and generate the saved motion data by using the latent variables and the decoder network. In the experiments, we collected data of writing a Kanji, trained the network using the saved data. We experimentally validated the generated data from the trained network by giving it to the robot.
Lead Relative Bioavailability in Lip Products and Their Potential Health Risk to Women (2016)

Recent studies have investigated lead (Pb) concentrations in lip products but little is known about its oral bioavailability. In this study, 75 lipsticks and 18 lip glosses were assessed for Pb concentration, while 15 samples were assessed for Pb relative bioavailability (RBA, relative to Pb acetate absorption) using a mouse femur assay. Lead concentrations were 0.2-10 185 mg kg(-1), with 21 samples exceeding the Chinese limit of 40 mg kg(-1). Samples with orange and pink colors and/or low cost contained higher Pb concentrations. For samples with Pb > 7500 mg kg(-1), Pb was present due to the addition of lead chromate (PbCrO4) as a colorant, which was confirmed by X-ray absorption near-edge structure analysis. Lead-RBA in 15 samples (87-10 185 mg kg(-1)) ranged from 23% to 95%, being significantly higher in moderate Pb (56-95%; 87-300 mg kg(-1)) than high Pb samples (23-48%; >300 mg kg(-1)). The calculation of Pb intake based on Pb-RBA showed that lip product ingestion contributed 5.4-68% of the aggregate Pb exposure for women depending on Pb concentration. The high Pb concentration in some lip products together with their moderate Pb-RBA suggests that lip product ingestion is a potential health concern to women.
Performance characteristics of fiber Bragg grating stabilized 980 nm diode lasers. Pump diode laser difference frequency generation as an efficient spectroscopic source (2002)

We utilize a fiber Bragg grating (FBG) stabilized diode laser at 980 nm that was designed for as a pump source for an erbium doped fiber amplifier (EDFA). Pump diode lasers with a DFG pump source have hundreds milliwatts of high optical power and are of a relatively reasonable cost compared to using YAG lasers, fiber lasers, or other diode lasers. Frequency stability performance by FBGs has been proven in the telecommunication field. Such pump diode lasers at 980 nm and circularized diode lasers at 780nm are difference frequency mixed in a temperature controlled Mg doped periodically poled LiNbO/sub 3/ crystal.
Solvent extraction of metallic anionic complexes with a quaternary amine (1968)

The behavior o f Zn, Cd, Co, f\ii, Cu, Fe, In , and A1 when e x tra c te d from aqueous s o lu tio n s w ith c h lo rid e or s u lfa t e as lig a n d by r n e th y ltr ic a p r y l amine mas s tu d ie d using a x y le n eisodecanol c a r r i e r .N i, F e ( I I ) , and A1 could not be e x tra c te d from c h lo rid e s o lu tio n s .The only m etal e x tra c te d from s u lfa t e s o lu tio n s mas iro n ( I I I ) .Dn the basis o f t h is study and o th e rs , i t is p o s tu la te d th a t in most cases f o r e x tr a c tio n to o ccur, the metal ionfe in n e r c o o rd in a tio n sphere must be s a tu ra te d by the.lig a n d in v o lv e d .This is to say th a t the complex anion e x tra c te d is unhydrated.Furtherm ore, evidence is presented mhich in d ic a te s the e x tra c tio n mechanism in v o lv e d .For example, in the z in c c h lo rid e system the e x tr a c tio n scheme proposed is : R, NCI o rg a n ic R. NCI b aqueous R, NCI aqueous aqueous 2R, N+ + ZnCl 7 b aqueous (Rz+N)2 ZnCl b aqueous b aqueous
Defining cell shape in 3D (2007)

rigidity, matrix composition, and cell shape, dimensionality is now considered an important physical property of the cell microenvironment which directs cell behavior. However, available
Investigations of the Exothermic Reactions of Natural Graphite Anode for Li-Ion Batteries during Thermal Runaway (2004)

Advances in the comparative study of the thermal behavior of graphite during the thermal runaway process are reviewed. The differential scanning calorimeter was used to evaluate the thermal runaway behavior of natural graphite (Mag-10) electrode material with different amounts of intercalated lithium ions. The effect of the polyvinylidene fluoride binder on the thermal behavior of a fully lithiated sample was also investigated. This is the first time it has been noted that graphite loses its structure with more than 0.7 intercalated lithium when electrolyte is present at high temperature by detecting the existence of (002) graphite X-ray diffraction peak. © 2004 The Electrochemical Society. All rights reserved.
Bio-Applications of Nanopillars (2016)

Bio-applications of nanopillars are discussed, with a focus on the advantages nanopillared surfaces compared to flat surfaces and the properties of nanopillars behind each application are explained.