gebhart/patrepeval huggingface dataset:
Deactivation of lipopolysaccharide by Ar and H2inductively coupled low-pressure plasma (2013)

Using an inductively coupled plasma system, we study the effects of direct plasma, plasma-generated high-energy photons in the ultraviolet and vacuum ultraviolet (UV/VUV), and radical treatments on lipopolysaccharide (LPS). LPS is a biomolecule found in the outer membrane of Gram-negative bacteria and a potent stimulator of the immune system composed of polysaccharide and lipid A, which contains six aliphatic chains. LPS film thickness spun on silicon was monitored by ellipsometry while the surface chemistry was characterized before and after treatments by x-ray photoelectron spectroscopy (XPS). Additionally, biological activity was measured using an enzyme-linked immunosorbent assay under (a) a sensitive regime (sub-µM concentrations of LPS) and (b) a bulk regime (above µM concentrations of LPS) after plasma treatments. Direct plasma treatment causes rapid etching and deactivation of LPS in both Ar and H2 feed gases. To examine the effect of UV/VUV photons, a long-pass filter with a cut-off wavelength of 112 nm was placed over the sample. H2 UV/VUV treatment causes material removal and deactivation due to atomic and molecular UV/VUV emission while Ar UV/VUV treatment shows minimal effects as Ar plasma does not emit UV/VUV photons in the transmitted wavelength range explored. Interestingly, radical treatments remove negligible material but cause deactivation. Based on the amphiphilic structure of LPS, we expect a lipid A rich surface layer to form at the air–water interface during sample preparation with polysaccharide layers underneath. XPS shows that H2 plasma treatment under direct and UV/VUV conditions causes oxygen depletion through removal of C–O and O–C = O bonds in the films, which does not occur in Ar treatments. Damage to these groups can remove aliphatic chains that contribute to the pyrogenicity of LPS. Radical treatments from both Ar and H2 plasmas remove aliphatic carbon from the near-surface, demonstrating the important role of neutral species.
Polymorphism in methylenetetrahydrofolate reductase, plasminogen activator inhibitor-1, and apolipoprotein E in hemodialysis patients. (2008)

The methylenetetrahydrofolate reductase (MTHFR) gene polymorphism, apolipoprotein E (apo epsilon4) gene polymorphism and polymorphism of plasminogen activator inhibitor-1 (PAI-1) have been shown to be associated with end-stage renal disease (ESRD). To determine the prevalence of these mutations in Saudi patients with ESRD on hemodialysis, we studied the allelic frequency and genotype distribution in patients receiving hemodialysis and in a control group, all residing in the Eastern Province of Saudi Arabia. The genotypes were determined using allele specific hybridization procedures and were confirmed by restriction fragment length polymorphism. The T allele frequency and homozygous genotype of MTHFR in ESRD patients were 14% and 2.4%, respectively compared to 13.4% and 0%, respectively in the control group. The allele frequency and homozygous genotype of 4G/4G PAI-1 gene polymorphism were 46.4% and 4.8% respectively in ESRD patients compared to 57.1% and 32% respectively in the control group. The apo s4 allele frequency and homozygous genotype distribution in hemodialysis patients were 7% and 2.4%, respectively compared to 13% and 2% in the control group. Although allele frequency of C677T of MTHFR was statistically similar in the hemodialysis patients and in the control group, the homozygotes T allele genotype was over represented in the hemodialysis group compared to normal. The prevalence of PAI-1 4G/4G polymorphism in ESRD patients was lower when compared to the control group. The prevalence of apo s4 allele did not differ significantly between the two groups. The present results demonstrate that all three studied polymorphic mutations are present in our population and that they may contribute to the etiology of the disease in our area.
3D analysis of MR readback on perpendicular medium (1991)

A 3-D analysis of magnetoresistive (MR) read on perpendicular media using the reciprocity method is presented. It is shown that the conduction of magnetic flux, obtained from an equivalent reciprocity field, away from the active area is an important phenomenon for this structure, and may introduce error if 2-D analysis is used. The authors examine the effect of shield width and show that when the shield width is equal to the width of the active area of the MR head, 3-D analysis closely resembles the 2-D results. This calculation is extended to a differentially connected dual element MR head for perpendicular recording.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cryopreservation of Penaeid Shrimp Embryos: Development of a Germplasm Cryo-Bank for Preservation of High Health and Genetically Improved Stocks (2002)

The objectives of the project were to develop a successful protocol for cryopreservation of penaeid germ plasm in order to preserve a pathogen-free broodstock nucleus for commercial exploitation of marine shrimp in aquaculture. The critical parameters to be characterized in the project were: 1. Determination of chill sensitivity and chill tolerant embryonic stages, including a full description and time course study of embryonic developmental stages. 2. Development of protocols for loading and removal of cryoprotectant agents (CPAs) from embryos; determination of optimal concentrations and duration of loading. 3. Characterization of the toxicity of the selected CP As and 4. Establishing optimal cooling and thawing procedures. Studies were performed on two penaeid species: Litopenaeus vannamei (in the USA) and P. semisulcatus (in Israel). The effect of incubation temperature on embryonic development rate and hatching success was studied in L. vannamei, showing that spawns maybe maintained at temperatures ranging from 24°C to 30°C, without compromising hatchability. Embryonic development extends from 12 hr to 19 hr at 30°C and 24°C, respectively. Studies showed that advanced embryonic developmental stages were chill tolerant in the two studied species, but P. semisulcatus could better endure lower temperatures than L. vannamei. A large number of experiments were performed to determine the optimal CP As, their concentration and duration of loading. Permeating (e.g. glycerol, methanol, DMSO, 1,2- propanediol, ethylene glycol, glucose) and non-permeating CPAs (sucrose, PVP, polyethylene glycol) were tested and several combinations of permeating and non-permeating CP As, on fertilized eggs (embryos), nauplii and protozoeae. In general, nauplii tolerated higher CPA concentrations than eggs and nauplii were also more permeable to radiolabeled methanol. Chlorine treatment intended to remove the chitinous envelop from eggs, did not increase dramatically the permeation of radiolabled methanol into eggs. Cooling eggs, nauplii or protozoeae to cryogenic temperatures, by either vitrification or slow cooling protocols, did not result in full survival of thawed samples, despite exhaustive attempts testing various protocols and CP As. Results seemed more encouraging in freezing of nauplii in comparison to eggs or protozoeae. Successful preliminary results in cryopreservation of spermatozoa of P. vannamei, will facilitate preservation of genetic specific to some extent.
Chaotic synchronization and modulation of nonlinear time-delayed feedback optical systems (1995)

We present a special chaos synchronization system based on coupled time-delayed feedback optical systems. As far as we know, this paper reports for the first time simulations of synchronization in such optical circuits. The unsolved problem of the channel in communication applications of chaos synchronization for electronic systems make the optical systems very attractive. The quasi-infinite bandwidth, very low attenuation and practically noiseless characteristic of single mode fiber, used as information transmission medium, are the three main advantages of our system. We show by simulations that synchronization is effective, use a chaos shift keying modulation/demodulation scheme for binary information transmission and present some estimation of the bit rate in a such system.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Zur Kenntnis der Dibenzoxanthyliumsalze II (1960)

Abstract Das bei der Einwirkung von Formaldehyd und konz. Schwefelsäure auf J‐Säure (2‐Amino‐5‐naphtol‐7‐sulfosäure) entstehende indigoblaue Produkt ist ein 3,4,5,6‐dibenzoxanthyliumfarbstoff, in welchem sich die Aminogruppen in amphi ‐Stellung zum Chromophor befinden. Analoge Farbstoffe werden mit Derivaten der J‐Säure erhalten. Die Reaktion ist spezifisch für Formaldehyd. 2‐Amino‐5‐naphtol und seine Derivate mit unbesetzter 7‐Stellung geben auch mit aromatischen Aldehyden Dibenzoxanthyliumfarbstoffe mit amphi ‐ständigen Auxochromen.
An Application of Lunar GIS with Visualized and Auditory Japan's Lunar Explorer "Kaguya" Data. (2008)

This paper describes an application of a geographical information system with visualized and sonification lunar remote sensing data provided by Japan’s lunar explorer (SELENE “KAGUYA”). Web based GIS is a very powerful tool which lunar scientists can use to visualize and access remote sensing data with other geospatial information. We discuss enhancement of the pseudo-colored visual map presentation of lunar topographical altimetry data derived from LALT and the map of the data to several sound parameters (Interval, harmony, and tempo). This paper describes an overview of this GIS with a sonification system, called “Moonbell”.
Sparse discriminative Fisher vectors in visual classification (2012)

Constructing global image representations from local feature descriptors is a common step in most visual classification tasks. Traditionally, the Bag of Features (BoF) representations involving hard vector quantization have been used ubiquitously for such tasks. Recent works have demonstrated superior performance of soft assignments over hard assignments. Fisher vector representations have been shown to outperform other global representations on most benchmark datasets. Fisher vectors (i) use soft assignments, and (ii) reduce information loss due to quantization by capturing the deviations from the mean. However, the Fisher vector representations are huge and the representation size increases linearly with the vocabulary size. Recent findings report that the classification performance of Fisher vectors is proportional to the vocabulary size. Computational and storage requirements, however, discourage the use of arbitrarily large vocabularies. Also, Fisher vectors are not inherently discriminative. In this paper, we devise a novel strategy to compute sparse Fisher representations. This allows us to increase the vocabulary size with little computation and storage overhead and still attain the performance of a larger vocabulary. Further, we describe an approach to encode class-discriminative information in the Fisher vectors. We evaluate our method on four popular datasets. Empirical results show that our representations consistently outperform the traditional Fisher Vector representations and are comparable to the state of art approaches.
Influence of basic residues on dissociation kinetics and dynamics of singly protonated peptides: time‐resolved photodissociation study (2009)

Product ion yields in postsource decay and time-resolved photodissociation at 193 and 266 nm were measured for some peptide ions with lysine ([KF6 + H]+, [F6K + H]+, and [F3KF3 + H]+) formed by matrix-assisted laser desorption ionization. The critical energy (E0) and entropy (DeltaS(double dagger)) were determined by RRKM fitting of the data. The results were similar to those found previously for peptide ions with histidine. To summarize, the presence of a basic residue, histidine or lysine, inside a peptide ion retarded its dissociation by lowering DeltaS(double dagger). On the basis of highly negative DeltaS(double dagger), presence of intramolecular interaction involving a basic group in the transition structure was proposed.
A bio-inspired 3D quasi-fractal nanostructure for an improved oxygen evolution reaction (2018)

We demonstrate a bio-inspired three-dimensional (3D) hierarchical catalyst, based on the Fe-doped nanoarrays of dendritic nickel trees, which provides large surface area, close to optimal electron transport, and large inter-branch open-channels for improving gas-bubble release, outperforming the benchmark catalyst of noble RuO2.
Flat lesion detection of white light cystoscopy with deep learning (2023)

Adequate lesion detection is critical in cystoscopy to improve bladder cancer resection and decrease recurrence. In particular, flat-appearing cancer such as carcinoma in situ is difficult to discern by standard white-light cystoscopy (WLC). The adoption of blue-light cystoscopy (BLC), an adjunct imaging technique, remains modest due to the expensive equipment required. We developed a deep-learning algorithm, CystoNet-F, for augmented detection of flat lesions on WLC. CystoNet-F was designed to augment WLC in lesion detection by incorporating domain translation of CycleGAN, transfer learning, and region of interest (ROI) detection. We constructed a development dataset of 40 patients for algorithm training and 10 patients for testing. In the training phase, features from both WLC and BLC were learned and embedded in the algorithm as the model weights of an ROI detector. Transfer learning was performed by fine-tuning CystoNet-F on BLC using the weights learned from WLC. We applied CycleGAN for domain translation between WLC and BLC. In the test phase, WLC input was first translated to the BLC domain and then served as the input of the ROI detector to finally generate a mask on the lesion area. CystoNet-F can produce flat lesion predictions close to urologist’s annotations on the validation set without paired BLC information. The proposed deep-learning algorithm may improve the diagnostic yield of standard WLC in a noninvasive and cost-effective fashion.
Plant Leaf Disease Detection Using Machine Learning. (2018)

The detection of plant leaf is very important factor to prevent serious outbreak. Automatic detection of plant disease is essential research topic. Most plant diseases are caused by fungi, bacteria, and viruses. Fungi are identified primarily from their morphology, with emphasis placed on their reproductive structures. Bacteria are considered more primitive than fungi and generally have simpler life cycles. With few exceptions, bacteria exist as single cells and increase in numbers by dividing into two cells during a process called binary fission. Viruses are extremely tiny particles consisting of protein and genetic material with no associated protein. The term disease is usually used only for the destruction of live plants. The proposed processing scheme uses machine learning and dynamic plants image model to predict disease related to the leaf. Using machine learning makes platform generic and useful. Adding and updating new diseases and datasets is easy if machine learning is use. Using cloud computing for storing retrieving and serving data from machine learning model is efficient choice and both technologies can be used to create system.
Saccade and Pursuit on an Active Head/Eye Platform (1993)

We describe the implementation of, and results from, a realtime active surveillance vision system which detects moving objects in an everyday environment, directs the gaze of a headkye platform towards the objects and subsequently pursues them smoothly. Target detection and pursuit arc performed purely on the basis of image motion, and can continue over extended periods. Two independent parallel processes derive (i) coarse resolution motion over the entire image to direct saccadic shifts in attention over a wide field of view, and (ii) fine resolution motion in a small central region of the image used to perform smooth-pursuit. A gaze controller which selects results from the two visual processes and controls the movement of the head platform is implemented as a finite state machine.
Effects of acute graft-versus-host-disease on physical and psychological functioning following hematopoietic stem cell transplantation. (2014)

7038 Background: Acute graft-versus-host-disease (aGVHD) is a significant early complication of allogeneic hematopoietic stem cell transplantation (HSCT). Little is known about the effects of aGVHD on quality of life, and no prior studies have examined psychological effects. We compared physical and psychological functioning of HSCT survivors who developed aGVHD to those who did not. Methods: Adults with hematologic malignancies were enrolled in this prospective, longitudinal study prior to allogeneic HSCT. Those alive without recurrence at 6 months post-HSCT (N=108) were included in the analyses. Participants completed well-validated self-report measures of physical functioning (fatigue, pain, sleep, physical and functional well-being) and psychological functioning (depression, anxiety, psychological well-being) pre-HSCT and 3 and 6 months post-HSCT. Those diagnosed with mild (grade 1-2) and severe (grade 3-4) aGVHD were compared to those with no aGVHD on all measures after controlling for pre-HSCT measures, age, HSCT regimen, and chronic GVHD. Results: 52 participants were diagnosed with mild (n=39) or severe (n=13) aGVHD. By 3 and 6 months post-HSCT, there were no significant differences between those with and without a history of aGVHD on physical functioning measures. There were significant differences in anxiety at 3 and 6 months post-HSCT (F(2, 103)=3.19; p=.049; F(2, 98)=4.99; p=.011). There was also a trend toward a difference in the psychological well-being measure of personal strength at 6 months (F(2, 97)=2.86; p=.070). Follow-up comparisons showed that those with a history of severe aGVHD reported significantly greater anxiety but also a greater sense of personal strength as compared to those with mild or no aGVHD (pvalues<.05). Conclusions: Findings indicate that HSCT survivors who developed aGVHD, even severe cases, were doing as well as those without aGVHD on all indices of physical functioning and most indices of psychological functioning by 3 and 6 months post-HSCT. However, the experience of severe aGVHD appeared to affect select aspects of psychological functioning, conferring greater anxiety but also an enhanced sense of personal strength.
(Me3Si)3SiH-Mediated Intermolecular Radical Perfluoroalkylation Reactions of Olefins in Water (2010)

Perfluoroalkyl-substituted compounds are regarded as important components of fluorophors and for the introduction of fluorous tags into organic substrates. Their syntheses in organic solvents are achieved through different methods, among which, the addition of perfluoroalkyl radicals to unsaturated bonds represents a convenient choice. On the other hand, intermolecular radical reactions in water have attracted the attention of synthetic chemists as a strategic route to carbon-carbon bond formation reactions. In this paper we undertook the intermolecular addition of perfluoroalkyl radicals on electron rich alkenes and alkenes with electron withdrawing groups in water, mediated by silyl radicals, and obtained perfluoroalkyl-substituted compounds in fairly good yields. The radical triggering events employed consist of the thermal decomposition of an azo compound and the dioxygen initiation. Our results indicate that for intermolecular carbon-carbon bond formation reactions mediated by (Me(3)Si)(3)SiH, the decomposition of the azo compound 1,1'-azobis(cyclohexanecarbonitrile) (ACCN) is the best radical initiator. We also found that water exerts a relevant solvent effect on the rates of perfluoroalkyl radical additions onto double bonds and the H atom abstraction from the silane. Our account provides a versatile and convenient method to achieve perfluoroalkylation reactions of alkenes in water to render perfluoroalkylated alkanes as key intermediates in the synthesis of fluorophors and other fluorinated materials. This is the first report where perfluoroalkyl-substituted alkanes are synthesized through intermolecular radical carbon-carbon bond formation reactions in water, mediated by silyl radicals.
Implementing federated database systems by compiling SchemaSQL (2003)

Federated systems integrating data from multiple sources must cope with semantic heterogeneity by reasoning over both the data and meta-data of their sources. SchemaSQL is one of a number of related higher-order languages, which have been proposed for succinctly expressing integrated views over heterogeneous sources. We define a method for compiling SchemaSQL into standard SQL. We show that the output of the compilation algorithm is of size O(m+p) where m is the size of the catalogs and p the size of input queries. The resulting code may be executed by existing conventional SQL query engines without modification. We extend our basic compilation method by including type driven optimizations which, empirical evaluation shows, yield an effective execution by native query engines. Prior efforts do not provide feasible guarantees on the size of the compiled programs or require the development of new query engines encompassing higher-order query operators.
Renormalization of the vortex diffusion constant in superfluid films (1981)

We study the dynamics of vortices in superfluid helium films, using a phenomenological Langevin equation to account for diffusive as well as convective motion of vortices. We show that in the long-wavelength limit, dynamic screening effects give rise to a renormalization of the diffusion constant, while the convective parameter remains unchanged. The critical behavior is analyzed with renormalization-group methods. In the limit $T\ensuremath{\rightarrow}{T}_{c}^{\ensuremath{-}}$, we find a universal cusp singularity for the diffusion constant, reaching a finite value at ${T}_{c}$.
Ultrafast structural studies on biological molecules by x-rays (1999)

Dramatic changes can be expected within the next few years in science that depends on synchrotron radiation today. An analysis of available data on short-pulse, high-intensity x-ray and electron sources indicate possibilities for imminent developments with x-ray free-electron lasers (driven primarily by the high energy physics community), and with table-top femtosecond x-ray sources based on laser-induced plasmas and wakefield acceleration. New sources could generate femtosecond x-ray pulses with as much as 12 orders of magnitude increase in peak brilliance and power over third-generation synchrotron storage rings. Such developments would create revolutionary new research opportunities in condensed matter physics, biology and medicine. Some of the possibilities are discussed here.
One‐Pot Synthesis of Aryl‐ and Alkyl S‐Perfluoroalkylated NH‐Sulfoximines from Sulfides (2018)

A general efficient one-pot synthesis of S-perfluoroalkylated NH-sulfoximines from sulfides has been developed using phenyliodine diacetate (PIDA) and ammonium carbamate. Remarkable rate enhancement with trifluoroethanol was observed, presumably due to H-bonding effects. These mild and metal-free conditions are compatible with -CH<sub>2</sub> F, -CFCl<sub>2</sub> , -CF<sub>2</sub> H, -CF<sub>2</sub> Br, -C<sub>4</sub> F<sub>9</sub> , and -CF<sub>3</sub> groups, in both the alkyl- and aryl series. Based on a <sup>19</sup> F NMR analysis, a λ<sup>6</sup> -acetoxysulfanenitrile intermediate was proposed.