gebhart/patrepeval huggingface dataset:
Fusarium-toksiinit : saanti viljasta ja viljatuotteista (2008)

Yleisiä suomalaisissa viljoissa esiintyviä homeiden tuottamia Fusarium-toksiineja&#13;\novat deoksinivalenoli, zearalenoni, nivalenoli sekä T-2- ja HT-2-toksiinit.&#13;\nFusarium-toksiineja esiintyy erityisesti kaurassa. EU:ssa on asetettu&#13;\nenimmäispitoisuusrajat deoksinivalenolille ja zearalenonille. T-2- ja HT-2-&#13;\ntoksiinien lainsäädäntö on EU:ssa työn alla.&#13;\nPitkäaikainen altistuminen Fusarium-toksiineille voi aiheuttaa terveydellisiä&#13;\nhaittavaikutuksia, kuten immuunijärjestelmän heikkenemistä. Kaikkia&#13;\npitkäaikaisen altistumisen vaikutuksia ei kuitenkaan toistaiseksi tunneta.&#13;\nAkuuteissa myrkytystapauksissa oireita ovat esimerkiksi pahoinvointi, oksentelu&#13;\nja vatsakivut.&#13;\nSuomalaisten altistuminen Fusarium-toksiineille arvioitiin Evirassa yhteistyössä&#13;\nMaa- ja elintarviketalouden tutkimuskeskuksen ja Kansanterveyslaitoksen&#13;\nkanssa. Saannit ovat alle siedettävän päivittäisen enimmäissaantimäärän&#13;\nlukuun ottamatta T-2- ja HT-2-toksiineja, joita kauran suurkuluttajat&#13;\nvoivat teoriassa saada raakaviljasta liikaa.&#13;\nToksiinipitoisuudet vaihtelevat vuosittain erityisesti satokauden sään perusteella.&#13;\nLisäksi viljan lajittelulla ja kuorinnalla voidaan vähentää toksiinien&#13;\nmäärää merkittävästi.&#13;\nViljoille asetettuja Fusarium-toksiinien enimmäispitoisuuksia on syytä valvoa&#13;\njatkuvasti. Valvonnan kohdentamista suositellaan erityisesti kauralle ja&#13;\nkauravalmisteille, joissa esiintyy suurimmat pitoisuudet toksiineja.
Preparation of mouse pancreatic tumor for single-cell RNA sequencing and analysis of the data (2021)

Preparation of single-cell suspension from primary tumor tissue can provide a valuable resource for functional, genetic, proteomic, and tumor microenvironment studies. Here, we describe an effective protocol for mouse pancreatic tumor dissociation with further processing of tumor suspension for single-cell RNA sequencing analysis of cellular populations. We further provide an outline of the bioinformatics processing of the data and clustering of heterogeneous cellular populations comprising pancreatic tumors using Common Workflow Language (CWL) pipelines within user-friendly Scientific Data Analysis Platform (https://SciDAP.com). For complete details on the use and execution of this protocol, please refer to Gabitova-Cornell et al. (2020).
Eff-3DPSeg: 3D Organ-Level Plant Shoot Segmentation Using Annotation-Efficient Deep Learning (2023)

Reliable and automated 3-dimensional (3D) plant shoot segmentation is a core prerequisite for the extraction of plant phenotypic traits at the organ level. Combining deep learning and point clouds can provide effective ways to address the challenge. However, fully supervised deep learning methods require datasets to be point-wise annotated, which is extremely expensive and time-consuming. In our work, we proposed a novel weakly supervised framework, Eff-3DPSeg, for 3D plant shoot segmentation. First, high-resolution point clouds of soybean were reconstructed using a low-cost photogrammetry system, and the Meshlab-based Plant Annotator was developed for plant point cloud annotation. Second, a weakly supervised deep learning method was proposed for plant organ segmentation. The method contained (a) pretraining a self-supervised network using Viewpoint Bottleneck loss to learn meaningful intrinsic structure representation from the raw point clouds and (b) fine-tuning the pretrained model with about only 0.5% points being annotated to implement plant organ segmentation. After, 3 phenotypic traits (stem diameter, leaf width, and leaf length) were extracted. To test the generality of the proposed method, the public dataset Pheno4D was included in this study. Experimental results showed that the weakly supervised network obtained similar segmentation performance compared with the fully supervised setting. Our method achieved 95.1%, 96.6%, 95.8%, and 92.2% in the precision, recall, F1 score, and mIoU for stem-leaf segmentation for the soybean dataset and 53%, 62.8%, and 70.3% in the AP, AP@25, and AP@50 for leaf instance segmentation for the Pheno4D dataset. This study provides an effective way for characterizing 3D plant architecture, which will become useful for plant breeders to enhance selection processes. The trained networks are available at https://github.com/jieyi-one/EFF-3DPSEG.
HIV/Hepatitis C Virus−Coinfected Virologic Responders to Pegylated Interferon and Ribavirin Therapy More Frequently Incur Interferon-Related Adverse Events Than Nonresponders Do (2010)

Our study demonstrates coupling of antiviral effect and occurrence of adverse events in HIV/HCV-coinfected patients. These patients with IFN-related adverse effects need a multidisciplinary treatment approach, hence, they are more likely to achieve sustained virologic response. Future studies are needed to evaluate the factors that predict the development of IFN-alpha-dependent adverse events before therapy.
Crystal structure of a MIC-reactive gamma-delta T cell receptor - insights into gamma-delta TCR antigen recognition (134.79) (2009)

Abstract Gamma-delta T cells play essential roles in the immune surveillance and elimination of tumor cells and various types of infection. However, little is known about the recognition mechanisms of human gamma-delta TCRs. MHC class I-related chain (MIC) is one of only two validated protein ligands for human gamma-delta TCRs. To investigate the recognition mechanism of gamma-delta TCR - MIC interaction, we have determined crystal structure of a MIC-reactive Vdelta1 gamma-delta TCR at 3.0 angstrom resolution. The structure reveals significantly altered loop conformations, particularly in CDR3 loops in both gamma and delta chains comparing to three other gamma-delta TCR structures that are available so far. Our structure suggests novel MIC antigen recognition mode. We further identified conserved surface patches in both Vdelta1 receptor and MIC antigen that may be important for recognition. To our knowledge, this is the first structure of a human gamma-delta TCR that recognizes human self-antigen. Supported by NIH grant AI48675.
Efficient N-Demethylation of Opiate Alkaloids Using a Modified Nonclassical Polonovski Reaction (2003)

A modified Polonovski reaction has been employed to N-demethylate several opiate alkaloids in moderate to high yield. This method provides an alternative to traditional N-demethylation procedures which utilize toxic reagents such as cyanogen bromide or expensive reagents such as vinyl chloroformate. The current synthesis involves N-oxide formation, isolation of the corresponding N-oxide hydrochloride, and an FeSO(4).7H(2)O mediated Polonovski reaction to afford the desired secondary amine.
Einleitung (1988)

Seit dem griechischen Philosophen Aristoteles wurde im Altertum und im Mittelalter, ja, noch bis in die Neuzeit hinein allgemein geglaubt, die Natur habe einen Abscheu vor dem absolut leeren Raum, dem Vakuum, oder — wie man es lateinisch nannte — einen „Horror vacui“. Man konnte sich entsprechend der damaligen spekulativen Naturbeobachtung nicht vorstellen, daß es ein Vakuum geben könne — und folgerte daraus, daß es auch keins geben dürfe. Selbst Galilei (1564–1642), der sich nicht mehr an die fast dogmatisch geltenden spekulativen Glaubenssätze der aristotelischen Naturphilosophie hielt, war noch ein Anhänger des „horror vacui“ [1] und dies, obwohl er durch Hineinpressen von Luft in eine Flasche eine Gewichtszunahme festgestellt, also bewiesen hatte, daß auch Luft ein Gewicht hat. Der erste, der den „horror vacui“ überwand, war Torricelli (1608–1647), ein Schüler Galileis. Er füllte eine lange Glasröhre mit Quecksilber, verschloß das untere Ende mit dem Daumen, tauchte dieses Ende in ein mit Quecksilber gefülltes Becken und ließ die Öffnung frei. Das Quecksilber sank bis zu einer Höhe von etwa 76 cm, darüber hatte sich das erste experimentell hergestellte Vakuum gebildet, mit dem später auch Torricellis Schüler experimentierten. Die Ansicht, daß die Natur einen Abscheu vor dem Vakuum habe, war damit wenigstens für einen Teil der Zeitgenossen widerlegt. Der andere Teil der damaligen wissenschaftlichen Welt bekämpfte diese Ansicht heftig. Deshalb wiederholte Blaise Pascal (623–1662) Torricellis Versuche und stellte zudem fest, daß der Luftdruck beim Besteigen eines Turmes oder eines Berges abnimmt.
Quantitation of Volatiles and Nonvolatile Acids in an Extract from Coffee Beverages:  Correlation with Antioxidant Activity (2006)

The antioxidant activities of a commercial brewed coffee were investigated by measuring malonaldehyde (MA) formation from oxidized cod liver oil using a gas chromatographic method (MA-GC assay) and a thiobarbituric acid method (TBA assay). The highest antioxidant activity obtained by the MA-GC assay was from regular whole brewed coffee (97.8%) at a level of 20%, and the highest antioxidant activity obtained by the TBA assay was from decaffeinated whole brewed coffee (96.6%) at a level of 5%. Among 31 chemicals identified in a dichloromethane extract, guaiacol, ethylguaiacol, and vinylguaiacol exhibited antioxidant activities, which were comparable to that of alpha-tocopherol. Among nine chlorogenic acids (three caffeoylquinic acids, three feruloylquinic acids, and three dicaffeoylquinic acids) identified, 5-caffeoylquinic acid contained the greatest amount both in regular (883.5 microg/mL) and in decaffeinated (1032.6 microg/mL) coffees; it exhibited 24.5% activity by the MA-GC assay and 45.3% activity by the TBA assay at a level of 10 microg/mL. Caffeic and ferulic acids showed moderate antioxidant activities in both assays.
Investigation on synthesis and properties of isosorbide based bis-GMA analogue (2012)

The aim of this work was to synthesize and investigate properties of a novel dimethacrylic monomer based on bioderived alicyclic diol--isosorbide. Its potential as a possible substitute of 2,2-bis[4-(2-hydroxy-3-methacryloyloxypropoxy)phenyl]propane (BISGMA), widely used in dental restorative materials and suspected for toxicity was assessed. The novel monomer was obtained in a three-step synthesis. First, isosorbide was etherified by a Williamson nucleophilic substitution and subsequently oxidized to isosorbide diglycidyl ether (ISDGE). A triphenyl phosphine catalyzed addition of methacrylic acid to ISDGE resulted in 2,5-bis(2-hydroxy-3-methacryloyloxypropoxy)- 1,4:3,6-dianhydro-sorbitol (ISDGMA). The monomer obtained was photopolymerized using camphorquinone/2-(dimethylamino)ethyl methacrylate initiating system. Next, compositions with triethylene glycol dimethacrylate (TEGDMA) were prepared and polymerized. Double bond conversion, polymerization shrinkage and water sorption of resulting polymers were determined. Selected mechanical (flexular strength and modulus, Brinell hardness) and thermomechanical (DMA analysis) properties were also investigated. BISGMA based materials were prepared as reference for comparison of particular properties.
Note on a Method of Determining the Distribution of Pore Sizes in a Porous Material (1921)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Introgression of the Florida Largemouth Bass Genome into Native Populations in Alabama Public Lakes (1992)

Many public fishing lakes constructed in Alabama first contained the state's native largemouth bass Micropterus salmoides, which has allozyme frequencies similar to those of the pure northern subspecies, M. s. salmoides. Many of these lakes then were supplementally stocked with largemouth bass fingerlings with allozyme frequencies similar to those of the Florida subspecies M. s. floridanus. The supplemental introductions had varying success, and 10 of 11 populations we examined had undergone significant (P < 0.05) allele-frequency changes–representing introgression of Florida alleles-at the diagnostic loci sAAT-B*, sIDHP*, and sSOD*. We evaluated several variables for their effects on introgression: number of years (6–18) since initial stockings of Florida largemouth bass, number of stockings (3–11), stocking densities (334–1,430/hectare), Secchi disk visibility (18–33 cm), and latitude (31°30'–34°90'N). All variables except latitude affected or were correlated with percent introgression, which ranged from 11 to 69%. Number of stockings was identified by step-wise multiple regression as the most influential variable (r2 = 0.77) on introgression. The best two-variable model (r2 = 0.82), which also incorporated years since initial stocking, was not different from the best one-variable model. Similar experiments previously reported from Texas also identified number of stockings as having the most influence on introgresSion; however, water clarity was positively correlated with introgression of Florida largemouth bass alleles in the Texas study but negatively correlated in ours.
Structures of metallic clusters: Mono- and polyvalent metals (2002)

We present detailed numerical results on the ground state structures of metallic clusters. The Gupta-type many-body potential is used to account for the interactions between atoms in the cluster. Both the genetic algorithm technique and the basin hopping method have been applied to search for the global energy minima of clusters. The excellent agreement found in both schemes for the global energy minima gives credence to the optimized energy values obtained. For four monovalent and one polyvalent metals studied in this work and within the accuracy of the energies presented here, we find that the global energy minima predicted by the basin hopping method are the same as those values obtained by the genetic algorithm. Our calculations for the ground state energies of alkali metallic clusters show regularities in the energy differences, and the cluster growth pattern manifested by this same group of clusters is generally icosahedral, which is quite different from the close-packed and decahedral preferentially exhibited by the tetravalent lead clusters. Considering the inherent disparities in the electronic properties and the bulk structures in these metals (body-centered cubic for alkali metals and face-centered cubic for the lead metal), it is not unreasonable to conjecture that the valence electrons do play a subtle role in the conformation of metallic clusters.
7.4 A 413&#x00D7;240-pixel sub-centimeter resolution Time-of-Flight CMOS image sensor with in-pixel background canceling using lateral-electric-field charge modulators (2014)

Time-of-Flight (ToF) range imagers have a wide range of applications, such as 3D mice, gesture-based remote controllers, amusement, robots, security systems, and automobiles. Numerous ToF range imager developments have been reported [1-4]. Recent developments are often based on CMOS image sensor technology with pinned photodiode options [5-7], which are suitable for cost-effective mass production. Reported CMOS ToF range imagers use single-tap or two-tap lock-in pixels; to cancel the influence of background light, two or four sub-frames are used to produce a background-canceled range image. These architectures, however, have difficulty with precise range measurements of moving objects, because background light cancelation is not guaranteed for moving objects. Lock-in pixels without any charge-draining gate suffer from background light during the readout time of the operation. Another important issue with CMOS ToF range imagers for high range resolution is the speed of lock-in pixels, which must be improved to use high-modulation-frequency light or short-duration light pulses.
n-Alkanoic Acid Monolayers on 316L Stainless Steel Promote the Adhesion of Electropolymerized Polypyrrole Films (2006)

The formation of a self-assembled monolayer significantly promotes the adhesion of electrodeposited polypyrrole on stainless steel. The monolayer affects the nucleation and growth mechanism of polypyrrole as a result of its hydrophobic nature. This was confirmed by analyzing current-time transients of the initial stages of electropolymerization and was in agreement with AFM images.
Supplementary Materials from Novel Mechanistic Insights into Ectodomain Shedding of EGFR Ligands Amphiregulin and TGF-α: Impact on Gastrointestinal Cancers Driven by Secondary Bile Acids (2023)

&lt;p&gt;PDF file - 66KB&lt;/p&gt;
Some Stability Criteria for Double Emulsions (1998)

Double W/O/W emulsions consist in an inverse emulsion which is dispersed within a water continuous phase as direct emulsion droplets. The aim of this paper is to explore the basic rules that govern the stability of double emulsions. By associating both water- and oil-soluble surfactants in various concentrations, we produce W/O/W double emulsions. We identify two types of instabilities that are responsible for the evolution of double emulsions: (i) coalescence of the small inner droplets with the globule interface or (ii) coalescence between the small inner droplets within the oil globule. The first type of instability leads to a complete delivering of the small inner droplets toward the external phase whereas the second one does not. We show that the kinetics associated with the release of the small inner droplets due to this former instability is clearly related to the hydrophilic surfactant concentration in the external phase. Depending on the value of this concentration, multiple emulsions may be destabilized with a time scale ranging from several months to a few minutes. We discuss the basic criteria which are responsible for the suppression or the starting of these instabilities, emphasizing the influence of the composition of the interfacial films.
Amino Acid Sequences of Cytochrome b5 from Human, Porcine, and Bovine Erythrocytes and Comparison with Liver Microsomal Cytochrome b51 (1985)

The amino acid sequences of human, porcine, and bovine erythrocyte cytochromes b5 which are soluble and present in the cytosol have been determined. In addition, the partial sequences of microsome-bound liver cytochrome b5, namely the sequence of the N-terminal region and joint region between the heme-containing and membranous part, have been established for human and porcine sources. All the cytochromes b5 from erythrocyte and liver contained N-acetylated N-termini. Of the 97 amino acid residues of erythrocyte cytochrome b5, residues 1-96 were identical with those of the liver protein of the same species. However, residue 97 (C-terminal residue) was proline for human erythrocyte cytochrome b5 and serine for the porcine protein, while residues 97 (joint region) of human and porcine liver cytochromes b5 were threonine. These findings indicate that the two forms of cytochrome b5 are encoded by two different but closely related mRNAs.
Hydrodynamic and Mass-Transfer Characteristics in Organic Liquid Mixtures in a Large-Scale Bubble Column Reactor for the Toluene Oxidation Process (2004)

The gas holdup (εG), Sauter mean bubble diameter (dS), and bubble size distribution, as well as the volumetric mass-transfer coefficient (kLa), gas−liquid interfacial area (a), and mass-transfer coefficient (kL), of N2 and air were measured in a large-scale (0.316-m inside diameter, 2.8-m height) bubble column reactor (BCR) in toluene and its mixtures (toluene−benzoic acid−benzaldehyde) under a wide range of pressure (0.2−0.8 MPa) and superficial gas velocities (0.06−0.14 m/s). The kLa data were determined using the transient physical gas absorption technique, whereas the bubble size distributions as well as the Sauter mean bubble diameters were obtained using the dynamic gas disengagement technique. The gas holdup values were measured employing the manometric method with two differential pressure cells located at different positions in the BCR. From the experimental gas holdup, Sauter mean bubble diameter, and kLa results, a and kL were extracted under various operating conditions. The central composite statistical design and analysis technique was used to study the effect of operating conditions on the hydrodynamic and mass-transfer parameters. Under the operating conditions used, the kLa, a, and εG values were found to increase with increasing gas superficial velocity and pressure, whereas the dS and kL values appeared to decrease with pressure and increase with superficial gas velocity. The effect of the nature of the gas on the hydrodynamic and mass-transfer parameters was found to be insignificant, whereas the effect of addition of benzaldehyde and benzoic acid to pure toluene, aimed at mimicking the actual continuous liquid-phase toluene oxidation process, appeared to have a strong impact on both parameters because of froth formation. The experimental data were also compared with the available literature, and statistical correlations were developed to predict the hydrodynamic and mass-transfer experimental parameters with confidence levels greater than 95%.
An activity-based sensor networks course for undergraduates with sun spot devices (2009)

Wireless sensor networks are revolutionizing the instrumentation of the physical world, across scientific, industrial and military applications. In this paper, we describe our efforts developing and classroom-testing hands-on materials for use in undergraduate-accessible courses on sensor networks. In Winter 2008 at Portland State University, we introduced an in-class laboratory component to a sensor networks course that had previously been entirely lecture-based. For the laboratory exercises, we utilized Sun's Java-programmable Sun SPOT [7] sensor network technology. We found the Sun SPOT based laboratory activities to be quite powerful as a teaching and excitement-fostering tool.
Treatment of Epilepsy With Diphenylhydantoin Sodium (1956)

(1956). Treatment of Epilepsy With Diphenylhydantoin Sodium. Postgraduate Medicine: Vol. 20, No. 6, pp. 584-590.
Automated measurement of polarization mode dispersion using Jones matrix eigenanalysis (1992)

Polarization mode dispersion (PMD), which can limit the bandwidth of optical transmission links, has been difficult to measure in a manner independent of human judgment, leading to difficulties in automating the measurement. It is shown that PMD in any linear, time-invariant network can be completely characterized by eigenanalysis of Jones matrices measured at a series of discrete wavelengths, even for networks exhibiting polarization-dependent loss. A fast, automated system using a tunable laser and an accurate, real-time polarimeter affords the temporal accuracy of approximately 2% down to a limit of several femtoseconds, as demonstrated by comparison with other techniques and comparison with known samples. Both the principal states of polarization and the group delay difference were measured as a function of optical frequency.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Physicochemical and Sensory Characteristics of Green Prunus mume Powder Granule (2012)

청매는 피로 회복에 좋고 체질 개선 효과에도 좋으며 해독작용에도 도움이 되며 그 외에도 여러 가지 기능성을 갖는 건강기능식품으로 알려져 있는 청매를 씨만 제거한 후 건조시켜 분쇄하여 청매분말(GPP)을 얻었다. 청매분말을 유동층 조립기에서 유동하면서 물(GPPGW)과 매실 농축액 20%를 분사액으로 하여 과립(GPPGE)을 제조하였다. 과립의 물성측정 결과 청매과립은 청매분말보다 용해성과 흐름성이 우수하였고, GPPGE는 GPPGW에 비하여 흐름성은 좋지 못하였으나 용해성은 우수하였다. 일반성분 분석 결과 GPPGE에 조지방과 구연산 함량이 가장 높았으며, GPP와 GPPGW 사이에는 성분에 큰 차이가 없었다. 관능특성 분석결과 GPPGE가 가장 반짝이는 녹색을 나타내었고 과립이 쉽게 깨지는 특성을 나타내었다. 관능특성과 소비자조사결과에 대한 상관분석결과 소비자들은 반짝이는 외관을 갖고 과립이 쉽게 깨지는 특성을 가진 GPPGE를 가장 선호하는 것을 알 수 있었다. 따라서 유동층 조립기에 청매분말을 유동시키면서 청매추출액을 분사하여 제조된 과립(GPPGE)은 청매과육전체를 섭취하면서 편리성이 증진된 새로운 형태의 제품으로 이용이 가능할 것으로 판단된다.