gebhart/patrepeval huggingface dataset:
Optimized application of surface-enhanced laser desorption/ionization time-of-flight MS to differentiate<i>Francisella tularensis</i>at the level of subspecies and individual strains (2007)

Francisella tularensis, the causative agent of tularaemia, is a potential agent of bioterrorism. The phenotypic discrimination of the closely related F. tularensis subspecies and individual strains with traditional methods is difficult and time consuming, often producing ambiguous results. Surface-enhanced laser desorption/ionization time-of-flight MS (SELDI-TOF MS) was used in this study to discriminate the different species and subspecies of the genus Francisella. We tested 18 Francisella strains including at least one representative of each species/subspecies on four different types of chromatographic chip surfaces. Multivariate analysis (hierarchical clustering and principal component analysis) allowed grouping of the strains according to their designated subspecies. Furthermore, single strains within F. tularensis subspecies could be discriminated.
A self-sufficient method for calibration of Varian electronic portal imaging device (2015)

Electronic portal imaging device (EPID) is currently used for dosimetric verification of IMRT fields and linac quality assurance (QA). It is critical to understand the dosimetric response and perform an accurate and robust calibration of EPID. We present the implementation of an efficient method for the calibration and the validation of a Varian EPID, which relies only on data collected with that specific device. The calibration method is based on images obtained with five shifts of EPID panel. With this method, the relative gain (sensitivity) of each element of a detector matrix is calculated and applied on top of the calibration determined with the flood-field procedure. The calibration procedure was verified using a physical wedge inserted in the beam line and the corrected profile shows consistent results with the measurements using a calibrated 2D array. This method does not rely on the beam profile used in the flood-field calibration process, which allows EPID calibration in 10 minutes with no additional equipment compared to at least 2 hours to obtain beam profile and scanning beam equipment requirement with the conventional method.
FGF-1–Induced Platelet-Derived Growth Factor-A Chain Gene Expression in Endothelial Cells Involves Transcriptional Activation by Early Growth Response Factor-1 (1997)

Fibroblast growth factor-1 (FGF-1), a prototype member of the heparin-binding growth factor family, is a potent mitogen for vascular endothelial cells and a variety of other cell types. FGF-1 can induce the expression of the platelet-derived growth factor-A chain (PDGF-A) gene in endothelial cells; however, the underlying transcriptional mechanisms are not known. We used serial 5' deletion and transient transfection analysis of the human PDGF-A promoter to demonstrate that a 16-bp element, located 55 to 71 bp upstream of the transcriptional start site, is required for FGF-1-inducible promoter-dependent expression. This region contains nucleotide recognition elements for the early growth response gene product, early growth response factor-1 (Egr-1), and the related zinc-finger transcription factor, Sp1. Reverse-transcription polymerase chain reaction revealed that FGF-1 induced Egr-1 mRNA expression within 30 minutes. Electrophoretic mobility shift, supershift, and Western blot analysis demonstrated that Egr-1 protein accumulated in the nuclei of endothelial cells exposed to the growth factor, whereas levels of Sp1 did not change. Egr-1 bound to the FGF-1 response element in the proximal PDGF-A promoter in a specific and time-dependent manner. These findings indicate that Egr-1 plays a key regulatory role in FGF-1-inducible endothelial PDGF-A expression and implicate this transcription factor in pathological settings in which these mitogens are both expressed.
Brassinosteroid Stimulation of Hypocotyl Elongation and Wall Relaxation in Pakchoi (Brassica chinensis cv Lei-Choi) (1993)

Hypocotyl elongation of pakchoi (Brassica chinensis cv Lei-Choi) was stimulated by applying 300 ng of brassinosteroid (2a,3a,22~,23~-tetrahydroxy-24~-methyl-B-homo-7-oxa-5cy-cholestan-6-one, BR) in 1 pL of 50% ethanol to the apex of hypocotyls. BR had its greatest effect on elongation of the apical 3-mm region below the cotyledonary node (75% stimulation) between 6 and 18 h after treatment. Stress/strain (Instron) analysis of this 3-mm region revealed that plastic and elastic components of extension were not significantly different between BR-treated and control seedlings. In pressure-block experiments, the initial rate of relaxation was 2-fold faster in BR-treated plants as compared with controls, whereas after 125 min the total amount of relaxation and the relaxation rate were the same for the two treatments. Osmotic pressure of cell sap expressed from this 3-mm region showed a large decrease (28%) in BR-treated seedlings compared to the controls. We conclude that BR stimulates growth in pakchoi by accelerating the biochemical processes that cause wall relaxation, without inducing a large change in wall mechanical properties.
Effect of Crystallinity on the Intercalation of Monoamine in α-Zirconium Phosphate Layer Structure (2005)

When the α-zirconium phosphate is of low crystallinity, guests are easy to intercalate into the entire gallery space, even at low intercalation ratio, and achieve a large interlayer distance. With increasing crystallinity, the intercalation turns out to be more difficult. A high degree of intercalation can only be achieved at a high intercalation ratio.
Convenient synthesis of 3,5-dialkoxy-4-hydroxy cinnamic acids (2007)

3,5-Dialkoxy-4-hydroxy cinnamic acids 8a-g have been conveniently synthesized from methyl 4-benzyloxy-3,5-dihydroxybenzoate 4. In five steps, cinamic acids 8a-g having various alkoxy groups on C-3 and C-5 positions of the phenyl ring were obtained in 33-70 % overall yields. The antioxidant properties of the newly synthesized amides and the effects on lipid peroxidation in rat brain homogenate will be examined by thiobarbituric acid reactive substances (TBARS) assay and other methods.
Standards for Reporting the Optical Aberrations of Eyes (2000)

In response to a perceived need in the vision community, an OSA taskforce was formed at the 1999 topical meeting on vision science and its applications (VSIA-99) and charged with developing consensus recommendations on definitions, conventions, and standards for reporting of optical aberrations of human eyes. Progress reports were presented at the 1999 OSA annual meeting and at VSIA-2000 by the chairs of three taskforce subcommittees on (1) reference axes, (2) describing functions, and (3) model eyes.
Infrared Spectra of Lignin and Related Compounds. II. Conifer Lignin and Model Compounds<sup>1,2</sup> (1960)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInfrared Spectra of Lignin and Related Compounds. II. Conifer Lignin and Model Compounds1,2HERBERT L. HERGERTCite this: J. Org. Chem. 1960, 25, 3, 405–413Publication Date (Print):March 1, 1960Publication History Published online1 May 2002Published inissue 1 March 1960https://pubs.acs.org/doi/10.1021/jo01073a026https://doi.org/10.1021/jo01073a026research-articleACS PublicationsRequest reuse permissionsArticle Views1751Altmetric-Citations124LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Role of beta-glucosidase in the bioconversion of cellulose to ethanol (1980)

The activity of beta-glucosidase from Trichoderma reesei was studied with respect to its inhibition by Et0H and its role in the degradation of cellulose. Ethanol and other alcohols increased the rate of hydrolysis of p-nitrophenyl-Beta-D-glucopyranoside by acting as acceptor molecules for the glucosyl cation. The presence of Et0H resulted in the formation of Et-Beta-D-glucopyranoside. Et0H inhibited the activity of the complete cellulase system, but the extent of inhibition was less than for glucose or cellobiose. Addition of Aspergillus niger Beta-glucosidase to a simultaneous saccharification/fermentation resulted in a 20% increase in conversion of cellulose to Et0H, whereas addition to saccharificatin resulted in a 53% increase in conversion.
Thin-layer supported nafion catalysts for the partial oxidation of light alkanes (1991)

Thin-layer carbon supported Nafion-H catalysts were found to be active and highly selective for the partial oxidation of C1–C3 alkanes under mild conditions and in the presence of aqueous H2O2. A three phase catalytic membrane reactor (3PCMR) has been used.
A Randomized, Double‐Blind, Placebo‐Controlled Study to Determine the Safety and Efficacy of Cultured and Expanded Autologous Fibroblast Injections for the Treatment of Interdental Papillary Insufficiency Associated With the Papilla Priming Procedure (2007)

This early-phase study using cell transplantation of autologous cultured and expanded fibroblasts following a papilla priming procedure suggests that the treatment is safe and may be efficacious for treating papillary insufficiency, especially in the early phases (2 months) of healing. The analysis of the investigator and subject VAS assessments indicates that the test treatment was superior to the placebo treatment. The finite measurement required to detect a change creates a problem that needs to be addressed in future studies.
Entropy loss in PUF-based key generation schemes: The repetition code pitfall (2014)

One of the promising usages of Physically Unclonable Functions (PUFs) is to generate cryptographic keys from PUFs for secure storage of key material. This usage has attractive properties such as physical unclonability and enhanced resistance against hardware attacks. In order to extract a reliable cryptographic key from a noisy PUF response a fuzzy extractor is used to convert non-uniform random PUF responses into nearly uniform randomness. Bösch et al. in 2008 proposed a fuzzy extractor suitable for efficient hardware implementation using two-stage concatenated codes, where the inner stage is a conventional error correcting code and the outer stage is a repetition code. In this paper we show that the combination of PUFs with repetition code approaches is not without risk and must be approached carefully. For example, PUFs with min-entropy lower than 66% may yield zero leftover entropy in the generated key for some repetition code configurations. In addition, we find that many of the fuzzy extractor designs in the literature are too optimistic with respect to entropy estimation. For high security applications, we recommend a conservative estimation of entropy loss based on the theoretical work of fuzzy extractors and present parameters for generating 128-bit keys from memory based PUFs.
Diffusion Strategies for Distributed Kalman Filtering and Smoothing (2010)

We study the problem of distributed Kalman filtering and smoothing, where a set of nodes is required to estimate the state of a linear dynamic system from in a collaborative manner. Our focus is on diffusion strategies, where nodes communicate with their direct neighbors only, and the information is diffused across the network through a sequence of Kalman iterations and data-aggregation. We study the problems of Kalman filtering, fixed-lag smoothing and fixed-point smoothing, and propose diffusion algorithms to solve each one of these problems. We analyze the mean and mean-square performance of the proposed algorithms, provide expressions for their steady-state mean-square performance, and analyze the convergence of the diffusion Kalman filter recursions. Finally, we apply the proposed algorithms to the problem of estimating and tracking the position of a projectile. We compare our simulation results with the theoretical expressions, and note that the proposed approach outperforms existing techniques.
Spatiotemporal Loss of <i>NF1</i> in Schwann Cell Lineage Leads to Different Types of Cutaneous Neurofibroma Susceptible to Modification by the Hippo Pathway (2018)

Neurofibromatosis type 1 (NF1) is a cancer predisposition disorder that results from inactivation of the tumor suppressor neurofibromin, a negative regulator of RAS signaling. Patients with NF1 present with a wide range of clinical manifestations, and the tumor with highest prevalence is cutaneous neurofibroma (cNF). Most patients harboring cNF suffer greatly from the burden of those tumors, which have no effective medical treatment. Ironically, none of the numerous NF1 mouse models developed so far recapitulate cNF. Here, we discovered that HOXB7 serves as a lineage marker to trace the developmental origin of cNF neoplastic cells. Ablating <i>Nf1</i> in the HOXB7 lineage faithfully recapitulates both human cutaneous and plexiform neurofibroma. In addition, we discovered that modulation of the Hippo pathway acts as a "modifier" for neurofibroma tumorigenesis. This mouse model opens the doors for deciphering the evolution of cNF to identify effective therapies, where none exist today. SIGNIFICANCE: This study provides insights into the developmental origin of cNF, the most common tumor in NF1, and generates the first mouse model that faithfully recapitulates both human cutaneous and plexiform neurofibroma. The study also demonstrates that the Hippo pathway can modify neurofibromagenesis, suggesting that dampening the Hippo pathway could be an attractive therapeutic target.<i>This article is highlighted in the In This Issue feature, p. 1</i>.
Epithelial inducible nitric oxide synthase activity is the major determinant of nitric oxide concentration in exhaled breath (2004)

Only NOS2 expression was associated with FeNO in respiratory epithelial cells obtained from children (R = 0.672; p<0.001). This suggests that FeNO variability is largely determined by epithelial NOS2 expression with little contribution from other isoforms.
Sound Information Notification System by Two-Channel Electrotactile Stimulation for Hearing Impaired Persons (2007)

Hearing impaired persons (HIPs) are afraid of walking along a street and living a life alone. If they can successfully get sound information via some machine interface, dangerous situations outdoors will be avoided, and their quality of life indoors will be improved. This paper describes a notification system for transmitting sound information to HIPs with two-channel electrotactile stimulation, assuming that it is used both outdoors and indoors. The proposed system consists of two subsystems: one is a block which detects sound information and another one is to transmit the detected sound information with electrotactile stimulation. In the system developed, sound information is provided with the attention arousal, notifying the direction of the sound source (four states) and the sound category (seven states). Thus, 28 states of sound information are sent. We adopted 12 stimulation patterns comprising several burst profiles, each burst composed of several pulses modulated in amplitude. In the first subsystem, recognition ratio of the direction was 90% and detection ratio of the sound category was 80%. In the second subsystem, recognition experiments for the direction of the sound source and the sound category performed for four healthy subjects showed that the average percentages of correct recognition were 91 % and 89 %, and the reaction times 1.21 seconds and 1.62 seconds. These results suggested the possible applicability of the proposed system to assist HIPs.
Responses of Fractionated Cells from Patients with Systemic Lupus Erythematosus and Normals to Plant Mitogen: Evidence for a Suppressor Population of Monocytes (1978)

In systemic lupus erythematosus (SLE) three populations of blood mononuclear cells from patients with systemic lupus erythematosus (SLE) and from normal controls were examined for their responses to graded concentrations of phytohemagglutinin (PHA). In normal controls, H3 thymidine uptake of unfractionated cells (FH) was greater than that of T cells (Fab Col). In contrast, SLE Fab Col cells responded better than FH cells in 44% of patients tested. SLE mononuclear cells devoid of adherent monocytes (NRIg) also responded better than FH cells.
Voxel planes: Rapid visualization and meshification of point cloud ensembles (2013)

Conversion of unorganized point clouds to surface reconstructions is increasingly required in the mobile robotics perception processing pipeline, particularly with the rapid adoption of RGB-D (color and depth) image sensors. Many contemporary methods stem from the work in the computer graphics community in order to handle the point clouds generated by tabletop scanners in a batch-like manner. The requirements for mobile robotics are different and include support for real-time processing, incremental update, localization, mapping, path planning, obstacle avoidance, ray-tracing, terrain traversability assessment, grasping/manipulation and visualization for effective human-robot interaction. We carry out a quantitative comparison of Greedy Projection and Marching cubes along with our voxel planes method. The execution speed, error, compression and visualization appearance of these are assessed. Our voxel planes approach first computes the PCA over the points inside a voxel, combining these PCA results across 2×2×2 voxel neighborhoods in a sliding window. Second, the smallest eigenvector and voxel centroid define a plane which is intersected with the voxel to reconstruct the surface patch (3-6 sided convex polygon) within that voxel. By nature of their construction these surface patches tessellate to produce a surface representation of the underlying points. In experiments on public datasets the voxel planes method is 3 times faster than marching cubes, offers 300 times better compression than Greedy Projection, 10 fold lower error than marching cubes whilst allowing incremental map updates.
Weight–length relationships and Fulton’s condition factors of skipjack tuna ( <i>Katsuwonus pelamis</i> ) in the western and central Pacific Ocean (2015)

This paper describes the weight-length relationships (WLRs) and Fulton's condition factors (K) of skipjack tuna (Katsuwonus pelamis) in purse seine fisheries from three cruises in the western and central Pacific Ocean (WCPO): August-September 2009 (AS09), November-December 2012 (ND12), and June-July 2013 (JJ13). The fork length and weight of a total of 1678 specimens were measured. The results showed that the fork length of more than 70% of specimens was below 60 cm (76% in AS09, 87% in ND12, and 73% in JJ13). The coefficient b in the combined sex group was 3.367, 3.300 and 3.234 in JJ13, AS09 and ND12, respectively. The b values of WLRs when fork length was >60 cm were significantly less than 3 (P = 0.062), but when fork length was <60 cm they were significantly greater than 3 (P = 0.028). The K value ranges of JJ13, AS09 and ND12 in different fork length groups were 1.3-1.84 (1.62 ± 0.18), 1.57-2.02 (1.86 ± 0.15), and 1.44-1.78 (0.65 ± 0.13), respectively. Moreover, K values in different fork length classes for each cruise had one turning point: 60-65 cm for JJ13; 60-65 cm for ND12; and 55-60 cm for AS09. The results of this study provide basic information on the WLRs and K values of skipjack tuna in different seasons and growth phases in the WCPO, which are useful for fishery biologists and fishery managers.
Rejection of fetal neocortical neural transplants by H-2 incompatible mice. (1987)

In order to examine questions concerning immunologic privilege of the central nervous system, we placed neocortical transplants into cerebral ventricles of mice. We compared the fates of transplants between fully H-2 compatible (isografts) and H-2 incompatible (allografts) animals. Histologic evaluation comparing animals from iso- and allograft groups revealed significant differences in the number of inflammatory cells and in the degree of necrosis within the grafts. Response to allografted tissue within the brain mimics that seen in several immune-mediated diseases of the nervous system in that neurons appear to be selectively spared. Only upon subsequent stimulation of the host's immune system with an orthotopic skin graft bearing the major histocompatibility complex antigens of the neural graft are neurons destroyed. Immunohistochemical evaluation revealed that the inflammatory cell infiltrates in and around the allografts were composed of Lyt-2+, L3T4+, and Mac-1+ cells. In addition, Ia+ endothelial cells as well as Ia+ parenchymal CNS cells were found in both donor and host tissue of allografted animals. Hence, H-2 incompatible neural tissue transplanted to the CNS is recognized and rejected by the immune system of the recipient animal. The cellular infiltrates seen within the first weeks to months following transplantation of allogeneic CNS tissue resemble those seen in other allografts undergoing rejection. We conclude that the CNS is not unconditionally privileged as either a transplant site or as a source of transplanted tissue.
Synthesis of an <i>N</i>-Alkyl Derivative of 2'-Deoxy<i>iso</i>guanosine (1997)

3',5'-O-bis-tert-butyldimethylsilyl-2'-deoxyguanosine is converted in two steps to 3',5'-O-tert-butyldimethylsilyl-6-O-aryl-2'-deoxyxanthosine. This compound is used to make a 2'-deoxyisoguanosine analog with a functionalized side chain.
Dynamical trajectories: the motion of a particle in an arbitrary field of force (1907)

where the dots indicate derivatives with respect to the time. The functions 4, *, X are assumned to have partial derivatives of first and second order in the region of space considered. The case where the force vanishes everywhere is excluded. The motion of the particle is determined when its initial position and initial velocity are given. By taking all possible initial conditions we obtain a definite quintuply infinite system of trajectories. Our object is to study the properties of such systems of curves with a view to obtaining a complete geometric characterization. The main result is stated in article 39 at the end of the paper. The first properties derived are consequences of the elementary fact that the osculating plane at any point of a trajectory is determined by its initial direction and by the direction of the force (articles 4-11). The next set relate to osculating, spheres.t With each lineal element there are associated oo1 osculating spheres whose centers lie on a straight line (articles 12-15). The straight lines corresponding to all the elements at a point form a congrulence of order one and class three determined by a twisted cubic curve (articles 16-23). The properties obtained at this stage belong to a more general class of curve systems than the dynamical class. The final characterization is attained by introducing certain related systems of plane curves, here termed S-systems, which have all the
SAGA: a subgraph matching tool for biological graphs (2006)

SAGA can be accessed freely via the web at http://www.eecs.umich.edu/saga. Binaries are also freely available at this website.