gebhart/patrepeval huggingface dataset:
Optical control of two-photon excitation efficiency of α-perylene crystal by pulse shaping (2004)

Optimized pulse shaping experiments were carried out on the control of two-photon excitation efficiency of an alpha-perylene crystal in the temperature region from 30 to 290 K. It was found that a pulse train with a pulse interval of 90 fs and an alternately reversing phase relation increased the excitation efficiency by a factor of 2 for the whole temperature region. The pulse shape characteristic for effective efficiency increase was reduced by double pulse experiments in which the dependence of the emission intensity on the pulse interval and relative phase between pulses were measured. The mechanism of the efficiency increase is briefly discussed using a sliding-window Fourier transform of the pulse shape.
Ordinal depth information from accommodation? (2000)

The ability to judge egocentric distance was assessed in two groups of six observers using a manual pointing task. The purpose of the study was to determine the extent to which blur-driven accommodation can provide information on target distance in the absence of any retinal cues to distance. Observers were extremely accurate when carrying out the pointing task in a ‘fullcue’ condition. In contrast, observers were extremely poor at carrying out the task when accommodation was the only distance cue available. Responses on individual trials bore little relationship to the actual target distance in any of the observers. On the other hand, accommodation weakly biased the mean responses in some observers. This bias appears to be due to the observers' effective use of accommodation to determine whether the target presented in one trial was nearer or further away than the target presented in the previous trial. Accommodation therefore appears to provide ordinal information, although the distance signal may actually arise from accommodation-driven vergence. The poverty of accommodation as a source of metric information was highlighted in a second group of observers who all demonstrated a strong bias when perceiving distance in the presence of an initially ambiguous retinal cue. It is concluded that accommodation can act as a source of ordinal distance information in the absence of other cues to distance but the contribution of accommodation to normal distance perception in full-cue conditions is questioned.
C-reactive protein binding to FcgRIIa on human monocytes (2000)

C-reactive protein (CRP) is involved in host defense, regulation of inflammation, and modulation of\nautoimmune disease. Although the presence of receptors for CRP on phagocytes has been inferred for\nyears, their identity was determined only recently. FcgRIa, the high-affinity IgG receptor, binds CRP\nwith low affinity, whereas FcgRIIa, the low-affinity IgG receptor, binds CRP with high affinity. Because\nthe single nucleotide polymorphism in FcgRIIA ??? which encodes histidine or arginine at position 131\n??? strongly influences IgG2 binding, we determined this polymorphism???s effect on CRP binding. CRP\nbound with high avidity to monocytes and neutrophils from FcgRIIA R-131 homozygotes, and binding\nwas inhibited by the R-specific mAb 41H16. CRP showed decreased binding to cells from FcgRIIA\nH-131 homozygotes (which bind IgG2 with high affinity). However, IFN-g enhanced FcgRI expression\nby H-131 monocytes and increased CRP binding. FcgRIIa heterozygotes showed intermediate binding.\nCRP initiated increases in [Ca2+]i in PMN from R-131, but not from H-131 homozygotes. These data\nprovide direct genetic evidence for FcgRIIa as the functional, high-affinity CRP receptor on leukocytes\nwhile emphasizing the reciprocal relationship between IgG and CRP binding avidities. This counterbalance\nmay affect the contribution of FcgRIIA alleles to host defense and autoimmunity.
Innate Immunity in Plants: An Arms Race Between Pattern Recognition Receptors in Plants and Effectors in Microbial Pathogens (2009)

For many years, research on a suite of plant defense responses that begin when plants are exposed to general microbial elicitors was underappreciated, for a good reason: There has been no critical experimental demonstration of their importance in mediating plant resistance during pathogen infection. Today, these microbial elicitors are named pathogen- or microbe-associated molecular patterns (PAMPs or MAMPs) and the plant responses are known as PAMP-triggered immunity (PTI). Recent studies provide an elegant explanation for the difficulty of demonstrating the role of PTI in plant disease resistance. It turns out that the important contribution of PTI to disease resistance is masked by pathogen virulence effectors that have evolved to suppress it.
An integrated metal-nitride-oxide-silicon (MNOS) memory (1969)

A nonvolatile integrated metal-nitride-oxide-silicon (MNOS) word organized memory was fabricated. The salient features of this integrated storage array are 1) WRITE cycle 2.0 microseconds, READ cycle 500 nanoseconds, 2) WRITE voltage ± 25V, 3) single device per storage bit, 4) MOS driving circuitry with no isolation between MOS and MNOS devices on the same chip, and 5) nonvolatile storage of information.
Antioxidant Activity in Fruits and Leaves of Blackberry, Raspberry, and Strawberry Varies with Cultivar and Developmental Stage (2000)

Fruits and leaves from different cultivars of thornless blackberry (Rubus sp.), red raspberry (Rubus idaeus L.), black raspberry (Rubus occidentalis L.), and strawberry (Fragaria x ananassa D.) plants were analyzed for total antioxidant capacity (oxygen radical absorbance capacity, ORAC) and total phenolic content. In addition, fruits were analyzed for total anthocyanin content. Blackberries and strawberries had the highest ORAC values during the green stages, whereas red raspberries had the highest ORAC activity at the ripe stage. Total anthocyanin content increased with maturity for all three species of fruits. Compared with fruits, leaves were found to have higher ORAC values. In fruits, ORAC values ranged from 7.8 to 33.7 micromol of Trolox equivalents (TE)/g of fresh berries (35. 0-162.1 micromol of TE/g of dry matter), whereas in leaves, ORAC values ranged from 69.7 to 182.2 micromol of TE/g of fresh leaves (205.0-728.8 micromol of TE/g of dry matter). As the leaves become older, the ORAC values and total phenolic contents decreased. The results showed a linear correlation between total phenolic content and ORAC activity for fruits and leaves. For ripe berries, a linear relationship existed between ORAC values and anthocyanin content. Of the ripe fruits tested, on the basis of wet weight of fruit, cv. Jewel black raspberry and blackberries may be the richest source for antioxidants. On the basis of the dry weight of fruit, strawberries had the highest ORAC activity followed by black raspberries (cv. Jewel), blackberries, and red raspberries.
A Framework for the Acquisition, Processing and Interactive Display of High Quality 3D Models (2001)

This tutorial highlights some recent results on the acquisition and\ninteractive display of high quality 3D models. For further use in\nphotorealistic rendering or object recognition, a high quality\nrepresentation must capture two different things: the shape of the\nmodel represented as a geometric description of its surface and on the\nother hand the appearance of the material or materials it is made of,\ne.g. the object's color, texture, or reflection properties.\n\nThe tutorial shows how computer vision and computer graphics\ntechniques can be seamlessly integrated into a single framework for\nthe acquisition, processing, and interactive display of high quality\n3D models.
Two separate DNA sequences within oriC participate in accurate chromosome segregation in Bacillus subtilis (2002)

Current views of bacterial chromosome segregation vary in respect of the likely presence or absence of an active segregation mechanism involving a mitotic-like apparatus. Furthermore, little is known about cis-acting elements for chromosome segregation in bacteria. In this report, we show that two separate DNA regions, a 3' coding region of dnaA and the AT-rich sequence between dnaA and dnaN (the initial opening site of duplex DNA during replication), are necessary for efficient segregation of the chromosome in Bacillus subtilis. When a plasmid replicon was integrated into argG, far from oriC, on the chromosome and then the oriC function was disrupted, the oriC-deleted mutant formed anucleate cells at 5% possibly because of defects in chromosome segregation. However, when the two DNA sequences were added near oriN, frequency of anucleate cells decreased to 1%. In these cells, the origin (argG) regions were localized near cell poles, whereas they were randomly distributed in cells without the two DNA sequences. These results suggest that the two DNA sequences in and downstream of the dnaA gene participate in correct positioning of the replication origin region within the cell and that this function is associated with accurate chromosome segregation in B. subtilis.
M-tree: An Efficient Access Method for Similarity Search in Metric Spaces (1997)

A new access meth d, called M-tree, is proposed to organize and search large data sets from a generic &amp;quot;metric space&amp;quot;, i.e. whE4 object proximity is only defined by a distance function satisfyingth positivity, symmetry, and triangle inequality postulates. We detail algorith[ for insertion of objects and split management, whF h keep th M-tree always balanced - severalheralvFV split alternatives are considered and experimentally evaluated. Algorithd for similarity (range and k-nearest neigh bors) queries are also described. Results from extensive experimentationwith a prototype system are reported, considering as th performance criteria th number of page I/O&amp;apos;s and th number of distance computations. Th results demonstratethm th Mtree indeed extendsth domain of applicability beyond th traditional vector spaces, performs reasonably well inhE[94Kv#E44V[vh data spaces, and scales well in case of growing files. 1
Synthesis and optical sensing properties of a boronic acid appended rhenium(I) complex for sugar (1998)

A rhenium(I) complex with boronic acid pendant is synthesized and characterized; the complex is shown to exhibit pH dependent electronic absorption characteristics; the photophysical properties and sugar sensing behaviour are also investigated.
Dynamics Analysis and Control of a Holonomic Vehicle With a Continuously Variable Transmission (2000)

This paper presents kinematic and dynamic analysis of a holonomic vehicle with continuously-variable transmission. Four ball wheels, independently actuated by DC motors, enable for moving the vehicle in any direction within the plane and rotating it around its center. The angle between the two beams holding the balls can be changed to alter the gear ratio and other dynamic characteristics of the vehicle. This feature is exploited in augmenting the vehicle stability, optimizing output power, selecting an appropriate gear ratio, and in impedance matching. A simple adaptive friction-compensation-based controller is proposed to handle the complex friction properties.
Separation of pyrroloimidazoles from indo-pacific marine sponges by high-speed countercurrent distribution (1989)

High-speed countercurrent distribution (HSGCD) with a multilayer coil plant centrifuge has been used for the isolation of pyrrololactams 1-3 from two marine sponges (Axinella sp. and Hymeniacidon sp.)
Neonatal mortality following transfusion of red cells with high plasma potassium levels (1993)

The death of a neonatal infant following cardiac surgery and the transfusion of packed red cells (RBCs) with high plasma potassium levels is reported. The patient had been diagnosed at 2 weeks of age as having multiple cardiac malformations. During cardiopulmonary bypass surgery, multiple units of packed RBCs less than 5 days old were transfused. In response to a "stat" order and after depletion of stock units prepared for neonatal usage, a 32-day-old unit of packed RBCs was issued for transfusion. After approximately 60 mL was rapidly transfused from this unit, the patient experienced cardiac arrest. Serum potassium concentration after transfusion and before death was 8.9 mmol per L. Plasma potassium concentration in the remainder of the transfused packed RBC unit was approximately 60 mmol per L. A model was created to calculate the posttransfusion plasma potassium concentration, and close correlation was found between the model and the observed potassium concentration, which assumes that the potassium load had not yet been distributed to the extravascular and intracellular fluid compartments. It is concluded that the transfusion of relatively large volumes of RBCs be limited to fresh packed RBCs or to packed RBCs that have been saline washed, to minimize the complications of electrolyte disturbances.
Design and Synthesis of Novel N-Hydroxy-Dihydronaphthyridinones as Potent and Orally Bioavailable HIV-1 Integrase Inhibitors (2011)

HIV-1 integrase (IN) is one of three enzymes encoded by the HIV genome and is essential for viral replication, and HIV-1 IN inhibitors have emerged as a new promising class of therapeutics. Recently, we reported the synthesis of orally bioavailable azaindole hydroxamic acids that were potent inhibitors of the HIV-1 IN enzyme. Here we disclose the design and synthesis of novel tricyclic N-hydroxy-dihydronaphthyridinones as potent, orally bioavailable HIV-1 integrase inhibitors displaying excellent ligand and lipophilic efficiencies.
Hoxa-5 in mouse developing lung: cell-specific expression and retinoic acid regulation (2000)

Hoxa-5 is a homeobox gene that is highly expressed in the developing mouse lung. However, little is known about the molecular mechanisms controlling expression. We characterized the ontogeny of Hoxa-5 gene and protein expressions during lung development and then studied the cell-specific effects of retinoic acid (RA) on Hoxa-5 mRNA in fetal lung fibroblasts and MLE-12 mouse lung epithelial cells. Strong but constant Hoxa-5 gene and protein expressions were detected from mouse lung on embryonic day 13.5 to postnatal day 2. At baseline, the gene was strongly expressed in the fibroblasts of day 17.5 fetal mouse lungs. A very weak but reproducible expression was present in the MLE-12 cells. RA stimulated gene expression in both cell types in a time- and dose-dependent manner. Peak expression occurred much later in the MLE-12 cells compared with that in fibroblasts. Cycloheximide and actinomycin D treatment studies suggested that the differences in RA effect on each cell type may involve the presence of a repressor that can be overcome by RA.
Selective Inhibitors of the Serine Protease Plasmin:  Probing the S3 and S3‘ Subsites Using a Combinatorial Library (2005)

A combinatorial library of 400 serine protease inhibitors with the general structure Cbz-X(aa)-Trp-cyclohexanone-Trp-Y(aa)-OH has been constructed. The library was synthesized on the solid phase using mix-and-split synthesis, where 20 different amino acids were incorporated at both the X(aa) and Y(aa) positions. These two positions correspond to the S3 and S3' subsites of the active site. Iterative deconvolution was used to identify hits from the library. The library was screened against four serine proteases: plasmin, kallikrein, thrombin, and trypsin. Seven inhibitors from the library that showed promising activities were resynthesized using solution-phase methods. Four of these compounds were good inhibitors of plasmin with IC(50) values in the range of 2.7-3.6 microM. The most potent of these inhibitors showed >150-fold selectivity for plasmin when compared to the other three serine proteases.
Two-color Quantitative Multiplex Methylation-Specific PCR (2006)

In recent years, several methylation-specific PCR-based techniques have been developed to identify and characterize hypermethylation of CpG dinucleotides with the primary goal of elucidating a better understanding of the role of DNA methylation in important biological processes, such as chromosome X inactivation and carcinogenesis. The specificity of methylation-specific PCR (MSP) techniques relies on amplifying sodium bisulfite-treated DNA with primers specific to predicted sequences of unmethylated and methylated DNA within the gene of interest. In the past, unmethylated and methylated reactions were singleplex and performed in separate wells. In this paper we report a modification of the real-time quantitative multiplex MSP (QM-MSP) technique of Fackler and colleagues that can be applied to any real-time MSP experiment. Although co-amplification with multiple fluorophores is common in standard reverse transcription PCR (RT-PCR), MSP presents unique challenges both mechanistically and operationally that must be overcome in order to successfully co-amplify two methylation-specific targets. In this two-color modification, unmethylated and methylated primer/probe sets are successfully co-amplified in the same reaction using FAM- and VIC-labeled probes. Our modification decreases the cost and time of each real-time experiment by allowing increased throughput of clinical samples and by doubling either the number of genes or the number of samples that can be analyzed per real-time plate.
A monoclonal antibody that recognizes a neo-antigen exposed in the E domain of fibrin monomer complexed with fibrinogen or its derivatives: its application to the measurement of soluble fibrin in plasma (1996)

Using urea-solubilized human fibrin monomer as an immunogen, we raised in mice a battery of monoclonal antibodies that reacted with the immunogen but not with urea-treated or native fibrinogen. Although they all failed to react with acid-solubilized fibrin monomer (acid-FM) alone, an antibody designated as IF-43 was found to recognize acid-FM, which was bound with fibrinogen or its derivatives to form a 1:2 complex of soluble fibrin. The epitope for this antibody, thus, appears to be exposed most probably by conformation changes induced in the acid-FM molecule upon formation of the complex. Because IF-43 was able to recognize fibrin-derived plasmic fragment E treated with urea but not the thrombin- and urea-treated amino-terminal disulfide knot of fibrinogen, the presence of the A alpha (52-78) residue segment seems to be prerequiste for the epitope expression. The antibody was found to react with soluble fibrin monomer spiked to normal plasma dose-dependently up to 200 micrograms/mL. By an aggregation assay using latex beads coated with IF-43, we found that concentrations of soluble fibrin monomer in plasma derived from patients with thrombotic diseases were mostly elevated, but not necessarily correlated with those of the D-dimer, reflecting another aspects of the disease. Furthermore, the soluble fibrin monomer in plasma derived from patients with thrombotic diseases was found to be depleted solely of the A peptides, but not the B peptides, based on its subunit polypeptide compositions lacking the beta-chain on immunoblotting.
A Voigt effect based 3D vector magnetometer (2019)

We describe a method to dispersively detect all three vector components of an external magnetic field using alkali atoms based on the Voigt effect. Our method relies on measuring the linear birefringence of the radio frequency dressed atomic medium via polarization homodyning. This gives rise to modulated polarization signals at the first and second harmonic of the dressing frequency. The vector components of the external magnetic field are mapped onto the quadratures of these harmonics. We find that our scheme can be utilised in both cold and hot atomic gases to detect such external fields in shielded and unshielded environments. In the shielded hot vapour case we achieve field sensitivities well below 1~pT/√ Hz range for all 3 vector components, using pump-probe cycles with 125 Hz repetition rate, and limited by the short coherence time of the cell. Finally, our scheme has a simple single axis beam geometry making it advantageous for miniature magnetic field sensors.
Improved Generation of Germline‐Competent Embryonic Stem Cell Lines from Inbred Mouse Strains (2003)

Genetically altered mice may exhibit highly variable phenotypes due to the variation in genetic background, which can only be circumvented by generation of inbred, isogenic gene-targeted and control mice. Here we report that an embryonic stem (ES) cell culture medium conditioned by a rabbit fibroblast cell line transduced with genomic rabbit leukemia inhibitory factor allows efficient derivation and maintenance of ES cell lines from all of 10 inbred mouse strains tested, including some that were presumed to be nonpermissive for ES cell derivation (129/SvEv, 129/SvJ, C57BL/6N, C57BL/6JOla, CBA/CaOla, DBA/2N, DBA/1Ola, C3H/HeN, BALB/c, and FVB/N). Germline transmission was established by blastocyst injection of established ES cell lines after 10 or more passages from all of seven strains tested (129/SvJ, C57BL/6N, C57BL/6JOla, DBA/2N, DBA/1Ola, BALB/c, and FVB/N), by diploid aggregation of ES cell lines from all of four strains tested (129/SvEv, C57BL/6N, CBA/ CaOla, and FVB/N), or by tetraploid aggregation of ES cell lines from all of three strains tested (129/SvEv, C57BL/6N, and CBA/CaOla). Thus, these inbred ES cell lines may constitute useful tools to derive gene-targeted mice and isogenic controls in selected genetic backgrounds.
The Bethesda System for Reporting Thyroid Cytopathology (2009)

To address terminology and other issues related to thyroid fine-needle aspiration (FNA), the National Cancer Institute (NCI) hosted the NCI Thyroid FNA State of the Science Conference. The conclusions regarding terminology and morphologic criteria from the NCI meeting led to the Bethesda Thyroid Atlas Project and form the framework for The Bethesda System for Reporting Thyroid Cytopathology (TBSRTC). For clarity of communication, TBSRTC recommends that each report begin with 1 of 6 general diagnostic categories. The project participants hope that the adoption of this flexible framework will facilitate communication among cytopathologists, endocrinologists, surgeons, radiologists, and other health care providers; facilitate cytologic-histologic correlation for thyroid diseases; facilitate research into the epidemiology, molecular biology, pathology, and diagnosis of thyroid diseases; and allow easy and reliable sharing of data from different laboratories for national and international collaborative studies.
Assessing the risk of early multiple sclerosis in patients with clinically isolated syndromes: the role of a follow up MRI (2001)

Serial imaging in patients with clinically isolated syndromes improved the positive predictive value, sensitivity, and specificity of MRI for the development of early multiple sclerosis and also identified patients at a lower risk of early multiple sclerosis than would have been expected from their abnormal baseline MRI. Selection of patients with clinically isolated syndromes for therapeutic intervention or clinical trials may benefit from serial MRI, to target those at greatest risk of early development of multiple sclerosis.