gebhart/patrepeval huggingface dataset:
Eyesafe pulsed microchip laser using semiconductor saturable absorber mirrors (1998)

We passively Q-switched a diode-pumped Er/Yb:glass microchip laser at a 1.535 μm wavelength using semiconductor saturable absorber mirrors and demonstrated pulses as short as 1.2 ns. By varying the design parameters of the saturable absorber, the pump power, and the pump spot size, we achieved repetition rates from 300 Hz to 100 kHz with pulse energies up to 4 μJ.
Development of a New Therapeutic Approach to B Cell Malignancy. The Induction of Immunity by the Host Against Cell Surface Receptor on the Tumor (1989)

(1989). Development of a New Therapeutic Approach to B Cell Malignancy. The Induction of Immunity by the Host Against Cell Surface Receptor on the Tumor. International Reviews of Immunology: Vol. 4, No. 4, pp. 251-270.
Transurethral Microwave Heating of the Prostate—Or from Hyperthermia to Thermotherapy (1991)

The authors studied microwave delivery by a flexible applicator providing simultaneous cooling for anesthesiafree outpatient single session treatment of benign prostatic hyperplasia (BPH) following preclinical trials in dogs and humans. The goal of transurethral microwave thermotherapy (TUMT) was to raise the temperature within the prostate to more than 45°C while maintaining the urethral temperature below 45°C. Histologically, the urethral mucosa and periurethral tissues were well preserved. There was a sharp transition (1-2 mm) to the microwave-treated area, where the normal cellular arrangement disappeared and small blood vessels were thrombosed. Smooth-muscle cells were seen to be more heat sensitive than glandular tissue. In 37 patients with BPH, the new device (Prostatron) produced significant improvements in the symptom score peak/low and post residual volume at 3 months. Seven patients required an indwelling catheter for 1 week after treatment, but four then voided satisfactorily. No infections occurred. Continued followup suggests enduring benefit.
Synthesis, photochemistry and enzymology of 2-O-(2-nitrobenzyl)-D-glucose, a photolabile derivative of D-glucose (1993)

Alkylation of the dibutylstannylene derivative of methyl 4,6-O-benzylidene-α-D-glucopyranoside 2a with 2-nitrobenzyl bromide gave a mixture of 2-O- and 3-O-(2-nitrobenzyl) derivatives 3b and 4b in the ratio ∼ 3 : 1. Chromatographic separation and removal of the protecting groups gave the title compound 1. Regiospecific synthesis by 2-nitrobenzylation of the monoalcohol 8a was examined but could not be achieved efficiently. Compound 1 was neither a substrate for nor an inhibitor of the coupled hexokinase/glucose-6-phosphate dehydrogenase enzyme system. On photolysis, it was converted into free glucose with 1 : 1 stoichiometry.
Implementing a unified approach to family-based tests of association (2000)

We describe a broad class of family-based association tests that are adjusted for admixture; use either dichotomous or measured phenotypes; accommodate phenotype-unknown subjects; use nuclear families, sibships or a combination of the two, permit multiple nuclear families from a single pedigree; incorporate di- or multi-allelic marker data; allow additive, dominant or recessive models; and permit adjustment for covariates and gene-by-environment interactions. The test statistic is basically the covariance between a user-specified function of the genotype and a user-specified function of the trait. The distribution of the statistic is computed using the appropriate conditional distribution of offspring genotypes that adjusts for admixture.
Hypogelsolinemia, a disorder of the extracellular actin scavenger system, in patients with multiple sclerosis (2010)

The decrease of GSN concentration in blood and CSF of MS subjects suggests that this protein may be involved in chronic inflammation associated with neurodegeneration. Additionally, the results presented here suggest the possible utility of GSN evaluation for diagnostic purposes. Reversing plasma GSN deficiency might represent a new strategy in MS treatment.
Site-specific integrase-mediated transgenesis in mice via pronuclear injection (2011)

Microinjection of recombinant DNA into zygotic pronuclei has been widely used for producing transgenic mice. However, with this method, the insertion site, integrity, and copy number of the transgene cannot be controlled. Here, we present an integrase-based approach to produce transgenic mice via pronuclear injection, whereby an intact single-copy transgene can be inserted into predetermined chromosomal loci with high efficiency (up to 40%), and faithfully transmitted through generations. We show that neighboring transgenic elements and bacterial DNA within the transgene cause profound silencing and expression variability of the transgenic marker. Removal of these undesirable elements leads to global high-level marker expression from transgenes driven by a ubiquitous promoter. We also obtained faithful marker expression from a tissue-specific promoter. The technique presented here will greatly facilitate murine transgenesis and precise structure/function dissection of mammalian gene function and regulation in vivo.
Assessing Variation in US Soybean Seed Composition (Protein and Oil) (2019)

Soybean [<i>Glycine max</i> (L.) Merr.] seed composition and yield are a function of genetics (G), environment (E), and management (M) practices, but contribution of each factor to seed composition and yield are not well understood. The goal of this synthesis-analysis was to identify the main effects of G, E, and M factors on seed composition (protein and oil concentration) and yield. The entire dataset (13,574 data points) consisted of 21 studies conducted across the United States (US) between 2002 and 2017 with varying treatments and all reporting seed yield and composition. Environment (E), defined as site-year, was the dominant factor accounting for more than 70% of the variation for both seed composition and yield. Of the crop management factors: (i) delayed planting date decreased oil concentration by 0.007 to 0.06% per delayed week (<i>R</i> <sup>2</sup>∼0.70) and a 0.01 to 0.04 Mg ha<sup>-1</sup> decline in seed yield per week, mainly in northern latitudes (40-45 N); (ii) crop rotation (corn-soybean) resulted in an overall positive impact for both seed composition and yield (1.60 Mg ha<sup>-1</sup> positive yield difference relative to continuous soybean); and (iii) other management practices such as no-till, seed treatment, foliar nutrient application, and fungicide showed mixed results. Fertilizer N application in lower quantities (10-50 kg N ha<sup>-1</sup>) increased both oil and protein concentration, but seed yield was improved with rates above 100 kg N ha<sup>-1</sup>. At southern latitudes (30-35 N), trends of reduction in oil and increases in protein concentrations with later maturity groups (MG, from 3 to 7) was found. Continuing coordinated research is critical to advance our understanding of G × E × M interactions.
Fundamental Neurological Research and Human Neurosurgery Using Intense Ultrasound (1960)

Focused high intensity ultrasound can be used, under accurately controlled dosage conditions, to produce either temporary or permanent changes in practically any desired brain structure. Volumes of tissue smaller than one tenth of a cubic millimeter can be affected in deep brain structures of experimental animals (cats and monkeys), and regions as large as desired can be changed by moving the focal spot of the ultrasonic beams through an appropriately chosen path. The changes can be induced without adversely affecting intervening brain structure and without interrupting the vascular system even within the site in which irreversible or permanent changes in the neural components are produced. The selectivity and absence of effects on the intervening tissue make focused ultrasound a tool of considerable power for investigating basic brain mechanisms. It is now being used in an extensive experimental animal program involving neuroanatomical, behavioral and physiological studies. It is also being used to study and modify the symptoms of various neurological disorders in humans. The signs and symptoms which have been and are under investigation in human patients at the present time include abnormal movements (tremor and nonpatterned), muscular rigidity), intractable pain (following amputations, cerebral vascular accidents, the acute phase of herpes zoster) and hypersensitivity to stimulation of the body surface.
pH-dependent Gating of ROMK (Kir1.1) Channels Involves Conformational Changes in Both N and C Termini (1998)

ROMK channels (Kir1.1) are members of the superfamily of inward rectifier potassium channels (Kir) and represent the channels underlying K+ secretion in the kidney. As their native counterparts, Kir1.1 channels are gated by intracellular pH, with acidification leading to channel closure. Although a lysine residue (Lys80) close to the first hydrophobic segment M1 has been identified as the pH sensor, little is known about how opening and closing of the channel is accomplished. Here we investigate the gating process of Kir1.1 channels exploiting their state-dependent modification by water-soluble oxidants and sulfhydryl reagents. Mutagenesis of all intracellular cysteines either alone or in combination revealed two residues targeted by these reagents, one in the N terminus (Cys49) and one in the C terminus (Cys308) of the channel protein. Both sites reacted with the thiol reagents only in the closed state and not in the open state. These results indicate that pH-dependent gating of Kir1.1 channels involves movement of protein domains in both N and C termini of the Kir1.1 protein.
Platelet-Rich Plasma: Quantification of Growth Factor Levels and the Effect on Growth and Differentiation of Rat Bone Marrow Cells (2006)

Platelet-rich plasma (PRP) is a new application of tissue engineering and a developing area for clinicians and researchers. It is a storage vehicle of growth factors (GFs) such as platelet-derived growth factor (PDGF)- AA, -BB, -AB; transforming growth factor (TGF)-beta1 and -2; platelet-derived epidermal growth factor (PDEGF); platelet-derived angiogenesis factor (PDAF); insulin growth factor-1 (IGF-1); and platelet factor- 4 (PF-4), which are known to influence bone regeneration. However, animal and clinical studies reveal different results with the use of PRP and its effect on bone healing. This could be due to the differences between species, that is, differences between species in GF concentrations or variation in presence of GFs between the various PRPs. In this study, rat bone marrow cells were cultured in PRP-coated wells or in uncoated wells for 16 days in osteogenic medium, and analyzed on cell growth (DNA content) and cell differentiation (alkaline phosphatase [ALP] activity, calcium content, scanning electron microscopy, and QPCR). The concentrations of TGF-beta1, PDGF-AA, PDGF-AB, and PDGF-BB in rat, goat, and human PRP were subsequently determined. The results showed that PRP stimulated initial cell growth and had no effect on ALP activity. The calcium measurements showed a significant increase in calcium at days 8, 12, and 16. The real-time PCR results showed that PRP upregulated osteocalcin at day 1 and collagen type I at day 8. Overall, the immunoassays revealed that human PRP contained higher concentrations of growth factors per platelet compared to rat and goat PRP. Goat PRP showed higher concentrations of growth factors per platelet as compared to rat PRP except for PDGF-BB, which had a higher concentration in rat PRP. TGF-beta1 was the most abundant growth factor in all 3 PRPs. On the basis of our results, we conclude that platelet-rich plasma contains osteo-inductive growth factors, which are probably species related. However, we cannot generalize the results because of large intraspecies variations. Further, we conclude that rat PRP gel stimulates initial growth and differentiation of rat bone marrow cells in vitro.
Periodicity of Female Sex Pheromone Titer and Release in Heliothis subflexa and H. virescens (Lepidoptera: Noctuidae) (1991)

Amounts of sex pheromone components in extracts of pheromone glands of virgin female Heliothis virescens (F.) and Heliothis subflexa (Guenee) and in the emissions of pheromone from individual females were sampled every 2 h of a 10-h scotophase and analyzed by capillary gas chromatography (GC) and GC-mass spectroscopy. Quantities of pheromone components in the emitted volatiles of H. subflexa from Florida were greatest during the 4th to 6th-h collection interval, whereas glands extracted with hexane at the 6th h contained the largest amounts of these chemicals. Pheromone-release behavior (calling) was at its maximum during the interval of the 4th to 6th h. The chemicals detected in the volatile collections from H. subflexa were: (Z)-11-hexadecenal (Z11-16:A1), (Z)-9-hexadecenal (Z9-16:A1), hexadecanal, (Z)-11-hexadecen-1-ol acetate, (Z)-9-hexadecen-1-ol acetate, (Z)-7- hexadecen-1-ol acetate, (Z)-11-hexadecen-1-ol (Z11-16:OH), and (Z)-9-hexadecen-1-ol. The pheromonal chemicals of H. virescens from Mississippi occurred in greatest quantity in emissions collected during the 6th to 8th h and 8th to 10th h intervals, and in the glands extracted at 8 and 10 h into the scotophase. H. virescens females produced and released pheromone over a broader period of time than H. subflexa females. The chemicals detected in the volatile collections from H. virescens were: tetradecanal (14: A1), (Z)-9-tetradecenal (Z9-14: A1), 16: A1, Z9-16: Al, Z11-16: A1, and Z11-16: OH. The alcohol/aldehyde and acetate/aldehyde ratios present in the extracts of glands from H. subflexa varied during the dark period, whereas those ratios in H. virescens were relatively constant. The ratios, relative to Z11-16:A1, of the acetates and of Z9-16:OH in extracts of glands of H. subflexa from Florida differed significantly from those of females from the U.S. Virgin Islands; the U.S. Virgin Islands glands contained 2.2 times more total amount of pheromonal chemicals than those from Florida. The ratio of Z11-16:OH, a critical chemical in sexual communication of H. subflexa , did not differ between the gland extracts obtained from two populations. Heliothis virescens from Mississippi and U.S. Virgin Islands contained similar amounts of total pheromonal components within their glands, and the relative ratios of components were the same between the populations.
Telomere Terminal Transferase Activity from Euplotes crassus Adds Large Numbers of TTTTGGGG Repeats onto Telomeric Primers (1989)

A telomere terminal transferase activity was identified in developing macronuclear extracts from Euplotes crassus. The activity was essentially unregulated in vitro: up to 50 tandem repeats of the Euplotes telomeric repeat sequence TTTTGGGG were added onto synthetic telomeric oligonucleotide primers. Both the structure of the telomere substrate and its 3'-terminal sequence were recognized. The activity was destroyed by low concentrations of RNase A.
Biochemical effects in normal and stone forming rats treated with the ripe kernel juice of plantain (musa paradisiaca). (1993)

The effect of Musa paradisiaca stem kernel juice was investigated in experimental urolithiatic rats. Stone forming rats exhibited a significant elevation in the activities of two oxalate synthesizing enzymes - Glycollic acid oxidase and Lactate dehydrogenase. Deposition and excretion of stone forming constituents in kidney and urine were also increased in these rats. The enzyme activities and the level of crystalline components were lowered with the extract treatment. The extract also reduced the activities of urinary alkaline phosphatase, lactate dehydrogenase, r-glutamyl transferase, inorganic pyrophosphatase and β-glucuronidase in calculogenic rats. No appreciable changes were noticed with leucine amino peptidase activity in treated rats.
Characterization of a human 5‐hydroxytryptamine3 receptor type A (h5‐HT3R‐AS) subunit stably expressed in HEK 293 cells (1996)

1. A cloned cDNA encoding a human 5-hydroxytryptamine3 receptor type A subunit (h5-HT3R-As) was transfected into human embryonic kidney (HEK 293) cells maintained in cell culture and a stable cell line expressing a high density of the recombinant receptor was selected. 2. Membrane homogenates prepared from transfected, but not untransfected, cells exhibited a homogeneous and saturable population (Bmax = 4.49 +/- 0.46 pmol mg-1 protein) of sites that bound the radiolabelled 5-HT3 receptor antagonist, [3H]-granisetron with high affinity (pKD = 8.87 +/- 0.08). Kinetic studies (at 37 degrees C) revealed rapid association (kappa +1 4.76 +/- 0.3 x 10(8) M-1 min-1) and dissociation (kappa -1 = 0.21 +/- 0.003 min-1) of the radioligand. 3. Selective and non-selective 5-HT3 receptor ligands competed for [3H]-granisetron binding with a rank order of potency (granisetron > ondansetron > meta-chlorophenylbiguanide > 5-HT > 2-methyl-5-HT > metoclopramide > > phenylbiguanide > cocaine > (+)-tubocurarine) identical to that established for 5-HT3 receptors endogenous to the human CNS. 4. In electrophysiological recordings performed on transfected cells, voltage-clamped at a holding potential of -60 mV, locally applied 5-HT (10 microM) evoked transient inward current responses that reversed in sign at a potential of -1.0 +/- 1.1 mV. Such responses were antagonized in a reversible manner by granisetron (1 nM). 5. The construction of a stable cell line expressing a high density of recombinant human 5-HT3 receptors which display appropriate pharmacology and function will assist in the further characterization of this receptor subtype and the exploration of species differences in 5-HT3 receptor pharmacology.
Graph-Based Background Suppression for Scene Text Detection (2012)

Detecting text in video or natural scene image is quite challenging due to the complex background, various fonts and illumination conditions. The preprocessing period, which suppresses the nontext areas so as to highlight the text areas, is the basis for further text detection. In this paper, a novel graph-based background suppression method for scene text detection is proposed. Considering each pixel as a node in the graph, our approach incorporates pixel-level and context-level features into a graph. Various factors contribute to the unary and pair wise cost function which is optimized via max-flow/min-cut algorithm [16] to get a binary image whose nontext pixels are suppressed so that text pixels are highlighted. Furthermore, the proposed background suppression method could be easily combined with other detection methods to improve the performance. Experimental results on ICDAR 2011 competition dataset show promising performance.
Light‐Responsive Biomaterials: Development and Applications (2009)

Novel biomaterials are beneficial to the growing fields of drug delivery, cell biology, micro-devices, and tissue engineering. With recent advances in chemistry and materials science, light is becoming an attractive option as a method to control biomaterial behavior and properties. In this Feature Article, we explore some of the early and recent advances in the design of light-responsive biomaterials. Particular attention is paid to macromolecular assemblies for drug delivery, multi-component surface patterning for advanced cell assays, and polymer networks that undergo chemical or shape changes upon light exposure. We conclude with some remarks about future directions of the field.
Protein Quality Control in the Bacterial Periplasm (2010)

Protein quality control involves sensing and treatment of defective or incomplete protein structures. Misfolded or mislocalized proteins trigger dedicated signal transduction cascades that upregulate the production of protein quality-control factors. Corresponding proteases and chaperones either degrade or repair damaged proteins, thereby reducing the level of aggregation-prone molecules. Because the periplasm of gram-negative bacteria is particularly exposed to environmental changes and respective protein-folding stresses connected with the presence of detergents, low or high osmolarity of the medium, elevated temperatures, and the host's immune response, fine-tuned protein quality control systems are essential for survival under these unfavorable conditions. This review discusses recent advances in the identification and characterization of the key cellular factors and the emerging general principles of the underlying molecular mechanisms.
Effects of Polycystic Ovary Syndrome (PCOS), Sex Hormones, and Obesity on Circulating miRNA-21, miRNA-27b, miRNA-103, and miRNA-155 Expression (2013)

The present results suggest that miRNAs that play an important role in metabolic and immune system processes are influenced by obesity and circulating androgen concentrations.
Discriminative Learning of Sum-Product Networks (2012)

Discriminatively-trained probabilistic models often outperform their generative counterparts on challenging tasks in computer vision and NLP. Conditional random elds have been a predomi-nant approach, but adapting them to richer structures further complicates learning with approximate inference [4]. Deep Networks have typically required both a generative and discriminative objec-tive involving approximate inference. The discriminative objective is usually reected in the use of backpropagation through softmax layers or support vector machines over network variables. The Sum-Product Network is a promising new deep architecture that can perform fast, exact inference on a representation that is broader than existing tractable graphical models [5]. For the rst time, we combine the advantages of SPNs with the advantages of discriminative learn-ing. We demonstrate the conditions under which an SPN represents the conditional partition func-tion and provide a discriminative training algorithm. In this setting, SPN nodes that exclusively cover variables conditioned upon need not be consistent or complete. This admits a larger class of discriminative SPNs with speedy inference. We dene an SPN that models the joint probability of three disjoint sets of hidden, query, and given variables: H, Y, and X respectively. The conditional probability of the query given the data is naturally P (Y jX) = P (Y;X) P (X) = P h
Epithelium percentage estimation facilitates epithelial quantitative protein measurement in tissue specimens (2013)

Our results show that estimation of tissue epithelium percentage using our color-based segmentation method correlates well with pathologists' estimation of tissue epithelium percentages. The epithelium contents estimated by color-based segmentation may be useful in immuno-based analysis or clinical proteomic analysis of tumor proteins. The codes used for epithelium estimation as well as the micrographs with estimated epithelium content are available online.
xBSP: an efficient BSP implementation for cLAN (2002)

Virtual Interface Architecture (VIA) is a light-weight protocol for protected user-level zero-copy communication. In spite of the high performance of VIA, the previous MPI implementation for GigaNet's cLAN revealed low communication performance. The main sources of the low performance are the discrepancy of communication model between MPI and VIA and multi-threading overhead. We propose a novel implementation of the Bulk Synchronous Parallel (BSP) programming library for VIA called xBSP for overcoming such problems. To the best of our knowledge, xBSP is the first implementation of the BSP library for VIA. xBSP demonstrates that selecting a proper library is important to exploit the features of light-weight protocols. The intensive use of RDMA operation leads to high performance, close to the native VIA performance with respect to round trip delay and bandwidth. Based on the study of the effects of multithreading, memory registration, and completion policy on performance, we could obtain an efficient BSP implementation for cLAN, which is confirmed by experimental results.