gebhart/patrepeval huggingface dataset:
Optical coherence tomography reveals light-dependent retinal responses in Alzheimer’s disease (2020)

Spectral-domain optical coherence tomography (SD-OCT) is an accessible clinical tool for measuring structural changes to the retina, and increasingly as a biomarker for brain-predominant neurodegenerative diseases like Alzheimer's. Information about retinal function can also be extracted from OCT images, but is under-studied, with literature examples often employing challenging protocols or requiring specialized hardware. The first goal of this study was to verify that functional retinal imaging was feasible with a commercially-available SD-OCT device and a clinically practical protocol. Inspired by methods from other functional imaging modalities, we acquired images while repeatedly cycling lights on and off, and spatially normalized retinas to facilitate intra- and inter-individual analyses. In eight healthy young adults, light-dependent increases in reflectivity were easily demonstrated at photoreceptor inner and outer segments, changing by ~7% in bright light and ~3% in dim light. Bright light elicited a subtle (~2%) but consistent light-dependent decrease in reflectivity through much of the rest of the retina, including the avascular outer nuclear layer (ONL). We speculated that some of these changes are influenced by glial function - as through water management - a topic of high interest in neurodegenerative diseases that may involve the glymphatic system. Functional abnormalities in patients with antibodies against aquaporin-4 (n ​= ​3) supported this interpretation. We next compared patients with early-onset Alzheimer's disease (n ​= ​14) to age-matched controls (n ​= ​14), revealing that patients had a relatively exaggerated light-induced change in ONL reflectivity (p ​< ​0.05). Because these measurements can be obtained within 30 ​min, regular use in research and limited clinical settings is feasible.
Surgical Anatomy of the Bile Ducts at the Hepatic Hilum as Applied to Living Donor Liver Transplantation (2003)

In harvesting the right liver from a donor without a right hepatic duct, 2 or more bile duct stumps will be present in the plane of transection in the graft in 3 patterns based on their relation to the portal vein. Accurate knowledge of the variations in the hepatic confluence is essential for successful living donor liver transplantation.
Conserved epitope on influenza-virus hemagglutinin head defined by a vaccine-induced antibody (2017)

Circulating influenza viruses evade neutralization in their human hosts by acquiring escape mutations at epitopes of prevalent antibodies. A goal for next-generation influenza vaccines is to reduce escape likelihood by selectively eliciting antibodies recognizing conserved surfaces on the viral hemagglutinin (HA). The receptor-binding site (RBS) on the HA "head" and a region near the fusion peptide on the HA "stem" are two such sites. We describe here a human antibody clonal lineage, designated CL6649, members of which bind a third conserved site ("lateral patch") on the side of the H1-subtype, HA head. A crystal structure of HA with bound Fab6649 shows the conserved antibody footprint. The site was invariant in isolates from 1977 (seasonal) to 2012 (pdm2009); antibodies in CL6649 recognize HAs from the entire period. In 2013, human H1 viruses acquired mutations in this epitope that were retained in subsequent seasons, prompting modification of the H1 vaccine component in 2017. The mutations inhibit Fab6649 binding. We infer from the rapid spread of these mutations in circulating H1 influenza viruses that the previously subdominant, conserved lateral patch had become immunodominant for individuals with B-cell memory imprinted by earlier H1 exposure. We suggest that introduction of the pdm2009 H1 virus, to which most of the broadly prevalent, neutralizing antibodies did not bind, conferred a selective advantage in the immune systems of infected hosts to recall of memory B cells that recognized the lateral patch, the principal exposed epitope that did not change when pdm2009 displaced previous seasonal H1 viruses.
Regulation of human ornithine decarboxylase expression by the c-Myc.Max protein complex. (1993)

The presence of a CACGTG element within a region of the human ornithine decarboxylase (ODC) promoter located at -491 to -474 base pairs 5' to the start site of transcription suggested that the c-Myc.Max protein complex may play a role in the regulation of ODC expression during growth. Electrophoretic mobility shift assays and methylation interference analysis showed that the nuclei of WI-38 cells expressing ODC contained proteins that bound to this region of the ODC gene in a manner that correlated with growth-associated ODC expression. Also, use of antibodies against c-Myc and Max and purified recombinant c-Myc and Max protein in the electrophoretic mobility shift assay confirmed that these proteins can specifically bind this portion of the human ODC promoter. Transient transfection studies showed that increase in the level of c-Myc and/or Max led to a significant enhancement of expression of a human ODC promoter-CAT reporter construct. Moreover, treatment of actively growing WI-38 cells with an antisense oligomer to c-Myc reduced the amount of endogenous protein complex formed and the amount of endogenous ODC mRNA expressed. These studies show that the c-Myc.Max protein complex plays a role in the transcriptional regulation of human ODC in vivo.
Comparing nitrate storage and remobilization in two rice cultivars that differ in their nitrogen use efficiency (2007)

Soil nitrogen (N) is available to rice crops as either nitrate or ammonium, but only nitrate can be accrued in cells and so factors that influence its storage and remobilization are important for N use efficiency (NUE). The hypothesis that the ability of rice crops to remobilize N storage pools is an indicator of NUE was tested. When two commonly grown Chinese rice cultivars, Nong Ken (NK) and Yang Dao (YD), were compared in soil and hydroponics, YD had significantly greater NUE for biomass production. The ability of each cultivar to remobilize nitrate storage pools 24 h after N supply withdrawal was compared. Although microelectrode measurements of the epidermal sub-cellular nitrate pools in leaves and roots showed similar patterns of vacuolar remobilization in both cultivars, whole-tissue analysis showed very little depletion of storage pools after 24 h. However, leaf epidermal cell cytosolic nitrate activities were significantly higher in YD when compared with NK. Before N starvation and growing in 10 mM nitrate, the xylem nitrate activity in YD was lower than that of NK. After 24 h of N starvation the xylem nitrate had decreased more in YD than in NK. Tissue analysis of stems showed that YD had accumulated significantly more nitrate than NK, and the remobilization pattern suggested that this store is important for both cultivars. Changes in nitrate reductase activity (NRA) and expression were measured. Growing in 10 mM nitrate, NRA was undetectable in roots of both cultivars, and the leaf total NRA of equivalent leaves was similar in NK and YD. When the N supply was withdrawn, after 24 h NRA in NK was reduced to 80% but no decrease was found in YD. The proportion of NRA in an active form in YD was significantly higher than that in NK under both nitrate supply and deprivation conditions. Checking NR gene expression showed that leaf expression of OsNia1 was faster to respond to nitrate deprivation than OsNia2 in both cultivars. These measurements are discussed in relation to cultivar differences and physiological markers for NUE in rice.
Statistical simulation: Adding efficiency to the computer designer's toolbox (2003)

Statistical simulation enables quick and accurate design decisions in the early stages of computer design, at the processor and system levels. it complements detailed but slower architectural simulations, reducing total design time and cost.
Total mass balances of SO2-ethanol-water (SEW) fractionation of forest biomass (2011)

Abstract The overall target of this project, called Bioforest, is to develop an economic process for the production of commodity chemicals from mixed forest biomass, consisting of logging residues of hardwoods (HW) and softwoods (SW) and also from recycled fibers. The aim is to dissolve the biomass lignin and to produce monosugars based on hemicelluloses and hydrolyzed cellulose in high yield. The hydrolyzate could subsequently be converted into chemicals by modified acetone-butanol-ethanol fermentation. Here, the total mass balances of SO 2 -ethanol-water fractionation of different types of biomass feedstocks, such as SW and HW biomass, and deinked pulp are presented. Chemical composition of the feedstocks, solid residues (pulps) and spent liquors of fractionation were analyzed to gain more understanding about the fractionation procedure. The analysis was focused on carbohydrates, lignin, ash, acetyl groups and sugar degradation products. It was also examined if all feedstocks could be treated simultaneously in one digester because a larger feedstock supply within an economic transport radius improves the viability of the process. The fractionation approach was successful and it can be concluded that the method presented is very versatile for future applications in lignocellulosic biorefineries.
PROCUSTE1 Encodes a Cellulose Synthase Required for Normal Cell Elongation Specifically in Roots and Dark-Grown Hypocotyls of Arabidopsis (2000)

Mathilde Fagard, Thierry Desnos, Thierry Desprez, Florence Goubet, Guislaine Refregier, Gregory Mouille, Maureen McCann, Catherine Rayon, Samantha Vernhettes, , PROCUSTE1 Encodes a Cellulose Synthase Required for Normal Cell Elongation Specifically in Roots and Dark-Grown Hypocotyls of Arabidopsis, The Plant Cell, Vol. 12, No. 12 (Dec., 2000), pp. 2409-2423
The anti-allergic drug, N-(3',4'-dimethoxycinnamonyl) anthranilic acid, exhibits potent anti-inflammatory and analgesic properties in arthritis (2007)

It is concluded that 3,4-DAA has both anti-inflammatory and analgesic properties, and may therefore be useful in filling an unmet need, in the treatment of rheumatoid and other forms of arthritis, especially in the light of its analgesic properties.
Advanced Integration Techniques on Broadband Millimeter-Wave Beam Steering for 5G Wireless Networks and Beyond (2015)

Recently, the desired very high throughput of 5G wireless networks drives millimeter-wave (mm-wave) communication into practical applications. A phased array technique is required to increase the effective antenna aperture at mm-wave frequency. Integrated solutions of beamforming/beam steering are extremely attractive for practical implementations. After a discussion on the basic principles of radio beam steering, we review and explore the recent advanced integration techniques of silicon-based electronic integrated circuits (EICs), photonic integrated circuits (PICs), and antenna-on-chip (AoC). For EIC, the latest advanced designs of on-chip true time delay (TTD) are explored. Even with such advances, the fundamental loss of a silicon-based EIC still exists, which can be solved by advanced PIC solutions with ultra-broad bandwidth and low loss. Advanced PIC designs for mm-wave beam steering are then reviewed with emphasis on an optical TTD. Different from the mature silicon-based EIC, the photonic integration technology for PIC is still under development. In this paper, we review and explore the potential photonic integration platforms and discuss how a monolithic integration based on photonic membranes fits the photonic mm-wave beam steering application, especially for the ease of EIC and PIC integration on a single chip. To combine EIC, for its accurate and mature fabrication techniques, with PIC, for its ultra-broad bandwidth and low loss, a hierarchical mm-wave beam steering chip with large-array delays realized in PIC and sub-array delays realized in EIC can be a future-proof solution. Moreover, the antenna units can be further integrated on such a chip using AoC techniques. Among the mentioned techniques, the integration trends on device and system levels are discussed extensively.
Efficient multidimensional volume rendering (1999)

In many medical fields, volume rendering is beneficial. For the effective surgery planning, interior objects as well as the surface must be rendered. However, direct volume rendering is computationally expensive and surface rendering cannot represent inside objects of the volume data. In addition, surface rendering has a disadvantage that the huge amount of generated polygons cannot be easily managed even on high-end graphics workstations. This paper presents a way of generating multi-planar imags efficiently. Multi-planar rendering consists of two parts, surface and cutting plane. To efficiently generate surface, our algorithm uses image- based rendering. Image-based rendering generates an image in constant time regardless of the complexity of the input scene. To speed up the performance, our algorithm uses intermediate image space instead of final image space. To reduce the space complexity , we use a new data structure that is based on delta-tree to represent volume. The algorithm was implemented on a Silicon Graphics Indigo 2 workstation with a single 195 MHz R10000 processor and 192MB Main Memory. For the experiments, we use 3 volume data sets, UNC head, engine and brain. Our algorithm takes 5-20 milliseconds to project reference images to the desired view. Including the warping time, 40 milliseconds are required to generate an image.
Mechanistic Studies on Three 2-Oxoglutarate-dependent Oxygenases of Flavonoid Biosynthesis (2004)

Anthocyanidin synthase (ANS), flavonol synthase (FLS), and flavanone 3beta-hydroxylase (FHT) are involved in the biosynthesis of flavonoids in plants and are all members of the family of 2-oxoglutarate- and ferrous iron-dependent oxygenases. ANS, FLS, and FHT are closely related by sequence and catalyze oxidation of the flavonoid "C ring"; they have been shown to have overlapping substrate and product selectivities. In the initial steps of catalysis, 2-oxoglutarate and dioxygen are thought to react at the ferrous iron center producing succinate, carbon dioxide, and a reactive ferryl intermediate, the latter of which can then affect oxidation of the flavonoid substrate. Here we describe work on ANS, FLS, and FHT utilizing several different substrates carried out in 18O2/16OH2, 16O2/18OH2, and 18O2/18OH2 atmospheres. In the 18O2/16OH2 atmosphere close to complete incorporation of a single 18O label was observed in the dihydroflavonol products (e.g. (2R,3R)-trans-dihydrokaempferol) from incubations of flavanones (e.g. (2S)naringenin) with FHT, ANS, and FLS. This and other evidence supports the intermediacy of a reactive oxidizing species, the oxygen of which does not exchange with that of water. In the case of products formed by oxidation of flavonoid substrates with a C-3 hydroxyl group (e.g. (2R,3R)-trans-dihydroquercetin), the results imply that oxygen exchange can occur at a stage subsequent to initial oxidation of the C-ring, probably via an enzyme-bound C-3 ketone/3,3-gem-diol intermediate.
Lumbar Spine Bone Mineral Density Changes in Patients with Primary Hyperparathyroidism According to Age and Gender (2007)

Primary hyperparathyroidism (PHPT) results from excessive secretion of parathyroid hormone (PTH), and catabolic and anabolic effects of PTH on bone may lead to overall deleterious effects on skeleton. The aim of this study was to analyze the changes in lumbar spine bone mineral density (BMD) in patients with PHPT who underwent parathyroidectomy (PTx), and to correlate the main demographics and biochemical parameters with pre- and postoperative BMD values. Two groups of age-matched patients (group A = 14 postmenopausal women; group B = 13 men, overall median age 53 years, range 26-56 years) with confirmed PHPT were enrolled in the study. All patients underwent lumbar (L2-L4 region) spine osteodensitometry using a dual-energy X-ray absorptiometry (DXA) prior to surgery. A significant correlation between alkaline phosphatase (ALP) and PTH (R = 0.73, P = 0.003) was found in group A patients. In group B correlations were found between calcemia and ALP (R = 0.71, P = 0.007), and between osteocalcin and both PTH (R = 0.65, P = 0.01) and ALP (R = 0.59, P = 0.03). No correlation (P = NS) was found between BMD, both basal and postoperative, and age or biochemical parameters. The 1-year BMD were 0.937 +/- 0.115 and 0.940 +/- 0.201 g/cm(2) (P = NS) in group A and B, respectively. A significant (P = 0.03) difference between basal and 1-year BMD was found only in group A, while in group B the difference was not significant. In conclusion, in patients with PHPT bone turnover is increased and consequently the BMD is reduced, but unfortunately PTx does not allow for complete bone restoring. However, in premenopausal women the BMD values of the lumbar spine significantly improve after PTx, suggesting a higher bone sensitivity to serum PTH normalization due to a synergic action with estrogens.
High-conversion-efficiency, diode-pumped continuous-wave Raman laser (2001)

We demonstrate a diode-pumped cw Raman laser in H(2) with photon-conversion efficiency of (66+/-8)%. Pumped by an injection-locked diode laser at 792 nm, the Stokes laser produces a peak output power of ~16mW at 1180 nm. Accompanying the high Stokes power are deviations from the existing theory, which are believed to be caused by the thermal-lensing effect of the Raman gas.
Stage- and subcellular-specific expression of Id proteins in male germ and Sertoli cells implicates distinctive regulatory roles for Id proteins during meiosis, spermatogenesis, and Sertoli cell function. (1998)

Immunohistological detection of each of the four Id proteins (Id1-Id4) in sections of mouse testis revealed a unique temporal and spatial expression pattern for each Id protein during spermatogenesis. Furthermore, each Id protein displayed a distinctive, dynamic pattern of subcellular distribution. Id1 was uniquely expressed in MI/MII spermatocytes undergoing meiotic division. Id4 protein was detectable in the cytoplasm of type A1 spermatogonia, as well as in late pachytene and in diplotene spermatocytes. Id2 protein, which was most abundant in Sertoli cell nuclei, was also detectable in pachytene and diplotene spermatocytes, but as with Id4, it was absent from MI/MII cells. In postmeiotic spermatids, Id1, Id2, and Id4 proteins were expressed in a stage- and subcellular-specific manner. Expression of Id3 was restricted to Sertoli cell cytoplasm. In malignant seminoma cells, all four Id proteins were abundantly expressed with accompanying changes in their subcellular distribution. The observed expression of Id proteins in postproliferative Sertoli cells and spermatids and during specific stages of meiosis implies novel functional roles for this class of transcriptional regulator during spermatogenesis.
Chapter 12: Arc Routing Problems with Profits (2015)

12.1 ▪ Introduction The class of routing problems with profits contains a large variety of problems which share the characteristic that, contrary to classical routing problems, the customers to serve have to be chosen from a set of potential customers. A profit is associated with each potential customer. The objective function may be the collected profit, the traveling cost, or a combination of both. The research activity has been mainly focused on node routing problems with profits, i.e., problems where customers are identified with specific locations which can be represented as vertices of a graph. The word “node” is usually not specified because having customers on nodes is the most common situation. We will specify it in this chapter as we will mention both classes of problems, with customers on nodes and on arcs. A first survey on single vehicle node routing problems with profits can be found in Feillet, Dejax, and Gendreau [21]. These problems are called Traveling Salesman Problems (TSPs) with profits. In this paper, the authors distinguish three classes of problems on the basis of the objective function. In the Orienteering Problem (OP) the objective is to maximize the collected profit with the constraint that the traveling time of the route does not exceed a given threshold. The Prize-Collecting Traveling Salesman Problem (PCTSP) is the problem of finding the route of minimum cost that collects a profit higher than a given lower bound. Finally, the Profitable Tour Problem (PTP) is the problem of finding the route that maximizes the difference between the total collected profit and the traveling cost. More recently, in Vansteenwegen, Souffriau, and Van Oudheusden [31] the authors focused on the OP and on its multiple vehicle version, i.e., the Team Orienteering Problem (TOP). A recent survey on node routing problems with profits, both with a single vehicle and with multiple vehicles, can be found in Archetti, Speranza, and Vigo [9].
Treatment of Fungal Infections with Semisynthetic Derivatives of Amphotericin Ba (1988)

AME appeared to be as effective as AmB in the treatment of mycoses in humans. AME was much less nephrotoxic than AmB, and was better tolerated in terms of rapid onset and reversible adverse reactions. AME may be more ototoxic than AmB. AME, even as AmB and OAME, may cause neurotoxicity and leukoencephalopathy, particularly when high doses are given for long periods.
Pharmacogenetics of ABCG2 and Adverse Reactions to Gefitinib (2006)

Gefitinib is an inhibitor of the epidermal growth factor receptor (EGFR) tyrosine kinase with activity in non-small-cell lung cancer. Diarrhea and skin toxicity are prominent gefitinib-related adverse events that potentially limit its use. Gefitinib is a substrate for ABCG2 (ABCP, BCRP, MXR), a polymorphic efflux transporter protein that is highly expressed in the intestines and liver. Here we investigated associations between allelic variants of EGFR, ABCG2, and the transporter protein ABCB1 with diarrhea and skin toxicity in gefitinib-treated patients. One variant, a common functional single-nucleotide polymorphism (SNP) in the ABCG2 gene, was associated with diarrhea in 124 patients treated with oral gefitinib 250 mg once daily; seven (44%) of 16 patients heterozygous for ABCG2 421C>A (Q141K) developed diarrhea, versus only 13 (12%) of 108 patients homozygous for the wild-type sequence (P = .0046). However, this SNP was not associated with skin toxicity (P = .99). The finding suggests that patients with reduced ABCG2 activity due to a common genetic variant are at increased risk for substrate drug-induced diarrhea, with implications for optimizing treatment with such agents.
Lidocaine, Monoethylglycinexylidide, and Isolated Human Uterine Muscle (1978)

The effects of lidocaine and its primary metabolite monoethylglycinexylidide (MEGX) on isolated human muscle strips from non-gravid and gravid uteri were evaluated. No differences between the effects of lidocaine and those of MEGX on gravid and non-gravid muscle strips were observed. Lidocaine produced significant (P less than 0.01) dose-related depression of uterine contractility, although significant pharamacologic depression occurred only at lidocaine concentrations in excess of 25 microgram/ml. MEGX produced no consistent changes in any of the responses measured.