gebhart/patrepeval huggingface dataset:
Glucose uptake and growth of glucose-limited chemostat cultures of Aspergillus niger and a disruptant lacking MstA, a high-affinity glucose transporter (2007)

This is a study of high-affinity glucose uptake in Aspergillus niger and the effect of disruption of a high-affinity monosaccharide-transporter gene, mstA. The substrate saturation constant (K(s)) of a reference strain was about 15 microM in glucose-limited chemostat culture. Disruption of mstA resulted in a two- to fivefold reduction in affinity for glucose and led to expression of a low-affinity glucose transport gene, mstC, at high dilution rate. The effect of mstA disruption was more subtle at low and intermediate dilution rates, pointing to some degree of functional redundancy in the high-affinity uptake system of A. niger. The mstA disruptant and a reference strain were cultivated in glucose-limited chemostat cultures at low, intermediate and high dilution rate (D=0.07 h(-1), 0.14 h(-1) and 0.20 h(-1)). Mycelium harvested from steady-state cultures was subjected to glucose uptake assays, and analysed for expression of mstA and two other transporter genes, mstC and mstF. The capacity for glucose uptake (v(max)) of both strains was significantly reduced at low dilution rate. The glucose uptake assays revealed complex uptake kinetics. This impeded accurate determination of maximum specific uptake rates (v(max)) and apparent affinity constants ( ) at intermediate and high dilution rate. Two high-affinity glucose transporter genes, mstA and mstF, were expressed at all three dilution rates in chemostat cultures, in contrast to batch culture, where only mstC was expressed. Expression patterns of the three transporter genes suggested differential regulation and functionality of their products.
Autoantibody Response to CD38 in Caucasian Patients With Type 1 and Type 2 Diabetes (2001)

Insulin secretion is one of the functions mediated by CD38, a nonlineage pleiotropic cell surface receptor. The molecule is the target of an autoimmune response, because serum autoantibodies (aAbs) to CD38 have been detected in diabetic patients. In the healthy Caucasian population, the CD38 gene is bi-allelic (86% CD38*B and 14% CD38*A), whereas an Arg140Trp mutation has been identified in Japanese diabetic patients. We investigated the relationship between CD38 and diabetes in Caucasian patients by characterizing anti-CD38 aAbs in terms of prevalence and function (agonistic/nonagonistic activity) and by exploring the potential influence of the CD38 genetic background. A novel enzymatic immunoassay, using recombinant soluble CD38 as the target antigen, was developed for the analysis of anti-CD38 aAb titers. Sera from 19.15% of type 1 and 16.67% of type 2 diabetic patients were positive. The majority of anti-CD38 aAbs (57.14%) displayed agonistic properties, i.e., they demonstrated the capability to trigger Ca2+ release in lymphocytic cell lines. In agreement with these functional features, the presence of anti-CD38 aAbs in type 2 diabetic patients was associated with significantly higher levels of fasting plasma C-peptide and insulin, as compared with anti-CD38-counterparts. No diabetic subject carrying the Arg140Trp mutation and no preferential association between diabetes or aAb status and the CD38*A allele was found in the study population. These results show the significance of anti-CD38 aAbs as a new diagnostic marker of beta-cell autoimmunity in diabetes. Moreover, the prevalent agonistic activity of these aAbs suggests that they could mediate relevant effects on target cells by means of Ca2+ mobilization.
Syringolin A, a new plant elicitor from the phytopathogenic bacterium Pseudomonas syringae pv. syringae, inhibits the proliferation of neuroblastoma and ovarian cancer cells and induces apoptosis (2006)

Abstract. Syringolin A is a new plant elicitor produced by the plant pathogen Pseudomonas syringae pv. syringae . The goal of this study was to investigate whether syringolin A exhibits anti‐proliferative properties in cancer cells. The treatment of human neuroblastoma (NB) cells (SK‐N‐SH and LAN‐1) and human ovarian cancer cells (SKOV3) with syringolin A (0–100 µm) inhibited cell proliferation in a dose‐dependent manner. The IC 50 (50% inhibition) for each cell line ranged between 20 µm and 25 µm. In SK‐N‐SH cells, the treatment with 20 µm syringolin A led to a rapid (24 h) increase of the apoptosis‐associated tumour suppressor protein p53. In addition, we found that the treatment of SK‐N‐SH cells caused severe morphological changes after 48 h such as rounding of cells and loss of adherence, both conditions observed during apoptosis. The induction of apoptosis by syringolin A was confirmed by both poly (ADP‐ribose) polymerase (PARP) cleavage and annexin V assay. Taken together, we show for the first time that the natural product syringolin A exhibits anti‐proliferative activity and induces apoptosis. Syringolin A and structurally modified syringolin A derivatives may serve as new lead compounds for the development of novel anticancer drugs.
Eliciting Consumer Preferences Using Robust Adaptive Choice Questionnaires (2008)

We propose a framework for designing adaptive choice-based conjoint questionnaires that are robust to response error. It is developed based on a combination of experimental design and statistical learning theory principles. We implement and test a specific case of this framework using Regularization Networks. We also formalize within this framework the polyhedral methods recently proposed in marketing. We use simulations as well as an online market research experiment with 500 participants to compare the proposed method to benchmark methods. Both experiments show that the proposed adaptive questionnaires outperform existing ones in most cases. This work also indicates the potential of using machine learning methods in marketing.
Preparation and Evaluation of a Radioisotope-Incorporated Iron Oxide Core/Au Shell Nanoplatform for Dual Modality Imaging (2008)

Magnetic gold-coated iron oxide nanoparticles (Fe@Au NPs) have recently emerged as a new type of iron oxide nanoparticle based magnetic resonance imaging (MRI) contrast agents, in which the gold shell provides a conveniently tunable surface for the presentation of multiple functional molecules. Given the versatility of this nanoplatform and the intrinsic sensitivity limitation of MRI contrast agents, a new approach was developed in this work to incorporate radioisotopes with suitable half-lives into the iron oxide core of Fe@Au NPs and impart the superior sensitivity of nuclear imaging to the nanoplatform. The incorporation of 67 Ga was successfully accomplished by co-precipitation of 67 Ga 3+ with Fe 3+ /Fe 2+ ions at a pH ranging from 4–10. The gold coating procedure was carried out by an iterative hydroxylamine seeding process. Upon the gold deposition, the hydrodynamic radius of the nanoparticles was changed from 23.2±2.2 nm to 31.7±2.3 nm, indicating an 8-nm thickness for the gold shell. The Fe@Au NPs were functionalized by lipoic acid (LA) and further conjugated with a polyarginine cell permeation peptide, NH 2 GR11. All the Fe@Au NPs stayed nearly 100% intact in either PBS or rat serum within 72 h. Cell labeling with the LA-modified Fe@Au NPs and NH 2 GR11-conjugated Fe@Au NPs was conducted by using a human prostate cancer cell line (PC-3). It was shown that NH 2 GR11 was able to increase the nanoparticle loading to PC-3 cells by 2–3 times. Shown in a pilot dual-modality imaging study, the LA-modified Fe@Au NP labeled cells could be visualized by both MRI and autoradiography imaging if the labeled PC-3 cell concentrations were above 1 × 10 5 cells/mL. The cell permeation peptide, NH 2 GR11, could significantly enhance the dual-modality detection sensitivity of the nanoplatform labeled PC-3 cells.
Aluminium compounds for use in vaccines (2004)

Aluminium adjuvants are the most widely used adjuvants in both human and veterinary vaccines. These adjuvants have been used in practical vaccination for more than 60 years and are generally recognized as safe and as stimulators of Th2 immunity. The present review gives a short introduction to the pioneering research at the start of the use of aluminium compounds as adjuvants, including references on the chemistry of these compounds. Analytical methods for identifying the most commonly used aluminium compounds, such as boehmite and aluminium hydroxyphosphate, are mentioned. Emphasis is placed on the important factors for antigen adsorption and on the latest work using gene-deficient mice in the research of the mechanism of aluminium adjuvants in terms of cytokine and T-cell subset stimulation. Key references on the ability of aluminium adjuvants to stimulate IgE and also in vivo clearing of aluminium adjuvants are discussed. Furthermore, the review addresses the issue of local reactions in the context of injection route and local tissue disturbance. Possible new applications of aluminium adjuvants in, for example, combined aluminium-adsorbed protein and DNA oligonucleotide vaccines as well as the possible use of aluminium adjuvants in combination with IL-12 to stimulate Th1-type immune responses are mentioned.
Donor CD4-enriched cells of Th2 cytokine phenotype regulate graft- versus-host disease without impairing allogeneic engraftment in sublethally irradiated mice (1994)

We have recently shown that donor CD4-enriched cells of Th2 cytokine phenotype, generated by treating mice in vivo with a combination of interleukin-2 (IL-2) and IL-4, prevent lipopolysaccharide-induced, tumor necrosis factor-alpha-mediated lethality during graft-versus-host reaction. To assess the potential regulatory role of such Th2-type cells in lethal graft-versus-host disease (GVHD) and graft rejection, we used a fully allogeneic murine transplant model using sublethally irradiated hosts (B6-->C3H, 500 cGy). Such recipients generated a strong host-versus-graft response, as reflected by their ability to reject T-cell-depleted inocula. The administration of T-cell-containing donor whole spleen inocula resulted in alloengraftment, but such recipients developed lethal GVHD. However, mice receiving sequential donor whole spleen (day 0) and CD4-enriched, Th2-type (day 1) populations engrafted, and had prolonged survival with protection from histologically defined tissue injury associated with GVHD. The findings in this fully allogeneic model thus extend our previous observations and indicate that the transfer of donor Th2-type cells may be an important strategy for regulating GVHD. Furthermore, the sequential "Th1(-)-->Th2-type" donor cell transfer described in this report represents a novel approach for abrogating graft rejection with concomitant control of GVHD and illustrates the importance of kinetics in the interaction of functionally distinct donor T-cell populations.
Determination of plasma amino acids by fluorescent derivatization and reversed-phase liquid chromatographic separation. (2004)

Amino acid analysis in physiological fluids remains expensive, as it usually requires a dedicated analyzer. We modified an RP-HPLC method originally devoted to peptide and protein hydrolysate analysis in order to apply it to plasma amino acid determination. The described method uses a commercial kit based on 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate derivatization followed by reversed-phase high-performance liquid chromatography. The described method is easy to use and allows the determination of twelve amino acids frequently involved in aminoacidopathies, thus enabling the diagnosis and follow-up of affected patients. The results obtained by this method are comparable to those obtained with a classical amino acid analyzer.
A high‐accuracy positioning service for land‐based mobile communication systems using the DGPS method (1994)

Abstract This paper proposes a high‐accuracy positioning service for terrestrial mobile communication systems which employs the global positioning system (GPS) with the differential method (DGPS). The proposed system provides a high‐accuracy navigation service to land‐based mobile communication users. The proposed system also provides a comprehensive vehicle control service to the transportation companies when both forward and return links are available in the terrestrial‐based mobile communication systems. This paper also assesses the performance of the DGPS method by computer simulations and a field experiment in an urban area to identify the viability of the proposed system under an actual environment. The relationship between average ranging time rate and the average visible number of satellites in various operating environments also is investigated.
Aberrant mRNAs with extended 3′ UTRs are substrates for rapid degradation by mRNA surveillance (1999)

The mRNA surveillance system is known to rapidly degrade aberrant mRNAs that contain premature termination codons in a process referred to as nonsense-mediated decay. A second class of aberrant mRNAs are those wherein the 3' UTR is abnormally extended due to a mutation in the polyadenylation site. We provide several observations that these abnormally 3'-extended mRNAs are degraded by the same machinery that degrades mRNAs with premature nonsense codons. First, the decay of the 3'-extended mRNAs is dependent on the same decapping enzyme and 5'-to-3' exonuclease. Second, the decay is also dependent on the proteins encoded by the UPF1, UPF2, and UPF3 genes, which are known to be specifically required for the rapid decay of mRNAs containing nonsense codons. Third, the ability of an extended 3' UTR to trigger decay is prevented by stabilizing sequences within the PGK1 coding region that are known to protect mRNAs from the rapid decay induced by premature nonsense codons. These results indicate that the mRNA surveillance system plays a role in degrading abnormally extended 3' UTRs. Based on these results, we propose a model in which the mRNA surveillance machinery degrades aberrant mRNAs due to the absence of the proper spatial arrangement of the translation-termination codon with respect to the 3' UTR element as defined by the utilization of a polyadenylation site.
Lecture Videos for E-Learning: Current Research and Challenges (2005)

E-learning is an emerging new education approach that augments learning experiences by integrating multimedia and network technologies. As an integrated part of e-learning, the lecture videos captured in classrooms contain most of the instructional content. Effective use of these videos, however, remains a challenging task. This paper reviews previous research work on capturing, analyzing, indexing, and retrieval of lecture (instructional) videos, and introduces on-going research efforts related with instructional videos. This paper compares instructional video to other video genres and addresses its special issues and difficulties. We present the current challenges in content-based indexing and retrieval of instructional videos. Improving these techniques for lecture videos has significant educational and social benefits.
Maternal Periodontitis and Prematurity. Part I: Obstetric Outcome of Prematurity and Growth Restriction (2001)

Oral Conditions and Pregnancy (OCAP) is a 5-year prospective study of pregnant women designed to determine whether maternal periodontal disease contributes to the risk for prematurity and growth restriction in the presence of traditional obstetric risk factors. Full-mouth periodontal examinations were conducted at enrollment (prior to 26 weeks gestational age) and again within 48 hours postpartum to assess changes in periodontal status during pregnancy. Maternal periodontal disease status at antepartum, using a 3-level disease classification (health, mild, moderate-severe) as well as incident periodontal disease progression during pregnancy were used as measures of exposures for examining associations with the pregnancy outcomes of preterm birth by gestational age (GA) and birth weight (BW) adjusting for race, age, food stamp eligibility, marital status, previous preterm births, first birth, chorioamnionitis, bacterial vaginosis, and smoking. Interim data from the first 814 deliveries demonstrate that maternal periodontal disease at antepartum and incidence/progression of periodontal disease are significantly associated with a higher prevalence rate of preterm births, BW < 2,500 g, and smaller birth weight for gestational age. For example, among periodontally healthy mothers the unadjusted prevalence of births of GA < 28 weeks was 1.1%. This was higher among mothers with mild periodontal disease (3.5%) and highest among mothers with moderate-severe periodontal disease (11.1%). The adjusted prevalence rates among GA outcomes were significantly different for mothers with mild periodontal disease (n = 566) and moderate-severe disease (n = 45) by pair-wise comparisons to the periodontally healthy reference group (n = 201) at P = 0.017 and P < 0.0001, respectively. A similar pattern was seen for increased prevalence of low birth weight deliveries among mothers with antepartum periodontal disease. For example, there were no births of BW < 1000 g among periodontally healthy mothers, but the adjusted rate was 6.1% and 11.4% for mild and moderate-severe periodontal disease (P = 0.0006 and P < 0.0001), respectively. Periodontal disease incidence/progression during pregnancy was associated with significantly smaller births for gestational age adjusting for race, parity, and baby gender. In summary, the present study, although preliminary in nature, provides evidence that maternal periodontal disease and incident progression are significant contributors to obstetric risk for preterm delivery, low birth weight and low weight for gestational age. These studies underscore the need for further consideration of periodontal disease as a potentially new and modifiable risk for preterm birth and growth restriction.
Free Tissue Failure Is Not an All-or-None Phenomenon (1995)

A common misconception among microsurgeons is that free tissue failure is an "all-or-none" phenomenon. In other words, there is an instantaneous cessation of blood flow to a flap primarily due to thrombosis at the arterial or venous anastomotic site (primary thrombosis) with complete flap loss as a result. Contrary to this belief, we have found that free tissue transfers occasionally "die" a slow, progressive, and partial death. This most likely is due to gradual "shutting down" of the microcirculation by the showering of microemboli downstream from the arterial anastomosis (secondary thrombosis). We discuss our clinical experience during the past 6 years with 10 patients in whom free flap failure was not an all-or-none phenomenon and describe the expectant management of these failing free flaps. Microvascular reconstruction of the lower extremities was performed for recalcitrant sickle cell ulceration, chronic venous stasis ulceration in a patient with anti-thrombin III deficiency, dry gangrene of the plantar surface of the foot and toes secondary to posterior tibial artery injection in an intravenous drug abuser, Gustillo type IIIc injury requiring reconstitution of the femoropopliteal artery after an automobile bumper injury, Gustillo type IIIb injury resulting from gunshot wounds, an open ankle joint in a patient with severe peripheral vascular disease, and osteomyelitis. Other cases included cheek soft tissue reconstruction after wide resection of a recurrent dermatofibrosarcoma protuberans of the parotid gland, chest wall coverage after claviculectomy for osteoradionecrosis, and thumb replantation complicated by refractory vasospasm. Latissimus dorsi (four patients), rectus abdominis (three patients), scapular (one patient), and radial forearm fasciocutaneous (one patient) flaps were used. Flap compromise was detected between 4 hours and 6 weeks after surgery. Salvage attempts included Fogarty thrombectomy (four patients), anastomotic revision (two patients), streptokinase instillation (one patient), and leech application (one patient). Failing free flaps were managed expectantly with the use of daily dressing changes. This allowed for the survival of sufficient soft tissue to effect coverage of exposed bone, tendon, or joint. Hyperbaric oxygen was not administered. Tangenital excision of the eschar was performed between 6 and 51 days after free tissue transfer. Skin grafting was delayed for 15 to 80 days. In all cases, a successful outcome was achieved ultimately by either a single skin-grafting procedure (seven patients) or groin flap coverage (one patient). Follow-up ranged from 2 to 35 months.(ABSTRACT TRUNCATED AT 250 WORDS)
Characterization of a purified bovine lung cGMP-binding cGMP phosphodiesterase. (1990)

A bovine lung cGMP-binding phosphodiesterase (cG-BPDE) was purified to homogeneity and exhibited specific cGMP hydrolytic (Km = 5.6 microM) and cGMP binding (half-maximum approximately 0.2 microM) activities which comigrated throughout the purification. A chimeric structure was suggested for cG-BPDE since DEAE chromatography of a partial alpha-chymotryptic digest of cG-BPDE separated cGMP-binding fragments from a cGMP hydrolytic fragment. Native cG-BPDE (178 kDa) appeared to be a homodimer comprised of two 93-kDa subunits. The order of potency of inhibitors of cG-BPDE hydrolysis of cGMP was as follows: zaprinast greater than dipyridamole greater than 3-isobutyl-1-methyl-8-methoxymethylxanthine greater than 3-isobutyl-1-methylxanthine greater than cilostamide greater than theophylline greater than rolipram. Minimum [3H]cGMP binding stoichiometry was 0.93 mol of cGMP bound/mol of monomer, but [3H]cGMP dissociation from cG-BPDE in the presence of excess unlabeled cGMP was curvilinear, suggesting multiple cGMP-binding sites. Two chymotryptic cGMP-binding fragments of 35 and 45 kDa were specifically photoaffinity labeled with [32P] cGMP, exhibited [3H]cGMP association and dissociation behavior indistinguishable from native cG-BPDE, and each had the amino-terminal sequence: Thr-Ser-Pro-Arg-Phe-Asp-Asn-Asp-Glu-Gly-. Cochromatography of the two cGMP-binding fragments suggested that both a dimerization domain and a cGMP-binding domain were located in a 35-kDa segment of cG-BPDE. Increased [3H]cGMP binding to or [32P]cGMP photoaffinity labeling of cG-BPDE binding sites in the presence of hydrolytic site-specific cyclic nucleotide analogs suggested communication between hydrolytic and binding sites. The principle of reciprocity thus predicts that cGMP binding to the binding sites may affect the hydrolytic site. In the presence of cGMP, the binding fragments or native cG-BPDE exhibited an electronegative shift on high performance liquid chromatography-DEAE, consistent with a cGMP-induced change in cG-BPDE conformation.
Learning Less is More - 6D Camera Localization via 3D Surface Regression (2018)

Popular research areas like autonomous driving and augmented reality have renewed the interest in image-based camera localization. In this work, we address the task of predicting the 6D camera pose from a single RGB image in a given 3D environment. With the advent of neural networks, previous works have either learned the entire camera localization process, or multiple components of a camera localization pipeline. Our key contribution is to demonstrate and explain that learning a single component of this pipeline is sufficient. This component is a fully convolutional neural network for densely regressing so-called scene coordinates, defining the correspondence between the input image and the 3D scene space. The neural network is prepended to a new end-to-end trainable pipeline. Our system is efficient, highly accurate, robust in training, and exhibits outstanding generalization capabilities. It exceeds state-of-the-art consistently on indoor and outdoor datasets. Interestingly, our approach surpasses existing techniques even without utilizing a 3D model of the scene during training, since the network is able to discover 3D scene geometry automatically, solely from single-view constraints.