gebhart/patrepeval huggingface dataset:
The mouse Fgf8 gene encodes a family of polypeptides and is expressed in regions that direct outgrowth and patterning in the developing embryo (1995)

Evidence is accumulating that members of the FGF gene family provide signals that act locally to regulate growth and patterning in vertebrate embryos. In this report, we provide a detailed analysis of the mouse Fgf8 gene. We have mapped the Fgf8 locus to the distal region of mouse chromosome 19, and sequenced the 5' coding region of the gene. Our data identify a new coding exon, and locate multiple splice donor and splice acceptor sites that can be used to produce at least seven transcripts encoding a family of secreted FGF8 proteins with different N termini. From these results, it appears that Fgf8 is structurally the most complex member of the FGF family described to date. In the embryo, many of the regions in which Fgf8 RNA is localized are known to direct outgrowth and patterning, including the apical ectodermal ridge of the limb bud, the primitive streak and tail bud, the surface ectoderm overlying the facial primorida and the midbrain-hindbrain junction, suggesting that FGF8 may be a component of the regulatory signals that emanate from these regions.
Electron-beam lithography damage and contact metallurgy in 1&amp;#181;m MOSFET technology (1981)

This work is motivated by the growing use of electron-beam lithography to fabricate high resolution MOSFET circuits. It deals with the introduction of damage into the gate oxides during resist exposure at the metal level and its subsequent removal by thermal annealing. Radiation damage to the gate oxides is shown to be caused not only by the primary beam electrons but also by electrons which are backscattered from the silicon substrate. This effect causes the threshold voltage of the MOSFET's on the chip to depend on the proximity of metal lines to the gate. The annealing cycles required to remove the damage from the gate oxides are described. The dependence of annealing on time, temperature and ambient are discussed. Anneals in pure hydrogen are shown to be superior to those in forming gas for removing damage from the gate oxide. A 400°C hydrogen anneal of a few hours reduces charge to negligible levels. The thermal stability and electrical properties of the Al/Ti metallurgy system are shown to be compatible with annealing cycles required for a 1 <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\micro</tex> m MOSFET technology. Annealing of damage is however impeded when Ti directly overlays the gate area on top of the field oxide. Consequently Ti is used only in the contact holes as a barrier metallurgy.
Cholix protein domain I functions as a carrier element for efficient apical to basal epithelial transcytosis (2020)

Cholix (Chx) is expressed by the intestinal pathogen <i>Vibrio cholerae</i> as a single chain of 634 amino acids (~70.7 kDa protein) that folds into three distinct domains, with elements of the second and third domains being involved in accessing the cytoplasm of nonpolarized cells and inciting cell death via ADP-ribosylation of elongation factor 2, respectively. In order to reach nonpolarized cells within the intestinal lamina propria, however, Chx must cross the polarized epithelial barrier in an intact form. Here, we provide <i>in</i><i>vitro</i> and <i>in</i><i>vivo</i> demonstrations that a nontoxic Chx transports across intestinal epithelium via a vesicular trafficking pathway that rapidly achieves vesicular apical to basal (A→B) transcytosis and avoids routing to lysosomes. Specifically, Chx traffics in apical endocytic Rab7<sup>+</sup> vesicles and in basal exocytic Rab11<sup>+</sup> vesicles with a transition between these domains occurring in the ER-Golgi intermediate compartment (ERGIC) through interactions with the lectin mannose-binding protein 1 (LMAN1) protein that undergoes an intracellular re-distribution that coincides with the re-organization of COPI<sup>+</sup> and COPII<sup>+</sup> vesicular structures. Truncation studies demonstrated that domain I of Chx alone was sufficient to efficiently complete A→B transcytosis and capable of ferrying genetically conjoined human growth hormone (hGH). These studies provide evidence for a pathophysiological strategy where native Chx exotoxin secreted in the intestinal lumen by nonpandemic <i>V. cholerae</i> can reach nonpolarized cells within the lamina propria in an intact form by using a nondestructive pathway to cross in the intestinal epithelial that appears useful for oral delivery of biopharmaceuticals.<b>One-Sentence Summary</b>: Elements within the first domain of the Cholix exotoxin protein are essential and sufficient for the apical to basal transcytosis of this <i>Vibrio cholerae</i>-derived virulence factor across polarized intestinal epithelial cells.
Reconfigurable microstrip antenna design based on genetic algorithm (2004)

At present, there are two main domains to be researched for reconfigurable antennas; one is to reconfigure the radiation patterns at fixed operating frequencies, the other is to reconfigure the operating frequencies with uniform radiation patterns. However, the core of the desired characteristics of a modern reconfigurable antenna is that the antenna can reconfigure the radiation patterns over an extremely wide band. There is a large gap between present research and the ultimate objective. A novel reconfigurable microstrip antenna scheme is presented; it has advantages of low profile, light weight, conformability, and, especially, ease of fabrication and integration with RF devices. The finite-difference time-domain (FDTD) method and GA optimizers are used to optimize the antenna states according to the selected goals. We attempt to explore the possibilities of a microstrip antenna for reconfiguring radiation characteristics over an extremely wide band. The design results indicate that this antenna can obtain the required goals over an ultra-wide band through reconfiguring the states of the switch array installed in the shared aperture when it operates with the higher order modes.
Antibiotic-impregnated beads. Part I: Bead implantation versus systemic therapy. (1991)

Parenteral antibiotic therapy for acute bone infections, soft-tissue infections, and osteomyelitis may result in high serum concentrations associated with nephrotoxic, ototoxic, and allergic complications. Conversely, the local release of antibiotics into the wound with the use of antibiotic-impregnated cement or antibiotic-impregnated polymethylmethacrylate beads has been found effective and does not induce negative effects or result in systemic concentrations of clinical significance. The antibiotic-impregnated cement beads are fabricated on a surgical steel wire, and they have bimodal elution properties. They provide local antibiotic concentrations that surpass the minimum inhibitory concentrations for pathogens commonly isolated in orthopaedic infections. Their use effectively controls chronic osteomyelitis and acute musculoskeletal infections. Compared with systemic antibiotic therapy, the incidence of nephrotoxic, ototoxic, and hypersensitivity reactions is significantly diminished. The beads release 5% of the antibiotic within the first 24 hours. The sustained elution then progressively diminishes to undetectable levels within a few weeks or months.
Evolution of HIV integrase resistance mutations (2012)

Because of the susceptibility to drug resistance, INSTIs should always be used together with other effective ARV drugs.
Role of the MET/HGF receptor in proliferation and invasive behavior of osteosarcoma (2003)

Signal transduction downstream HGF receptor (MET) activation involves multiple pathways that account for mitogenesis, motility and morphogenesis in a cell type-dependent fashion. MET receptor is aberrantly expressed in almost 100% of human osteosarcomas. We analyzed the effect of the MET receptor activation in five human osteosarcoma cell lines evaluating the levels of HGF-dependent activation of MAPK and PKB/AKT as biochemical readouts of mitogenic and invasive responses, respectively. All the cell lines tested expressed high levels of the MET proto-oncogene. Four cell lines showed activation of the MAPK cascade upon HGF stimulation, suggesting that this growth factor serves a common proliferative function in osteosarcomas. Two lines showed activation of PKB/AKT that is known to be involved in migration mediated by HGF receptor. Accordingly, cell lines where MAPK cascade was activated responded to HGF with increased proliferation, while induction and inhibition of PKB/AKT activity corresponded to acquisition or block of the invasive-motile response to HGF, respectively. Both the HGF dependent responses were reverted by the specific MET inhibitor K252a. These data show that HGF activates both the mitogen and motogen machinery in osteosarcoma cells and suggest that HGF might promote their malignant behavior by concomitant activation of different pathways and biological functions.
Self-assembly of core-polyethylene glycol-lipid shell (CPLS) nanoparticles and their potential as drug delivery vehicles (2016)

Herein a new multifunctional formulation, referred to as a core-polyethylene glycol-lipid shell (CPLS) nanoparticle, has been proposed and studied in silico via large scale coarse-grained molecular dynamics simulations. A PEGylated core with surface tethered polyethylene glycol (PEG) chains is used as the starting configuration, where the free ends of the PEG chains are covalently bonded with lipid molecules (lipid heads). A complete lipid bilayer is formed at the surface of the PEGylated particle core upon addition of free lipids, driven by the hydrophobic properties of the lipid tails, leading to the formation of a CPLS nanoparticle. The self-assembly process is found to be sensitive to the grafting density and molecular weight of the tethered PEG chains, as well as the amount of free lipids added. At low grafting densities the assembly of CPLS nanoparticles cannot be accomplished. As demonstrated by simulations, a lipid bud/vesicle can be formed on the surface when an excess amount of free lipids is added at high grafting density. Therefore, the CPLS nanoparticles can only be formed under appropriate conditions of both PEG and free lipids. The CPLS nanoparticle has been recognized to be able to store a large quantity of water molecules, particularly with high molecular weight of PEG chains, indicating its capacity for carrying hydrophilic molecules such as therapeutic biomolecules or imaging agents. Under identical size and surface chemistry conditions of a liposome, it has been observed that the CPLS particle can be more efficiently wrapped by the lipid membrane, indicating its potential for a greater efficiency in delivering its hydrophilic cargo. As a proof-of-concept, the experimental realization of CPLS nanoparticles is explicitly demonstrated in this study. To test the capacity of the CPLS to store small molecule cargo a hydrophilic dye was successfully encapsulated in the particles' water soluble layer. The results of this study show the power and potential of simulation-driven approaches for guiding the design of more efficient nanomaterial delivery platforms.
Distribution of Research Awards from the National Institutes of Health among Medical Schools (2000)

Research funded by the NIH is becoming more concentrated in the medical schools that are most active in research.
Effects of Computer Assisted Visual Scanning Training in the Treatment of Visual Neglect: (1996)

This article reports the effects of visual scanning training using a computer software program with three patients with right-brain damage following stroke. This preliminary case study focuses on the possibility of the near transfer effects of visual scanning training. Study results showed some treatment effect in three patients following visual scanning skills training after four weeks. The results of this study add to the data available on computer applications for visual perceptual remediation.
Iron-Source Preference of Staphylococcus aureus Infections (2004)

Although bacteria use different iron compounds in vitGro, the possibility that microbes distinguish between these iron sources during infection has hitherto not been examined. We applied stable isotope labeling to detect source-specific iron by mass spectrometry and show that Staphylococcus aureus preferentially imports heme iron over transferrin iron. By combining this approach with computational genome analysis, we identified hts (heme transport system), a gene cluster that promotes preferred heme iron import by S. aureus. Heme iron scavenging by means of hts is required for staphylococcal pathogenesis in animal hosts, indicating that heme iron is the preferred iron source during the initiation of infection.
Auto-Encoding Twin-Bottleneck Hashing (2020)

Conventional unsupervised hashing methods usually take advantage of similarity graphs, which are either pre-computed in the high-dimensional space or obtained from random anchor points. On the one hand, existing methods uncouple the procedures of hash function learning and graph construction. On the other hand, graphs empirically built upon original data could introduce biased prior knowledge of data relevance, leading to sub-optimal retrieval performance. In this paper, we tackle the above problems by proposing an efficient and adaptive code-driven graph, which is updated by decoding in the context of an auto-encoder. Specifically, we introduce into our framework twin bottlenecks (i.e., latent variables) that exchange crucial information collaboratively. One bottleneck (i.e., binary codes) conveys the high-level intrinsic data structure captured by the code-driven graph to the other (i.e., continuous variables for low-level detail information), which in turn propagates the updated network feedback for the encoder to learn more discriminative binary codes. The auto-encoding learning objective literally rewards the code-driven graph to learn an optimal encoder. Moreover, the proposed model can be simply optimized by gradient descent without violating the binary constraints. Experiments on benchmarked datasets clearly show the superiority of our framework over the state-of-the-art hashing methods. Our source code can be found at https://github.com/ymcidence/TBH.
A molecular model for the genetic and phenotypic characteristics of the mouse lethal yellow (Ay) mutation. (1994)

Lethal yellow (Ay) is a mutation at the mouse agouti locus in chromosome 2 that causes a number of dominant pleiotropic effects, including a completely yellow coat color, obesity, an insulin-resistant type II diabetic condition, and an increased propensity to develop a variety of spontaneous and induced tumors. Additionally, homozygosity for Ay results in preimplantation lethality, which terminates development by the blastocyst stage. The Ay mutation is the result of a 170-kb deletion that removes all but the promoter and noncoding first exon of another gene called Raly, which lies in the same transcriptional orientation as agouti and maps 280 kb proximal to the 3' end of the agouti gene. We present a model for the structure of the Ay allele that can explain the dominant pleiotropic effects associated with this mutation, as well as the recessive lethality, which is unrelated to the agouti gene.
Post-Translational Processing :A Practical Approach (1999)

1. Sequence Analysis of Expressed Proteins 2. Protein Folding and Import into Organelles 4. Protein Glycosylation 5. Lipid Modification of Proteins 6. Proteolytic Processing 8. Protein Degradation and Proteinases in Yeast
Vaccines and melanoma (2002)

Melanoma is one of the prototypic immunogenic tumors. Various immunotherapeutic approaches for melanoma have been developed in the past decades. Recent scientific progress includes the discovery of defined melanoma antigens, new tools for monitoring of an anti-cancer immune response and application of novel adjuvants for amplification of the immune response such as dendritic cells. These and other advances in the field of melanoma vaccines will be discussed.
Selective Dehydrogenative Silylation–Hydrogenation Reaction of Divinyldisiloxane with Hydrosilane Catalyzed by an Iron Complex (2011)

A hydride and a silyl group of hydrosilane is introduced into 1,3-divinyldisiloxane in the presence of a catalytic amount of (η(5)-C(5)H(5))Fe(CO)(2)Me. Instead of the product expected from the well-known hydrosilylation reaction, the product obtained is that characteristic of dehydrogenative silylation at one vinyl group and hydrogenation at the other vinyl group of 1,3-divinyldisiloxane. Based on deuterium labeling experiments, a catalytic cycle for this new reaction has been proposed.
Pharmacokinetics of cefoperazone in newborn infants. (1984)

We studied the disposition of two 100 mg/kg doses of cefoperazone given intravenously 12 hr apart in ten newborn infants. Peak levels were a mean 352 +/- SD 75 and 371 +/- 68 micrograms/ml immediately after the first and second dose, respectively, with corresponding troughs of 60 +/- 10 and 76 +/- 28 mcg/ml 12 hr later. Mean half-life was 6.5 +/- 0.9 hr and decreased with increasing gestational age and birthweight. Steady-state volume of distribution averaged 410 +/- 40 ml/kg and total clearance 0.78 +/- 0.13 ml/min X kg and neither varied with gestational age nor birthweight. No untoward physical or laboratory effects were noted. Additional studies including postnatal age effects on kinetics, efficacy, and cerebrospinal fluid penetrance are necessary prior to widespread use of this potentially valuable antibiotic in newborn infants.
A Self-contained Active Sensor System for Health Monitoring of Civil Infrastructures (2006)

A self-contained active sensor system is proposed for the practical use of an electro-mechanical impedance-based structural health monitoring (SHM) technique for civil infrastructures. This system, which consists of a miniaturized impedance measuring chip (AD5933) and a self-sensing macro-fiber composite (MFC) patch, can be a powerful tool for a variety of in-situ SHM applications in civil, mechanical, and aerospace systems, since (1) the AD5933 is low-cost, portable, and readily combined with a wireless telemetry and (2) the MFC patch can be permanently attached to a structure and provide meaningful information regarding the structure's integrity through its self-sensing function. In this study, the effectiveness of the proposed active sensor device has been verified through a series of experimental studies: (a) inspecting loosening bolts in a bolt-jointed structure and (b) detecting corrosion in an aluminum beam.
Microalgae: biotechnology and microbiology (1994)

1. Introduction 2. Algal production systems 3. Culture media 4. Cultivation methods (indoors) 5. Scaling up 6. Algal grouping 7. Strain selection 8. Growth kinetics 9. Measurement of algal growth 10. Large scale cultivation 11. Yield 12. Chemical composition 13. Nutrition 14. Applications of algae 15. Addresses of algae culture collections.
Down-regulation of cell cycle control genes by ionizing radiation. (1992)

The cellular responses to ionizing radiation include growth arrest, DNA repair, and lethality. However, little is known about the signaling events responsible for these responses. The present studies have examined the effects of ionizing radiation on the expression of genes involved in cell cycle control. The results demonstrate that the treatment of asynchronous cells with 20 Gy ionizing radiation is associated with transient down-regulation of the cdc2, cyclin A, cyclin B, and cdc25 genes. This effect was associated with transient induction of the c-jun gene. RNA stability studies demonstrate that the down-regulation of gene expression following ionizing radiation exposure is at least in part due to a decrease in transcript half-life. Other studies were performed with elutriated cells enriched for populations in G1 and S phases. Treatment of G1 enriched cell populations with 10 Gy resulted in a selective decrease in cyclin B mRNA levels, whereas this effect on cyclin B expression was less pronounced at 5 Gy and undetectable at 1 Gy. Similar results were obtained with S phase enriched cells. Taken together with clonogenic survival studies, these findings indicate that down-regulation of cell cycle control gene expression is associated with lethality, whereas lower doses of ionizing radiation have little, if any, effect on the expression of these genes. The findings also suggest that DNA damage may activate signaling events which regulate expression of cell cycle control genes.
A collaborative web-based help-system (2012)

In this paper we present a novel help system that integrates material provided by various contributors into a single point of reference for user assistance. Therefore different kinds of resources are organized by means of collaborative tagging. To retrieve the content natural language is used to communicate with an avatar on a web page. The advantage of our approach has been verified by user testing. First-time users assisted by our system were able to perform a given task more efficiently than those performing the same task employing a system based on traditional help texts.
The role of BK virus in acute respiratory tract disease and the presence of BKV DNA in tonsils (1982)

The significance of BKV infections relative to infections by generally tested respiratory agents was investigated in children with acute respiratory disease. Paired sera from 177 children admitted to a hospital for acute respiratory disease were tested for significant rises in antibodies. Sera from seven patients showed a seroconversion to BKV and clinical signs of acute upper respiratory tract infection were exhibited by each of these patients. BKV infections were present in 8% of the patients with upper respiratory tract disease while seroconversions to adenovirus (2%), influenza A virus (1%), parainfluenza virus (5%), RS virus (6%) and mycoplasma pneumoniae (1%) were observed in 15% of the patients with upper respiratory tract disease. BKV was isolated from the urine of one child with tonsillitis with a concomitant seroconversion to BKV. Tonsils from children with recurrent attacks of acute respiratory disease were tested for the presence of BKV DNA by hybridization with a cloned genomic 32P-labeled DNA of prototype BKV. Five of twelve tonsil DNAs showed hybridization with BKV DNA. Each tonsil showing hybridization with BKV DNA contained multiple nonintegrated copies of the BKV genome per diploid amount of host cell DNA. Attempts to recover infective BKV by transfection of primary human embryonic cells with tonsil DNAs or by co-cultivation of tonsillar cells with primary human embryonic cells were unsuccessful.