gebhart/patrepeval huggingface dataset:
Cloning and Characterization of a Rice cDNA Encoding Glutamate Decarboxylase (2005)

In this study, we have isolated a rice (Oryza sativa L.) glutamate decarboxylase (RicGAD) clone from a root cDNA library, using a partial Arabidopsis thaliana GAD gene as a probe. The rice root cDNA library was constructed with mRNA, which had been derived from the roots of rice seedlings subjected to phosphorus deprivation. Nucleotide sequence analysis indicated that the RicGAD clone was 1,712 bp long, and harbors a complete open reading frame of 505 amino acids. The 505 amino acid sequence deduced from this RicGAD clone exhibited 67.7 % and 61.9 % identity with OsGAD1 (AB056060) and OsGAD2 (AB056061) in the database, respectively. The 505 amino acid sequence also exhibited 62.9, 64.1, and 64.2 % identity to Arabidopsis GAD (U9937), Nicotiana tabacum GAD (AF020425), and Petunia hybrida GAD (L16797), respectively. The RicGAD was found to possess a highly conserved tryptophan residue, but lacks the lysine cluster at the C-proximal position, as well as other stretches of positively charged residues. The GAD sequence was expressed heterologously using the high copy number plasmid, pVUCH. Our activation analysis revealed that the maximal activation of the RicGAD occurred in the presence of both Ca(2+) and calmodulin. The GAD-encoded 56 approximately 58 kDa protein was identified via Western blot analysis, using an anti-GAD monoclonal antibody. The results of our RT-PCR analyses revealed that RicGAD is expressed predominantly in rice roots obtained from rice seedlings grown under phosphorus deprivation conditions, and in non-germinated brown rice, which is known to have a limited phosphorus bioavailability. These results indicate that RicGAD is a Ca(2+)/ calmodulin-dependent enzyme, and that RicGAD is expressed primarily under phosphate deprivation conditions.
Learning for Autonomous Navigation (2010)

Autonomous navigation by a mobile robot through L natural, unstructured terrain is one of the premier k challenges in field robotics. Tremendous advances V in autonomous navigation have been made recently in field robotics. Machine learning has played an increasingly important role in these advances. The Defense Advanced Research Projects Agency (DARPA) UGCV-Perceptor Integration (UPI) program was conceived to take a fresh approach to all aspects of autonomous outdoor mobile robot design, from vehicle design to the design of perception and control systems with the goal of achieving a leap in performance to enable the next generation of robotic applications in commercial, industrial, and military applications. The essential problem addressed by the UPI program is to enable safe autonomous traverse of a robot from Point A to Point B in the least time possible given a series of waypoints in complex, unstructured terrain separated by 0.2-2 km. To accomplish this goal, machine learning techniques were heavily used to provide robust and adaptive performance, while simultaneously reducing the required development and deployment time. This article describes the autonomous system, Crusher, developed for the UPI program and the learning approaches that aided in its successful performance.
Human glioma cells overexpress receptors for interleukin 13 and are extremely sensitive to a novel chimeric protein composed of interleukin 13 and pseudomonas exotoxin. (1995)

Recently, we have demonstrated that a spectrum of human adenocarcinoma cell lines express binding sites for interleukin 13 (IL-13). These cells are killed by a chimeric protein composed of human (h) IL-13 and a derivative of Pseudomonas exotoxin, PE38QQR (Debinski et al., J. Biol. Chem., 270: 16775-16780, 1995). The cell killing was hIL-13- and hIL-4-specific, indicating that a common binding site for the two cytokines is present in several solid tumor cell lines. Herein, we report that an array of established glioma cell lines is killed by very low concentrations of hIL-13-PE38QQR, often reaching <1 ng/ml (<20 pM). Glioma cells express up to 30,000 molecules of IL-13 receptor/cell which has intermediate affinity toward hIL-13. hIL-13-PE38QQR is more active (up to 3 logs difference in cytotoxic activities) than are the corresponding chimeric toxins containing hIL-4 or hIL-6. The cytotoxic action of hIL-13-PE38QQR is blocked by an excess of hIL-13 on all cell lines studied, and it is not neutralized by hIL-4 on some of these cells. Our results show that human brain cancers richly express receptors for IL-13. Furthermore, the interaction detected previously between receptors for IL-13 and IL-4 on solid tumors cell lines is of a qualitatively different character in U-251 MG and U-373 MG glioma cells. The receptor for IL-13 may represent a new marker of brain cancers and an attractive target for anticancer therapies.
Speckle statistics in optical coherence tomography (2005)

The two previously reported calculations of the amplitude distribution of speckles in optical coherence tomography, each based on a different mathematical formulation, yield different results. We show that a modification of an initial assumption in one of the formulations leads to equivalent results.
Evidence that the N-terminal domain of nonstructural protein NS3 from yellow fever virus is a serine protease responsible for site-specific cleavages in the viral polyprotein. (1990)

Sequence homology and molecular modeling studies have suggested that the N-terminal one-third of the flavirvirus nonstructural protein NS3 functions as a trypsin-like serine protease. To examine the putative proteolytic activity of NS3, segments of the yellow fever virus genome were subcloned into plasmid transcription/translation vectors and cell-free translation products were characterized. The results suggest that a protease activity encoded within NS2B and the N-terminal one-third of yellow fever virus NS3 is capable of cis-acting site-specific proteolysis at the NS2B-NS3 cleavage site and dilution-insensitive cleavage of the NS2A-NS2B site. Site-directed mutagenesis of the His-53, Asp-77, and Ser-138 residues of NS3 that compose the proposed catalytic triad implicates this domain as a serine protease. Infectious virus was not recovered from mammalian cells transfected with RNAs transcribed from full-length yellow fever virus cDNA templates containing mutations at Ser-138 (which abolish or dramatically reduce protease activity in vitro), suggesting that the protease is required for viral replication.
Full COLD-PCR Protocol for Noninvasive Prenatal Diagnosis of Genetic Diseases (2010)

To the Editor:

After the discovery of fetal DNA in maternal plasma, investigators reported different strategies for the noninvasive prenatal diagnosis of genetic diseases (1). Despite the advances in improving the analytical sensitivity of methods, distinguishing between fetal and maternal sequences remains very challenging, and the field of noninvasive prenatal diagnosis of genetic diseases has yet to attain a routine application in clinical diagnostics. An innovative strategy that has been reported is based on COLD-PCR (coamplification at a lower denaturation temperature PCR),1 which exploits melting temperature ( T m) differences between variant or mismatched sequences and wild-type sequences. This approach uses a critical denaturation temperature ( T c) lower than the T m to selectively amplify minority mutated alleles (2).

We have developed assays for the identification of fetal paternally inherited mutations in maternal plasma. These assays use full COLD-PCR for the detection of IVSI.110 (G>A) and Cd39 (C>T) HBB (globin, beta) gene mutations that cause β-thalassemia.

Full COLD-PCR is based on the generation of heteroduplexes between mutant and wild-type sequences. These heteroduplexes melt at lower temperatures than the wild-type homoduplexes. They are selectively denatured at the T c and then subsequently amplified. Given that both the fetal and maternal DNA content in maternal plasma has been demonstrated to vary from pregnancy to …
DUX4 , a candidate gene of facioscapulohumeral muscular dystrophy, encodes a transcriptional activator of PITX1 (2007)

Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant disorder linked to contractions of the D4Z4 repeat array in the subtelomeric region of chromosome 4q. By comparing genome-wide gene expression data from muscle biopsies of patients with FSHD to those of 11 other neuromuscular disorders, paired-like homeodomain transcription factor 1 (PITX1) was found specifically up-regulated in patients with FSHD. In addition, we showed that the double homeobox 4 gene (DUX4) that maps within the D4Z4 repeat unit was up-regulated in patient myoblasts at both mRNA and protein level. We further showed that the DUX4 protein could activate transient expression of a luciferase reporter gene fused to the Pitx1 promoter as well as the endogenous Pitx1 gene in transfected C2C12 cells. In EMSAs, DUX4 specifically interacted with a 30-bp sequence 5'-CGGATGCTGTCTTCTAATTAGTTTGGACCC-3' in the Pitx1 promoter. Mutations of the TAAT core affected Pitx1-LUC activation in C2C12 cells and DUX4 binding in vitro. Our results suggest that up-regulation of both DUX4 and PITX1 in FSHD muscles may play critical roles in the molecular mechanisms of the disease.
Biochemical characterization of the soluble form of tumor antigen MUC1 isolated from sera and ascites fluid of breast and pancreatic cancer patients. (2001)

Transmembrane glycoprotein tumor antigen MUC1 that is overexpressed on pancreatic and breast tumor cells can be found in large amounts in soluble form in serum and ascites fluid. MUC1 has been identified as a target of human antitumor antibody and CTL responses that are generated in the absence of helper T cells. The soluble form of MUC1 should support generation of helper T cells, but we have found recently that this form, although effectively endocytosed by dendritic cells, remains trapped in early endosomes and is not trafficked to antigen-processing compartments. The exact biochemical structure of this form of MUC1 has not been elucidated to date, and it is thus not clear what structural characteristics may be responsible for its retention in early endosomes. We have purified soluble MUC1 from ascites fluid of breast/pancreatic cancer patients (ASC-MUC1) and quantitated O-linked carbohydrates. We have altered ASC-MUC1 by enzymatic treatment: trypsin or clostripain digestion, desialylation, and further in vitro glycosylation. We have found that desialylated ASC-MUC1 was further glycosylated by peptidyl N-acetylgalactosamine transferases and was not when sialic acid was present. These alterations created new forms of ASC-MUC1 that might be handled more efficiently by antigen-presenting cells to generate better tumor-specific immunity and used to identify structures that are directly involved in retention of this antigen in early endosomes.
Molecular mechanisms involved in the regulation of gene expression during cell differentiation and development. (1990)

One general point to emerge from this review is that each step in the pathway for gene expression from DNA to final polypeptide via chromosome structure, primary transcript, mRNA processing, stability, and translation is exploited in some developmental context as a means of regulation. Moreover, there is little evidence that the regulation of different stages in this pathway is associated consistently with particular classes of genes or developmental processes: for example, homeotic and other regulatory genes, which are important in early development and in determining the overall structures of organisms, are regulated by both transcriptional and posttranscriptional mechanisms, as are many other genes encoding cell-type-specific proteins expressed late during terminal differentiation. There are also instances in which transcription factors regulating tissue-specific transcription are present constitutively but are activated only in certain cell types by posttranslational events, and in yeast, coordinate regulation of amino-acid biosynthesis genes involves the translation control of a transcription factor. Second, as far as transcriptional control is concerned, it is now clear that in most instances cell-type specificity arises from the activities of multiple cis-control elements that can act either positively or negatively: The precise way in which the gene functions depends on what combination of cis-control elements it possesses. A third somewhat negative point is that in general the mechanisms responsible for the coordinate expression of genes during cell differentiation and development are not yet understood. In view of the complexities of possible mechanisms noted above, it may be that closely related genes (such as those encoding the alpha- and beta-globins, for example) in fact come to be coordinately expressed via a complex, indirect route. Indeed, it is quite possible that such mechanisms will not be revealed simply by a reductionist approach studying relatively short regions of DNA and that some form of overall "systems analysis" will be required. Finally, what we know relates mainly to expression of genes within particular cell types. How groups of cells are organized into complex structures remains a mystery at the molecular level, although progress into the genetic principles involved in the regulation of such "compartments" is being made, mainly in insects, reviewed recently by Brower, although to some extent also in the mouse [discussed by Hogan and co-workers].
교회의 지향점: 하나님의 공의와 정의 -창세기 18:16-20:18에 대한 칼빈의 성경 해석 방법의 적용- (2009)

논문 목적은 칼빈의 성경 해석 방법을 사용하여 창세기 18-20장을 해석하여 본문의 역사와 교회의 맥락에서 그 기능을 고찰하는 것이다. 칼빈은 성경 해석에 있어서 `맥락`(context)을 매우 중요시 했다. 필자는 칼빈이 주목한 `문맥`에 주목하여 창세기 18-19장과 20장이 한 본문으로 연구되지 않고 두 본문으로서 각기 다른 방면에서 연구된 문제를 해결하려고 했다. 문학적 전략상 창세기 18:16-33은 서론적으로 문제를 제기하고 창세기 19장과 20장은 그 문제를 해결한다. 창세기 18:18에서 제기된 모든 족속이 아브라 함을 통하여 복을 받게 된다는 약속은 창세기 19장과 20장에서 롯의 구원과 아비멜렉이 구출되는 이야기에서 해결된다. 또한 창세기 18:22b-33에서 제기된 하나님의 정의 문제는 창세기 19장 소돔의 심판과 롯의 구원과 창세기 20장에서 사라와 아비멜렉의 구원과 아브라함에 대한 간접적 책망을 통해서 이루어진다. 창세기 18:20-22에서 제기된 소돔의 죄는 창세기 19장에서 그들의 죄가 집단적이며 동성애적이며 폭력적인 죄임을 폭로함으로 해결된다. 결과적으로 창세기 19장과 20장은 하나님의 공의와 정의가 무엇인지를 독자들에게 말한다. 필자는 창세기 18:16-20:18의 역사적 맥락이 출애굽 시대라고 주장했다. 또한 창세기 18:16-20:18은 출애굽 독자와 현대 교회의 독자들에게 세가지 중요한 기능을 한다고 보았다. 첫째, 창세기 18:16-20:18은 언약 백성의 정체성과 사명을 일깨운다. 둘째, 창세기 18:16-20:18은 언약 백성이 하나님 앞에서 취할 태도에 대해 교훈한다. 셋째, 창세기 18:16-20:18은 모든 민족 가운데서 언약백성의 위치를 규정해 준다. 그러므로 창세기 18:16-20:18은 두 본문이 아니라 하나의 본문이며 그것은 아브라함의 후손으로서 교회의 궁극적인 사명을 일깨운다. 즉 그것은 교회의 지향점은 하나님의 공의와 정의를 행하는 것이다.
Development of iron chelators to treat iron overload disease and their use as experimental tools to probe intracellular iron metabolism (1998)

The development of an orally effective iron (Fe) chelator for the treatment of Fe overload diseases such as beta-thalassemia has been a difficult challenge. Even though the drug in current clinical use, desferrioxamine (DFO), is efficient and remarkably free of toxicity, it suffers from not being orally effective and requiring long subcutaneous infusion to mobilize sufficient quantities of Fe. In addition, DFO is very expensive, which precludes it from treating most of the world's thalassemic population. Therefore, the development of an economical and orally effective Fe chelator is of great importance. Despite the screening of a wide range of structurally diverse ligands from both natural and synthetic sources, few compounds have been promising enough to proceed to clinical trials. In the current review, the properties of an ideal chelator are discussed, followed by a description of the most successful ligands that have been identified. Apart from the use of Fe chelators as therapeutic agents, some of these compounds have also been useful as experimental probes to investigate cellular Fe metabolism. We describe here the most important of these studies.
Tissue-Nonspecific Alkaline Phosphatase with an Asp289->Val Mutation Fails to Reach the Cell Surface and Undergoes Proteasome-Mediated Degradation (2003)

A missense mutation in the gene of tissue-nonspecific alkaline phosphatase, which replaces aspartic acid at position 289 with valine [TNSALP (D289V)], was reported in a lethal hypophosphatasia patient [Taillandier, A. et al. (1999) Hum. Mut. 13, 171-172]. To define the molecular defects of TNSALP (D289V), this mutant protein in transiently transfected COS-1 cells was analyzed biochemically and morphologically. TNSALP (D289V) exhibited no alkaline phosphatase activity and mainly formed a disulfide-linked high molecular mass aggregate. Cell-surface biotinylation, digestion with phosphatidylinositol-specific phospholipase C and an immunofluorescence study showed that the mutant protein failed to appear on the cell surface and was accumulated intracellularly. In agreement with this, pulse/chase experiments demonstrated that TNSALP (D289V) remained endo-beta-N-acetyl- glucosaminidase H-sensitive throughout the chase and was eventually degraded, indicating that the mutant protein is unable to reach the medial-Golgi. Proteasome inhibitors strongly blocked the degradation of TNSALP (D289V), and furthermore the mutant protein was found to be ubiquitinated. Besides, another naturally occurring TNSALP with a Glu(218)-->Gly mutation was also found to be polyubiquitinated and degraded in the proteasome. Since the acidic amino acids at positions 218 and 289 of TNSALP are thought to be directly involved in the Ca(2+) coordination, these results suggest the critical importance of calcium binding in post-translational folding and assembly of the TNSALP molecule.
Internal medicine : CD-ROM (1998)

The Stein CD contains all the huge wealth and illustrations on disease pathophysiology, diagnosis and treatment contained in Internal Medicine, 5/e. From the opening screen, it is possible to go to whichever section of information from Stein that the user wants to access. Alternatively, the user can opt to enter the Diagnostic Algorithms section first, to help with a diagnosis, then hotlink to sections in Stein for further information on specific disorders mentioned in the algorithm (then to GenRX for specific drug information, etc.).
Targeting Bacillosamine Biosynthesis in Bacterial Pathogens: Development of Inhibitors to a Bacterial Amino-Sugar Acetyltransferase from Campylobacter jejuni (2017)

The glycoproteins of selected microbial pathogens often include highly modified carbohydrates such as 2,4-diacetamidobacillosamine (diNAcBac). These glycoconjugates are involved in host-cell interactions and may be associated with the virulence of medically significant Gram-negative bacteria. In light of genetic studies demonstrating the attenuated virulence of bacterial strains in which modified carbohydrate biosynthesis enzymes have been knocked out, we are developing small molecule inhibitors of selected enzymes as tools to evaluate whether such compounds modulate virulence. We performed fragment-based and high-throughput screens against an amino-sugar acetyltransferase enzyme, PglD, involved in biosynthesis of UDP-diNAcBac in Campylobacter jejuni. Herein we report optimization of the hits into potent small molecule inhibitors (IC<sub>50</sub> < 300 nM). Biophysical characterization shows that the best inhibitors are competitive with acetyl coenzyme A and an X-ray cocrystal structure reveals that binding is biased toward occupation of the adenine subpocket of the AcCoA binding site by an aromatic ring.
Electrochemical Reaction of Lithium with Cobalt Fluoride Thin Film Electrode (2005)

To extend the electrochemical reaction mechanisms of transition-metal compounds based on metal cobalt as the anode with Li, the electrochemical reaction of with Li was first investigated. A lithium phosphorous oxynitride (Lipon) thin film coating on the surface of was fabricated as a separator between and liquid electrolyte to avoid a solution of Interestingly, the electrochemical behavior of the cell was reversible. The as-deposited, lithiated, and delithiated thin film electrode was characterized by ex situ scanning electron microscopy, X-ray diffraction, and X-ray photoelectron spectroscopy measurements. It is very difficult to understand the reversible decomposition of LiF under potentials less than 6.1 V vs. so an attempt was made to theoretically analyze the reaction of LiF with metal Co. The stable formation and further dissociation of CoLiF may be one of the main pathways in the reversible electrochemical reaction of with Li. © 2004 The Electrochemical Society. All rights reserved.
Clinical features of children and adolescents with multiple sclerosis (2007)

There is increasing appreciation that multiple sclerosis (MS) can begin in childhood or adolescence, but pediatric MS continues to be a rare entity, with an estimated 2 to 5% of patients with MS experiencing their first clinical symptoms before age 16. A prompt diagnosis of pediatric MS is important to optimize overall management of both the physical and social impact of the disease. The widespread use of disease-modifying therapies (DMT) for MS in adults, as early as following an initial isolated episode, has led to the use of DMT in children and adolescents with MS. However, it is imperative to distinguish pediatric MS from other childhood CNS inflammatory demyelinating disorders such as acute disseminated encephalomyelitis. Although increasing evidence suggests a slower disease course in children with MS compared to adults, significant disability can still accumulate by early adulthood. Furthermore, associated neurocognitive deficits can impair both academic and psychosocial function at a critical juncture in a young person's life. This article reviews the clinical characteristics, neuroimaging, paraclinical findings, disease course, epidemiology, genetics, and pathophysiology of pediatric MS vis-à-vis adult MS. Further research of pediatric MS may advance our understanding of MS pathophysiology in general, as well as improve the long-term health care outcomes of children and adolescents diagnosed with MS.
Strain and charge distribution in GaN-AlN-GaN semiconductor-insulator-semiconductor structure for arbitrary growth orientation (1993)

We demonstrate that, in a GaN-AlN-GaN semiconductor-insulator-semiconductor structure, the strain-induced electric fields across the interface depend on the angle, θ, between the c axis and the growth direction. The magnitude of the strain induced polarization has a maximum in (0001) crystallographic direction (θ=0°) and a subsidiary maximum near θ=70°. This angular dependence is a unique feature of wurtzite-type structures. Considering θ as an independent parameter for device design, one can obtain structures with flat band voltage shift from 0 to 1.5 V for 30 Å AlN film, with different positions of accumulation-depletion regions, and with electron (hole) charge varying from 0 to more than 1012 cm−2.
Fabrication of electron injecting Mg:Ag alloy electrodes for organic light-emitting diodes with radio frequency magnetron sputter deposition (1996)

Electron injecting electrodes made of magnesium and silver alloys (Mg:Ag) with a wide range of Ag concentration from 0 to 26.6 at. % were successfully fabricated for organic light-emitting diodes (LEDs) by using the radio frequency sputter deposition technique. The LED characteristics such as intensity, turn-on voltage, and durability of electroluminescence were strongly dependent on the Mg:Ag composition. Both the work function and the structural order of these Mg:Ag electrodes played a crucial role in determining the LED characteristics.