gebhart/patrepeval huggingface dataset:
Isolation and characterization of a major tandem repeat family from the human X chromosome (1983)

We report the identification and characterization of a family of repeated restriction fragments whose molecular organization is apparently specific to the human X chromosome. This fragment, identified as an ethidium bromide-staining 2.0 kilobase (kb) band in BamHI-digested DNA from a Chinese hamster-human somatic cell hybrid containing a human X chromosome, has been cloned into pBR325 and characterized. The 2.0 kb repeated family has been assigned to the Xp11 leads to Xq12 region on the X by Southern blot analysis of somatic cell hybrids and is predominantly arranged in tandem clusters of up to seven 2.0 kb monomers. Homologous DNA sequences, not organized as 2.0 kb BamHI fragments, are found elsewhere on the X chromosome and on at least some autosomes, but are not found on the Y chromosome. From a dosing experiment using various amounts of the cloned repeat, we estimate that there are 5,000-7,500 copies of the 2.0 kb BamHI repeat per haploid genome. Since the vast majority, if not all, of these are confined to the X chromosome, this repeated DNA family must account for 5-10% of all X chromosome DNA and must constitute the major sequence component of the pericentromeric region of the X.
The Value of FDG Positron Emission Tomography in the Management of Patients with Breast Cancer (2005)

Increasing experience with positron emission tomography (PET) scanning in breast cancer patients is revealing a significant role for this imaging modality. This report summarizes the experience of 2-[F18]fluoro-2-deoxy-D-glucose (FDG) PET scanning in 165 breast cancer patients from the BC Cancer Agency, British Columbia, Canada, and reviews the literature on this topic. Using the database at PETSCAN Vancouver, we identified imaged patients with a diagnosis of breast cancer. We then conducted a retrospective review of these patients' BC Cancer Agency charts to extract demographic and follow-up information. Between November 2000 and March 2003 we identified 165 patients with histologically confirmed breast cancer who had undergone PET scanning, were registered at the BC Cancer Agency, and had follow-up information. The median patient age was 52 years. The sensitivity of PET in detecting axillary metastases was 28%, and the specificity was 86%. At diagnosis, 5% of patients were diagnosed with distant metastases. In patients undergoing PET scanning because of suspected recurrence, the sensitivity and specificity for detecting recurrence were 89% and 88%, respectively. Distant metastases were demonstrated in 30% of patients who were thought only to have local-regional recurrence. The results suggest that there are two clinical situations in which PET appears to be particularly valuable. The first is in the evaluation of patients who are suspected of having a tumor recurrence. The other is in identifying patients with multifocal or distant sites of malignancy who otherwise appear to have an isolated, potentially curable, local-regional recurrence.
Characterization of the Escherichia coli thyA gene and its amplified thymidylate synthetase product. (1983)

The 7.8-kilobase HindIII insert in phage lambda NM589thyA [Borck, K., Beggs, J.D., Brammar, W.J., Hopkins, A.S. & Murray, N. (1976) Mol. Gen. Genet. 146, 199] was confirmed as originating from Escherichia coli by hybridization analysis and was shown to encode the thymidylate synthetase (5,-10-methylenetetrahydrofolate:dUMP C-methyltransferase EC 2.1.1.45) of E. coli K-12 by using biochemical, structural, and immunologic criteria. The 7.8-kilobase insert was reduced in size to a quasi-random population of DNA subfragments by partial digestion with the 4-base-pair recognition enzymes Alu I and Hae III. A clone containing a 1.1- to 1.2-kilobase fragment that encompassed the gene was obtained from this mixture by selecting for Thy+ recombinants. Fusion of this DNA fragment to the phage lambda rho L promoter in plasmid pKC30 revealed the direction of transcription of the thyA gene, and, in a phage lambda lysogen containing a thermolabile repressor, intracellular synthetase levels were increased about 700-fold. The enzyme was purified to homogeneity from this source by affinity chromatography, and some of its properties are described.
A Gene Encoding the Cytokinin Enzyme ZeatinO-Xylosyltransferase of Phaseolus vulgaris1 (1999)

Zeatin is the most active and ubiquitous form of the naturally occurring cytokinins. Glycosyl conjugates of zeatin are found in many plant tissues and are considered important for storage and protection against degradative enzymes. Two enzymes catalyzing the formation of O-glycosyl derivatives of zeatin have been characterized, O-glucosyltransferase and O-xylosyltransferase, occurring in seeds of lima bean (Phaseolus lunatus) and bean (Phaseolus vulgaris), respectively. Recently, the ZOG1 gene (zeatin O-glucosyltansferase) was isolated from P. lunatis (). Based on the ZOG1 sequence, the ZOX1 gene (zeatin O-xylosyltransferase) was cloned from P. vulgaris. ZOX1 contains an open reading frame of 1362 bp that codes for a 454-amino acid peptide of 51 kD. The recombinant protein has properties identical to the native enzyme: it catalyzes O-xylosylzeatin formation with UDP-Xyl as a glycosyl donor but does not recognize UDP-Glucose as a substrate. The ZOX1 and ZOG1 genes exhibit 93% identity at the nucleotide level and 90% similarity at the amino acid level. Neither gene contains introns. These zeatin-specific genes and their promoters will be useful for studies of the regulation of active versus storage forms of cytokinins. Comparison of sequences encoding similar enzymes with distinct substrate specificity may lead to identification of epitopes specific to cytokinin and glycosyl donor molecules.
Nonradiating edges and four edges gap-coupled multiple resonator broad-band microstrip antennas (1985)

Two novel configurations for increasing the impedance bandwidth of the microstrip patch antennas are described. One of these configurations uses two additional resonators which are gap-coupled to the nonradiating edges of a rectangular patch, whereas in the second case, four additional resonators are gap-coupled to the four edges of a rectangular patch. Green's function approach and segmentation method are used for analysis. The experimental results are in reasonable agreement with analysis and impedance bandwidths of 480 MHz and 815 MHz are obtained for the three resonators and five resonators configurations, respectively (in <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">S</tex> -band with substrate <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\epsilon_{r} = 2.55</tex> and thickness = 0.318 cm).
Human Early Placental Development: Potential Roles of the Endometrial Glands (2007)

There is strong evidence that the endometrial glands play a key role in regulating placental development in many domestic species, but their contribution in the human has largely been ignored once implantation is complete. Here we re-evaluate their role during the first trimester. Connections between the glands and the intervillous space have been observed from day 17 post-conception through to the end of the first trimester. In the absence of a maternal arterial supply to the early placenta it is believed that the carbohydrate- and lipid-rich secretions represent an important source of nutrients during the first trimester, and possibly the beginning of the second trimester. The secretions also contain a variety of growth factors that may regulate placental morphogenesis since their receptors are present on villous and extravillous trophoblast, and villous endothelial cells. Other components of the secretions may modulate immune responses and trophoblast invasion at the materno-fetal interface. We speculate that lactogenic hormones secreted by decidual cells and the syncytiotrophoblast may act in concert with human chorionic gonadotropin to stimulate the secretory activity of glandular epithelial cells during the first trimester. There is circumstantial evidence, but as yet no conclusive proof, that deficient glandular activity is associated with pregnancy failure in the human.
A Unique Hydrophobic Cluster Near the Active Site Contributes to Differences in Borrelidin Inhibition among Threonyl-tRNA Synthetases (2004)

Borrelidin, a compound with anti-microbial and anti-angiogenic properties, is a known inhibitor of bacterial and eukaryal threonyl-tRNA synthetase (ThrRS). The inhibition mechanism of borrelidin is not well understood. Archaea contain archaeal and bacterial genre ThrRS enzymes that can be distinguished by their sequence. We explored species-specific borrelidin inhibition of ThrRSs. The activity of ThrRS from Sulfolobus solfataricus and Halobacterium sp. NRC-1 was inhibited by borrelidin, whereas ThrRS enzymes from Methanocaldococcus jannaschii and Archaeoglobus fulgidus were not. In Escherichia coli ThrRS, borrelidin binding induced a conformational change, and threonine was not activated as shown by ATP-PP(i) exchange and a transient kinetic assay measuring intrinsic tryptophan fluorescence changes. These assays further showed that borrelidin is a noncompetitive tight binding inhibitor of E. coli ThrRS with respect to threonine and ATP. Genetic selection of borrelidin-resistant mutants showed that borrelidin binds to a hydrophobic region (Thr-307, His-309, Cys-334, Pro-335, Leu-489, Leu-493) proximal to the zinc ion at the active site of the E. coli ThrRS. Mutating residue Leu-489 --> Trp reduced the space of the hydrophobic cluster and resulted in a 1500-fold increase of the K(i) value from 4 nM to 6 microm. An alignment of ThrRS sequences showed that this cluster is conserved in most organisms except for some Archaea (e.g. M. jannaschii, A. fulgidus) and some pathogens (e.g. Helicobacter pylori). This study illustrates how one class of natural product inhibitors affects aminoacyl-tRNA synthetase function, providing potentially useful information for structure-based inhibitor design.
Oligonucleotide Sequential Bis-Conjugation via Click−Oxime and Click−Huisgen Procedures (2010)

A novel procedure has been developed for the bis-conjugation of oligonucleotides using CuAAC (click-H) and oxime (click-O) tethering strategies. Oligonucleotides bearing a 5'-alkyne function and a 3'-aldehyde precursor were synthesized and were bis-conjugated with various reporters including azido carbohydrate or fluorescent dye and aminooxy peptide or carbohydrate. Versatility of the method was demonstrated by performing click-O prior to click-H and vice versa. Interestingly, when click-O is achieved prior to click-H, no purification is required in between, allowing a sequential one-pot protocol.
The Na-K-Cl Cotransporter of Secretory Epithelia (2000)

The Na-K-Cl cotransporters are a class of ion transport proteins that transport Na, K, and Cl ions into and out of cells in an electrically neutral manner, in most cases with a stoichiometry of 1Na:1K:2Cl. To date, two Na-K-Cl cotransporter isoforms have been identified: NKCC1, which is present in a wide variety of secretory epithelia and non-epithelial cells; and NKCC2, which is present exclusively in the kidney, in the epithelial cells of the thick ascending limb of Henle's loop and of the macula densa. Both NKCC isoforms represent part of a diverse family of cation-chloride cotransport proteins that share a common predicted membrane topology; this family also includes Na-Cl cotransporters and multiple K-Cl cotransporter isoforms. In secretory epithelia, the regulation of NKCC1, which is typically present on the basolateral membrane, is tightly coordinated with that of other transporters, including apical Cl channels, to maintain cell volume and integrity during active salt and fluid secretion. Changes in intracellular [Cl] ([Cl]i) appear to be involved in this regulation of NKCC1, which is directly phosphorylated by an unknown protein kinase in response to various secretagogues as well as reductions in [Cl]i and cell volume. This review focuses on structure-function relationships within NKCC1 and on recent developments pertaining to NKCC1 regulation at cellular and molecular levels.
Embroidering electrical interconnects with conductive yarn for the integration of flexible electronic modules into fabric (2005)

This paper shows how common embroidery can be used to integrate electronics into textile environment in a light and cost efficient way. A mechanism has been developed to embroider through flexible electronic modules using conductive yarn, thus creating an interconnection with other modules like sensors, batteries, textile keyboards, etc. Mold encapsulation has been found to improve the electrical contact and support the reliability of the whole system.
Location cache (2004)

While set-associative caches incur fewer misses than direct-mapped caches, they typically have slower hit times and higher power consumption, when multiple tag and data banks are probed in parallel. This paper presents the location cache structure which significantly reduces the power consumption for large set-associative caches. We propose to use a small cache, called location cache to store the location of future cache references. If there is a hit in the location cache, the supported cache is accessed as a direct-mapped cache. Otherwise, the supported cache is referenced as a conventional set-associative cache.The worst case access latency of the location cache system is the same as that of a conventional cache. The location cache is virtually indexed so that operations on it can be performed in parallel with the TLB address translation. These advantages make it ideal for L2 cache systems where traditional way-predication strategies perform poorly.We used the CACTI cache model to evaluate the power con-sumption and access latency of proposed cache architecture. Simplescalar CPU simulator was used to produce final results. It is shown that the proposed location cache architecture is power-efficient. In the simulated cache configurations, up-to 47% of cache accessing energy and 25% of average cache access latency can be reduced.
A phase-based approach to the estimation of the optical flow field using spatial filtering (2002)

We introduce a new technique for estimating the optical flow field, starting from image sequences. As suggested by Fleet and Jepson (1990), we track contours of constant phase over time, since these are more robust to variations in lighting conditions and deviations from pure translation than contours of constant amplitude. Our phase-based approach proceeds in three stages. First, the image sequence is spatially filtered using a bank of quadrature pairs of Gabor filters, and the temporal phase gradient is computed, yielding estimates of the velocity component in directions orthogonal to the filter pairs' orientations. Second, a component velocity is rejected if the corresponding filter pair's phase information is not linear over a given time span. Third, the remaining component velocities at a single spatial location are combined and a recurrent neural network is used to derive the full velocity. We test our approach on several image sequences, both synthetic and realistic.
Biochemical and structural exploration of the catalytic capacity of Sulfolobus KDG aldolases (2007)

Aldolases are enzymes with potential applications in biosynthesis, depending on their activity, specificity and stability. In the present study, the genomes of Sulfolobus species were screened for aldolases. Two new KDGA [2-keto-3-deoxygluconate (2-oxo-3-deoxygluconate) aldolases] from Sulfolobus acidocaldarius and Sulfolobus tokodaii were identified, overexpressed in Escherichia coli and characterized. Both enzymes were found to have biochemical properties similar to the previously characterized S. solfataricus KDGA, including the condensation of pyruvate and either D,L-glyceraldehyde or D,L-glyceraldehyde 3-phosphate. The crystal structure of S. acidocaldarius KDGA revealed the presence of a novel phosphate-binding motif that allows the formation of multiple hydrogen-bonding interactions with the acceptor substrate, and enables high activity with glyceraldehyde 3-phosphate. Activity analyses with unnatural substrates revealed that these three KDGAs readily accept aldehydes with two to four carbon atoms, and that even aldoses with five carbon atoms are accepted to some extent. Water-mediated interactions permit binding of substrates in multiple conformations in the spacious hydrophilic binding site, and correlate with the observed broad substrate specificity.
Bioabsorbable Coronary Stents (2009)

An ideal stent should furnish best acute outcomes after PCI by sealing intimal flaps and optimizing lumen size. It should control restenosis by limiting negative remodeling and by controlling excessive healing by delivery of an antiproliferative drug. Beyond 6 months, a permanent implant has no useful function and has possible disadvantages including the potential for late thrombosis. The concept of a stent that does its job and disappears has appeal.44 A number of different materials ranging from magnesium to a variety of polymers have been used to construct stents of different designs. Some of these are being tested in clinical trials. The best outcomes to date have been with the BVS everolimus-eluting PLLA stent where in the Absorb trial, cohort A at 2 years, the stent was safe in the small number of patients with simple lesions.9,11 Indeed, there is a suggestion of luminal enlargement between 6 months and 2 years, return of vasomotion, and endothelial function. These findings need to be confirmed in larger trials in more complex lesions. A hope is that a healed, normally functioning vessel free of foreign body and restenosis will be free of the risk of late thrombosis. Time will tell if this dream will come true.
1:1 Complex of Octadecanoic Acid and 3-Pyridinecarboxamide (1998)

An equimolar mixture of stearic acid (octadecanoic acid) and nicotinamide (3-pyridinecarboxamide) in acetone yields crystals of a 1:1 complex, C18H36O2·C6H6N2O. In this structure, the 1:1 complex forms a dimer through hydrogen bonds between the amide groups, thus forming a lamellar structure. The alkyl chain of stearic acid has an all-trans conformation.
Genome-wide association study identifies germline polymorphisms associated with relapse of childhood acute lymphoblastic leukemia (2012)

With the use of risk-directed therapy for childhood acute lymphoblastic leukemia (ALL), outcome has improved dramatically in the past 40 years. However, a substantial portion of patients, many of whom have no known risk factors, experience relapse. Taking a genome-wide approach, in the present study, we evaluated the relationships between genotypes at 444 044 single nucleotide polymorphisms (SNPs) with the risk of relapse in 2535 children with newly diagnosed ALL after adjusting for genetic ancestry and treatment regimen. We identified 134 SNPs that were reproducibly associated with ALL relapse. Of 134 relapse SNPs, 133 remained prognostic after adjusting for all known relapse risk factors, including minimal residual disease, and 111 were significant even among patients who were negative for minimal residual disease after remission induction therapy. The C allele at rs7142143 in the PYGL gene was associated with 3.6-fold higher risk of relapse than the T allele (P = 6.7 × 10(-9)). Fourteen of the 134 relapse SNPs, including variants in PDE4B and ABCB1, were also associated with antileukemic drug pharmacokinetics and/or pharmacodynamics. In the present study, we systematically identified host genetic variations related to treatment outcome of childhood ALL, most of which were prognostic independent of known risk factors for relapse, and some of which also influenced outcome by affecting host dis-position of antileukemic drugs. All trials are registered at www.clinicaltrials.gov or www.cancer.gov (COG P9904: NCT00005585; COG P9905: NCT00005596; COG P9906: NCT00005603; St Jude Total XIIIB: NCI-T93-0101D; and St Jude Total XV: NCT00137111).
LIFRβ and gp130 as Heterodimerizing Signal Transducers of the Tripartite CNTF Receptor (1993)

The ciliary neurotrophic factor (CNTF) receptor complex is shown here to include the CNTF binding protein (CNTFR alpha) as well as the components of the leukemia inhibitory factor (LIF) receptor, LIFR beta (the LIF binding protein) and gp130 [the signal transducer of interleukin-6 (IL-6)]. Thus, the conversion of a bipartite LIF receptor into a tripartite CNTF receptor apparently occurs by the addition of the specificity-conferring element CNTFR alpha. Both CNTF and LIF trigger the association of initially separate receptor components, which in turn results in tyrosine phosphorylation of receptor subunits. Unlike the IL-6 receptor complex in which homodimerization of gp130 appears to be critical for signal initiation, signaling by the CNTF and LIF receptor complexes depends on the heterodimerization of gp130 with LIFR beta. Ligand-induced dimerization of signal-transducing receptor components, also seen with receptor tyrosine kinases, may provide a general mechanism for the transmission of a signal across the cell membrane.
A High Glucose Concentration Stimulates the Expression of Monocyte Chemotactic Peptide 1 in Human Mesangial Cells (1998)

The mechanism of glomerular infiltration of monocytes remains unknown in diabetic nephropathy. We examined the effect of a high glucose concentration on monocyte chemotactic peptide 1 (MCP-1) expression in human mesangial cells (MCs) by using enzyme-linked immunosorbent assay and reverse transcription coupled with polymerase chain reaction (PCR). More than a 50% increase in the MCP-1 protein production was observed in MCs cultured in high-glucose medium (450 mg/dl) as compared to normal glucose (100 mg/dl; 1,496 +/- 75 vs. 966 +/- 15 pg/ml after 24 h, 1,910 +/- 93 vs. 1,250 +/- 55 pg/ml after 48 h). Semiquantitative PCR showed that phorbol myristate acetate (100 nM) increased the ratio of PCR products for MCP-1 to housekeeping gene glyceraldehyde-3-phosphate dehydrogenase on densitometric results at 24 h by 2.7-fold, which was prevented by calphostin C (200 nM) pretreatment. High glucose increased the ratio by 3-fold as compared to normal glucose at 24 h (0.72 +/- 0.11 vs. 0.24 +/- 0.01). This was also suppressed by calphostin C pretreatment. These findings demonstrate that high glucose can directly increase MCP-1 expression in MCs, which may contribute to monocyte infiltration in diabetic nephropathy, and this is regulated by protein kinase C.
Filamentous bacterial viruses (1969)

The filamentous bacterial virus is a simple and well-characterized model system for studying how genetic information is transformed into molecular machines. The viral DNA is a single-stranded circle coding for about 10 proteins. The major viral coat protein is largely α-helical, with about 46 amino acid residues. Several thousand identical copies of this protein in a helical array form a hollow cylindrical tube 1–2μ long, of outer diameter 60 A and inner diameter 20 A, with the twisted circular DNA extending down the core of the tube. Before assembly, the viral coat protein spans the cell membrane, and assembly involves extrusion of the coat from the membrane. X-ray fibre diffraction patterns of the Pf 1 species of virus at 4°C, oriented in a strong magnetic field, give three-dimensional data to 4 A resolution. An electron density map calculated from native virus and a single iodine derivative, using the maximum entropy technique, shows a helix pitch of 5.9 A. This may indicate a stretched A-helix, or it may indicate a partially 310 helix conformation, resulting from the fact that the coat protein is an integral membrane protein before assembly, and is still in the hydrophobic environment of other coat proteins after assembly.