gebhart/patrepeval huggingface dataset:
A Three-Megabase Yeast Artificial Chromosome Contig Spanning the C57BL Mouse Igh Locus (2002)

The mouse Ig H chain (Igh) complex locus is composed of >100 gene segments encoding the variable, diversity, joining, and constant portions of the Ab H chain protein. To advance the characterization of this locus and to identify all the V(H) genes, we have isolated the entire region from C57BL/6 and C57BL/10 as a yeast artificial chromosome contig. The mouse Igh locus extends approximately three megabases and contains at least 134 V(H) genes classified in 15 partially interspersed families. Two non-Igh pseudogenes (Odc-rs8 and Rpl32-rs14) were localized in the distal part of the locus. This physical yeast artificial chromosome map will provide important structure and guidance for the sequencing of this large, complex, and highly repetitive locus.
Autoxidation of human low density lipoprotein: loss of polyunsaturated fatty acids and vitamin E and generation of aldehydes (1987)

The alteration of structural and biological properties of human plasma low density lipoprotein (LDL) exposed to oxidative conditions is in part ascribed to lipid peroxidation. The objective of this investigation was to measure quantitatively several parameters in oxidizing LDL indicative for lipid peroxidation. Exposure of freshly prepared EDTA-free LDL to an oxygen-saturated buffer led to a complete depletion of alpha- and gamma-tocopherol within 6 hr, thereafter lipid peroxidation commenced as indicated by the kinetics of the loss of linoleic (18:2) and arachidonic (20:4) acids, the formation of aldehydic lipid peroxidation products and fluorescent apoB. Within 24 hr of oxidation, on average 79 nmol of 18:2 (initial 345) and 12.8 nmol of 20.4 (initial 25.6) were oxidized per mg of LDL and the sample contained in total 7.1 nmol of aldehydes with the following molar distribution: 36.6% malonaldehyde, 25% hexanal, 8.9% propanal, 8.2% 4-hydroxynonenal, 7.6% butanal, 4.1% 2.4-heptadienal, 3.4% pentanal, 3.4% 4-hydroxyhexenal, and 2.5% 4-hydroxyoctenal. Malonaldehyde was predominantly (93%) in the aqueous phase, whereas the other aldehydes remained mostly (34-98%) within the LDL particle, where the total aldehyde concentration was in the range of 12 mM. Oxidized LDL exhibited a 1.6-fold enhanced electrophoretic mobility. Similarily, native LDL incubated for 5 hr with aldehydes showed increased electrophoretic mobility. At equal concentrations (5 mM) 4-hydroxynonenal was most effective, followed by 2,4-heptadienal, hexanal, and malonaldehyde. This study reports for the first time the rate and extent of the change of LDL constituents occurring during lipid peroxidation.
An economic paradigm for query processing and data migration in Mariposa (2002)

Many new database applications require very large volumes of data. Mariposa is a database system under construction at Berkeley responding to this need. This system combines the best features of traditional distributed database systems, object-oriented DBMSs, tertiary memory file systems and distributed file systems. Mariposa objects can be stored over thousands of autonomous sites and on memory hierarchies with very large capacity. This scale of the system leads to complex query execution and storage management issues, unsolvable in practice with traditional techniques. We propose an economic paradigm as the solution. A query receives a budges which it spends to obtain the answers. Each site attempts to maximize income by buying and selling storage objects, and processing queries for locally stored objects. We present the protocols which underlie the Mariposa economy.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Stabilization of coordinatively unsaturated Ir4clusters with bulky ligands: a comparative study of chemical and mechanical effects (2011)

The synthesis and characterization of new cluster compounds represented by the series Ir(4)(CO)(12-x)L(x) (L = tert-butyl-calix[4]-arene(OPr)(3)(OCH(2)PPh(2)); x = 2 and 3) is reported using ESI mass spectrometry, NMR spectroscopy, IR spectroscopy and single-crystal X-ray diffraction. Thermally driven decarbonylation of the cluster compound series represented by x = 1-3 according to the formula above is followed via FTIR and NMR spectroscopies, and dynamic light scattering in toluene solution. The propensity of these clusters to decarbonylate in solution is shown to be directly correlated with number density of adsorbed calixarene phosphine ligands and controlled via Pauli repulsion between metal d and CO 5σ orbitals. The tendency for cluster aggregation unintuitively follows a trend that is exactly opposite to the cluster's propensity to decarbonylate. No cluster aggregation is observed for clusters consisting of x = 3, even after extensive decarbonylation via loss of all bridging CO ligands and coordinative unsaturation. Some of the CO lost during thermal treatment via decarbonylation can be rebound to the coordinatively unsaturated cluster consisting of x = 3. In contrast, the clusters consisting of x = 1 and x = 2 both aggregate into large nanoparticles when treated under identical conditions. Clusters in which the calixarene phosphine ligand is replaced with a sterically less demanding PPh(2)Me ligand 6 lead to significantly less coordinative unsaturation upon thermal treatment. Altogether, these data support a mechanical model of accessibility in coordinatively unsaturated metal clusters in solution, which hinges on having at least three sterically bulky organic ligands per Ir(4) core.
Isolation and characterization of cDNA clones derived from the divergently transcribed gene in the region upstream from the human dihydrofolate reductase gene (1989)

Transcripts initiated in the region immediately upstream from the human dihydrofolate reductase gene but transcribed from the opposite strand have been identified in human cells. These divergent upstream transcripts are polyadenylated, start at 89 base pairs upstream from the dihydrofolate reductase major initiation site, and are composed of two species of 5.0 and 3.8 kilobases in length. We have isolated complementary DNA clones derived from the divergent transcripts and identified a 3.5-kilobase open reading frame in one of these clones. Computer-assisted sequence analyses have shown that there is no significant sequence homology between the putative amino acid sequence and known protein sequences. This arrangement of two divergent transcriptional units suggests that the expression of these two genes may be regulated by a bidirectional promoter with common sequence elements.
[Surgical therapy strategies in carcinoma in situ of the breast]. (1998)

The surgical treatment of carcinoma in situ of the breast depends on the histological type. After detecting a lobular carcinoma in situ (CLIS) either an intensive (aftercare) follow-up is recommended or a bilateral mastectomy. The choice for one of these two very different forms of therapy can be done only after intensive psychological dialog with patient. The reason for the different forms of further treatment is the multicentric and often bilateral occurrence of CLIS and the potential risk of developing an invasive cancer. The therapy of the ductal carcinoma in situ (DCIS), which often spread out in a segment of one breast, is the total excision of the lesion with clear margins. The Van Nuys Prognostic Index depending on the histological results (tumor-diameter, thickness of clear margins, pathocytologic classification) indicates further treatment such as radiotherapy or mastectomy to lower the chance of local recurrence.
Size dependent platelet subpopulations: relationship of platelet volume to ultrastructure, enzymatic activity, and function (1982)

A method for the separation of platelets on the basis of their size has been developed using counterflow centrifugation. Platelets were separated, free of plasma proteins and other cells, into seven subpopulations. The smallest‐sized platelets, designated as Fraction 1, had a mean platelet volume (MPV) of 3.94 ± 0.60 μm 3 (SD). Each successive fraction had a progressively larger MPV. The MPV for the largest‐sized platelets, designated Fraction 7, was 8.19 ± 0.64 μm 3 . The MPV for the original platelets prior to fractionation was 6.57 ± 0.61 μm 3 . The mean density of Fraction 1 platelets was 1.067 ± 0.002 g/cm 3 , while Fraction 7 had a mean density of 1.072 ± 0.001 g/cm 3 . Transmission electron microscopy demonstrated that Fraction 1 had 4.3 ± 0.9 dense bodies per platelet, and Fraction 7 had 12.6 ± 2.4 dense bodies per platelet. Platelet LDH activity showed that the Fraction 1 platelets had 4.77 ± 0.92 iu per 10 10 platelets; Fraction 7 platelets had 14.88 ± 1.23 iu per 10 10 platelets. The LDH activity in the platelets before separation into subpopulations was 9.47 ± 1.45 iu per 10 10 platelets.
Repression of Acetolactate Synthase Activity through Antisense Inhibition (Molecular and Biochemical Analysis of Transgenic Potato (Solanum tuberosum L. cv Desiree) Plants) (1995)

Acetolactate synthase (ALS), the first enzyme in the biosynthetic pathway of leucine, valine, and isoleucine, is the biochemical target of different herbicides. To investigate the effects of repression of ALS activity through antisense gene expression we cloned an ALS gene from potato (Solanum tuberosum L. cv Desiree), constructed a chimeric antisense gene under control of the cauliflower mosaic virus 35S promoter, and created transgenic potato plants through Agrobacterium tumefaciens-mediated gene transfer. Two regenerants revealed severe growth retardation and strong phenotypical effects resembling those caused by ALS-inhibiting herbicides. Antisense gene expression decreased the steady-state level of ALS mRNA in these plants and induced a corresponding decrease in ALS activity of up to 85%. This reduction was sufficient to generate plants almost inviable without amino acid supplementation. In both ALS antisense and herbicide-treated plants, we could exclude accumulation of 2-oxobutyrate and/or 2-aminobutyrate as the reason for the observed deleterious effects, but we detected elevated levels of free amino acids and imbalances in their relative proportions. Thus, antisense inhibition of ALS generated an in vivo model of herbicide action. Furthermore, expression of antisense RNA to the enzyme of interest provides a general method for validation of potential herbicide targets.
Nano-Featured Scaffolds for Tissue Engineering: A Review of Spinning Methodologies (2006)

Tissue engineering is a multidisciplinary field that is rapidly emerging as a promising new approach in the restoration and reconstruction of imperfect tissues. In this approach, scaffolds play a pivotal role in supporting the cells to accommodate and guide their growth into a specific tissue; therefore, designing scaffolds that are favorable to cellular growth is of great importance. Electrospinning is a straightforward, cost-effective, and versatile technique that has been applied recently for the fabrication of nano-featured scaffolds suitable for tissue engineering. By mimicking a natural extracellular matrix, it offers many advantages over conventional scaffold methodologies. This paper reviews the current state of art of designing nanostructure scaffolds by using the electrospinning technique. Furthermore, an overview of this technique and its spinning mechanism is described, with special attention to areas of interest to the readers.
Cell Depletion Due to Diphtheria Toxin Fragment A after Cre-Mediated Recombination (2004)

Abnormal cell loss is the common cause of a large number of developmental and degenerative diseases. To model such diseases in transgenic animals, we have developed a line of mice that allows the efficient depletion of virtually any cell type in vivo following somatic Cre-mediated gene recombination. By introducing the diphtheria toxin fragment A (DT-A) gene as a conditional expression construct (floxed lacZ-DT-A) into the ubiquitously expressed ROSA26 locus, we produced a line of mice that would permit cell-specific activation of the toxin gene. Following Cre-mediated recombination under the control of cell-type-specific promoters, lacZ gene expression was efficiently replaced by de novo transcription of the Cre-recombined DT-A gene. We provide proof of this principle, initially for cells of the central nervous system (pyramidal neurons and oligodendrocytes), the immune system (B cells), and liver tissue (hepatocytes), that the conditional expression of DT-A is functional in vivo, resulting in the generation of novel degenerative disease models.
Active zone self-similarity of fractal-Sierpinskiantenna verified using infra-red thermograms (1999)

The surface current distribution of a Sierpinski fractal antenna shows a self-similar behaviour determined by the self-similar properties of its geometry. The application of infra-red thermography to electromagnetic near field detection allows the experimental verification of the active region scaling of a fractal antenna operating at different bands.
Biotechnological applications of mobile group II introns and their reverse transcriptases: gene targeting, RNA-seq, and non-coding RNA analysis (2014)

Mobile group II introns are bacterial retrotransposons that combine the activities of an autocatalytic intron RNA (a ribozyme) and an intron-encoded reverse transcriptase to insert site-specifically into DNA. They recognize DNA target sites largely by base pairing of sequences within the intron RNA and achieve high DNA target specificity by using the ribozyme active site to couple correct base pairing to RNA-catalyzed intron integration. Algorithms have been developed to program the DNA target site specificity of several mobile group II introns, allowing them to be made into 'targetrons.' Targetrons function for gene targeting in a wide variety of bacteria and typically integrate at efficiencies high enough to be screened easily by colony PCR, without the need for selectable markers. Targetrons have found wide application in microbiological research, enabling gene targeting and genetic engineering of bacteria that had been intractable to other methods. Recently, a thermostable targetron has been developed for use in bacterial thermophiles, and new methods have been developed for using targetrons to position recombinase recognition sites, enabling large-scale genome-editing operations, such as deletions, inversions, insertions, and 'cut-and-pastes' (that is, translocation of large DNA segments), in a wide range of bacteria at high efficiency. Using targetrons in eukaryotes presents challenges due to the difficulties of nuclear localization and sub-optimal magnesium concentrations, although supplementation with magnesium can increase integration efficiency, and directed evolution is being employed to overcome these barriers. Finally, spurred by new methods for expressing group II intron reverse transcriptases that yield large amounts of highly active protein, thermostable group II intron reverse transcriptases from bacterial thermophiles are being used as research tools for a variety of applications, including qRT-PCR and next-generation RNA sequencing (RNA-seq). The high processivity and fidelity of group II intron reverse transcriptases along with their novel template-switching activity, which can directly link RNA-seq adaptor sequences to cDNAs during reverse transcription, open new approaches for RNA-seq and the identification and profiling of non-coding RNAs, with potentially wide applications in research and biotechnology.
Proteolysis of human eukaryotic translation initiation factor eIF4GII, but not eIF4GI, coincides with the shutoff of host protein synthesis after poliovirus infection (1998)

Eukaryotic initiation factor (eIF) 4GI is a component of the cap-binding protein complex eIF4F, which is required for cap-dependent translation. Infection of cells by poliovirus results in a precipitous decline of host cell protein synthesis, which is preceded by the cleavage of eIF4GI. Cleavage of eIF4GI results in the inhibition of cap-dependent translation. Poliovirus translation is not affected by eIF4GI cleavage, however, because poliovirus mRNA is translated by a cap-independent mechanism. Cleavage of eIF4GI alone cannot explain the shutoff of host protein synthesis, because after infection in the presence of inhibitors of virus replication, eIF4GI is cleaved, yet host protein synthesis is only partially inhibited. Here we show that eIF4GII, a recently discovered functional homolog of eIF4GI, is more resistant to poliovirus-mediated cleavage than eIF4GI, and that its proteolysis is concomitant with the shutoff of host cell protein synthesis. Moreover, infection with poliovirus in the presence of inhibitors of virus replication resulted in efficient cleavage of eIF4GI, but only partial proteolysis of eIF4GII. Thus, cleavage of both eIF4GI and eIF4GII appears to be required for the shutoff of host protein synthesis after poliovirus infection. These results explain several earlier reports documenting the lack of correlation between eIF4GI cleavage and inhibition of cellular mRNA translation after poliovirus infection.
Discovery and Characterization of Catalysts for Azide−Alkyne Cycloaddition by Fluorescence Quenching (2004)

Copper-based catalysts for the 1,3-dipolar cycloaddition of azides and alkynes were screened in parallel fashion using a fluorescence quenching assay. The method was designed to identify systems able to accelerate the coupling of reactants at micromolar concentrations in aqueous mixtures and to obtain quantitative comparisons of their activities. In addition to the tris(triazolylamines) previously reported, two types of compounds (bipy/phen and 2-pyridyl Schiff bases) were found to exhibit significant ligand-accelerated catalysis, with one complex showing especially dramatic rate enhancements. Preliminary explorations of the dependence of reaction rate on pH, ligand:Cu ratio, and Cu concentration are described.
An analytic model for the polymer grid triode (1996)

The polymer grid triode (PGT) is a novel semiconductor device constructed using a self-assembling porous conducting polyaniline (PANI) network placed between two semiconducting polymer layers, and sandwiched between metal electrodes. The structure behaves as a three-terminal device capable of current amplification, with the PANI network functioning as the control grid. An analysis of the generalized field-assisted carrier injection by tunneling, controlled by the grid voltage, is presented to model the charge injection and transport in the PGT. The results are in good agreement with the measured current–voltage characteristics. Further, an effective diode model for the PGT is introduced, and a simple, intuitive expression for charge transport in the presence of the grid network is obtained. In the effective diode regime, the current through the PGT is a function of (Vac−PVag); i.e., Iac≊I(Vac−PVag) where P is a geometric factor, as required for use in image processing applications. Other application possibilities for the PGT are surveyed, and the limitations of this device when placed in common circuit configurations are discussed.
High-performance sub-quarter-micrometer PMOSFET's on SOI (1993)

PMOS transistors with effective channel lengths down to 0.15 mu m have been fabricated on silicon-on-insulator (SOI) films. Gate oxide thicknesses of 5.5 and 10 nm are used. These P/sup +/ gate PMOS devices exhibit excellent short-channel behavior, low-source-drain resistance, and remarkably large current drive and transconductance. for T/sub ox/=5.5 nm, saturation transconductances of 274 mS/mm at 300 K and 352 mS/mm at 80 K are achieved, which are the highest reported values for this oxide thickness. The result is attributed to low series resistance, forward-bias body effect, and the reduction of body charge effect.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Wound healing : alternatives in management (1990)

Part 1 The wound healing environment: normal healing nutrition and wound healing factoring affecting repair bacteriology and infection control growth factors, extracellular matrix and wound healing. Part 2 Evaluation: methods of wound evaluation. Part 3 Principles and techniques: wound debridement and irrigation dressings electrical stimulation for wound healing adjunctive interventions for wound healing. Part 4 Case management and documentation: management of the insensate foot management of wounds secondary to vascular disease prevention and treatment of wounds cause by pressure documentation for reimbursement.
Associative Induction of Posttetanic and Long-Term Potentiation in CA1 Neurons of Rat Hippocampus (1986)

Electrical stimulation of fibers in the stratum radiatum causes an excitatory postsynaptic potential in CA1 neurons of the hippocampus. Other excitatory inputs to or direct depolarization of these CA1 neurons during stimulation of the stratum radiatum caused a subsequent increase in the excitatory postsynaptic potential. This enhancement was characterized as a brief potentiation (2 to 3 minutes, similar to posttetanic potentiation) and a long-term potentiation (presumed to be involved in learning and memory). These potentiations are probably induced by an interaction of the postsynaptic cell or other presynaptic terminals with the test presynaptic terminals.
Bi-substituted Effect on Phenylisoquinoline Iridium(III) Complexes (2005)

This paper studies the synthesis and photophysical properties of a series of bi-substituted phenylisoquinoline iridium(III) complexes. Interestingly, the bis[3-methyl-1-p-tolylisoquinolinato-N,C2‘] iridium(III) (acetylacetonate) (6a1) could be prepared even though the single-crystal X-ray crystallography data showed that there was steric hindrance due to the methyl group on the C-3 position to isoquinoline. Noticeably, the cyclic voltammetric (CV) measurements indicated that although these iridium(III) complexes have similar energy gaps, their E1/2(ox) are different from the mono-substituted (in phenyl ring) phenylisoquinoline iridium(III) complexes. This illustrates that the major influence of oxidation potential for iridium(III) complexes is the substituted isoquinoline ring. While all these complexes emitted in the red region, the bis[5-methyl-1-p-tolylisoquinolinato-N,C2‘] iridium(III) (acetylacetonate) (6c1) showed a higher brightness of 9299.36 cd/m2 at a higher current density of J = 63.69 mA/cm2 and a better luminance efficiency of 21.96 cd/A at a current density of J = 0.28 mA/cm2. The corresponding CIE (Commission International de L'Eclairage) coordinates are x = 0.67, y = 0.33.
Saser (Sound Amplification by Stimulated Emission of Radiation) (1997)

A theoretical scheme of a saser (Sound Amplification by Stimulated Emission of Radiation) is proposed. A liquid with gas bubbles is used as the active medium. Pumping is performed with an alternating electric field or mechanical vibrations of the resonator. Phase bunching of initially incoherent radiators (bubbles) occurs under the action of acoustic radiation forces. The proposed scheme is similar to that of a free-electron laser. Two models of an active medium are studied. In the first model it is assumed that all bubbles have the same radius. In the second model a continuous distribution of bubble radii is studied. The starting values for sasers with square and cylindrical resonators are calculated. It is shown that in all cases studied these conditions are identical, to within a numerical factor. The operation of a saser in a nonlinear regime and the directional pattern of a saser in the saturation regime are studied.
Synovial lymphoid neogenesis does not define a specific clinical rheumatoid arthritis phenotype (2008)

These findings indicate that synovial lymphoid neogenesis is associated with more severe synovial and systemic inflammation, but this is not confined to a specific clinical subset of RA.