gebhart/patrepeval huggingface dataset:
Cloning and molecular characterization of a novel chromosome specific centromere sequence of Chinese hamster (1994)

We isolated and characterized the first chromosome-specific satellite DNA (HC2sat) of Chinese hamster. This novel satellite was localized to the pericentric region of hamster chromosome 2. The 2.8 kb long repeat unit of HC2sat was identified and two such units were sequenced. Extended short range periodicity could not be revealed in repeat units. These elements are amongst the largest satellite repeat units reported from mammals to date. HC2sat is a major constituent of the pericentric region of CHO chromosome 2 representing a 7-14 Mb long DNA segment. Studies of long range organization of HC2sat indicated that the formation of the satellite array might occur in different phases and involved different amplification mechanisms.
Reducing Storage Management Costs via Informed User-Based Policies (2004)

Storage consumption continues to grow rapidly, especially with the popularity of multimedia files. Storage hardware costs represent a small fraction of overall management costs, which include frequent maintenance and backups. Our key approach to reducing total storage management costs is to reduce actual storage consumption. We achieve this in two ways. First, we classify files into categories of importance. Based on these categories, files can be backed up with various frequencies, or even not at all. Second, the system may also reclaim space based on a file’s importance (e.g., transparently compress old files). Our system provides a rich set of policies. We allow users to tailor their disk usage policies, offloading some of the management burdens from the system and its administrators. We have implemented the system and evaluated it. Performance overheads under normal use are negligible. We report space savings on modern systems ranging from 25 % to 76%, which result in extending storage lifetimes by 72%. 1
Determination of optical scattering properties of highly-scattering media in optical coherence tomography images (2004)

We developed a new algorithm that fits optical coherence tomography (OCT) signals as a function of depth to a general theoretical OCT model which takes into account multiple scattering effects. With use of this algorithm, it was possible to extract both the scattering coefficient and anisotropy factor from a particular region of interest in an OCT image. The extraction algorithm was evaluated against measurements from an integrating sphere on a set of tissue phantoms and yielded valid results. Finally, a preliminary ex vivo OCT investigation on human aortic specimen indicated that the algorithm may contribute importantly to differentiation between normal and atherosclerotic arteries. We conclude that this algorithm may facilitate tissue characterization by OCT.
The First Polar Body Can Be Used for the Production of Normal Offspring in Mice1 (1998)

The purpose of this study was to determine whether chromosomes in the first polar body can participate in normal embryonic development. In the mouse the majority of first polar bodies degenerate soon after ovulation, but a few remain viable for 10 h or more. When the contents of a live polar body were injected into an enucleated mature oocyte and examined 2 h later, the polar body chromosomes were arranged on a metaphase plate as seen prior to the secondary meiotic division. Such oocytes were fertilized normally by sperm injection. When 2-cell embryos were transferred to foster females, 30-57% developed into fertile offspring. This outcome supports a longstanding belief that chromosomes ejected into the first polar body have the same genetic potential as those remaining in the oocyte after the first meiotic division. As the chromosomes in the second polar body are known to have full potential to participate in normal embryonic development, it is theoretically possible to reproduce four offspring by using chromosomes in one oocyte.
A method for modulation transfer function determination from edge profiles with correction for finite-element differentiation (1987)

In this paper we describe a technique for determining the modulation transfer function (MTF) of an imaging system from an experimentally obtained edge profile. The technique includes an exact correction for the frequency passband of the finite-element differentiation required to obtain the line spread function from the edge spread function. This correction has been ignored by investigators in the past and is required whenever finite-element differentiation is used rather than analytic differentiation of a model fitted to the edge response data. The magnitude of the MTF correction is approximately 11% at f = fc/2 and approximately 57% at f = fc, where fc = fs/2 is the maximum frequency reproducible without aliasing with a sampling rate of fs. The correction is performed in the spatial frequency domain by multiplying the uncorrected MTF by 1/sinc (pi f/2fc). A computer simulation is presented to demonstrate the effect and the correction procedure. An experimental MTF of an x-ray image intensifier system obtained using this technique is found to be consistent with an MTF obtained using a bar pattern test phantom.
Cryo-EM structure of a 3D DNA-origami object (2012)

A key goal for nanotechnology is to design synthetic objects that may ultimately achieve functionalities known today only from natural macromolecular complexes. Molecular self-assembly with DNA has shown potential for creating user-defined 3D scaffolds, but the level of attainable positional accuracy has been unclear. Here we report the cryo-EM structure and a full pseudoatomic model of a discrete DNA object that is almost twice the size of a prokaryotic ribosome. The structure provides a variety of stable, previously undescribed DNA topologies for future use in nanotechnology and experimental evidence that discrete 3D DNA scaffolds allow the positioning of user-defined structural motifs with an accuracy that is similar to that observed in natural macromolecules. Thereby, our results indicate an attractive route to fabricate nanoscale devices that achieve complex functionalities by DNA-templated design steered by structural feedback.
Synthesis of novel, highly potent cyclic-hexapeptide analogs of somatostatin. Potential application of orthogonal protection for affinity chromatography (1991)

The syntheses of new cyclic hexapeptides are described. These peptides potently displace [125I] CGP-23996 (des-Ala1, Gly2-desamino-Cys3[Tyr11]-dicarba3,14 SRIF) from SRIF receptors on AtT-20 cells. Two of these compounds are of potential value for the isolation of SRIF receptors by affinity chromatography. A key feature in the design was the use of orthogonal protection to provide selective covalent bonding to the solid support.
Liquid chromatography/tandem mass spectrometry analysis of long‐chain oxidation products of cardiolipin induced by the hydroxyl radical (2010)

The anionic phospholipid cardiolipin (CL) is found almost exclusively in the inner membrane of mitochondria, playing an important role in energy metabolism. Oxidation of CL has been associated with apoptotic events and various pathologies. In this study, electrospray ionization mass spectrometry coupled with liquid chromatography (LC/ESI-MS) was used to identify tetralinoleoyl-cardiolipin (TLCL) modifications induced by the OH(·) radical generated under Fenton reaction conditions (H(2)O(2) and Fe(2+)). The identified oxidation products of TLCL contained 2, 4, 6 and 8 additional oxygen atoms. These long-chain oxidation products were characterized by LC/ESI-MS/MS as doubly [M-2H](2-) and singly charged [M-H](-) ions. A detailed analysis of the fragmentation pathways of these precursor ions allowed the identification of hydroperoxy derivatives of CL. MS/MS analysis indicated that CL oxidation products with 4, 6 and 8 oxygen atoms have one fatty acyl chain bearing 4 oxygen atoms ([RCOO+4O](-)). Even when the TLCL molecule was oxidized by the addition of eight oxygen atoms, one of the acyl chains remained non-modified and one fatty acyl chain contained three or four oxygen atoms. This led us to conclude that under oxidative conditions by the OH(·) radical, the distribution of oxygens/peroxy groups in the CL molecule is not random, even when CL has the same fatty acyl chains in all the positions. Using mass spectrometry, the oxidation products have been unequivocally assigned, which may be useful for their detection in biological samples.
A functional on-chip pressure generator using solid chemical propellant for disposable lab-on-a-chip (2003)

This paper presents a functional on-chip pressure generator using a solid chemical propellant for the applications of plastic-based disposable biochips or lab-on-a-chips. In this functional on-chip pressure generator, azobis-isobutyronitrile (AIBN) as the solid chemical propellant is deposited on a microheater, which can heat the AIBN to produce nitrogen gas. The output pressure of nitrogen gas, which is generated from the solid chemical propellant, is adjustable to a desired pressure by controlling the input power of the heater. Due to its compact size, easy fabrication, fully integration, high reliability, biologically inert gas output, and functionality of gas generation, this pressure generator will be an excellent pressure source for handling the fluids of the disposable lab-on-a-chips and biochemical analysis systems.
New antibody approaches to lymphoma therapy (2014)

The CD20-directed monoclonal antibody rituximab established a new era in lymphoma therapy. Since then other epitopes on the lymphoma surface have been identified as potential targets for monoclonal antibodies (mAb). While most mAbs eliminate lymphoma cells mainly by antibody-dependent cellular cytotoxicity, complement-dependent cytotoxicity or direct cell death, others counter mechanisms utilized by malignant cells to evade immune surveillance. Expression of PD-L1 on malignant or stromal cells in the tumor environment for example leads to T-cell anergy. Targeting either PD-1 or PD-L1 via mAbs can indirectly eliminate cancer cells by unblocking the host intrinsic immune response. Yet another mechanism of targeted therapy with mAbs are bi-specific T-cell engagers (BiTE) such as blinatumomab, which directly engages the host immune cells. These examples highlight the broad spectrum of available therapies targeting the lymphoma surface with mAbs utilizing both passive and active immune pathways. Many of these agents have already demonstrated significant activity in clinical trials. In this review we will focus on novel CD20-directed antibodies as well as mAbs directed against newer targets like CD19, CD22, CD40, CD52 and CCR4. In addition we will review mAbs unblocking immune checkpoints and the BiTE blinatumomab. Given the success of mAbs and the expansion in active and passive immunotherapies, these agents will play an increasing role in the treatment of lymphomas.
Generation of 11-fs pulses from a Ti:sapphire laser without the use of prisms (1994)

The generation of highly stable optical pulses as short as 11 fs from a Kerr-lens mode-locked Ti:sapphire laser containing no intracavity prisms is demonstrated. In the femtosecond oscillator design reported, novel dielectric mirrors provide broadband dispersion control for solitonlike pulse formation.
Salmonella : from Pathogenesis to Therapeutics (2006)

Although Salmonella enterica serovars are some of the beststudied bacterial pathogens, the field still has a long way to go, especially when one considers that (i) they cause significant morbidity and mortality worldwide; (ii) they have broad host ranges, but for unknown reasons, infections result in different diseases in different hosts; (iii) they are able to establish persistent infections, which serve as reservoirs for transmission/ shedding; and (iv) they are increasingly resistant to many antibiotics.The Second Conference on Salmonella, sponsored by the American Society for Microbiology, was held in Victoria, Canada, from 9 to 13 September 2006.Over 200 participants from around the world gathered at the historic Empress Hotel to discuss their latest findings on Salmonella population biology, animal models, pathogenic mechanisms, clinical disease, and vaccination.The first highlight of the conference was the keynote address by Roy Curtiss III (Arizona State University, Temple).He embodied the spirit of the conference "from pathogenesis to therapeutics," as his life with Salmonella has taken him from investigating bacterial genetics and pathogenic mechanisms to translating this research into therapeutic approaches and vaccine development.This review will highlight some of the central themes that arose during the course of the conference; however, as it is so brief, it will describe only a fraction of the many excellent talks and posters presented. CLINICAL MANIFESTATIONS OF TYPHOIDAL AND NONTYPHOIDAL SALMONELLADiseases caused by S. enterica serovars are especially prevalent in developing areas, such as Southeast Asia, Africa, and South America.Challenges such as antibiotic-resistant Salmonella strains pose a significant threat to the development of reliable therapies.In this section, we highlight the work of groups that presented research dedicated to understanding the prevalence, spread, and control of both typhoidal and nontyphoidal salmonelloses in the developing world.Typhoidal Salmonella serovars, such as Salmonella enterica serovars Typhi and Paratyphi, cause systemic illness that leads to an estimated 20 million cases and 200,000 deaths worldwide each year (5).In Southeast Asian countries, such as Vietnam,
Effects of Continuous Positive Airway Pressure on Sleep Apnea and Ventricular Irritability in Patients With Heart Failure (2000)

In 55% of patients with heart failure and sleep apnea, first-night nasal CPAP eliminates disordered breathing and reduces ventricular irritability.
Dynamics of polynucleotide transport through nanometre-scale pores (2003)

The transport of biopolymers through large membrane channels is a ubiquitous process in biology. It is central to processes such as gene transfer by transduction and RNA transport through nuclear pore complexes. The transport of polymers through nanoscopic channels is also of interest to physicists and chemists studying the effects of steric, hydrodynamic, and electrostatic interactions between polymers and confining walls. Single-channel ion current measurements have been recently used to study the transport of biopolymers, and in particular single-stranded DNA and RNA molecules, through nanometre-size channels. Under the influence of an electric field, the negatively charged polynucleotides can be captured and drawn through the channel in a process termed 'translocation'. During translocation, the ion current flowing through the channel is mostly blocked, indicating the presence of the polymer inside the channel. The current blockades were found to be sensitive to the properties of the biopolymers such as their nucleotide composition, length, and secondary structure, and to physical parameters such as the driving field intensity, temperature, and ionic strength. These blockades are therefore a rich source of information regarding the dynamics of polynucleotides in the pore. The translocation process is separated into its two main steps: (a) polymer 'capture' in which one of the polymer's ends is threaded a small distance through the channel, and (b) polymer sliding through the channel. The experimental and theoretical efforts to elucidate polymer capture and the transport dynamics of biopolymers in nanoscopic pores are reviewed in this article.
New principle for optical filters (1992)

A theoretical characterization of the guided-mode resonance properties of planar dielectric waveguide gratings is presented. Efficient exchange of energy between forward and backward propagating diffracted waves is shown to be possible with smooth line shapes. The linewidths of the resonances can be controlled by the grating modulation amplitude. Due to the inherent separation between the TE and TM modes associated with the waveguide grating, these elements can provide polarization separation. Applications to polarization sensitive filtering and to electro-optic switching are suggested. The guided-mode resonance filter represents a basic new optical element.
Protein engineering modulates the transport properties and ion selectivity of the pores formed by staphylococcal γ‐haemolysins in lipid membranes (2002)

Staphylococcal gamma-haemolysins are bicomponent toxins in a family including other leucocidins and alpha-toxin. Two active toxins are formed combining HlgA or HlgC with HlgB. Both open pores in lipid membranes with conductance, current voltage characteristics and stability similar to alpha-toxin, but different selectivity (cation instead of anion). Structural analogies between gamma-haemolysins and alpha-toxin indicate the presence, at the pore entry, of a conserved region containing four positive charges in alpha-toxin, but either positive or negative in gamma-haemolysins. Four mutants were produced (HlgA D44K, HlgB D47K, HlgB D49K and HlgB D47K/D49K) converting those negative charges to positive in HlgA and HlgB. When all charges were positive, the pores had the same selectivity and conductance as alpha-toxin, suggesting that the cluster may form an entrance electrostatic filter. As mutated HlgC-HlgB pores were less affected, additional charges in the lumen of the pore were changed (HlgB E107Q, HlgB D121N, HlgB T136D and HlgA K108T). Removing a negative charge from the lumen made the selectivity of both HlgA-HlgB D121N and HlgC-HlgB D121N more anionic. Residue D121 of HlgB is compensated by a positive residue (HlgA K108) in the HlgA-HlgB pore, but isolated in the more cation-selective HlgC-HlgB pore. Interestingly, the pore formed by HlgA K108T-HlgB, in which the positive charge of HlgA was removed, was as cation selective as HlgC-HlgB. Meanwhile, the pore formed by HlgA K108T-HlgB D121N, in which the two charge changes compensated, retrieved the properties of wild-type HlgA-HlgB. We conclude that the conductance and selectivity of the gamma-haemolysin pores depend substantially on the presence and location of charged residues in the channel.
Isolation and complete sequence of a functional human glyceraldehyde-3-phosphate dehydrogenase gene. (1988)

Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.2.12) (GAPDH) mRNA levels, protein, and enzymatic activity increase in 3T3-F442A adipocytes after exposure to physiological concentrations of insulin (Alexander, M., Curtis, G., Avruch, J., and Goodman, H. (1985) J. Biol. Chem. 260, 11978-11985). In order to understand the mechanism of this regulation, we have isolated and sequenced 5.4 kilobase pairs of a 12-kilobase pair human genomic clone encoding a functional GAPDH gene. The gene consists of 9 exons and 8 introns with eukaryotic signals necessary for the transcription and translation of GAPDH mRNA. The exon sequence confirms previously published cDNA sequences for human GAPDH in muscle, liver, and erythrocytes. The organization of the human and the unique chicken GAPDH genes is strikingly similar. Although chicken exons VIII-XI have been fused into human exon 8, introns which separate exons encoding the NAD binding, catalytic, and helical domains of the GAPDH protein have been retained. Stable transfection of rodent cells with the intact human GAPDH gene resulted in the expression of a correctly initiated human GAPDH mRNA and an enzymatically active human GAPDH polypeptide. Thus, the gene contains a functional promoter and intact coding sequences. Although many processed GAPDH pseudogenes and GAPDH-like sequences are present in the human genome, Southern blot analysis of human genomic DNA using a probe derived from the 3'-untranslated region of the GAPDH gene detected only two genes, a 10-copy processed pseudogene and a single copy of the isolated gene. In contrast, a probe derived from an intron segment of the isolated gene detected only a single copy of the GAPDH gene. Collectively, these findings strongly suggest that the human genome encodes a single functional GAPDH gene.
<title>Self-calibration in two dimensions: the experiment</title> (1996)

A two-dimensional self-calibration experiment obtains Cartesian traceability for high-precision tools. The calibration procedure incorporates group theory principles to solve our industry's two-dimensional calibration problem. With group theory, a Cartesian system is obtainable through mathematics; thus, eliminating the need for any certified standards. The calibration algorithm was developed by Jun Ye at Stanford University and funded by the Semiconductor Research Corporation (SRC) with collaboration from Hewlett Packard (HP) and IBM. The data was collected from Leica's LMS2000 and LMS2020 systems.
An anti-platelet-endothelial cell adhesion molecule-1 antibody inhibits leukocyte extravasation from mesenteric microvessels in vivo by blocking the passage through the basement membrane. (1996)

Platelet-endothelial cell adhesion molecule-1 (PECAM-1, CD31) plays an active role in the process of leukocyte migration through cultured endothelial cells in vitro and anti-PECAM-1 antibodies (Abs) inhibit accumulation of leukocytes into sites of inflammation in vivo. Despite the latter, it is still not clear at which stage of leukocyte emigration in vivo PECAM-1 is involved. To address this point directly, we studied the effect of an anti-PECAM-1 Ab, recognizing rat PECAM-1, on leukocyte responses within rat mesenteric microvessels using intravital microscopy. In mesenteric preparations activated by interleukin (IL)-1 beta, the anti-PECAM-1 Ab had no significant effect on the rolling or adhesion of leukocytes, but inhibited their migration into the surrounding extravascular tissue in a dose-dependent manner. Although in some vessel segments these leukocytes had come to a halt within the vascular lumen, often the leukocytes appeared to be trapped within the vessel wall. Analysis of these sections by electron microscopy revealed that the leukocytes had passed through endothelial cell junctions but not the basement membrane. In contrast to the effect of the Ab in mesenteric preparations treated with IL-1 beta, leukocyte extravasation induced by topical or intraperitoneal administration of the chemotactic peptide formyl-methionyl-leucyl-phenylalanine was not inhibited by the anti-PECAM-1 Ab. These results directly demonstrate a role for PECAM-1 in leukocyte extravasation in vivo and indicate that this involvement is selective for leukocyte extravasation elicited by certain inflammatory mediators. Further, our findings provide the first in vivo indication that PECAM-1 may have an important role in triggering the passage of leukocytes through the perivascular basement membrane.
Contribution of preterm delivery to perinatal mortality. (1976)

A detailed retrospective analysis was made of the records of 486 preterm infants, who accounted for 5-1% of all births during 1973 and 1974. Whereas preterm delivery did not contribute to perinatal mortality in terms of stillbirth, it outweighed all other causes in terms of early neonatal deaths. Preterm birth was responsible for 85% of the early neonatal deaths not due to lethal congenital deformities. Early neonatal mortality rates were closely linked both to gestational age and birth weight and to the reason for preterm birth. Early neonatal mortality was high (97 per 1000) when preterm labour was spontaneous, whether or not associated with material or fetal disease or with multiple pregnancy, but low (27 per 1000) when preterm delivery was elective. Preventing spontaneous preterm labour would considerably reduce neonatal mortality in our community.