gebhart/patrepeval huggingface dataset:
Loss of Atrx Affects Trophoblast Development and the Pattern of X-Inactivation in Extraembryonic Tissues (2006)

ATRX is an X-encoded member of the SNF2 family of ATPase/helicase proteins thought to regulate gene expression by modifying chromatin at target loci. Mutations in ATRX provided the first example of a human genetic disease associated with defects in such proteins. To better understand the role of ATRX in development and the associated abnormalities in the ATR-X (alpha thalassemia mental retardation, X-linked) syndrome, we conditionally inactivated the homolog in mice, Atrx, at the 8- to 16-cell stage of development. The protein, Atrx, was ubiquitously expressed, and male embryos null for Atrx implanted and gastrulated normally but did not survive beyond 9.5 days postcoitus due to a defect in formation of the extraembryonic trophoblast, one of the first terminally differentiated lineages in the developing embryo. Carrier female mice that inherit a maternal null allele should be affected, since the paternal X chromosome is normally inactivated in extraembryonic tissues. Surprisingly, however, some carrier females established a normal placenta and appeared to escape the usual pattern of imprinted X-inactivation in these tissues. Together these findings demonstrate an unexpected, specific, and essential role for Atrx in the development of the murine trophoblast and present an example of escape from imprinted X chromosome inactivation.
Local application of recombinant human fibroblast growth factor‐2 on bone repair: A dose–escalation prospective trial on patients with osteotomy (2007)

Based on preclinical evidence in animal models, the present study examined the clinical efficacy and safety of recombinant human fibroblast growth factor-2 (rhFGF-2) to accelerate bone repair in a dose-escalation prospective trial. One of three dosages (200, 400 or 800 microg) of rhFGF-2 in a biodegradable gelatin hydrogel was injected during surgery into the osteotomy site of 59 knee osteoarthritis patients undergoing high tibial osteotomy, and 57 of them were monitored for 16 weeks. The rhFGF-2 dose dependently increased the percentage of patients with radiographic bone union, and decreased the average time needed for such union. The percentages of patients with an absence of pain and full-weight bearing were also greater in the higher dosage groups than in the low dosage group, especially in the clinically critical periods 6, 8, and 10 weeks. Neither blood chemistries nor clinical adverse events were associated with the rhFGF-2 dosages. We therefore conclude that the rhFGF-2 in gelatin hydrogel dose dependently accelerated radiographic bone union of a surgical osteotomy with a safety profile at least at the dosages used, suggesting the clinical efficacy of this agent for bone repair.
Characterization of Closterovirus‐like Particles Associated with Grapevine Leafroll Disease (1990)

Abstract A purification procedure (Z ee et al. 1987) for closterovirus‐like particles associated with grapevine leafroll disease was improved after various sources of plant tissues, extraction buffers, pH values, and centrifugation techniques had been examined. An antiserum against the CA‐4 isolate was produced and used in ELISA. The virus‐like particles of the NY‐1 isolate measured in crude plant preparations were about 1,800 to 1,900 nm long. The molecular weight of coat protein of the NY‐1and NY‐2 isolates were ca. 43 × 10 3 daltons in SDS‐PAGE analysis; and bands having this molecular weight reacted in Western blotting tests with specific polyclonal and monoclonal antibodies. A large dsRNA molecule (ca. 10 × 10 6 Mr) along, with lower molecular weight species were isolated from leafroll diseased grapevines, but not from healthy grapevines. Seven leafroll isolates were tested for their serological relatedness in a protein A‐gold labelling immunosorbent electron microscopy, assay. Results indicated that serologically distinct serotypes existed, and mixed infection of grapevines with different scrotypes was common. A grouping of isolates into serotype I, II, III, IV is proposed.
Release of chemoattractants for human monocytes from endothelial cells by interaction with neutrophils (1998)

Interaction of PMNL with endothelium induces the release of functionally active MCP-1 suggesting that in the vascular wall, PMNL may play a role in the recruitment of MNC.
The in vivo gene expression signature of oxidative stress (2008)

How higher organisms respond to elevated oxidative stress in vivo is poorly understood. Therefore, we measured oxidative stress parameters and gene expression alterations (Affymetrix arrays) in the liver caused by elevated reactive oxygen species induced in vivo by diquat or by genetic ablation of the major antioxidant enzymes CuZn-superoxide dismutase (Sod1) and glutathione peroxidase-1 (Gpx1). Diquat (50 mg/kg) treatment resulted in a significant increase in oxidative damage within 3-6 h in wild-type mice without any lethality. In contrast, treatment of Sod1(-/-) or Gpx1(-/-) mice with a similar concentration of diquat resulted in a significant increase in oxidative damage within an hour of treatment and was lethal, i.e., these mice are extremely sensitive to the oxidative stress generated by diquat. The expression response to elevated oxidative stress in vivo does not involve an upregulation of classic antioxidant genes, although long-term oxidative stress in Sod1(-/-) mice leads to a significant upregulation of thiol antioxidants (e.g., Mt1, Srxn1, Gclc, Txnrd1), which appears to be mediated by the redox-sensitive transcription factor Nrf2. The main finding of our study is that the common response to elevated oxidative stress with diquat treatment in wild-type, Gpx1(-/-), and Sod1(-/-) mice and in untreated Sod1(-/-) mice is an upregulation of p53 target genes (p21, Gdf15, Plk3, Atf3, Trp53inp1, Ddit4, Gadd45a, Btg2, Ndrg1). A retrospective comparison with previous studies shows that induction of these p53 target genes is a conserved expression response to oxidative stress, in vivo and in vitro, in different species and different cells/organs.
A novel energy recycling clamp circuit (2005)

The reverse recovery of the output rectifying diodes in converters often causes excessive power loss in semiconductor devices and voltage spikes across the diodes, resulting in lower efficiency. There are many kinds of snubber circuits used to clamp voltage spike across the diodes and recycle the reverse recovery energy, which have many limitations such as the bad effect for spike killing, not working in output short circuit. To overcome the limitations a novel snubber circuit is put forward in the paper, which is lossless and more effective than the prior ones. In addition, during the main circuit operates in the current limit mode, the snubber circuit operates normally. The principle and analysis of the snubber circuit are presented in the paper. In a 3 kW telecom power supply very good results are obtained by applying the circuit.
Prednisolone acetate or prednisolone phosphate concurrently administered with ciprofloxacin for the therapy of experimental Pseudomonas aeruginosa keratitis (1993)

This study was conducted to determine the therapeutic efficacy of 3.0 mg/ml ciprofloxacin administered concurrently with one of two salts of prednisolone for the treatment of experimental pseudomonal keratitis. Rabbit corneas were injected intrastromally with Pseudomonas aeruginosa ATCC strain 27853. Sixteen hr after injection, rabbits were randomly divided into four treatment groups (3 rabbits, 6 eyes per group): 1) ciprofloxacin plus prednisolone acetate; 2) ciprofloxacin plus prednisolone phosphate; 3) ciprofloxacin only; 4) untreated. Signs of inflammation were graded in a masked fashion by slit lamp examination (SLE) and by estimating polymorphonuclear leukocyte (PMN) numbers in corneas 27 hr after injection. SLE scores and PMN numbers were significantly lower (P < 0.02) in eyes receiving either salt of prednisolone plus ciprofloxacin compared to the untreated controls. In contrast, SLE scores and PMN numbers were not significantly different in eyes treated with ciprofloxacin alone, compared to untreated controls (P > 0.13). No viable bacteria were recovered from any eye treated with ciprofloxacin (groups 1, 2, and 3). Ciprofloxacin concentrations in the aqueous humor of eyes in groups 1, 2, and 3 were greater than 15-fold higher than the MIC for P. aeruginosa 27853. These results suggest that either salt of prednisolone, when combined with ciprofloxacin, reduces ocular inflammation without affecting the antimicrobial efficacy of the antibiotic.
Nonlinear focusing of DNA macromolecules (2001)

The present paper reports the nonlinear electrophoretic focusing techniques developed after an original idea by Chacron and Slater [Phys. Rev. E 56, 3436 (1997)]. Focusing of DNA molecules is achieved in an alternating nonuniform electric field, created in a wedge gel with hyperbolic boundaries. The fractions separated on such a wedge retained their rectilinear shape during the electrophoresis. Experiments with gel electrophoresis confirm the possibility of a noticeable nonlinear focusing of DNA molecules.
New York In June (1965)

On June 21-23, 1965, the scientific community will again have an opportunity to appreciate the increasingly close relationship between research and the care of patients when the Association for Research in Ophthalmology (ARO) and the American Medical Association Section on Ophthalmology meet at New York's Plaza Hotel. Scheduled to assemble in the morning hours, the ARO will feature the Proctor Lecture by Dr. Zacharias Dische. Meeting during the afternoon periods, the AMA Section on Ophathalmology will highlight the address of the invited guest, Professor Isaac Michaelson. Noteworthy, as an innovation this year, the program of both groups will be coordinated on June 22nd to provide for the timely presentation of basic science and clinical papers related to retinal vascular disease. Considered in conjunction with the simultaneous array of exhibits, specialty programs and interdisciplinary forums that constitute the annual meeting of the American Medical Association, this assembly of the AMA Section
Comparison of granulocyte-macrophage colony stimulating factor and interleukin-1 production from human peripheral blood mononuclear cells as measured by specific radioimmunoassays. (1992)

Attention has focused on cytokine networks in which gene and protein expression of some cytokines is under the influence of other cytokines. In the present studies, we addressed the relationship between the synthesis of granulocyte-macrophage colony stimulating factor (GM-CSF) and interleukin-1 (IL-1) in human peripheral blood mononuclear cells (PBMC) stimulated with mitogens. Since bioassays for cytokines are sensitive to more than one of these factors, it was necessary to measure the amounts of IL-1 and GM-CSF independent of bioassays. A specific and sensitive (40 pg/ml) radioimmunoassay (RIA) was developed for human GM-CSF. The sensitivity of the RIA was greater when lysine residues were iodinated with Bolton-Hunter reagent than tyrosine residues using chloramine T. After stimulating PBMC with concanavalin A (Con A), the biological activity of GM-CSF was determined in bone marrow cultures and compared to immunoreactive GM-CSF; GM-CSF levels detected by bioassays and RIAs were highly correlated in two separate sets of experiments (r2 = 0.95 and 0.43). Incubation with Con A for 48 h induced more GM-CSF than stimulation by phytohemagglutinin (PHA) despite the fact that PHA stimulates large amounts of IL-1 alpha; indomethacin had no effect on Con A stimulated synthesis of GM-CSF or IL-1 alpha. In two separate studies, PBMC from 14 donors and a second group of 12 donors were incubated with Con A for 48 h and the total amount of immunoreactive IL-1 alpha and GM-CSF was determined in the same cell cultures. There was no correlation of the amount of either cytokines in these cultures.(ABSTRACT TRUNCATED AT 250 WORDS)
The I/LWEQ module: a conserved sequence that signifies F-actin binding in functionally diverse proteins from yeast to mammals (1997)

Talin is an actin-binding protein involved in integrin-mediated cell adhesion and spreading. The C-terminal 197 amino acids of vertebrate talin are 45% similar to the C-terminal residues of Sla2, a yeast protein implicated in polarized assembly of the yeast actin cytoskeleton. Talin is also homologous in this region to nematode talin, cellular slime mold filopodin, and an Sla2 homolog from nematode. Analysis of the conserved C-terminal sequences of these five proteins with BLOCK MAKER reveals a series of four blocks, which we name the I/LWEQ module after the conserved initial residues in each block. Experiments presented here show that the conserved protein domain represented by the I/LWEQ module competes quantitatively with native talin for binding to F-actin in vitro. Furthermore, the corresponding domain of Sla2 binds to both yeast and vertebrate F-actin in vitro. Mutation of one of the conserved residues in the fourth conserved block abolishes the interaction of the Sla2 I/LWEQ module with F-actin. These results establish the location of an F-actin binding domain in native talin, demonstrate that direct interaction of Sla2 with actin is a possible basis for its effect on the actin cytoskeleton in vivo, and define the I/LWEQ consensus as a new actin-binding motif.
Visualization and analysis of gene expression in tissue sections by spatial transcriptomics (2016)

Analysis of the pattern of proteins or messengerRNAs (mRNAs) in histological tissue sections is a cornerstone in biomedical research and diagnostics. This typically involves the visualization of a few proteins or expressed genes at a time. We have devised a strategy, which we call "spatial transcriptomics," that allows visualization and quantitative analysis of the transcriptome with spatial resolution in individual tissue sections. By positioning histological sections on arrayed reverse transcription primers with unique positional barcodes, we demonstrate high-quality RNA-sequencing data with maintained two-dimensional positional information from the mouse brain and human breast cancer. Spatial transcriptomics provides quantitative gene expression data and visualization of the distribution of mRNAs within tissue sections and enables novel types of bioinformatics analyses, valuable in research and diagnostics.
Binding Affinity and Specificity of Escherichia coli RNase H1:  Impact on the Kinetics of Catalysis of Antisense Oligonucleotide−RNA Hybrids (1997)

In this study we report for the first time the binding affinity of RNase H1 for oligonucleotide duplexes. We used a previously described 17-mer antisense sequence [Monia, B. P., Johnston, J. F., Ecker, D. J., Zounes, M. A., Lima, W. F., & Freier, S. M. (1992) J. Biol. Chem. 267, 19954-19962] hybridized to a complementary oligoribonucleotide to evaluate both the binding affinity and the catalytic rate of RNase H1. The dissociation constants (Kd) of RNase H1 for the various substrates tested were determined by inhibition analysis using chemically modified noncleavable oligonucleotide heteroduplexes. Catalytic rates were determined using heteroduplex substrates containing chimeric antisense oligonucleotides composed of a five-base deoxynucleotide sequence flanked on either side by chemically modified nucleotides. We find that the enzyme preferentially binds A-form duplexes: RNase H bound A-form duplexes (RNA:RNA and DNA:RNA) approximately 60-fold tighter than B-form duplexes (DNA:DNA) and approximately 300-fold tighter than single-strand oligonucleotides. The enzyme exhibited equal affinity for both the wild type (RNA:DNA) oligonucleotide substrate and heteroduplexes containing various 2'-sugar modifications, while the cleavage rates for these chemically modified substrates were without exception slower than for the wild type substrate. The introduction of a single positively charged 2'-propoxyamine modification into the chimeric antisense oligonucleotide portion of the heteroduplex substrate resulted in both decreased binding affinity and a slower rate of catalysis by RNase H. The cleavage rates for heteroduplexes containing single-base mismatch sequences within the chimeric oligonucleotide portion varied depending on the position of the mismatch but had no effect on the binding affinity of the enzyme. These results offer further insights into the physical binding properties of the RNase H-substrate interaction as well as the design of effective antisense oligonucleotides.
mTORC1 Phosphorylation Sites Encode Their Sensitivity to Starvation and Rapamycin (2013)

The mechanistic target of rapamycin (mTOR) complex 1 (mTORC1) protein kinase promotes growth and is the target of rapamycin, a clinically useful drug that also prolongs life span in model organisms. A persistent mystery is why the phosphorylation of many bona fide mTORC1 substrates is resistant to rapamycin. We find that the in vitro kinase activity of mTORC1 toward peptides encompassing established phosphorylation sites varies widely and correlates strongly with the resistance of the sites to rapamycin, as well as to nutrient and growth factor starvation within cells. Slight modifications of the sites were sufficient to alter mTORC1 activity toward them in vitro and to cause concomitant changes within cells in their sensitivity to rapamycin and starvation. Thus, the intrinsic capacity of a phosphorylation site to serve as an mTORC1 substrate, a property we call substrate quality, is a major determinant of its sensitivity to modulators of the pathway. Our results reveal a mechanism through which mTORC1 effectors can respond differentially to the same signals.
Preparation of cyclo-octyn-3-ol, cyclononyn-3-ol, and derivatives (1970)

Cyclo-octyne and cyclononyne derivatives have been prepared by the action of KOBut–Me2SO on the corresponding 1-bromo-trans-cyclo-octenes and -cyclononenes: the elimination reaction was very fast at 20°, and high yields of products were generally obtained.
A new MOSFET with large-tilt-angle implanted drain (LATID) structure (1988)

The LATID device features the elimination of the sidewall spacer and self-alignment of n/sup -/ large tilt angle (LAT) and n/sup +/ implants to the same gate edge. Even without a spacer and a heavy drive-in, the LATID can achieve both a sufficiently long L/sub n-/ and an n/sup +/ gate overlap. The LATID achieves improved current drive by more than 50% and improved hot-carrier lifetime by more than three orders of magnitude as compared with a conventional lightly doped drain. The LATID technique is most promising for applications to submicrometer ULSI under 5-V operation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Antigenic relationships between measles and canine distemper viruses: comparison of immune response in animals and humans to individual virus-specific polypeptides. (1979)

Precipitation with hyperimmune rabbit sera, sera from patients convalescing from measles, and sera from patients with subacute sclerosing panencephalitis, followed by electrophoresis, enabled antigenic relationships between the individual polypeptides of measles and canine distemper viruses to be examined. Virus isolates from patients with acute measles or subacute sclerosing panencephalitis showed no antigenic differences. With rabbit hyperimmune sera, antigenic crossreactivity was present between all polypeptides of measles and canine distemper viruses except H. The N polypeptides showed the highest degree of crossreactivity and were interpreted as group-specific antigens. Both convalescent measles sera and sera from subacute sclerosing panencephalitis showed high antibody titers to all measles polypeptides except L and M. However, these sera contained only low activities to the N and F1 polypeptides from canine distemper virus.
Gastrointestinal transit and 5‐ASA release from a new mesalazine extended‐release formulation (2003)

The administration of the new mesalazine formulation was well tolerated, and 5-ASA was continuously released along the whole colon, a favourable prerequisite for the therapy of distally located inflammatory bowel disease.
SecA interacts with secretory proteins by recognizing the positive charge at the amino terminus of the signal peptide in Escherichia coli. (1990)

SecA is an acidic, peripheral membrane protein involved in the translocation of secretory proteins across the cytoplasmic membrane. The direct interaction of SecA with secretory proteins was demonstrated by means of chemical cross-linking with 1-ethyl-3-(3-dimethylaminoprophyl)carbodiimide. OmpF-Lpp, a model secretory protein, carries either an uncleavable or cleavable signal peptide, and mutant secretory proteins derived from uncleavable OmpF-Lpp were used as translocation substrates. The interaction was SecA-specific. None of the control proteins, which are as acidic as SecA, was cross-linked with uncleavable OmpF-Lpp. The interaction was signal peptide-dependent. The interaction was increasingly enhanced as the number of positively charged amino acid residues at the amino-terminal region of the signal peptide was increased, irrespective of the species of amino acid residues donating the charge. Finally, parallelism was observed between the efficiency of interaction and that of translocation among mutant secretory proteins. It is suggested that precursors of secretory proteins interact with SecA to initiate the translocation reaction.
The MVP sensor planning system for robotic vision tasks (1995)

The MVP (machine vision planner) model-based sensor planning system for robotic vision is presented. MVP automatically synthesizes desirable camera views of a scene based on geometric models of the environment, optical models of the vision sensors, and models of the task to be achieved. The generic task of feature detectability has been chosen since it is applicable to many robot-controlled vision systems. For such a task, features of interest in the environment are required to simultaneously be visible, inside the field of view, in focus, and magnified as required. In this paper, we present a technique that poses the vision sensor planning problem in an optimization setting and determines viewpoints that satisfy all previous requirements simultaneously and with a margin. In addition, we present experimental results of this technique when applied to a robotic vision system that consists of a camera mounted on a robot manipulator in a hand-eye configuration.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Characteristic Analysis of Wind Turbine Gearbox Considering Non-Torque Loading (2013)

In the design of wind turbine gearboxes, the most important objective is to improve the durability to guarantee a service life of more than 20 years. This work investigates how external loads caused by wind fluctuation influence both the load distribution over the gear tooth flank and the planet load sharing. A whole system model is developed to analyze a wind turbine gearbox (WTG) that consists of planetary gearsets. Two models for different design loads are employed to quantify how external loads acting on the input shaft of the WTG affect the load distribution of the gears and the load sharing among the planets under quasi-static conditions. One model considers only the torque for the design load, whereas the other model also considers non-torque loads. For two models, the results for the gear mesh misalignment, contact pattern, load distribution, and load sharing are different, and this leads to different gear safety factors. Therefore, the results indicate that it is appropriate to consider the non-torque loads in addition to the torque as the design load for a WTG, and that this is very important to accurately determine the design load that guarantee the service life of a WTG.