gebhart/patrepeval huggingface dataset:
Derivation of Porcine Embryonic Stem-Like Cells from In Vitro-Produced Blastocyst-Stage Embryos (2016)

Efficient isolation of embryonic stem (ES) cells from pre-implantation porcine embryos has remained a challenge. Here, we describe the derivation of porcine embryonic stem-like cells (pESLCs) by seeding the isolated inner cell mass (ICM) from in vitro-produced porcine blastocyst into α-MEM with basic fibroblast growth factor (bFGF). The pESL cells kept the normal karyotype and displayed flatten clones, similar in phenotype to human embryonic stem cells (hES cells) and rodent epiblast stem cells. These cells exhibited alkaline phosphatase (AP) activity and expressed pluripotency markers such as OCT4, NANOG, SOX2, SSEA-4, TRA-1-60, and TRA-1-81 as determined by both immunofluorescence and RT-PCR. Additionally, these cells formed embryoid body (EB), teratomas and also differentiated into 3 germ layers in vitro and in vivo. Microarray analysis showed the expression of the pluripotency markers, PODXL, REX1, SOX2, KLF5 and NR6A1, was significantly higher compared with porcine embryonic fibroblasts (PEF), but expression of OCT4, TBX3, REX1, LIN28A and DPPA5, was lower compared to the whole blastocysts or ICM of blastocyst. Our results showed that porcine embryonic stem-like cells can be established from in vitro-produced blastocyst-stage embryos, which promote porcine naive ES cells to be established.
The ripX Locus of Bacillus subtilis Encodes a Site-Specific Recombinase Involved in Proper Chromosome Partitioning (1999)

The Bacillus subtilis ripX gene encodes a protein that has 37 and 44% identity with the XerC and XerD site-specific recombinases of Escherichia coli. XerC and XerD are hypothesized to act in concert at the dif site to resolve dimeric chromosomes formed by recombination during replication. Cultures of ripX mutants contained a subpopulation of unequal-size cells held together in long chains. The chains included anucleate cells and cells with aberrantly dense or diffuse nucleoids, indicating a chromosome partitioning failure. This result is consistent with RipX having a role in the resolution of chromosome dimers in B. subtilis. Spores contain a single uninitiated chromosome, and analysis of germinated, outgrowing spores showed that the placement of FtsZ rings and septa is affected in ripX strains by the first division after the initiation of germination. The introduction of a recA mutation into ripX strains resulted in only slight modifications of the ripX phenotype, suggesting that chromosome dimers can form in a RecA-independent manner in B. subtilis. In addition to RipX, the CodV protein of B. subtilis shows extensive similarity to XerC and XerD. The RipX and CodV proteins were shown to bind in vitro to DNA containing the E. coli dif site. Together they functioned efficiently in vitro to catalyze site-specific cleavage of an artificial Holliday junction containing a dif site. Inactivation of codV alone did not cause a discernible change in phenotype, and it is speculated that RipX can substitute for CodV in vivo.
Design of a Synthetic Collagen-Binding Peptidoglycan that Modulates Collagen Fibrillogenesis (2008)

The ubiquity of collagen in mammalian tissues, with its host of structural and chemical functions, has motivated its research in many fields, including tissue engineering. The organization of collagen is known to affect cell behavior and the resulting structural integrity of tissues or tissue engineered scaffolds. Of particular interest are proteoglycan (PG) interactions with collagen and their influence on collagen assembly. These natural molecules provide unique chemical and mechanical cues and are known to modulate collagen fibrillogenesis. Research has been limited to PGs extracted and purified from animal sources and has the drawbacks of limited design control and costly purification. Consequently, we have designed a synthetic peptidoglycan based on decorin, a collagen-binding PG. The synthetic peptidoglycan containing a collagen-binding peptide with a single dermatan sulfate side chain specifically binds to collagen, delays fibrillogenesis, and increases collagen gel stiffness as decorin does. This design can be tailored with respect to the peptide sequence and attached glycosaminoglycan chain, offering unique control with relative ease of manufacturing.
PAPR Reduction Method for OFDM Signal by Using Dummy Sub-carriers (2006)

One of the disadvantages of using OFDM is the larger peak to averaged power ratio (PAPR) in its time domain signal. The larger PAPR signal would course the fatal degradation of bit error rate performance (BER) due to the inter-modulation noise in the non-linear channel. This paper proposes an improved DSI (Dummy Sequence Insertion) method, which can achieve the better PAPR and BER performances. The feature of proposed method is to optimize the phase of each dummy sub-carrier so as to reduce the PAPR performance by changing all predetermined phase coefficients in the time domain signal, which is calculated for data sub-carriers and dummy sub-carriers separately. To achieve the better PAPR performance, this paper also proposes to employ the time-frequency domain swapping algorithm for fine adjustment of phase coefficient of the dummy subcarriers, which can achieve the less complexity of processing and achieves the better PAPR and BER performances than those for the conventional DSI method. This paper presents various computer simulation results to verify the effectiveness of proposed method as comparing with the conventional methods in the non-linear channel.
Kurzmitteilung / Short Communication A Convenient Preparation of Acetone Solutions of Dimethyldioxirane (1991)

Abstract A novel simplified procedure affords consistently 0.09‐0.10 M solutions of distilled dimethyldioxirane in acetone; other than control of the reaction temperature below 15° and vigorous mechanical stirring, no other precautions are maniatory.
Spatial and temporal transformation of femtosecond laser pulses by lenses and lens systems (1992)

A Fourier-optical analysis of the transformation of ultrashort light pulses by lenses is given. Inserting the material dispersion up to second order, we find a coupling between the temporal, spectral, and spatial properties of the light pulse. In general, this coupling leads to a drastic increase in pulse duration and width of the spatial intensity distribution in the focal plane of the lens, which can be avoided with the use of achromatic lens doublets. The results are discussed for Gaussian-shaped input pulses.
Three‐dimensional fluorescence lifetime tomography (2005)

Near-infrared fluorescence tomography using molecularly targeted lifetime-sensitive, fluorescent contrast agents have applications for early-stage cancer diagnostics. Yet, although the measurement of fluorescent lifetime imaging microscopy (FLIM) is extensively used in microscopy and spectroscopy applications, demonstration of fluorescence lifetime tomography for medical imaging is limited to two-dimensional studies. Herein, the feasibility of three-dimensional fluorescence-lifetime tomography on clinically relevant phantom volumes is established, using (i) a gainmodulated intensified charge coupled device (CCD) and modulated laser diode imaging system, (ii) two fluorescent contrast agents, e.g., Indocyanine green and 3-3'-Diethylthiatricarbocyanine iodide differing in their fluorescence lifetime by 0.62 ns, and (iii) a two stage approximate extended Kalman filter reconstruction algorithm. Fluorescence measurements of phase and amplitude were acquired on the phantom surface under different target to background fluorescence absorption (70:1, 100:1) and fluorescence lifetime (1:1, 2.1:1) contrasts at target depths of 1.4-2 cm. The Bayesian tomography algorithm was employed to obtain three-dimensional images of lifetime and absorption owing to the fluorophores.
Calin???a platelet adhesion inhibitor from the saliva of the medicinal leech (1991)

The saliva of the medicinal leech, Hirudo medicinalis, contains a potent, hitherto unsuspected, inhibitor of collagen-mediated platelet adhesion/aggregation. Calin, of molecular size approximately 65,000 (reduced), has a rapid (1-10 min) effect on collagen which is reflected in its ability to suppress collagen-induced platelet aggregation, as well as adhesion of platelets to collagen-coated microcarrier beads. It also causes flocculation of Type I collagen fibril suspensions. Calin is differentiated from leech collagenase in two ways: (1) by demonstrating, by SDS-PAGE analysis of the products of incubations of Calin with Type I collagen at 37 degrees C, that Calin binds to but does not cleave collagen; and (2) by showing that Calin cannot be purified using the methods used to isolate leech collagenase. Calin's rapid and unusual interaction with collagen makes it a prime candidate for one of the agents that are the causative factors of the prolonged bleeding phenomenon seen after leech bites.
Reversible cell cycle inhibition and premature aging features imposed by conditional expression of p16Ink4a (2014)

The cyclin-dependent kinase (Cdk) inhibitor p16(Ink4a) (p16) is a canonical mediator of cellular senescence and accumulates in aging tissues, where it constrains proliferation of some progenitor cells. However, whether p16 induction in tissues is sufficient to inhibit cell proliferation, mediate senescence, and/or impose aging features has remained unclear. To address these issues, we generated transgenic mice that permit conditional p16 expression. Broad induction at weaning inhibited proliferation of intestinal transit-amplifying and Lgr5+ stem cells and rapidly imposed features of aging, including hair loss, skin wrinkling, reduced body weight and subcutaneous fat, an increased myeloid fraction in peripheral blood, poor dentition, and cataracts. Aging features were observed with multiple combinations of p16 transgenes and transactivators and were largely abrogated by a germline Cdk4 R24C mutation, confirming that they reflect Cdk inhibition. Senescence markers were not found, and de-induction of p16, even after weeks of sustained expression, allowed rapid recovery of intestinal cell proliferation and reversal of aging features in most mice. These results suggest that p16-mediated inhibition of Cdk activity is sufficient to inhibit cell proliferation and impose aging features in somatic tissues of mammals and that at least some of these aging features are reversible.
Stacked Attention Networks for Image Question Answering (2016)

This paper presents stacked attention networks (SANs) that learn to answer natural language questions from images. SANs use semantic representation of a question as query to search for the regions in an image that are related to the answer. We argue that image question answering (QA) often requires multiple steps of reasoning. Thus, we develop a multiple-layer SAN in which we query an image multiple times to infer the answer progressively. Experiments conducted on four image QA data sets demonstrate that the proposed SANs significantly outperform previous state-of-the-art approaches. The visualization of the attention layers illustrates the progress that the SAN locates the relevant visual clues that lead to the answer of the question layer-by-layer.
Metabolic Engineering of Poly(3-Hydroxyalkanoates): From DNA to Plastic (1999)

Poly(3-hydroxyalkanoates) (PHAs) are a class of microbially produced polyesters that have potential applications as conventional plastics, specifically thermoplastic elastomers. A wealth of biological diversity in PHA formation exists, with at least 100 different PHA constituents and at least five different dedicated PHA biosynthetic pathways. This diversity, in combination with classical microbial physiology and modern molecular biology, has now opened up this area for genetic and metabolic engineering to develop optimal PHA-producing organisms. Commercial processes for PHA production were initially developed by W. R. Grace in the 1960s and later developed by Imperial Chemical Industries, Ltd., in the United Kingdom in the 1970s and 1980s. Since the early 1990s, Metabolix Inc. and Monsanto have been the driving forces behind the commercial exploitation of PHA polymers in the United States. The gram-negative bacterium Ralstonia eutropha, formerly known as Alcaligenes eutrophus, has generally been used as the production organism of choice, and intracellular accumulation of PHA of over 90% of the cell dry weight have been reported. The advent of molecular biological techniques and a developing environmental awareness initiated a renewed scientific interest in PHAs, and the biosynthetic machinery for PHA metabolism has been studied in great detail over the last two decades. Because the structure and monomeric composition of PHAs determine the applications for each type of polymer, a variety of polymers have been synthesized by cofeeding of various substrates or by metabolic engineering of the production organism. Classical microbiology and modern molecular bacterial physiology have been brought together to decipher the intricacies of PHA metabolism both for production purposes and for the unraveling of the natural role of PHAs. This review provides an overview of the different PHA biosynthetic systems and their genetic background, followed by a detailed summation of how this natural diversity is being used to develop commercially attractive, recombinant processes for the large-scale production of PHAs.
Fluorine-19 chemical shifts in saturated systems (1970)

A series of cis-3 substituted trifluoromethylcyclohexanes has been synthesized and the l9F chemical shifts determined. The data reveal that in this system the field effect of sterically remote substituents has little influence on the shielding of the fluorine nucleus.
Plastics Technology Handbook (2006)

Because the field of plastics is one of the fastest changing areas today, the need arises to offer relevant, comprehensive material on polymers. An established source of information on modern plastics, the Plastics Technology Handbook continues to provide up-to-date coverage on the properties, processing methods, and applications of polymers
Development of a complementing cell line and a system for construction of adenovirus vectors with E1 and E2a deleted (1996)

Although adenovirus vectors offer many advantages, it would be desirable to develop vectors with improved expression and decreased toxicity. Toward this objective, an adenovirus vector system with deletion of both the El and E2a regions was developed. A 5.9-kb fragment of the adenovirus type 5 (Ad5) genome containing the E2a gene and its early and late promoters was transfected into 293 cells. A complementing cell line, designated 293-C2, expressed the E2a mRNA and protein and was found to complement the defect in Ad5 viruses with temperature-sensitive or deletion mutations in E2a. A deletion of 1.3 kb removing codons 40 to 471 of the 529 amino acids of E2a was introduced into plasmids for preparation of viruses and vectors. An Ad5 virus with disruption of the El gene and deletion of E2a grew on 293-C2 cells but not on 293 cells. Vectors with E1 and E2a deleted expressing Escherichia coli beta-galactosidase or human alpha1-antitrypsin were prepared and expressed the reporter genes after intravenous injection into mice. This vector system retains sequences in common between the complementing cell line and the vectors, including 3.4 kb upstream and 1.1 kb downstream of the deletion. These vectors have potential advantages of increased capacity for insertion of transgene sequences, elimination of expression of E2a, and possibly reduction in expression of other viral proteins. Although the titers of the vectors with deleted are about 10- to 30-fold below those of vectors with E2a wild-type regions, the former vectors are suitable for detailed studies with animals to evaluate the effects on host immune responses, on duration of expression, and on safety.
Effects of Salts on the Properties of Sols and Gels Prepared from Whey Protein Isolate and Process Whey Protein (1998)

Process whey protein was prepared by heat treatment of whey protein isolate under salt-free conditions. Addition of sodium chloride, trisodium cit-rate, potassium chloride, or calcium chloride to a process whey protein solution increased the viscosity and resulted in gelation at 25C. In contrast, the viscosity of whey protein isolate solutions was not changed. The properties of whey protein isolate and process whey protein gels prepared by heating at 80C for 60 min with 25 different salts were measured and compared. Although process whey protein produced gels with the addition of any of the salts examined, whey protein isolate solution did not gel with some salts. The tendency of both protein solutions to gel apparently depended on the lyotropic nature of the cation. Inorganic salts produced firmer gels than did organic salts. The gel strength and water-holding capacity of both proteins decreased as salt concentration increased. When the transparent gels prepared from process whey protein were heated again, the gel firmness increased, adhesiveness decreased, and transparency and cohesiveness slightly decreased, depending on the temperature and duration of the second heating. (
Nanostructure Initiator Mass Spectrometry: Tissue Imaging and Direct Biofluid Analysis (2009)

Nanostructure initiator mass spectrometry (NIMS) is a recently introduced matrix-free desorption/ionization platform that requires minimal sample preparation. Its application to xenobiotics and endogenous metabolites in tissues is demonstrated, where clozapine and N-desmethylclozapine were observed from mouse and rat brain sections. It has also been applied to direct biofluid analysis where ketamine and norketamine were observed from plasma and urine. Detection of xenobiotics from biofluids was made even more effective using a novel NIMS on-surface extraction method taking advantage of the hydrophobic nature of the initiator. Linear response and limit of detection were also evaluated for xenobiotics such as methamphetamine, codeine, alprazolam, and morphine, revealing that NIMS can be used for quantitative analysis. Overall, our results demonstrate the capacity of NIMS to perform sensitive, simple, and rapid analyses from highly complex biological tissues and fluids.
Suppression of Thromboxane A2but Not of Systemic Prostacyclin by Controlled-Release Aspirin (1991)

Maximal inhibition of platelet thromboxane A2 production was sustained during long-term dosing with controlled-release aspirin, whereas basal prostacyclin biosynthesis fell only slightly and systemic synthesis of prostacyclin stimulated by bradykinin was preserved. Controlled-release aspirin may facilitate determination of the clinical importance of preserving prostacyclin during platelet inhibition in humans.
Buying Time for Recanalization in Acute Stroke: Arterial Blood Infusion Beyond the Occluding Clot as a Neuroprotective Strategy (2009)

Momentary reperfusion of ischemic penumbra with oxygenated blood is feasible and may allow to "buy time" until definitive reperfusion is achieved.
Localized substrate removal technique enabling strong-confinement microphotonics in bulk Si CMOS processes (2008)

A novel post-processing fabrication technique, based on XeF <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> etching, has been developed to locally remove the silicon substrate beneath polysilicon waveguides, enabling integration of low-loss strong-confinement microphotonics into standard bulk-silicon CMOS process flows.
Deletion mapping of chromosome 8p in colorectal carcinoma and dysplasia arising in ulcerative colitis, prostatic carcinoma, and malignant fibrous histiocytomas. (1994)

Short tandem repeat polymorphism markers on the short arm of chromosome 8 were used to search for loss of heterozygosity (LOH) in colorectal carcinoma and dysplasia complicating ulcerative colitis, in prostatic carcinoma, and in malignant fibrous histiocytoma (MFH). Fifty percent of prostatic carcinomas (13/26), 44% of carcinomas or dysplasias arising in ulcerative colitis (7/16), and 30% (4/12) of MFH cases showed LOH for markers on 8p. Detailed mapping demonstrated variability in the size of the chromosomal region showing LOH; however, the data suggest a common 30-centimorgan region of LOH on chromosome 8p between the LPL locus and pter in colorectal and prostatic cancers. In addition, LOH was observed on 8p in both high-grade and low-grade dysplasia in ulcerative colitis, indicating that LOH on 8p may occur at an early stage of neoplastic development in this disorder. In contrast, MFH cases exhibited LOH for marker D8S87, which has been identified as being near the putative Werner's syndrome locus. These results suggest that a tumor suppressor gene, located on the distal portion of chromosome 8p, exists in common for prostatic and colorectal carcinomas, and a second tumor suppressor gene may exist linked to the Werner's syndrome locus.
Hemoglobin interference from in vivo hemolysis. (1985)

Laboratory values for specimens from a case of intravascular hemolysis showed that hemoglobin was significantly increased and thus could interfere with the determination of other analytes. We studied this problem by adding increasing amounts of purified hemoglobin (to a maximum concentration of 19.3 mg/L) to aliquots of pooled serum samples. The hemoglobin significantly interfered with the determination of only five analytes: albumin, aspartate aminotransferase, direct bilirubin, and total protein on the SMAC, and creatinine on the Astra. We propose that for cases of proven intravascular hemolysis, values for only the analytes not affected by hemoglobin should be reported. We find lactate dehydrogenase activity useful in assessing the components of in vivo hemolysis; the differences between serum and plasma values for potassium, lactate dehydrogenase, and hemoglobin are related to in vitro hemolysis. Criteria for specimen collection and assessment of type of hemolysis are proposed.
Laboratory monitoring of heparin therapy--the effect of different salts of heparin on the activated partial thromboplastin time. (1980)

Data from the 1978 CAP Hematology Survey were analyzed for the effect of sodium and calcium salts of heparin on the activated partial thromboplastin time (APTT). The results indicate that the sodium salt of heparin prolongs the APTT more than the calcium salt at a heparin concentration of 0.2 units/ml. Furthermore, there was a variable response of the different APTT reagents to the different heparin salts. Data from the 1979 CAP Hematology Survey showed a greater sensitivity of the Automated APTT reagent and the Platelin Plus Activator of General Diagnostics compared with Actin (Dade) and Thrombofax (Ortho) at therapeutic heparin levels of 0.2 units/ml to 0.4 units/ml. The 1979 CAP heparin questionnaire results are presented and analyzed.
Increased Expression of Phosphatidylcholine (16:0/18:1) and (16:0/18:2) in Thyroid Papillary Cancer (2012)

A good prognosis can be expected for most, but not all, cases of thyroid papillary cancer. Numerous molecular studies have demonstrated beneficial treatment and prognostic factors in various molecular markers. Whereas most previous reports have focused on genomics and proteomics, few have focused on lipidomics. With the advent of mass spectrometry (MS), it has become possible to identify many types of molecules, and this analytical tool has become critical in the field of omics. Recently, imaging mass spectrometry (IMS) was developed. After a simple pretreatment process, IMS can be used to examine tissue sections on glass slides with location information.Here, we conducted an IMS analysis of seven cases of thyroid papillary cancer by comparison of cancerous with normal tissues, focusing on the distribution of phospholipids. We identified that phosphatidylcholine (16:0/18:1) and (16:0/18:2) and sphingomyelin (d18:0/16:1) are significantly higher in thyroid papillary cancer than in normal thyroid tissue as determined by tandem mass (MS/MS) analysis. These distributional differences may be associated with the biological behavior of thyroid papillary cancer.