gebhart/patrepeval huggingface dataset:
Introduction of Extra Telomeric DNA Sequences into Saccharomyces cerevisiae Results in Telomere Elongation (1989)

The termini of Saccharomyces cerevisiae chromosomes consist of tracts of C1-3A (one to three cytosine and one adenine residue) sequences of approximately 450 base pairs in length. To gain insights into trans-acting factors at telomeres, high-copy-number linear and circular plasmids containing tracts of C1-3A sequences were introduced into S. cerevisiae. We devised a novel system to distinguish by color colonies that maintained the vector at 1 to 5, 20 to 50, and 100 to 400 copies per cell and used it to change the amount of telomeric DNA sequences per cell. An increase in the number of C1-3A sequences caused an increase in the length of telomeric C1-3A repeats that was proportional to plasmid copy number. Our data suggest that telomere growth is inhibited by a limiting factor(s) that specifically recognizes C1-3A sequences and that this factor can be effectively competed for by long tracts of C1-3A sequences at telomeres or on circular plasmids. Telomeres without this factor are exposed to processes that serve to lengthen chromosome ends.
Nutrient content and distribution in milling fractions of rice grain (1979)

Abstract Nutrient content and distribution in a low‐protein (7.5%) rice and a high‐protein (10.8 %) rice were studied by analysing successive abrasive milling fractions of brown rice. Non‐starch constituents decreased from the surface to the centre of the grain in both rices, except that the highest protein fraction in high‐protein rice was the sub‐aleurone layer. Starch and amylose contents of starch increased progressively from the surface to the centre of the grain and were lower in high‐protein grain. Although this low‐protein rice had lower total ash content than the high‐protein rice, other samples of the same low‐protein rice had comparable ash content to the high‐protein rice. Glutelin accounted for 87–93% of milled rice protein. Protein and protein bodies of the sub‐aleurone layer and inner endosperm have similar amino‐grams, and electrophoretic patterns using analytical and SDS‐polyacrylamide disc gels.
H+-myo-Inositol Transporter SLC2A13 as a Potential Marker for Cancer Stem Cells in an Oral Squamous Cell Carcinoma (2011)

Cancer Stem Cells (CSCs) from tumors of different phenotypes possess a marked capacity for proliferation, self-renewal, and differentiation. They also play a critical role in cancer recurrence. Although CSC has been regarded as a new target for cancer therapy, the fundamental questions in the CSC study have not been resolved mainly due to the lack of proper CSC markers. To find new CSC markers for oral squamous cell carcinoma (OSCC), we cultured the primary tumor cells from OSCC patients the regular culture condition and the sphere-forming culture condition to enrich primary tumor cells and potential CSCs. We compared gene expression profiles between sphere-forming and non-forming cells, thus identifying that 23 membrane protein-coding genes were over-expressed in the sphere-forming cells. Among them, 8 belonged to the solute carrier (SLC) protein family. H⁺-myo-inositol transporter SLC2A13 and monocarbohydrate transporter SLC16A6 genes that were consistently increased in the sphere-forming cells in the primary cultures of OSCC samples. Confocal microscopy revealed that SLC2A13-expressing cells were embedded in the limited areas of tumor tissue as a cluster, while SLC16A6 was uniformly detected in hyperplastic epithelium. Moreover, SLC2A13 an expression was induced in human breast adenocarcinoma MCF7 cells after serum starvation. Taken together, our results suggest that SLC2A13 can be a potential markers for CSC in various tumors.
<title>Stereo camera calibration with distortion model and using forgetting factor</title> (1993)

In this paper, we present a calibration technique for cameras with several types of distortion lenses. The algorithm decomposes the calibration parameters into nondistortion parameters and distortion parameters, and the estimation is performed using the weighted least-squares method. The validity and the performance of the calibration algorithm is tested on two stereo cameras mounted in a stereoscopic bank. Experimental results show the feasibility and the performance of the calibration algorithm.
G protein diversity: a distinct class of alpha subunits is present in vertebrates and invertebrates. (1990)

Heterotrimeric guanine nucleotide-binding proteins (G proteins) are integral to the signal transduction pathways that mediate the cell's response to many hormones, neuromodulators, and a variety of other ligands. While many signaling processes are guanine nucleotide dependent, the precise coupling between a variety of receptors, G proteins, and effectors remains obscure. We found that the family of genes that encode the alpha subunits of heterotrimeric G proteins is much larger than had previously been supposed. These novel alpha subunits could account for some of the diverse activities attributed to G proteins. We have now obtained cDNA clones encoding two murine alpha subunits, G alpha q and G alpha 11, that are 88% identical. They lack the site that is ordinarily modified by pertussis toxin and their sequences vary from the canonical Gly-Ala-Gly-Glu-Ser (GAGES) amino acid sequence found in most other G protein alpha subunits. Multiple mRNAs as large as 7.5 kilobases hybridize to G alpha q specific probes and are expressed at various levels in many different tissues. G alpha 11 is encoded by a single 4.0-kilobase message which is expressed ubiquitously. Amino acid sequence comparisons suggest that G alpha q and G alpha 11 represent a third class of alpha subunits. A member of this class was found in Drosophila melanogaster. This alpha subunit, DG alpha q, is 76% identical to G alpha q. The presence of the Gq class in both vertebrates and invertebrates points to a role that is central to signal transduction in multicellular organisms. We suggest that these alpha subunits may be involved in pertussis toxin-insensitive pathways coupled to phospholipase C.
MRI-PET Registration with Automated Algorithm (1993)

The method has been validated quantitatively using data from patients with stereotaxic fiducial markers rigidly fixed in the skull. Maximal three-dimensional errors of < 3 mm and mean three-dimensional errors of < 2 mm were measured. Computation time on a SPARCstation IPX varies from 3 to 9 min to align MR image sets with [18F]fluorodeoxyglucose PET images. The MR alignment with noisy H2(15)O PET images typically requires 20-30 min.
Effects of Moderate Hypothermia on Proinflammatory Cytokine Production in a Rat Model of Caerulein-Induced Pancreatitis (2003)

Our results suggest that MH may be clinically applicable for reducing the severity of AP.
A Variable-Ratio Microwave Power Divider and Multiplexer (1957)

A microwave circuit is presented which provides continuous variation of microwave power between two outputs in any desired ratio. A typical device utilizing the circuit is described, and other uses of the circuit are discussed. An X-band power divider was constructed which had a vswr of less than 1.2 at all times over the frequency range of 8.6 to 9.6 kmc, divided the total input energy between the outputs in any ratio from 1/10,000 to 1, and had less than 0.4-db total insertion loss. No other losses were present. Adjustment could be made under maximum power levels of the waveguide. Another use of the circuit is to couple two high-power transmitters into one output, thus providing a dual frequency antenna coupler or diplexer. By cascading diplexers, multiplexing can be accomplished.
Delineation of the intronless nature of the genes for the human and hamster beta 2-adrenergic receptor and their putative promoter regions. (1987)

The beta 2-adrenergic receptor is the first adenylate cyclase-coupled receptor to be cloned. We provide here a detailed characterization of its complete gene in both the human and hamster which reveals several unusual and provocative features. The genes are present in a single copy, are intronless, and are bounded by homologous 18-bp (base pair) direct repeats. These findings suggest that the beta 2-adrenergic receptor may have arisen as a processed gene for another related gene. Genomic Southern blots done at reduced stringency in fact reveal additional weak signals. The human and hamster gene sequences 5' to the principal site of transcription initiation are highly homologous and share many characteristics of promoters for housekeeping genes. Moreover, there is present in the human genome a long (777 bp) open reading frame which is in frame with the beta-adrenergic receptor coding block and which ends only 234 bp 5' to the initiator methionine of the receptor. An unusual cDNA has been found, transcribed from a putative second more 5' promoter which contains the 5' half of the beta-adrenergic receptor as well as 1065-bp 5' to the receptor coding region, including the entire upstream long open reading frame (sufficient to encode a putative protein of Mr approximately 28,000).
Matrix Metalloproteinase-9 Is Required for Adequate Angiogenic Revascularization of Ischemic Tissues (2003)

Angiogenesis, an essential component of a variety of physiological and pathological processes, offers attractive opportunities for therapeutic regulation. We hypothesized that matrix metalloproteinase-9 genetic deficiency (MMP-9-/-) will impair angiogenesis triggered by tissue ischemia, induced experimentally by femoral artery ligation in mice. To investigate the role of MMP-9, we performed a series of biochemical and histological analyses, including zymography, simultaneous detection of perfused capillaries, MMP-9 promoter activity, MMP-9 protein, and macrophages in MMP-9-/- and wild-type (WT) mice. We found that ischemia resulted in doubling of capillary density in WT and no change in the MMP-9-/- ischemic tissues, which translated into increased (39%) perfusion capacity only in the WT at 14 days after ligation. We also confirmed that capillaries in the MMP-9-/- presented significantly (P<0.05) less points of capillary intersections, interpreted by us as decreased branching. The combined conclusions from simultaneous localizations of MMP-9 expression, capillaries, and macrophages suggested that macrophage MMP-9 participates in capillary branching. Transplantation of WT bone marrow into the MMP-9-/-, restored capillary branching, further supporting the contribution of bone marrow-derived macrophages in supplying the necessary MMP-9. Our study indicates that angiogenesis triggered by tissue ischemia requires MMP-9, which may be involved in capillary branching, a potential novel role for this MMP that could be exploited to control angiogenesis.
Herpes simplex virus trans-regulatory protein ICP27 stabilizes and binds to 3' ends of labile mRNA (1995)

Previous work demonstrated that a herpes simplex virus type 1 (HSV-1) immediate-early function up-regulates beta interferon but not chloramphenicol acetyltransferase reporter genes driven by the strong simian virus 40 (SV40) or cytomegalovirus promoter-enhancer regions in both transient assays and stable cell lines. The different 3' mRNA stabilization and RNA-processing signals from these two reporter genes appeared to be primarily responsible for this phenomenon. We now report that the HSV-1 ICP27 itself is sufficient to stimulate both steady-state accumulation and increased half-life of beta interferon reporter gene mRNA. Furthermore, the ability to respond directly to cotransfected ICP27 can be transferred to chloramphenicol acetyltransferase reporter genes by replacement of their SV40-derived splicing and poly(A) signals with the 3' AU-rich and poly(A) RNA-processing signals from the normally highly labile beta interferon and c-myc mRNA species. ICP27 expressed in bacteria bound specifically to in vitro-generated RNA from both the beta interferon and c-myc intronless AU-rich 3' RNA-processing regions, but not to the SV40-derived early-region splice signal and poly(A) sequences. By site-specific mutagenesis, we also show that individual ICP27 C-terminal amino acid residues that are positionally conserved in ICP27 homologs in other herpesviruses (D-357, E-358, H-479, C-400, C-483, and C-488) are critical for trans-regulatory activity. Importantly, several of these positions match mutations that are known to be essential for the role of ICP27 in the early-to-late switch during the virus lytic cycle. Therefore, our findings support the notion that HSV ICP27 modulates gene expression posttranscriptionally in part by targeting RNA.
Induction of Adipocyte‐Like Phenotype in Human Mesenchymal Stem Cells by Hypoxia (2004)

Human mesenchymal stem cells (hMSCs) have the capacity to differentiate along several pathways to form bone, cartilage, tendon, muscle, and adipose tissues. The adult hMSCs reside in vivo in the bone marrow in niches where oxygen concentration is far below the ambient air, which is the most commonly encountered laboratory condition. The study reported here was designed to determine whether oxygen has a role in the differentiation of hMSCs into adipocytes. Indeed, when exposed to atmosphere containing only 1% of oxygen, the formation of adipocyte-like phenotype with cytoplasmic lipid inclusions was observed. The effect of hypoxia on the expression of adipocyte-specific genes was determined by real-time reverse transcription polymerase chain reaction. Interestingly, neither of the two central regulators of adipogenesis--the transcription factors peroxisome proliferator-activated receptor gamma2 (PPAR-gamma2) and ADD1/SREBP1c-was induced. Furthermore, hypoxia did not have any effect on the transcription of early (lipoprotein lipase) or late (aP2) marker genes. By the same token, neither of the mature adipocyte-specific genes--leptin and adipophilin--was found responsive to the treatment. High level of induction, however, was observed with the PPAR-gamma-induced angiopoietin-related gene, PGAR. The lack of an adipocyte-specific transcription pattern thus indicates that despite accumulation of the lipid, true adipogenic differentiation did not take place. In conclusion, hypoxia appears to exert a potent lipogenic effect independent of PPAR-gamma2 maturation pathway.
Atom Transfer Polymerization:  Use of Uridine and Adenosine Derivatized Monomers and Initiators (1999)

The multifunctional monomers 5‘-methacryloyluridine and 5‘-methacryloyladenosine have been polymerized under atom transfer polymerization conditions, giving products of narrow polydispersities as consistent with living polymerization. Initiators derived from both uridine and adenosine have also been used to terminally functionalize poly(methyl methacrylate) and poly(styrene). Both hydroxyl-protected and unprotected initiators successfully gave polymers of predictable and narrow PDI. Atom transfer polymerization of methyl methacrylate with the protected 5‘-bromoisobutyroyluridine initiator 2 with NMPI ligand in conjunction with copper(I) bromide gives polymer with an Mn of 13 100 with a very narrow PDI of 1.06 (Mn of 11 000 1H NMR). The initiator efficiency is less than unity (e.g., 0.81 for the above reaction), similar to that observed with nonfunctional initiators. 1H NMR is used to demonstrate the presence of the initiator in the polymer. The results demonstrate that this living polymerization system is inert to a multitude of functionality in the initiator, including secondary hydroxyl, silyl ether, tertiary amine, primary amine, secondary amide, etc. Atom transfer polymerization has been used to synthesize well-defined poly(nucleoside)-based polymers which have tremendous potential for templating and polymers used in applications that require biorecognition.
Optimization Manufacture of Virus- and Tumor-Specific T Cells (2011)

Although ex vivo expanded T cells are currently widely used in pre-clinical and clinical trials, the complexity of manufacture remains a major impediment for broader application. In this review we discuss current protocols for the ex vivo expansion of virus- and tumor-specific T cells and describe our experience in manufacture optimization using a gas-permeable static culture flask (G-Rex). This innovative device has revolutionized the manufacture process by allowing us to increase cell yields while decreasing the frequency of cell manipulation and in vitro culture time. It is now being used in good manufacturing practice (GMP) facilities for clinical cell production in our institution as well as many others in the US and worldwide.
Effects of combined arginine vasopressin and levosimendan on organ function in ovine septic shock* (2010)

First-line cardiovascular support with combined arginine vasopressin and levosimendan supplemented with norepinephrine improves myocardial, vascular, pulmonary, and renal function as compared with arginine vasopressin + norepinephrine in septic shock.
TDP-43 transgenic mice develop spastic paralysis and neuronal inclusions characteristic of ALS and frontotemporal lobar degeneration (2010)

Neuronal cytoplasmic and intranuclear aggregates of RNA-binding protein TDP-43 are a hallmark feature of neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). ALS and FTLD show a considerable clinical and pathological overlap and occur as both familial and sporadic forms. Though missense mutations in TDP-43 cause rare forms of familial ALS, it is not yet known whether this is due to loss of TDP-43 function or gain of aberrant function. Moreover, the role of wild-type (WT) TDP-43, associated with the majority of familial and sporadic ALS/FTLD patients, is also currently unknown. Generating homozygous and hemizygous WT human TDP-43 transgenic mouse lines, we show here a dose-dependent degeneration of cortical and spinal motor neurons and development of spastic quadriplegia reminiscent of ALS. A dose-dependent degeneration of nonmotor cortical and subcortical neurons characteristic of FTLD was also observed. Neurons in the affected spinal cord and brain regions showed accumulation of TDP-43 nuclear and cytoplasmic aggregates that were both ubiquitinated and phosphorylated as observed in ALS/FTLD patients. Moreover, the characteristic approximately 25-kDa C-terminal fragments (CTFs) were also recovered from nuclear fractions and correlated with disease development and progression in WT TDP-43 mice. These findings suggest that approximately 25-kDa TDP-43 CTFs are noxious to neurons by a gain of aberrant nuclear function.
Shared Control between Human and Machine: Using a Haptic Steering Wheel to Aid in Land Vehicle Guidance (2001)

When humans interface with machines, the control interface is usually passive and its response contains little information pertinent to the state of the environment. Usually, information flows through the interface from human to machine but not so often in the reverse direction. This work proposes a control architecture in which bi-directional information transfer occurs across the control interface, allowing the human to use the interface to simultaneously exert control and extract information. In this alternative control architecture, which we call shared control, the human utilizes the haptic sensory modality to share control of the machine interface with an automatic controller. We present a fixed-base driving simulator experiment in which subjects take advantage of a haptic steering wheel, which aids them in a path following task. Results indicate that the haptic steering wheel allows a significant reduction in visual demand while improving path following performance.
[Epidemiology, origin and genetic diversity of HTLV-1 retrovirus and STLV-1 simian affiliated retrovirus]. (2000)

Human T Cell leukemia/lymphoma virus type I, the first human oncogenic retrovirus, is the aetiological factor of Adult T cell leukemia (ATL), a CD4+ malignant lymphoproliferative disease and of a chronic neuromyelopathy, the tropical spastic paraparesis or HTLV-1 associated myelopathy (TSP/HAM). HTLV-1, which infects from 15 to 25 million individuals world-wide, is highly endemic in certain areas such as south-western Japan, Central Africa, the Caribbean basin and some regions of South America, Melanesia and of the middle East (for example the Mashhad area of Iran). The three major modes of transmission for HTLV-1 infection are perinatal, sexual and by blood transfusion. Recent molecular studies on HTLV-1 have shown the existence of several molecular subtypes (genotypes). These are related to the geographical origin of the infected populations and not to the associated diseases. The virus has a very high genetic stability. Viral amplification via clonal expansion of infected cells, rather than by use of reverse transcription could explain this remarkable phenomenon which can be used as a molecular tool for gaining new insights into the origin, evolution and modes of dissemination of HTLV-1. Analyses of HTLV-1 and STLV-1 (the simian counterpart) viral strains from throughout the world suggest that four events are responsible for this pattern of dissemination: 1) the transmission in the wild of STLV-1 between simian species, 2) the transmission of STLV-1 to humans as exemplified by the high percentage of identity between STLV-1 strains from chimpanzees or from mandrills with some HTLV-1 strains present in inhabitants of Central Africa, 3) persistence of HTLV-1 over a long period of time (by sexual and perinatal transmissions) in remote populations, as seen in the Australo-Melanesian region and 4) a global distribution of HTLV-1 via large scale human migrations, e.g., the slave trade from Africa to the New World.
Facile Conversion of Alcohols into Esters and Dihydrogen Catalyzed by New Ruthenium Complexes (2005)

An efficient, environmentally benign method for the preparation of esters from alcohols under mild, neutral conditions without the need for carboxylic acid derivatives and condensing agents was developed. Catalyst design, based on new Ru(II) hydrido carbonyl complexes incorporating electron-rich PNP and PNN ligands has resulted in the novel complex (I) which is an outstanding catalyst for the dehydrogenation of primary alcohols to esters and H(2) under neutral conditions.