Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrated Defective Polyomavirus Genomet

We have characterized the viral sequences integrated in a polyomavirus-transformed mouse cell line, Py-3T3 (clone Py-6), and followed their excision and packaging upon superinfection. The polyomavirus sequences contained in Py-6 cells are present as a single insert of nonidentical tandem copies which includes, in addition to a normal middle T-antigen-coding region, some very rearranged sequences. Infection of Py-6 cells with polyomavirus strains encoding a normal large T antigen leads to the reproducible recovery in the resulting viral stock of specific defective viral genomes. The defective genomes contain a wild-type coding region for middle and small T antigens and intact viral origin and enhancer sequences. The remainder of the viral genome is rearranged or lost, so that there is no capacity to code for large T antigen or viral capsid proteins. The recovered defective sequences are also found integrated in Py-6 genomic DNA. Presumably, in infections of Py-6 cells, large T antigen, provided by the superinfecting virus, amplifies and excises the integrated viral sequences. The superinfecting helper virus must also produce viral capsids for packaging of the defective viral DNA and thus provides a means to shuttle the defective sequences from the mouse cells into other hosts, such as rat cells. In the latter host, the defective sequences are able to induce transformation.
Electron Microscopy of the Lysis of Staphylococcus auireus

Isolated and purified cell walls of Staphlylococcus aureus were treated with a purified fraction of the culture supernatant fluid of a species of Aeromlionas. The course of lysis of the cell walls was followed over a period of time by examination of samples under an electron microscope. The undifferentiated cell wall was rapidly digested, but the equatorial rings were more resistant. The undifferentiated cell wall became a very thin sheet before completely dissolving, leaving a series of equatorial rings of various widths. As digestion proceeded, solubilization of the entire cell wall occurred. Analogous findings were obtained with purified S. auureus mucopeptide. It is concluded that the Aeromonas lytic principle is an enzyme, and that susceptible bonds are more concentrated in the undifferentiated cell wall mucopeptide.
Physical Linkage of Mouse A Genes by Pulsed-Field Gel

The first complete map of a mammalian immunoglobulin gene locus is presented. Mouse A genes were mapped by pulsed-field gel electrophoresis. The gene order is V2-Vx-C2-C4-Vl-C3-Cl. The distance between V2 or Vx and the C2-C4 cluster is 74 or 55 kilobases (kb), respectively, whereas that between Vl and C3-C1 is only 19 kb; V2 and C3-Cl are at least 190 kb apart. Thus, the distances between the A subloci are inversely proportional to their frequencies of rearrangement. The related gene A5 is not within the 500 kb of the A locus mapped here.
Genetics of the fuzzless ovule phenotype of Gossypium arboreum accession PI 615733 (cv

Lint and fuzz are the two types of fiber that develop on cotton seeds. Lint is an economically important fiber used in the textile industry. Fuzz fibers remain attached to seeds, and reducing the amount of fuzz could improve ginning efficiency. The Gossypium arboreum accession PI 615733 from the United States Department of Agriculture cotton germplasm collection showed the fuzzless trait, where no fuzz fibers were observed on seeds. Accession PI 615733 was crossed with the fuzzy seeded G. arboreum accession PI 529729 to develop an F2 population. Seeds from F1 plants showed no fuzz fiber. For the F2 population of 409 plants, 239 plants were classified as fuzzless and 170 were classified as fuzzy. These data support a two-gene model with incomplete dominance. A greater understanding of the genetic mechanisms controlling fiber development on cotton seeds could contribute to breeding efforts to improve lint fiber yields and quality.
Regulatory Protein of Herpes Simplex Virus 1, Regulate Late Genes

Earlier studies have described the a4/c113 baby hamster kidney cell line which constitutively expresses the a4 protein, the major regulatory protein of herpes simplex virus 1 (HSV-1). Introduction of the HSV-1 glycoprotein B (gB) gene, regulated as a 'yl gene, into these cells yielded a cell line which constitutively expressed both the a4 and 'yl gB genes. The expression of the gB gene was dependent on the presence of functional a4 protein. In this article we report that we introduced into the a4/cll3 and into the parental BHK cells, the HSV-1 BamHI J fragment, which encodes the domains of four genes, including those of glycoproteins D, G, and I (gD, gG, and gI), and most of the coding sequences of the glycoprotein E (gE) gene. In contrast to the earlier studies, we obtained significant constitutive expression of gD (also a 'yl gene) in a cell line (BJ) derived from parental BHK cells, but not in a cell line (a4IBJ) which expresses functional a4 protein. RNA homologous to the gD gene was present in significant amounts in the BJ cell line; smaller amounts of this RNA were detected in the a4/BJ cell line. RNA homologous to gE, presumed to be polyadenylated from signals in the vector sequences, was present in the BJ cells but not in the a4IBJ cells. The expression of the HSV-1 gD and gE genes was readily induced in the aL4IBJ cells by superinfection with HSV-2. The BJ cell line was, in contrast, resistant to expression of HSV-1 and HSV-2 genes. The BamHI J DNA fragment copy number was approximately 1 per BJ cell genome equivalent and 30 to 50 per oL4/BJ cell genome equivalent. We conclude that (i) the genes specifying gD and gB belong to different viral regulatory gene subsets, (ii) the gD gene is subject to both positive and negative regulation, (iii) both gD and gE mRNAs are subject to translational controls although they may be different, and (iv) the absence of expression of gD in the a4/BJ cells reflects the expression of the cL4 protein in these cells.
The Ultrasonic P-Wave Velocity-Stress Relationship and Energy Evolution of Sandstone under Uniaxial Loading-Unloading Conditions

State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource & Hydropower, Sichuan University, Chengdu 610065, China MOE Key Laboratory of Deep Earth Science and Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu 610065, China Guangdong Provincial Key Laboratory of Deep Earth Science and Geothermal Energy Exploitation and Utilization, Institute of Deep Earth Science and Green Energy, Shenzhen University, Shenzhen 518060, China
Adenovirus Gene Products in the Helper Effect for Adeno-

Several adenovirus early genes act together to promote growth of the helper-dependent adeno-associated virus (AAV). Data from several laboratories have implicated adenovirus early regions la, lb, 2a, and 4 in the helper effect, as well as the small RNA polymerase III transcript, virus-associated RNA I. Although a subset of these must participate directly in the AAV life cycle, some may play an indirect role by influencing expression of the others. This paper is concerned particularly with the roles of early regions la and lb in the helper effect. We introduced DNA fragments representing the various early regions into AAV-infected or uninfected Vero cells, by the manual microinjection procedure. After labeling the cells with [35S]methionine, we visualized immunoprecipitates of AAV or adenovirus proteins on sodium dodecyl sulfate-polyacrylamide gels. When over 200 copies of each DNA fragment per cell were injected, early regions 2a and 4 were themselves sufficient to provide the helper effect. At 100 copies per cell, however, a third gene became essential, and this could be either early region la or lb. The role of early region la is easily explained by its known ability to stimulate transcription of the other early genes. The function of early region lb is less clear, but it does not simply mimic the action of early region la. Instead, there appear to be at least two distinct regulatory pathways which can lead to expression of AAV. To investigate the sequence of regulatory interactions, we microinjected purified adenovirus mRNAs, or combinations of mRNA and DNA, into AAV-infected cells. Our results suggest that adenovirus early products enhance viral gene expression by several mechanisms which can operate independently, but whose effects may be cumulative.
Partition of ElA Proteins between Soluble and Structural Fractions

The partition ofElA proteins between soluble and structural framework fractions of human cells infected or transformed by subgroup C adenoviruses was investigated by using gentle cell fractionation conditions. A polyclonal antibody raised against a trpE-ElA fusion protein (K. R. Spindler, D. S. E. Rosser, and A. J. Berk, J. Virol. 132-141, 1984) synthesized in Escherichia coli was used to measure the steady-state levels of ElA proteins recovered in the various fractions by immunoblotting. The relative concentration of ElA proteins recovered in the soluble fraction of adenovirus type 2-infected cells was at least fivefold greater than the relative concentration in the corresponding fraction of transformed 293 cells. The observed distribution of ElA proteins was not altered by the sulfhydryl-blocking reagent N-ethylmaleimide. ElA proteins were recovered in nuclear matrix, chromatin, and cytoskeleton fractions after further fractionation of the structural framework fraction. However, the ElA protein species that could be identified by one-dimensional gel electrophoresis were not uniformly distributed among the subcellular fractions examined. The results obtained when fractionation was performed in the presence of the oxidation catalysts Cu2+ or (ortho-phenanthroline)2 Cu2+ indicate that ElA proteins can be efficiently cross-linked, via disulfide bonds, to the structural framework of both adenovirusinfected and adenovirus-transformed cells.
α-Phenylalanyl tRNA synthetase attenuates Notch signaling by competing with Notch through its N-terminal domain

The alpha subunit of the cytoplasmic Phenylalanyl tRNA synthetase (α-PheRS) displays cell growth and proliferation activities and its elevated levels can induce cell fate changes and tumor-like phenotypes that do neither dependent on the canonical function of charging tRNAPhe with phenylalanine nor on stimulating general translation. In intestinal stem cells of Drosophila midguts, α-PheRS levels are naturally slightly elevated and in multiple human cancers the mRNA levels of the human homolog, FARSA, are also elevated. In the Drosophila midgut model, even moderately elevating α-PheRS levels caused the accumulation of many additional proliferating cells resembling intestinal stem cells (ISCs) and enteroblasts (EBs). This phenotype resembles the tumor-like phenotype described as Notch RNAi phenotype for the same cells. Genetic interactions between α-PheRS and Notch suggest that their activities neutralize each other and that elevated α-PheRS levels attenuate Notch signaling whether Notch induces differentiation into enterocytes, neuroblast stem cell proliferation, or transcription of a Notch reporter. These non-canonical functions all map to the N-terminal part of α-PheRS. An N-terminal α-PheRS polypeptide of approximately 200 amino acids (α-S) accumulates also naturally in the intestine and displays a weak sequence similarity to the Notch intracellular domain (NICD), suggesting that α-S competes with the NICD for binding to the BTD domain of the transcription factor Su(H)/CSL. Supporting this hypothesis, the key tryptophan (W) residue for this suggested interaction is not only conserved in α-PheRS and α-S, but also essential for attenuating Notch signaling.
Brønsted Acid-Catalyzed Epimerization-Free Preparation of Dual-Protected Amino Acid Derivatives

An organocatalytic protocol, employing the commercially available EDC as coupling agent, has been developed for the preparation of dual-protected amino acid derivatives without epimerization. This methodology was then applied to different Boc-amino acid and amine derivatives in moderate to excellent isolated yields. In addition, racemization-free Boc deprotection was also demonstrated. Mechanism investigation through electrospray ionization (+)-mass spectrometry/mass spectrometry revealed an acyclic intermediate (no azlactone formation) activated by the camphorsulfonic acid as an organocatalyst as a key step for the sequential attack of the nucleophile.
Coherent theta activity in the medial and orbital frontal cortices encodes reward value

This study examined how the medial frontal (MFC) and orbital frontal (OFC) cortices process reward information. We simultaneously recorded local field potentials in the two areas as rats consumed liquid sucrose rewards. Both areas exhibited a 4-8 Hz “theta” rhythm that was phase locked to the lick cycle. The rhythm tracked shifts in sucrose concentrations and fluid volumes, demonstrating that it is sensitive to differences in reward magnitude. The coupling between the rhythm and licking was stronger in MFC than OFC and varied with response vigor and absolute reward value in the MFC. Spectral analysis revealed zero-lag coherence between the cortical areas, and found evidence for a directionality of the rhythm, with MFC leading OFC. Our findings suggest that consummatory behavior generates simultaneous theta range activity in the MFC and OFC that encodes the value of consumed fluids, with the MFC having a top-down role in the control of consumption.
Transcription Factor in Tyl Elements

The Ty transposable elements of Saccharomyces cerevisiae consist of a single large transcription unit whose expression is controlled by a combination of upstream and downstream regulatory sequences. Errede (B. Errede, Mol. Cell. Biol. 13:57-62, 1993) has shown that among the downstream control sequences is a binding site for the transcription factor, MCM1. A small restriction fragment containing the Tyl MCMI-binding site exhibits very weak activation of heterologous gene expression. The absence of SPT13 (GAL1l) causes a dramatic increase in activity directed by these sequences. This effect is mediated through the MCM1-binding site itself. MCM1 mRNA and protein levels, as well as its affinity for its binding site, are unchanged in the absence of SPT13. Our results suggest that SPT13 has a role in the negative control of MCM1 activity that is likely to be posttranslational. A role for SPT13 in the negative regulation of the activity of the Tyl MCMI-binding site is consistent with our previous proposal that sptl3-mediated suppression of Ty insertion mutations could be attributed to the loss of negative regulation of genes adjacent to Ty elements.
Destructive and constructive cheater suppression through quorum sensing

The evolutionary consequences of quorum sensing in regulating bacterial cooperation are not fully understood. In this study, we reveal unexpected consequences of regulating public good production through quorum sensing on bacterial population dynamics, showing that quorum sensing can be a collectively harmful alternative to unregulated production. We analyze a birth-death model of bacterial population dynamics accounting for public good production and the presence of non-producing cheaters. Our model demonstrates that when demographic noise is a factor, the consequences of controlling public good production according to quorum sensing depend on the cost of public good production and the presence of non-public fitness benefits. When public good production is inexpensive, quorum sensing is a destructive alternative to unconditional production, in terms of the mean population extinction time. When costs are higher, quorum sensing becomes a constructive strategy for the producing strain, both stabilizing cooperation and decreasing the risk of population extinction.
Antigen-Driven Disease: Major Histocompatibility Complex Class and CD4+ T Cells Requirements for II Expression

Murine AIDS (MAIDS) is a complex syndrome of lymphoproliferation and immunodeficiency induced by a replication-defective murine leukemia virus (BM5def) that encodes Pr6O'g as its only product. It has been suggested that the gag polyprotein is responsible for vigorous antigenic stimulation of CD4+ T cells and generalized secondary activation of the immune system. This model was tested first by infecting mice (C2K/0) that lack class II major histocompatibility complex molecules required for presentation of antigens to CD4+ T cells. C2K/O mice expressed BM5def at high levels but did not develop MAIDS either when unmanipulated
Phenotypic characterization of the Guaymi breed in conservation centers of Panama

1 Conservation and Animal Improvement, City of Knowledge, IDIAP, LABMA, IDIAP, LABMA, Research Institute in Panama. 2 Veterinary Medicine, Faculty of Veterinary Medicine, University of Panama. 3 Ruminant Nutrition, Agricultural Innovation Center for Genetic Resources, IDIAP, Research Institute in Panama. 4 Tropical Veterinary Diseases, Laboratory of Animal Health Currency, IDIAP, Research Institute in Panama.
Insight Into the Posthospital Syndrome: A 3-Month Longitudinal Follow up on Geriatric Syndromes and Their Association With Functional Decline, Readmission, and Mortality

Background: Acute hospitalization may lead to posthospital syndrome, but no studies have investigated how this syndrome manifests and geriatric syndromes are often used as synonym. However, studies on longitudinal associations between syndromes and adverse outcomes are scarce. We aimed to analyze longitudinal associations between geriatric syndromes and functional decline (FD), readmission, and mortality. Methods: Prospective cohort study, including 401 acutely hospitalized patients (aged ≥ 70). We performed: (i) logistic regression analyses to assess associations between patterns of geriatric syndromes as they develop over time (between admission and 1 month postdischarge), and FD and readmission; (ii) generalized estimating equations to assess longitudinal associations between geriatric syndromes over five time points (admission, discharge, 1, 2, and 3 months postdischarge) and FD, mortality, and readmission at 3 months postdischarge. Results: After syndrome absent, syndrome present at both admission and 1 month postdischarge was most prevalent. Persistent patterns of apathy (odds ratio [OR] = 4.35, 95% confidence interval [CI] = 1.54–12.30), pain (OR = 3.26, 95% CI = 1.21–8.8), malnutrition (OR = 3.4, 95% CI = 1.35–8.56), mobility impairment (OR = 6.65, 95% CI = 1.98–22.38), and fear of falling (OR = 3.17, 95% CI = 1.25–8.02) were associated with FD. Developing cognitive impairment (OR = 6.40, 95% CI = 1.52–26.84), fatigue (OR = 4.71, 95% CI = 1.03–21.60), and fall risk (OR = 4.30, 95% CI = 1.21–16.57) postdischarge, was associated with readmission; however, only 4%–6% developed these syndromes. Over the course of five time points, mobility impairment, apathy, and incontinence were longitudinally associated with FD; apathy, malnutrition, fatigue, and fall risk with mortality; malnutrition with readmission. D ow naded rom http/academ ic.p.com /iom edgerontologle/75/7/1403/5740211 by U nivrsiteit an Am srdam user on 18 D ecem er 2020 Conclusion: Most geriatric syndromes are present at admission and patients are likely to retain them postdischarge. Several geriatric syndromes are longitudinally associated with mortality and, particularly, persistently present syndromes place persons are at risk of FD. Although few persons develop syndromes postdischarge, those developing cognitive impairment, fatigue, and fall risk were at increased readmission risk.
tRNAPro Primer-Binding Site

Synthetic oligonucleotides complementary to putative retroviral primer-binding sites were used as hybridization probes to detect novel retroviruslike sequences. An 8.1-kilobase element with structural features of a retroviral provirus was isolated from a human genomic library by this approach. Nucleotide sequence analysis of its 600-base-pair long terminal repeats revealed characteristic motifs known as regulatory signals for RNA polymerase II transcription: CCAAT, TATA, and ATTAAA. In addition, a putative pol gene displays apparent homologies to conserved regions of retroviral reverse transcriptase. The 5' long terminal repeat is flanked at its 3' end by a putative primer-binding site for reverse transcription with homology to tRNApr0. This element is therefore termed HuRRS-P (human retrovirus-related sequence-proline). There are 20 to 40 copies of HuRRS-P homologous sequences in DNAs of human and simian origin.
Quantifying Vision through Language Demonstrates that Visionary Ideas Come from the Periphery

Where do visionary ideas come from? Although the products of vision as manifested in technical innovation are readily observed, the ideas that eventually change the world are often obscured. Here we develop a novel method that uses deep learning to identify visionary ideas from the language used by individuals and groups. Quantifying vision this way unearths prescient ideas, individuals, and documents that prevailing methods would fail to detect. Applying our model to corpora spanning the disparate worlds of politics, law, and business, we demonstrate that it reliably detects vision in each domain. Moreover, counter to many prevailing intuitions, vision emanates from each domain’s periphery rather than its center. These findings suggest that vision may be as much as property of contexts as of individuals.
Dependence of TiO 2 Film Thickness on Photocurrent-Voltage Characteristics of Dye-Sensitized S 이 ar Cells

To realize high energy conversion efficiency, mesoporous TiO2 nanocrystalline electrodes of a large surface area have been investigated extensively as a key material for dyesensitized solar cells (DSSC). 1 One of the strategies to improve conversion efficiencies is to increase light harvest­ ing efficiency by increasing the amount of dye in the electrodes using thick TiO2 films. A thick nanocrystalline film may, however, increase charge recombination between injected electrons and electroactive agents arising from low drift mobility of electrons in the film (10-4-10-7cm/Vs),2 which limits the conversion efficiency. Furthermore, surface states increase with increasing film thickness, offsetting the injection efficiency achieved by the large surface area. Though it would be interesting to evaluate the TiO2 film thickness for optimum conversion efficiency, systematic studies on thickness dependence of photocurrent-voltage are limited. Hara et al. reported that short-circuit photocurrent density Jsc) increased up to about 16 ^m-thick film for a mercurochrome-sensitized TiO2 solar cell due to an increased amount of dye, but corresponding energy conversion efficiencies (n) and fill factors (FF) were not examined.3 Park and coauthors correlated J increase of a dye, cisdithiocyanate-NN-bis(4-carboxylate-4-tetrabutylammoniumcarboxylate-2,2'-bipyridine)-Ru(II) (N719), sensitized rutile TiO2 solar cell with two different film thickness, 6.6 and 11.5 〃m.4 Recently, Yanagida and collaborators reported that light-to-electricity conversion efficiencies (n) decreased in films beyond about 12-^m thickness that were fabricated by repetitive coating followed by combusting at 500 °C for 30 min, but thickness-dependent Jsc and open-circuit voltage (VQ were not analyzed.5 The most commonly utilized TiO2 thickness in the various studies has been around 11 〃m, although it can be thicker than that because the diffusion length of injected electrons in DSSC is expected to be longer than 20 〃m, according to a recent report.6 In this paper, the effect of increasing thickness of nano­ crystalline anatase TiO2 film of DSSC on photocurrent­ voltage (J-V) characteristics and incident-photon-to-current conversion efficiency (IPCE) was studied. The films ranging from 6 to 27 ^m in thickness, were fabricated by repetitive coating with TiO2 colloids made by a sol-gel hydrolysis and characterized by SEM and electrochemical impedance spectroscopy. Optimum conditions are reported regarding the film thickness.