Miracle-dz/UniFAR-FTUs huggingface dataset:
Composite transposable elements in the Xenopus laevis genome

Members of two related families of transposable elements, Tx1 and Tx2, were isolated from the genome of Xenopus laevis and characterized. In both families, two versions of the elements were found. The smaller version in each family (Tx1d and Tx2d) consisted largely of two types of 400-base-pair tandem internal repeats. These elements had discrete ends and short inverted terminal repeats characteristic of mobile DNAs that are presumed to move via DNA intermediates, e.g., Drosophila P and maize Ac elements. The longer versions (Tx1c and Tx2c) differed from Tx1d and Tx2d by the presence of a 6.9-kilobase-pair internal segment that included two long open reading frames (ORFs). ORF1 had one cysteine-plus-histidine-rich sequence of the type found in retroviral gag proteins. ORF2 showed more substantial homology to retroviral pol genes and particularly to the analogs of pol found in a subclass of mobile DNAs that are supposed retrotransposons, such as mammalian long interspersed repetitive sequences, Drosophila I factors, silkworm R1 elements, and trypanosome Ingi elements. Thus, the Tx1 elements present a paradox by exhibiting features of two classes of mobile DNAs that are thought to have very different modes of transposition. Two possible resolutions are considered: (i) the composite versions are actually made up of two independent elements, one of the retrotransposon class, which has a high degree of specificity for insertion into a target within the other, P-like element; and (ii) the composite elements are intact, autonomous mobile DNAs, in which the pol-like gene product collaborates with the terminal inverted repeats to cause transposition of the entire unit.
HLA class I heavy-chain gene promoter elements mediating synergy between tumor necrosis factor and interferons

The cytokines tumor necrosis factor (TNF), beta interferon (IFN-beta), and IFN-gamma increase major histocompatibility complex class I molecule expression. A greater than additive (i.e., synergistic) induction of class I heavy-chain mRNA is observed in HeLa cells treated with TNF in combination with either type of IFN. To define the cis-acting elements mediating cytokine synergy, the promoter of a human major histocompatibility complex class I heavy-chain gene (HLA-B7) was placed in front of a reporter gene and transfected into HeLa cells. Deletion analysis mapped the elements required for synergy to a 40-bp region containing a kappa B-like element, which is necessary for the response to TNF, and an interferon consensus sequence (ICS), which is necessary for the responses to IFNs. When the orientation of these elements was reversed or their normal 20-bp spacing was reduced by 5 or 10 bp, i.e., one half or one full turn of the DNA helix, essentially equivalent responses were obtained, suggesting that these parameters are not critical. In electromobility shift assays, a p50-containing NF-kappa B nuclear factor from TNF-treated cells binds kappa B-containing probes, and ISGF-2 from IFN-gamma-treated cells binds ICS-containing probes. A probe containing both the kappa B and ICS elements (kappa B-ICS) forms a novel complex with nuclear factors isolated from cells treated with both TNF and IFN-gamma; this complex also forms when nuclear factors from individually cytokine-treated cells are mixed in vitro. The natural variant ICS found in HLA-A responds to IFN-gamma and can mediate synergy with TNF. However, the variant kappa B found in HLA-C does not respond to TNF, nor can it mediate synergy between TNF and IFN-gamma. These observations suggest that synergy between TNF and IFNs in the induction of HLA class I gene expression results from the sum of individual interactions of cytokine-activated enhancer-binding factors with the transcription initiation complex.
Far1 and Fus3 link the mating pheromone signal transduction pathway to three G1-phase Cdc28 kinase complexes

In the yeast Saccharomyces cerevisiae, the Cdc28 protein kinase controls commitment to cell division at Start, but no biologically relevant G1-phase substrates have been identified. We have studied the kinase complexes formed between Cdc28 and each of the G1 cyclins Cln1, Cln2, and Cln3. Each complex has a specific array of coprecipitated in vitro substrates. We identify one of these as Far1, a protein required for pheromone-induced arrest at Start. Treatment with alpha-factor induces a preferential association and/or phosphorylation of Far1 by the Cln1, Cln2, and Cln3 kinase complexes. This induced interaction depends upon the Fus3 protein kinase, a mitogen-activated protein kinase homolog that functions near the bottom of the alpha-factor signal transduction pathway. Thus, we trace a path through which a mitogen-activated protein kinase regulates a Cdc2 kinase.
Direct Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Testing from Positive Blood Cultures for Rapid Identification of Bloodstream Infection-Causing Anaerobic Bacteria

Direct use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) on positive blood culture (PBC) bottles may accelerate the identification of bloodstream infection (BSI) causing organisms (1), particularly anaerobic bacteria for which BSI-associated mortality rates are high (2). ….
Defects in mitochondrial protein synthesis and respiratory chain activity segregate with the tRNA(Leu(UUR)) mutation associated with mitochondrial myopathy, encephalopathy, lactic acidosis, and strokelike episodes

Cytoplasts from two unrelated patients with MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis, and strokelike episodes) harboring an A----G transition at nucleotide position 3243 in the tRNA(Leu(UUR)) gene of the mitochondrial genome were fused with human cells lacking endogenous mitochondrial DNA (mtDNA) (rho 0 cells). Selected cybrid lines, containing less than 15 or greater than or equal to 95% mutated genomes, were examined for differences in genetic, biochemical, and morphological characteristics. Cybrids containing greater than or equal to 95% mutant mtDNA, but not those containing normal mtDNA, exhibited decreases in the rates of synthesis and in the steady-state levels of the mitochondrial translation products. In addition, NADH dehydrogenase subunit 1 (ND 1) exhibited a slightly altered mobility on polyacrylamide gel electrophoresis. The mutation also correlated with a severe respiratory chain deficiency. A small but consistent increase in the steady-state levels of an RNA transcript corresponding to 16S rRNA + tRNA(Leu(UUR)) + ND 1 genes was detected. However, there was no evidence of major errors in processing of the heavy-strand-encoded transcripts or of altered steady-state levels or ratios of mitochondrial rRNAs or mRNAs. These results provide evidence for a direct relationship between the tRNALeu(UUR) mutation and the pathogenesis of this mitochondrial disease.
Cadmium-free CuInS2/ZnS quantum dots as efficient and robust photosensitizers in combination with a molecular catalyst for visible light-driven H2 production in water

We demonstrate that cadmium-free core–shell CuInS2/ZnS quantum dots (QDs) are very efficient and robust visible-light absorbing photosensitizers for photocatalytic hydrogen production in a fully aqueous solution when associated with a molecular catalyst, a cobalt tetraazamacrocyclic complex. In the presence of ascorbate as a sacrificial electron donor, this new hybrid system exhibits a remarkable activity for hydrogen production under visible light irradiation at pH 5.0 with up to 7700 and 1010 turnover numbers versus catalyst and QDs, respectively, and with an initial turnover frequency per QD of 1.59 mmolH2 gQD−1 h−1. These are the best performances reported so far with cadmium-free QDs in combination with a molecular catalyst, highlighting the great potential of ternary chalcopyrite nanocrystals as efficient and robust materials for solar fuel production.
Nonsense codons within the Rous sarcoma virus gag gene decrease the stability of unspliced viral RNA

The intracellular accumulation of the unspliced RNA of Rous sarcoma virus was decreased when translation was prematurely terminated by the introduction of nonsense codons within its 5' proximal gene, the gag gene. In contrast, the levels of spliced viral RNAs were not affected in our transient expression assays in chicken cells. Experiments using the transcription inhibitor dactinomycin showed that mutant unspliced RNAs were degraded more rapidly than wild-type RNA. Furthermore, mutant RNAs could be partially stabilized by coexpression of wild-type gag proteins in trans; however, intact gag proteins were not required to maintain the stability of RNAs which did not contain premature termination codons. Thus, termination codons seemed to destabilize the RNA not because of their effect on gag protein function but instead because they disrupted the process of translating the gag region of the RNA. Analysis of double-mutant constructs containing both deletions and termination codons within the gag gene also suggested that the stability of the unspliced RNA was affected by a cis-acting interaction between the RNA and ribosomes.
Repression of cyclin D1: a novel function of MYC

Constitutive expression of human MYC represses mRNA levels of cyclin D1 in proliferating BALB/c-3T3 fibroblasts. We expressed a series of mutant alleles of MYC and found that downregulation of cyclin D1 is distinct from previously described properties of MYC. In particular, we found that association with Max is not required for repression of cyclin D1 by MYC in vivo. Conversely, the integrity of a small amino-terminal region (amino acids 92 to 106) of MYC is critical for repression of cyclin D1 but dispensable for transformation of established RAT1A cells. Runoff transcription assays showed that repression occurs at the level of transcription initiation. We cloned the promoter of the gene for human cyclin D1 and found that it lacks a canonical TATA element. Transcription starts at an initiator element similar to that of the adenovirus major late promoter; this element can be directly bound by USF in vitro. Expression of MYC represses the cyclin D1 promoter via core promoter elements and antagonizes USF-mediated transactivation. Taken together, our data define a new pathway for gene regulation by MYC and show that the cyclin D1 gene is a target gene for repression by MYC.
Layer-number dependent reflection spectra of WS2 and WSe2 flakes on SiO2/Si substrate

Tremendous interest has recently focused on the layered TMDs. Layer number is one of the fundamental parameters in TMDs. In this paper, layer-number dependent reflectivity of WS2 and WSe2 flakes on SiO2/Si substrate were measured by a simple and fast reflection spectrum probing technique. Characteristic excitonic peaks, A and B, and some higher energy density of states excitonic peaks were observed and their properties as a function of layer number were studied. Our results are in agreement with the previous reports.
Markers Differentiating Type 3 Parainfluenza Virus Grown at 25 and 37 C

Serial passage of the 64-2389 strain of type 3 parainfluenza virus in cercopithecus monkey kidney tissue cultures at low temperatures resulted in the selection of a variant which had a higher efficiency of plaque formation at 25 C than the parent line grown at 37 C. The cold variant, unlike the parent strain, plaqued readily at 25 C, and at 37 C it produced significantly larger plaques. Virus titers of the cold variant in hamster lungs were significantly lower and this was probably caused by the stimulation of interferon by the cold variant during the early phase of the infection. The cold variant, like the virus grown at 37 C, also induced the synthesis of interferon late in the infection. Hamsters responded to the intranasal inoculation of each virus line by the development of hemagglutinating-inhibiting antibodies in the sera.
DeGNN : Characterizing and Improving Graph Neural Networks with Graph Decomposition

Despite the wide application of Graph Convolutional Network (GCN), one major limitation is that it does not beneﬁt from the increasing depth and suffers from the oversmoothing problem. In this work, we ﬁrst characterize this phenomenon from the information-theoretic perspective and show that under certain conditions, the mutual information between the output after l layers and the input of GCN converges to 0 exponentially with respect to l . We also show that, on the other hand, graph decomposition can potentially weaken the condition of such convergence rate, which enabled our analysis for GraphCNN. While different graph structures can only beneﬁt from the corresponding decomposition, in practice, we propose an automatic connectivity-aware graph decomposition algorithm, DeGNN , to improve the performance of general graph neural networks. Extensive experiments on widely adopted benchmark datasets demonstrate that often DeGNN can not only signiﬁcantly boost the performance of corresponding GNNs, but also achieves the state-of-the-art performances.
Formation and Elimination of Anti-site Defects during Crystallization in Perovskite Ba1–xSrxLiF3

The defect density of a material is decisive for its physical, chemical, and mechanical properties. Accordingly, defect tuning is desirable for applications spanning, e.g., batteries, fuel cells, electronics, optics, catalysis, and mechanical strength and resilience. Here, we simulate the mechanochemical synthesis of the perovskite Ba1–xSrxLiF3 by compressing a BaLiF3 nanoparticle with a SrLiF3 nanoparticle under conditions likely to occur during high-energy ball milling. We investigate the crystallization process and the ionic mobility of the system and compare with experiment. Animations of the crystallization, simulated under high pressure, revealed that cations, within the crystallization front, would commonly condense onto “incorrect” lattice sites, in some cases eventually leading to the formation of anti-site defects. However, most of these cations would then re-amorphize and the “correct” cation would take its place—rectifying the defect. Crucially, it is the amorphous/crystalline interface that e.
SYMPOSIUM ON THE BIOLOGY OF BACTERIAL SPORES

E. STATEN WYNNE2 Department of Pathology (Division of Experimental Pathology), University of Texas M. D. Anderson Hospital for Cancer Research, Houston, Texas C. F. SCHMIDT' Research Department, Continental Can Company, Chicago, Illinois HAROLD R. CURRAN' Bureau of Dairy Industry, Agricultural Research Administration, United States Department of Agriculture, Washington, D. C. MAX LEVINE Bureau of Laboratories, Territorial Department of Health, Honolulu H. SUGIYAMA' Food Research Institute, University of Chicago, Chicago, Illinois HOWARD REYNOLDS AND HAROLD LICHTENSTEIN Bureau of Human Nutrition and Home Economics, Agricultural Research Administration, United States Department of Agriculture, Washington, D. C. CHARLES R. PHILLIPS' Camp Detrick, Frederick, Maryland
Biostable Aptamer Rings Conjugated for Targeting Two Biomarkers on Circulating Tumor Cells in Vivo with Great Precision

Cancer metastatic spread is life-threatening and caused by circulating tumor cells (CTCs) that are very difficult to precisely capture in vivo. Here we show that two aptamer rings targeting different CTC biomarker epitopes conjugated on dendrimers capture CTCs with enhanced precision even in the presence of 108 interfering cells, or blood cells, and in mice or patient samples when compared with their single aptamer counterparts. The aptamer-conjugate inhibited in vivo metastasis and demonstrated enhanced biostability by resisting biodegradation caused by the endogenous nucleases. The capture arms of the aptamer conjugates could simultaneously and specifically seize two biomarkers (EpCAM and Her2). The double seizure resulted in significant cell-cycle arrest, apoptosis, and growth inhibition of the captured CTCs. The aptamer-conjugate highly penetrated and accumulated in mouse tumors. This study provides the first conceptual evidence that two aptamer rings, inexpensive but bioequivalent to their antibodies.
Development of Fully Automated Determination of Marker-Specific Immunoglobulin G (IgG) Avidity Based on the Avidity Competition Assay Format: Application for Abbott Architect Cytomegalovirus and Toxo IgG Avidity Assays

Determination of the avidity of immunoglobulin G (IgG) directed against a specific marker has become an established diagnostic tool for identifying or excluding acute infections with pathogens. A novel assay format termed AVIcomp (avidity competition based on mass action) circumventing the conventional chaotropic format has been developed for determination of the avidity of marker-specific IgG in patient specimens. Its applications for cytomegalovirus (CMV) and Toxoplasma gondii are presented. Specific high-avidity IgG from the patient specimen is selectively blocked using a soluble antigen in a sample pretreatment reagent, and the amount of remaining specific low-avidity IgG is determined relative to that in an untreated control. The comparison of the conventional chaotropic format, represented by the Radim CMV IgG Avidity assay, and the newly developed AVIcomp method, as exemplified by the Architect CMV IgG Avidity assay, on blood drawn within 4 months after seroconversion revealed a sensitivity of 100% (97.3% by an alternative calculation) for the AVIcomp format versus 87.5% (75.7% by an alternative calculation) for the chaotropic avidity assay. The specificity on 312 CMV IgG reactive and CMV IgM nonreactive specimens from pregnant women was 100% for the AVIcomp assay and 99.7% for the conventional avidity assay. The Architect Toxo IgG Avidity assay showed an agreement of 97.2% with the bioMérieux Vidas Toxo IgG Avidity Assay employing chaotropic reagents. These performance data suggest that the AVIcomp format shows superior sensitivity and equivalent specificity for the determination of IgG avidity to assays based on the chaotropic method and that the AVIcomp format may also be applicable to other disease states.
Preparation and Standardization of an Australia Antigen Antibody of Equine Origin

A horse has been immunized with Australia antigen (Au/SH) purified 20-fold by a procedure employing gel filtration of Cohn fraction IV derived from an Au/SH-positive human plasma pool. Hyperimmunization was initiated by the intramuscular injection of 20 ml of a mixture of equal parts of purified Au/SH and complete Freund's adjuvant. The 20-ml volume was divided into four 5-ml doses, two of which were administered on each side of the horse's neck. Booster doses of antigen alone were given as follows: 10 ml intravenously 30 days later and 5 ml intramuscularly on each of days 77 and 205. Au/SH antibody formed readily, beginning on day 17, and was demonstrated by the agar gel double-diffusion technique and the complement fixation test during the subsequent 6 months. Antihuman plasma protein antibodies were effectively removed from the horse serum by one absorption with 1 to 3 volumes of normal human plasma. Abrupt rises in anticomplementary activity observed shortly after the third and fourth antigen injections, when the horse had developed elevated and steady levels of Au/SH antibody, could possibly be due to formation of antigen-antibody complexes. After optimal conditions were determined, an Au/SH antibody reagent pool which met official requirements was prepared. It was found equally suitable for the agar gel double-diffusion, complement fixation, and counterimmunoelectrophoresis test procedures.
Growth of Indigenous Organisms in Aerated Filtrate of Feedlot Waste

Filtrates from feedlot waste were incubated under aerobic conditions to evaluate the availability of nutrients for cell production and to assess the capacity of indigenous flora to produce stabilized effluents. Incubation was carried out in 9-liter aerated jar fermentors. Three-fourths of the organic material and one-third of the nitrogen were taken up in 4 days; 90% utilization of organic material and nitrogen required almost a month. Acid was produced initially, but aerated liquid thereafter rapidly became alkaline. With pH controlled at 7.0, a comparable pattern of carbon utilization occurred, but nitrogen was incompletely used. The numerically dominant organisms in the waste inoculum were almost immediately displaced by an emergent population of a few types of organisms not originally evident. Maximal viable populations of 109 to 3 � 109 cells/ml were obtained in aerated waste liquid within 48 h; subsequently, numbers declined quickly to initial levels. Numbers of fungi, yeasts, and streptomycetes slowly increased but never exceeded their initial concentration by more than tenfold.
Growth of Human Lymphoid Cells (Raji Strain) in a Five-Liter Fermentor

Procedures used to produce an established line of mammalian cells (L cell) in a New Brunswick fermentor were adapted to propagate human lymphoid cells in suspended culture. Control of pH within defined limits was more effective for regulation of cell metabolism than control of oxidation-reduction potential. An unusually high rate of agitation was required.
Genetically Alterable Transport of Amethopterin in Diplococcus pneumoniae I. Physiological Properties and Kinetics of the Wild-type System

A system of H3-amethopterin uptake, physiologically and kinetically resembling active transport, has been described in Diplococcus pneumoniae. Uptake by this system has a pH optimum near 6.0, is temperature-dependent, requires a readily available source of energy, and conforms to Michaelis-Menten kinetics. The system showed a Km of 0.9 × 10−6m and a Vmax of 1.9 × 10−13 moles per min per mg (dry weight). Both folate and H2-folate compete with H3-amethopterin for the same system, but to a limited degree. The intracellular concentration of H3-amethopterin accumulated at equilibrium was 1.06 × 10−9 moles/ml or fivefold the external concentration when the latter was limiting, but at least 60-fold the internal concentration attained solely by diffusion in the same time interval at 0 C.
Epidemiological Surveillance of Serratia marcescens Infections by Bacteriocin Typing

During 10 months, 155 isolates of Serratia marcescens were cultured from 105 patients, of whom 49 were considered to have significant infection. The 155 isolates were typed by bacteriocin sensitivity, and 137 (88.4%) were assigned to 37 provisional bacteriocin groups; 18 isolates were nontypable. No major outbreaks of nosocomial infection were demonstrable; however, there were four chronologically separate minor episodes of cross-infection that involved two or three patients per room or unit, respectively.
Learning Efficiency of Multiagent Information Structures

Which information structures are more effective at eliminating first- and higher-order uncertainty and hence at facilitating efficient play in coordination games? We consider a learning setting where players observe many private signals about the state. First, we characterize multiagent learning efficiency, that is, the rate at which players approximate common knowledge. We find that this coincides with the rate at which first-order uncertainty disappears, as higher-order uncertainty vanishes faster than first-order uncertainty. Second, we show that with enough signal draws, information structures with higher learning efficiency induce higher equilibrium welfare. We highlight information design implications for games in data-rich environments.