Miracle-dz/UniFAR-FTUs huggingface dataset:
Truncations and Deletions Expressed by Recombinant

Glycoprotein gIV is an envelope component of bovine herpesvirus type 1 and appears to be involved in attachment, penetration, and cell fusion. Four antigenic domains which include both continuous and discontinuous epitopes have been previously defined by competition binding assays using gIV-specific monoclonal antibodies (MAbs). Here we describe the construction of C-terminal truncations and internal deletions in the gIV-encoding gene and analyses of the effects of these mutations on the synthesis, processing, transport, and antigenicity of glycoprotein glV as expressed by recombinant vaccinia viruses. Wild-type glV expressed by recombinant vaccinia virus STg1V was indistinguishable from authentic glV produced in bovine herpesvirus 1-infected cells with respect to molecular weight, processing, transport, and antigenicity. Analysis of the mutant proteins showed that the binding sites for MAbs 9D6 and 3D9S, which recognize linear epitopes, lie between amino acids 164 and 216 and amino acids 320 and 355, respectively. Discontinuous epitopes recognized by MAbs 3E7, 4C1, 2C8, and 3C1 were located between amino acids 19 and 320, whereas amino acids 320 to 355 were critical for binding of MAb 136. All mutant proteins containing amino acids 245 to 320 were processed, possess endo-13-N-acetylglucosaminidase H-resistant oligosaccharides, and were transported to the cell surface or secreted into the medium. In contrast, mutant proteins missing amino acids 245 to 320 were retained in the rough endoplasmic reticulum. These findings suggest that residues 245 to 320 are important for proper processing and transport of gIV to the cell surface.
Interaction of Glycoprotein glll

Glycoprotein glll is one of the major envelope glycoproteins of pseudorabies virus (PrV) (Suid herpesvirus 1). Although it is dispensable for viral growth, it has been shown to play a prominent role in the attachment of the virus to target cells, since gIIIdeletion mutants are severely impaired in adsorption (C. Schreurs, T. C. Mettenleiter, F. Zuckermann, N. Sugg, and T. Ben-Porat, J. Virol. 62:2251-2257, 1988). We show here that during the process of adsorption of PrV, the viral glycoprotein gIlH interacts with a cellular heparinlike receptor. This conclusion is based on the following findings. (i) Heparin inhibits plaque formation of PrV by preventing the adsorption of wild-type virions to target cells. However, heparin does not interfere with the plaque formation of PrV mutants that lack glycoprotein glll. (ii) Wild-type virions readily adsorb to matrix-bound heparin, whereas gIllmutants do not. (iii) Pretreatment of cells with heparinase reduces considerably the ability of wild-type PrV to adsorb to these cells and to form plaques but does not negatively affect glllmutants. (iv) Glycoprotein gIII binds to heparin and appears to do so in conjunction with glycoprotein gIl. Although heparin significantly reduces the adsorption of wild-type virus to all cell types tested, quantitative differences in the degree of inhibition of virus adsorption by heparin to different cell types were observed. Different cell types also retain their abilities to adsorb wild-type PrV to a different extent after treatment with heparinase and differ somewhat in their relative abilities to adsorb gIlmutants. Our results show that while the primary pathway of adsorption of wild-type PrV to cells occurs via the interaction of viral glycoprotein glll with a cellular heparinlike receptor, an alternative mode of adsorption, which is not dependent on either component, exists. Furthermore, the relative abilities of different cell types to adsorb PrV by the gIlH-dependent or the alternative mode vary to some extent.
Glial Cell Line Persistently Infected with Borna Disease Virus (BDV): Influence of Neurotrophic Factors

Borna disease virus (BDV) infects cells of the nervous system in a wide range of species. Previous work suggests that there are differences in BDV replication in neuronal cells and glial cells. Many neurons are lysed by the immunopathologic response to BDV; lysis of dentate gyrus neurons in the absence of encephalitis is seen in rats inoculated with BDV as neonates. In contrast, persistently BDV-infected astrocytes increase over the course of BDV infection. Therefore, we compared BDV replication in neuronal (SK-N-SH and SK-N-SHEP) and astrocytic (C6) cell lines. While SK-N-SH cells produced more infectious virions per cell, the C6 cells contained more BDV proteins and RNA. BDV sequences in the supernatants of both cell types were identified, despite low titers of infectious virus, suggesting the release of incomplete virions into the medium. C6 cells secreted a factor or factors into the medium that enhanced the production of BDV proteins and RNA in other cell lines. In addition, nerve growth factor treatment produced the same enhancement. Thus, BDV replication in certain neural cells in vitro may be linked to the production of cell-specific factors which affect viral replication.
Role of Extracellular Virus in the Maintenance of the Persistent Infection Induced in Aedes

Sindbis virus infection of cultured mosquito cells was found to have no effect on the growth ofthese cells; instead, a persistent infection ofthe culture followed an initial acute phase ofrapid virus synthesis. Nearly all ofthe cells in the acute stage of infection were found to actively release virus in an infectious-center assay and to contain significant amounts of virus antigen as determined by immunofluorescence. Cells in the persistent phase of infection released few virions into the media, and only a small percentage ofthe cultured cells could be demonstrated to contain detectable amounts of virus antigen by immunofluorescence assay. In spite of the fact that nearly 100% of the cells in the persistent phase of infection were found to be virus negative by the two assays described above, the culture as a whole totally excluded the expression of superinfecting virus, as did cells in the acute phase, suggesting that most of the persistently infected cells did, indeed, contain virus information. Prevention of reinfection of the cells in the persistent phase by eliminating extracellular virus resulted in a curing of the culture such that it responded to infection by added virus much as would an uninfected culture.
Ultra-fast HPM detectors improve NAD(P)H FLIM

Metabolic imaging by NAD(P)H FLIM requires the decay functions in the individual pixels to be resolved into the decay components of bound and unbound NAD(P)H. Metabolic information is contained in the lifetime and relative amplitudes of the components. The separation of the decay components and the accuracy of the amplitudes and lifetimes improves substantially by using ultra-fast HPM-100-06 and HPM-100-07 hybrid detectors. The IRF width in combination with the Becker & Hickl SPC-150N and SPC-150NX TCSPC modules is less than 20 ps. An IRF this fast does not interfere with the fluorescence decay. The usual deconvolution process in the data analysis then virtually becomes a simple curve fitting, and the parameters of the NAD(P)H decay components are obtained at unprecedented accuracy.
Egocentric Global Pose Estimation

The input pose sequence with n frames is firstly reshaped to (3× 15, n) and fed into the encoder with 45 input channels. The encoder has five 1D conv blocks with 64, 64, 128, 256 and 512 output channels. Each conv block contains one 1D conv layer (kernel size=3, stride=1 and padding=1), one batch norm layer and one leaky relu layer with negative slope=0.01. The output of the encoder is sent into two linear layers giving μ, σ ∈ R. The latent vector z is sampled with μ, σ with the reparameterization trick. For the decoder, the sampled latent vector z is firstly fed into a linear layer with output dimension n × 512, and five 1D de-conv blocks with 256, 128, 64, 64 and 64 output channels. Each block contains one 1D de-conv layer, one batch norm layer and one leaky relu layer with the same hyper-parameters as the encoder. The output vector with 45 channels is obtained from a final conv layer (kernel size=3, stride=1 and padding=1). The output vector is eventually reshaped to (n, 15, 3), representing a pose sequence as the input. During training, the weight of reconstruction loss and KL divergence loss is set to 1 and 5 × 10−3 respectively. The code will be released in the future.
3 ' Sequences by the Hypermodified Oxopyrimidine in Bacillus subtilis Bacteriophage SP 10 DNA

The DNA of Bacillus subtilis bacteriophage SP10 is partially resistant to cleavage and methylation in vitro by restriction enzyme R * BsuRI and its cognate methylase even though >20 copies of the target sequence, 5'. GGCC . 3', are present on the phage genome. YThy, a hypermodified oxopyrimidine that replaces a fraction of the thymine residues in SP10 DNA, was responsible for this protection, since YThy-free DNA was no longer resistant. Sites that were normally resistant could nevertheless be cleaved or methylated in vitro if the salt concentration was reduced or dimethyl sulfoxide was added to the reaction buffer. Analysis of the termini produced by cleavage suggested that resistant sites occurred in the sequence 5' . o. GGCC-YThy . 3', whereas sensitive sites, of which there were only two per genome, occurred in the sequence 5' . GGCCG . 3'. These in vitro results provide an explanation for the in vivo resistance of SP10 to restriction-modification by B. subtilis R. They also suggest ways in which the presence of the atypical base YThy in regions that flank the target might upset critical DNA-enzyme interactions necessary to locate and recognize the specific site of cleavage or methylation. YThy also strongly protected 5' . GCNGC . 3' (R * Fnu4HI) sequences on SP10 DNA, but the biological relevance of this protection is unclear.
Inactivation by L-(+)-Glutamate

A previously unrecognized enzyme, citrate lyase deacetylase, has been purified about 140-fold from cell extracts of Rhodopseudomonas gelatinosa. It catalyzed the conversion of enzymatically active acetyl-S-citrate lyase into the inactive HS-form and acetate. The enzyme exhibited an optimal rate of inactivation at pH 8.1. Because of the instability of acetyl-S-citrate lyase at acidic and alkaline pH values, all assays were carried out at pH 7.2, where the spontaneous hydrolysis of the acetyl-S-citrate lyase was negligible and deacetylase showed 70% of the activity at pH 8.1. The apparent Km value for citrate lyase was 10-7 M at pH 7.2 and 30 C. The activity of the deacetylase was restricted to the citrate lyase from R. gelatinosa. The corresponding lyases from Enterobacter aerogenes (formerly Klebsiella aerogenes) and Streptococcus diacetilactis were not deacetylated; likewise, thioesters such as acetyl-S coenzyme A, acetoacetyl-S coenzyme A, and N-acetyl-S-acetyl-cysteamine were also not hydrolyzed. Citrate lyase deacetylase was present in very small amounts in cells of R. gelatinosa grown with acetate or succinate; it was induced by citrate along with the citrate lyase. L-(+)-Glutamate strongly inhibited the deacetylase. Fifty percent inhibition was obtained at a concentration of 1.4 x 10-i L-(+)-glutamate. D-(-)Glutamate, a-ketoglutarate, L-a-hydroxyglutarate, L-(-)-proline, and other metabolites were less effective.
Cryptic RNA-Binding Domain in the Pol Region of the L-A

The Pol region of the Gag-Pol fusion protein of the L-A double-stranded (ds) RNA virus of Saccharomyces cerevisiae has (i) a domain essential for packaging viral positive strands, (ii) consensus amino acid sequence patterns typical of RNA-dependent RNA polymerases, and (iii) two single-stranded RNA binding domains. We describe here a third single-stranded RNA binding domain (Pol residues 374 to 432), which is unique in being cryptic. Its activity is revealed only after deletion of an inhibitory region C terminal to the binding domain itself. This cryptic RNA binding domain is necessary for propagation of M1 satellite dsRNA, but it is not necessary for viral particle assembly or for packaging of viral positive-strand single-stranded RNA. The cryptic RNA binding domain includes a sequence pattern common among positive-strand single-stranded RNA and dsRNA viral RNA-dependent RNA polymerases, suggesting that it has a role in RNA polymerase activity.
From rocks to walls: a machine learning approach for lunar base construction

In-situ resource utilization is a key aspect for an eﬃcient human exploration of extraterrestrial environments. A cost-eﬀective method for the construction of preliminary structures is dry stacking with locally found unprocessed rocks, which is a challenging task. This thesis focus on learning this task from scratch. Former approaches rely on previously acquired models, which may be hard to obtain in the context of a mission. In alternative, we propose a model-free, data-driven approach. We formulate an abstraction of the problem as the task of selecting the position to place each rock, presented to the robot in a sequence, on top of the currently built structure. The goal is to assemble a wall that approximates a target volume, given the 3D perception of the currently built structure, the next object and the target volume. An agent is developed to learn this task using reinforcement learning. The Deep Q-networks algorithm is used, where the Q-network outputs a value map corresponding to the expected return of placing the object in each position of a top-view depth image. The learned q-function is able to capture the goal and dynamics of the environment. The emerged behaviour is, to some extent, consistent with dry stacking theory. The learned policy outperforms engineered heuristics, both in terms of stability of the structure and similarity with the target volume. Despite the simpliﬁcation of the task, the policy learned with this approach could be applied to a realistic setting as the high level planner in an autonomous construction pipeline.
Mitochondrial oL-Ketoglutarate Dehydrogenase Complex

genes for a-ketoglutarate dehydrogenase (KE1) and dihydrolipoyl transsuccinylase (KE2) components, respectively. Mutants unable to express KEl or KE2 form partial complexes similar to those reported in earlier studies on the resolution and reconstitution of bacterial and mammalian KGDC. Thus mutants lacking KE1 assemble a high-molecular-weight subcomplex consisting of a KE2 core particle with bound dihydrolipoyl dehydrogenase (E3). Similarly, mitochondrial extracts of mutants lacking KE2 contain dimeric KE1 and E3. These components, however, are not associated with each other. The partial complexes detected in the mutants
Probabilistic Feature Attention as an Alternative to Variables in Phonotactic Learning

Since Halle 1962, explicit algebraic variables (often called alpha notation) have been commonplace in phonological theory. However, Hayes and Wilson (2008) proposed a variable-free model of phonotactic learning, sparking a debate about whether such algebraic representations are necessary to capture human phonological acquisition. While past experimental work has found evidence that suggested a need for variables in models of phonology (Berent et al. 2012, Moreton 2012, Gallagher 2013), this article presents a novel mechanism, Probabilistic Feature Attention, that allows a variable-free model of phonotactics to predict a number of these phenomena. This approach also captures experimental results involving phonological generalization that cannot be explained by variables. These results cast doubt on whether variables are necessary to capture human-like phonotactic learning and provide a useful alternative to such representations.
Transforming DNA into Yeast Chromosomes and In Vivo

When the yeast Saccharomyces cerevisiae was transformed with DNA that shares no homology to the genome, three classes of transformants were obtained. In the most common class, the DNA was inserted as the result of a reaction that appears to require base pairing between the target sequence and the terminal few base pairs of the transforming DNA fragment. In the second class, no such homology was detected, and the transforming DNA was integrated next to a CTT or GTT in the target; it is likely that these integration events were mediated by topoisomerase I. The final class involved the in vivo ligation of transforming DNA with nucleus-localized linear fragments of mitochondrial DNA.
Monitoring the quality of software development and thereby anticipating the defects before release: Examples from the Service Sector

: Existing error prediction methods based on change metrics and code must rely on source code and software evaluation information and are not always available. The ability to assess software defects at the beginning of an ongoing project allows the development team to effectively allocate resources and efforts. We assessed the correlation between pre-release defects, funding, integration points and final defect units, i.e., the number of defects. Results at earlier integration points may reflect corresponding defects at later integration points. A sample size of 86 subsystems and 108 features were analyzed at subsystem and feature granularity at eight integration points. The final results show that the defects found at integration points IP-3 and IP-4 can be used as good predictors of the total number of defects expected in the final version. The correlation of the defects found in the integration points can be examined in order to identify high-risk modules at the beginning of the development cycle.
Simultaneous Detection of Total Coliforms and Escherichia coli

A defined substrate method was applied to drinking water to simultaneously enumerate total coliforms and total Escherichia coli directly from samples. After incubation at 35°C for 24 h, the development of yellow in an initially colorless solution was specific for total coliforms; fluorescence at 366 nm in the same tube(s) or vessel demonstrated the presence of E. coli. No confirmatory or completed steps were necessary. Known as autoanalysis colilert (AC), this method was constituted as a presence-absence test and compared with the methods described in Standard Methods (SM) in the P-A format. Seven water utilities representing a wide geological and hydrological spectrum participated in the evaluation. A total of 702 split drinking water samples were analyzed. Of these, 358 were negative in both tests (SMand AC-); 302 were positive (SM+ and AC+); and 42 were mixed (SM+ and AC-, 20; AC+ and SM-, 22). The overall agreement rate was 94%. Comparison of the SM and AC results by nonparametric statistics demonstrated no differences. Heterotrophic plate count bacteria exerted no discernible effect on the AC test. By subculture, each time the AC test was yellow, a total coliform was present; when the test was fluorescent, E. coli was isolated.
7-Kilodalton Subunit of Vaccinia Virus DNA- Dependent RNA Polymerase with Structural Similarities

A previousl unrecognized 7-kDa polypeptide copurified with the DNA-dependent RNA polymerase of vaccinia virus virions. Internal amino acid sequences of the small protein matched a viral genomic open reading frame of 63 codons. Antipeptide antiserum was used to confirm the specific and complete association of the 7-kDa protein with RNA polymerase. The amino acid sequence predicted from the viral gene, named rpo7, was 23% identical to that of the smallest subunit of Saccharomyces cerevisiae RNA polymerase II, and a metal-binding motif, Cys-X-X-Cys-Gly, was located at precisely the same location near the N terminus in the two proteins. RNA analyses demonstrated early transcriptional initiation and termination signals in the rpo7 gene sequence. The viral RNA polymerase subunit was synthesized during the early phase of infection and continued to accumulate during the late phase.
Anaerobic Oxidation of Ornithine by Clostridium sticklandii1

The oxidation of ornithine in the presence of proline by crude extracts of Clostridium sticklandii cells was stimulated by nicotinamide adenine dinucleotide, coenzyme A, a-ketoglutarate, dimethylbenzimidazolyl cobamide (DBC) coenzyme, MgC12, and adenosine diphosphate. Deletion of various cofactors resulted in the accumulation of a new dibasic amino acid which was identified as 2, 4-diaminovaleric acid. Both the oxidation of ornithine to alanine and acetate and the conversion of ornithine to 2, 4-diaminovaleric acid were stimulated by addition of DBC coenzyme, and both were inhibited by intrinsic factor, an inhibitor of cobamide coenzyme-dependent reactions. This inhibition was reversed by addition of DBC coenzyme. However, the oxidation of 2, 4-diaminovaleric acid was insensitive to added intrinsic factor. The data indicate that 2,4-diaminovaleric acid represents the first intermediate in the oxidation of ornithine by C. sticklandii.
Tax Induces Nuclear Translocation of NF-KB through Dissociation

The activity of the NF-KB transcription factor is controlled through cytoplasmic retention by either of two types of molecules: the inhibitor IKBaIMAD3 or the p105 and pl00 precursors of the p50 and p52 DNA-binding subunits. Treatment of cells with classical NF-KB inducers such as tumor necrosis factor, interleukin-1, phorbol myristate acetate, and lipopolysaccharide results in MAD3 degradation followed by nuclear translocation of NF-KB. On the other hand, the mechanisms involved in the dissociation of the cytoplasmic p105/p100-containing complexes are largely unknown. The Tax protein encoded by human T-cell leukemia virus type 1 is a potent activator of viral and cellular gene transcription. It does not bind DNA directly but seems to activate transcription indirectly either by enhancing the activities of the transcription factors that recognize responsive elements located in the promoters of the Tax-responsive genes or by forming ternary complexes with these factors and DNA. It has been previously shown that Tax is able to induce nuclear translocation of NF-KB. We demonstrate here that Tax can induce translocation of members of the NF-KcB family retained in the cytoplasm through their interaction with either p105 or plO0. On the other hand, Tax induces no apparent degradation of MAD3, although experiments using cycloheximide indicate that it decreases the half-life ofMAD3. However, this activity is shared by a mutant of Tax which is unable to activate NF-KB. These results suggest that Tax activates NF-KB essentially through the p105/pl00 retention pathway.
Genetic Region from Pseudomonas putida Involved in the Stimulation of Plant Root

Transposon (Tn5) mutagenesis was applied to Pseudomonas putida GR12-2R3, which promotes root elongation (a phenotype designated Pre) of Brassica campestris under gnotobiotic conditions. Of 3,000 TnS transconjugants, only one mutant that lost Pre activity but remained prototrophic and capable of plant root colonization was detected. This mutant was complemented by plasmid pRE53, which contained a 15.0-kilobase DNA insert isolated from a parental strain. The complemented mutant regained full Pre activity comparable to that of the wild type.
Primary Porcine Kidney Cell Culturest

A porcine enteric calicivirus-like virus was adapted to serial propagation in primary porcine kidney cell cultures. Attempts to propagate this virus in primary porcine kidney cells in the presence of trypsin or pancreatin or without medium supplementation were unsuccessful. A low-pH medium (pH 6.8) was also ineffective in virus propagation. Successful serial propagation of the virus required the presence of an intestinal-content preparation, derived from uninfected gnotobiotic pigs, in the cell culture medium. The best results were obtained with six-well plate cultures which were centrifuged after virus inoculation. Infected cells