Miracle-dz/UniFAR-FTUs huggingface dataset:
Together Are Necessary and Sufficient for Transformation

The early human papillomavirus type 16 genes that directly participate in the in vitro transformation of primary human keratinocytes have been defined. In the context of the full viral genome, mutations in either the E6 or E7 open reading frame completely abrogated transformation of these cells. Mutations in the El, E2, and E2-E4 open reading frames, on the other hand, had no effect. Thus, both the full-length E6 and E7 genes were required for the induction of keratinocyte immortalization and resistance to terminal differentiation. The E6 and E7 genes expressed together from the human ,-actin promoter were sufficient for this transformation; mutation of either gene in the context of this recombinant plasmid eliminated the ability to induce stable differentiation-resistant transformants.
Aspergillus niger and Saccharomyces cerevisiaet

Direct fermentation of unhydrolyzed potato starch to ethanol by monocultures of an amylolytic fungus, Aspergilus niger, and cocultures ofA. niger and Saccharomyces cerevisiae was investigated. Amylolytic activity, rate and amount of starch utilization, and ethanol yields increased several-fold in coculture versus the monoculture due to the synergistic metabolic interactions between the species. Optimal ethanol yields were obtained in the pH range 5 to 6 and amylolytic activity was obtained in the pH range 5 to 8. Ethanol yields were maximal when fermentations were conducted anaerobically. Increasing S. cerevisiae inoculum in the coculture from 4 to 12% gave a dramatic increase in the rate of ethanol production, and ethanol yields of >96% of the theoretical maximum were obtained within 2 days of fermentation. These results indicate that simultaneous fermentation of starch to ethanol can be conducted efficiently by using cocultures of the amylolytic fungus A. niger and a nonamylolytic sugar fermenter, S. cerevisiae.
Diamidino-2-Phenylindole and Fluorescent Oligonucleotide Probes Targeting Kingdom-Level 16S rRNA Sequencest

A method for quantifying eubacterial cell densities in dilute communities of small bacterioplankton is presented. Cells in water samples were stained with 4',6-diamidino-2-phenylindole (DAPI), transferred to gelatin-coated slides, and hybridized with rhodamine-labeled oligonucleotide probes specific for kingdom-level 16S rRNA sequences. Between 48 and 69%o of the cells captured on membrane filters were transferred to gelatin-coated slides. The number of DAPI-stained cells that were visualized with eubacterial probes varied from 35 to 67%. Only 2 to 4% of these cells also fluoresced following hybridization with a probe designed to target a eukaryotic 16S rRNA sequence. Between 0.1 and 6% of the bacterioplankton in these samples were autofluorescent and may have been mistaken as cells that hybridized with fluorescent oligonucleotide probes. Dual staining allows precise estimates of the efficiency of transfers of cells to gelatin films and can be used to measure the percentage of the total bacterioplankton that also hybridize with fluorescent oligonucleotide probes, indicating specific phylogenetic groups.
Bacteriocin Produced by Lactobacillus acidophilus 11088t

Lactacin F, a bacteriocin produced by Lactobacillus acidophilus 11088 (NCK88), was purified and characterized. Lactacin F is heat stable, proteinaceous, and inhibitory to other lactobacilli as well as Enterococcusfaecalis. The bacteriocin was isolated as a floating pellet from culture supernatants brought to 35 to 40% saturation with ammonium sulfate. Native lactacin F was sized at approximately 180 kDa by gel filtration. Column fractions having lactacin F activity were examined by electron microscopy and contained micelle-like globular particles. Purification by ammonium sulfate precipitation, gel filtration, and highperformance liquid chromatography resulted in a 474-fold increase in specific activity of lactacin F. The purified bacteriocin was identified as a 2.5-kDa peptide by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The lactacin F peptide retained activity after extraction from SDS-PAGE gel slices, confirming the identity of the 2.5-kDa peptide. Variants of NCK88 that failed to exhibit lactacin F activity did not produce the 2.5-kDa band. Sequence analysis of purified lactacin F identified 25 N-terminal amino acids containing an arginine residue at the N terminus. Composition analysis indicates that lactacin F may contain as many as 56 amino acid residues.
Growth responses of strains of Desulfovibrio spp . a Desulfovibrio Desulfovibrio " De . br Desulfovibrio Desulfovibrio Desulfovibrio besii Medium compositionb desulfuricans desulfuricans eultspiras desulfuricans desulfuricans baculatus

The different nutritional properties of several Desulfovibrio desulfuricans strains suggest that either the strains are misclassified or there is a high degree of phenotypic diversity within the genus Desulfovibrio. The results of partial 16S rRNA and 23S rRNA sequence determinations demonstrated that Desulfovibrio desulfuricans ATCC 27774 and "Desulfovibrio multispirans" are closely related to the type strain (strain Essex 6) and that strains ATCC 7757, Norway 4, and El Agheila Z are not. Therefore, these latter three strains of Desulfovibrio desulfuricans are apparently misclassified. A comparative analysis of nearly complete 16S rRNA sequences in which we used a least-squares analysis method for evolutionary distances, an unweighted pair group method, a signature analysis method, and maximum parsimony was undertaken to further investigate the phylogeny of Desulfovibrio species. The species analyzed were resolved into two branches with origins deep within the 8 subdivision of the purple photosynthetic bacteria. One branch contained five deep lineages, which were represented by (i) Desulfovibrio salexigens and Desulfovibrio desulfuricans El Agheila Z; (ii) Desulfovibrio africanus; (iii) Desulfovibrio desulfuricans ATCC 27774, Desulfomonas pigra, and Desulfovibrio vulgaris; (iv) Desulfovibtio gigas; and (v) Desulfomicrobium baculatus (Desulfovibrio baculatus) and Desulfovibrio desulfuricans Norway 4. A correlation between 16S rRNA sequence similarity and percentage of DNA relatedness showed that these five deep lineages are related at levels below the minimum genus level suggested by Johnson (in Bergey's Manual of Systematic Bacteriology, vol. 1, 1984). We propose that this branch should be grouped into a single family, the Desulfovibrionaceae. The other branch includes other genera of sulfate-reducing bacteria (e.g., Desulfobacter and Desulfococcus) and contains Desulfovibrio sapovorans and Desulfovibrio baarsii as separate, distantly related lineages.
Genetically Engineered Escherichia coli Introduced into Soilt

a most-probable-number-polymerase chain reaction method. Whereas the E. coli population density declined below the plate-counting-technique detection threshold (102 CFU g-1) after 15 days, 103 extracellular and 5 x 102 total DNA target sequences were still detected after 40 days. Additionally, the E. coli cell counts fell below the detection limit of the immunofluorescence method (105 cells. g-1) before the end of the experiment. Colony hybridizations did not reveal gene transfer to the indigenous microflora. These results confirm the persistence of residual E. coli target sequences that could not be detected by the classical cell counting method and offer promising applications for the environmental detection of microorganisms, either engineered, pathogenic, or released for beneficial effects.
Cloning and Analysis of Duplicated rJbM and rJbK Genes Involved in the Formation of GDP-Mannose in Eschenrchia coli

The rfbg,, gene cluster, which is responsible for the synthesis of the lipopolysaccharide 09 antigen, was cloned from Escherichia coi 09:130. The gnd gene, encoding 6-phosphogluconate dehydrogenase, was identified adjacent to the rJb09 cluster, and by DNA sequence analysis the gene order gnd-rJbM-rjbK was established. This order differs from that described for other members of the family Enterobacteriaceae. Nucleotide sequence analysis was used to identify the rftK and rJbM genes, encoding phosphomannomutase and GDP-mannose pyrophosphorylase, respectively. In members of the family Enterobacteriaceae, these enzymes act sequentially to form GDP-mannose, which serves as the activated sugar nucleotide precursor for mannose residues in cell surface polysaccharides. In the E. coli 09:K30 strain, a duplicated rJbM2-rJbK2 region was detected approximately 3 kbp downstream of rJbM'-dbK' and adjacent to the remaining genes of the rib09 cluster. The rJbM isogenes differed in upstream flanking DNA but were otherwise highly conserved. In contrast, the rfbK isogenes differed in downstream flanking DNA and in 3'-terminal regions, resulting in slight differences in the sizes of the predicted RfbK proteins. RfbMog and RfbKog are most closely related to CpsB and CpsG, respectively. These are isozymes of GDP-mannose pyrophosphorylase and phosphomannomutase, respectively, which are thought to be involved in the biosynthesis of the slime polysaccharide colanic acid in E. coi K-12 and Salmonella enterica serovar Typhimurium. An E. col 0-:K30 mutant, strain CWG44, lacks rJbM2-rJb0K2 and has adjacent essential rib09 sequences deleted. The remaining chromosomal genes are therefore suflicieift for GDP-mannose formation and K30 capsular polysaccharide synthesis. A mutant of E. coli CWG44, strain CWG152, was found to lack GDP-anannose pyrophosphorylase and lost the ability to synthesize K30 capsular polysaccharide. Wild-type capsular polysaccharide could be restored in CWG152, by transformation with plasmids containing either fM' or JM2. Introduction of a complete rib09 gene cluster into CWG152 restored synthesis of both 09 and K30 polysaccharides. Consequently, rJbM is sufficient for the biosynthesis of GDP-mannose for both 0 antigen and capsular polysaccharide in E. coil 09:K30. Analysis of a collection of serotype 08 and 09 isolates by Southern hybridization and PCR amplification experiments demonstrated extensive polymorphism in the rJbM-rJbK region.
Reaction in the Cerebrospinal Fluid of Patients Suffering from Neurological Complications Associated with Chicken

The polymerase chain reaction (PCR) was used to detect varicella-zoster virus (VZV) DNA in the cerebrospinal fluid of patients with VZV infection associated with neurological symptoms. Positive results were obtained in three of five children with post-chicken pox cerebellitis and in seven of seven herpes zoster patients with neurological symptoms. The PCR thus provides a useful tool for the early diagnosis of VZV-associated neurological disease.
Adherence of an Enterotoxigenic Escherichia coli Strain, Serotype 078:H11,

The human enterotoxigenic Escherichia coli pathogen designated H10407 expresses two different types of surface pili, one designated type 1 pili and the other designated colonization factor antigen I (CFA/I). CFA/I pili are thought to promote the adherence of H10407 to the mucosa of the human small bowel. H10407 was grown under conditions which promoted the expression of either type 1 pili or CFA/I pili, and in each case, the adherence of H10407 to purified human intestinal brush borders was quantitated. The adherence assays revealed that H10407 adhered to human brush borders only when it expressed CFA/I pili. It appears that in vitro adherence of H10407 to human intestinal epithelial cells is dependent on the expression of CFA/I.
UK-Dependent Gene Expression from Dependence on Intercompartmental Communication

During sporulation of Bacillus subtilis, proteolytic activation of pro-rK and ensuing fK-dependent gene expression normally require the activity ofmany sporulation gene products. We report here that overproducing pro-oK at the onset of sporulation substantially uncouples orK-dependent gene expression from its normal dependency. Overproducing pro-oK in strains with a mutation in spoIIIG, spoIIL, spoIIIE, or spoIVB partially restored CK-dependent gene expression in the mother cell and resulted in accumulation of a small amount of polypeptide that comigrated with CfK, but these mutants still failed to form spores. In contrast, sporulation of K spoIVF mutants was greatly enhanced by pror overproduction. The products of the spoIVF operon are made in the mother cell and normally govern pro-ciK processing, but overproduction of pro-ci K appears to allow accumulation of a small amount of iK, which is sufficient to partially restore mother cell gene expression and spore formation. This spoIVF-independent mechanism for processing pro_oK depends on ifE, an earlier-acting mother cell-specific sigma factor. The spoIIID gene, which encodes a mother cell-specific DNA-binding protein that is normally required for pro-cK production, was shown to be required for efficient pro-rK processing as well. bof (bypass of forespore) mutations bypassed this requirement for spoIIID, suggesting that SpoMID is less directly involved in pro-cK processing than are spoIVF gene products. However, bof spoIIID double mutants overproducing pro-irK still failed to sporulate, indicating that SpolIID serves another essential role(s) in sporulation in addition to its multiple roles in the production of if
Negative for F1651 Fimbriae in Septicemia of Gnotobiotic Pigs

To evaluate the role of the F1651 fimbrial system in the pathogenesis of septicemia, 2-day-old germfree pigs were inoculated intragastrically with Escherichia coli 0115:K"V165":F165 wild-type strain 5131, its F1651negative TnphoA mutant M48, or E. coli 0115:K(-):F165(-) wild-type strain 862B. Pigs were sacrificed at different times (3, 6, 12, 24, 48, and 96 h) postinfection (p.i.). Pigs inoculated with strain 5131 developed clinical signs (anorexia, lameness, reluctance to move, or lack of motor coordination) and were moribund within 48 h p.i. , and, at necropsy, infecting bacteria were isolated in various extraintestinal organs. Strain 5131 was isolated as early as 6 h p.i. from the blood of inoculated pigs. Pigs inoculated with mutant M48 developed only mild clinical signs at 96 h p.i. Mutant M48 colonized extraintestinal organs of pigs but to a lesser extent than the parent strain did. In contrast to the parent strain, this mutant was not isolated in the blood of inoculated pigs. Pigs inoculated with strain 862B remained normal during the experiment. All of the strains colonized the mucus layer of the intestine, but no histological changes of intestinal mucosa were observed by either light or electron microscopy. The parent strain, but not the mutant M48, expressed F1651 in vivo. In a competitive study in which the parent strain and its afimbrial mutant were inoculated simultaneously, clinical signs of septicemia developed 24 h after inoculation, and only the parent strain 5131 was isolated from the blood of inoculated pigs. Our results suggest that the F1651 fimbrial system of E. coli 0115:K"V165" strains may play
Chains among Different Heat-Stable Serotypes of Campylobacterjejuni by Silver Staining of Polyacrylamide Gels

Lipopolysaccharide (LPS) from three human and four monkey isolates of Campylobacterjejuni was extracted in high yields that revealed ladder-like structures in polyacrylamide gels by direct silver staining. These observations demonstrate that C. jejuni possesses LPS with 0-chain repeating units typical of the family Enterobacteriaceae. The isolates showed differences in the number and electrophoretic mobility of bands in silver-stained gels.
ALLWAS: Active Learning on Language models in WASserstein space

Active learning has emerged as a standard paradigm in areas with scarcity of labeled training data, such as in the medical domain. Language models have emerged as the prevalent choice of several natural language tasks due to the performance boost offered by these models. However, in several domains, such as medicine, the scarcity of labeled training data is a common issue. Also, these models may not work well in cases where class imbalance is prevalent. Active learning may prove helpful in these cases to boost the performance with a limited label budget. To this end, we propose a novel method using sampling techniques based on submodular optimization and optimal transport for active learning in language models, dubbed ALLWAS. We construct a sampling strategy based on submodular optimization of the designed objective in the gradient domain. Furthermore, to enable learning from few samples, we propose a novel strategy for sampling from the Wasserstein barycenters. Our empirical evaluations on standard benchmark datasets for text classification show that our methods perform significantly better (>20% relative increase in some cases) than existing approaches for active learning on language models.
Transcription of rRNA and tRNA Operons in Escherichia colit

We have recently proposed a model for the negative feedback control of rRNA and tRNA synthesis in Escherichia coli by products of rRNA operons or their derivatives (e.g., nontranslating ribosomes) (S. JinksRobertson, R. L. Gourse, and M. Nomura, Cell 33:865-876, 1983). In this paper, we examined the following questions. (i) Are the spacer tRNAs carried within rRNA operons the products responsible for the regulation of rRNA and tRNA transcription? (ii) Are tRNAs capable of regulating their own syntheses? We measured tRNA accumulations in cells containing plasmids with intact or defective rRNA operons or with tRNA operons. From the results obtained, we conclude that neither the tRNAs encoded within rRNA operons nor the tRNAs encoded in non-rRNA operons are capable of controlling rRNA or tRNA transcription. Therefore, the products responsible for the initial step leading to rRNA and tRNA regulation are rRNAs (or their derivatives).
Surface Antigens of Herpesvirus Type

persons with known type 1 virus infections, 20 sera from persons with known type 2 virus infections, 30 sera from women with cervical cancer, and 30 sera from matched control women. There was a good correlation between antibody activity to the surface antigens and neutralizing antibody activity for both herpesvirus type 1 and herpesvirus type 2 in all groups of sera examined. Women with cervical cancer did not have unusually high or low titers of antibody activity to the surface antigens. In the selected sera examined, analysis of antibodies to the surface antigens was not superior to the microneutralization test in distinguishing women with cervical cancer from control women.
28-Kilodalton Hemolytic and Mosquitocidal Protein Toxin of Bacillus thuringiensis subsp

The mosquitocidal crystal of Bacillus thuringiensis subsp. darmstadiensis 73-E10-2 was purified, bioassayed against third-instar Aedes aegypti larvae (50% lethal concentration, 7.5 ,ug/ml), and subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis, revealing polypeptides of 125, 50, 47, and 28 kilodaltons (kDa). When solubilized and proteolytically activated by insect gut proteases or proteinase K, the crystal was cytotoxic to insect and mammalian cells in vitro and was hemolytic. By using nondenaturing polyacrylamide gel electrophoresis, a polypeptide of 23 kDa, derived from the 28-kDa protoxin, was identified which was hemolytic and cytotoxic to Aedes albopictus, A. aegypti, and Choristoneurafumiferana CF1 insect cell lines. The 23-kDa polypeptide was purified by ion-exchange chromatography and gave 50% lethal dose values of 3.8, 3.3, and 6.9 ,ug/ml against A. albopictus, A. aegypti, and C. fumiferana CF1 cells lines, respectively. Cytotoxicity in vitro
Incompatibility Determinant Specific for IncHIl Plasmids

Two replicons were isolated independently from different IncHIl plasmids. One was isolated from R27, and a second was isolated from pIP522. We demonstrate, by DNA-DNA hybridization experiments, that these maintenance regions are different and that they are specific to, and carried by, all IncHIl plasmids tested. In view of this specificity we decided to designate the replicon isolated from R27 as RepHIlA and the replicon isolated from pIP522 as RepHI1B. These two autoreplicative regions are not related to a third replicon present in all IncHIl plasmids that bears homology with RepFIA and that expresses the characteristic incompatibility of IncHIl subgroup plasmids toward F factor (D. Saul, D. Lane, and P. L. Bergquist, Mol. Microbiol. 2:219-225, 1988; D. E. Taylor, R. W. Hedges, and P. L. Bergquist, J. Gen. Microbiol. 131:1523-1530, 1985). These results demonstrate that all IncHIl plasmids tested contain at least three replicons. An incompatibility (Inc) region that hybridizes specifically to all the IncHIl plasmids was previously isolated (M. Couturier, F. Bex, P. L. Bergquist, and W. K. Maas, Microbiol. Rev. 52:375-395, 1988). Although this Inc locus is not located in an autoreplicative region of IncHIl plasmids, we observed that this locus stabilizes a low-copy-number replicon. This Inc locus is probably a component of an active partition locus involved in the maintenance of IncHIl plasmids. The nucleotide sequence of the Inc region contains direct repeats of 31 bp. In addition, this incompatibility determinant hybridizes specifically with IncHIl plasmids but expresses incompatibility toward plasmids of both IncHI subgroups (IncHIl and IncHI2). In this communication, we present the mapping of these maintenance elements on the R27 genome.
Characterization of Hybrid Toxins Produced in Eschernchia coli by Assembly of A and B

The genes encoding the individual A and B polypeptides of the type I enterotoxin LTp-I and type II enterotoxins LT-HIa and LT-IIb were cloned and tested for complementation in Escherichia coli. Each gene encoding anA polypeptide was cloned into pACYC184, and each gene encoding a B polypeptide was cloned into the compatible plasmid Bluescript KS+. In addition, operon fusions representing all combinations ofA and B genes were constructed in Bluescript KS+. Extracts from strains of E. coli expressing each combination of A and B genes, either from compatible plasmids or from operon fusions, were tested for immunoreactive holotoxin by radioimmunoassays and for toxicity by Y1 adrenal cell assays. Biologically active holotoxin was detected in each case, but the toxicity of extracts containing the hybrid toxins was usually less than that of extracts containing the wild-type holotoxins. The ganglioside-binding activity of each holotoxin was tested, and in each case, the B polypeptide determined the ganglioside-binding specificity. The A and B polypeptides of the type II heat-labile enterotoxins were also shown to form holotoxin in vitro without exposure to denaturing conditions, in contrast to the polypeptides of the type I enterotoxins that failed to form holotoxin in vitro under comparable conditions. These findings suggest that type I and type II enterotoxins have conserved structural features that permit their A and B polypeptides to form hybrid holotoxins, although the B polypeptides of the type I and type II enterotoxins have very little amino acid sequence homology.
Field Isolates by Using Field Inversion Gel Electrophoresist

The genomes of 11 Bradyrhizobium japonicum serocluster 123 field isolates were analyzed by using field inversion gel electrophoresis. Genomic fingerprints produced by digestion of intact genomic DNA in agarose plugs with the rare-cutting restriction enzymes AseI, DraI, SpeI, and XbaI showed that the isolates were genetically diverse. Few (30 to 50%) isolates exhibited the same fingerprint as the USDA serogroup strain with which they are antigenically related. Southern hybridization with a nifHD gene probe to the blotted field inversion electrophoresis gels provided further evidence of the relatedness between members of serogroups 123 and 127.