gebhart/patrepeval huggingface dataset:
Mutants of Bacillus subtilis 168 Thermosensitive for Growth and Wall Teichoic Acid Synthesis (1989)

A protocol designed to isolate mutants with thermosensitive (Ts) synthesis of the bacteriophage 𝜙29 receptor, which includes the major wall teichoic acid in Bacillus subtilis 168, yielded a significant enrichment for Ts growth mutants among colonies surviving 𝜙29 treatment. Nine mutants, Ts for both 𝜙29 susceptibility and cell growth, harboured mutations which were located in the tag locus by PBS1 transduction and recombination index with the tag-1 marker. Physical mapping revealed that they were distributed on a segment of more than 4 kb. Chemical analysis of cell walls showed a marked reduction in phosphate relative to diaminopimelic acid content of all mutants at the non-permissive temperature. Differences between mutants were correlated with the distribution of tag mutations on the genetic map. We conclude (i) that the newly identified markers affect several genes involved in poly(glycerol phosphate) synthesis, and (ii) that on phosphate-rich media, cell growth cannot occur without the synthesis of the latter polymer.
Isolation of prostate-derived single cells and cell clusters from human peripheral blood. (1996)

The detection of blood-borne prostate cancer (PCA) cells may help with clinical staging and the further understanding of PCA metastases. We discovered prostate-specific antigen (PSA)-positive stained but not PSA mRNA-expressing blood cells by means of cell sorting and PSA reverse transcription-PCR in patients. Therefore, we developed a cytokeratin immunomagnetic method to isolate PSA-positive epithelial cells from the circulating blood of PCA patients. We obtained blood-borne single cells from 6 of 10 PCA patients and clustered cells from 8 of 10 PCA patients. Patients with benign prostate hyperplasia tested negative for cell clusters. The reported isolation method yielded prostate-derived cells or clusters of them from PCA-diagnosed patients.
Challenges and opportunities in supporting video streaming over infrastructure wireless mesh networks (2009)

Multi-hop wireless mesh networks (WMNs) are emerging as a promising technology with applications in last mile Internet access, public safety, disaster response, battlefield, etc. The unique characteristics of WMNs such as limited and dynamic bandwidth, error prone nature, interferences, and user mobility, however, pose a number of significant challenges for high quality video streaming. In this paper, we discuss the major challenges, review some general approaches, and present a Unified Cache and Peer-to-Peer (UNICAP) framework we developed recently to support high quality streaming over WMNs. Issues addressed in UNICAP include the architecture, cache server/peer/route selection with cross-layer optimization, and admission control. Some future research directions are also discussed.
Generation of a large library of point mutations in polymamiddle T antigen (1991)

Polyoma middle T antigen (MTAg) transforms cells by associating with and activating a variety of intracellular proteins, including src family members and a phosphatidylinositol-3 kinase. In order to assist in the study of the relative importance of the various associated biochemical activities for transformation by polyomavirus MTAg, a library of MTAg mutants was constructed. Chemically mutagenized MTAg DNA was purified from wild-type DNA by separation on denaturing gradient gels and placed into a recombinant retrovirus vector. Utilizing the resultant library of MTAg-expressing retroviruses, fibroblast cell lines expressing retroviruses, fibroblast cell lines expressing individual MTAg mutants were generated and screened for a non-transformed morphology. Of the first seven non-transformed clones tested, all express the MTAg protein. We estimate that approximately 24% of the G418-resistant colonies contain a transformation-defective MTAg mutant. A more thorough evaluation of one such clone revealed four single base-pair changes as compared to wild-type. Further genetic dissection of this mutant reveals that substituting leucine for proline at amino acid 248 results in a completely transformation defective MTAg. The utility of this mutagenesis and screening procedure as well as the description of several new MTAg mutants is described. This library of mutations should be of general interest for studying the transforming ability of MTAg.
Quantitative genome-wide methylation analysis of high-grade non-muscle invasive bladder cancer (2016)

High-grade non-muscle invasive bladder cancer (HG-NMIBC) is a clinically unpredictable disease with greater risks of recurrence and progression relative to their low-intermediate-grade counterparts. The molecular events, including those affecting the epigenome, that characterize this disease entity in the context of tumor development, recurrence, and progression, are incompletely understood. We therefore interrogated genome-wide DNA methylation using HumanMethylation450 BeadChip arrays in 21 primary HG-NMIBC tumors relative to normal bladder controls. Using strict inclusion-exclusion criteria we identified 1,057 hypermethylated CpGs within gene promoter-associated CpG islands, representing 256 genes. We validated the array data by bisulphite pyrosequencing and examined 25 array-identified candidate genes in an independent cohort of 30 HG-NMIBC and 18 low-intermediate-grade NMIBC. These analyses revealed significantly higher methylation frequencies in high-grade tumors relative to low-intermediate-grade tumors for the ATP5G2, IRX1 and VAX2 genes (P<0.05), and similarly significant increases in mean levels of methylation in high-grade tumors for the ATP5G2, VAX2, INSRR, PRDM14, VSX1, TFAP2b, PRRX1, and HIST1H4F genes (P<0.05). Although inappropriate promoter methylation was not invariantly associated with reduced transcript expression, a significant association was apparent for the ARHGEF4, PON3, STAT5a, and VAX2 gene transcripts (P<0.05). Herein, we present the first genome-wide DNA methylation analysis in a unique HG-NMIBC cohort, showing extensive and discrete methylation changes relative to normal bladder and low-intermediate-grade tumors. The genes we identified hold significant potential as targets for novel therapeutic intervention either alone, or in combination, with more conventional therapeutic options in the treatment of this clinically unpredictable disease.
Unsupervised local color correction for coarsely registered images (2011)

The current paper proposes a new parametric local color correction technique. Initially, several color transfer functions are computed from the output of the mean shift color segmentation algorithm. Secondly, color influence maps are calculated. Finally, the contribution of every color transfer function is merged using the weights from the color influence maps. The proposed approach is compared with both global and local color correction approaches. Results show that our method outperforms the technique ranked first in a recent performance evaluation on this topic. Moreover, the proposed approach is computed in about one tenth of the time.
Peptidyl Vinyl Ester Derivatives:  New Class of Selective Inhibitors of Proteasome Trypsin-Like Activity (2005)

The proteasome is a multicatalytic proteinase complex which plays a central role in intracellular protein degradation. We report here the synthesis and biological activities of a new class of specific proteasome inhibitors selective for trypsin-like activity. These tripeptide-based compounds bearing a C-terminal vinyl ester are nontoxic, and do not affect cell proliferation, but are able to modulate the generation and presentation of immunogenic peptides presented by MHC class I molecules.
Identification and cloning of a novel plasmid-encoded enterotoxin of enteroinvasive Escherichia coli and Shigella strains (1995)

We have employed a molecular genetic approach to characterize the nature of enteroinvasive Escherichia coli (EIEC) enterotoxic activity, as previously observed in Ussing chambers (A. Fasano, B.A. Kay, R.G. Russell, D.R. Maneval, Jr., and M.M. Levine, Infect. Immun. 58:3717-3723, 1990). The screening of TnphoA mutants of EIEC yielded a single insertion mutant which had significantly reduced levels of enterotoxic activity in the Ussing chamber assay. DNA flanking the insertion was used as a probe to screen for EIEC cosmid clones which conferred secretogenic activity. Such screening resulted in the identification of two overlapping cosmid clones which elicited significant changes in mucosal short-circuit current (Isc). Subcloning and nucleotide sequence analysis of a DNA fragment from one of the cosmid clones led to the identification of a single open reading frame which conferred this enterotoxic activity. By DNA hybridization, this gene (designated sen for shigella enterotoxin) was found in 75% of EIEC strains and 83% of Shigella strains and was localized to the inv plasmid of Shigella flexneri 2457T. By PCR, a sen gene with 99.7% nucleotide identity was cloned and sequenced from 2457T. A deletion in the EIEC sen gene was constructed by allelic exchange, resulting in significantly lower rises in Isc than were elicited by the wild-type parent; however, significant enterotoxic activity remained in the sen deletion mutant. To purify the Sen protein, the gene was cloned into the multiple cloning site of the expression vector pKK223-3. Purification of the sen gene product yielded a protein with a molecular mass of 63 kDa which elicited rises in Isc in the Ussing chamber. We believe that the sen gene product may constitute all or part of a novel enterotoxin in EIEC and Shigella spp.
Pterin metabolism in normal subjects and hyperphenylalaninaemic patients (1981)

The application of high performance liquid chromatography to the estimation of urinary pterins is illustrated by results from normal subjects and from patients with phenylketonuria, dihydropteridine reductase deficiency and biopterin synthetase deficiency. In normal subjects following a phenylalanine load the is a temporary increase in pterin elimination, the pattern being different to that seen in chronic hyperphenylalaninaemia.
Antimyelin Antibodies as a Predictor of Clinically Definite Multiple Sclerosis after a First Demyelinating Event (2003)

Analysis of antibodies against MOG and MBP in patients with a clinically isolated syndrome is a rapid, inexpensive, and precise method for the prediction of early conversion to clinically definite multiple sclerosis. This finding may be important for the counseling and care of patients with a first demyelinating event suggestive of multiple sclerosis.
DBTSS, DataBase of Transcriptional Start Sites: progress report 2004 (2003)

DBTSS (http://dbtss.hgc.jp) was originally constructed based on a collection of experimentally determined TSSs of human genes. Since its first release in 2002, it has been updated several times. First, the amount of stored data has increased significantly: e.g. the number of clones that match both the RefSeq mRNA set and the genome sequence has increased from 111,382 to 190,964, now covering 1,234 genes. Second, the positions of SNPs in dbSNP were displayed on the upstream regions of contained human genes. Third, DBTSS now covers other species such as mouse and the human malaria parasite. It will become a central database containing data for many more species with oligo-capping and related methods. Lastly, the database now serves for comparative promoter analyses: in the current version, comparative views of potentially orthologous promoters from human and mouse are presented with an additional function of searching potential transcription-factor binding sites, which are either conserved or diverged between species.
Structure and function of the hepatic form of 11 beta-hydroxysteroid dehydrogenase in the squirrel monkey, an animal model of glucocorticoid resistance (1993)

Both cortisol and aldosterone bind to and activate the mineralocorticoid receptor. Cortisol concentrations are generally 100- to 200-fold higher than aldosterone concentrations, yet mineralocorticoids clearly exert effects different from glucocorticoids. One hypothesis is that 11 beta-hydroxysteroid dehydrogenase (11 beta-HSD), which converts cortisol to biologically inactive cortisone, protects the mineralocorticoid receptor from cortisol. The circulating concentrations of cortisol in the squirrel monkey are 20- to 50-fold higher than human cortisol concentrations, yet this animal has no evidence of glucocorticoid or mineralocorticoid excess. We used this experiment of nature to test the hypotheses that the known (hepatic) form of 11 beta-HSD protects renal mineralocorticoid receptors from the action of cortisol and that it modulates glucocorticoid concentrations in target tissues. Using a long oligonucleotide based on the rat sequence, we cloned the squirrel monkey 11 beta-HSD complementary DNA and gene. The encoded monkey amino acid sequence is 75% and 91% identical to the corresponding rat and human sequences, respectively. The tissue abundance of the messenger RNA for the monkey enzyme was similar to or less than that seen for the rat and human enzymes. Both the monkey and human 11 beta-HSD complementary DNAs were cloned into an expression vector and used to transfect cultures of Chinese hamster ovary cells. Both vectors were transcribed and translated into equivalent amounts of 11 beta-HSD enzyme. The monkey enzyme was slightly more efficient than the human enzyme in converting [3H]cortisol to cortisone, and estimates of the Michaelis-Menten constant and maximum velocity of both enzymes are similar. These data indicate that the abundance and activity of the hepatic form of 11 beta-HSD are insufficient to inactivate the very high concentrations of cortisol in the squirrel monkey, suggesting that this form of 11 beta-HSD does not defend the mineralocorticoid receptor or protect tissues from high cortisol concentrations. Rather, this enzyme appears to favor conversion of cortisone to cortisol, thus maximizing tissue concentrations of cortisol to overcome glucocorticoid resistance associated with a 50% reduction in glucococorticoid receptors.
Membrane filter method to study the effects of Lactobacillus acidophilus and Bifidobacterium longum on fecal microbiota (2015)

A large number of commensal bacteria inhabit the intestinal tract, and interbacterial communication among gut microbiota is thought to occur. In order to analyze symbiotic relationships between probiotic strains and the gut microbiota, a ring with a membrane filter fitted to the bottom was used for in vitro investigations. Test strains comprising probiotic nitto strains (Lactobacillus acidophilus NT and Bifidobacterium longum NT) and type strains (L. acidophilus JCM1132(T) and B. longum JCM1217(T) ) were obtained from diluted fecal samples using the membrane filter to simulate interbacterial communication. Bifidobacterium spp., Streptococcus pasteurianus, Collinsella aerofaciens, and Clostridium spp. were the most abundant gut bacteria detected before coculture with the test strains. Results of the coculture experiments indicated that the test strains significantly promote the growth of Ruminococcus gnavus, Ruminococcus torques, and Veillonella spp. and inhibit the growth of Sutterella wadsworthensis. Differences in the relative abundances of gut bacterial strains were furthermore observed after coculture of the fecal samples with each test strain. Bifidobacterium spp., which was detected as the dominant strain in the fecal samples, was found to be unaffected by coculture with the test strains. In the present study, interbacterial communication using bacterial metabolites between the test strains and the gut microbiota was demonstrated by the coculture technique. The detailed mechanisms and effects of the complex interbacterial communications that occur among the gut microbiota are, however, still unclear. Further investigation of these relationships by coculture of several fecal samples with probiotic strains is urgently required.
The Polycystic Kidney Disease-1 Promoter Is a Target of the β-Catenin/T-cell Factor Pathway (2002)

Polycystic kidney disease (PKD) results from loss-of-function mutations in the PKD1 gene. There are also reports showing abnormally high levels of PKD1 expression in cystic epithelial cells. At present, nothing is known about the molecular mechanisms regulating the normal expression of the PKD1 gene or whether transcriptional disregulation of the PKD1 gene has a role in cyst formation. We have analyzed a 3.3-kb 5'-proximal portion of the human PKD1 gene. Sequence analysis revealed the presence of consensus sequences for numerous transactivating factors, including four T-cell factor (TCF) binding elements (TBEs). Transcriptional activity of the 3.3-kb fragment and a series of deletion constructs was assayed in HEK293T cells. A 2.0-kb proximal promoter region containing one of the four TBEs (TBE1) was inducible up to 6-fold by cotransfection with beta-catenin. beta-catenin-mediated induction was inhibited by dominant-negative TCF and by deletion of the TBE1 sequence. 15- or 109-bp sequences containing the TBE1 site, when cloned upstream of a minimal promoter, were shown to respond to beta-catenin induction. Gel shift assays confirmed that the TBE1 site is capable of forming complexes with TCF and beta-catenin. To determine whether expression of the endogenous PKD1 gene responds to beta-catenin, HT1080 cells were treated with LiCl, and HeLa cells were stably transfected with beta-catenin. In both cases, endogenous PKD1 mRNA levels were elevated in response to these treatments. Taken together, these studies define an active PKD1 promoter region and suggest that the PKD1 gene is a target of the beta-catenin/TCF pathway.
Augmented reality based on estimation of defocusing and motion blurring from captured images (2006)

Photometric registration is as important as geometric registration to generate a seamless augmented reality scene. Especially the difference in image quality between a real image and virtual objects caused by defocusing and motion blurring in capturing a real scene image easily exhibits the seam between real and virtual worlds. To avoid this problem in video see-through augmented reality, it is necessary to simulate the optical system of camera when virtual objects are rendered. This paper proposes an image composition method for video see-through augmented reality, which is based on defocusing and motion blurring estimation from the captured real image and rendering of virtual objects with blur effects. In experiments, the effectiveness of the proposed method is confirmed by comparing a real image with virtual objects rendered by the proposed method.
Vector engineering to improve a staphylococcal surface display system (2002)

A previously developed expression system for surface display of heterologous proteins on the surface of Staphylococcus carnosus employs the secretion signals from a Staphylococcus hyicus lipase and the cell wall anchoring part of Staphylococcus aureus protein A (SpA) to achieve surface display of expressed recombinant proteins. The system has been successfully used in various applications but the vector has not been considered genetically stable enough to allow protein library display applications, which would be of obvious interest. A new set of vectors, differing in size and devoid of a phage f1 origin of replication, were constructed and evaluated in terms of bacterial growth characteristics and vector stability. Furthermore, surface expression of a model surface protein was monitored by an enzymatic whole-cell assay and flow cytometry. The engineered expression vectors demonstrated dramatically improved stability and growth properties and two of the novel vectors demonstrated retained high surface density of the displayed model protein. The flow cytometry was found to be a powerful tool for observing the surface density of displayed heterologous proteins, and would thus be a rational strategy for monitoring the optimisation of any surface display system. The implications of these improved display vectors for future protein library applications are discussed.
Greedy Layer-Wise Training of Deep Networks (2007)

Complexity theory of circuits strongly suggests that deep architectures can be much more efficient (sometimes exponentially) than shallow architectures, in terms of computational elements required to represent some functions. Deep multi-layer neural networks have many levels of non-linearities allowing them to compactly represent highly non-linear and highly-varying functions. However, until recently it was not clear how to train such deep networks, since gradient-based optimization starting from random initialization appears to often get stuck in poor solutions. Hinton et al. recently introduced a greedy layer-wise unsupervised learning algorithm for Deep Belief Networks (DBN), a generative model with many layers of hidden causal variables. In the context of the above optimization problem, we study this algorithm empirically and explore variants to better understand its success and extend it to cases where the inputs are continuous or where the structure of the input distribution is not revealing enough about the variable to be predicted in a supervised task. Our experiments also confirm the hypothesis that the greedy layer-wise unsupervised training strategy mostly helps the optimization, by initializing weights in a region near a good local minimum, giving rise to internal distributed representations that are high-level abstractions of the input, bringing better generalization.
Heparin-binding protein as a biomarker of circulatory failure during severe infections: A report of three cases (2010)

We report 3 cases of disease - leptospirosis, tropical malaria and fulminant meningococcaemia - associated with high serum concentrations of heparin-binding protein (HBP) and haemodynamic instability. Furthermore, HBP kinetics were observed for the first 3 days in survivors and were correlated with improvement in clinical condition.
A deletion in the extracellular domain of the alpha platelet-derived growth factor (PDGF) receptor differentially impairs PDGF-AA and PDGF-BB binding affinities. (1992)

32D cells transfected with the human alpha platelet-derived growth factor receptor (alpha PDGFR) bind PDGF-AA, -AB, and -BB isoforms with high affinity, and the binding of each can be efficiently competed by all three isoforms. In an effort to develop better understanding of spatial relationships of binding sites for PDGF-AA and -BB, we constructed an alpha PDGFR mutant which deleted amino acids 150-189 within its extracellular domain. This mutant showed a marked decrease in high affinity binding sites for PDGF-AA without comparable alteration in affinity for PDGF-BB. These findings imply that the high affinity binding sites for PDGF-AA and PDGF-BB in the alpha PDGFR extracellular domain are not structurally coincident.