gebhart/patrepeval huggingface dataset:
Subtractive Hybridization Identifies a Novel Predicted Protein Mediating Epithelial Cell Invasion by Virulent Serotype III Group B Streptococcus agalactiae (2003)

Group B Streptococcus agalactiae bacteria (group B streptococci [GBS]) are the most common cause of serious bacterial infection in newborn infants. The majority of serotype III-related cases of neonatal disease are caused by a genetically related subgroup of bacteria, restriction fragment digest pattern (RDP) type III-3, suggesting that these strains possess unique genes contributing to virulence. We used genomic subtractive hybridization to identify regions of genomic DNA unique to virulent RDP type III-3 GBS strains. Within one of these III-3-specific regions is a 1,506-bp open reading frame, spb1 (surface protein of group B streptococcus 1). A mutant type III GBS strain lacking Spb1 was constructed in virulent RDP type III-3 strain 874391, and the interactions of the wild-type and spb1 isogenic mutant with a variety of epithelial cells important to GBS colonization and infection were compared. While adherence of the spb1 isogenic mutant to A549 respiratory, C2Bbe1 colonic, and HeLa cervical epithelial cells was slightly lower than that of the 874391 strain, invasion of the Spb1(-) mutant was significantly reduced with these cell lines compared to what was seen with 874391. The defect in epithelial invasion was corrected by supplying spb1 in trans. These observations suggest that Spb1 contributes to the pathogenesis of neonatal GBS infection by mediating internalization of virulent serotype III GBS and confirm that understanding of the population structure of bacteria may lead to insights into the pathogenesis of human infections.
Shuttle mutagenesis: a method of transposon mutagenesis for Saccharomyces cerevisiae. (1986)

We have extended the method of transposon mutagenesis to the eukaryote, Saccharomyces cerevisiae. A bacterial transposon containing a selectable yeast gene can be transposed into a cloned fragment of yeast DNA in Escherichia coli, and the transposon insertion can be returned to the yeast genome by homologous recombination. Initially, the cloned yeast DNA fragment to be mutagenized was transformed into an E. coli strain containing an F factor derivative carrying the transposable element. The culture was grown to allow transposition and cointegrate formation and, upon conjugation, recipients were selected that contained yeast sequences with transposon insertions. The yeast DNA was removed from the vector by restriction endonuclease digestion, and the transposon insertion was transformed into yeast. The procedure required a minimum number of manipulations, and each transconjugant colony contained an independent insertion. We describe 12 transposon Tn3 derivatives for this procedure as well as several cloning vectors to facilitate the method.
Site-specific cleavage of DNA–RNA hybrids by zinc finger/FokI cleavage domain fusions (1997)

Zinc-finger proteins of the Cys2His2 type bind DNA-RNA hybrids with affinities comparable to those for DNA duplexes. Such zinc-finger proteins were converted into site-specific cleaving enzymes by fusing them to the FokI cleavage domain. The fusion proteins are active and under optimal conditions cleave DNA duplexes in a sequence-specific manner. These fusions also exhibit site-specific cleavage of the DNA strand within DNA-RNA hybrids albeit at a lower efficiency (approximately 50-fold) compared to the cleavage of the DNA duplexes. These engineered endonucleases represent the first of their kind in terms of their DNA-RNA cleavage properties, and they may have important biological applications.
Study of low energy emulsification methods for the preparation of narrow size distribution W/O emulsions (2008)

The main aim of this work was to prepare W/O emulsions by low-energy emulsification methods to be used as reaction media for the preparation of silica particles. In this reaction work the system H2O/C12E5/isooctanol/isooctane was chosen as a model system. The emulsification methods assayed were: (1) addition of water to a surfactant solution in oil and (2) addition of oil to an aqueous surfactant solution. Emulsions prepared according to method (1) were highly polydisperse, both droplet size and polydispersity were found to be dependent on mechanical stirring. In contrast, monodisperse emulsions could be obtained with method (2). The influence of parameters such as stirring speed and the order of addition of the components (in method (2)), were evaluated. The results have been interpreted according to the phase transitions induced during emulsification, that is the changes in the natural curvature of the surfactant during the process.
Characterization of a fabrication process for the integration of superconducting qubits and rapid-single-flux-quantum circuits (2006)

In order to integrate superconducting qubits with rapid-single-flux-quantum (RSFQ) control circuitry, it is necessary to develop a fabrication process that fulfills at the same time the requirements of both elements: low critical current density, very low operating temperature (tens of milliKelvin) and reduced dissipation on the qubit side; high operation frequency, large stability margins, low dissipated power on the RSFQ side. For this purpose, VTT has developed a fabrication process based on Nb trilayer technology, which allows the on-chip integration of superconducting qubits and RSFQ circuits even at very low temperature. Here we present the characterization (at 4.2 K) of the process from the point of view of the Josephson devices and show that they are suitable to build integrated superconducting qubits.
Few-cycle mid-infrared pulse generation, characterization, and coherent propagation in optically dense media (2002)

The generation of four- to five-cycle mid-infrared pulses using a single-stage potassium niobate optical parametric amplifier (OPA) is demonstrated. The OPA is pumped by a gain-switched Ti:Sapphire regenerative amplifier and is seeded with the near-infrared portion of a white light continuum. The OPA is continuously tunable from 2700 to 4700 nm, and maintains sub-65 fs pulses that are fully characterized using cross-correlation frequency-resolved optical gating (XFROG). These are the shortest near-transform-limited pulses reported over this large infrared spectral range. This apparatus is used to measure ultrafast vibrational responses, specifically, pulse profiles modified by the free-induction decay (FID) of O–H oscillators. Both the intensity and instantaneous phase of these pulses are determined after traversing samples of isotopically diluted water (HDO in D2O) using XFROG, representing a new application of the XFROG technique to the study of (dipolar) molecular responses. Pronounced beating of the trailing edges of FID-modified pulses is observed even below optical densities of one, and the details of these features are found to depend on the chirp of the field used to generate the FID. These results indicate that discretion should be used in the selection of sample conditions for nonlinear infrared spectroscopic measurements.
Microfluidic technologies for structural biology (2004)

In the post-genomic era, X-ray crystallography has emerged as the workhorse of large-scale structural biology initiatives that seek to understand protein function and interaction at the atomic scale. Despite impressive technological advances in X-ray sources, phasing techniques, and computing power, the determination of protein structure has been severely hampered by the difficulties in obtaining high-quality protein crystals. Emergent technologies utilizing microfluidics now have the potential to solve these problems on several levels, both by allowing researchers to conduct efficient assays in nanoliter reaction volumes, and by exploiting the properties of mass-transport at the micron scale to improve the crystallization process. The technique of Multilayer Soft Lithography (MSL) has been used to developed a set of microfluidic tools suitable for all stages of protein crystallogenesis, including protein solubility phase-space mapping, crystallization screening, harvesting, and in silicone diffraction studies. These tools represent the state of the art in on-chip fluid handling functionality and have been demonstrated to dramatically improve protein crystallization.
Learning Bounds for Importance Weighting (2010)

This paper presents an analysis of importance weighting for learning from finite samples and gives a series of theoretical and algorithmic results. We point out simple cases where importance weighting can fail, which suggests the need for an analysis of the properties of this technique. We then give both upper and lower bounds for generalization with bounded importance weights and, more significantly, give learning guarantees for the more common case of unbounded importance weights under the weak assumption that the second moment is bounded, aconditionrelatedtotheRényidivergenceofthetrainingand test distributions. These results are based on a series of novel and general boundswederiveforunbounded loss functions, which are of independent interest. We use these bounds to guide the definition of an alternative reweighting algorithm andreporttheresults of experiments demonstrating its benefits. Finally, we analyze the properties of normalized importance weights which are also commonly used. 1
<title>Development of a smart workstation for use in mammography</title> (1991)

We are developing various computer-vision schemes for the detection of masses and microcalcifications in digital mammograms. However, for the effective and efficient implementation of computer-aided diagnosis (CAD), appropriate man-machine interfaces must be developed. Thus, our plan is to incorporate our schemes into a dedicated workstation for use as a 'second opinion' in a mammographic screening program. Output from the computer would be displayed as an aid, leaving the final diagnostic decision with the radiologist.
The B Subunit of Shiga Toxin Fused to a Tumor Antigen Elicits CTL and Targets Dendritic Cells to Allow MHC Class I-Restricted Presentation of Peptides Derived from Exogenous Antigens (2000)

Abstract Immunization with peptide or recombinant proteins generally fails to elicit CTL, which are thought to play a key role in the control of virus-infected cells and tumor growth. In this study we show that the nontoxic B subunit of Shiga toxin fused to a tumor peptide derived from the mouse mastocytoma P815 can induce specific CTL in mice without the use of adjuvant. The Shiga B subunit acts as a vector rather than as an adjuvant, because coinjection of the tumor peptide and the B subunit as separate entities does not lead to CTL induction. We also demonstrated that in vitro the B subunit mediates the delivery of various exogenous CD8 T cell epitopes into the conventional MHC class I-restricted pathway, as this process is inhibited by brefeldin A and lactacystin and requires a functional TAP system. In contrast to other nonviral methods for transport of exogenous Ags into the endogenous MHC class I pathway that involve macropinocytosis or phagocytosis, the Shiga B subunit targets this pathway in a receptor-dependent manner, namely via binding to the glycolipid Gb3. Because this receptor is highly expressed on various dendritic cells, it should allow preferential targeting of the Shiga B subunit to these professional APCs. Therefore, the Shiga B subunit appears to represent an attractive vector for vaccine development due to its ability to target dendritic cells and to induce specific CTL without the need for adjuvant.
Expression of HER/erbb family of receptor tyrosine kinases and induction of differentiation by glial growth factor 2 in human rhabdomyosarcoma cells (2000)

Five human rhabdomyosarcoma cell lines were used to investigate the surface expression of HER/erbB receptors, particularly of HER-2, HER-3 and HER-4, by flow cytometry. HER-2 was expressed in 3/5 rhabdomyosarcoma cell lines. HER-3 was expressed in all rhabdomyosarcoma cell lines. None of the rhabdomyosarcoma cell lines investigated showed HER-4 surface expression. To study the biological activity of HER/erbB receptors in rhabdomyosarcomas, cells were cultured in the presence of glial growth factor 2 (GGF-2), a specific ligand of HER-3 that is able to stimulate myogenesis in normal myoblasts. In 3 of 3 human rhabdomyosarcoma cell lines positive for both HER-2 and HER-3 receptors, the treatment with GGF-2 induced a significant increase in myogenic differentiation.
Loss of Zona Pellucida Binding Proteins in the Acrosomal Matrix Disrupts Acrosome Biogenesis and Sperm Morphogenesis (2007)

Zona pellucida binding protein 1 (ZPBP1), a spermatid and spermatozoon protein that localizes to the acrosome, was originally identified in pigs and named for its binding to the oocyte zona pellucida. In an in silico search for germ cell-specific genes, Zpbp1 and its novel paralog, Zpbp2, were discovered and confirmed to be expressed only in the testes in both mice and humans. To study the in vivo functions of both ZPBP proteins, we disrupted Zpbp1 and Zpbp2 in mice. Males lacking ZPBP1 were sterile, with abnormal round-headed sperm morphology and no forward sperm motility. Ultrastructural studies demonstrated that absence of ZPBP1 prevents proper acrosome compaction, resulting in acrosome fragmentation and disruption of the Sertoli-spermatid junctions. Males null for ZPBP2 were subfertile, demonstrated aberrant acrosomal membrane invaginations, and produced dysmorphic sperm with reduced ability to penetrate zona pellucida. Molecular phylogenetic analysis of ZPBPs from amphibians, birds, and mammals suggests that these paralogous genes coevolved to play cooperative roles during spermiogenesis. Whereas ZPBP1 was discovered for an in vitro role in sperm-egg interactions, we have shown that both ZPBP proteins play an earlier structural role during spermiogenesis.
Testing, correcting, and extending the Woodworth model for interaural time difference (2014)

The Woodworth model and formula for interaural time difference is frequently used as a standard in physiological and psychoacoustical studies of binaural hearing for humans and other animals. It is a frequency-independent, ray-tracing model of a rigid spherical head that is expected to agree with the high-frequency limit of an exact diffraction model. The predictions by the Woodworth model for antipodal ears and for incident plane waves are here compared with the predictions of the exact model as a function of frequency to quantify the discrepancy when the frequency is not high. In a second calculation, the Woodworth model is extended to arbitrary ear angles, both for plane-wave incidence and for finite point-source distance. The extended Woodworth model leads to different formulas in six different regions defined by ear angle and source distance. It is noted that the characteristic cusp in Woodworth's well-known function comes from ignoring the longer of the two paths around the head in circumstances when the longer path is actually important. This error can be readily corrected.
Functional Avidity: A Measure to Predict the Efficacy of Effector T Cells? (2012)

The functional avidity is determined by exposing T-cell populations in vitro to different amounts of cognate antigen. T-cells with high functional avidity respond to low antigen doses. This in vitro measure is thought to correlate well with the in vivo effector capacity of T-cells. We here present the multifaceted factors determining and influencing the functional avidity of T-cells. We outline how changes in the functional avidity can occur over the course of an infection. This process, known as avidity maturation, can occur despite the fact that T-cells express a fixed TCR. Furthermore, examples are provided illustrating the importance of generating T-cell populations that exhibit a high functional avidity when responding to an infection or tumors. Furthermore, we discuss whether criteria based on which we evaluate an effective T-cell response to acute infections can also be applied to chronic infections such as HIV. Finally, we also focus on observations that high-avidity T-cells show higher signs of exhaustion and facilitate the emergence of virus escape variants. The review summarizes our current understanding of how this may occur as well as how T-cells of different functional avidity contribute to antiviral and anti-tumor immunity. Enhancing our knowledge in this field is relevant for tumor immunotherapy and vaccines design.
Applying massive parallel sequencing to molecular diagnosis of Marfan and Loeys-Dietz syndromes (2011)

The Marfan (MFS) and Loeys-Dietz (LDS) syndromes are caused by mutations in the fibrillin-1 (FBN1) and Transforming Growth Factor Beta Receptor 1 and 2 (TGFBR1 and TGFBR2) genes, respectively. With the current conventional mutation screening technologies, analysis of this set of genes is time consuming and expensive. We have tailored a cost-effective and reliable mutation discovery strategy using multiplex PCR followed by Next Generation Sequencing (NGS). In a first stage, genomic DNA from five MFS or LDS patient samples with previously identified mutations and/or polymorphisms in FBN1 and TGFBR1 and 2 were analyzed and revealed all expected variants. In a second stage, we validated the technique on 87 samples from MFS patients fulfilling the Ghent criteria. This resulted in the identification of 75 FBN1 mutations, of which 67 were unique. Subsequent Multiplex Ligation-dependent Probe Amplification (MLPA) analysis of the remaining negative samples identified four large deletions/insertions. Finally, Sanger sequencing identified a missense mutation in FBN1 exon 1 that was not included in the NGS workflow. In total, there was an overall mutation identification rate of 92%, which is in agreement with data published previously. We conclude that multiplex PCR of all coding exons of FBN1 and TGFBR1/2 followed by NGS analysis and MLPA is a robust strategy for time- and cost-effective identification of mutations.
Scaffold-Free Three-Dimensional Cell Culture Utilizing Micromolded Nonadhesive Hydrogels (2007)

Techniques that allow cells to self-assemble into three-dimensional (3-D) spheroid microtissues provide powerful in vitro models that are becoming increasingly popular--especially in fields such as stem cell research, tissue engineering, and cancer biology. Unfortunately, caveats involving scale, expense, geometry, and practicality have hindered the widespread adoption of these techniques. We present an easy-to-use, inexpensive, and scalable technology for production of complex-shaped, 3-D microtissues. Various primary cells and immortal cell lines were utilized to demonstrate that this technique is applicable to many cell types and highlight differences in their self-assembly phenomena. When seeded onto micromolded, nonadhesive agarose gels, cells settle into recesses, the architectures of which optimize the requisite cell-to-cell interactions for spontaneous self-assembly. With one pipeting step, we were able to create hundreds of uniform spheroids whose size was determined by seeding density. Multicellular tumor spheroids (MCTS) were assembled or grown from single cells, and their proliferation was quantified using a modified 4-[3-(4-iodophenyl)-2-(4-nitrophenyl)-2H-5-tetrazolio]-1,3-benzene disulfonate (WST-1) assay. Complex-shaped (e.g., honeycomb) microtissues of homogeneous or mixed cell populations can be easily produced, opening new possibilities for 3-D tissue culture.
Differential gene expression profiles of invasive and non-invasive non-functioning pituitary adenomas based on microarray analysis (2010)

Non-functioning pituitary adenomas (NFPAs) may be locally invasive. Markers of invasiveness are needed to guide patient management and particularly the use of adjuvant radiotherapy. To examine whether invasive NFPAs display a specific gene expression profile relative to non-invasive tumors, we selected 40 NFPAs (38 of the gonadotroph type) and classified them as invasive (n=22) or non-invasive (n=18) on the basis of magnetic resonance imaging and surgical findings. We then performed pangenomic analysis with the 44k Agilent human whole genome expression oligonucleotide microarray in order to identify genes with differential expression between invasive and non-invasive NFPAs. Candidate genes were then tested in qRT-PCR. Prediction class analysis showed that the expression of 346 genes differed between invasive and non-invasive NFPAs (P<0.001), of which 233 genes were up-regulated and 113 genes were down-regulated in invasive tumors. On the basis of Ingenuity networks and the degree of up- or down-regulation in invasive versus non-invasive tumors, 35 genes were selected for expression quantification by qRT-PCR. Overexpression of only four genes was confirmed, namely IGFBP5 (P=0.02), MYO5A (P=0.04), FLT3 (P=0.01), and NFE2L1 (P=0.02). At the protein level, only myosin 5A (MYO5A) immunostaining was stronger in invasive than in non-invasive NFPAs. Molecular signature allows to differentiate 'grossly' invasive from non-invasive NFPAs. The product of one of these genes, MYO5A, may be a useful marker of tumor invasiveness.
Computational Design of a Circular RNA with Prionlike Behavior (2016)

RNA molecules engineered to fold into predefined conformations have enabled the design of a multitude of functional RNA devices in the field of synthetic biology and nanotechnology. More complex designs require efficient computational methods, which need to consider not only equilibrium thermodynamics but also the kinetics of structure formation. Here we present a novel type of RNA design that mimics the behavior of prions, that is, sequences capable of interaction-triggered autocatalytic replication of conformations. Our design was computed with the ViennaRNA package and is based on circular RNA that embeds domains amenable to intermolecular kissing interactions.
Functional interleukin-7 receptors (IL-7Rs) are expressed by marrow stromal cells: binding of IL-7 increases levels of IL-6 mRNA and secreted protein (2002)

DNA spotted microarrays were used to compare gene expression profiles from 2 functionally distinct human marrow stromal cell lines: HS-27a, which supports cobblestone area formation by early hematopoietic progenitors, and HS-5, which secretes multiple cytokines that support the proliferation of committed progenitors. One unexpected result was the high level of interleukin-7 receptor (IL-7R) gene expression in HS-27a stromal cells. Northern blot analysis confirmed the IL-7R RNA expression, and Western blots for the IL-7R protein detected both a full-length (90-kd) IL-7R and a smaller 30-kd fragment in both HS-27a cells and primary stromal cell cultures, whereas only the 90-kd receptor protein was detected in peripheral blood mononuclear cells. Biotinylated IL-7 was shown to bind to HS-27a cells under physiologic conditions, and this binding was inhibited by blocking anti-IL-7 antibodies. Tyrosine phosphorylation of several proteins (55 kd, 30 kd, and 24 kd) in HS-27a cells was rapidly increased after incubation with recombinant IL-7. One of the phosphorylated proteins proved to be the 30-kd IL-7R fragment. Exposure of HS-27a cells to IL-7 resulted in a 10-fold increase in secretion of IL-6 into culture supernatants but no increase in the cytokines stromal cell-derived factor 1, macrophage inflammatory protein 1 alpha, or IL-1 beta. The up-regulation of IL-6 secretion is associated with a rapid but transient increase in detectable levels of IL-6 messenger RNA. These data suggest that IL-7 may function to regulate the milieu of the microenvironment by modulating IL-6 secretion by the IL-7R-expressing stromal elements.