gebhart/patrepeval huggingface dataset:
Quantification of Intestinal Bacterial Populations by Real-Time PCR with a Universal Primer Set and Minor Groove Binder Probes: a Global Approach to the Enteric Flora (2004)

The composition of the human intestinal flora is important for the health status of the host. The global composition and the presence of specific pathogens are relevant to the effects of the flora. Therefore, accurate quantification of all major bacterial populations of the enteric flora is needed. A TaqMan real-time PCR-based method for the quantification of 20 dominant bacterial species and groups of the intestinal flora has been established on the basis of 16S ribosomal DNA taxonomy. A PCR with conserved primers was used for all reactions. In each real-time PCR, a universal probe for quantification of total bacteria and a specific probe for the species in question were included. PCR with conserved primers and the universal probe for total bacteria allowed relative and absolute quantification. Minor groove binder probes increased the sensitivity of the assays 10- to 100-fold. The method was evaluated by cross-reaction experiments and quantification of bacteria in complex clinical samples from healthy patients. A sensitivity of 10(1) to 10(3) bacterial cells per sample was achieved. No significant cross-reaction was observed. The real-time PCR assays presented may facilitate understanding of the intestinal bacterial flora through a normalized global estimation of the major contributing species.
Chemoselective Approaches to Glycoprotein Assembly (2001)

Oligosaccharides on proteins and lipids play central roles in human health and disease. The molecular analysis of glycoconjugate function has benefited tremendously from new methods for their chemical synthesis, which provides homogeneous material not attainable from biosynthetic systems. Still, glycoconjugate synthesis requires the manipulation of multiple stereocenters and protecting groups and remains the domain of a few expert laboratories around the world. This Account summarizes chemoselective approaches for assembling homogeneous glycoconjugates that attempt to reduce the barriers to their synthesis. The objective of these methods is to make glycoconjugate synthesis accessible to a broader community, thereby accelerating progress in glycobiology.
Gene Fusion (2013)

Abstract Gene fusion is a process by which the complete or partial sequences of two or more distinct genes are fused into a single chimeric gene or transcript, as a result of deoxyribonucleic acid ‐ or ribonucleic acid ‐derived rearrangements. This phenomenon is widespread and has been observed across all domains of life. Comparative genomics studies reveal high and persistent incidence of gene fusions and identify lineage‐specific factors that promote or hinder the formation of chimeric genes. Studies of recent gene fusions expose the mechanisms of their origin and the diversity of functional changes that accompany their formation. Gene fusions prominently contribute to evolutionary change by providing a continuous source of new genes. Gene duplications often precede gene fusions, permitting the evolution of chimeric genes, but at the same time preserving the original functions. Despite the reputation of gene fusions as drivers of adaptive evolution, gene fusions can have devastating consequences, often leading to genomic disorders or cancer. Key Concepts: Gene fusions form through DNA‐derived rearrangements or through transcription‐mediated mechanisms (novel cis ‐ or trans ‐splicing). Gene or domain duplications often precede gene fusions preserving the original functions of parental genes and therefore facilitating the evolution of new functions by chimeric gene products. Young gene fusions (polymorphic or recently fixed) retain molecular signatures of their formations revealing the mechanisms of origin. The formation of chimeric genes generally involves two steps: juxtaposition of the sequences involved in fusion and subsequent mutations that generate a single chimeric transcriptional unit under the control of a single regulatory system. Various replicative (i.e. replication related) and nonreplicative mechanisms of DNA break repair can result in gene duplication and gene movement. Transposable elements greatly facilitate gene fusions by (1) mediating gene duplication and gene movements, (2) providing the source of reverse transcriptase required for retropositions and (3) directly participating in gene fusions. Gene fusion often generates a novel product with functional capabilities distinct from those of its parental genes, ensuring frequent contribution of chimeric genes to adaptive evolution. Gene fusions in the germline can lead to genomic disorders, whereas gene fusions in somatic cells are associated with many different cancers, frequently as mutations that initiate tumourigenesis.
A MRF Formulation for Coded Structured Light (2005)

Multimedia projectors and cameras make possible the use of structured light to solve problems such as 3D reconstruction, disparity map computation and camera or projector calibration. Each projector displays patterns over a scene viewed by a camera, thereby allowing automatic computation of camera-projector pixel correspondences. This paper introduces a new algorithm to establish this correspondence in difficult cases of image acquisition. A probabilistic model formulated as a Markov random field uses the stripe images to find the most likely correspondences in the presence of noise. Our model is specially tailored to handle the unfavorable projector-camera pixel ratios that occur in multiple-projector single-camera setups. For the case where more than one camera is used, we propose a robust approach to establish correspondences between the cameras and compute an accurate disparity map. To conduct experiments, a ground truth was first reconstructed from a high quality acquisition. Various degradations were applied to the pattern images which were then solved using our method. The results were compared to the ground truth for error analysis and showed very good performances, even near depth discontinuities.
Myocardial tissue reconstruction: The cell sheet engineering approach (2007)

Regenerative medicine has currently emerged as one of the most promising therapies for patients suffering from severe heart failure. Direct implantation of isolated skeletal myoblasts and bone-marrow derived cells has already been clinically performed and research on fabricating three-dimensional (3-D) cardiac grafts using tissue engineering technologies has also now been initiated. In contrast to scaffold-based methods, we have proposed cell sheet-based tissue engineering, which involves stacking confluently cultured cell sheets to construct 3-D cell-dense tissues. Upon layering, individual cardiomyocyte sheets integrate to form a single, continuous, cell-dense tissue that resembles native cardiac muscle. When transplanted directly to host hearts, these engineered myocardial tissues are able to form morphological connections to the host with the presence of functional gap junctions. The transplantation of layered cardiomyocyte sheets has also been shown to be able to repair damaged cardiac muscle. As a next step, we have attempted to promote neovascularization within bioengineered myocardial tissues to overcome the longstanding limitations on engineered tissue thickness. Finally as a possible advanced therapy, we are now trying to fabricate functional myocardial tubes which may have the potential for circulatory support. Cell sheet engineering technologies therefore shows enormous promise as a novel approach in the field of myocardial tissue engineering.
Fluid Transport Mechanisms in Microfluidic Devices (1998)

Abstract Most microfluidic systems rely on one of two manners of fluid transport: pressure-driven or electrokinetically-driven flow. This investigation focuses on describing these flows in microfabricated channels and small diameter capillary tubes. Flow characterization is accomplished by interrogation of micron-scale fluid regions through a powerful, non-intrusive flow imaging technique. Interesting phenomena have been observed from these detailed examinations. Our results are presented in conjunction with an evaluation of mechanisms that potentially explain observed deviations from the Helmholtz-Smoluchowski equation. In particular, we show that observed perturbations of electrokinetic flow in open capillaries might be caused by induced pressure gradients. We also show how these induced pressure gradients may globally perturb the flow in an electrokinetically-driven microfluidic system.
Interleukin-8 production via protease-activated receptor 2 in human esophageal epithelial cells (2007)

Interaction between proteases and protease-activated receptor (PAR) 2 has been proposed to mediate inflammatory and immune response in the gastrointestinal tract. Recently, increase in interleukin (IL)-8 in the esophageal mucosa has been associated with the pathogenesis of esophagitis induced by reflux of gastric acids, bile acids or trypsin. The aims of the present study were to determine PAR2 expression in normal human esophageal epithelial cells (HEEC) and to evaluate the mediation of IL-8 production by trypsin-PAR2 interaction in HEEC. Reverse transcription polymerase chain reaction (RT-PCR) and Western blot analysis revealed that PAR2 mRNA and protein were constitutively expressed in HEEC without upregulation by the stimulation with tumor necrosis factor alpha or trypsin. IL-8 was produced in a dose-dependent fashion when cells were stimulated with a PAR2 agonist such as trypsin or SLIGKV-amide. Blocking antibody to PAR2, camostat mesilate (a trypsin inhibitor), p-38 mitogen-activated protein kinase (MAPK) inhibitors or ERK1/2 inhibitors reduced IL-8 production from trypsin-stimulated HEEC. Mutation of the NFkappaB-, AP-1- and NF-IL-6-binding site on the IL-8 gene promoter abrogated the induction of luciferase activities stimulated with trypsin by 100, 80 and 50%, respectively. These results indicate that PAR2 activation in HEEC by trypsin induces NFkappaB- and AP-1-dependent IL-8 production in association with activation of p38 MAPK and ERK1/2, suggesting that esophageal inflammation may be induced by PAR2 activation via reflux of trypsin.
Vesicle interactions with polyamino acids and antibody: in vitro and in vivo studies. (1975)

Artificial spherules or vesicles of 900 A in diameter formed from phosphatidylcholine and gangliosides and enclosing 99mTcO4 - (standard preparation) survive intact in the circulation of the mouse. Polyamino acids and protein have been incorporated into and onto the vesicles; such vesicles remain intact as determined by diffusion dialysis studies and by electron paramagnetic resonance studies of vesicles enclosing spin label. In studying the distribution of polyamino acid-vesicles and protein vesicles in vivo, it was found that the latter distribute differently from standard vesicles or free protein alone whereas aromatic polyamino acid-vesicles concentrate in the liver and spleen to a greater extent than standard vesicles. We conclude that the permeability and stability characteristics of vesicles may be preserved when they are modified by the addition of protein or polyamino acids and that such modification of vesicles may be associated with an alteration of their fate in vivo. The potential exists to use vesicles as carriers of radiopharmaceuticals and other drugs and to direct the vesicles preferentially to tissue targets in vivo.
Discovering multi-purpose modules through deep multitask learning (2018)

Machine learning scientists aim to discover techniques that can be applied across diverse sets of problems. Such techniques need to exploit regularities that are shared across tasks. This begs the question: What shared regularity is not yet being exploited? Complex tasks may share structure that is difficult for humans to discover. The goal of deep multitask learning is to discover and exploit this structure automatically by training a joint model across tasks. To this end, this dissertation introduces a deep multitask learning framework for collecting generic functional modules that are used in different ways to solve different problems. Within this framework, a progression of systems is developed based on assembling shared modules into task models and leveraging the complementary advantages of gradient descent and evolutionary optimization. In experiments, these systems confirm that modular sharing improves performance across a range of application areas, including general video game playing, computer vision, natural language processing, and genomics; yielding state-of-the-art results in several cases. The conclusion is that multi-purpose modules discovered by deep multitask learning can exceed those developed by humans in performance and generality.
Fluorescence-guided resection of glioblastoma multiforme utilizing 5-ALA-induced porphyrins: a prospective study in 52 consecutive patients (2000)

The observations in this study indicate the usefulness of 5-ALA-induced tumor fluorescence for guiding tumor resection. The completeness of resection, as determined intraoperatively from residual tissue fluorescence, was related to postoperative MR imaging findings and to survival in patients suffering from GBM.
Mechanical properties of the skin: A comparison between two suction cup methods (2003)

The results indicate that both methods are useful in the study of the mechanical aspects of the skin, especially for detecting age-related changes. The Dermaflex seems to produce more accurate for data. This is thought to be due to the conceptual design differences between the two methods. The methods measure related but not identical values of the mechanical properties of the skin, as reflected by the limited positive correlation between them.
Down-Regulation of Tyrosine Aminotransferase at A Frequently Deleted Region 16Q22 Contributes to the Pathogenesis of Hepatocellular Carcinoma (2010)

Taken together, our findings suggest that TAT plays an important suppressive role in the development and progression of HCC.
Identification of the ligand‐binding domain of human vascular‐endothelial‐growth‐factor receptor Flt‐1 (2001)

The vascular-endothelial-growth-factor (VEGF) receptor Flt-1 has been shown to be involved in vasculogenesis and angiogenesis. The receptor is characterized by seven immunoglobulin-like loops within the extracellular domain and the first three N-terminal immunoglobulin-like loops are involved in high-affinity binding of VEGF. The minimal extracellular domains of Flt-1 to achieve VEGF binding were screened using the yeast two-hybrid system. The result showed that the binding capacity of loop2-3 was close to that of loop1-3. The two truncated mutants consisting of loop2-3 and loop1-3 were expressed in the methylotrophic yeast Pichia pastoris at high levels (0.3 g[corrected]/litre). The corresponding proteins, named soluble (s)Flt-1(2-3) and sFlt-1(1-3), were purified. An in vitro biological activity assay showed that the binding capacity of sFlt-1(2-3) to human VEGF(165) and the inhibiting effect of it on human umbilical-vein endothelial cell proliferation stimulated by human VEGF(165) were close to those of sFlt-1(1-3). Animal tests showed that sFlt-1(2-3) could significantly inhibit the formation of regenerated blood vessels stimulated by hVEGF(165).
A distributed object model for the java TM system (1996)

We show a distributed object model for the JavaTM System [1,6] (hereafter referred to simply as Java) that retains as much of the semantics of the Java object model as possible, and only includes differences where they make sense for distributed objects. The distributed object system is simple, in that a) distributed objects are easy to use and to implement, and b) the system itself is easily extensible and maintainable. We have designed such a model and implemented a system that supports remote method invocation (RMI) for distributed objects in Java. This system combines aspects of both the Modula-3 Network Objects system [3] and Spring's subcontract [8] and includes some novel features.

To achieve its goal of seamless integration in the language, the system exploits the use of pickling [14] to transmit arguments and return values and also exploits unique features of Java in order to dynamically load stub code to clients. The final system will include distributed reference-counting garbage collection for distributed objects as well as lazy activation [11,16].
Nonvolatile Memory Design (2011)

The manufacture of flash memory, which is the dominant nonvolatile memory technology, is facing severe technical barriers. So much so, that some emerging technologies have been proposed as alternatives to flash memory in the nano-regime. Nonvolatile Memory Design: Magnetic, Resistive, and Phase Changing introduces three promising candidates: phase-change memory, magnetic random access memory, and resistive random access memory. The text illustrates the fundamental storage mechanism of these technologies and examines their differences from flash memory techniques. Based on the latest advances, the authors discuss key design methodologies as well as the various functions and capabilities of the three nonvolatile memory technologies.
SOME ASPECTS OF RGB VISION AND ITS APPLICATIONS IN INDUSTRY (1996)

RGB machine vision overlaps both colorimetry instrumentation and gray scale machine vision, and offers advantages over both. Proper calibration of the color camera which makes measurements independent of changes in illumination is essential for the reliability of color machine vision. A practical approach to on-line color camera calibration under unstable illumination conditions is presented and the performance of the procedure is evaluated. New potential applications of RGB machine vision are discussed from the perspective of physics-based vision and the calibration procedure developed here.
Designing Inhibitors of Cyclin-Dependent Kinases (2002)

Cyclin-dependent kinases (cdks) play a pivotal role in controlling progression through the cell cycle. The complex mechanisms that control cdks have been elucidated and, in the case of cdk2, explained with reference to X-ray crystal structures of the catalytically active and inactive kinase. Deregulation of the cell cycle is commonly observed in cancer, so cdks are potential targets for experimental therapeutic agents. A number of distinct structural classes of cdk inhibitors have been discovered. Good selectivity among these ATP competitive inhibitors for cdks over other kinases has been established, and selectivity between individual cdks is often observed. The crystal structures of a number of key inhibitors bound to cdk2 can be used to explain the observed structure-activity relationships within the compound series and to guide the design of more potent inhibitors.
Microfabricated atomic clocks and magnetometers (2006)

We demonstrate the critical subsystems of a compact atomic clock based on a microfabricated physics package. The clock components have a total volume below 10 cm3, a fractional frequency instability of 6 × 10−10/τ1/2, and consume 200 mW of power. The physics package is easily adapted to function as a magnetometer with sensitivity below 50 pT Hz−1/2 at 10 Hz.
Advancing chimeric antigen receptor T cell therapy with CRISPR/Cas9 (2017)

The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (CRISPR/Cas9) system, an RNA-guided DNA targeting technology, is triggering a revolution in the field of biology. CRISPR/Cas9 has demonstrated great potential for genetic manipulation. In this review, we discuss the current development of CRISPR/Cas9 technologies for therapeutic applications, especially chimeric antigen receptor (CAR) T cell-based adoptive immunotherapy. Different methods used to facilitate efficient CRISPR delivery and gene editing in T cells are compared. The potential of genetic manipulation using CRISPR/Cas9 system to generate universal CAR T cells and potent T cells that are resistant to exhaustion and inhibition is explored. We also address the safety concerns associated with the use of CRISPR/Cas9 gene editing and provide potential solutions and future directions of CRISPR application in the field of CAR T cell immunotherapy. As an integration-free gene insertion method, CRISPR/Cas9 holds great promise as an efficient gene knock-in platform. Given the tremendous progress that has been made in the past few years, we believe that the CRISPR/Cas9 technology holds immense promise for advancing immunotherapy.
The laminin B2 chain has a multidomain structure homologous to the B1 chain. (1987)

Laminin (Mr = 850,000) is a large basement membrane-specific glycoprotein composed of three chains: A, B1, and B2. Previously, we have reported the primary structure of the B1 chain of mouse laminin deduced from sequencing cDNA clones (Sasaki M., Kato, S., Kohno, K., Martin, G. R., and Yamada, Y. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 935-939). Here we report the isolation of overlapping cDNA clones spanning 7642 bases which encode the entire B2 chain. The nucleotide sequence of the clones contains an open reading frame of 4821 bases coding for a protein of 1607 amino acids including 33 amino acids of a presumptive signal peptide. The mRNA for the B2 chain contains 2.5 kilobases of 3'-untranslated region. The deduced amino acid sequence indicates that the B2 chain consists of six distinct domains, including two domains with alpha-helical, coiled-coil structures, two domains with cysteine-rich homologous repeats, and two globular domains. These structural features of the B2 chain are similar to those of the B1 chain. In addition, the amino acid sequences of the B2 and B1 chains demonstrate considerable homology, suggesting that the genes for these two chains arose from a common ancestor.
Glucosylation of Deoxyribonucleic Acid by Enzymes from Bacteriophage-infected Escherichia coli (1961)

The deoxyribonucleic acid of bacteriophages T2, T4, and T6 contains glucose linked to the hydroxymethyl groups of hydroxymethylcytosine.The work of Sinsheimer, Volkin, Jesaitis, and of Lichtenstein and Cohen (l-4) established the presence of glucosyl-hydroxymethylcytosine residues in the deoxyribonucleic acid and indicated that there is a characteristic glucose to hydroxymethylcytosine ratio for each phage.Lehman and Pratt ( 5) have now published a detailed analysis showing four types of hydroxymethylcytosine residues which have the following distribution in these phages : Unglucosylated.in T2 25%, in T4 0, in T6 25% cr-Glucosyl.in T2 70'%, in T4 70%, in TG 3% P-Glucosyl.. in T2 0, in T4 30%, in TG 0 &Glucosyl-or-glucosyl (diglucosyl) in T2 5y0, in T4 0, in T6 72%
Animal Models of Human Psychology: Critique of Science, Ethics and Policy (1998)

When is animal research necessity and when is it cruelty? Animal Models of Human Psychology is a breakthrough text that presents the first empirically based system of analysis to determine the answer to this much-debated question. Taking psychological eating disorders as a case study, Shapiro examines the costs and benefits associated with using nonhuman animals to study human phenomena. He uses social scientific analytic methods and original data to assess the effectiveness of current research, applying a combination of historical, conceptual, ethical, and political analyses to the use of animal models. This combination of elements makes Animal Models of Human Psychology a revolutionary text, which criticizes both the scientists who use animal models, as well as animal support groups which condemn such activities without a rigorous analysis of each situation.