gebhart/patrepeval huggingface dataset:
MINING GENE-DISEASE RELATIONSHIPS FROM BIOMEDICAL LITERATURE: WEIGHTING PROTEIN–PROTEIN INTERACTIONS AND CONNECTIVITY MEASURES (2006)

Top-ranked proteins from the method are related to atherosclerosis with accuracy between 0.85 to 1.00 for the top 20 and 0.64 to 0.80 for the top 90 if duplicates are ignored, with 45% of the top 20 and 75% of the top 90 derived by the method, not extracted from text. Thus, though the initial gene set and interactions were automatically extracted from text (and subject to the impreciseness of automatic extraction), their use for further hypothesis generation is valuable given adequate computational analysis.
Production of Corneal Lesions Using High-Intensity Focused Ultrasound (1990)

In order to study the potential use of ultrasound as a noninvasive system for altering corneal curvature, we used high-density focused ultrasound at a frequency of 4.8 MHz and 7.9 MHz to produce corneal lesions in the rabbit eye. Intensity and duration threshold exposure conditions were determined for the production of minimally visible lesions. Threshold lesions were initially apparent as discrete white opacities resulting from stromal edema and disruption. Light and scanning electron microscopy of higher-energy, suprathreshold lesions revealed more extensive disruption, including the formation of a superficial stromal depression and a larger zone of edema and disorganization surrounding each lesion. Posterior stromal lamellae, endothelium, and Descemet's membrane were intact. Healing and reepithelialization resulted in a smooth corneal surface with no residual opacification. Threshold determinations predict safe exposure levels to the cornea during insonification of other ocular structures. Selective heating of the peripheral cornea using focused ultrasound may be a useful technique for correcting astigmatism.
Pneumococcal Antibody Levels in Children With PID Receiving Immunoglobulin (2013)

In IVIG-treated children with PID, protective PnPsAb levels for most pathogenic serotypes were obtained. A correlation was observed between PnPsAb levels in patients and in the IVIG product. This offers the potential to improve infection prevention by adapting the IVIG product and dose according to epidemiology.
Interfacing Droplet Microfluidics with Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry: Label-Free Content Analysis of Single Droplets (2013)

Droplet-based microfluidic systems have become a very powerful tool to miniaturize chemical and biological reactions. However, droplet content analysis remains challenging and relies almost exclusively on optical methods such as fluorescence spectroscopy. Hence, labeling of the analyte is typically required which impedes a more universal applicability of microdroplets. Here we present a novel interface coupling droplet microfluidics and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for label-free content analysis of single droplets. Nanoliter aqueous droplets immersed in perfluorinated oil are created in a microfluidic T-junction, transferred into a capillary, and deposited on a high-density microarray MALDI plate mounted on a motorized xy-stage. The fully automated system is robust and reliable due to two unique features. First, a simple optical droplet detection system is used to synchronize stage movement and exit of droplets from the capillary. Second, the microarray plate contains an array of over 26,000 hydrophilic spots within a hydrophobic coating, each spot acting as a recipient to confine the droplets and to prevent cross-contamination. The MALDI matrix can also be applied using our system by spotting matrix droplets on the microarray in a separate run. To demonstrate the potential of our system, we studied the enzymatic cleavage of angiotensin I by angiotensin converting enzyme and monitored the increasing concentration of the product angiotensin II over time. The interface provides a robust and fully automated method for rapid label-free and information-rich content analysis of single droplets. With the high number of droplets per plate, this method is particularly suitable for high-throughput screening applications.
Review of laser speckle contrast techniques for visualizing tissue perfusion (2008)

When a diffuse object is illuminated with coherent laser light, the backscattered light will form an interference pattern on the detector. This pattern of bright and dark areas is called a speckle pattern. When there is movement in the object, the speckle pattern will change over time. Laser speckle contrast techniques use this change in speckle pattern to visualize tissue perfusion. We present and review the contribution of laser speckle contrast techniques to the field of perfusion visualization and discuss the development of the techniques.
Head-to-head arrangement of murine type IV collagen genes. (1988)

The genes for the two dissimilar subunits of type IV collagen are organized in a head-to-head manner with their translation initiation codons within 874 base pairs. Murine genomic clones which contain portions of both genes have been isolated and characterized. These clones contain the first exon of the alpha 1(IV) chain and the first 3 exons for the alpha 2(IV) chain within a 1.7-kilobase HindIII fragment. The intergenic region appears not to resemble previously described bidirectional promoters. The HindIII fragment is present as a single copy in the mouse genome ruling out the presence of one of these gene fragments as a pseudogene. These findings agree with linkage studies of these two genes and differ from the known organization of human fibrillar collagen genes which have been found to be dispersed within the human genome.
The CD19/CR2/TAPA-1 Complex of B Lymphocytes: Linking Natural to Acquired Immunity (1995)

B lymphocytes must respond to low concentrations of antigen despite having low affinity antigen receptors during the primary immune response. CD19, a B cell-restricted membrane protein of the immunoglobulin superfamily that associates with the antigen receptor complex, may help the B cell meet this requirement. Cross-linking CD19 to membrane immunoglobulin (mIg) lowers, by two orders of magnitude, the number of mIg that must be ligated to activate phospholipase C (PLC) or to induce DNA synthesis. CD19 is coupled, via protein tyrosine kinases (PTKs), to PLC and phosphatidylinositol 3' kinase (PI3' kinase), and it interacts with the Src-type nonreceptor PTK lyn. It also associates with two other membrane proteins, CR2 (complement receptor type 2, CD21), which permits nonimmunologic ligation of CD19, and TAPA-1, a member of the tetraspan family of membrane proteins. CR2 binds fragments of C3 that are covalently attached to glycoconjugates. This indirectly enables CD19 to be cross-linked to mIg after preimmune recognition of an immunogen by the complement system. CR2 also can be ligated by CD23, a lectin-like membrane protein that resides on cells that may present antigen to B cells. TAPA-1 associates with several other membrane proteins on B and T cells, including MHC class II, CD4, and CD8, and it promotes Ca2(+)- and LFA-1-independent homotypic aggregation when ligated directly or indirectly through CD19 or CR2. This may facilitate interaction of the B cell with other cells essential for cellular activation. The formation of this membrane protein complex by representatives of three different protein families helps the B cell resolve its dilemma of combining broad specificity with high sensitivity.
Production of glucolipids and specialty fatty acids from sophorolipids by Penicillium decumbens naringinase: Optimization and kinetics (2009)

In view of global environmental concerns and the awakening to the exhaustibility of our natural resources, an increasing importance of biologically derived surfactants can be expected in the near future. Enzymatic modification of these biosurfactants allows to improve their characteristics and so extend their application field. In view of this, glucolipids are interesting substrates e.g., for the synthesis of new glycolipids with increased biological activity. Here, we describe the optimization of glucolipid production from Candida bombicola sophorolipids by Penicillium decumbens naringinase and show that the enzyme might be useful for production of specialty fatty acids as well. Optimum conditions for production of glucolipids were found to be pH 7.0 and 50 degrees C with a yield of 80% (w/w) glucolipids after 3 h of incubation. The K(m) for sophorolipids was 1.67 mM, while V(max) was 0.035 mM sophorolipids/min. At pH 3.0, glucolipids were immediately further hydrolyzed and completely converted to fatty acids after 24 h of incubation, offering a biological route to the synthesis of unique specialty fatty acids. The K(m) for glucolipids was 11 mM while V(max) was 0.21 mM glucolipids/min. Glucose inhibited the enzyme in a competitive way with K(I) around 10-15 mM glucose. Surfactant properties of the produced glucolipids were comparable to those of the acidic sophorolipids.
CXCR4 neutralization, a novel therapeutic approach for non-Hodgkin's lymphoma. (2002)

The chemokine stromal cell-derived factor-1 (CXCL12/SDF-1) and its monogamous receptor CXCR4 are involved in trafficking of B cells and hematopoietic progenitors. CXCR4 expression was found in the large majority of non-Hodgkin's lymphoma (NHL) cell lines and primary cells, and CXCR4 neutralization by monoclonal antibodies had profound in vitro effects on NHL cells including inhibition of transendothelial/stromal migration, enhanced apoptosis, decreased proliferation, and inhibition of pseudopodia formation. In a nonobese diabetes/severe combined immunodeficiency (NOD/SCID) mouse model of human high-grade NHL, CXCR4 neutralization had an impressive efficacy. In a first tumor-challenge trial, CXCR4 neutralization of Namalwa cells injected i.p. delayed tumor growth and reduced tumor weight. In a second tumor-challenge trial, NOD/SCID mice received Namalwa cells i.v. All of the controls died of neoplasia within day 36, whereas 83% of mice injected with cells incubated with anti-CXCR4 were still alive and disease-free >150 days after transplant. The crucial role of CXCR4 in tumor cell extravasation was confirmed by the finding that CXCR4 neutralization before i.v. injection of Namalwa cells in NOD/SCID mice increased the number of cancer cells circulating 24 h after injection. In additional preclinical trials, the therapeutic effect of anti-CXCR4 antibodies was evaluated in mice bearing Namalwa cells injected 3 days before. Tumor growth was abrogated in the majority of treated mice and significantly delayed in the remaining group. Taken together, these data support clinical studies on CXCR4 neutralization in NHL patients by monoclonal antibodies or CXCR4 antagonists.
Enhanced Supercontinuum Generation through Dispersion-Management (2005)

We show in theory and simulation that the supercontinuum generation from an initial continuous wave field in a highly nonlinear fiber operating near the zero-dispersion point can be significantly enhanced with the aid of dispersion management. We characterize the spectral broaden-ing as a process initiated by modulational instability, but driven by the zero-dispersion dynamics of an N-soliton interacting with the asymmetric phase profile generated by the Raman effect, self-steepening effect, and/or higher-order dispersion. Higher N-soliton values lead to shorter pulses and a broader spectrum. This insight allows us to use dispersion management in conjunction with modulational instability to effectively increase the N value and greatly enhance the supercontiuum generation process.
Direct RF to optical frequency measurements with a femtosecond laser comb (2001)

By spanning an optical octave (>300 THz) with a broadened femtosecond laser frequency comb, we directly measure the frequencies of optical standards at 1064/532 nm, 633 nm and 778 nm in terms of the microwave frequency that controls the comb spacing. This microwave frequency can be linked directly to the cesium standard.
Synthesis of 2,2′‐Bipyridines: Versatile Building Blocks for Sexy Architectures and Functional Nanomaterials (2004)

Abstract The latest synthetic strategies to prepare 2,2′‐bipyridine and its mono‐substituted, symmetrical and unsymmetrical 3,3′‐, 4,4′‐, 5,5′‐, and 6,6′‐disubstituted derivatives are critically discussed and evaluated. Different coupling procedures to achieve new symmetrical and unsymmetrical functionalized 2,2′‐bipyridines, such as Stille‐type, Negishi‐type, and Suzuki‐type cross‐coupling reactions are discussed in detail. Moreover, condensation procedures that allow further variations are presented. The application of functional group transformations for access to additional groups is examined. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2004)
The p53-Estrogen Receptor Loop in Cancer (2013)

Tumor suppressor p53 maintains genome stability by regulating diverse cellular functions including cell cycle arrest, apoptosis, senescence and metabolic homeostasis. Mutations in the p53 gene occur in almost all human cancers with a frequency of up to 80%. However, it is only 20% in breast cancers, 18% in endometrial cancers and 1.5% in cervical cancers. Estrogen receptor alpha (ERα) plays a pivotal role in hormone-dependent cancer development and the status of ERα is used for designing treatment strategy and for prognosis. A closer look at the cross-talk between p53 and ERα has revealed that their activities are mutually regulated. This review will summarize the current body of knowledge on p53, ERα and ERβ in cancer. Clinical correlations between estrogen receptors and p53 status have also been reported. Thus, this review will discuss the relationship between p53 and ERs at both the molecular and clinical levels.
Service configurator: a pattern for dynamic configuration of services (1997)

This paper describes the Service Configurator pattern, which decouples the implementation of services from the time when they are configured. This pattern increases the flexibility and extensibilityof applicationsby enabling their constituent services to be configured at any point in time. The Service Configurator pattern is widely used in application environments (e.g., to configure Java applets into WWW browsers), operating systems (e.g., to configure device drivers), and distributed systems (e.g., to configure standard Internet communication services).
Reinforcement Learning in a Nutshell (2007)

Abstract. We provide a concise introduction to basic approaches to reinforcement learning from the machine learning perspective. The focus is on value function and policy gradient methods. Some selected recent trends are highlighted. 1
XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data (2008)

XplorSeq should benefit researchers who are engaged in analyses of environmental sequence data, especially those with little experience using bioinformatics software. Although XplorSeq was developed for management of rDNA sequence data, it can be applied to most any sequencing project. The application is available free of charge for non-commercial use at http://vent.colorado.edu/phyloware.
Optical Levitation of Liquid Drops by Radiation Pressure (1975)

Charged and neutral liquid drops in the diameter range from 1 to 40 microns can be stably levitated and manipulated with laser beams. The levitation technique has been extended toward smaller particles (about 1 micron), lower laser power (less than 1 milliwatt), and deeper traps (greater than ten times the particle's weight). The techniques developed here have particular importance in cloud physics, aerosol science, fluid dynamics, and optics. The interactions of the drops with light, the electric field, the surrounding gas, and one another can be observed with high precision.
[The clinical features and prognosis of drug-induced liver disease]. (2008)

A variety of medicines may cause DILD; herbal medicines, anti-tuberculosis drugs and immunosuppressive drugs were frequently found to be responsible, the hepatocellular type was the most common, while the mixed type and cholestatic type were somewhat less. Serum albumin, total bile acids, direct bilirubin and blood prothrombin time are important predictors of the prognosis of DILD.
Automated Synthesis of Peptides (1965)

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Association between features of the insulin resistance syndrome and alzheimer's disease independently of apolipoprotein e4 phenotype: cross sectional population based study (1997)

Features of the insulin resistance syndrome are associated with Alzheimer's disease independently of apolipoprotein E4 phenotype.
QseA Directly Activates Transcription of LEE1 in Enterohemorrhagic Escherichia coli (2007)

Quorum sensing (QS) in enterohemorrhagic Escherichia coli (EHEC) regulates the expression of the locus of enterocyte effacement (LEE). The LEE contains five major operons named LEE1 through LEE5. QseA was previously shown to be activated through QS and to activate the transcription of LEE1. The LEE1 operon encodes Ler, the transcription activator of all other LEE genes, and has two promoters: a distal promoter (P1) and a proximal promoter (P2). We have previously reported that QseA acts on P1 and not P2. To identify the minimal region of LEE1 that is necessary for QseA-mediated activation, a series of nested-deletion constructs of the LEE1 promoter fused to a lacZ reporter were constructed in both the EHEC and E. coli K-12 backgrounds. In an EHEC background, QseA-dependent activation of LEE1 can be observed for the entire regulatory region (beginning at nucleotide -393 and ending at nucleotide -123). In contrast to what occurred in EHEC, in K-12 there was no QseA-dependent activation of LEE1 transcription between base pairs -393 and -343. These data indicate that a QseA-dependent EHEC-specific regulator is required for the activation of transcription in this region. We also observed QseA-dependent LEE1 activation from nucleotides -218 to -123 in K-12, similar to results of the nested-deletion analysis performed with EHEC. Electrophoretic mobility shift assays established that QseA directly binds to the region of LEE1 from bp -173 to -42 and not to the region from bp -393 to -343. These studies suggest that QseA activates the transcription of LEE1 by directly binding upstream of its P1 promoter region.
Human cytoplasmic superoxide dismutase cDNA clone: a probe for studying the molecular biology of Down syndrome. (1982)

The gene locus for human cytoplasmic superoxide dismutase (SOD-1; superoxide:superoxide oxidoreductase, EC 1.15.1.1) is located in or near a region of chromosome 21 known to be involved in Down syndrome. To approach the molecular biology of this genetic disease we have constructed a SOD-1 cDNA clone. Poly(A)-containing RNA enriched for human SOD-1 mRNA was isolated, used to synthesize double-stranded cDNA, and inserted into the endonuclease Pst I site of the plasmid pBR322. The chimeric molecules were used to transform Escherichia coli. Two clones containing SOD-1 cDNA inserts were identified by their ability to hybridize specifically with mRNA coding for SOD-1. Each of these clones carries a 650-base-pair insert, as was determined by restriction enzyme digestion and electron microscopic heteroduplex analysis. Hybridization of labeled cloned cDNA to RNA blots revealed two distinct SOD-1 mRNA classes of 500 and 700 nucleotides. The data suggest that both are polyadenylylated and are coded by chromosome 21.
Cardiovascular Risk Associated with Celecoxib in a Clinical Trial for Colorectal Adenoma Prevention (2005)

Celecoxib use was associated with a dose-related increase in the composite end point of death from cardiovascular causes, myocardial infarction, stroke, or heart failure. In light of recent reports of cardiovascular harm associated with treatment with other agents in this class, these data provide further evidence that the use of COX-2 inhibitors may increase the risk of serious cardiovascular events.
Polymerization of diacetylenes in multilayers (1979)

Abstract A series of amphiphilic diacetylene monocarbonic acids was synthesized, and their ability to form monolayers at the air–water interphase was investigated. Acids with total number of C atoms ≥20 and mp &gt;45°C form surface states suitable to be used for buildup of multilayers by the Langmuir–Blodgett technique. Using the LB technique, multilayers of defined thickness were built up on quartz substrates. The multilayers were polymerized by exposure to a UV light source according to the mechanism of solid‐state polymerization of diacetylenes without destruction of the layer structure and with retention of the packing in the individual layers. Thus well‐defined polymer multilayers were obtained. The monomer and polymer multilayers were characterized by UV spectra, x‐ray small‐angle diffraction, and interference microscopic and electron microscopic techniques. The polyconjugated backbones of the polymer chains are all stretched out in the plane of the substrate but not over macroscopic dimensions because the multilayers have a crystalline domain structure. The polymer multilayer films are quite stable under ambient conditions.
Placental mRNA in maternal plasma as a predictor of ectopic pregnancy (2012)

Placental mRNA is present in the maternal circulation in significantly lower copies in cases of ectopic pregnancy compared with cases of intrauterine pregnancy. Measurement of placental mRNA in the maternal circulation may help to distinguish between intrauterine and ectopic pregnancies.
Low‐Density Parity‐Check Codes: Design and Decoding (2003)

Abstract In this chapter, we treat code design and decoding for a family of error correction codes known as low‐density parity‐check (LDPC) codes. The chapter begins with an introduction to error correction in telecommunications with the focus on parity‐check equations and codes defined by their parity‐check matrices. To introduce the concepts behind iterative decoding, a hard‐decision iterative algorithm is discussed before the soft‐decision sum‐product decoding algorithm is presented. Following sections focus on the relationship of graph‐based representations of codes to the development of both the theoretical understanding and implementation of iterative decoders, and current methods for design of LDPC codes. The chapter concludes with the connections of LDPC codes and their decoding to other topics and likely future directions in the area.