gebhart/patrepeval huggingface dataset:
Rearrangements of Chromosome Band 3q21 in Myeloid Leukemia (2002)

Chromosome rearrangements affecting band 3q21, namely, the inv(3)(q21q26), the t(3;3)(q21;q26), and the t(1;3)(p36;q21), are associated with a particularly poor prognosis in myeloid leukemia or myelodysplasia. Originally, inv(3) and t(3;3) breakpoints have been reported to cluster in a region (breakpoint cluster region, BCR) of approximately 30 kb, which is located centromeric and downstream of the ribophorin I (RPN-I) gene. More recently, we established a PAC contig that includes the 3q21 BCR, and used these PAC clones to map breakpoints in patient samples by both metaphase and interphase fluorescence in situ hybridization (FISH) analysis. A significant proportion of inv(3) and t(3;3) breakpoints was located at sometimes considerable distances centromeric of the originally described BCR, in a region recently also implicated in t(1;3) rearrangements. These breakpoints may thus define a second, centromeric BCR (BCR-C), or extend the original 3q21 BCR to a size of approximately 100 kb. Activation of the EVI-1 gene in 3q26 by regulatory sequences of the housekeeping gene RPN-I has been suggested as a leukemogenic mechanism in patients with inv(3) and t(3;3). However, despite a number of characteristics that make EVI-1 an attractive candidate oncogene, its biological properties fail to fully explain the phenotype of leukemias carrying 3q rearrangements. Several additional candidate genes have been identified in or near the 3q21 breakpoint region, but their possible contribution to the characteristics of leukemias with 3q21 rearrangements remains to be explored.
Special diffractive lenses (1993)

The method has been proposed for computing Fresnel-type multi-focal lenses on the basis of special-type phase nonlinearity. Multi-focal lens is represented as a mathematical superposition of a thin lens and nonlinearity distorted Fresnel lens. Selection of the nonlinearity-type is reduced to the problem of the groove form determination for the phase diffraction grating with pre-set energy distribution between orders. In particular, bifocal lens and multi-focal lens have been investigated.
Enantioselective Synthesis of Fused Cycloheptadienes by a Tandem Intramolecular Cyclopropanation/Cope Rearrangement Sequence (1999)

The asymmetric induction in the intramolecular cyclopropanations of allyl vinyldiazoacetates catalyzed by tetrakis[N-[4-dodecylphenyl)sulfonyl]-(S)-prolinato]dirhodium [Rh2(S-DOSP)4] is very dependent on the allyl substitution pattern. The reactions of cis-alkenes result in much higher asymmetric induction than trans-alkenes while the highest enantioselectivity was obtained with a disubstituted terminal alkene. The intramolecular cyclopropanation of dienylmethyl vinyldiazoacetates results in the synthesis of fused cycloheptadiene ring systems with full control of relative stereochemistry and variable enantioselectivity. The synthetic utility of this process was demonstrated by a short synthesis of 5-epi-tremulenolide in 93% ee.
Curved acceleration path of ultrasound-driven air flow (2019)

We established a method for generating an ultrasound beam that propagates along a narrow, isolated curved path and is accompanied by an arc-shaped airflow, and experimentally confirmed the actual generation of such a beam. The method employs a two-dimensional orthogonal phased array of ultrasound transducers, whose individual columns correspond to a line segment in a given beam trajectory. Each column of transducers yields a “ring” in which acoustic energy is concentrated. A cluster of these ultrasound rings arranged at sufficiently small spatial intervals interfere with adjacent rings, consequently forming a fine curved path of propagating ultrasound accompanied by an ultrasound-driven air flow. The positions of these rings can be electronically controlled and so can the position of the resulting beam path. We obtained isolated sharp arc-shaped airflows propagating over nearly 1 m in open space. Such airflows have never been reported and are extremely difficult to generate by the superposition of ordinary jet-driven airflows. Our achievement will lead to the ability to generate airflows along an arbitrarily designed three-dimensional arc-shaped path. This technique will be utilized in such unprecedented applications as midair transportation of gaseous substance or control of heat in the air while circumventing obstacles, which are intuitive, yet hard to achieve by other methods.
Distribution of myoepithelial cells and basement membrane proteins in the normal breast and in benign and malignant breast diseases. (1982)

An immunocytochemical method for fixed and paraffin-embedded human breast biopsies is reported for the detection of myoepithelial and epithelial cells using antibodies to myosin and keratin, respectively, and of basement membranes using antibodies to laminin and type IV collagen. Using these markers, myoepithelial cells can be clearly distinguished in the normal breast and in the benign breast diseases sclerosing adenosis, epitheliosis, and fibroadenoma. In sclerosing adenosis, myoepithelial cells form a major cellular component. A stromally derived spindle cell is identified which stains with myosin but not with keratin antibodies (myofibroblast). These cells are seen in one-fifth of the fibroadenomas. Although cells staining with myosin antibodies are seen in the infiltrating component of all 18 carcinomas examined, elongated cells staining with both myosin and keratin antibodies (myoepithelial-like) are seen in only one infiltrating carcinoma where they are interposed at the stromal-epithelial junction of the infiltrating tumor cells. In contrast to the situation in benign breast diseases, mature myoepithelial cells form a very minor component of the majority of infiltrating ductal carcinomas. Basement membrane proteins, laminin, and type IV collagen are present in normal breast, benign breast disease, and grade I infiltrating ductal carcinomas but are absent in carcinomas of grades II and III.
Clinical Significance of Glucose Transporter 1 (GLUT1) Expression in Human Breast Carcinoma (2002)

Glucose uptake and glycolytic metabolism are enhanced in cancer cells compared to normal cells and tissues. Increased expression of glucose transporter 1 (GLUT1) has been reported in human malignant cells. The aim of this study is to determine the expression of the facilitative glucose transporter protein GLUT1 in human breast carcinomas and a possible correlation between GLUT1 expression and clinical outcome including disease-free or overall survival. One hundred consecutive formalin-fixed, paraffin-embedded sections of invasive breast carcinomas were evaluated by means of immunohistochemical staining of GLUT1. Forty-seven (47%) of 100 breast carcinomas showed positive staining for GLUT1. Expression of GLUT1 correlated significantly with nuclear grade (P < 0.001), estrogen receptor status (P = 0.002), and progesterone receptor status (P = 0.001). The mean disease-free survival periods of GLUT1-positive and -negative patients were 47 +/- 2.4 months and 54.3 +/- 1.3 months, respectively (P = 0.017). The mean overall survival periods of GLUT1-positive and -negative patients were 48.7 +/- 2.2 and 56.1+/- 1.3 months, respectively (P = 0.043). In the multivariate analysis, disease-free survival correlated significantly with GLUT1, tumor size, and lymph node involvement (P = 0.043, P = 0.014, and P = 0.045, respectively). In analysis of overall survival, however, lymph node involvement, tumor size, and nuclear grade were statistically significant (P = 0.024, P = 0.023, and P = 0.003, respectively). Our data suggest that absence of GLUT1 expression significantly increases disease-free survival. These findings demonstrate that GLUT1 expression in breast carcinoma can be a marker of aggressive biological behavior and identifies a worse prognosis in breast carcinoma patients.
Rapid scanning fluorescence spectroscopy using an acousto-optic tunable filter (1987)

A new method for rapidly acquiring fluorescence spectra from optical probes using an acousto-optic tunable filter (AOTF) has been developed. The AOTF consists of a piezoelectric transducer bonded to a birefringent crystal. Acoustic waves are generated in the crystal by an applied radio frequency. For a given radio frequency, only a narrow band of optical frequencies will be diffracted. Unlike normal Bragg diffraction which can only be used with collimated light, the AOTF has a large angular aperture (up to 28 deg) and can therefore be coupled to an uncollimated broadband white light source, photomultiplier tube, or camera. Using the device and a xenon–mercury arc lamp, excitation and emission spectra of the fluorescent pH probe BCECF were acquired in 17 ms (spectral resolution=4 nm). Rapid wavelength switching or modulation of selected wavelengths was achieved at ∼105 Hz. The device is also capable of spectral imaging with a spatial resolution of greater than 100 lines/mm.
Genome Sequence of Non-O1 Vibrio cholerae PS15 (2013)

The draft genome sequence of a non-O1 Vibrio cholerae strain, PS15, organized into 3,512 open reading frames within a 3.9-Mb genome, was determined. The PS15 genome sequence will allow for the study of the evolution of virulence and environmental adaptation in V. cholerae.
Oxidized Phospholipids Are More Potent Antagonists of Lipopolysaccharide than Inducers of Inflammation (2010)

Polyunsaturated fatty acids are precursors of multiple pro- and anti-inflammatory molecules generated by enzymatic stereospecific and positionally specific insertion of oxygen, which is a prerequisite for recognition of these mediators by cellular receptors. However, nonenzymatically oxidized free and esterified polyunsaturated fatty acids also demonstrate activities relevant to inflammation. In particular, phospholipids containing oxidized fatty acid residues (oxidized phospholipids; OxPLs) were shown to induce proinflammatory changes in endothelial cells but paradoxically also to inhibit inflammation induced via TLR4. In this study, we show that half-maximal inhibition of LPS-induced elevation of E-selectin mRNA in endothelial cells developed at concentrations of oxidized 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (OxPAPC) 10-fold lower than those required to induce proinflammatory response. Similar concentration difference was observed for other classes and molecular species of OxPLs. Upon injection into mice, OxPAPC did not elevate plasma levels of IL-6 and keratinocyte chemoattractant but strongly inhibited LPS-induced upregulation of these inflammatory cytokines. Thus, both in vitro and in vivo, anti-LPS effects of OxPLs are observed at lower concentrations than those required for their proinflammatory action. Quantification of the most abundant oxidized phosphatidylcholines by HPLC/tandem mass spectrometry showed that circulating concentrations of total oxidized phosphatidylcholine species are close to the range where they demonstrate anti-LPS activity but significantly lower than that required for induction of inflammation. We hypothesize that low levels of OxPLs in circulation serve mostly anti-LPS function and protect from excessive systemic response to TLR4 ligands, whereas proinflammatory effects of OxPLs are more likely to develop locally at sites of tissue deposition of OxPLs (e.g., in atherosclerotic vessels).
Soluble E-Selectin and Intercellular Adhesion Molecule-1 Plasma Levels Increase During Acute Myocardial Infarction (1997)

Previous studies have shown that adhesion molecules play a crucial role in leukocyte-endothelium interactions that occur during myocardial ischemia and reperfusion. We assessed the plasma levels of the soluble form of E-selectin (sE-selectin) and intercellular adhesion molecule-1 (sICAM-1) in 15 patients with acute myocardial infarction (AMI) and in 15 controls with chronic stable angina. In patients with AMI, the levels of sE-selectin and sICAM-1 increased significantly during the first 8 h after infarction and subsequently decreased. Soluble E-selectin levels were inversely related to the peak plasma levels of creatine kinase-MB (CK-MB), and the time course of their appearance in plasma correlated with that of neutrophil count and plasma D-dimer. In individual patients, peak and mean sICAM-1 levels correlated respectively with plasma D-dimer concentrations and monocyte count, but no correlation were found when their time courses were analyzed. Eight hours after symptom onset, the mean plasma sE-selectin levels were higher in patients with AMI than in those with stable angina, whereas no significant differences were found in mean plasma sICAM-1 levels between the two groups at every time analyzed. In the acute phase of MI (a) sE-selectin and sICAM-1 levels increase during the first 8 h and subsequently decrease; (b) the increase in sE-selectin probably reflects activation of endothelial cells, correlates with other inflammatory and coagulation parameters, and is inversely related to the degree of myocardial damage; and (c) sICAM-1 plasma levels do not represent a good marker of "cell activation" because they reflect activation of different cells and may be affected by different conditions.
Tumor Necrosis Factor‐α, an Initiator, and Etanercept, an Inhibitor of Cochlear Inflammation (2002)

Interleukin-1beta expression is a general cochlear response to trauma, whereas tumor necrosis factor-alpha expression in the infiltrated immunocompetent cells is the cytokine that induces amplification of the response that leads to cochlear disease.
Fourier-transform, integrated-optic spatial heterodyne spectrometer on a silica-based planar waveguide with 1 GHz resolution (2011)

Spatial heterodyne spectrometers (SHS) can achieve high resolution with excellent optical throughput. We demonstrate a planar waveguide SHS incorporating 64 asymmetric Mach-Zehnder interferometers and show measurements that verify 1 GHz resolution across a 64 GHz measurement range.
Characterization of polymers by multi‐step thermal desorption/programmed pyrolysis gas chromatography using a high temperature PTV injector (1996)

Abstract Thermal treatment hyphenated with gas chromatography is a versatile and powerful tool in the study of polymer characterization. An inexpensive system where thermal treatment at different temperatures occurs inside a Programmable Temperature Vaporization injector (PTV) is described. The samples investigated, commercial plastics, are complex mixtures that contain several polymers and additives. These plastics as well as their pure constituents are subjected to multi‐step thermal treatment. The individual chromatograms of the various constituents of the polymeric sample are correlated with those of the final material in order to identify additives (thermal desorption) and degradation products (pyrolysis). Results obtained with the new method indicate the interesting potentials of the technique for the characterization of polymer compositions. Reproducibility of absolute and relative peak areas has been considered and found to be acceptable. The absence of a heated transfer line and switching valves, which are always present in conventional set‐ups, eliminates the risk of losses of high molecular weight components. Further advantages of the technique proposed are simplicity, versatility, and its inexpensive nature.
The Wall Street Journal experiment (and useful programs) (2004)

This document gives information on parsing experiments applied to the standard Wall Street Journal corpus (``Standard'' means that this corpus has been widely used for exhibiting parsing tests of various models). The tested syntactic models are : standard Stochastic Context-Free Grammars, standard Tree Substitution Grammars, Gibbsian Context-Free Grammars and Gibbsian Tree Substitution Grammars. The parsing experiments are described with deep details so as to enable reader to easily redo the experiments from scratch (i.e. preparing the database, training and evaluating the models). The programs developped for these experiments are also described.
Mobile RFID Tracking System (2008)

This paper describes the design of an RFID kids tracking system. It is designed to track a moving child in a wide area, such as a park or mall, using RFID technology. The proposed system has hardware and software components. The hardware architecture consists of an RFID active tag, RFID tag reader, Web server and database server. The Web server and database server are located in the master station. The tag readers are distributed around the open area, e.g. park. The tags are programmed with kid's profiles and are worn by the kids. Communication between the tag reader and the Web server is done via wireless LANs. The software architecture consists of a communication driver that handles all communication functions done at the master station, an application programming interface (API) that handles and analyzes the data, a friendly GUI and a database that saves all readings and client information.
Human milk oligosaccharides: Every baby needs a sugar mama (2012)

Human milk oligosaccharides (HMOs) are a family of structurally diverse unconjugated glycans that are highly abundant in and unique to human milk. Originally, HMOs were discovered as a prebiotic "bifidus factor" that serves as a metabolic substrate for desired bacteria and shapes an intestinal microbiota composition with health benefits for the breast-fed neonate. Today, HMOs are known to be more than just "food for bugs". An accumulating body of evidence suggests that HMOs are antiadhesive antimicrobials that serve as soluble decoy receptors, prevent pathogen attachment to infant mucosal surfaces and lower the risk for viral, bacterial and protozoan parasite infections. In addition, HMOs may modulate epithelial and immune cell responses, reduce excessive mucosal leukocyte infiltration and activation, lower the risk for necrotizing enterocolitis and provide the infant with sialic acid as a potentially essential nutrient for brain development and cognition. Most data, however, stem from in vitro, ex vivo or animal studies and occasionally from association studies in mother-infant cohorts. Powered, randomized and controlled intervention studies will be needed to confirm relevance for human neonates. The first part of this review introduces the pioneers in HMO research, outlines HMO structural diversity and describes what is known about HMO biosynthesis in the mother's mammary gland and their metabolism in the breast-fed infant. The second part highlights the postulated beneficial effects of HMO for the breast-fed neonate, compares HMOs with oligosaccharides in the milk of other mammals and in infant formula and summarizes the current roadblocks and future opportunities for HMO research.
Characterization of RNA sequence determinants and antideterminants of processing reactivity for a minimal substrate of Escherichia coli ribonuclease III (2006)

Members of the ribonuclease III family are the primary agents of double-stranded (ds) RNA processing in prokaryotic and eukaryotic cells. Bacterial RNase III orthologs cleave their substrates in a highly site-specific manner, which is necessary for optimal RNA function or proper decay rates. The processing reactivities of Escherichia coli RNase III substrates are determined in part by the sequence content of two discrete double-helical elements, termed the distal box (db) and proximal box (pb). A minimal substrate of E.coli RNase III, muR1.1 RNA, was characterized and used to define the db and pb sequence requirements for reactivity and their involvement in cleavage site selection. The reactivities of muR1.1 RNA sequence variants were examined in assays of cleavage and binding in vitro. The ability of all examined substitutions in the db to inhibit cleavage by weakening RNase III binding indicates that the db is a positive determinant of RNase III recognition, with the canonical UA/UG sequence conferring optimal recognition. A similar analysis showed that the pb also functions as a positive recognition determinant. It also was shown that the ability of the GC or CG bp substitution at a specific position in the pb to inhibit RNase III binding is due to the purine 2-amino group, which acts as a minor groove recognition antideterminant. In contrast, a GC or CG bp at the pb position adjacent to the scissile bond can suppress cleavage without inhibiting binding, and thus act as a catalytic antideterminant. It is shown that a single pb+db 'set' is sufficient to specify a cleavage site, supporting the primary function of the two boxes as positive recognition determinants. The base pair sequence control of reactivity is discussed within the context of new structural information on a post-catalytic complex of a bacterial RNase III bound to the cleaved minimal substrate.
Regulatory Network Connecting Two Glucose Signal Transduction Pathways in Saccharomyces cerevisiae (2004)

The yeast Saccharomyces cerevisiae senses glucose, its preferred carbon source, through multiple signal transduction pathways. In one pathway, glucose represses the expression of many genes through the Mig1 transcriptional repressor, which is regulated by the Snf1 protein kinase. In another pathway, glucose induces the expression of HXT genes encoding glucose transporters through two glucose sensors on the cell surface that generate an intracellular signal that affects function of the Rgt1 transcription factor. We profiled the yeast transcriptome to determine the range of genes targeted by this second pathway. Candidate target genes were verified by testing for Rgt1 binding to their promoters by chromatin immunoprecipitation and by measuring the regulation of the expression of promoter lacZ fusions. Relatively few genes could be validated as targets of this pathway, suggesting that this pathway is primarily dedicated to regulating the expression of HXT genes. Among the genes regulated by this glucose signaling pathway are several genes involved in the glucose induction and glucose repression pathways. The Snf3/Rgt2-Rgt1 glucose induction pathway contributes to glucose repression by inducing the transcription of MIG2, which encodes a repressor of glucose-repressed genes, and regulates itself by inducing the expression of STD1, which encodes a regulator of the Rgt1 transcription factor. The Snf1-Mig1 glucose repression pathway contributes to glucose induction by repressing the expression of SNF3 and MTH1, which encodes another regulator of Rgt1, and also regulates itself by repressing the transcription of MIG1. Thus, these two glucose signaling pathways are intertwined in a regulatory network that serves to integrate the different glucose signals operating in these two pathways.