gebhart/patrepeval huggingface dataset:
Genomic organization of human surfactant protein D (SP-D). SP-D is encoded on chromosome 10q22.2-23.1. (1993)

Surfactant protein D (SP-D) is a member of the family of mammalian C-type lectins. SP-D is secreted into the pulmonary airspaces by lung epithelial cells and is believed to contribute to the lung's defense against inhaled microorganisms. We have previously characterized cDNAs specific for human SP-D (hSP-D). We now describe the partial characterization of genomic clones for hSP-D and present evidence for an SP-D gene with coding sequences spanning > 11 kilobases on the long arm of chromosome 10. Genomic sequencing demonstrated that the signal peptide/amino-terminal domain, the carbohydrate recognition domain, and the linking sequence between the collagen domain, and carbohydrate recognition domain are each encoded by a single exon, as for surfactant protein A and the mannose-binding protein C. However, sequencing also demonstrated a unique intron-exon structure for the collagen domain which is encoded on five exons, including four tandem exons of 117 bp. The latter exons show marked conservation in the predicted distribution of hydrophilic amino acids, consistent with tandem replication of this collagen gene sequence during evolution. Segregation analysis of HindIII digests of genomic DNA using specific cDNA probes demonstrated selective hybridization of radiolabeled hSP-D cDNA to chromosome 10- and 10q-containing human/hamster somatic hybrids. The presence of SP-D gene sequences was confirmed by DNA amplification using oligomers specific for sequences within the collagen domain of the hSP-D gene. Fluorescence in situ hybridization of metaphase chromosomes using genomic probes gave selective labeling of 10q22.2-23.1. We speculate that SP-D is encoded at a locus on 10q that includes the genes for surfactant protein A.
Non-nucleosomal packaging of a tandemly repeated DNA sequence at termini of extrachromosomal DNA coding for rRNA in Tetrahymena. (1981)

A tandemly repeated DNA hexanucleotide sequence, 5'C-C-C-C-A-A3', that occurs at the termini of extrachromosomal DNA molecules coding for rRNA (rDNA) in Tetrahymena macronuclei was examined to determine whether it is packaged as nucleosomes. This repeated DNA sequence comprises the terminal few hundred base pairs at each end of the linear rDNA molecules. Digestion of macronuclei with micrococcal nuclease showed that this DNA sequence is protected from digestion but is left, following digestion, as a single but broad size class of DNA fragments several hundred base pairs long, under conditions in which bulk macronuclear DNA and rDNA were digested to fragments that were multiples of approximately 200 base pairs in length. The repeated C-C-C-C-A-A was found protected as fragments longer than the bulk macronuclear DNA digestion products at all times during digestion. Together with putative associated protein(s), this protected DNA was soluble after lysis of micrococcal nuclease-digested macronuclei at low salt concentrations but was insoluble in 0.075--0.2 M KCl, regardless of the extend of digestion. The size and solubility properties of the repeated C-C-C-C-A-A DNA nucleoprotein complex after micrococcal nuclease digestion of macronuclei are clearly distinguishable from those of nucleosomes, and it is inferred that this DNA sequence in macronuclei is packaged in chromatin by proteins other than histones.
Repulsive Guidance Molecule (RGM) Gene Function Is Required for Neural Tube Closure But Not Retinal Topography in the Mouse Visual System (2004)

The establishment of topographic projections in the developing visual system depends on the spatially and temporally controlled expression of axon guidance molecules. In the developing chick tectum, the graded expression of the repulsive guidance molecule (RGM) has been proposed to be involved in controlling the topography of the retinal ganglion cell (RGC) axon termination zones along the anteroposterior axis of the tectum. We now show that there are three mouse proteins homologous to chick RGM displaying similar proteolytic processing but exhibiting differential cell-surface targeting by glycosyl phosphatidylinositol anchor addition. Two members of this gene family (mRGMa and mRGMb) are expressed in complementary patterns in the nervous system, and mRGMa is expressed prominently in the superior colliculus at the time of anteroposterior targeting of RGC axons. The third member of the family (mRGMc) is expressed almost exclusively in skeletal muscles. Functional studies in the mouse reveal a role for mRGMa in controlling cephalic neural tube closure, thus defining an unexpected role for mRGMa in early embryonic development. In contrast, mRGMa mutant mice did not exhibit defects in anteroposterior targeting of RGC axons to their stereotypic termination zones in the superior colliculus.
Mechanism of Protein Modification by Glyoxal and Glycolaldehyde, Reactive Intermediates of the Maillard Reaction (1995)

The role of glyoxal and glycolaldehyde in protein cross-linking and N epsilon-(carboxymethyl)lysine (CML) formation during Maillard reaction under physiological conditions was investigated. Incubation of bovine serum albumin with these reagents lead to rapid formation of C-2-imine cross-links and CML. Initial CML formation rate from glyoxal was not dependent on oxidation, suggesting an intramolecular Cannizzaro reaction. CML formation from glucose/lysine or Amadori product of both was strongly dependent on oxidation. Blocking of Amadori product by boric acid totally suppressed CML formation from Amadori product, but only by 37% in the glucose/lysine system. Trapping of glyoxal with aminoguanidine hardly suppressed CML formation from Amadori product, whereas it blocked 50% of CML production in the glucose/lysine system. While these results would support a significant role for glucose autoxidation in CML formation, the addition of lysine to a glucose/aminoguanidine incubation system catalyzed glyoxal-triazine formation 7-fold, thereby strongly suggesting that glucose autoxidation is not a factor for glyoxal-mediated CML formation. Based on these results, it can be estimated that approximately 50% of the CML forming in a glucose/lysine system originates from oxidation of Amadori product, and 40-50% originates from a pre-Amadori stage largely independent from glucose autoxidation. This step may be related to the so-called Namiki pathway of the Maillard reaction.
A “Turn-On” Fluorescent Sensor for Selective Hg(II) Detection in Aqueous Media Based on Metal-Induced Dye Formation (2006)

A Hg-promoted desulfurization reaction of a thiocarbazone derivative was introduced in the design of a fluorescent sensor for selective Hg(II) detection. Crystal structural and spectroscopic investigations demonstrated the formation of a triazanaphthalene ring and the "turn-on" responding for Hg(II) in aqueous media.
Drug-induced acute angle closure glaucoma (2007)

Most attacks of acute angle closure glaucoma involving pupillary block occur in individuals that are unaware that they have narrow iridocorneal angles. Practitioners using any of the above drugs should be aware of their potential to cause acute angle closure.
Magnetic resonance imaging of gastric cancer in Tff1 knock‐out mice (2003)

In this work, the use of MRI to stage gastric neoplasia in a mouse model of spontaneous gastric cancer is demonstrated. The methodology involves 1) the use of deuterated water ((2)H(2)O) to distend the stomach, and to provide negative contrast between the stomach and the lumen without inducing susceptibility-based field shifts; 2) GlucaGen to minimize motion artifacts that arise from peristalsis; and 3) Gd-DTPA to enhance contrast between the dysplasia/tumor and the normal wall. Initial images are presented from a Tff1 -/- homozygous knock-out model of gastric cancer and a heterozygous C57BL6/J control mouse. There are clear differences between the two types of animals in the MR appearance of the stomach. The distended stomach of the control mouse has a smooth perimeter and a thin wall, and an absence of nodules. The stomach of the Tff1 -/- mouse demonstrates a thickened wall; a jagged, irregular surface; and protruding nodules that are bright after injection of Gd-DTPA.
Cyclophilin–CD147 interactions: a new target for anti-inflammatory therapeutics (2010)

CD147 is a widely expressed plasma membrane protein that has been implicated in a variety of physiological and pathological activities. It is best known for its ability to function as extracellular matrix metalloproteinase inducer (hence the other name for this protein, EMMPRIN), but has also been shown to regulate lymphocyte responsiveness, monocarboxylate transporter expression and spermatogenesis. These functions reflect multiple interacting partners of CD147. Among these CD147-interacting proteins cyclophilins represent a particularly interesting class, both in terms of structural considerations and potential medical implications. CD147 has been shown to function as a signalling receptor for extracellular cyclophilins A and B and to mediate chemotactic activity of cyclophilins towards a variety of immune cells. Recent studies using in vitro and in vivo models have demonstrated a role for cyclophilin-CD147 interactions in the regulation of inflammatory responses in a number of diseases, including acute lung inflammation, rheumatoid arthritis and cardiovascular disease. Agents targeting either CD147 or cyclophilin activity showed significant anti-inflammatory effects in experimental models, suggesting CD147-cyclophilin interactions may be a good target for new anti-inflammatory therapeutics. Here, we review the recent literature on different aspects of cyclophilin-CD147 interactions and their role in inflammatory diseases.
Effect of sulodexide in patients with non-proliferative diabetic retinopathy: diabetic retinopathy sulodexide study (DRESS) (2014)

Oral sulodexide therapy over 12 months improved macular HE in patients with mild-to-moderate NPDR, without leading to detectable adverse events. The study protocol was registered on clinicaltrial.gov under identifier NCT01295775.
Different Human Gut Models Reveal the Distinct Fermentation Patterns of Arabinoxylan versus Inulin (2013)

Different in vitro models have been developed to assess how food compounds affect the human gut microbiota. Using two such models (SHIME(R) and TIM-2), we compared how long-chain arabinoxylan (LC-AX), a wheat-derived potentially prebiotic fiber, and inulin (IN), a well-established prebiotic compound, modulate SCFA production and bifidobacteria composition. While both the SHIME and TIM-2 differ in experimental design, they both demonstrated that LC-AX and IN specifically increased the health-promoting metabolites propionate and butyrate, respectively. Furthermore, LC-AX stimulated Bifidobacterium longum, while IN stimulated other bifidobacteria including Bifidobacterium adolescentis. The SHIME experiment also revealed that effects of LC-AX were more persistent during the 2-week wash-out period. These results confirm a recent in vivo study, during which humanized rats were treated with the same LC-AX/IN. In conclusion, results from different human gut models suggest that, besides IN, LC-AX are promising prebiotic candidates with high specificity toward Bifidobacterium longum and a selective propionate increase.
Photo-induced trimming of coupled ring-resonator filters and delay lines in As_2S_3 chalcogenide glass (2011)

Selective exposure to visible light is used to permanently trim the resonant wavelengths of coupled ring-resonator filters and delay-lines realized on a chalcogenide As2S3 platform. Post-fabrication manipulation of the circuit parameters has proved an effective tool to compensate for technological tolerances, targeting demanding specifications in photonic integrated circuits with no need for always-on power-hungry actuators. The same approach opens a way to realize photonic integrated circuits that can be reconfigured after fabrication to fulfill specific applications.
Crosslinguistic Influence and Multilingualism (2012)

Abstract Crosslinguistic influence is the often preferred term for a phenomenon more commonly known as transfer , which is the influence of one language on another, as witnessed in the language use (both comprehension and production) and other language‐related behavior (e.g., categorization, gesturing, similarity and typicality judgments, reaction times) of both individuals and discourse communities. The former term is often preferred because it more naturally refers to a wider variety of crosslinguistic effects—including the overuse, underuse, and avoidance of language forms, functions, and structures in one language due to the influence of another language, as well as crosslinguistic effects at the level of conceptualization and mental processing—whereas the latter term is often interpreted as the literal transfer of a form, structure, or meaning from a person's knowledge of one language to their use of another (Kellerman &amp; Sharwood Smith, 1986). Nevertheless, the two terms are often used interchangeably to cover the same range of meanings, and this convention will be followed here as well. Interference is another term that has frequently been used to refer to this phenomenon, but its use is naturally limited to the negative effects of crosslinguistic influence, which may represent only a minority portion of the ways in which one language affects another. For convenience, in this entry, crosslinguistic influence as a general phenomenon will be referred to interchangeably as CLI, CLI effects , and transfer .
Positional Isomers of Linear Sodium Dodecyl Benzene Sulfonate:  Solubility, Self-Assembly, and Air/Water Interfacial Activity (2006)

Commercial linear alkyl benzene sulfonates (ABS) are a very important class of anionic surfactants that are employed in a wide variety of applications, especially those involving wetting and detergency. Linear ABS surfactants generally consist of a complex mixture of different chain lengths and positional isomers. This diversity and level of complexity makes it difficult to develop fundamental structure-property correlations for the commercial surfactants. In this work, six monodisperse headgroup positional isomers of sodium para-dodecyl benzene sulfonate (Na-x-DBS, x = 1-6) have been studied. The influence of headgroup position and added electrolyte (NaCl) on the solubility and self-assembly (micellar and vesicular aggregation and lyotropic liquid crystalline phase behavior) in the temperature range from 10 to 90 degrees C have been investigated. Additionally, the air-aqueous solution interfacial adsorption at 25 (no added NaCl) and 50 degrees C (from 0 to 1.0 M added NaCl) has been examined. The observed physicochemical behavior is interpreted in terms of local molecular packing constraints, and in the case of the lyotropic liquid crystalline behavior global aggregate packing constraints as well.
Molecular mechanisms of melanoma metastasis (1997)

The molecular changes associated with the transition of melanoma cells from radial growth phase to vertical growth phase (metastatic phenotype) are not very well defined. Expression of the tyrosine-kinase receptor c-KIT progressively decreases during local tumor growth and invasion of human melanomas. To provide direct evidence that c-KIT plays a role in metastasis of human melanoma, we transfected the c-KIT gene into c-KIT-negative, highly metastatic human melanoma cells and subsequently analyzed their tumorigenic and metastatic potential in nude mice. Enforced c-KIT expression significantly inhibited tumor growth and metastasis. Exposure of c-KIT-positive melanoma cells in vitro and in vivo to stem cell factor (SCF), the ligand for c-KIT, triggered apoptosis of these cells but not of normal melanocytes. These results suggest that the loss of c-KIT receptor may allow malignant melanoma cells to escape SCF/c-KIT-mediated apoptosis, thus contributing to tumor growth and eventually metastasis. The expression of c-KIT and other genes associated with malignant melanoma (such as MCAM/MUC18) is highly regulated by the transcription factor AP-2. The AP-2 protein is not expressed in malignant melanoma cells. Therefore, loss of AP-2 expression might be a crucial event in the progression of human melanoma.
Neuronal Regeneration after Stroke (2003)

Neurogenesis in the mammalian central nervous system was formerly considered to end shortly after birth. We now know that neural stem cells exist not only in the developing nervous system, but also in the nervous systems of all adult mammalian organisms, including humans.1 In the adult brain, new neurons are generated primarily in two regions: the subventricular zone and the subgranular zone1 of the hippocampal dentate gyrus. This neurogenesis occurs under normal conditions, and the generation of new neurons can increase under pathologic conditions, such as the brain ischemia that typifies a stroke.2 Whether newly formed neurons migrate to the . . .
Idoxifene: report of a phase I study in patients with metastatic breast cancer. (1995)

Idoxifene, a novel antiestrogen with reduced estrogenic activity when compared to tamoxifen, has been given to 20 women with metastatic breast cancer, 19 of whom had received tamoxifen previously, in doses between 10-60 mg. Idoxifene had an initial half-life of 15 h and a terminal half-life of 23.3 days. At a maintenance dose of 20 mg, a mean steady-state level of 173.5 ng/ml was achieved. Significant falls in luteinizing hormone and follicle-stimulating hormone were seen, but the falls were not dose related. Idoxifene was well tolerated, with 11 patients complaining of mild symptoms similar to those seen with tamoxifen. Fourteen patients continued idoxifene therapy for 1-56 weeks; 4 patients showed stabilization of disease for 6-56 weeks and 2 patients showed a partial response.
A Regression Approach to Music Emotion Recognition (2008)

Content-based retrieval has emerged in the face of content explosion as a promising approach to information access. In this paper, we focus on the challenging issue of recognizing the emotion content of music signals, or music emotion recognition (MER). Specifically, we formulate MER as a regression problem to predict the arousal and valence values (AV values) of each music sample directly. Associated with the AV values, each music sample becomes a point in the arousal-valence plane, so the users can efficiently retrieve the music sample by specifying a desired point in the emotion plane. Because no categorical taxonomy is used, the regression approach is free of the ambiguity inherent to conventional categorical approaches. To improve the performance, we apply principal component analysis to reduce the correlation between arousal and valence, and RReliefF to select important features. An extensive performance study is conducted to evaluate the accuracy of the regression approach for predicting AV values. The best performance evaluated in terms of the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">R</i> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> statistics reaches 58.3% for arousal and 28.1% for valence by employing support vector machine as the regressor. We also apply the regression approach to detect the emotion variation within a music selection and find the prediction accuracy superior to existing works. A group-wise MER scheme is also developed to address the subjectivity issue of emotion perception.
1,3‐Dipolar Cycloadditions of Azides and Alkynes: A Universal Ligation Tool in Polymer and Materials Science (2007)

In 2001, Sharpless and co-workers introduced "click" chemistry, a new approach in organic synthesis that involves a handful of almost perfect chemical reactions. Among these carefully selected reactions, Huisgen 1,3-dipolar cycloadditions were shown to be the most effective and versatile and thus became the prime example of click chemistry. Hence, these long-neglected reactions were suddenly re-established in organic synthesis and, in particular, have gained popularity in materials science. The number of publications dealing with click chemistry has grown exponentially over the last two years. The Minireview discusses whether click chemistry is a miracle tool or an ephemeral trend.
Cell-penetrating peptides as transporters for morpholino oligomers: effects of amino acid composition on intracellular delivery and cytotoxicity (2007)

Arginine-rich cell-penetrating peptides (CPPs) are promising transporters for intracellular delivery of antisense morpholino oligomers (PMO). Here, we determined the effect of L-arginine, D-arginine and non-alpha amino acids on cellular uptake, splice-correction activity, cellular toxicity and serum binding for 24 CPP-PMOs. Insertion of 6-aminohexanoic acid (X) or beta-alanine (B) residues into oligoarginine R8 decreased the cellular uptake but increased the splice-correction activity of the resulting compound, with a greater increase for the sequences containing more X residues. Cellular toxicity was not observed for any of the conjugates up to 10 microM. Up to 60 microM, only the conjugates with > or = 5 Xs exhibited time- and concentration-dependent toxicity. Substitution of L-arginine with D-arginine did not increase uptake or splice-correction activity. High concentration of serum significantly decreased the uptake and splice-correction activity of oligoarginine conjugates, but had much less effect on the conjugates containing X or B. In summary, incorporation of X/B into oligoarginine enhanced the antisense activity and serum-binding profile of CPP-PMO. Toxicity of X/B-containing conjugates was affected by the number of Xs, treatment time and concentration. More active, stable and less toxic CPPs can be designed by optimizing the position and number of R, D-R, X and B residues.
Molecular Chaperones—Cellular Machines for Protein Folding (2002)

Proteins are linear polymers synthesized by ribosomes from activated amino acids. The product of this biosynthetic process is a polypeptide chain, which has to adopt the unique three-dimensional structure required for its function in the cell. In 1972, Christian Anfinsen was awarded the Nobel Prize for Chemistry for showing that this folding process is autonomous in that it does not require any additional factors or input of energy. Based on in vitro experiments with purified proteins, it was suggested that the correct three-dimensional structure can form spontaneously in vivo once the newly synthesized protein leaves the ribosome. Furthermore, proteins were assumed to maintain their native conformation until they were degraded by specific enzymes. In the last decade this view of cellular protein folding has changed considerably. It has become clear that a complicated and sophisticated machinery of proteins exists which assists protein folding and allows the functional state of proteins to be maintained under conditions in which they would normally unfold and aggregate. These proteins are collectively called molecular chaperones, because, like their human counterparts, they prevent unwanted interactions between their immature clients. In this review, we discuss the principal features of this peculiar class of proteins, their structure-function relationships, and the underlying molecular mechanisms.