gebhart/patrepeval huggingface dataset:
The Genomic Region Encompassing the Nephropathic Cystinosis Gene (CTNS): Complete Sequencing of a 200-kb Segment and Discovery of a Novel Gene within the Common Cystinosis-Causing Deletion (2000)

Nephropathic cystinosis is an autosomal recessive disorder caused by the defective transport of cystine out of lysosomes. Recently, the causative gene (CTNS) was identified and presumed to encode an integral membrane protein called cystinosin. Many of the disease-associated mutations in CTNS are deletions, including one >55 kb in size that represents the most common cystinosis allele encountered to date. In an effort to determine the precise genomic organization of CTNS and to gain sequence-based insight about the DNA within and flanking cystinosis-associated deletions, we mapped and sequenced the region of human chromosome 17p13 encompassing CTNS. Specifically, a bacterial artificial chromosome (BAC)-based physical map spanning CTNS was constructed by sequence-tagged site (STS)-content mapping. The resulting BAC contig provided the relative order of 43 STSs. Two overlapping BACs, which together contain all of the CTNS exons as well as extensive amounts of flanking DNA, were selected and subjected to shotgun sequencing. A total of 200,237 bp of contiguous, high-accuracy sequence was generated. Analysis of the resulting data revealed a number of interesting features about this genomic region, including the long-range organization of CTNS, insight about the breakpoints and intervening DNA associated with the common cystinosis-causing deletion, and structural information about five genes neighboring CTNS (human ortholog of rat vanilloid receptor subtype 1 gene, CARKL, TIP-1, P2X5, and HUMINAE). In particular, sequence analysis detected the presence of a novel gene (CARKL) residing within the most common cystinosis-causing deletion. This gene encodes a previously unknown protein that is predicted to function as a carbohydrate kinase. Interestingly, both CTNS and CARKL are absent in nearly half of all cystinosis patients (i.e., those homozygous for the common deletion). [The sequence data described in this paper have been submitted to the GenBank data library under accession nos. AF168787 and AF163573.]
Revisiting Batch Normalization For Practical Domain Adaptation (2016)

Deep neural networks (DNN) have shown unprecedented success in various computer vision applications such as image classification and object detection. However, it is still a common annoyance during the training phase, that one has to prepare at least thousands of labeled images to fine-tune a network to a specific domain. Recent study (Tommasi et al. 2015) shows that a DNN has strong dependency towards the training dataset, and the learned features cannot be easily transferred to a different but relevant task without fine-tuning. In this paper, we propose a simple yet powerful remedy, called Adaptive Batch Normalization (AdaBN) to increase the generalization ability of a DNN. By modulating the statistics in all Batch Normalization layers across the network, our approach achieves deep adaptation effect for domain adaptation tasks. In contrary to other deep learning domain adaptation methods, our method does not require additional components, and is parameter-free. It archives state-of-the-art performance despite its surprising simplicity. Furthermore, we demonstrate that our method is complementary with other existing methods. Combining AdaBN with existing domain adaptation treatments may further improve model performance.
FUT2 Nonsecretor Status Links Type 1 Diabetes Susceptibility and Resistance to Infection (2011)

Our findings linking FUT2 and type 1 diabetes highlight the intriguing relationship between host resistance to infections and susceptibility to autoimmune disease.
Prognostic Significance of Occult Metastases Detected by Sentinel Lymphadenectomy and Reverse Transcriptase–Polymerase Chain Reaction in Early-Stage Melanoma Patients (1999)

H&E staining and IHC underestimate the true incidence of melanoma metastases. MM expression in the SN more accurately reflects melanoma micrometastases and is also a more powerful predictor of disease relapse than are H&E staining and IHC alone.
Wave field synthesis of a sound field described by spherical harmonics expansion coefficients (2012)

Near-field compensated higher order Ambisonics (NFC-HOA) and wave field synthesis (WFS) constitute the two best-known analytic sound field synthesis methods. While WFS is typically used for the synthesis of virtual sound scenes, NFC-HOA is typically employed in order to synthesize sound fields that have been captured with appropriate microphone arrays. Such recorded sound fields are essentially represented by the coefficients of the underlying surface spherical harmonics expansion. A sound field described by such coefficients cannot be straightforwardly synthesized in WFS. This is a consequence of the fact that, unlike in NFC-HOA, it is critical in WFS to carefully select those loudspeakers that contribute to the synthesis of a given sound source in a sound field under consideration. In order to enable such a secondary source selection, it is proposed to employ the well-known concept of decomposing the sound field under consideration into a continuum of plane waves, for which the secondary source selection is straightforward. The plane wave representation is projected onto the horizontal plane and a closed form expression of the secondary source driving signals for horizontal WFS systems of arbitrary convex shape is derived.
Deaths related to iodinated contrast media reported spontaneously to the U.S. Food and Drug Administration, 1978-1994: effect of the availability of low-osmolality contrast media. (1997)

Despite the availability of LOCM in the United States, data for 1978-1994 do not show a marked decrease in contrast medium-related deaths. Since 1990, more deaths have been associated with LOCM than with conventional contrast media. Although these data have substantial limitations, they shed some light on contrast medium use and safety.
Identification of mutations in regions corresponding to the two putative nucleotide (ATP)-binding folds of the cystic fibrosis gene. (1990)

Additional mutations in the cystic fibrosis (CF) gene were identified in the regions corresponding to the two putative nucleotide (ATP)-binding folds (NBFs) of the predicted polypeptide. The patient cohort included 46 Canadian CF families with well-characterized DNA marker haplotypes spanning the disease locus and several other families from Israel. Eleven mutations were found in the first NBF, 2 were found in the second NBF, but none was found in the R-domain. Seven of the mutations were of the missense type affecting some of the highly conserved amino acid residues in the first NBF; 3 were nonsense mutations; 2 would probably affect mRNA splicing; 2 corresponded to small deletions, including another 3-base-pair deletion different from the major mutation (delta F508), which could account for 70% of the CF chromosomes in the population. Nine of these mutations accounted for 12 of the 31 non-delta F508 CF chromosomes in the Canadian families. The highly heterogeneous nature of the remaining CF mutations provides important insights into the structure and function of the protein, but it also suggests that DNA-based genetic screening for CF carrier status will not be straightforward.
Highly reactive organolanthanides. Synthesis, chemistry, and structures of 4f hydrocarbyls and hydrides with chelating bis(polymethylcyclopentadienyl) ligands (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHighly reactive organolanthanides. Synthesis, chemistry, and structures of 4f hydrocarbyls and hydrides with chelating bis(polymethylcyclopentadienyl) ligandsGerald Jeske, Laurel E. Schock, Paul N. Swepston, Herbert Schumann, and Tobin J. MarksCite this: J. Am. Chem. Soc. 1985, 107, 26, 8103–8110Publication Date (Print):December 1, 1985Publication History Published online1 May 2002Published inissue 1 December 1985https://pubs.acs.org/doi/10.1021/ja00312a051https://doi.org/10.1021/ja00312a051research-articleACS PublicationsRequest reuse permissionsArticle Views864Altmetric-Citations325LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Nasal eosinophilia: an indicator of eosinophilic inflammation in asthma (2010)

This study brings further evidence that upper airway diseases are an important component of the asthma syndrome. Furthermore, monitoring of nasal eosinophilia by quantitative cytology may be useful as a surrogate of sputum cytology in as a component of composite measurement for determining airway inflammation.
The Extent of Linkage Disequilibrium and Haplotype Sharing Around a Polymorphic Site (2003)

Various expressions related to the length of a conserved haplotype around a polymorphism of known frequency are derived. We obtain exact expressions for the probability that no recombination has occurred in a sample or subsample. We obtain an approximation for the probability that no recombination that could give rise to a detectable recombination event (through the four-gamete test) has occurred. The probabilities can be used to obtain approximate distributions for the length of variously defined haplotypes around a polymorphic site. The implications of our results for data analysis, and in particular for detecting selection, are discussed.
DIVERGENT ROLES FOR FcRECEPTORS AND COMPLEMENT IN VIVO (1998)

Recent results obtained in mice deficient in either FcRs or complement have revealed distinct functions for these two classes of molecules. While each is capable of interacting with antibodies or immune complexes, the two systems mediate distinct biological effector responses. Complement-deficient mice are unable to mediate innate immune responses to several bacterial pathogens and bacterial toxins, yet respond normally to the presence of cytotoxic antibodies and pathogenic immune complexes. In contrast, FcR-deficient mice display no defects in innate immunity or susceptibility to a variety of pathogens, yet they are unable to mediate inflammatory responses to cytotoxic IgG antibodies or IgG immune complexes, despite the presence of a normal complement system. These results lead to the surprising conclusion that these two systems have evolved distinct functions in host immunity, with complement and its receptors mediating the interaction of natural antibodies (IgM) with pathogens to effect protection, while FcRs couple the interaction of IgG antibodies to effector cells to trigger inflammatory sequelae. These results necessitate a fundamental revision of the role of these antibody-binding systems in the immune response.
The Binding Site of Sodium in the Gramicidin A Channel (2007)

The available information concerning the structure and location of the main binding site for sodium in the gramicidin A channel is reviewed and discussed. Results from molecular dynamics simulations using an atomic model of the channel embedded in a lipid bilayer are compared with experimental observations. The combined information from experiment and simulation suggests that the main binding sites for sodium are near the channel's mouth, approximately 9.2 A from the centre of the dimer channel, although the motion along the axis could be as large as 1 to 2 A. In the binding site, the sodium ion is lying off axis, making contact with two carbonyl oxygens and two single-file water molecules. The main channel ligand is provided by the carbonyl group of the Leu10-Trp11 peptide linkage, which exhibits the largest deflection from the ion-free channel structure.
Imparting Multivalency to a Bifunctional Chelator: A Scaffold Design for Targeted PET Imaging Probes (2009)

Two are better than one: Multivalent scaffolds for targeted PET imaging probes not only feature chelators that form stable and neutral complexes with a radiometal but also contain functional groups for presentation of multiple targeting molecules. A bivalent scaffold was synthesized and coupled with a targeting ligand to afford the probe, which was used to efficiently image tumors in vivo (see picture). Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Contribution of fibrin stabilization to clot strength. Supplementation of factor XIII-deficient plasma with the purified zymogen. (1983)

The contribution of fibrin stabilization to clot strength, measured as the static elastic modulus, was evaluated in human plasma by two independent procedures. In the first approach, amine inhibitors of fibrin stabilization were examined for their effects on the rigidity of normal plasma clots. It is a unique property of these inhibitors that they do not interfere with the reversible aggregation of fibrin molecules, i.e., do not delay clotting time, but selectively prevent only the formation of gamma-glutamyl-epsilon-lysine protein-to-protein linkages. Though the compounds tested were of different chemical structures and potencies, a fivefold reduction in clot strength was obtained in each instance. This value of 20% of normal seems to correspond to the rigidity of the Factor XIII-deficient plasma clot because, as demonstrated by the second approach, when a plasma specimen that genetically lacked the fibrin stabilizing factor was supplemented by the addition of measured amounts of the purified zymogen, a fivefold increase in clot strength could be achieved. The described procedure of evaluating Factor XIII in terms of correcting the elastic modulus of a deficient plasma clot is considered an important assay for the functional competence of purified preparations of the zymogen for the purpose of therapeutic application.
Parenteral and enteral metabolism of anaplerotic triheptanoin in normal rats (2006)

A new chronic treatment for inherited disorders of long-chain fatty acid oxidation involves administering up to one-third of dietary calories as triheptanoin, a medium-odd-chain triglyceride (Roe CR, Sweetman L, Roe DS, David F, and Brunengraber H. J Clin Invest 110: 259-269, 2002). Heptanoate and C(5)-ketone bodies derived from its partial oxidation in liver are precursors of anaplerotic propionyl-CoA in peripheral tissues. It was hypothesized that increasing anaplerosis in peripheral tissues would boost energy production. In the present study, we tested the potential of a triheptanoin emulsion as an intravenous nutrient. Normal rats were infused with triheptanoin intravenously or intraduodenally at up to 40% of caloric requirement. The blood concentration ratio (heptanoate/C(5)-ketone bodies) was high with intravenous and low with intraduodenal triheptanoin infusion. During intravenous infusion of triheptanoin, lipolysis was stimulated but appeared compensated by fatty acid reesterification. During intraduodenal infusion of triheptanoin, lipolysis was not stimulated. Our data support the hypothesis that intravenous triheptanoin could be used to treat decompensated patients with long-chain fatty acid oxidation disorders.
Pharmacological Activation of Liver X Receptors Promotes Reverse Cholesterol Transport In Vivo (2005)

These results demonstrate that administration of the LXR agonist GW3965 increases the rate of RCT from macrophages to feces in vivo.
Exploring interactions between rat hepatocytes and nonparenchymal cells using gene expression profiling (2004)

Cocultivation of primary hepatocytes with a plethora of nonparenchymal cells (from within and outside the liver) has been shown to support hepatic functions in vitro. Despite significant investigation into this phenomenon, the molecular mechanism underlying epithelial-nonparenchymal interactions in hepatocyte cocultures remains poorly understood. In this study, we present a functional genomic approach utilizing gene expression profiling to isolate molecular mediators potentially involved in induction of liver-specific functions by nonparenchymal cells. Specifically, primary rat hepatocytes were cocultivated with closely related murine fibroblast cell types (3T3-J2, NIH-3T3, mouse embryonic fibroblasts) to allow their classification as "high," "medium," or "low" inducers of hepatic functions. These functional responses were correlated with fibroblast gene expression profiles obtained using Affymetrix GeneChips. Microarray data analysis provided us with 17 functionally characterized candidate genes in the cell communication category (cell surface, extracellular matrix, secreted factors) that may be involved in induction of hepatic functions. Further analysis using various databases (i.e., PubMed, GenBank) facilitated prioritization of the candidates for functional characterization. We experimentally validated the potential role of two candidates in our coculture model. The cell surface protein, neural cadherin (N-cadherin), was localized to hepatocyte-fibroblast junctions, while adsorbed decorin up-regulated hepatic functions in pure cultures as well as cocultures with low-inducing fibroblasts. In the future, identifying mediators of hepatocyte differentiation may have implications for both fundamental hepatology and cell-based therapies (e.g., bioartificial liver devices). In conclusion, the functional genomic approach presented in this study may be utilized to investigate mechanisms of cell-cell interaction in a variety of tissues and disease states.
Chemistry, Physical Nature, and Rheology of Aqueous Stimulation Foams (1981)

Abstract Laboratory equipment has been designed specifically to study effectively the microscopic structure of flowing foams at high pressures. In addition, application of foaming-agent optimization techniques to design stable foams at varying foam qualities is demonstrated at high pressures – i.e., 500 to 2,000 psig (3448 to 13 792 kPa). Capillary viscosity data for these foams is established and correlated with a video-photomicroscopic study of the flowing foam and their designated bubble qualities. Foaming-agent screening information from the tests is provided indicating the foaming-agent generic chemistry that allows optimal foam stability under high-pressure conditions.
Population Differences in the Human Functional Olfactory Repertoire (2003)

Olfactory receptors (OR) constitute the molecular basis for the sense of smell. They are encoded by a large multigene family that in humans includes approximately 400 functional genes and approximately 600 putative pseudogenes, distributed on all but two chromosomes. To examine the ethnogeographic variability in the functional chemosensory repertoire, we resequenced 32 OR loci reported to contain a single coding region disruption in seven Caucasians and seven Pygmies. Thirteen of the 32 OR loci were found to have an interrupted coding region in all 28 alleles sampled, seven had an intact form in all the individuals examined, and 12 were polymorphic, segregating both the intact and the null variants. Among the latter loci, the frequency of the null allele was higher in Caucasians than in Pygmies, suggesting that African populations may have a larger repertoire of functional OR genes. Interestingly, when analyzing the entire OR coding regions, we find an excess of high-frequency derived alleles at many loci in the Caucasian sample but less so in the Pygmy sample. Our observations are unlikely to be accounted for by simple demographic models but may be explained by positive selection acting on OR loci in Caucasians.
The Forkhead Box m1b transcription factor is essential for hepatocyte DNA replication and mitosis during mouse liver regeneration (2002)

The Forkhead Box (Fox) proteins are an extensive family of transcription factors that shares homology in the winged helix DNA-binding domain and whose members play essential roles in cellular proliferation, differentiation, transformation, longevity, and metabolic homeostasis. Liver regeneration studies with transgenic mice demonstrated that FoxM1B regulates the onset of hepatocyte DNA replication and mitosis by stimulating expression of cell cycle genes. Here, we demonstrate that albumin-promoter-driven Cre recombinase-mediated hepatocyte-specific deletion of the Foxm1b Floxed (fl) targeted allele resulted in significant reduction in hepatocyte DNA replication and inhibition of mitosis after partial hepatectomy. Reduced DNA replication in regenerating Foxm1b(-/-) hepatocytes was associated with sustained increase in nuclear staining of the cyclin-dependent kinase (Cdk) inhibitor p21(Cip1) (p21) protein between 24 and 40 h after partial hepatectomy. Furthermore, increased nuclear p21 levels and reduced expression of Cdc25A phosphatase coincided with decreases in Cdk2 activation and hepatocyte progression into S-phase. Moreover, the significant reduction in hepatocyte mitosis was associated with diminished mRNA levels and nuclear expression of Cdc25B phosphatase and delayed accumulation of cyclin B1 protein, which is required for Cdk1 activation and entry into mitosis. Cotransfection studies demonstrate that FoxM1B protein directly activated transcription of the Cdc25B promoter region. Our present study shows that the mammalian Foxm1b transcription factor regulates expression of cell cycle proteins essential for hepatocyte entry into DNA replication and mitosis.