gebhart/patrepeval huggingface dataset:
Bending insensitive, highly Yb-Doped LMA triple-clad fiber for nearly diffraction-limited laser output (2006)

The new highly rare-earth doped triple-clad fiber design comprises a first clad next to the core of the well-known double-clad design. The added clad allows to reduce and to better control the core effective numerical aperture for achieving a highly doped large mode area amplifying fiber with a very low numerical aperture (~0.07). The triple-clad design is optimized to obtain a nearly bending insensitive fiber output while keeping excellent beam quality through proper ytterbium doping. The high ytterbium concentration allows for very high gain from a short (~1 m) fiber length which, in many applications, is required to prevent the onset of nonlinear effects such as stimulated Brillouin scattering. A polarization-maintaining 22-&#956;m core Yb-doped triple-clad fiber was first tested. A laser slope efficiency of up to 86% with a polarization extinction ratio exceeding 24 dB and a M2 output beam quality factor below 1.1, for both laser and amplifier configurations, have been measured. Moreover, beam quality and output power were not significantly affected when coiling the fiber down to a 1.2 cm diameter, thus showing the optical robustness of the triple clad fiber design and offering the opportunity to build very compact high power fiber amplifiers and laser sources.
Enhanced sensitivity of PTEN-deficient tumors to inhibition of FRAP/mTOR (2001)

Recent evidence places the FRAP/mTOR kinase downstream of the phosphatidyl inositol 3-kinase/Akt-signaling pathway, which is up-regulated in multiple cancers because of loss of the PTEN tumor suppressor gene. We performed biological and biochemical studies to determine whether PTEN-deficient cancer cells are sensitive to pharmacologic inhibition of FRAP/mTOR by using the rapamycin derivative CCI-779. In vitro and in vivo studies of isogenic PTEN(+/+) and PTEN(-/-) mouse cells as well as human cancer cells with defined PTEN status showed that the growth of PTEN null cells was blocked preferentially by pharmacologic FRAP/mTOR inhibition. Enhanced tumor growth caused by constitutive activation of Akt in PTEN(+/+) cells also was reversed by CCI-779 treatment, indicating that FRAP/mTOR functions downstream of Akt in tumorigenesis. Loss of PTEN correlated with increased S6 kinase activity and phosphorylation of ribosomal S6 protein, providing evidence for activation of the FRAP/mTOR pathway in these cells. Differential sensitivity to CCI-779 was not explained by differences in biochemical blockade of the FRAP/mTOR pathway, because S6 phosphorylation was inhibited in sensitive and resistant cell lines. These results provide rationale for testing FRAP/mTOR inhibitors in PTEN null human cancers.
The uridine in “U-turn”: Contributions to tRNA-ribosomal binding (1999)

"U-turns" represent an important class of structural motifs in the RNA world, wherein a uridine is involved in an abrupt change in the direction of the polynucleotide backbone. In the crystal structure of yeast tRNAPhe, the invariant uridine at position 33 (U33), adjacent to the anticodon, stabilizes the exemplar U-turn with three non-Watson-Crick interactions: hydrogen bonding of the 2'-OH to N7 of A35 and the N3-H to A36-phosphate, and stacking between C32 and A35-phosphate. The functional importance of each noncanonical interaction was determined by assaying the ribosomal binding affinities of tRNAPhe anticodon stem and loop domains (ASLs) with substitutions at U33. An unsubstituted ASL bound 30S ribosomal subunits with an affinity (Kd = 140+/-50 nM) comparable to that of native yeast tRNAPhe (Kd = 100+/-20 nM). However, the binding affinities of ASLs with dU-33 (no 2'-OH) and C-33 (no N3-H) were significantly reduced (2,930+/-140 nM and 2,190+/-300 nM, respectively). Surprisingly, the ASL with N3-methyluridine-33 (no N3-H) bound ribosomes with a high affinity (Kd = 220+/-20 nM). In contrast, ASLs constructed with position 33 uridine analogs in nonstacking, nonnative, and constrained conformations, dihydrouridine (C2'-endo), 6-methyluridine (syn) and 2'O-methyluridine (C3'-endo) had almost undetectable binding. The inability of ASLs with 6-methyluridine-33 and 2'O-methyluridine-33 to bind ribosomes was not attributable to any thermal instability of the RNAs. These results demonstrate that proton donations by the N3-H and 2'OH groups of U33 are not absolutely required for ribosomal binding. Rather, the results suggest that the overall uridine conformation, including a dynamic (C3'-endo > C2'-endo) sugar pucker, anti conformation, and ability of uracil to stack between C32 and A35-phosphate, are the contributing factors to a functional U-turn.
The Role of Human Immunodeficiency Virus Type 1 Envelope Glycoproteins in Virus Infection (1995)

Enveloped viruses enter cells by a two-step process. The first step involves the binding of a viral surface protein to receptors on the plasma membrane of the host cell. After receptor binding, a membrane fusion reaction takes place between the lipid bilayer of the viral envelope and host cell membranes. This fusion reaction can occur either at the plasma membrane or in acidic endosomes following receptor-mediated endocytosis. In either case, the membrane fusion reaction delivers the viral nucleocapsid into the host cytoplasm, allowing the infection to proceed.
Inception-v4, Inception-ResNet and the Impact of Residual Connections on Learning (2017)

Very deep convolutional networks have been central to the largest advances in image recognition performance in recent years. One example is the Inception architecture that has been shown to achieve very good performance at relatively low computational cost. Recently, the introduction of residual connections in conjunction with a more traditional architecture has yielded state-of-the-art performance in the 2015 ILSVRC challenge; its performance was similar to the latest generation Inception-v3 network. This raises the question: Are there any benefits to combining Inception architectures with residual connections? Here we give clear empirical evidence that training with residual connections accelerates the training of Inception networks significantly. There is also some evidence of residual Inception networks outperforming similarly expensive Inception networks without residual connections by a thin margin. We also present several new streamlined architectures for both residual and non-residual Inception networks. These variations improve the single-frame recognition performance on the ILSVRC 2012 classification task significantly. We further demonstrate how proper activation scaling stabilizes the training of very wide residual Inception networks. With an ensemble of three residual and one Inception-v4 networks, we achieve 3.08% top-5 error on the test set of the ImageNet classification (CLS) challenge.
Pre-organization induced synthesis of a crossed alkene-bridged nisin Z DE-ring mimic by ring-closing metathesis (2004)

An alkene-bridged mimic of the complex DE-bisthioether-ring system of the antibiotic nisin was prepared in one step from the linear precursor.
Phylogenetic Distribution of Potential Cellulases in Bacteria (2012)

Many microorganisms contain cellulases that are important for plant cell wall degradation and overall soil ecosystem functioning. At present, we have extensive biochemical knowledge of cellulases but little is known about the phylogenetic distribution of these enzymes. To address this, we analyzed the distribution of 21,985 genes encoding proteins related to cellulose utilization in 5,123 sequenced bacterial genomes. First, we identified the distribution of glycoside hydrolases involved in cellulose utilization and synthesis at different taxonomic levels, from the phylum to the strain. Cellulose degradation/utilization capabilities appeared in nearly all major groups and resulted in strains displaying various enzyme gene combinations. Potential cellulose degraders, having both cellulases and β-glucosidases, constituted 24% of all genomes whereas potential opportunistic strains, having β-glucosidases only, accounted for 56%. Finally, 20% of the bacteria have no relevant enzymes and do not rely on cellulose utilization. The latter group was primarily connected to specific bacterial lifestyles like autotrophy and parasitism. Cellulose degraders, as well as opportunists, have multiple enzymes with similar functions. However, the potential degraders systematically harbor about twice more β-glucosidases than their potential opportunistic relatives. Although scattered, the distribution of functional types, in bacterial lineages, is not random but mostly follows a Brownian motion evolution model. Degraders form clusters of relatives at the species level, whereas opportunists are clustered at the genus level. This information can form a mechanistic basis for the linking of changes in microbial community composition to soil ecosystem processes.
上位 德里克·罗斯 (2011)

说起来很巧,这是我今年第二次写罗斯翻看旧杂志,有时候真是件很有意思的事。当新闻过时,一些话也变成了事实——有时你成了预言家,而有些话却不幸成了狗屎,也许这就是杂志的魅力所在吧!它定格的只是一个时刻,但值得你回味的远远不只如此。看看我之前写罗斯的文章,我很幸运自己的话没有成为狗屎。没错,罗斯朝着我的预期在前进,不过当赛季即将结束,猛回头再看一眼罗斯,他早已把我给他定格的那条线甩得太远。我承认我太小看他了,我说罗斯会成为公牛合格的领袖,他不仅做到了,还成为本赛季MVP的最大热门;我还说公牛会扰乱东部的格局,他也做到了,但他们已经是东部第一（和凯
THE DEVELOPMENT OF THE GUIDELINE VDI 2221 - THE CHANGE OF DIRECTION (2006)

Design guidelines, especially the VDI 2221, have been developed over the past 50 years. Analyzing this development gives interesting insights into the changing character of the design guidelines. Special insights are obtained concerning the intention and direction of the guidelines. These insights give, on the one hand, explanations for the still reserved application and acceptance of design guidelines, and on the other hand, evidence of their improvement. This paper aims to give an overview of the development of the design guidelines in German-speaking lands, point out certain aspects of changes (aim, advice, instructions, terminology, and description) and provide ideas about the consequences and potentials of these changes.
Transmission of Human Immunodeficiency Virus (HIV) by Blood Transfusions Screened as Negative for HIV Antibody (1988)

Since early 1985, blood donations in the United States have been screened for antibody to human immunodeficiency virus (HIV). To identify instances of HIV transmission by antibody-negative donations, we investigated 13 persons seropositive for HIV who had received blood from 7 donors who were screened as negative for HIV antibody at the time of donation. Twelve of the 13 recipients had no identifiable risk factors for HIV infection other than the transfusions they had received. On evaluation 8 to 20 months after transfusion, HIV-related illnesses had developed in three recipients, and the acquired immunodeficiency syndrome had developed in one. All seven donors were found to be infected with HIV. On interview, six reported a risk factor for HIV infection, and five had engaged in high-risk activities or had had an illness suggestive of acute retroviral syndrome within the four months preceding their HIV-seronegative donation. Thus, these donors had apparently been infected only recently, and so were negative at the time of blood donation according to available antibody tests. We conclude that there is a small but identifiable risk of HIV infection for recipients of screened blood. To minimize this risk, the reasons for deferral of donation need to be communicated more effectively to blood donors who are at high risk of HIV infection, and new assays that detect HIV infection earlier should be evaluated for their effectiveness in screening donated blood.
Signaling through human killer cell activating receptors triggers tyrosine phosphorylation of an associated protein complex (1998)

Our understanding of the biology of human natural killer (NK) cells has significantly advanced in recent years upon identification of a family of NK cell-expressed genes that encode killer cell inhibitory receptors (KIR). Individual KIR can selectively bind various HLA class I allotypes and consequently transduce inhibitory signals that block NK cell lysis of ligand-bearing target cells. A distinct subset of related and linked genes express truncated versions of KIR that are otherwise highly homologous in amino acid sequence. Interestingly, these receptors appear to transmit stimulatory signals into NK cells and have been termed killer cell activating receptors (KAR). In this report, we demonstrate that recognition of HLA-Cw3 by the p50 KAR, NKAT8, can potentiate the cytotoxic response of appropriate NK cell clones. Specific cross-linking of this KAR with a monoclonal antibody resulted in intracellular calcium mobilization, protein tyrosine phosphorylation, and phosphorylation of the MAP kinases, ERK1 and ERK2. In addition, we identified a KAR-associated disulfide-linked dimer of a 13-kDa protein that was absent in the Jurkat T cell line and is predicted to participate in these activation signaling events. Upon treatment of NK cells with pervanadate, the disulfide-linked p13 and additional proteins of 25, 30, 37 and 50-95 kDa were identified as KAR-associated tyrosine phosphoproteins. Importantly, p13 was inducibly tyrosine phosphorylated upon cross-linking of NKAT8, which strongly suggests that the associated p13 provides KAR with appropriate cytoplasmic structure to couple with tyrosine kinase-mediated signaling effectors.
TAILOR: a record linkage toolbox (2003)

Data cleaning is a vital process that ensures the quality of data stored in real-world databases. Data cleaning problems are frequently encountered in many research areas, such as knowledge discovery in databases, data warehousing, system integration and e-services. The process of identifying the record pairs that represent the same entity (duplicate records), commonly known as record linkage, is one of the essential elements of data cleaning. In this paper, we address the record linkage problem by adopting a machine learning approach. Three models are proposed and are analyzed empirically. Since no existing model, including those proposed in this paper, has been proved to be superior, we have developed an interactive record linkage toolbox named TAILOR (backwards acronym for "RecOrd LInkAge Toolbox"). Users of TAILOR can build their own record linkage models by tuning system parameters and by plugging in in-house-developed and public-domain tools. The proposed toolbox serves as a framework for the record linkage process, and is designed in an extensible way to interface with existing and future record linkage models. We have conducted an extensive experimental study to evaluate our proposed models using not only synthetic but also real data. The results show that the proposed machine-learning record linkage models outperform the existing ones both in accuracy and in performance.
Transportation Utility Fees: The Newest Revenue Enhancement (1991)

Abstract The intense pressure upon local governments to raise revenues to compensate for deficiencies and support new developmenthas spawned innovative financing techniques. The property tax, the traditional basefor local government financing, is playing a proportionally lesser role and, instead, impact and user fees are becoming more popular. The quest for funding has inspired the creation of a variant of a user fee—the transportation utility fee.
The growth of vibrissa dermal papilla cells in vitro (1981)

Journal Article The growth of vibrissa dermal papilla cells in vitro Get access C. JAHODA, C. JAHODA Department of Biological Sciences, University of Dundee, Dundee, Scotland Search for other works by this author on: Oxford Academic Google Scholar R.F. OLIVER R.F. OLIVER Department of Biological Sciences, University of Dundee, Dundee, Scotland Search for other works by this author on: Oxford Academic Google Scholar British Journal of Dermatology, Volume 105, Issue 6, 1 December 1981, Pages 623–627, https://doi.org/10.1111/j.1365-2133.1981.tb00971.x Published: 01 December 1981 Article history Accepted: 04 February 1981 Published: 01 December 1981
Genetic Incorporation of Human Metallothionein into the Adenovirus Protein IX for Non-Invasive SPECT Imaging (2011)

As the limits of existing treatments for cancer are recognized, clearly novel therapies must be considered for successful treatment; cancer therapy using adenovirus vectors is a promising strategy. However tracking the biodistribution of adenovirus vectors in vivo is limited to invasive procedures such as biopsies, which are error prone, non-quantitative, and do not give a full representation of the pharmacokinetics involved. Current non-invasive imaging strategies using reporter gene expression have been applied to analyze adenoviral vectors. The major drawback to approaches that tag viruses with reporter genes is that these systems require initial viral infection and subsequent cellular expression of a reporter gene to allow non-invasive imaging. As an alternative to conventional vector detection techniques, we developed a specific genetic labeling system whereby an adenoviral vector incorporates a fusion between capsid protein IX and human metallothionein. Our study herein clearly demonstrates our ability to rescue viable adenoviral particles that display functional metallothionein (MT) as a component of their capsid surface. We demonstrate the feasibility of (99m)Tc binding in vitro to the pIX-MT fusion on the capsid of adenovirus virions using a simple transchelation reaction. SPECT imaging of a mouse after administration of a (99m)Tc-radiolabeled virus showed clear localization of radioactivity to the liver. This result strongly supports imaging using pIX-MT, visualizing the normal biodistribution of Ad primarily to the liver upon injection into mice. The ability we have developed to view real-time biodistribution in their physiological milieu represents a significant tool to study adenovirus biology in vivo.
Crowdsourcing for Affective Annotation of Video: Development of a Viewer-reported Boredom Corpus (2010)

Predictions of viewer affective response to video are an important source of information that can be used to enhance the performance of multimedia retrieval and recommendation systems. The development of algorithms for robust prediction of viewer affective response requires corpora accompanied by appropriate ground truth. We report on the development a new corpus to be used to evaluate algorithms for prediction of viewer-reported boredom.We make use of crowdsourcing in order to address two shortcomingsof previous affective video corpora: small number of annotators and gap between annotators and target viewer group. We describe the design of the Mechanical Turk setup that we used to generate the affective annotations for the corpus. We discuss specific issues that arose and how we resolve them and then present an analysis of the annotations collected. The paper closes with a list of recommended practices for the collection of self-reported affective annotations using crowdsourcing techniques and an outlookon future work.
Gastrointestinal Microbiota in Irritable Bowel Syndrome: Their Role in Its Pathogenesis and Treatment (2008)

Irritable bowel syndrome (IBS) is a chronic disorder characterized by abdominal pain, change in bowel habit, and bloating. It has traditionally been viewed as a disorder of visceral hypersensitivity heavily influenced by stress, and therefore therapeutic strategies to date have largely reflected this. However, more recently, there is good evidence for a role of the gastrointestinal (GI) microbiota in its pathogenesis. Changes in fecal microbiota, the use of probiotics, the phenomenon of postinfectious IBS, and the recognition of an upregulated host immune system response suggest that an interaction between the host and GI microbiota may be important in the pathogenesis of IBS. This article explores the role of the GI microbiota in IBS and how their modification might lead to therapeutic benefit.
A bovine papillomavirus constitutive enhancer is negatively regulated by the E2 repressor through competitive binding for a cellular factor (1990)

The bovine papillomavirus type 1 long control region (LCR) contains DNA sequence elements involved in the regulation of viral transcription and replication. Differences in the levels of transcription have previously been noted between bovine papillomavirus type 1-infected rodent cell lines and bovine cells. To investigate these differences, fragments of the LCR were cloned into an enhancer-deleted chloramphenicol acetyltransferase expression vector and assayed for enhancer activity. A strong constitutive enhancer was found in the 5' portion of the LCR that was most active in primary bovine fibroblasts and had little activity in other cell types. Deletion mapping localized most of the activity to a 113-bp fragment from nucleotides (nt) 7162 to 7275, a region of the viral sequence that also contains the P7185 promoter and an E2-binding site at nt 7203. The enhancer activity of this element could be positively modulated by the full-length E2 transactivator or negatively modulated by the E2 repressor. Site-directed mutagenesis defined two cis elements, CE1 and CE2, which were both necessary for enhancer activity. The CE1 element was required for P7185 activity, whereas the CE2 element was dispensable for P7185 activity. The CE1 and CE2 elements both overlap the E2-binding site at nt 7203. In vitro DNA-binding studies revealed (i) a specific gel retardation complex associated with cellular factor binding at the CE1 element, (ii) a correlation between enhancer activity and the binding of factors to the CE1 element, and (iii) competitive binding between the E2 repressor and the cellular factor at the CE1 element.
Cellular localization and regional distribution of an angiotensin II-forming chymase in the heart. (1993)

The human heart is a target organ for the octapeptide hormone, angiotensin II (Ang II). Recent studies suggest that the human heart contains a dual pathway of Ang II formation in which the major Ang II-forming enzymes are angiotensin I-converting enzyme (ACE) and chymase. Human heart chymase has recently been purified and its cDNA and gene cloned. This cardiac serine proteinase is the most efficient and specific Ang II-forming enzyme described. To obtain insights into the cardiac sites of chymase-dependent Ang II formation, we examined the cellular localization and regional distribution of chymase in the human heart. Electron microscope immunocytochemistry using an anti-human chymase antibody showed the presence of chymase-like immunoreactivity in the cardiac interstitium and in cytosolic granules of mast cells, endothelial cells, and some mesenchymal interstitial cells. In the cardiac interstitium, chymase-like immunoreactivity is associated with the extracellular matrix. In situ hybridization studies further indicated that chymase mRNA is expressed in endothelial cells and in interstitial cells, including mast cells. Tissue chymase levels were determined by activity assays and by Western blot analyses. Chymase levels were approximately twofold higher in ventricles than in atria. There were no significant differences in chymase levels in ventricular tissues obtained from non-failing donor hearts, failing ischemic hearts, or hearts from patients with ischemic cardiomyopathy. These findings suggest that a major site of chymase-dependent Ang II formation in the heart is the interstitium and that cardiac mast cells, mesenchymal interstitial cells, and endothelial cells are the cellular sites of synthesis and storage of chymase. In the human heart, because ACE levels are highest in the atria and chymase levels are highest in ventricles, it is likely that the relative contribution of ACE and chymase to cardiac Ang II formation varies with the cardiac chamber. Such differences may lead to differential suppression of cardiac Ang II levels during chronic ACE inhibitor therapy in patients with congestive heart failure.