gebhart/patrepeval huggingface dataset:
Capacity Limits of Optical Fiber Networks (2010)

We describe a method to estimate the capacity limit of fiber-optic communication systems (or ¿fiber channels¿) based on information theory. This paper is divided into two parts. Part 1 reviews fundamental concepts of digital communications and information theory. We treat digitization and modulation followed by information theory for channels both without and with memory. We provide explicit relationships between the commonly used signal-to-noise ratio and the optical signal-to-noise ratio. We further evaluate the performance of modulation constellations such as quadrature-amplitude modulation, combinations of amplitude-shift keying and phase-shift keying, exotic constellations, and concentric rings for an additive white Gaussian noise channel using coherent detection. Part 2 is devoted specifically to the "fiber channel.'' We review the physical phenomena present in transmission over optical fiber networks, including sources of noise, the need for optical filtering in optically-routed networks, and, most critically, the presence of fiber Kerr nonlinearity. We describe various transmission scenarios and impairment mitigation techniques, and define a fiber channel deemed to be the most relevant for communication over optically-routed networks. We proceed to evaluate a capacity limit estimate for this fiber channel using ring constellations. Several scenarios are considered, including uniform and optimized ring constellations, different fiber dispersion maps, and varying transmission distances. We further present evidences that point to the physical origin of the fiber capacity limitations and provide a comparison of recent record experiments with our capacity limit estimation.
Spread-time code division multiple access (2002)

An alternative code division multiple access (CDMA) scheme to spread spectrum (SS), called spread-time (ST), is proposed for bandlimited multiple access channels. ST-CDMA can be considered the time-frequency dual of SS-CDMA. Implementations are described in which surface acoustic wave (SAW) devices are used to perform the matched filtering or Fourier transformation. A first-order comparison of signal-to-interference ratio and spectral efficiency is given for ST- and conventional asynchronous SS-CDMA, assuming an ideal bandlimited channel.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
T134, a Small-Molecule CXCR4 Inhibitor, Has No Cross-Drug Resistance with AMD3100, a CXCR4 Antagonist with a Different Structure (1999)

T22, an analog of polyphemusin II (18 amino acid residues), was found to block T-tropic human immunodeficiency virus type 1 (HIV-1) entry into target cells as a CXCR4 inhibitor. We synthesized T134, a small analog (14 amino acid residues) of T22 with reduced positive charges. T134 exhibited highly potent activity and significantly less cytotoxicity in comparison to that of T22. T134 prevents the anti-CXCR4 monoclonal antibody from binding to peripheral blood mononuclear cells but has no effect on the binding of anti-CCR5 monoclonal antibodies. Since T134 inhibits the binding of stromal cell-derived factor-1 (SDF-1) to MT-4 cells, it seems that T134 prevents HIV-1 entry by binding to CXCR4. The bicyclam AMD3100 has also been shown to block HIV-1 entry via CXCR4 but not via CCR5. Both T134 and AMD3100 are CXCR4 antagonists and low-molecular-weight compounds but have different structures. Our results indicate that T134 is active against wild-type T-tropic HIV-1 strains and against AMD3100-resistant strains.
A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota (2005)

The ongoing characterization of novel species creates the need for a molecular marker which can be used for species- and, simultaneously, for mega-systematics. Recently, the use of the internal transcribed spacer 2 (ITS2) sequence was suggested, as it shows a high divergence in sequence with an assumed conservation in structure. This hypothesis was mainly based on small-scale analyses, comparing a limited number of sequences. Here, we report a large-scale analysis of more than 54,000 currently known ITS2 sequences with the goal to evaluate the hypothesis of a conserved structural core and to assess its use for automated large-scale phylogenetics. Structure prediction revealed that the previously described core structure can be found for more than 5000 sequences in a wide variety of taxa within the eukaryotes, indicating that the core secondary structure is indeed conserved. This conserved structure allowed an automated alignment of extremely divergent sequences as exemplified for the ITS2 sequences of a ctenophorean eumetazoon and a volvocalean green alga. All classified sequences, together with their structures can be accessed at http://www.biozentrum.uni-wuerzburg.de/bioinformatik/projects/ITS2.html. Furthermore, we found that, although sample sequences are known for most major taxa, there exists a profound divergence in coverage, which might become a hindrance for general usage. In summary, our analysis strengthens the potential of ITS2 as a general phylogenetic marker and provides a data source for further ITS2-based analyses.
A complete set of repeat-depleted, PCR-amplifiable, human chromosome-specific painting probes (1999)

We describe the generation of a complete set of human chromosome-specific painting probes depleted in repetitive sequences. These probes yield highly specific signals when hybridized without the addition of a blocking agent, such as Cot-1 DNA, and without probe preannealing prior to hybridization. Fluorescent intensities and signal-to-background ratios for these probes are comparable to those of untreated probes hybridized with Cot-1 DNA. We demonstrate the suitability of these probes for applications with very complex probe sets, such as multiplex-FISH.
Faecal microbiota profile of Crohn’s disease determined by terminal restriction fragment length polymorphism analysis (2008)

Terminal restriction fragment length polymorphism analyses showed that the diversity of faecal microbiota in patients with CD differed from that of healthy individuals. Furthermore, elemental diets modulated faecal microbiota composition, and this effect may be involved in mechanisms of clinical effects of elemental diet.
Single-agent expansion cohort of lenvatinib (LEN) and combination dose-finding cohort of LEN + etoposide (ETP) + ifosfamide (IFM) in patients (pts) aged 2 to ≤25 years with relapsed/refractory osteosarcoma (OS). (2018)

11527 Background: LEN is a multikinase inhibitor of VEGFR1-3, FGFR1-4, PDGFRα, KIT, and RET. In human pediatric OS xenograft models, LEN enhanced the antitumor activity of IFM + ETP. In a phase (Ph) 2 study of sorafenib in pts with unresectable high-grade OS, progression-free survival at 4 months (PFS-4) was 46%. We report emerging data from a Ph 2 single-agent LEN expansion cohort and Ph 1b combination dose-finding cohort of LEN + ETP + IFM in pts with relapsed/refractory OS. Methods: Pts were age 2 to ≤25 years, had relapsed OS, and had < 2 prior VEGF-targeted therapies. The recommended dose (RD; 14 mg/m2) from Ph 1 was used in Ph 2. In Ph 1b, a 20% reduction of LEN (11 mg/m2/day) was used as starting dose in combination with IFM 3000 mg/m2 + ETP 100 mg/m2 daily/3 days. Ph 2 and Ph 1b primary endpoints were PFS-4 per RECIST 1.1 and RD of the combination. Secondary objectives included best overall response (BOR), objective response rate, PFS, safety, and PK. Data cutoff was October 6, 2017. Results: In Ph 2, 16 pts received LEN 14 mg/m2. Median (min, max) number of cycles received was 3.0 (1, 9). Most common any-grade TEAEs were diarrhea, hypothyroidism, and proteinuria (43.8% each). Most common Grade (G) 3 or 4 TEAEs were back pain and dyspnea (12.5% each). One pt discontinued due to TEAEs (myelodysplastic syndrome); 5 of 15 evaluable pts achieved PFS-4 and BOR was PR (n = 1) and SD (n = 7). In Ph 1b, 7 pts received LEN 11 (LEN 11 mg/m2 + IFM + ETP) and 6 pts received LEN 14 (LEN 14 mg/m2 + IFM + ETP). 1 pt had a DLT at LEN 11 (G3 thrombocytopenia) and 2 pts had DLTs at LEN 14 (G4 thrombocytopenia with G3 bleeding in 1 pt; G2 oral dysesthesia, G2 back pain, and G1 muscle spasms in 1 pt). G ≥3 TEAEs occurred in 85.7% and 66.7% of LEN 11 and LEN 14 pts, respectively. No pts discontinued due to TEAEs. BOR was PR (n = 1) and SD (n = 5). AUC at steady state of LEN and distributions of interindividual variability of oral clearance were comparable between LEN single agent and the combination. Conclusions: In Ph 2, LEN at 14 mg/m2 achieved PFS-4 in 5 pts; BOR was PR in 1 pt and SD in 7 pts. In Ph 1b, LEN + chemotherapy had a manageable safety profile. The study is ongoing and updated data will be presented. Clinical trial information: NCT02432274.
Regulatory T Cells in Autoimmmunity (2000)

Clonal deletion of autoreactive T cells in the thymus is not the sole mechanism for the induction of tolerance to self-antigens since partial depletion of peripheral CD4(+) T cells from neonatal and adult animals results in the development of organ-specific autoimmunity. Reconstitution of these immunodeficient animals with populations of regulatory CD4(+)T cells prevents the development of autoimmunity. The lineage of regulatory CD4(+) T cells is generated in the thymus and can be distinguished from effector cells by the expression of unique membrane antigens. The target antigens for these suppressor populations and their mechanisms of action remain poorly defined. Depletion of regulatory T cells may be useful in the induction of immunity to weak antigens, such as tumor-specific antigens. Conversely, enhancement of regulatory T cell function may be a useful adjunct to the therapy of autoimmune diseases and for prevention of allograft rejection.
Kermas for Various Substances Averaged Over the Energy Spectra of Fast Neutron Therapy Beams: A Study in Uncertainties (1982)

Abstract Not Provided
Topical negative pressure therapy. A very useful new method to treat severe infected vascular approaches in the groin. (2003)

This study establishes VAC as a very valuable tool for managing severe complications of groin vascular surgery sites even in patients with obesity and/or diabetes mellitus.
Identification of a membrane adenosine deaminase binding protein from human placenta (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIdentification of a membrane adenosine deaminase binding protein from human placentaPaul P. TrottaCite this: Biochemistry 1982, 21, 17, 4014–4023Publication Date (Print):August 17, 1982Publication History Published online1 May 2002Published inissue 17 August 1982https://pubs.acs.org/doi/10.1021/bi00260a017https://doi.org/10.1021/bi00260a017research-articleACS PublicationsRequest reuse permissionsArticle Views44Altmetric-Citations24LEARN 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-Alertsclose Get e-Alerts
Hexapeptide Combinatorial Ligand Libraries: The March for the Detection of the Low-Abundance Proteome Continues (2008)

After 10 years of extensive proteomic research, it has become increasingly apparent that new technologies are sorely needed for detecting the low-abundance proteome-those proteins (up to 50% in any proteome) whose concentration in tissues or cells falls below the detection limits of currently available methodologies. Here we survey one such method: a combinatorial ligand library (called ProteoMiner), comprising dozens of millions of hexapeptides capable of interacting with most, if not all, proteins in any given proteome. They act by drastically reducing the signal of high-abundance species while increasing the level of the low-abundance components to bring their signal within the detection limit of present-day tools. Such a library has been tested against a number of human biological fluids, such as sera, urine, cerebrospinal fluid as well as against cell lysates (e.g., platelets, red blood cells) with interesting results.
Duchenne muscular dystrophy: Gene and gene product; mechanism of mutation in the gene (1992)

The X-linked gene responsible for Duchenne muscular dystrophy encodes dystrophin, a high-molecular-weight cytoskeletal protein. Studies in several laboratories have revealed deletion of one or more exons in 60% of affected boys; quantitative analysis in our laboratory has detected duplication of exons in another 6%. The severe Duchenne phenotype is associated with deletions or duplications that shift the reading frame of the message, whereas the milder Becker muscular dystrophy is associated with deletions or duplications that maintain the reading frame. Patients who have neither deletion nor duplication may have nonsense mutations, one of which has been detected by predicting the site of the mutation from the size of the truncated protein. Rare females with the disease have a translocation that disrupts the dystrophin gene on one X chromosome and causes non-random inactivation of the normal X, resulting in the expression of the disease. The high frequency of new mutation provides an opportunity to study the mechanism of chromosomal rearrangement that is characteristic of the disease. Our laboratory has focused on the translocations in females and on duplications in affected males. The X-autosome translocations of affected females are all de novo events that originated in the paternal set of chromosomes. Molecular characterization of the translocation junctions revealed reciprocal translocation with both deletion and addition of nucleotides at the junction, suggestive of a breakage and reunion mechanism. Duplications studied to date are all tandem in nature and sequence analysis of duplication junctions has revealed both homologous and non-homologous recombination. Marker segregation analysis has revealed that five out of five duplications originated in a single X chromosome of one of the maternal grandparents, suggesting that the recombination event is unequal sister chromatid exchange.
Distinct clonotypes of anti-DNA antibodies in mice with lupus nephritis. (1985)

Clonotypes of IgG anti-DNA antibodies were studied by isoelectric focusing in various autoimmune mice with or without lethal lupus nephritis. MRL/MpJ-lpr/lpr mice exhibited the most heterogeneous spectrotypes of anti-DNA antibodies in the pH range from 6.5 to 8.5, with marked variation in individual mice. Female (NZB X NZW)F1 mice expressed rather uniform DNA-binding bands composed of at least five to six distinct subgroups, having isoelectric points from 6.5 to 8.0. Male BXSB mice showed major characteristic bands confined to alkaline pH range from 7.8 to 8.5, similar to C57BL/6J-lpr/lpr mice, which showed markedly restricted bands in this region. Both AKR/J-lpr/lpr and C3H/HeJ-lpr/lpr mice expressed DNA-binding bands mostly focused between pH 6.5 and 8.2. The aging study indicated that three autoimmune mice (MRL/MpJ-lpr/lpr, [NZB X NZW]F1, and male BXSB) that developed fatal glomerulonephritis showed clonal expansion of anti-DNA antibodies throughout their life. In contrast, such age-dependent expansion of anti-DNA clonotypes was not evident in three lpr cogenic mice (C57BL/6J-lpr/lpr, AKR/J-lpr/lpr, and C3H/HeJ-lpr/lpr) that developed only mild glomerulonephritis; rather, their expression of anti-DNA spectrotypes diminished as they aged. Anti-DNA activities in renal eluates from nephritic autoimmune mice were mostly distributed in the pH range from 6.5 to 8.0, without significant concentrations in the high alkaline range of more than pH 8.0. These results suggest that there exist distinct anti-DNA clonotypes in each mouse strain and that the development of lupus nephritis does not appear to be associated with particular spectrotypes of anti-DNA antibodies. Rather, the age-dependent expansion of anti-DNA clonotypes may be a feature more characteristic of mice developing lethal lupus nephritis.
Support of human hematopoiesis in long-term bone marrow cultures by murine stromal cells selectively expressing the membrane-bound and secreted forms of the human homolog of the steel gene product, stem cell factor. (1992)

The maintenance and differentiation of hematopoietic stem cells is influenced by cells making up the hematopoietic microenvironment (HM), including bone marrow-derived stromal cells. We and several other investigators have recently demonstrated the molecular basis of abnormal HM observed in the steel mutant mouse and cloned the normal cDNA products of this gene (termed SCF, KL, or MCF). In this report, we focus on the human counterpart of the mouse Steel (Sl) gene. Alternative splicing of the human SCF pre-mRNA transcript results in secreted and membrane-bound forms of the protein. To investigate the role of these two forms of human SCF, we targeted an immortalized stromal cell line derived from fetal murine homozygous (Sl/Sl) SCF-deficient embryos for gene transfer of various human cDNAs encoding SCF. We report that stable stromal cell transfectants can differentially process the two forms of human SCF protein product. We also demonstrate that both soluble SCF and membrane-bound SCF are active in increasing the number of human progenitor cells in the context of stromal cell cultures, although in a qualitatively different manner. Hence, the membrane-bound form of SCF may play an important role in the cell-cell interactions observed between stromal and hematopoietic cells both in vitro and in vivo.
Fibromodulin-null Mice Have Abnormal Collagen Fibrils, Tissue Organization, and Altered Lumican Deposition in Tendon (1999)

Fibromodulin is a member of a family of connective tissue glycoproteins/proteoglycans containing leucine-rich repeat motifs. Several members of this gene family bind to fibrillar collagens and are believed to function in the assembly of the collagen network in connective tissues. Here we show that mice lacking a functional fibromodulin gene exhibit an altered morphological phenotype in tail tendon with fewer and abnormal collagen fiber bundles. In fibromodulin-null animals virtually all collagen fiber bundles are disorganized and have an abnormal morphology. Also 10-20% of the bundles in heterozygous mice are similar to the abnormal bundles in fibromodulin-null tail tendon. Ultrastructural analysis of Achilles tendon from fibromodulin-null mice show collagen fibrils with irregular and rough outlines in cross-section. Morphometric analysis show that fibromodulin-null mice have on the average thinner fibrils than wild type animals as a result of a larger preponderance of very thin fibrils in an overall similar range of fibril diameters. Protein and RNA analyses show an approximately 4-fold increase in the content of lumican in fibromodulin-null as compared with wild type tail tendon, despite a decrease in lumican mRNA. These results demonstrate a role for fibromodulin in collagen fibrillogenesis and suggest that the orchestrated action of several leucine-rich repeat glycoproteins/proteoglycans influence the architecture of collagen matrices.
Elastic properties of bimesogenic liquid crystals (2013)

The second nematic phase found in some bimesogenic liquid crystals with an odd flexible spacer has aroused considerable interest due to many unusual properties exhibited by them. However, the reason for such molecules to exhibit transitions to the modulated phase is still unclear. Dozov [Europhys Lett. 2001;56:247] predicted that negative K 33 can lead to a modulated phase where the director has either splay-bend or twist-bend distribution. Though various theoretical studies have suggested that this scenario may be valid, no experimental evidence has so far been given. In order to study the influence of the elastic constants, we measured the splay and bend elastic constants in the ordinary nematic phase of a dimer material, CBC11CB, for temperatures down to 0.6°C above the Nx–Nu transition. Our results show that the bend constant is reduced by a factor of 2 compared with that closer to the I-Nu transition but is positive and the trend does not seem that K 33 will extrapolate to zero or fall below it for the temperature range investigated. Compared to K 11, K 33 is reduced by a factor of 3, close to the Nu–Nx transition temperature.
Current topics in plant biochemistry and physiology: Volume 4: Proceedings (1985)

These proceedings represent papers presented at the Fourth Annual Plant Biochemistry and Physiology Symposium held at the University of Missouri-Columbia, April 10-12, 1985 and hosted by the Interdisciplinary Plant Biochemistry and Physiology Group. This Interdisciplinary Group was organized to facilitate research and train-ing through interdisciplinary and cooperative approaches to problems facing Plant Biochemistry and Physiology. A key objective of this group is to maintain an awareness of the advances in research in this field. This annual symposium is one means of meeting this objective. Topics are selected each year in three to five areas in order to broaden our individual horizons.
The Problem of Overfitting (2003)

ADVERTISEMENT RETURN TO ISSUEArticleNEXTThe Problem of OverfittingDouglas M. HawkinsView Author Information School of Statistics, University of Minnesota, Minneapolis, Minnesota 55455 Cite this: J. Chem. Inf. Comput. Sci. 2004, 44, 1, 1–12Publication Date (Web):December 2, 2003Publication History Received30 October 2003Published online2 December 2003Published inissue 1 January 2004https://pubs.acs.org/doi/10.1021/ci0342472https://doi.org/10.1021/ci0342472research-articleACS PublicationsCopyright © 2004 American Chemical SocietyRequest reuse permissionsArticle Views19627Altmetric-Citations1642LEARN 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 options SUBJECTS:Calibration,Hydrocarbons,Quality management,Testing and assessment,Transition temperature Get e-Alerts