gebhart/patrepeval huggingface dataset:
MIRD Pamphlet No. 20: The Effect of Model Assumptions on Kidney Dosimetry and Response—Implications for Radionuclide Therapy (2008)

Radionuclide therapy dose-response data, when expressed in terms of biologically effective dose, have been found to be consistent with external-beam experience for predicting kidney toxicity. Model predictions using both the multiregion kidney and linear quadratic models may serve to guide the investigator in planning and optimizing future clinical trials of radionuclide therapy.
Addressing Big Data Time Series (2013)

Most time series data mining algorithms use similarity search as a core subroutine, and thus the time taken for similarity search is the bottleneck for virtually all time series data mining algorithms, including classification, clustering, motif discovery, anomaly detection, and so on. The difficulty of scaling a search to large datasets explains to a great extent why most academic work on time series data mining has plateaued at considering a few millions of time series objects, while much of industry and science sits on billions of time series objects waiting to be explored. In this work we show that by using a combination of four novel ideas we can search and mine massive time series for the first time. We demonstrate the following unintuitive fact: in large datasets we can exactly search under Dynamic Time Warping (DTW) much more quickly than the current state-of-the-art <i>Euclidean distance</i> search algorithms. We demonstrate our work on the largest set of time series experiments ever attempted. In particular, the largest dataset we consider is larger than the combined size of all of the time series datasets considered in all data mining papers ever published. We explain how our ideas allow us to solve higher-level time series data mining problems such as motif discovery and clustering at scales that would otherwise be untenable. Moreover, we show how our ideas allow us to efficiently support the uniform scaling distance measure, a measure whose utility seems to be underappreciated, but which we demonstrate here. In addition to mining massive datasets with up to one trillion datapoints, we will show that our ideas also have implications for real-time monitoring of data streams, allowing us to handle much faster arrival rates and/or use cheaper and lower powered devices than are currently possible.
Investigation of the putative immunodominant T cell epitopes in coeliac disease (2003)

Peptide G4 is highly immunogenic. Certain amino acid substitutions in peptide G4 abolish T cell reactivity while others are partial agonists which may have potential in immunomodulation in this condition.
Near-infrared fluorescent sensor for in vivo copper imaging in a murine Wilson disease model (2012)

Copper is an essential metal nutrient that is tightly regulated in the body because loss of its homeostasis is connected to severe diseases such as Menkes and Wilson diseases, Alzheimer's disease, prion disorders, and amyotrophic lateral sclerosis. The complex relationships between copper status and various stages of health and disease remain challenging to elucidate, in part due to a lack of methods for monitoring dynamic changes in copper pools in whole living organisms. Here we present the synthesis, spectroscopy, and in vivo imaging applications of Coppersensor 790, a first-generation fluorescent sensor for visualizing labile copper pools in living animals. Coppersensor 790 combines a near-infrared emitting cyanine dye with a sulfur-rich receptor to provide a selective and sensitive turn-on response to copper. This probe is capable of monitoring fluctuations in exchangeable copper stores in living cells and mice under basal conditions, as well as in situations of copper overload or deficiency. Moreover, we demonstrate the utility of this unique chemical tool to detect aberrant increases in labile copper levels in a murine model of Wilson disease, a genetic disorder that is characterized by accumulation of excess copper. The ability to monitor real-time copper fluxes in living animals offers potentially rich opportunities to examine copper physiology in health and disease.
Single‐dose dexmedetomidine reduces agitation and provides smooth extubation after pediatric adenotonsillectomy (2005)

We conclude that 0.5 microg.kg(-1) dexmedetomidine reduces agitation after sevoflurane anesthesia in children undergoing adenotonsillectomy.
The primary structure of human liver manganese superoxide dismutase. (1984)

The complete amino acid sequence of manganese superoxide dismutase from human liver was determined. The sequence was deduced following characterization of the peptides obtained from tryptic, chymotryptic, and Staphylococcus aureus digests of the apoprotein. Chemical cleavage with dimethyl sulfoxide-hydrobromic acid was also carried out. The amino acid sequence listed below is made up of 196 amino acids and the two subunit polypeptides in the native enzyme appear to be identical. No homology was observed with copper/zinc containing class of superoxide dismutase. Lys-His-Ser-Leu-Pro-Asp-Leu-Pro-Tyr-Asp-Tyr-Gly-Ala-Leu-Glu-Pro-His-Il e -Asn-Ala-Gln-Ile-Met-Gln-Leu-His-His-Ser-Lys-His-His-Ala-Ala-Tyr-Val-Asn -Asn-Leu-Asn-Val-Thr-Gln-Glu-Lys-Tyr-Gln-Glu-Ala-Leu-Ala-Lys-Gly-Asp-Val -Thr-Ala-Gln-Ile-Ala-Leu-Gln-Pro-Ala-Leu-Lys-Phe-Asn-Gly-Gly-Gly-His-Ile -Asn-His-Ser-Ile-Phe-Trp-Thr-Asn-Leu-Ser-Pro-Asn-Gly-Gly-Gly-Gln-Pro-Lys -Gly-Glu-Leu-Leu-Glu-Ala-Ile-Lys-Arg-Asp-Phe-Gly-Ser-Phe-Asp-Lys-Phe-Lys -Gln-Lys-Leu-Thr-Ala-Ala-Ser-Val-Gly-Val-Gln-Gly-Ser-Gly-Trp-Leu-Gly-Phe -Asn-Lys-Gln-Arg-Gly-His-Leu-Gln-Ile-Ala-Ala-Cys-Pro-Asn-Gln-Asp-Pro-Leu -Gln-Gly-Thr-Thr-Gly-Leu-Ile-Pro-Leu-Leu-Gly-Ile-Asp-Val-Trp-Glu-His-Ala -Tyr-Tyr-Leu-Gln-Tyr-Lys-Asn-Val-Arg-Pro-Asp-Tyr-Leu-Lys-Ala-Ile-Trp-Asn -Val-Ile-Asn-Trp-Glu-Asn-Val-Thr-Glu-Arg-Tyr-Met-Ala-Cys-Lys-Lys.
Global gene expression analysis identifies molecular pathways distinguishing blastocyst dormancy and activation (2004)

Delayed implantation (embryonic diapause) occurs when the embryo at the blastocyst stage achieves a state of suspended animation. During this period, blastocyst growth is very slow, with minimal or no cell division. Nearly 100 mammals in seven different orders undergo delayed implantation, but the underlying molecular mechanisms that direct this process remain largely unknown. In mice, ovariectomy before preimplantation ovarian estrogen secretion on day 4 of pregnancy initiates blastocyst dormancy, which normally lasts for 1-2 weeks by continued progesterone treatment, although blastocyst survival decreases with time. An estrogen injection rapidly activates blastocysts and initiates their implantation in the progesterone-primed uterus. Using this model, here we show that among approximately 20,000 genes examined, only 229 are differentially expressed between dormant and activated blastocysts. The major functional categories of altered genes include the cell cycle, cell signaling, and energy metabolic pathways, particularly highlighting the importance of heparin-binding epidermal growth factor-like signaling in blastocyst-uterine crosstalk in implantation. The results provide evidence that the two different physiological states of the blastocyst, dormancy and activation, are molecularly distinguishable in a global perspective and underscore the importance of specific molecular pathways in these processes. This study has identified candidate genes that provide a scope for in-depth analysis of their functions and an opportunity for examining their relevance to blastocyst dormancy and activation in numerous other species for which microarray analysis is not available or possible due to very limited availability of blastocysts.
Evaluation of the functional equivalence of major histocompatibility complex class II A and E complexes. (1992)

Most mice display two conventional major histocompatibility complex class II isotypes, A and E. Several A+E- strains have been observed, but never any that are A-E+. Because of this and because of hints from several lines of functional analysis, it has been proposed that the two isotypes might not operate equivalently. This proposition has not been directly testable until now because of the lack of an E-only strain. We report the production of such mice, exploiting previously created class II-transgenic and class II-"knock-out" lines. A+E-, A-E-, and A-E+ littermates have been compared by a number of parameters. We find that E and A molecules are, for the most part, functionally equivalent. However, subtle differences are seen in their ability to engage CD4 molecules on immature thymocytes, and in the profile of receptors on T cells selected into the periphery.
Sex hormones modulate brain damage in multiple sclerosis: MRI evidence (2005)

The hormone related modulation of pathological changes supports the hypothesis that sex hormones play a role in the inflammation, damage, and repair mechanisms typical of MS.
Preparative production of optically active esters and alcohols using esterase-catalyzed stereospecific transesterification in organic media (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparative production of optically active esters and alcohols using esterase-catalyzed stereospecific transesterification in organic mediaBernard Cambou and Alexander M. KlibanovCite this: J. Am. Chem. Soc. 1984, 106, 9, 2687–2692Publication Date (Print):May 1, 1984Publication History Published online1 May 2002Published inissue 1 May 1984https://pubs.acs.org/doi/10.1021/ja00321a033https://doi.org/10.1021/ja00321a033research-articleACS PublicationsRequest reuse permissionsArticle Views1037Altmetric-Citations245LEARN 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
A role for APP in Wnt signalling links synapse loss with β-amyloid production (2018)

In Alzheimer's disease (AD), the canonical Wnt inhibitor Dickkopf-1 (Dkk1) is induced by β-amyloid (Aβ) and shifts the balance from canonical towards non-canonical Wnt signalling. Canonical (Wnt-β-catenin) signalling promotes synapse stability, while non-canonical (Wnt-PCP) signalling favours synapse retraction; thus Aβ-driven synapse loss is mediated by Dkk1. Here we show that the Amyloid Precursor Protein (APP) co-activates both arms of Wnt signalling through physical interactions with Wnt co-receptors LRP6 and Vangl2, to bi-directionally modulate synapse stability. Furthermore, activation of non-canonical Wnt signalling enhances Aβ production, while activation of canonical signalling suppresses Aβ production. Together, these findings identify a pathogenic-positive feedback loop in which Aβ induces Dkk1 expression, thereby activating non-canonical Wnt signalling to promote synapse loss and drive further Aβ production. The Swedish familial AD variant of APP (APP<sub>Swe</sub>) more readily co-activates non-canonical, at the expense of canonical Wnt activity, indicating that its pathogenicity likely involves direct effects on synapses, in addition to increased Aβ production. Finally, we report that pharmacological inhibition of the Aβ-Dkk1-Aβ positive feedback loop with the drug fasudil can restore the balance between Wnt pathways, prevent dendritic spine withdrawal in vitro, and reduce Aβ load in vivo in mice with advanced amyloid pathology. These results clarify a relationship between Aβ accumulation and synapse loss and provide direction for the development of potential disease-modifying treatments.
Structure and Developmental Regulation of a Wheat Gene Encoding the Major Chlorophyll a/b-Binding Polypeptide (1985)

A genomic clone for a major chlorophyll a/b-binding polypeptide of the light-harvesting complex has been sequenced from wheat. This gene, whAB1.6, encodes a 70-nucleotide 5'-nontranslated spacer, a 34-amino-acid NH2-terminal extension, i.e., the transit peptide, and a mature coding protein of 232 amino acid residues. The exact molecular weight of the precursor polypeptide is 28,560. The transit peptide is basic and is rich in serines. No intervening sequences are found in this gene. The transcription start site of the whAB1.6 gene occurs at AAAC as determined by S1 nuclease analysis. Putative regulatory sequences occur upstream of the gene at -25 (TTTAAATA) and at -72 (CCAACCA). Northern blots show a single RNA species estimated to be 1,100 nucleotides. Heterogeneity of the RNA population is demonstrated in S1 nuclease analyses with a 5'-end-labeled fragment that extends 191 nucleotides into the mature protein coding sequence. At least seven different transcripts can be recognized. The highest levels of RNA transcribed from the whAB1.6 gene are found in the basal segments of the wheat leaf, whereas other chlorophyll a/b-binding transcripts in the cell show a different pattern of abundance. As a control, we show that roots do not contain chlorophyll a/b-binding RNA. The most abundant RNA species shows an interrupted homology with the whAB1.6 gene at the start of the mature protein coding sequence; another species shows homology beginning at the start of the transit peptide and does not include the nontranslated region. Chlorophyll a/b-binding polypeptides accumulate toward the tip of the leaf as shown by Western blot analysis of total thylakoid proteins.
Engine Cooling by Direct Injection of Cooling Water (1970)

&lt;div class="htmlview paragraph"&gt;A computer program has been developed to analyze the Otto cycle for an engine where water can be injected directly into the cylinder. The program can treat arbitrary amounts of water injection at any point in the cycle. Results show that a main factor is the timing of the water injection; optimum injection is early in the compression stroke.&lt;/div&gt;
SLC5A8 Triggers Tumor Cell Apoptosis through Pyruvate-Dependent Inhibition of Histone Deacetylases (2006)

Tumor cells up-regulate glycolysis but convert pyruvate into lactate instead of oxidizing it. Here, we show that pyruvate, but not lactate, is an inhibitor of histone deacetylases (HDAC) and an inducer of apoptosis in tumor cells and that SLC5A8, a Na(+)/monocarboxylate cotransporter, is obligatory for this process. We found that SLC5A8 is expressed in nontransformed breast epithelial cell lines but silenced by DNA methylation in tumor cell lines. The down-regulation of the gene is also evident in primary breast tumors. When MCF7 breast tumor cells are transfected with SLC5A8 cDNA, the cells undergo pyruvate-dependent apoptosis. Butyrate and propionate also induce apoptosis in SLC5A8-expressing cells, whereas lactate does not. The differential ability of these monocarboxylates to cause apoptosis in SLC5A8-expressing MCF7 cells correlates with their ability to inhibit HDACs. Apoptosis induced by SLC5A8/pyruvate in MCF7 cells is associated with up-regulation of p53, Bax, tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), TRAIL receptor (TRAILR) 1, and TRAILR2 and down-regulation of Bcl2 and survivin. Lactate dehydrogenase isozymes are differentially expressed in nontransformed cells and tumor cells such that the latter convert pyruvate into lactate. Silencing of SLC5A8 coupled with conversion of pyruvate into lactate in tumor cells correlates with increased HDAC activity in these cells compared with nontransformed cells. Our studies thus identify pyruvate as a HDAC inhibitor and indicate that the Na(+)-coupled pyruvate transport underlies the tumor-suppressive role of SLC5A8. We propose that tumor cells silence SLC5A8 and convert pyruvate into lactate as complementary mechanisms to avoid pyruvate-induced cell death.
Nitric Oxide: A Key Mediator of Biofilm Dispersal with Applications in Infectious Diseases (2014)

Studies of the biofilm life cycle can identify novel targets and strategies for improving biofilm control measures. Of particular interest are dispersal events, where a subpopulation of cells is released from the biofilm community to search out and colonize new surfaces. Recently, the simple gas and ubiquitous biological signaling molecule nitric oxide (NO) was identified as a key mediator of biofilm dispersal conserved across microbial species. Here, we review the role and mechanisms of NO mediating dispersal in bacterial biofilms, and its potential for novel therapeutics. In contrast to previous attempts using high dose NO aimed at killing pathogens, the use of low, non-toxic NO signals (picomolar to nanomolar range) to disperse biofilms represents an innovative and highly favourable approach to improve infectious disease treatments. Further, several NO-based technologies have been developed that offer a versatile range of solutions to control biofilms, including: (i) NO-generating compounds with short or long half-lives and safe or inert residues, (ii) novel compounds for the targeted delivery of NO to infectious biofilms during systemic treatments, and (iii) novel NO-releasing materials and surface coatings for the prevention and dispersal of biofilms. Overall the use of low levels of NO exploiting its signaling properties to induce dispersal represents an unprecedented and promising strategy for the control of biofilms in clinical and industrial contexts.
RFID Implementation (2006)

Complete coverage of this widespread technology 

This is the only book available to offer in-depth, practical details for implementing an RFID project from start to finish. From Wal-Mart and beyond, RFID (Radio Frequency Identification) is in use everywhere--enabling superior supply-chain management by tracking inventory via microchip-tagged products. RFID Implementation delivers step-by-step instructions for initiating, installing, and managing an RFID rollout.

 

Table of contents

Part I: The Basics
Chapter 1. RFID Physics, Standards, and Regulations
Chapter 2. The EPCglobal Network
Chapter 3. Components of an RFID System
Chapter 4. Bar Codes and RFID Tags
Part II: Applications
Chapter 5: RFID Applications
Chapter 6: RFID at the United States Department of Defense
Chapter 7: The Pharmaceutical Industry
Chapter 8: RFID in the Supply Chain
Part III: Your Project
Chapter 9: Business Justification for RFID
Chapter 10: Plan Your Project
Chapter 11: Tag-and-Ship
Chapter 12: Engineering Tag Performance
Chapter 13: Data Integrity and Data Synchronization
Chapter 14: Privacy
Part IV: References
Appendix A: Typical Application Profiles
Appendix B: Bibliography
Glossary
Index
Somatic Gene Therapy in Gastroenterology (1992)

Summary Somatic gene therapy represents a new approach for treating a variety of genetic and acquired diseases and has many potential applications in gastroenterology. Somatic gene therapy is based on the ability to transfer recombinant genes efficiently into somatic tissues, such as the liver or intestine, and achieve expression of the recombinant gene product. Gene transfer could be used to replace genetically defective gene functions or prevent the progression of acquired or multifactorial diseases. The therapeutic application of gene transfer technologies requires development of methods for achieving efficient transfer and expression of recombinant gene products, research directed at developing strategies for altering the course of disease, and clinical research aimed at assessing both the technical feasibility and therapeutic efficacy of this approach.
Increased bone density in sclerosteosis is due to the deficiency of a novel secreted protein (SOST) (2001)

Sclerosteosis is a progressive sclerosing bone dysplasia with an autosomal recessive mode of inheritance. Radiologically, it is characterized by a generalized hyperostosis and sclerosis leading to a markedly thickened and sclerotic skull, with mandible, ribs, clavicles and all long bones also being affected. Due to narrowing of the foramina of the cranial nerves, facial nerve palsy, hearing loss and atrophy of the optic nerves can occur. Sclerosteosis is clinically and radiologically very similar to van Buchem disease, mainly differentiated by hand malformations and a large stature in sclerosteosis patients. By linkage analysis in one extended van Buchem family and two consanguineous sclerosteosis families we previously mapped both disease genes to the same chromosomal 17q12-q21 region, supporting the hypothesis that both conditions are caused by mutations in the same gene. After reducing the disease critical region to approximately 1 Mb, we used the positional cloning strategy to identify the SOST gene, which is mutated in sclerosteosis patients. This new gene encodes a protein with a signal peptide for secretion and a cysteine-knot motif. Two nonsense mutations and one splice site mutation were identified in sclerosteosis patients, but no mutations were found in a fourth sclerosteosis patient nor in the patients from the van Buchem family. As the three disease-causing mutations lead to loss of function of the SOST protein resulting in the formation of massive amounts of normal bone throughout life, the physiological role of SOST is most likely the suppression of bone formation. Therefore, this gene might become an important tool in the development of therapeutic strategies for osteoporosis.
Molecular Parameters of Hyperbranched Polymers Made by Self-Condensing Vinyl Polymerization. 2. Degree of Branching (1997)

Using a modified definition, the average degree of branching, , the fraction of branchpoints, , as well as the fractions of various structural units are calculated as a function of conversion of double bonds for hyperbranched polymers formed by self-condensing vinyl polymerization (SCVP) of monomers (or “inimers”) with the general structure AB*, where A is a vinyl group and B* is an initiating group. The results are compared to those for the polycondensation of AB2-type monomers. At full conversion, is somewhat smaller for SCVP ( ∞ ≈ 0.465) than for AB2 systems ( ∞ = 0.5). There are two kinds of linear groups in SCVP whereas there is only one kind in AB2 systems. Since there are two different active centers in SCVP, i.e., initiating B* and propagating A* centers, the effect of nonequal reactivities on is also discussed. At a reactivity ratio of the two kinds of active centers, r = kA/kB ≈ 2.59, a maximum value of ∞ = 0.5 is reached. For the limiting case r << 1, a linear polymer resembling a polycondensate will be formed whereas for r >> 1 a weakly branched vinyl polymer is expected. NMR experiments allow for the determination of reactivity ratio r.