gebhart/patrepeval huggingface dataset:
Information Value Theory (1966)

The information theory developed by Shannon was designed to place a quantitative measure on the amount of information involved in any communication. The early developers stressed that the information measure was dependent only on the probabilistic structure of the communication process. For example, if losing all your assets in the stock market and having whale steak for supper have the same probability, then the information associated with the occurrence of either event is the same. Attempts to apply Shannon's information theory to problems beyond communications have, in the large, come to grief. The failure of these attempts could have been predicted because no theory that involves just the probabilities of outcomes without considering their consequences could possibly be adequate in describing the importance of uncertainty to a decision maker. It is necessary to be concerned not only with the probabilistic nature of the uncertainties that surround us, but also with the economic impact that these uncertainties will have on us. In this paper the theory of the value of information that arises from considering jointly the probabilistic and economic factors that affect decisions is discussed and illustrated. It is found that numerical values can be assigned to the elimination or reduction of any uncertainty. Furthermore, it is seen that the joint elimination of the uncertainty about a number of even independent factors in a problem can have a value that differs from the sum of the values of eliminating the uncertainty in each factor separately.
Platelet-derived Growth Factor Induces Phosphorylation of a 64-kDa Nuclear Protein (1989)

The platelet-derived growth factor (PDGF) stimulated the phosphorylation of a nuclear protein of 64 kDa (pp64) in nuclei of nontransformed normal rat kidney (NRK) cells. Low levels of phosphorylation of pp64 were observed in nuclei of serum-starved NRK cells. Fetal calf serum (FCS), PDGF, and homodimeric v-sis and PDGF A-chain protein enhanced the incorporation of 32P into pp64 over 4-fold within 30 min and over 8-fold within 2 h of exposure of NRK cells to the growth factors. In contrast, constitutive phosphorylation of 32P-labeled pp64 in nuclei of NRK cells transformed by the simian sarcoma virus (SSV) was high and only minimally stimulated by PDGF and FCS. 32P-Labeled pp64 was isolated from nuclei of PDGF-stimulated nontransformed NRK cells; the 32P of pp64 was labile in 1 M KOH, and pp64 was not significantly recognized by anti-phosphotyrosine antisera, suggesting that the PDGF-induced phosphorylation of pp64 occurred on serine or on threonine residues. However, pp64 from SSV-transformed NRK cell nuclei was significantly stable to base hydrolysis and was immunoprecipitated with anti-phosphotyrosine antisera, suggesting that pp64 from SSV-transformed cell nuclei is phosphorylated also on tyrosine. FCS, PDGF, and PDGF A- and B-chain homodimers thus stimulate the rapid time-dependent phosphorylation of a 64-kDa nuclear protein shortly after stimulation of responsive cells. The growth factor-stimulated phosphorylation of pp64 and the constitutive high levels of pp64 phosphorylation in cells transformed by SSV suggest important roles for pp64 and perhaps regulated nuclear protein kinases and phosphatases in cell division and proliferation.
Polyazanaphthalenes. Part I. Some derivatives of 1:4:5-triazanaphthalene and quinoxaline (1955)

C. L. Leese and H. N. Rydon, J. Chem. Soc., 1955, 303 DOI: 10.1039/JR9550000303
On Having No Head: Cognition throughout Biological Systems (2016)

The central nervous system (CNS) underlies memory, perception, decision-making, and behavior in numerous organisms. However, neural networks have no monopoly on the signaling functions that implement these remarkable algorithms. It is often forgotten that neurons optimized cellular signaling modes that existed long before the CNS appeared during evolution, and were used by somatic cellular networks to orchestrate physiology, embryonic development, and behavior. Many of the key dynamics that enable information processing can, in fact, be implemented by different biological hardware. This is widely exploited by organisms throughout the tree of life. Here, we review data on memory, learning, and other aspects of cognition in a range of models, including single celled organisms, plants, and tissues in animal bodies. We discuss current knowledge of the molecular mechanisms at work in these systems, and suggest several hypotheses for future investigation. The study of cognitive processes implemented in aneural contexts is a fascinating, highly interdisciplinary topic that has many implications for evolution, cell biology, regenerative medicine, computer science, and synthetic bioengineering.
The response of Culex quinquefasciatus (Diptera: Culicidae) to traps baited with carbon dioxide, 1-octen-3-ol, acetone, butyric acid and human foot odour in Tanzania (2000)

The responses of Culex quinquefasciatus Say to traps baited with carbon dioxide, 1-octen-3-ol, acetone, butyric acid and human foot odour were studied in the field in Muheza, north-east Tanzania using Counterflow Geometry (CFG) and Centers for Disease Control (CDC) traps. It was found that significantly more C. quinquefasciatus responded to foot odour collected on nylon stockings than to clean nylon stockings (P < 0.05). Significantly more mosquitoes were caught in a CFG trap baited with carbon dioxide than in traps with either human foot odour, acetone or butyric acid. It was also found that in an outdoor situation a carbon dioxide baited CDC unlit trap collected over 12 times more C. quinquefasciatus than an unbaited CDC unlit trap and nine times more mosquitoes than CDC traps baited with 1-octen-3-ol alone (P < 0.05). The number of mosquitoes caught in a CDC trap baited with 1-octen-3-ol did not differ significantly from that of the unbaited CDC trap (P > 0.05). These results indicate that the Afrotropical C. quinquefasciatus respond significantly better to traps baited with carbon dioxide than to either octenol, acetone or butyric acid, and that human foot odour contains stimuli to which C. quinquefasciatus is attracted under field conditions.
Quantitative Measurement of the Electron and Hole Mobility−Lifetime Products in Semiconductor Nanowires (2006)

The mobility−lifetime products (μτ) for electrons and holes in CdS nanowires were quantitatively determined by scanning photocurrent microscopy of devices with ohmic contacts. Ohmic contacts were fabricated by ion bombardment of the contact regions. By analyzing the spatial profiles of the local photoconductivity maps, we determined that electron transport (μeτe ≈ 5 × 10-7 cm2/V) was more efficient than hole transport (μhτh ≈ 10-7 cm2/V). The results demonstrate that photocurrent mapping can provide quantitative insight into intrinsic carrier transport properties of semiconductor nanostructures.
Effect of substrate RNA sequence on the cleavage reaction by a short ribozyme (1998)

Leadzyme is a ribozyme that requires Pb2+. The catalytic sequence, CUGGGAGUCC, binds to an RNA substrate, GGACC downward arrowGAGCCAG, cleaving the RNA substrate at one site. We have investigated the effect of the substrate sequence on the cleavage activity of leadzyme using mutant substrates in order to structurally understand the RNA catalysis. The results showed that leadzyme acted as a catalyst for single site cleavage of a C5 deletion mutant substrate, GGAC downward arrowGAGCCAG, as well as the wild-type substrate. However, a mutant substrate GGACCGACCAG, which had G8 deleted from the wild-type substrate, was not cleaved. Kinetic studies by surface plasmon resonance indicated that the difference between active and inactive structures reflected the slow association and dissociation rate constants of complex formation induced by Pb2+rather than differences in complex stability. CD spectra showed that the active form of the substrate-leadzyme complex was rearranged by Pb2+binding. The G8 of the wild-type substrate, which was absent in the inactive complex, is not near the cleavage site. Thus, these results show that the active substrate-leadzyme complex has a Pb2+binding site at the junction between the unpaired region (asymmetric internal loop) and the stem region, which is distal to the cleavage site. Pb2+may play a role in rearranging the bases in the asymmetric internal loop to the correct position for catalysis.
Introductory Lecture : Surface enhanced Raman spectroscopy: new materials, concepts, characterization tools, and applications (2005)

Surface-enhanced Raman spectroscopy (SERS) is currently experiencing a renaissance in its development driven by the remarkable discovery of single molecule SERS (SMSERS) and the explosion of interest in nanophotonics and plasmonics. Because excitation of the localized surface plasmon resonance (LSPR) of a nanostructured surface or nanoparticle lies at the heart of SERS, it is important to control all of the factors influencing the LSPR in order to maximize signal strength and ensure reproducibility. These factors include material, size, shape, interparticle spacing, and dielectric environment. All of these factors must be carefully controlled to ensure that the incident laser light maximally excites the LSPR in a reproducible manner. This article describes the use of nanosphere lithography for the fabrication of highly reproducible and robust SERS substrates for both fundamental studies and applications. Atomic layer deposition (ALD) is introduced as a novel fabrication method for dielectric spacers to study the SERS distance dependence and control the nanoscale dielectric environment. Wavelength scanned SER excitation spectroscopy (WS SERES) measurements show that enhancement factors approximately 10(8) are obtainable from NSL-fabricated surfaces and provide new insight into the electromagneticfield enhancement mechanism. Tip-enhanced Raman spectroscopy (TERS) is an extremely promising new development to improve the generality and information content of SERS. A 2D correlation analysis is applied to SMSERS data. Finally, the first in vivo SERS glucose sensing study is presented.
49.4L: Late‐News Paper : Highly Transmissive One Side Emission OLED Panel for Novel Lighting Applications (2013)

Abstract We fabricated a transmissive one‐side‐emission organic light emitting diode (OLED) based on a stripe‐shaped cathode. The fabricated transmissive OLED whose panel size is 180 × 90 mm 2 showed high transmittance of 68% with the luminance ratio of the bright side to the dark side of 70.
Can a Metastatic Gene Expression Profile Outperform Tumor Size as a Predictor of Occult Lymph Node Metastasis in Oral Cancer Patients? (2011)

These results suggest that our gene expression markers of OSCC metastasis hold promise for improving current clinical practice. Confirmation by others and functional studies of CTONG2002744 is warranted.
Ecological "Blind Spots" in the Structure and Content of Recent Evangelical Systematic Theologies (2000)

Almost a generation ago Francis Schaeˆer issued a challenge for the evangelical church to take more seriously issues of environmental stewardship: “God’s calling to the . . . Christian community . . . is that we should exhibit a substantial healing, here and now, between man and nature and nature itself, as far as Christians can bring it to pass.” 1 Many segments of the evangelical community have in fact responded positively to Schaeˆer’s challenge in the last two decades. Evangelical theologians, however, have exhibited a rather uneven record in their incorporation of environmental concerns into the basic fabric of their theologies. The purpose of this paper is to argue that certain “blind spots” in the structure and content of recent evangelical systematic theologies have contributed to the neglect of environmental issues and environmental stewardship in certain segments of the evangelical subculture. 2 More speci cally, it will be argued that de ciencies in the doctrines of creation and the atonement in evangelical systematic theology textbooks have contributed to this problem. After a brief introduction to the historical background of evangelical theological re ection on environmental issues, an “ecological audit” of the treatment of these two critical theological loci will be undertaken for twenty representative evangelical systematic theology texts published since 1970. The paper will conclude with an analysis of the results, and with a call for evangelical theologians to correct an imbalance in the treatment of the doctrine of creation and an omission in the doctrine of the atonement, so as to provide a more adequate theological basis for evangelical environmental ethics.
Exploiting basic block value locality with block reuse (1999)

Value prediction at the instruction level has been introduced to allow more aggressive speculation and reuse than previous techniques. We investigate the input and output values of basic blocks and find that these values can be quite regular and predictable, suggesting that using compiler support to extend value prediction and reuse to a coarser granularity may have substantial performance benefits. For the SPEC benchmark programs evaluated, 90% of the basic blocks have fewer than 4 register inputs, 5 live register outputs, 4 memory inputs and 2 memory outputs. About 16% to 41% of all the basic blocks are simply repeating earlier calculations when the programs are compiled with the -O2 optimization level in the GCC compiler. We evaluate the potential benefit of basic block reuse using a novel mechanism called a block history buffer. This mechanism records input and live output values of basic blocks to provide value prediction and reuse at the basic block level. Simulation results show that using a reasonably sized block history buffer to provide basic block reuse in a 4-way issue superscalar processor can improve execution time for the tested SPEC programs by 1% to 14% with an overall average of 9%.
Larotrectinib efficacy and safety in TRK fusion cancer: An expanded clinical dataset showing consistency in an age and tumor agnostic approach (2018)

Background: TRK fusion cancer results from gene fusions involving NTRK1, NTRK2 or NTRK3. Larotrectinib, the first selective TRK inhibitor, has demonstrated an overall response rate (ORR) of 75% with a favorable safety profile in the first 55 consecutively enrolled adult and pediatric patients with TRK fusion cancer (Drilon et al.,NEJM2018). Here, we report the clinical activity of larotrectinib in an additional 35 TRK fusion cancer patients and provide updated follow-up of the primary analysis set (PAS) of 55 patients as of 19thFeb 2018. Methods: Patients with TRK fusion cancer detected by molecular profiling from 3 larotrectinib clinical trials (NCT02122913, NCT02637687, and NCT02576431) were eligible.Larotrectinib was administered until disease progression, withdrawal, or unacceptable toxicity. Disease status was assessed using RECIST version 1.1. Results: As of Feb 2018, by independent review, 6 PRs in the PAS deepened to CRs. The median duration of response (DoR) and progression-free survival in the PAS had still not been reached, with 12.9 months median follow-up. At 1 year, 69% of responses were ongoing, 58% of patients remained progression-free and 90% of patients were alive. An additional 19 children and 25 adults (age range, 0.1-78 years) with TRK fusion cancer were enrolled after the PAS, and included cancers of the salivary gland, thyroid, lung, colon, melanoma, sarcoma, GIST and congenital mesoblastic nephroma. In 35 evaluable patients, the ORR by investigator assessment was 74% (5 CR, 21 PR, 6 SD, 2 PD, 1 not determined). In these patients, with median follow-up of 5.5 months, median DoR had not yet been reached, and 88% of responses were ongoing at 6 months, consistent with the PAS. Adverse events (AEs) were predominantly grade 1, with dizziness, increased AST/ALT, fatigue, nausea and constipation the most common AEs reported in ≥ 10% of patients. No AE of grade 3 or 4 related to larotrectinib occurred in more than 5% of patients. Conclusions: TRK fusions are detected in a broad range of tumor types. Larotrectinib is an effective age- and tumor-agnostic treatment for TRK fusion cancer with a positive safety profile. Screening patients for NTRK gene fusions in solid- and brain tumors should be actively considered. Clinical trial identification: NCT02122913, NCT02637687, and NCT02576431. Legal entity responsible for the study: Loxo Oncology, Inc. Funding: Loxo Oncology, Inc. Disclosure: S.G. Dubois: Fees for consulting and advisory board roles: Loxo Oncology. N. Federman: Honoraria from ad boards: Bayer AG and Loxo Oncology. S. Cruickshank: Paid consultant: Loxo Oncology, Inc. N.C. Ku, M.C. Cox: Employee and stockholder: Loxo Oncology, Inc. All other authors have declared no conflicts of interest.
Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis (2018)

During embryogenesis, cells acquire distinct fates by transitioning through transcriptional states. To uncover these transcriptional trajectories during zebrafish embryogenesis, we sequenced 38,731 cells and developed URD, a simulated diffusion-based computational reconstruction method. URD identified the trajectories of 25 cell types through early somitogenesis, gene expression along them, and their spatial origin in the blastula. Analysis of Nodal signaling mutants revealed that their transcriptomes were canalized into a subset of wild-type transcriptional trajectories. Some wild-type developmental branch points contained cells that express genes characteristic of multiple fates. These cells appeared to trans-specify from one fate to another. These findings reconstruct the transcriptional trajectories of a vertebrate embryo, highlight the concurrent canalization and plasticity of embryonic specification, and provide a framework with which to reconstruct complex developmental trees from single-cell transcriptomes.
3-Cyclohexene-1-glycine, an Isoleucine Antagonist (1958)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT3-Cyclohexene-1-glycine, an Isoleucine AntagonistJerome Edelson, John D. Fissekis, Charles G. Skinner, and William ShiveCite this: J. Am. Chem. Soc. 1958, 80, 11, 2698–2700Publication Date (Print):June 1, 1958Publication History Published online1 May 2002Published inissue 1 June 1958https://pubs.acs.org/doi/10.1021/ja01544a028https://doi.org/10.1021/ja01544a028research-articleACS PublicationsRequest reuse permissionsArticle Views144Altmetric-Citations28LEARN 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
Germ-line mutations of the APC gene in 53 familial adenomatous polyposis patients. (1992)

We searched for germ-line mutations of the APC gene in 79 unrelated patients with familial adenomatous polyposis using a ribonuclease protection analysis coupled with polymerase chain reaction amplifications of genomic DNA. Mutations were found in 53 patients (67%); 28 of the mutations were small deletions and 2 were 1- to 2-base-pair insertions; 19 were point mutations resulting in stop codons and only 4 were missense point mutations. Thus, 92% of the mutations were predicted to result in truncations of the APC protein. More than two-thirds (68%) of the mutations were clustered in the 5' half of the last exon, and nearly two-fifths of the total mutations occurred at one of five positions. This information has significant implications for understanding the role of APC mutation in inherited forms of colorectal neoplasia and for designing effective methods for genetic counseling and presymptomatic diagnosis.
The Treatment of Chlorosis by Iron and some Other Drugs (1893)

IT is generally agreed that chlorosis may be cured by the administration of iron preparations by the mouth, but opinions differ widely and fundamentally as to the way in which the cure is brought about. So long ago as 1821 Wohler advanced the opinion that iron is not absorbed from the alimentary canal, because he failed to detect it in the urine after giving it per o8, while Kletzinsky (1854) experimenting on himself, and finding in his fmeces as much iron as het had previously swallowed, came to the same conclusion. These views have received support from a considerable number of cotemporary and later observers. On the other hand, Becquerel, Herberger, Naase, Quevenne, and many others have believed it to be absorbed, but no rigorous proof of its absorption has ever been given. It is unnecessary to discuss the older literaturp, as the whole question has been reworked in recent years with iimproved methods and much greater accuracy. At the present time there are three chief thieories as to the modus operandi of iron. I. THB ABSORPTION THEORY.
Titanium–Salan‐Catalyzed Asymmetric Epoxidation with Aqueous Hydrogen Peroxide as the Oxidant (2006)

Keep it simple: A titanium complex with a salan ligand bearing phenyl groups at C3 and C3′ is an efficient catalyst for the enantioselective epoxidation of unfunctionalized olefins with aqueous hydrogen peroxide (see scheme); furthermore, the epoxidation was stereospecific. The C3 and C3′ substituents stabilize this complex and enhance the asymmetric induction.
Virtual Adversarial Training: A Regularization Method for Supervised and Semi-Supervised Learning (2017)

We propose a new regularization method based on virtual adversarial loss: a new measure of local smoothness of the conditional label distribution given input. Virtual adversarial loss is defined as the robustness of the conditional label distribution around each input data point against local perturbation. Unlike adversarial training, our method defines the adversarial direction without label information and is hence applicable to semi-supervised learning. Because the directions in which we smooth the model are only "virtually" adversarial, we call our method virtual adversarial training (VAT). The computational cost of VAT is relatively low. For neural networks, the approximated gradient of virtual adversarial loss can be computed with no more than two pairs of forward- and back-propagations. In our experiments, we applied VAT to supervised and semi-supervised learning tasks on multiple benchmark datasets. With a simple enhancement of the algorithm based on the entropy minimization principle, our VAT achieves state-of-the-art performance for semi-supervised learning tasks on SVHN and CIFAR-10.