gebhart/patrepeval huggingface dataset:
Characterization of Saccharomyces cerevisiae genes encoding subunits of cyclic AMP-dependent protein kinase. (1987)

Mutations in the SRA1 or SRA3 gene eliminate the requirement for either RAS gene (RAS1 or RAS2) in Saccharomyces cerevisiae. We cloned SRA1 and SRA3 and determined their DNA sequences. SRA1 encodes the regulatory subunit of the cyclic AMP (cAMP)-dependent protein kinase and therefore is identical to REG1 and BCY1. This gene is not essential, but its deletion confers many traits: reduction of glycogen accumulation, temperature sensitivity, reduced growth rate on maltose and sucrose, inability to grow on galactose and nonfermentable carbon sources, and nitrogen starvation intolerance. SRA3 is homologous to protein kinases that phosphorylate serine and threonine and likely encodes the catalytic subunit of the cAMP-dependent protein kinase. The wild-type SRA3 gene either triplicated in the chromosome or on episomal, low-copy plasmids behaves like spontaneous dominant SRA3 mutations by suppressing ras2-530 (RAS2::LEU2 disruption), cdc25, and cdc35 mutations. These findings indicate that the yeast RAS genes are dispensable if there is constitutive cAMP-dependent protein kinase activity.
Blend surfaces for set theoretic volume modelling systems (1985)

Most volume modelling systems are very limited in the complexity of the surfaces which they support. This is satisfactory for basic models of most mechanical components, since the functional surfaces are not usually complex. However, there are often blends between simple base surfaces. This paper presents a technique appropriate for blend definition and profile control. A discussion of blend conics is used to develop analogous surfaces for use in typical volume modelling systems. These surfaces are then used to set theoretically define bounded volumes for fillets and chamfers. Empirical results show that the method described suits many engineering applications.
A Comprehensive Analysis of IMD Behavior in RF CMOS Power Amplifiers (2004)

This paper presents a comprehensive analysis of nonlinear intermodulation distortion (IMD) behavior in RF CMOS power amplifiers (PAs). Separate analyses are presented for small- and large-signal operation regimes. Especially, a new, simple, large-signal behavioral IMD analysis method is presented that allows the mechanisms dominant for IMD generation to be identified and their individual contributions to be studied. By combining these analyses, typical IMD versus input power characteristics of MOSFET PAs can be predicted and understood for different classes of operation. Various measurements made on a 950-MHz RF CMOS PA are used to demonstrate typical behavior and validate the proposed theory. Prediction of IMD using a standard CMOS transistor model is also evaluated and is shown to give good agreement with the measurements.
RNA−Ligand Interactions:  Affinity and Specificity of Aminoglycoside Dimers and Acridine Conjugates to the HIV-1 Rev Response Element (2003)

Semisynthetic aminoglycoside derivatives may provide a means to selectively target viral RNA sites, including the HIV-1 Rev response element (RRE). The design, synthesis, and evaluation of derivatives based upon neomycin B, kanamycin A, and tobramycin conjugates of 9-aminoacridine are presented. To evaluate the importance of the acridine moiety, a series of dimeric aminoglycosides as well as unmodified "monomeric" aminoglycosides have also been evaluated for their nucleic acid affinity and specificity. Fluorescence-based binding assays that use ethidium bromide or Rev peptide displacement are used to quantify the affinities of these compounds to various nucleic acids, including the RRE, tRNA, and duplex DNA. All the modified aminoglycosides exhibit a high affinity for the Rev binding site on the RRE (K(d) <or= 10 nM), but few compounds have a high specificity for the RRE. Compared to the acridine conjugates, the dimeric and unmodified aminoglycosides exhibit good RNA over DNA selectivity, but show little differentiation between different RNA molecules. Neomycin-based derivatives consistently have the highest RNA and DNA affinities, but the lowest RRE specificity. To optimize these derivatives for RRE specificity, a series of neomycin-acridine conjugates with variable linker lengths were synthesized and evaluated. The neo-acridine conjugate with the shortest linker length has the optimal RRE specificity. Duplex DNA, on the other hand, prefers the acridine conjugate with the longest linker length, and duplex RNA (poly r[A]-r[U]) has the highest affinity for the conjugate with an intermediate linker length. Compared to neomycin B, the derivatives based upon tobramycin and kanamycin A have slightly lower RRE affinities, but better RRE specificities. These results illustrate how the binding affinity and specificity of aminoglycoside intercalator conjugates can be tuned by optimizing the linker length and by changing the identity of the aminoglycoside moiety. These results also indicate that many aminoglycoside-based ligands are capable of high-affinity binding of RNA, but achieving high site specificity remains a challenging objective.
Intraocular lens power calculation for lens exchange (2001)

Axial length and IOL manufacturer were important factors in predicting refraction power in eyes requiring IOL exchange.
European Union Regulations on Algorithmic Decision Making and a “Right to Explanation” (2017)

We summarize the potential impact that the European Union's new General Data Protection Regulation will have on the routine use of machine‐learning algorithms. Slated to take effect as law across the European Union in 2018, it will place restrictions on automated individual decision making (that is, algorithms that make decisions based on user‐level predictors) that “significantly affect” users. When put into practice, the law may also effectively create a right to explanation, whereby a user can ask for an explanation of an algorithmic decision that significantly affects them. We argue that while this law may pose large challenges for industry, it highlights opportunities for computer scientists to take the lead in designing algorithms and evaluation frameworks that avoid discrimination and enable explanation.
Δ9‐Tetrahydrocannabinol induces apoptosis in human prostate PC‐3 cells via a receptor‐independent mechanism (1999)

The effect of delta9-tetrahydrocannabinol (THC), the major psycho-active component of marijuana, in human prostate cancer cells PC-3 was investigated. THC caused apoptosis in a dose-dependent manner. Morphological and biochemical changes induced by THC in prostate PC-3 cells shared the characteristics of an apoptotic phenomenon. First, loss of plasma membrane asymmetry determined by fluorescent anexin V binding. Second, presence of apoptotic bodies and nuclear fragmentation observed by DNA staining with 4',6-diamino-2-phenylindole (DAPI). Third, presence of typical 'ladder-patterned' DNA fragmentation. Central cannabinoid receptor expression was observed in PC-3 cells by immunofluorescence studies. However, several results indicated that the apoptotic effect was cannabinoid receptor-independent, such as lack of an effect of the potent cannabinoid agonist WIN 55,212-2, inability of cannabinoid antagonist AM 251 to prevent cellular death caused by THC and absence of an effect of pertussis toxin pre-treatment.
Efficient Delivery of Sticky siRNA and Potent Gene Silencing in a Prostate Cancer Model Using a Generation 5 Triethanolamine-Core PAMAM Dendrimer (2011)

Successful achievement of RNA interference in therapeutic applications requires safe and efficient vectors for siRNA delivery. In the present study, we demonstrate that a triethanolamine (TEA)-core PAMAM dendrimer of generation 5 (G(5)) is able to deliver sticky siRNAs bearing complementary A(n)/T(n) 3'-overhangs effectively to a prostate cancer model in vitro and in vivo and produce potent gene silencing of the heat shock protein 27, leading to a notable anticancer effect. The complementary A(n)/T(n) (n = 5 or 7) overhangs characteristic of these sticky siRNA molecules help the siRNA molecules self-assemble into "gene-like" longer double-stranded RNAs thus endowing a low generation dendrimer such as G(5) with greater delivery capacity. In addition, the A(n)/T(n) (n = 5 or 7) overhangs act as protruding molecular arms that allow the siRNA molecule to enwrap the dendrimer and promote a better interaction and stronger binding, ultimately contributing toward the improved delivery activity of G(5). Consequently, the low generation dendrimer G(5) in combination with sticky siRNA therapeutics may constitute a promising gene silencing-based approach for combating castration-resistant prostate tumors or other cancers and diseases, for which no effective treatment currently exists.
arcA (dye), a global regulatory gene in Escherichia coli mediating repression of enzymes in aerobic pathways. (1988)

In Escherichia coli the levels of numerous enzymes associated with aerobic metabolism are decreased during anaerobic growth. In an arcA mutant the anaerobic levels of these enzymes are increased. The enzymes, which are encoded by different regulons, include members that belong to the tricarboxylic acid cycle, the glyoxylate shunt, the pathway for fatty acid degradation, several dehydrogenases of the flavoprotein class, and the cytochrome o oxidase complex. Transductional crosses placed the arcA gene near min O on the chromosomal map. Complementation tests showed that the arcA gene corresponded to the dye gene, which is also known as fexA, msp, seg, or sfrA because of various phenotypic properties [Bachmann, B. (1983) Microbiol. Rev. 47, 180-230]. A dye-deletion mutant was derepressed in the aerobic enzyme system. The term modulon is proposed to describe a set of regulons that are subject to a common transcriptional control.
Advantages of Perfectly Ordered 2-D Porous Pillar Arrays over Packed Bed Columns for LC Separations:  A Theoretical Analysis (2003)

A series of theoretical calculations is presented to quantify the gain in LC separation efficiency that can be expected if the traditionally used packed bed columns were replaced by columns with a perfectly ordered flow-through pore network. It is shown that a perfectly ordered 2-D array of porous cylindrical pillars could yield reduced plate heights as small as h = 0.65 (for k' ' = 0.75) to h = 0.85 (for k' ' = 2) and separation impedances as small as E = 200 (for k' ' = 0.75) to E = 300 (for k' ' = 2) without having to compromise on the porosity (epsilon = 0.4) and the retention capacity of the packed bed of spheres. Fitting the calculated van Deemter plots with Knox's equation especially shows a strong decrease of the A-term contribution, hence confirming that the improved column performance indeed stems from the increased homogeneity of the packing. The presented results, hence, provide a clear quantitative support for Knox's recent argumentation that the use of more uniform beds could greatly enhance the efficiency of pressure-driven LC.
CBTRUS Statistical Report: Primary Brain and Central Nervous System Tumors Diagnosed in the United States in 2006-2010 (2013)

The Central Brain Tumor Registry of the United States (CBTRUS), in collaboration with the CDC and NCI, is the largest population-based registry focused exclusively on primary brain and other central nervous system (CNS) tumors in the United States (US) and represents the entire US population. This report contains the most up-to-date population-based data on primary brain tumors available and supersedes all previous reports in terms of completeness and accuracy and is the first CBTRUS Report to provide the distribution of molecular markers for selected brain and CNS tumor histologies. All rates are age-adjusted using the 2000 US standard population and presented per 100,000 population. The average annual age-adjusted incidence rate (AAAIR) of all malignant and non-malignant brain and other CNS tumors was 24.25 (Malignant AAAIR=7.06, Non-malignant AAAIR=17.18). This overall rate was higher in females compared to males (26.95 versus 21.35) and non-Hispanics compared to Hispanics (24.68 versus 22.12). The most commonly occurring malignant brain and other CNS tumor was glioblastoma (14.3% of all tumors and 49.1% of malignant tumors), and the most common non-malignant tumor was meningioma (39% of all tumors and 54.5% of non-malignant tumors). Glioblastoma was more common in males, and meningioma was more common in females. In children and adolescents (age 0-19 years), the incidence rate of all primary brain and other CNS tumors was 6.21. An estimated 88,190 new cases of malignant and non-malignant brain and other CNS tumors are expected to be diagnosed in the US population in 2021 (25,690 malignant and 62,500 non-malignant). There were 83,029 deaths attributed to malignant brain and other CNS tumors between 2014 and 2018. This represents an average annual mortality rate of 4.43 per 100,000 and an average of 16,606 deaths per year. The five-year relative survival rate following diagnosis of a malignant brain and other CNS tumor was 66.9%, for a non-malignant brain and other CNS tumors the five-year relative survival rate was 92.1%.
Mode of Action of 5-Fluorocytosine and Mechanisms of Resistance (1975)

Mode of action of 5-fluorocytosine (5-FC) and mechanisms of resistance to the drug are discussed on the basis of experiments performed with Candida albicans ATCC 26790 and with 50 selected clinical isolates of C. albicans belonging to serological type A or B and representing various degrees and models of 5-FC resistance (sensitivity). Incorporation of 5-fluorouridylic acid into RNA appeared as a prerequisite to antifungal activity, although at a given incorporation rate, growth inhibition varied considerably from one strain to the other. The amino acid pool was unbalanced, and there was evidence for disturbance of protein synthesis. These dysfunctions of RNA probably account for growth inhibition and cell death, whereas up to the present, there was no proof of formation of 5-fluorodeoxyuridylic acid nor of subsequent inhibition of thymidylate synthetase. Incorporation of fluorinated pyrimidine into RNA was lower in normally sensitive type B strains than in normally sensitive ones of type A, whereas the frequency of 5-FC-resistant mutants was the same. The two serological types did not differ in the activity of cytosine permease nor in that of cytosine deaminase. Among 29 clinical isolates with 6-FC resistance (or impaired sensitivity) no instance of cytosine permease deficiency was found. Two isolates (belonging to the serological type A) were deficient in cytosine deaminase, whereas the majority was probably deficient in uridine monophosphate pyrophosphorylase or had a surplus of de novo synthesis of pyrimidines. Relative 5-FC resistance was more common than complete resistance.
Clinical, Cellular, and Molecular Aspects of Cancer Invasion (2003)

Invasion causes cancer malignancy. We review recent data about cellular and molecular mechanisms of invasion, focusing on cross-talk between the invaders and the host. Cancer disturbs these cellular activities that maintain multicellular organisms, namely, growth, differentiation, apoptosis, and tissue integrity. Multiple alterations in the genome of cancer cells underlie tumor development. These genetic alterations occur in varying orders; many of them concomitantly influence invasion as well as the other cancer-related cellular activities. Examples discussed are genes encoding elements of the cadherin/catenin complex, the nonreceptor tyrosine kinase Src, the receptor tyrosine kinases c-Met and FGFR, the small GTPase Ras, and the dual phosphatase PTEN. In microorganisms, invasion genes belong to the class of virulence genes. There are numerous clinical and experimental observations showing that invasion results from the cross-talk between cancer cells and host cells, comprising myofibroblasts, endothelial cells, and leukocytes, all of which are themselves invasive. In bone metastases, host osteoclasts serve as targets for therapy. The molecular analysis of invasion-associated cellular activities, namely, homotypic and heterotypic cell-cell adhesion, cell-matrix interactions and ectopic survival, migration, and proteolysis, reveal branching signal transduction pathways with extensive networks between individual pathways. Cellular responses to invasion-stimulatory molecules such as scatter factor, chemokines, leptin, trefoil factors, and bile acids or inhibitory factors such as platelet activating factor and thrombin depend on activation of trimeric G proteins, phosphoinositide 3-kinase, and the Rac and Rho family of small GTPases. The role of proteolysis in invasion is not limited to breakdown of extracellular matrix but also causes cleavage of proinvasive fragments from cell surface glycoproteins.
TNK–Tissue Plasminogen Activator Compared With Front-Loaded Alteplase in Acute Myocardial Infarction (1998)

TNK-tPA, given as a single 40-mg bolus, achieved rates of TIMI grade 3 flow similar to those of the 90-minute bolus and infusion of tPA. Weight-adjusting TNK-tPA appears to be important in achieving optimal reperfusion; reduced heparin dosing appears to improve safety for both agents. Together with the safety results from the parallel Assessment of the Safety of a New Thrombolytic: TNK-tPA (ASSENT I) trial, an appropriate dose of this single-bolus thrombolytic agent has been identified for phase III testing.
Computer assisted screening for lung cancer based on helical CT images (2002)

Describes a computer assisted automatic diagnosis system for lung cancer that detects tumor candidates at an early stage using helical computed tomography (CT) images. This automation of the process reduces the time and complexity and increases the confidence of diagnosis. The authors' algorithm consists of an analysis part and a diagnosis part. In the analysis part, the authors' method extracts the lung regions and the pulmonary blood vessels regions and analyzes the features of these regions using an image processing technique. In the diagnosis part, diagnostic rules are defined based on these features, and tumor candidates are detected using these rules. The authors apply their algorithm to the data of 450 mass screening patients. The results show that the algorithm detects lung cancer candidates successfully.
Social Attention: Modeling Attention in Human Crowds (2018)

Robots that navigate through human crowds need to be able to plan safe, efficient, and human predictable trajectories. This is a particularly challenging problem as it requires the robot to predict future human trajectories within a crowd where everyone implicitly cooperates with each other to avoid collisions. Previous approaches to human trajectory prediction have modeled the interactions between humans as a function of proximity. However, that is not necessarily true as some people in our immediate vicinity moving in the same direction might not be as important as other people that are further away, but that might collide with us in the future. In this work, we propose Social Attention, a novel trajectory prediction model that captures the relative importance of each person when navigating in the crowd, irrespective of their proximity. We demonstrate the performance of our method against a state-of-the-art approach on two publicly available crowd datasets and analyze the trained attention model to gain a better understanding of which surrounding agents humans attend to, when navigating in a crowd.
Lessons from hydrodynamic turbulence (2006)

Turbulent flows, with their irregular behavior, confound any simple attempts to understand them. But physicists have succeeded in identifying some universal properties of turbulence and relating them to broken symmetries.
Diverse Heterocyclic Scaffolds as Allosteric Inhibitors of AKT (2012)

Wide-ranging exploration of potential replacements for a quinoline-based inhibitor of activation of AKT kinase led to number of alternative, novel scaffolds with potentially improved potency and physicochemical properties. Examples showed predictable DMPK properties, and one such compound demonstrated pharmacodynamic knockdown of phosphorylation of AKT and downstream biomarkers in vivo and inhibition of tumor growth in a breast cancer xenograft model.
Identification of a virulence locus encoding a second type III secretion system in Salmonella typhimurium. (1996)

Mapping the insertion points of 16 signature-tagged transposon mutants on the Salmonella typhimurium chromosome led to the identification of a 40-kb virulence gene cluster at minute 30.7. This locus is conserved among all other Salmonella species examined but is not present in a variety of other pathogenic bacteria or in Escherichia coli K-12. Nucleotide sequencing of a portion of this locus revealed 11 open reading frames whose predicted proteins encode components of a type III secretion system. To distinguish between this and the type III secretion system encoded by the inv/spa invasion locus known to reside on a pathogenicity island, we refer to the inv/spa locus as Salmonella pathogenicity island (SPI) 1 and the new locus as SPI2. SPI2 has a lower G+C content than that of the remainder of the Salmonella genome and is flanked by genes whose products share greater than 90% identity with those of the E. coli ydhE and pykF genes. Thus SPI2 was probably acquired horizontally by insertion into a region corresponding to that between the ydhE and pykF genes of E. coli. Virulence studies of SPI2 mutants have shown them to be attenuated by at least five orders of magnitude compared with the wild-type strain after oral or intraperitoneal inoculation of mice.
Plasmin-Sensitive Dibasic Sequences in the Third Fibronectin-like Domain of L1–Cell Adhesion Molecule (Cam) Facilitate Homomultimerization and Concomitant Integrin Recruitment (2000)

L1 is a multidomain transmembrane neural recognition molecule essential for neurohistogenesis. While moieties in the immunoglobulin-like domains of L1 have been implicated in both heterophilic and homophilic binding, the function of the fibronectin (FN)-like repeats remains largely unresolved. Here, we demonstrate that the third FN-like repeat of L1 (FN3) spontaneously homomultimerizes to form trimeric and higher order complexes. Remarkably, these complexes support direct RGD-independent interactions with several integrins, including alpha(v)beta(3) and alpha(5)beta(1). A pep- tide derived from the putative C-C' loop of FN3 (GSQRKHSKRHIHKDHV(852)) also forms trimeric complexes and supports alpha(v)beta(3) and alpha(5)beta(1) binding. Substitution of the dibasic RK(841) and KR(845) sequences within this peptide or the FN3 domain limited multimerization and abrogated integrin binding. Evidence is presented that the multimerization of, and integrin binding to, the FN3 domain is regulated both by conformational constraints imposed by other domains and by plasmin- mediated cleavage within the sequence RK( downward arrow)HSK( downward arrow)RH(846). The integrin alpha(9)beta(1), which also recognizes the FN3 domain, colocalizes with L1 in a manner restricted to sites of cell-cell contact. We propose that distal receptor ligation events at the cell-cell interface may induce a conformational change within the L1 ectodomain that culminates in receptor multimerization and integrin recruitment via interaction with the FN3 domain.