gebhart/patrepeval huggingface dataset:
MutS HOMOLOG1 Is a Nucleoid Protein That Alters Mitochondrial and Plastid Properties and Plant Response to High Light (2011)

Mitochondrial-plastid interdependence within the plant cell is presumed to be essential, but measurable demonstration of this intimate interaction is difficult. At the level of cellular metabolism, several biosynthetic pathways involve both mitochondrial- and plastid-localized steps. However, at an environmental response level, it is not clear how the two organelles intersect in programmed cellular responses. Here, we provide evidence, using genetic perturbation of the MutS Homolog1 (MSH1) nuclear gene in five plant species, that MSH1 functions within the mitochondrion and plastid to influence organellar genome behavior and plant growth patterns. The mitochondrial form of the protein participates in DNA recombination surveillance, with disruption of the gene resulting in enhanced mitochondrial genome recombination at numerous repeated sequences. The plastid-localized form of the protein interacts with the plastid genome and influences genome stability and plastid development, with its disruption leading to variegation of the plant. These developmental changes include altered patterns of nuclear gene expression. Consistency of plastid and mitochondrial response across both monocot and dicot species indicate that the dual-functioning nature of MSH1 is well conserved. Variegated tissues show changes in redox status together with enhanced plant survival and reproduction under photooxidative light conditions, evidence that the plastid changes triggered in this study comprise an adaptive response to naturally occurring light stress.
Assays for laboratory confirmation of novel human coronavirus (hCoV-EMC) infections (2012)

We present a rigorously validated and highly sensitive confirmatory real-time RT-PCR assay (1A assay) that can be used in combination with the previously reported upE assay. Two additional RT-PCR assays for sequencing are described, targeting the RdRp gene (RdRpSeq assay) and N gene (NSeq assay), where an insertion/deletion polymorphism might exist among different hCoV-EMC strains. Finally, a simplified and biologically safe protocol for detection of antibody response by immunofluorescence microscopy was developed using convalescent patient serum.
Clock distribution design and verification for PowerPC microprocessors (1995)

With the increase of clock speeds, clock skew has become a significant part of the cycle time of high speed microprocessors. While many clock tree routing techniques promise zero or minimal skew, algorithm assumptions or design methodology constraints often prevent a single approach from being suitable for the entire clock design. In this paper we describe a collection of strategies for designing low skew clock distributions. These techniques are applied at various levels of design (synthesis, placement, routing etc.) to yield clock distribution networks of acceptable skew for the two different clock design styles used by PowerPC processors. We also describe a static timing based approach for analyzing the clock network to detect the various clock violations of interest. Finally we outline current deficiencies in our methodology.
SUB1, an Arabidopsis Ca 2+ -Binding Protein Involved in Cryptochrome and Phytochrome Coaction (2001)

Cryptochromes and phytochromes are the major photosensory receptors in plants and often regulate similar photomorphogenic responses. The molecular mechanisms underlying functional interactions of cryptochromes and phytochromes remain largely unclear. We have identified an Arabidopsis photomorphogenic mutant, sub1, which exhibits hypersensitive responses to blue light and far-red light. Genetic analyses indicate that SUB1 functions as a component of a cryptochrome signaling pathway and as a modulator of a phytochrome signaling pathway. The SUB1 gene encodes a Ca2+-binding protein that suppresses light-dependent accumulation of the transcription factor HY5.
Cellular Antioxidant Activity (CAA) Assay for Assessing Antioxidants, Foods, and Dietary Supplements (2007)

A cellular antioxidant activity (CAA) assay for quantifying the antioxidant activity of phytochemicals, food extracts, and dietary supplements has been developed. Dichlorofluorescin is a probe that is trapped within cells and is easily oxidized to fluorescent dichlorofluorescein (DCF). The method measures the ability of compounds to prevent the formation of DCF by 2,2'-azobis(2-amidinopropane) dihydrochloride (ABAP)-generated peroxyl radicals in human hepatocarcinoma HepG2 cells. The decrease in cellular fluorescence when compared to the control cells indicates the antioxidant capacity of the compounds. The antioxidant activities of selected phytochemicals and fruit extracts were evaluated using the CAA assay, and the results were expressed in micromoles of quercetin equivalents per 100 micromol of phytochemical or micromoles of quercetin equivalents per 100 g of fresh fruit. Quercetin had the highest CAA value, followed by kaempferol, epigallocatechin gallate (EGCG), myricetin, and luteolin among the pure compounds tested. Among the selected fruits tested, blueberry had the highest CAA value, followed by cranberry > apple = red grape > green grape. The CAA assay is a more biologically relevant method than the popular chemistry antioxidant activity assays because it accounts for some aspects of uptake, metabolism, and location of antioxidant compounds within cells.
Current Strategies and Perspectives for Correcting Endothelial Dysfunction in Atherosclerosis (2001)

The vascular endothelium synthesizes and releases a spectrum of vasoactive substances such as nitric oxide and endothelin. In atherosclerosis, the delicate balance between endothelium-derived factors is disturbed. Endothelin acts as the natural counterpart to endothelium-derived nitric oxide, which exerts vasodilating, antithrombotic and antiproliferative effects, and inhibits leukocyte adhesion to the vascular wall. Besides its blood pressure increasing effect in man, endothelin also induces vascular and myocardial hypertrophy, which are independent risk factors for cardiovascular morbidity and mortality. The derangement of endothelial function in atherosclerosis is likely to be caused in part by genetic factors, but is also due to cardiovascular risk factors. Endothelial dysfunction in atherosclerosis is crucial for the development of the disease process in the vasculature and is therefore an important therapeutic target. However, the efficacy of pharmacotherapy aimed at an improvement in endothelial function depends on the individual risk factor profile of the patient.
Sequences near the 3' secretion-specific polyadenylation site influence levels of secretion-specific and membrane-specific IgG2b mRNA in myeloma cells. (1986)

The expressed immunoglobulin gamma 2b (IgG2b) heavy-chain gene of 4T001 was cloned into the shuttle vector pSV2-gpt and transfected into myeloma J558L and lymphoma A20.2J. Northern blots indicated that the transfected gamma 2b gene was processed in a manner similar to the endogenous heavy chain in both lymphoma and myeloma cells. To identify sequences important for immunoglobulin mRNA processing, we constructed deletions around the secretion-specific polyadenylation site and introduced the deleted genes into J558L cells. The BAL deletion lacked 670 base pairs of intervening sequence between secreted and membrane regions; the Kpn deletion lacked 830 base pairs in this region. J558L cells transfected with either the entire gamma 2b gene or the delta BAL vector produced predominantly secretion-specific gamma 2b mRNA and protein. J558L cells transfected with the delta Kpn vector produced approximately equimolar amounts of secretion-specific and membrane-specific gamma 2b mRNA. Both 55,000-dalton secreted and 62,000-dalton putative surface IgG2b proteins were detected in the delta Kpn transfectants. We conclude that sequences absent in the Kpn deletion but present in the BAL deletion exert an important role in the production of secretion-specific mRNA. The Kpn deletion removes the normal site of cleavage and poly(A) addition, and it is possible that it is the absence of this site which changes the processing pattern. Alternatively, it is possible that sequences absent in the Kpn deletion but present in the BAL deletion function in regulating the production of predominantly secretion-specific mRNA in myeloma cells. The possible role of a highly conserved sequence found in this region is discussed.
Prevention of Chemotherapy-Induced Alopecia in Rats by CDK Inhibitors (2001)

Most traditional cytotoxic anticancer agents ablate the rapidly dividing epithelium of the hair follicle and induce alopecia (hair loss). Inhibition of cyclin-dependent kinase 2 (CDK2), a positive regulator of eukaryotic cell cycle progression, may represent a therapeutic strategy for prevention of chemotherapy-induced alopecia (CIA) by arresting the cell cycle and reducing the sensitivity of the epithelium to many cell cycle-active antitumor agents. Potent small-molecule inhibitors of CDK2 were developed using structure-based methods. Topical application of these compounds in a neonatal rat model of CIA reduced hair loss at the site of application in 33 to 50% of the animals. Thus, inhibition of CDK2 represents a potentially useful approach for the prevention of CIA in cancer patients.
Multisite dephosphorylation and desensitization of conventional protein kinase C isotypes (1999)

The generation of antisera specific for the priming phosphorylation sites on protein kinase Calpha (PKCalpha) has permitted analysis of the dephosphorylation of these sites in relation to the down-regulation of the protein. It was demonstrated that these priming sites are subject to agonist-induced dephosphorylation, consistent with inactivation of the protein. Further, the process is shown to be blocked by a PKC inhibitor, indicating a requirement for PKC catalytic activity. This was corroborated by showing that a constitutively active fragment of PKCalpha is able to stimulate the dephosphorylation of wild-type PKCalpha in transfected cells. Consistent with a membrane-traffic event, the process controlled by PKC that leads to dephosphorylation is shown to be temperature-sensitive and to correlate with transient accumulation of PKCalpha on cytoplasmic vesicular structures. It was established that the dephosphorylation of priming sites in PKCalpha is not unique and occurs with other conventional PKC isotypes, demonstrating that this is a general desensitization process for this subclass of kinases. The physiological importance of this desensitization is evidenced by the behaviour of PKCbeta1 in U937 cells, where dephosphorylation of the activation loop site is shown to be a function of cell density.
Diffractive optics for Moon topography mapping (2006)

This paper presents the design, analysis, and testing of a diffractive optical element (DOE) to be part of the Lunar Orbiter Laser Altimeter (LOLA) instrument scheduled to launch in 2008. LOLA will be one of six instruments to orbit the Moon for a year or more as part of the Lunar Reconnaissance Orbiter (LRO). The various scientific instruments aboard the LRO will map the lunar environment in greater detail than ever before. LOLA will produce a topographic map of the Moon from a nominal 50km orbit during the one-year mission. LOLA works by bouncing laser pulses off the lunar surface as it orbits the Moon. By measuring the time it takes for light to travel to the surface and back, LOLA can calculate the roundtrip distance. Each pulse consists of five laser spots in a cross-like pattern spanning about 50 meters of the lunar surface. The spots are generated by a DOE from the single, collimated LOLA laser input beam. It is projected that LOLA will gather more than a billion measurements of the Moon's surface elevation creating a high resolution three-dimensional map of the surface.
Cyclophosphate, III. Synthese und Eigenschaften von Uridin‐3′,5′‐cyclophosphat‐estern (1977)

Abstract Die Uridin‐3′,5′‐cyclophosphat‐ester 4–11 wurden durch Reaktion der freien Säure des Uridin‐3′,5′‐cyclophosphates ( 1–3 ) mit den entsprechenden Diazoalkanen erhalten. Die Zuordnung der stereoisomeren 1,3,2λ 5 ‐Dioxaphosphorinane läßt sich mit Hilfe der 31 P‐NMR‐Spektren aufgrund einer Röntgenstrukturanalyse zeigen. Eine stereoselektive Beeinflussung durch Variation der Reaktivität der Diazokomponente oder durch sterische Hinderung an der 2′‐Position der Ribose, sowie in Abhängigkeit von der Temperatur, konnte partiell erzielt werden. Sämtliche synthetisierten Verbindungen wurden durch UV‐ und 31 P‐NMR‐Spektren charakterisiert.
Conventional explanation for ‘crossed field antenna’ (1992)

Recent papers have described the ‘crossed field antenna’, and have offered an explanation of its properties in terms of ‘Poynting vector synthesis’. In this Letter the antenna is analysed in a more conventional manner, providing an alternative explanation of its operation. The importance of the alternative is its compatibility with the Wheeler criteria for electrically small antennas. Extrapolation to very small antennas then encounters the expected efficiency-bandwidth limitations.
Ion projection lithography (1998)

In spite of the comparatively modest level of effort devoted to ion projection lithography, the results obtained so far indicate that the technology is highly promising. Accordingly, a $36M program has been launched in Europe to develop a full field, IPL process tool.
Collagen cross-linking compounds in human urine (1981)

We report the isolation and chemical characterization of collagen cross-linking compounds, 3-hydroxypyridinium and dihydroxylysinonorleucine, from human urine.
Pivotal Phase III Trial of Two Dose Levels of Denileukin Diftitox for the Treatment of Cutaneous T-Cell Lymphoma (2001)

Denileukin diftitox has been shown to be a useful and important agent in the treatment of patients whose CTCL is persistent or recurrent despite other therapeutic interventions.
Systematic and stochastic influences on the performance of the MinION nanopore sequencer across a range of nucleotide bias (2018)

Emerging sequencing technologies are allowing us to characterize environmental, clinical and laboratory samples with increasing speed and detail, including real-time analysis and interpretation of data. One example of this is being able to rapidly and accurately detect a wide range of pathogenic organisms, both in the clinic and the field. Genomes can have radically different GC content however, such that accurate sequence analysis can be challenging depending upon the technology used. Here, we have characterized the performance of the Oxford MinION nanopore sequencer for detection and evaluation of organisms with a range of genomic nucleotide bias. We have diagnosed the quality of base-calling across individual reads and discovered that the position within the read affects base-calling and quality scores. Finally, we have evaluated the performance of the current state-of-the-art neural network-based MinION basecaller, characterizing its behavior with respect to systemic errors as well as context- and sequence-specific errors. Overall, we present a detailed characterization the capabilities of the MinION in terms of generating high-accuracy sequence data from genomes with a wide range of nucleotide content. This study provides a framework for designing the appropriate experiments that are the likely to lead to accurate and rapid field-forward diagnostics.
Spatially Distinct Binding of Cdc42 to PAK1 and N-WASP in Breast Carcinoma Cells (2005)

While a significant amount is known about the biochemical signaling pathways of the Rho family GTPase Cdc42, a better understanding of how these signaling networks are coordinated in cells is required. In particular, the predominant subcellular sites where GTP-bound Cdc42 binds to its effectors, such as p21-activated kinase 1 (PAK1) and N-WASP, a homolog of the Wiskott-Aldritch syndrome protein, are still undetermined. Recent fluorescence resonance energy transfer (FRET) imaging experiments using activity biosensors show inconsistencies between the site of local activity of PAK1 or N-WASP and the formation of specific membrane protrusion structures in the cell periphery. The data presented here demonstrate the localization of interactions by using multiphoton time-domain fluorescence lifetime imaging microscopy (FLIM). Our data here establish that activated Cdc42 interacts with PAK1 in a nucleotide-dependent manner in the cell periphery, leading to Thr-423 phosphorylation of PAK1, particularly along the lengths of cell protrusion structures. In contrast, the majority of GFP-N-WASP undergoing FRET with Cy3-Cdc42 is localized within a transferrin receptor- and Rab11-positive endosomal compartment in breast carcinoma cells. These data reveal for the first time distinct spatial association patterns between Cdc42 and its key effector proteins controlling cytoskeletal remodeling.
Cardiovascular and Endocrine Alterations After Masturbation-Induced Orgasm in Women (1999)

Sexual arousal and orgasm produce a distinct pattern of neuroendocrine alterations in women, primarily inducing a long-lasting elevation in plasma prolactin concentrations. These results concur with those observed in men, suggesting that prolactin is an endocrine marker of sexual arousal and orgasm.
A multiscale approach for modeling actuation response of polymeric artificial muscles (2015)

Artificial muscles are emerging materials in the field of smart materials with applications in aerospace, robotic, and biomedical industries. Despite extensive experimental investigations in this field, there is a need for numerical modeling techniques that facilitate cutting edge research and development. This work aims at studying an artificial muscle made of twisted Nylon 6.6 fibers that are highly cold-drawn. A computationally efficient phenomenological thermo-mechanical constitutive model is developed in which several physical properties of the artificial muscles are incorporated to minimize the trial-and-error numerical curve fitting processes. Two types of molecular chains are considered at the micro-scale level that control training and actuation processes viz. (a) helically oriented chains which are structural switches that store a twisted shape in their low temperature phase and restore their random configuration during the thermal actuation process, and (b) entropic chains which are highly drawn chains that could actuate as soon as the muscle heats up, and saturates when coil contact temperature is reached. The thermal actuation response of the muscle over working temperatures has been elaborated in the Modeling section. The performance of the model is validated by available experiments in the literature. The model may provide a design platform for future artificial muscle developments.
Synergistic Antitumor Effect of Bispecific CD19 × CD3 and CD19 × CD16 Diabodies in a Preclinical Model of Non-Hodgkin’s Lymphoma (2002)

To target NK cells against non-Hodgkin's lymphoma, we constructed a bispecific diabody (BsDb) with reactivity against both human CD19 and FcgammaRIII (CD16). Bacterially produced CD19 x CD16 BsDb specifically interacted with both CD19(+) and CD16(+) cells and exhibited significantly higher apparent affinity and slower dissociation from the tumor cells than from effector cells. It was able to induce specific lysis of tumor cells in the presence of isolated human NK cells or nonfractionated PBLs. The combination of the CD19 x CD16 BsDb with a previously described CD19 x CD3 BsDb and CD28 costimulation significantly increased the lytic potential of human PBLs. Treatment of SCID mice bearing an established Burkitt's lymphoma (5 mm in diameter) with human PBLs, CD19 x CD16 BsDb, CD19 x CD3 BsDb, and anti-CD28 mAb resulted in the complete elimination of tumors in 80% of animals. In contrast, mice receiving human PBLs in combination with either diabody alone showed only partial tumor regression. These data clearly demonstrate the synergistic effect of small recombinant bispecific molecules recruiting different populations of human effector cells to the same tumor target.
Hetero Atomic-Layer Epitaxy of Ge on Si(100) (2000)

Hetero atomic-layer epitaxy of Ge on the Si(100) surface has been successfully demonstrated. The Si underlayer was found to have strong influences on the adsorption kinetics of a Ge precursor, but a discrete increase in the grown-film thickness was achieved with a one-monolayer step up to the critical thickness of the Ge layer. The periodicity of vacancy lines in the grown Ge layer is shortened in pitch with increasing the number of Ge growth cycles, reconfirming that the Ge layer was grown in a layer-by-layer manner. C atoms were not introduced in the grown film when the growth temperature was about 420°C.
Acne: Androgens and microbiology (1988)

Abstract Acne, the most prevalent disease of the skin, is a multifactorial follicular disorder in which androgens and microbiology are essential for the occurrence of the pathogenic events that characterize it. The role of the androgen is to stimulate the development and secretory activity of the sebaceous gland, which performs several important actions in the etiopathogenesis of acne. The anaerobic diphtheroid Propionibacterium acnes , a resident organism in acne‐susceptible follicles, is directly responsible for much of the inflammation in acne. This review deals with a description of these events and the therapeutic modalities that have been developed in an attempt to counteract them.
Serine at Position 2 in the DNA Recognition Helix of a Cys2-His2Zinc Finger Peptide is Not, in General, Responsible for Base Recognition (1995)

The roles of certain amino acids within zinc finger peptides of the Cys2His2 type in determining DNA-binding site specificity were investigated. A variety of three domain peptides designed using a consensus sequence framework were prepared with different potential DNA-contacting residues and tested in a recently developed specificity determination assay. Proteins with recognition helix sequence Q-1S1S2N3L4Q5K6 and QSSDLQK prefer binding subsites 5'-GAA-3' and 5'-(G/T)C(A/G)-3', respectively. Changing the Ser residues in position 2 to Ala in these proteins did not significantly affect the DNA binding site preferences, indicating that Ser residues, which occur frequently in position 2 in known zinc finger proteins are not, in general, responsible for determining binding site preferences. Examination of proteins with recognition helices HSSNLQK and ASSNLQK revealed considerable loss of binding site discrimination throughout the binding subsite. These observations provide further evidence for the importance of residues in positions -1 and 3 in determining DNA binding specificity. Moreover, these results illustrate the effects of changes of one residue in the recognition helix on binding site preferences throughout the recognition subsite.