gebhart/patrepeval huggingface dataset:
Reflexion and transmission at a plane screen with periodically arranged circular or elliptical apertures (1973)

A plane harmonic sound wave is considered to be incident upon a rigid plane screen that contains a periodic rectangular array of circular or elliptical apertures, and a characterization is sought for the reflexion and transmission coefficients of the scattered waves when the relationships aperture dimension [Lt ] spacing [Lt ] wavelength apply. The problem is analysed with the help of an integral equation over a single aperture and, as a consequence of the determination of the leading terms in its asymptotic solution, some prior results for more general (that is, irregular) aperture spacing are confirmed and specific features of the interaction in the periodic arrangement are established. Similar formulations are devised and given attention for the related problems in which (i) the screen is backed by a rigid infinite plane and (ii) the apertures contain rigid pistons capable of executing normal displacements compatible with an assigned and common impedance. A section is devoted to the solution, based on expansion of its kernel, for an integral equation of the first kind with a plane circular or elliptical domain.
Elucidation of crystal form diversity of the HIV protease inhibitor ritonavir by high-throughput crystallization (2003)

Pharmaceutical compounds are molecular solids that frequently exhibit polymorphism of crystal form. One high profile case of polymorphism was ritonavir, a peptidomimetic drug used to treat HIV-1 infection and introduced in 1996. In 1998, a lower energy, more stable polymorph (form II) appeared, causing slowed dissolution of the marketed dosage form and compromising the oral bioavailability of the drug. This event forced the removal of the oral capsule formulation from the market. We have carried out high-throughput crystallization experiments to comprehensively explore ritonavir form diversity. A total of five forms were found: both known forms and three previously unknown forms. The novel forms include a metastable polymorph, a hydrate phase, and a formamide solvate. The solvate was converted to form I via the hydrate phase by using a simple washing procedure, providing an unusual route to prepare the form I "disappearing polymorph" [Dunitz, J. D. & Bernstein, J. (1995) Acc. Chem. Res. 28, 193-200]. Crystals of form I prepared by using this method retained the small needle morphology of the solvate and thus offer a potential strategy for particle size and morphology control.
Thermoresponsive Polymers for Biomedical Applications (2011)

Thermoresponsive polymers are a class of “smart” materials that have the ability to respond to a change in temperature; a property that makes them useful materials in a wide range of applications and consequently attracts much scientific interest. This review focuses mainly on the studies published over the last 10 years on the synthesis and use of thermoresponsive polymers for biomedical applications including drug delivery, tissue engineering and gene delivery. A summary of the main applications is given following the different studies on thermoresponsive polymers which are categorized based on their 3-dimensional structure; hydrogels, interpenetrating networks, micelles, crosslinked micelles, polymersomes, films and particles.
Mechanism of the dicrotic pulse. (1986)

The dicrotic pulse is an abnormal carotid pulse found in conjunction with certain conditions characterised by low cardiac output. It is distinguished by two palpable pulsations, the second of which is diastolic and immediately follows the second heart sound. In the course of open chest canine studies of the second heart sound, micromanometers and an electromagnetic flow meter were used to study proximal aortic haemodynamic function in both strong and weak beats. It was found that the incisural notch of the aortic pressure signal is not strongly dependent on the extent of left ventricular ejection, and is of essentially normal amplitude even in beats having greatly reduced aortic flow. In contrast, the magnitude of the systolic upstroke of the aortic pressure pulse is strongly determined by the magnitude of left ventricular ejection and is considerably reduced in weak beats. With low cardiac output the relative size of the incisural notch becomes exaggerated in comparison with the overall pulsation, thus creating the characteristic M shaped waveform of the dicrotic pulse.
Phosphatidylinositol 3-Kinase Is Necessary but Not Sufficient for Thrombopoietin-induced Proliferation in Engineered Mpl-bearing Cell Lines as Well as in Primary Megakaryocytic Progenitors (2001)

Thrombopoietin and its receptor (Mpl) support survival and proliferation in megakaryocyte progenitors and in BaF3 cells engineered to stably express Mpl (BaF3/Mpl). The binding of thrombopoietin to Mpl activates multiple kinase pathways, including the Jak/STAT, Ras/Raf/MAPK, and phosphatidylinositol 3-kinase pathways, but it is not clear how these kinases promote cell cycling. Here, we show that thrombopoietin induces phosphatidylinositol 3-kinase and that phosphatidylinositol 3-kinase is required for thrombopoietin-induced cell cycling in BaF3/Mpl cells and in primary megakaryocyte progenitors. Treatment of BaF3/Mpl cells and megakaryocytes with the phosphatidylinositol 3-kinase inhibitor LY294002 inhibited mitotic and endomitotic cell cycl-ing. BaF3/Mpl cells treated with thrombopoietin and LY294002 were blocked in G(1), whereas megakaryocyte progenitors treated with thrombopoietin and LY294002 showed both a G(1) and a G(2) cell cycle block. Expression of constitutively active Akt in BaF3/Mpl cells restored the ability of thrombopoietin to promote cell cycling in the presence of LY294002. Constitutively active Akt was not sufficient to drive proliferation of BaF3/Mpl cells in the absence of thrombopoietin. We conclude that in BaF3/Mpl cells and megakaryocyte progenitors, thrombopoietin-induced phosphatidylinositol 3-kinase activity is necessary but not sufficient for thrombopoietin-induced cell cycle progression. Phosphatidylinositol 3-kinase activity is likely to be involved in regulating the G(1)/S transition.
Small genes/gene-products in Escherichia coli K-12 (1998)

Forty-two protein spots of observed Mr 6–15 kDa were resolved by two-dimensional gel electrophoresis, stained by Coomassie blue and subjected to Edman microsequencing. All of the proteins could be related back to their encoding open reading frames, thereby vindicating the bioinformatic tools currently utilised in their identification. However, only 14/42 gene-products were expressed as annotated. Translation was confirmed for 14 open reading frames with no attributed function (EcoGene Y-entries), while N-terminal sequence allowed the start codon to be accurately annotated for the genes yjgF, yccU, yqiC, ynfD, and yeeX. The methionine start codon was cleaved in 11 gene-products (AtpE, Hns, RpoZ, RplL, CspC, YccJ, YggX, YjgF, HimA, InfA, RpsQ) and a further five showed loss of a signal peptide (PspE, HdeB, HdeA, YnfD, YkfE). Internal (Tig, AtpA, TufA) and N-terminal fragmentation (CspD, RpsF, AtcU) of much larger proteins was also detected, which may have resulted from physiological or translational processes. Mr and pI isoforms were detected respectively for PtsH and GatB, each being phosphoproteins, as well as RplY which manifested differences with respect to predicted Mr and pI. In addition, YjgF was shown to belong to a small gene family of unknown function with ancient conserved regions across procaryotes and eucaryotes. YgiN was revealed to have a paralogue and orthologues in Bacillus subtilis, Synechocystis sp., Mycobacterium tuberculosis, Neisseria gonorrhoea, and Rhodococcus erythropolis. Orthologues are also reported for YihD, YccU and YeeX. Of the 14 Y-genes, only YkfE possessed no detectable orthologues. These results highlight the need to complement genomic analysis with detailed proteomics in order to gain a better understanding of cellular molecular biology, while the confirmation of the open reading frame start codon using Edman degradation protein microsequencing has yet to be superseded by recent advances in mass spectrometry.
Hepatotoxicity of Chemotherapy (2001)

After assessment of tumor histology, the next important factor to consider in the selection of a chemotherapy regime is organ function. Patients who are to receive chemotherapy require careful assessment of liver function prior to treatment to determine which drugs may not be appropriate, and which drug doses should be modified. Following therapy abnormalities of liver function tests may be due to the therapy rather than to progressive disease, and this distinction is of critical importance. Furthermore, not all abnormalities in liver function are due to the tumor or its treatment, and other processes, such as hepatitis, must be kept in mind. This article reviews the hepatic toxicity of chemotherapeutic agents, and suggests dose modifications based upon liver function abnormalities. Emphasis is placed on agents known to be hepatotoxic, and those agents with hepatic metabolism.
Comparison of three rapid methods for detection of antibodies to streptolysin O and DNase B (1988)

Three commercial systems were compared for ability to detect antibodies to streptolysin O (ASO) and DNase B (ADB). Streptozyme (Wampole Laboratories, Cranbury, N.J.) exhibited high sensitivity (100%) for detecting ASO but low sensitivity for ADB (22.2%). The LeapStrep (Organon Teknika, Malvern, Pa.) and Check-Spectra (Diagnostic Technology, Hauppauge, N.Y.) tests had low sensitivities for detecting ASO (35.3 and 21.4%, respectively) and ADB (22.2 and 33.3%, respectively).
Mineralogy and Isotopic Composition of Pyrites-Bearing Ejects from a Mud Volcano, Baratang, Andaman Islands (1999)

Abstract The Jarawa Creek mud volcano on Baratang Island has produced a variety of ejecta including mud containing illite, kaolinite and microfossils, volcanic glass, brine, methane gas and sulfide nodules. The nodules are of pyrite with a d34S ranging from -3.6 to 25.4‰. Sulfate leached from the mud has d34S values of -9.3 and -11.37‰. Our study reveals that the sulfate could not have been derived either from the nodules themselves or from the sea water or from connate brine. The nodules are of sedimentary origin and the most likely source of sulfate is sedimentary sulfide implying subsurface oxidation and a supply of oxidant possibly in groundwater.
Hepatocyte nuclear factor 4α in the intestinal epithelial cells protects against inflammatory bowel disease (2008)

While HNF4alpha does not have a major role in normal function of the intestine, it protects the gut against DSS-induced colitis.
Phosphorylation-Independent Regulation of the Diguanylate Cyclase WspR (2008)

Environmental signals that trigger bacterial pathogenesis and biofilm formation are mediated by changes in the level of cyclic dimeric guanosine monophosphate (c-di-GMP), a unique eubacterial second messenger. Tight regulation of cellular c-di-GMP concentration is governed by diguanylate cyclases and phosphodiesterases, which are responsible for its production and degradation, respectively. Here, we present the crystal structure of the diguanylate cyclase WspR, a conserved GGDEF domain-containing response regulator in Gram-negative bacteria, bound to c-di-GMP at an inhibitory site. Biochemical analyses revealed that feedback regulation involves the formation of at least three distinct oligomeric states. By switching from an active to a product-inhibited dimer via a tetrameric assembly, WspR utilizes a novel mechanism for modulation of its activity through oligomerization. Moreover, our data suggest that these enzymes can be activated by phosphodiesterases. Thus, in addition to the canonical pathways via phosphorylation of the regulatory domains, both product and enzyme concentration contribute to the coordination of c-di-GMP signaling. A structural comparison reveals resemblance of the oligomeric states to assemblies of GAF domains, widely used regulatory domains in signaling molecules conserved from archaea to mammals, suggesting a similar mechanism of regulation.
Sequencing of K60, Type Strain of the Major Plant Pathogen Ralstonia solanacearum (2012)

Ralstonia solanacearum is a widespread and destructive plant pathogen. We present the genome of the type strain, K60 (phylotype IIA, sequevar 7). Sequevar 7 strains cause ongoing tomato bacterial wilt outbreaks in the southeastern United States. K60 generally resembles R. solanacearum CFBP2957, a Caribbean tomato isolate, but has almost 360 unique genes.
Acquirement of Brown Fat Cell Features by Human White Adipocytes (2003)

Obesity, i.e. an excess of white adipose tissue (WAT), predisposes to the development of type 2 diabetes and cardiovascular disease. Brown adipose tissue is present in rodents but not in adult humans. It expresses uncoupling protein 1 (UCP1) that allows dissipation of energy as heat. Peroxisome proliferator-activated receptor gamma (PPAR gamma) and PPAR gamma coactivator 1 alpha (PGC-1 alpha) activate mouse UCP1 gene transcription. We show here that human PGC-1 alpha induced the activation of the human UCP1 promoter by PPAR gamma. Adenovirus-mediated expression of human PGC-1 alpha increased the expression of UCP1, respiratory chain proteins, and fatty acid oxidation enzymes in human subcutaneous white adipocytes. Changes in the expression of other genes were also consistent with brown adipocyte mRNA expression profile. PGC-1 alpha increased the palmitate oxidation rate by fat cells. Human white adipocytes can therefore acquire typical features of brown fat cells. The PPAR gamma agonist rosiglitazone potentiated the effect of PGC-1 alpha on UCP1 expression and fatty acid oxidation. Hence, PGC-1 alpha is able to direct human WAT PPAR gamma toward a transcriptional program linked to energy dissipation. However, the response of typical white adipocyte targets to rosiglitazone treatment was not altered by PGC-1 alpha. UCP1 mRNA induction was shown in vivo by injection of the PGC-1 alpha adenovirus in mouse white fat. Alteration of energy balance through an increased utilization of fat in WAT may be a conceivable strategy for the treatment of obesity.
Expression and initial characterization of five site-directed mutants of the N-terminal half-molecule of human transferrin (1991)

Five site-directed mutants of the N-terminal half-molecule of human serum transferrin have been expressed in baby hamster kidney cells and purified to homogeneity. Expression levels and overall yields varied considerably from the wild-type protein, depending on the mutant in question. The mutants are D63S, D63C, G65R, K206Q, and H207E and are based on mutations observed in a variety of transferrins of known sequence. Their molecular masses, determined by electrospray mass spectrometry, agree with theory, except for the D63C mutant, which appears to be cysteinylated. All mutants bind iron but with varying affinities; qualitatively, in increasing order D63S approximately D63C approximately G65R much less than wild type less than or equal to H207E much less than K206Q. In general, reduction of formal negative charge within the binding cleft shifts the visible spectral maximum of the iron complex toward the blue and reduces the affinity for iron, and increasing the formal negative charge shifts the visible maximum toward the red and increases the affinity for iron. The K206Q mutant is exceptional inasmuch as its visible maximum shows a blue shift, but its affinity for iron is the greatest of all of the mutants studied. All mutants reported, in addition to the wild-type protein, exhibit very similar visible molar extinction coefficients for the iron complex and very similar changes in extinction coefficients at 240 nm on binding Fe(III) or Ga(III). These results suggest that in all cases the bound metal ion is coordinated by two tyrosyl side chains.
DNA Microarrays (1999)

The complete human genes (ca. 100 000) as well as the whole spectrum of biological diversity should soon be able to be analyzed simultaneously by means of DNA microarrays using the fast technical advances that are occurring in this area. The particular strength of array analysis, typically based on the hybridization of nucleic acid probes attached to microchips with labeled RNA or DNA samples, results from the highly redundant measurement of many parallel hybridization events (see picture), which leads to an extraordinary level of assay validation.
Ag8Fluorescence in Argon (2001)

The fluorescence of Ag8 in an argon matrix and in argon droplets is reported. This is the first unambiguous assignment of the fluorescence of a metal cluster larger than the tetramer, indicating that the excited state lifetime is longer than previously thought. It is discussed as a possible result of a matrix cage effect. The excitation spectrum is compared with two-photon-ionization measurements of Ag8 in helium droplets and to known absorption data. The agreement is excellent. We propose that the excited states relax rapidly through vibrational coupling to a long-lived state, from which the fluorescence occurs.
'An act hath three branches': Being and acting in Hamlet (2012)

Not all the ‘forms, moods, shapes of grief’ can denote Hamlet truly (or so he insists) ‘for these are actions that a man might play’. This article looks at the pun on acting that is verbally and conceptually focal to Shakespeare’s 'Hamlet', starting with the fascination with Hamlet the character manifest in the nineteenth century – when the play became the central text, not just of the Shakespeare canon, but of modernity itself – and ending with speculation about Hamlet’s emotional and ideological paternity.
Ruthenium Carbene Mediated Metathesis of Oleate-Type Fatty Compounds (2008)

The complexes RuCl(2)(PCy(3))(2)(=CHPh), 1, and RuCl(2)(PCy(3))(H(2)IMes)(=CHPh), 2, proved to be active catalysts for the self-metathesis of oleate-type fatty compounds containing the ester, hydroxyl, epoxy and carboxylic acid functional groups. At elevated reaction temperatures 2 showed a higher activity, stability and lower selectivity for primary metathesis products compared to 1. A profound influence of organic functional groups on catalyst activity and selectivity was found and from relative activities and selectivities 2 has proved to be more resistant to deactivation by polar functional groups and more inclined to promote double bond isomerisation than 1. The observed catalyst deactivation by oxygen-containing functional groups could be attributed to a phosphine displacement side reaction.
Cytokines in the peritoneal fluid of patients with endometriosis (1993)

These findings support the concept that IL-5 and IL-6 but not IL-1 are associated with endometriosis.
SOI for digital CMOS VLSI: design considerations and advances (1998)

This paper reviews the recent advances of silicon-on-insulator (SOI) technology for complementary metal-oxide-semiconductor (CMOS) very-large-scale-integration memory and logic applications. Static random access memories (SRAMs), dynamic random access memories (DRAMs), and digital CMOS logic circuits are considered. Particular emphases are placed on the design issues and advantages resulting from the unique SOI device structure. The impact of floating-body in partially depleted devices on the circuit operation, stability, and functionality are addressed. The use of smart-body contact to improve the power and delay performance is discussed, as are global design issues.
Isolation of a Novel Oil Globule Protein from the Green Alga Haematococcus pluvialis (Chlorophyceae) (2011)

Cytoplasmic oil globules of Haematococcus pluvialis (Chlorophyceae) were isolated and analyzed for pigments, lipids and proteins. Astaxanthin appeared to be the only pigment deposited in the globules. Triacyglycerols were the main lipids (more than 90% of total fatty acids) in both the cell-free extract and in the oil globules. Lipid profile analysis of the oil globules showed that relative to the cell-free extract, they were enriched with extraplastidial lipids. A fatty acids profile revealed that the major fatty acids in the isolated globules were oleic acid (18:1) and linoleic acid (18:2). Protein extracts from the globules revealed seven enriched protein bands, all of which were possible globule-associated proteins. A major 33-kDa globule protein was partially sequenced by MS/MS analysis, and degenerate DNA primers were prepared and utilized to clone its encoding gene from cDNA extracted from cells grown in a nitrogen depleted medium under high light. The sequence of this 275-amino acid protein, termed the Haematococcus Oil Globule Protein (HOGP), revealed partial homology with a Chlamydomonas reinhardtii oil globule protein and with undefined proteins from other green algae. The HOGP transcript was barely detectable in vegetative cells, but its level increased by more than 100 fold within 12 h of exposure to nitrogen depletion/high light conditions, which induced oil accumulation. HOGP is the first oil-globule-associated protein to be identified in H. pluvialis, and it is a member of a novel gene family that may be unique to green microalgae.
A Phase I, Two-center Study of the Pharmacokinetics and Pharmacodynamics of Dexmedetomidine in Children (2006)

The pharmacokinetics of dexmedetomidine in children are predictable with a terminal half-life of 1.8 h. Hemodynamic responses decreased with increasing doses of dexmedetomidine. Respiratory responses were maintained, whereas sedation was transient.
Cleavage and Shedding of E-cadherin after Induction of Apoptosis (2001)

Apoptotic cell death induces dramatic molecular changes in cells, becoming apparent on the structural level as membrane blebbing, condensation of the cytoplasm and nucleus, and loss of cell-cell contacts. The activation of caspases is one of the fundamental steps during programmed cell death. Here we report a detailed analysis of the fate of the Ca(2+)-dependent cell adhesion molecule E-cadherin in apoptotic epithelial cells and show that during apoptosis fragments of E-cadherin with apparent molecular masses of 24, 29, and 84 kDa are generated by two distinct proteolytic activities. In addition to a caspase-3-mediated cleavage releasing the cytoplasmic domain of E-cadherin, a metalloproteinase sheds the extracellular domain from the cell surface during apoptosis. Immunofluorescence analysis confirmed that concomitant with the disappearance of E-cadherin staining at the cell surface, the E-cadherin cytoplasmic domain accumulates in the cytosol. In the presence of inhibitors of caspase-3 and/or metalloproteinases, cleavage of E-cadherin was almost completely blocked. The simultaneous cleavage of the intracellular and extracellular domains of E-cadherin may provide a highly efficient mechanism to disrupt cadherin-mediated cell-cell contacts in apoptotic cells, a prerequisite for cell rounding and exit from the epithelium.
Structure, Functional Expression, and Cerebral Localization of the Levocabastine-Sensitive Neurotensin/Neuromedin N Receptor from Mouse Brain (1996)

This work describes the cloning and expression of the levocabastine-sensitive neurotensin (NT) receptor from mouse brain. The receptor protein comprises 417 amino acids and bears the characteristics of G-protein-coupled receptors. This new NT receptor (NTR) type is 39% homologous to, but pharmacologically distinct from, the only other NTR cloned to date from the rat brain and the human HT29 cell line. When the receptor is expressed in Xenopus laevis oocytes, the H1 antihistaminic drug levocabastine, like NT and neuromedin N, triggers an inward current. The pharmacological properties of this receptor correspond to those of the low-affinity, levocabastine-sensitive NT binding site described initially in membranes prepared from rat and mouse brain. It is expressed maximally in the cerebellum, hippocampus, piriform cortex, and neocortex of adult mouse brain.