gebhart/patrepeval huggingface dataset:
DETERMINATION OF SERUM PROTEINS BY MEANS OF THE BIURET REACTION (1949)

In the course of an investigation of the biochemical changes following experimental liver injury we felt the need of a simple, rapid, and accurate method for determining the protein fractions in small amounts of serum. Among the simpler procedures known, the biuret reaction seemed to offer the most encouraging possibilities. Variations and improvements in the application of the biuret reaction to clinical chemistry can be traced in the works of Autenrieth (l), Hiller (2), Fine (3), Kingsley (4), and Robinson and Hogden (5). Kingsley (6) simplified the technique by adding serum directly to a “one piece” reagent. Efforts have been made to increase the stability of such biuret reagents with ethylene glycol (7), tartrate (8), and citrate (9)) We began our investigation with Kingsley’s (6) method and report briefly on the two main difficulties encountered in its use. The first is that the total protein (TP) reagent and, to a lesser extent, the albumin (ALB) reagent are not sufficiently stable. The length of time they remain so depends upon the technique of their preparation. One consequence of this variable stability is a difficulty in duplicating calibration curves with different lots of reagent. Errors may arise when results with a new reagent are read from an old calibration curve. Serious errors occur if a reagent is used after the separation of any black deposit gives evidence of deterioration. A second difficulty has been that total protein estimations made with the TP reagent and read, as prescribed, from calibration curves prepared with the ALB reagent have tended to be too low. Recorded in Table I are the results of a number of analyses in which Kingsley’s biuret procedure has been compared with the Kjeldahl method2 on both normal and ab-
Potassium ion recognition by 15-crown-5 functionalized CdSe/ZnS quantum dots in H2O (2005)

Based on 15-crown-5 functionalized CdSe/ZnS quantum dots (QDs), we report a novel fluorogenic sensor to probe K+ ions in H2O; recognition of K+ can be achieved via the Förster type of energy transfer between two different color QDs, so that [K+] of the order of 10(-6) M can be promptly detected.
Anti-α4 integrin antibody suppresses the development of multiple myeloma and associated osteoclastic osteolysis (2004)

Supporting roles of stromal cells in preferential colonization of myeloma cells in bone marrow and development of associated osteoclastic osteolysis through cell-cell interactions have been indicated. Here we examined the effects of a monoclonal antibody to alpha4 integrin (anti-alpha4 Ab) that disrupts myeloma cell-stromal cell interactions mediated via alpha4beta1 integrin and vascular cell adhesion molecule-1 (VCAM-1) on myeloma cell growth in bone marrow and accompanying osteolysis. The anti-alpha4 Ab decreased VCAM-1-stimulated 5TGM1/luc cell growth in culture. The 5TGM1 murine myeloma cells stably transfected with the firefly luciferase (5TGM1/luc) were inoculated from tail vein in bg/xid/nd mice. Preventative administration of the anti-alpha4 Ab suppressed the elevation of serum IgG2b levels, decreased 5TGM1/luc tumor burden with increased apoptosis in bone and spleen, reduced bone destruction with diminished number of osteoclasts, and prolonged survival of 5TGM1/luc-bearing mice. In contrast, therapeutic administration of the antibody failed to show these effects. However, therapeutic administration of the antibody combined with melphalan significantly suppressed serum IgG2b levels and tumor burden in bone. Our results suggest that the interactions with stromal cells via alpha4beta1/VCAM-1 are critical to the development of myeloma and associated osteolysis and that disruption of these interactions using anti-alpha4 Ab is a potential therapeutic approach for myeloma.
Nod1, an Apaf-1-like Activator of Caspase-9 and Nuclear Factor-κB (1999)

Ced-4 and Apaf-1 belong to a major class of apoptosis regulators that contain caspase-recruitment (CARD) and nucleotide-binding oligomerization domains. Nod1, a protein with an NH2-terminal CARD-linked to a nucleotide-binding domain and a COOH-terminal segment with multiple leucine-rich repeats, was identified. Nod-1 was found to bind to multiple caspases with long prodomains, but specifically activated caspase-9 and promoted caspase-9-induced apoptosis. As reported for Apaf-1, Nod1 required both the CARD and P-loop for function. Unlike Apaf-1, Nod1 induced activation of nuclear factor-kappa-B (NF-kappaB) and bound RICK, a CARD-containing kinase that also induces NF-kappaB activation. Nod1 mutants inhibited NF-kappaB activity induced by RICK, but not that resulting from tumor necrosis factor-alpha stimulation. Thus, Nod1 is a leucine-rich repeat-containing Apaf-1-like molecule that can regulate both apoptosis and NF-kappaB activation pathways.
Hormone-induced meiotic maturation in Xenopus oocytes occurs independently of p70s6k activation and is associated with enhanced initiation factor (eIF)-4F phosphorylation and complex formation (1995)

Hormone-induced meiotic maturation of the Xenopus oocyte is regulated by complex changes in protein phosphorylation. It is accompanied by a stimulation in the rate of translation, manifest at the level of polypeptide chain initiation. At laser times in the maturation process, this reflects an increased ability for mRNA to interact with the 40 S ribosomal subunit. In mammalian cells there is growing evidence for the regulation of translation by phosphorylation of ribosomal protein S6 and of initiation factors responsible for the binding of mRNA to ribosomes. In this report, we show that although the 70 kDa form of S6 kinase is activated within 1.5 hours in response to progesterone or insulin, a time critical for protein synthesis, its activation is not required for hormone-induced stimulation of translation rates or maturation. In response to progesterone, activation of translation occurs in parallel with enhanced phosphate labelling of eIF-4 alpha and eIF-4 gamma and eIF-4F complex formation, events which are thought to facilitate the interaction of eIF-4F with the mRNA cap structure. However, with insulin, activation of translation occurs prior to detectable de novo phosphorylation of eIF-4F, although a small enhancement of turnover of phosphate on eIF-4 alpha may occur at this early time. With either hormone, enhanced phosphate labelling of eIF-4 alpha is shown to reflect activation of eIF-4 alpha kinase(s), which coincides temporally with activation of p42 MAP and p90rsk kinases. The possible role of initiation factor modification on increased translation rates during meiotic maturation is discussed.
Nature of electrical contacts in a metal–molecule–semiconductor system (2003)

The effects of the top electrode fabrication method on the transport properties of Au–alkanedithiol–GaAs junctions are examined. We found that diodes made by evaporating Au on 1,8-octanedithiol monolayer behave similarly to Au–GaAs junctions without the molecular layer. The direct Au–GaAs contact dominates the electrical conduction in these evaporated devices despite the presence of the molecular layer. In contrast, Au–dithiol–GaAs diodes made by nanotransfer printing (nTP) exhibit no direct contact between Au and GaAs. Electrical transport in the nTP junctions occurs through the 1,8-octanedithiol insulating layer. The low current levels and the high barrier-height values in the current–voltage results and the exponential energy dependence in the photoreponse yield that are observed in the nTP diodes support this conclusion. Since transport through the molecular layer is much less conductive, even a miniscule region of direct contact between the two electrodes will make it impossible to observe electrical transport through molecules. Fractional amounts of the different types of contacts for each kind of sample were obtained from the experimental results.
On the naturalness of software (2016)

Natural languages like English are rich, complex, and powerful. The highly creative and graceful use of languages like English and Tamil, by masters like Shakespeare and Avvaiyar, can certainly delight and inspire. But in practice, given cognitive constraints and the exigencies of daily life, most human utterances are far simpler and much more repetitive and predictable. In fact, these utterances can be very usefully modeled using modern statistical methods. This fact has led to the phenomenal success of statistical approaches to speech recognition, natural language translation, question-answering, and text mining and comprehension. We begin with the conjecture that most software is also natural , in the sense that it is created by humans at work, with all the attendant constraints and limitations---and thus, like natural language, it is also likely to be repetitive and predictable. We then proceed to ask whether (a) code can be usefully modeled by statistical language models and (b) such models can be leveraged to support software engineers. Using the widely adopted n -gram model, we provide empirical evidence supportive of a positive answer to both these questions. We show that code is also very regular, and, in fact, even more so than natural languages. As an example use of the model, we have developed a simple code completion engine for Java that, despite its simplicity, already improves Eclipse's completion capability. We conclude the paper by laying out a vision for future research in this area.
Destabilized green fluorescent protein for monitoring dynamic changes in yeast gene expression with flow cytometry (2000)

Green fluorescent protein (GFP) has many advantages as a reporter molecule, but its stability makes it unsuitable for monitoring dynamic changes in gene expression, among other applications. Destabilized GFPs have been developed for bacterial and mammalian systems to counter this problem. Here, we extend such advances to the yeast model. We fused the PEST-rich 178 carboxyl-terminal residues of the G(1) cyclin Cln2 to the C terminus of yEGFP3 (a yeast- and FACS-optimized GFP variant), creating yEGFP3-Cln2(PEST). We tested the hybrid protein after integrating modules harbouring the yEGFP3 or yEGFP3-CLN2(PEST) ORFs into the Saccharomyces cerevisiae genome. yEGFP3- Cln2(PEST) had a markedly shorter half-life (t(1/2)) than yEGFP3; inhibition of protein synthesis with cycloheximide lead to a rapid decline in GFP content and fluorescence (t(1/2) approximately 30 min) in cells expressing yEGFP3-Cln2(PEST), whereas these parameters were quite stable in yEGFP3-expressing cells (t(1/2) approximately 7 h). We placed yEGFP3-CLN2(PEST) under the control of the CUP1 promoter, which is induced only transiently by copper. This transience was readily discernible with yEGFP3-Cln2(PEST), whereas yEGFP3 reported only on CUP1 switch-on, albeit more slowly than yEGFP3-Cln2(PEST). Cell cycle-regulated transcriptional activation/inactivation of the CLN2 promoter was also discernible with yEGFP3- Cln2(PEST), using cultures that were previously synchronized with nocodazole. In comparison to CLN2, expression from the ACT1 promoter was stable after release from nocodazole. We also applied a novel flow-cytometric technique for cell cycle analysis with asynchronous cultures. The marked periodicities of CLN2 and CLB2 (mitotic cyclin) transcription were readily evident from cellular yEGFP3-Cln2(PEST) levels with this non-perturbing approach. The results represent the first reported successful destabilization of a yeast-GFP. This new construct expands the range of GFP applications open to yeast workers.
Modified enterotoxin signal sequences increase secretion level of the recombinant human epidermal growth factor in Escherichia coli (1991)

Amino acid substitutions were made in the heat-labile enterotoxin signal sequence of Escherichia coli by recombinant DNA techniques, and their influence on the secretion of recombinant human epidermal growth factor by E. coli was examined. The heat-labile enterotoxin signal sequence is an amino-terminal extension of the octadecapeptide chain and is comprised of three distinct regions: a positively charged amino-terminal region, a central hydrophobic region, and a carboxyl-terminal region with the cleavage site recognized by the signal peptidase. Some alterations in the signal sequence caused a 1.5-3.5-fold increase in the secretion of recombinant human epidermal growth factor. These were the introduction of: (i) polar and small residues into the carboxyl-terminal region (replacement of Pro-1 Leu-3 with Asn-Ala or Ser-Ala), which may give a favorable structure for the recognition and cleavage by the signal peptidase; and (ii) a polar residue into the central hydrophobic region (replacement of Ile-9 with Ser), which may cause an increase of the affinity to the cytoplasmic membrane. In the latter case, a large amount of the unprocessed "precursor" was accumulated. The combination of these modifications, however, did not work additively. An increase in the amino-terminal positive charge (insertion of Lys) had no effect on secretion. These results prove that the level of protein secretion is greatly dependent on the polarity of the carboxyl-terminal region and the hydrophobicity and/or the amphiphilicity of the central region. Moreover, the overall balance of the physicochemical properties of respective regions is important.
Purification and amino acid analysis of two human monocyte chemoattractants produced by phytohemagglutinin-stimulated human blood mononuclear leukocytes. (1989)

Physicochemical characteristics of monocyte chemotactic activity in the culture fluid of PHA-stimulated human mononuclear leukocytes (MNL) were investigated. Among several chemotactic activity peaks eluted from a TSK-2000 gel filtration column, one peak, corresponding to a molecular mass of 17 kDa, accounted for about 40% of total chemotactic activity. On a chromatofocusing column, most of the 17-kDa activity eluted in a pH range of 9.4 to 7.9. It could bind to Orange-A Sepharose. These three characteristics--molecular mass, basic isoelectric point, and dye column binding--were similar to those of human glioma-derived monocyte chemotactic factor (GDCF), recently purified in our laboratory. Therefore, the MNL-derived chemoattractant was purified by the same procedures used for purification of GDCF, namely Orange-A Sepharose chromatography, carboxymethyl (CM)-HPLC, and reverse phase (RP) HPLC. About 50% of the culture fluid chemotactic activity bound to Orange-A Sepharose and was eluted in a single peak by a NaCl gradient. The active pool from the Orange-A column was separated into two sharp peaks by CM-HPLC, each of which eluted at identical acetonitrile concentrations from a RP HPLC column. By SDS-PAGE, the peptides had apparent molecular masses of 15 and 13 kDa and appeared homogeneous. Amino acid analysis showed that the composition of the two peptides was almost identical; and the N terminus of each peptide was apparently blocked. Shared characteristics of these peptides and the GDCF peptides include identical elution patterns from CM- and RP HPLC columns, identical SDS-PAGE migration, almost identical amino acid composition, and blocked N terminus. This suggests that the monocyte attractants isolated from culture fluid of PHA-stimulated MNL are identical to those derived from human glioma cells.
Treatment of radiation side effects with oral pilocarpine (1989)

Radiation therapy is commonly utilized either alone or in combination with surgery in the treatment of malignancies arising in the upper aerodigestive tract. Frequent post-treatment sequelae include xerostomia, dysgeusia, and dysphagia. Numerous commercial products designed to decrease these symptoms have not been uniformly successful. This pilot study was designed to evaluate prospectively oral pilocarpine as a means of stimulating minor and major salivary gland flow to eradicate these radiation-induced symptoms. The results of this pilot study support the hypothesis that the salivary glands are capable of responding to oral pilocarpine, and this therapeutic approach warrants further study.
A new potent angiogenesis inhibitor,FR-118487 (1991)

A new angiogenesis inhibitor, FR-118487 was obtained by chemical modification of FR-111142 which was isolated from the fermentation products of Scolecobasidium arenarium F-2015. The antiangiogenic activity of FR-118487 was compared with that of the parent compound, FR-111142. In the endothelial cell proliferation test in vitro and the angiogenesis in the chick embryo chorioal-lantoic membrane assay, FR-118487 had about 5∼10 times stronger antiangiogenic activities than FR-111142. In addition, FR-118487 inhibited the angiogenesis in the rabbit corneal assay and suppressed the solid tumor growth in mice. These findings showed that FR-118487 would be a unique antiangiogenic agent with promising antitumor activity.
Quantitative and qualitative in vivo angiogenesis assay (2002)

We describe the development and optimization of an in vivo angiogenesis assay utilizing gelfoam sponges impregnated with 0.4% agarose and different proangiogenic factors, such as basic fibroblast growth factor (bFGF), vascular epidermal growth factor (VEGF), tumor growth factor-alpha (TGF-alpha), and endothelial growth factor (EGF). The sponges are implanted into the subcutis of mice and harvested after different times. The gelfoam sponges are fixed, sectioned, and stained with fluorescent antibodies against CD31. The median number of CD31+ cells is determined in 10 different 0.159-mm2 fields. Proangiogenic molecules induced significant migration and proliferation of endothelial cells. To demonstrate the utility of this assay for evaluation of an antiangiogenic agent, mice were implanted with gelfoam sponges containing different proangiogenic factors and treated orally with water or PTK 787, a novel tyrosine kinase inhibitor with specific activity against the VEGF-R. PTK 787 significantly inhibited angiogenesis in sponges containing agarose + VEGF but not other proangiogenic molecules. The data show that the implanted gelfoam sponges provide a reliable quantitative assay to study in vivo angiogenesis.
Purification, Properties, and Transglycosylation Reaction ofβ-N-Acetylhexosaminidase fromNocardia orientalis (1990)

β-N-Acetylhexosaminidase (EC 3.2.1.52) from the culture filtrate of Nocardia orientalis was purified to homogeneity by precipitation with ammonium sulfate followed by column chromatography on CM-Sephadex, Bio-Gel P-60, and phenyl-Sepharose CL-4B. The molecular weight of the enzyme was about 56,000 by gel filtration and 54,000 by SDS polyacrylamide gel electrophoresis. The enzyme showed about 1.6-fold higher β-N-acetylglucosaminidase activity than β-N-acetylgalactosaminidase activity. The optimum pH and temperature were 5.0 and around 70–75°C for PNP-GlcNAc, and 4.0 and 60°C for PNP–GalNAc. The enzyme was stable in the pH range from 4.0 to 8.0 and below 45°C. The enzyme hydrolyzed N-acetyl-chitooligosaccharides, di-N-acetyl-chitobiose through hexa-N-acetyl-chitohexaose. The enzyme showed glycosyl transferase activity during the hydrolysis of di-N-acetyl-chitobiose. Two major transfer products were isolated and identified as the β-(1 → 6)-linked disaccharide of N-acetylglucosamine and tri-N-acetyl-chitotriose.
Plasmonic enhanced quantum well infrared photodetector with high detectivity (2010)

We report a normal-incident quantum well infrared photodetector (QWIP) strongly coupled with surface plasmon modes. A periodic hole array perforated in gold film was integrated with In0.53Ga0.47As/InP QWIP to convert normal-incident electromagnetic waves into surface plasmon waves, and to excite the intersubband transition of carriers in the quantum wells. The peak responsivity of the photodetector at ∼8 μm was ∼7 A/W at the bias of 0.7 V at 78 K with the peak detectivity as high as ∼7.4×1010 cm Hz1/2/W. The full width at half maximum of the response spectrum was only ∼0.84 μm due to a narrow plasmonic resonance.
Effects of Antioxidant Therapy in Women Exposed to Eccentric Exercise (2004)

The purpose of this study was to determine the effects of antioxidant therapy on indirect markers of muscle damage following eccentric exercise (EE). Eighteen women were randomized to an antioxidant supplement or a placebo before a bout of EE. Plasma creatine kinase (CK) activity, muscle soreness (MS), maximal isometric force (MIF), and range of motion (ROM) were assessed before and through 14 d postexercise. Eccentric exercise resulted in an increase in CK activity and MS, and a drop in MIF and ROM during the days following EE, which returned to baseline values 14 d after EE in both groups. Antioxidants attenuated the CK activity and MS response to the EE, while little difference was noted between groups in MIF or ROM. These findings suggest that antioxidant supplementation was helpful in reducing the elevations in plasma CK activity and MS, with little impact on MIF and ROM loss.
Persistent elevations of cerebrospinal fluid concentrations of corticotropin-releasing factor in adult nonhuman primates exposed to early-life stressors: implications for the pathophysiology of mood and anxiety disorders. (1996)

There is increasing evidence for an important role of adverse early experience on the development of major psychiatric disorders in adulthood. Corticotropin-releasing factor (CRF), an endogenous neuropeptide, is the primary physiological regulator of the mammalian stress response. Grown nonhuman primates who were exposed as infants to adverse early rearing conditions were studied to determine if long-term alterations of CRF neuronal systems had occurred following the early stressor. In comparison to monkeys reared by mothers foraging under predictable conditions, infant monkeys raised by mothers foraging under unpredictable conditions exhibited persistently elevated cerebrospinal fluid (CSF) concentrations of CRF. Because hyperactivity of CRF-releasing neurons has been implicated in the pathophysiology of certain human affective and anxiety disorders, the present finding provides a potential neurobiological mechanism by which early-life stressors may contribute to adult psychopathology.
ChemInform Abstract: FOLIC ACID ANALOGS, MODIFICATIONS IN THE BENZENE‐RING REGION PART 3, NEOHOMOFOLIC AND NEOBISHOMOFOLIC ACIDS, AN IMPROVED SYNTHESIS OF FOLIC ACID AND ITS ANALOGS (1973)

Abstract Die substituierten Aniline (I) werden mit dem Aldehyd (II) zu den Anilen (III) kondensiert und diese mit Natriumborhydrid bei nachfolgender Hydrolyse in die Folsäure‐Analoga (IVa)‐(IVc) wie Neohomofolsäure (IVb) und Neobishomofolsäure (IVc) übergeführt, die an der Maus e en Leukämie L12l0‐Zellen unwirksam sind.
Muscle Weakness in Myositis: MicroRNA‐Mediated Dystrophin Reduction in a Myositis Mouse Model and Human Muscle Biopsies (2020)

These data demonstrate that an acquired dystrophin deficiency may occur through NF-κB-regulated miRNAs in myositis, thereby suggesting a unifying theme in which muscle injury, inflammation, and weakness are perpetuated both in myositis and in DMD.