gebhart/patrepeval huggingface dataset:
[Structural and functional organization of ACTH: synthesis and properties of analogs of ACTH-(11-24)-tetradeca- and ACTH-(1-24)-tetracosapeptides containing hexa-amino acids instead of a natural sequence of ACTH 19-24 amino acids]. (1984)

To assess the role of amino acid sequence ACTH 19-24 in the corticotropin structure and steroidogenic activity, the analogues of ACTH-(11-24)-tetradeca- and ACTH-(1-24)-tetracosapeptides containing hexaglycine, hexaphenylalanine, hexaglutamic acid or hexalysine instead of the natural 19-24 sequence have been synthesized by conventional methods. All these compounds in water have the CD curves characteristic of random coil, CD spectra of analogue ACTH-(1-24)-tetracosapeptide and hexalysine-containing analogue ACTH-(11-24)-tetradecapeptide in trifluoroethanol indicate the presence of alpha-helices. The latter compound manifested higher steroidogenic activity than ACTH-(11-24)-tetradecapeptide. All the other analogues were either less active than ACTH-(1-24)-tetracosapeptide or inactive over the concentration range 10(-5)-10(2) mg/ml, thereby testifying to functional importance of the 19-24 sequence for manifesting full steroidogenic activity.
Hydrogen sulfide: A multifunctional gaseous molecule in plants (2013)

Hydrogen sulfide (H2S), a gaseous transmitter, has long been considered as a phytotoxin, but nowadays as a small molecule with multiple functions fulfilled at low concentrations. H2S has many positive effects on plant growth, development, and the acquisition of plant stress tolerance. The focus of this review is to summarize the generation and properties of hydrogen sulfide and its potential physiological functions, including mediating stomatal movements; mediating the responses to abiotic stressors, such as heavy metals, salt, drought, and heating; involving in organogenesis and growth; regulating senescence; priming seed germination; and enhancing photosynthesis. Future prospects are also presented.
Back and forth (1994)

That some membranes restrict certain lipid species to one side of the bilayer and others to the opposite side has been known for two decades. However, how this asymmetric transbilayer distribution is generated and controlled, how many and what type of membranes are so structured, and even the reason for its existence is just now beginning to be understood. It has been a decade since the discovery of an activity which transports in an ATP-dependent manner only the aminophospholipids from the outer to the inner leaflet of the plasma membrane. This aminophospholipid translocase has yet to be isolated, reconstituted, and identified molecularly. Elevating intracellular Ca2+ allows all the major classes of phospholipids to move freely across the bilayer, scrambling lipids and dissipating asymmetry. The nature of this pathway and its mode of activation by Ca2+ remain to be determined. Though loss of transbilayer asymmetry by blood cells clearly produces a procoagulant surface and increases interactions with the reticuloendothelial system, it remains to be elucidated whether maintenance of blood homeostasis is just one expression of a more general raison d'être for lipid asymmetry. It is these persisting uncertainties and gaps in our knowledge which make the field such an interesting and exciting challenge at the present time.
Characterization of the Domain Structure of Chick c-erbA by Deletion Mutation:in VitroTranslation and Cell Transfection Studies (1989)

Chicken c-erbA (Ck-c-erbA) cDNA (1250 base pairs), a cellular homologue of the avian erythroblastosis virus v-erbA gene, encodes a 408 amino acid protein which binds L-T3 and its analogs with affinities similar to that of endogenous thyroid hormone nuclear receptors. By analogy with steroid receptors, Ck-c-erbA(Met1-Val408) contains an A and B domain (amino acids 1-50); a putative DNA binding C domain (amino acids 51-118); a hydrophilic D domain (amino acids 119-189); and a putative ligand binding E domain (amino acids 187-408). To further characterize the ligand binding region of Ck-c-erbA, two deletion mutations were constructed: Ck-c-erbA(Met120-Val408) which encodes a 289 amino acid protein lacking regions A, B, and C; and Ck-c-erbA-(Met199-Val408) which encodes a 210 amino acid protein lacking regions A, B, C, D, and the first 12 amino acids of the E region. The in vitro translation products ([35S]methionine) of cDNA transcripts of a human placental c-erbA, Ck-c-erbA (Met1-Val408), and Ck-c-erbA(Met120-Val408) efficiently bind L-[125I]T3, whereas Ck-c-erbA(Met199-Val408) does not bind L-[125I]T3. In frame substitution of the last 14 C-terminal amino acids of Ck-c-erbA(Met1-Val408) for the last 7 C-terminal amino acids of v-erbA reduces but does not eliminate L[125I]T3 binding. These results indicate that a broad region of the E domain is important for ligand binding.(ABSTRACT TRUNCATED AT 250 WORDS)
CRISPR Cpf1 proteins: structure, function and implications for genome editing (2019)

CRISPR and CRISPR-associated (Cas) protein, as components of microbial adaptive immune system, allows biologists to edit genomic DNA in a precise and specific way. CRISPR-Cas systems are classified into two main classes and six types. Cpf1 is a putative type V (class II) CRISPR effector, which can be programmed with a CRISPR RNA to bind and cleave complementary DNA targets. Cpf1 has recently emerged as an alternative for Cas9, due to its distinct features such as the ability to target T-rich motifs, no need for trans-activating crRNA, inducing a staggered double-strand break and potential for both RNA processing and DNA nuclease activity. In this review, we attempt to discuss the evolutionary origins, basic architectures, and molecular mechanisms of Cpf1 family proteins, as well as crRNA designing and delivery strategies. We will also describe the novel Cpf1 variants, which have broadened the versatility and feasibility of this system in genome editing, transcription regulation, epigenetic modulation, and base editing. Finally, we will be reviewing the recent studies on utilization of Cpf1as a molecular tool for genome editing.
THE ROLE OF FIBROBLAST TRANSDIFFERENTIATION IN LUNG EPITHELIAL CELL PROLIFERATION, DIFFERENTIATION, AND REPAIR IN VITRO (2003)

Parathyroid hormone-related protein (PTHrP) expression is necessary for differentiation of mesenchymal lipofibroblasts, which induce epithelial type II (TII) cell differentiation, both of which are necessary for alveolarization. PTHrP deficiency may be associated with bronchopulmonary dysplasia (BPD), characterized by truncation of alveolarization among preterm infants. This is supported by the baboon model of BPD (failure of alveolarization) that manifests PTHrP deficiency. We provide evidence that TII cell PTHrP expression is downregulated by alveolar overdistension, resulting in the transdifferentiation of lipofibroblasts to myofibroblasts, characterized by progressive loss of PTHrP receptor expression and triglyceride content, and sequential upregulation of alpha-smooth muscle actin (alphaSMA), typifying fibrosis. PTHrP reverses the downregulation of the PTHrP receptor and upregulation of alphaSMA, reverting myofibroblasts to a lipofibroblast genotype. When TII cells are co-cultured with lipofibroblasts, they proliferate and differentiate, expressing surfactant protein-B; in contrast, TII cells co-cultured with myofibroblasts fail to develop, mimicking the failed alveolarization associated with BPD. Treatment of myofibroblasts with 15-deoxy-Delta 12, 14 prostaglandinJ(2) (PGJ(2)) stimulates ADRP expression, reconstituting the lipofibroblast phenotype. PGJ(2)-treated myofibroblasts promote TII cell growth and surfactant protein-B expression, indicating that failed alveolarization due to transdifferentiation is reversible. We conclude that alveolar overdistension can cause fibroblast transdifferentiation, resulting in failed alveolarization.
The current state of xenotransplantation (2014)

Pigs as a source of grafts for xenotransplantation can help to overcome the rapidly growing shortage of human donors. However, in the case of pig-to-human transplantation, the antibody-xenoantigen complexes lead to the complement activation and immediate hyperacute rejection. Methods eliminating hyperacute rejection (HAR) include α1,3-galactosyltransferase (GGTA1) inactivation, regulation of the complement system and modification of the oligosaccharide structure of surface proteins. The humoral immune response control and reduction of the risk of coagulation disorders are the priority tasks in attempts to overcome acute humoral xenograft rejection that may occur after the elimination of HAR. The primary targets for research are connected with the identification of obstacles and development of strategies to tackle them. Because of the magnitude of factors involved in the immune, genetic engineers face a serious problem of producing multitransgenic animals in the shortest possible time.
Multiplex Detection of Bacteria Associated with Normal Microbiota and with Bacterial Vaginosis in Vaginal Swabs by Use of Oligonucleotide-Coupled Fluorescent Microspheres (2009)

Bacterial vaginosis (BV) is a recurrent condition that is associated with a range of negative outcomes, including the acquisition of human immunodeficiency virus and other sexually transmitted diseases, preterm births, and pelvic inflammatory disease. In contrast to the Lactobacillus-dominated normal vaginal microbiota, BV is characterized by a lack of lactobacilli and an abundance of anaerobic and gram-negative organisms, including Gardnerella vaginalis and Atopobium vaginae. To date, the laboratory diagnosis of BV has relied upon the fulfillment of criteria determined by microscopic observation of Gram-stained vaginal swabs. We describe a molecular-based method for the easy determination of the species profile within the vaginal microbiota based on the amplification of the chaperonin-60 genes of all bacteria present in the swab and hybridization of the amplicon to species-specific oligonucleotide-coupled fluorescent beads that are identified by flow cytometry with a Luminex instrument. We designed a nineplex Luminex array for characterization of the vaginal microbiota and applied it to the analysis of vaginal swabs from individuals from Africa and North America. Using the presence of A. vaginae or G. vaginalis, or both, as the defining criterion for BV, we found that the method was highly specific and sensitive for the diagnosis of BV using microscopy as a gold standard.
Concepts and Categories: A Cognitive Neuropsychological Perspective (2008)

One of the most provocative and exciting issues in cognitive science is how neural specificity for semantic categories of common objects arises in the functional architecture of the brain. More than two decades of research on the neuropsychological phenomenon of category-specific semantic deficits has generated detailed claims about the organization and representation of conceptual knowledge. More recently, researchers have sought to test hypotheses developed on the basis of neuropsychological evidence with functional imaging. From those two fields, the empirical generalization emerges that object domain and sensory modality jointly constrain the organization of knowledge in the brain. At the same time, research within the embodied cognition framework has highlighted the need to articulate how information is communicated between the sensory and motor systems, and processes that represent and generalize abstract information. Those developments point toward a new approach for understanding category specificity in terms of the coordinated influences of diverse regions and cognitive systems.
A radioscientist's reaction to Marconi's first transatlantic wireless experiment-revisited (2002)

On 12 December 1901 signals from a high power spark transmitter located at Poldhu, Cornwall, were reported to have been heard by Marconi and his assistant George Kemp at a receiving site on Signal Hill near St. John's, Newfoundland. For this reception experiment, Marconi used a kite supported wire aerial, an untuned receiver, a detector of uncertain performance and a telephone receiver. The signals, if heard, would have traveled a distance of 3500 kilometres. Even at the time of the experiment there were those who said, indeed there are some who still say, that he misled himself and the world into believing that atmospheric noise crackling was in fact the Morse code letter "S". A little later, in February 1902, when Marconi was returning to North America on the SS Philadelphia, using a tuned ship-borne antenna, he received signals using his filings coherer from the same sender up to distances of 1120 km by day and 2500 km by night. Even these distances are rather remarkable considering the receiving apparatus he used. This paper revisits that first transatlantic experiment and concludes that it is difficult to believe that signals could have been heard on Signal Hill.
Mutant SV40 large T antigen as a therapeutic agent for HER-2/neu-overexpressing ovarian cancer. (1996)

The HER-2/neu gene is frequently amplified and/or its protein product, p185, is overexpressed in a number of human cancers. Overexpression of p185 correlates with poor prognosis and low survival rates in ovarian cancer patients. We previously found that the K1 mutant of SV40 large T antigen inhibits rat neu promoter and suppresses mutation-activated rat neu transformation in mouse fibroblasts. We show here that K1 also inhibits human HER-2/neu promoter in human ovarian cancer cells. To investigate whether K1 can suppress HER-2/neu transformation and thus is a potential therapeutic agent, we used an orthotopic ovarian cancer model in which mice were injected intraperitoneally with HER-2/neu-overexpressing human ovarian cancer cells to induce tumor development. The tumor-bearing mice were then treated with K1-liposome complex weekly. We found that liposome-mediated K1 gene transfer decreased the p185 protein level by K1 expression in these cancer cells and significantly prolonged mice survival; about 40% of these treated mice were alive for more than 1 year without any tumor development. On the other hand, the animals from control groups that did not receive this gene therapy all developed tumors and died within 7 months. The results indicate that liposome-mediated K1 gene transfer is able to suppress tumor development from HER-2/neu-overexpressing ovarian cancer cells in mice.
Androgens contribute to the stimulation of cancellous bone formation by ovarian hormones in female rats (1996)

We investigated whether androgens, for which the ovaries are the major source in female rats, contribute to the stimulation of cancellous bone formation by ovarian hormones in female rats. Ovariectomized animals were administered 5alpha-dihydrotestosterone (DHT; 10 and 100 microgram/kg) by daily subcutaneous injection for 13 days, after which histomorphometric analysis was performed at the proximal tibial metaphysis. To prevent ovariectomy from stimulating bone turnover, and hence complicating the interpretation of changes in bone formation, animals were also given the resorption inhibitor 3-amino-1-hydroxypropylidene-1-bisphosphonate. We found that ovariectomy markedly suppressed cancellous bone formation, which was partially prevented by DHT (100 microgram/kg). To further address whether androgens contribute to the stimulation of bone formation by ovarian hormones, we treated intact and ovariectomized female rats with the androgen antagonist flutamide (15 mg/kg/day) for 28 days. Whereas flutamide had no effect in ovariectomized rats, it significantly reduced cancellous bone formation in intact animals. We conclude that, in the female rat, androgens contribute under physiological conditions to the stimulation of cancellous bone formation by ovarian hormones.
Effect of storage in short‐ and long‐term commercial semen extenders on the motility, plasma membrane and chromatin integrity of boar spermatozoa (2006)

For artificial insemination (AI) in pigs, preservation of liquid boar semen at 16-20 degrees C is still common practice as sperm cryopreservation remains suboptimal in this species. To meet the different needs of the swine industry, several extenders have been developed to preserve semen in liquid form for short--and long-term storage. In the present study, three different commercial extenders devised for short-term (BTS+) or long-term preservation (MR-A and X-Cell), were used to test whether storage of semen from four mature, fertile boars at 17 degrees C for 96 h would affect sperm characteristics relevant for fertility, such as motility, membrane integrity and chromatin stability. Computer-assisted sperm analysis, and stainings with the acylated membrane dye SYBR-14/propidium iodide, and acridine orange in connection with flow cytometry were used to evaluate these variables. Percentages of total motile spermatozoa decreased slightly, but significantly, after 72-96 h. While membrane integrity values varied during the period of study, no significant changes in either membrane integrity or chromatin stability were, however, registered. This suggests a customary 96-day storage at 17 degrees C in these extenders was too short an interval to cause losses of integrity in nuclear DNA in the boar population studied.
A Calibrated Phase and Amplitude Control System for a 1.9 GHz Phased-Array Transmitter Element (2009)

A system is proposed to allow the phase and amplitude of a signal to be accurately set and regulated over process and power supply variations. It uses a variable gain amplifier (VGA) in conjunction with the phase shifter to compensate for the variable losses of the phase shifter and simultaneously provide a means of adjusting the amplitude of the signal. The system has been fabricated in a 0.18 ¿m CMOS process, and operates at 1.9 GHz. The phase can be set with 5 bits of control over a 240° range and the amplitude can be varied over a 20 dB range. The feedback loops reduce the variation in | <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">S</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">21</sub> | across the phase control range from 12.1 to 0.4 dB. For a changing power supply voltage the feedback loops reduce the maximum phase deviation from 28° to 7° , and across different test chips the maximum standard deviation over the phase control range is reduced from 12° to 3°.
Aspiration Pneumonitis and Aspiration Pneumonia (2001)

Aspiration is defined as the inhalation of oropharyngeal or gastric contents into the larynx and lower respiratory tract.1,2 Several pulmonary syndromes may occur after aspiration, depending on the amount and nature of the aspirated material, the frequency of aspiration, and the host's response to the aspirated material.2 Aspiration pneumonitis (Mendelson's syndrome) is a chemical injury caused by the inhalation of sterile gastric contents, whereas aspiration pneumonia is an infectious process caused by the inhalation of oropharyngeal secretions that are colonized by pathogenic bacteria. Although there is some overlap between these syndromes, they are distinct clinical entities (Table 1). Other . . .
A spontaneous mutation of integrin alpha IIb beta 3 (platelet glycoprotein IIb-IIIa) helps define a ligand binding site. (1992)

This work characterizes a mutant integrin alpha IIb beta 3 (glycoprotein (GP) IIb-IIIa) from a thrombasthenic patient, ET, whose platelets fail to aggregate in response to stimuli. The nature of defect was defined by the reduced ability of synthetic peptide ligands, corresponding to the carboxyl terminus of the fibrinogen gamma chain (gamma 402-411) and Arg-Gly-Asp (RGD), to increase the binding of the occupancy-dependent anti-LIBS1 antibody to mutant alpha IIb beta 3 and the reduced binding of mutant alpha IIb beta 3 to an immobilized RGD peptide. In addition, ET's platelets failed to bind the ligand-mimetic monoclonal anti-alpha IIb beta 3, PAC1. DNA sequence analysis of amplified ET genomic DNA revealed a single G----A base change which encoded substitution of R214 by Q in mature beta 3. Introduction of this point mutation into recombinant wild type alpha IIb beta 3 expressed in Chinese hamster ovary cells reproduced the ET platelet alpha IIb beta 3 deficits in binding of fibrinogen, mAb PAC1, and synthetic peptide ligands. Furthermore, substitution of R214 by Q in the synthetic peptide containing the sequence of beta 3(211-222) resulted in decreased ability of this peptide to block fibrinogen binding to purified alpha IIb beta 3. These findings suggest that substitution of beta 3 R214 by Q is responsible for the functional defect in alpha IIb beta 3 and that R214 is proximal to or part of a ligand binding domain in alpha IIb beta 3.
Dimerization of the bacterial effector protein AvrBs3 in the plant cell cytoplasm prior to nuclear import (2005)

The effector protein AvrBs3 from the bacterial phytopathogen Xanthomonas campestris pv. vesicatoria is translocated into the plant cell where it specifically induces hypertrophy symptoms or the hypersensitive reaction. Activity of AvrBs3 depends on nuclear localization signals (NLSs) and an acidic activation domain, suggesting a role in regulation of plant transcription. Here, we show that AvrBs3 dimerizes in the plant cell prior to its nuclear import. AvrBs3 deletion derivatives were tested in the yeast two-hybrid system revealing that the repeat region, which confers specific recognition in resistant plants and is crucial for virulence function, is also essential for the self-interaction. GST pull-down assays showed that the AvrBs3-AvrBs3 interaction occurs independent of plant proteins. Coexpression of two different inactive mutant AvrBs3 derivatives in Bs3-resistant pepper plants resulted in 'trans-complementation', i.e., the induction of a hypersensitive reaction. This clearly indicates that AvrBs3-dimerization occurs in planta. Interestingly, 'trans-complementation' was not observed in susceptible plants suggesting that wild-type homodimers are needed for the AvrBs3 virulence function in plants. Furthermore, a green fluorescent protein (GFP) fusion of AvrBs3 deleted in the NLSs (AvrBs3DeltaNLS-GFP), normally localized in the cytoplasm, was imported into the nucleus upon coexpression with wild-type AvrBs3 in Nicotiana benthamiana. Thus, AvrBs3 dimerization takes place in the cytoplasm of the plant cell prior to nuclear import. Given the fact that dimerization is a common feature of transcriptional regulators, our data are consistent with the idea that AvrBs3 manipulates expression of plant genes involved in the establishment of compatible and incompatible interactions.
Pagerank for product image search (2008)

In this paper, we cast the image-ranking problem into the task of identifying "authority" nodes on an inferred visual similarity graph and propose an algorithm to analyze the visual link structure that can be created among a group of images. Through an iterative procedure based on the PageRank computation, a numerical weight is assigned to each image; this measures its relative importance to the other images being considered. The incorporation of visual signals in this process differs from the majority of large-scale commercial-search engines in use today. Commercial search-engines often solely rely on the text clues of the pages in which images are embedded to rank images, and often entirely ignore the content of the images themselves as a ranking signal. To quantify the performance of our approach in a real-world system, we conducted a series of experiments based on the task of retrieving images for 2000 of the most popular products queries. Our experimental results show significant improvement, in terms of user satisfaction and relevancy, in comparison to the most recent Google Image Search results.