gebhart/patrepeval huggingface dataset:
The Transcriptional Activator GCN4 Contains Multiple Activation Domains That Are Critically Dependent on Hydrophobic Amino Acids (1995)

GCN4 is a transcriptional activator in the bZIP family that regulates amino acid biosynthetic genes in the yeast Saccharomyces cerevisiae. Previous work suggested that the principal activation domain of GCN4 is a highly acidic segment of approximately 40 amino acids located in the center of the protein. We conducted a mutational analysis of GCN4 with a single-copy allele expressed under the control of the native promoter and translational control elements. Our results indicate that GCN4 contains two activation domains of similar potency that can function independently to promote high-level transcription of the target genes HIS3 and HIS4. One of these domains is coincident with the acidic activation domain defined previously; the other extends over the N-terminal one-third of the protein. Both domains are partially dependent on the coactivator protein ADA2. Each domain appears to be composed of two or more small subdomains that have additive effects on transcription and that can cooperate in different combinations to promote high-level expression of HIS3 and HIS4. At least three of these subdomains are critically dependent on bulky hydrophobic amino acids for their function. Five of the important hydrophobic residues, Phe-97, Phe-98, Met-107, Tyr-110, and Leu-113, fall within a region of proposed sequence homology between GCN4 and the herpesvirus acidic activator VP16. The remaining three residues, Trp-120, Leu-123, and Phe-124, are highly conserved between GCN4 and its Neurospora counterpart, cpc-1. Because of the functional redundancy in the activation domain, mutations at positions 97 and 98 must be combined with mutations at positions 120 to 124 to observe a substantial reduction in activation by full-length GCN4, and substitution of all eight hydrophobic residues was required to inactivate full-length GCN4. These hydrophobic residues may mediate important interactions between GCN4 and one or more of its target proteins in the transcription initiation complex.
Calcium in Ischemic Cell Death (1998)

Calcium is one of the triggers involved in ischemic cell death, whatever the mechanism.
Structural organization of the Helicoverpa zea gene encoding the precursor protein for pheromone biosynthesis-activating neuropeptide and other neuropeptides. (1994)

Sex pheromone biosynthesis in a number of moth species is induced by a conserved 33-amino acid amidated neuropeptide PBAN (pheromone biosynthesis-activating neuropeptide). We have isolated and characterized the Helicoverpa zea PBAN cDNA corresponding to a 766-nucleotide mRNA that is expressed in the subesophageal ganglion of adult moths. This mRNA is encoded on a transcription unit comprising 6 exons. The longest open reading frame of the cDNA encodes a 194-amino acid precursor protein that contains the PBAN peptide sequence. Proteolytic processing of this protein, which has structural features consistent with its being a preprohormone, is predicted to generate Hez-PBAN and four additional neuropeptides having a common C-terminal pentapeptide motif, Phe-Xaa-Pro-(Arg or Lys)-Leu (Xaa = Gly, Ser, or Thr), which is also found in insect pyrokinin and myotropin peptide families.
The signal peptidase II (lsp) gene of Bacillus subtilis (1997)

The gene encoding the type II signal peptidase (SPase II) of Bacillus subtilis was isolated by screening a genomic DNA library of this bacterium for the ability to increase the levels of globomycin resistance in Escherichia coli, and to complement the growth deficiency at the non-permissive temperature of E. coli strain Y815 carrying a temperature-sensitive mutation in its Isp gene for SPase II. The deduced amino acid sequence of the B. subtilis SPase II showed significant similarity with those of other known SPase II enzymes. Activity of the B. subtilis SPase II was demonstrated by a pulse-labelling experiment in E. coli. In B. subtilis, the Isp gene is flanked by the isoleucyl-tRNA synthetase (ileS) gene and the pyrimidine biosynthetic (pyr) gene cluster, which is known to map at 139 degrees of the chromosome. In the Gram-positive bacteria studied thus far, Isp appears to be the first gene in an operon. The promoter-distal gene ("orf4') of this operon specifies a hypothetical protein in bacteria and yeast.
The Evolution of the Brain, the Human Nature of Cortical Circuits, and Intellectual Creativity (2011)

The tremendous expansion and the differentiation of the neocortex constitute two major events in the evolution of the mammalian brain. The increase in size and complexity of our brains opened the way to a spectacular development of cognitive and mental skills. This expansion during evolution facilitated the addition of microcircuits with a similar basic structure, which increased the complexity of the human brain and contributed to its uniqueness. However, fundamental differences even exist between distinct mammalian species. Here, we shall discuss the issue of our humanity from a neurobiological and historical perspective.
Detection of minimal residual disease in acute promyelocytic leukemia by a reverse transcription polymerase chain reaction assay for the PML/RAR-alpha fusion mRNA (1993)

The characteristic reciprocal translocation t(15;17) of acute promyelocytic leukemia (APL) disrupts the PML gene on chromosome 15 and the retinoic acid receptor-alpha (RAR-alpha) gene on chromosome 17. PML/RAR-alpha fusion mRNAs are then transcribed and can be detected by a newly described reverse transcription polymerase chain reaction (RT-PCR) assay. Using RT followed by nested PCR amplification for PML/RAR-alpha, we serially evaluated bone marrow aspirates from patients with APL who were treated with all-trans retinoic acid (RA) for induction, followed by all-trans RA as maintenance or cytotoxic drugs as consolidation. At diagnosis, PML/RAR-alpha mRNA was detected in all patients. After initial therapy with all-trans RA, the RT-PCR assay remained positive after induction of complete remission in 31 of 32 evaluable patients. Maintenance treatment by all-trans RA alone was associated with persistent assay positivity and subsequent clinical relapse in 13 of 13 patients. By contrast, the test became negative in 19 of 20 newly diagnosed patients who received consolidation chemotherapy; the 1 patient who remained positive relapsed at 12 months. Three of the 19 assay-negative patients later converted to positive and subsequently relapsed; the remaining 16 patients have remained RT-PCR negative in sustained first remission, with a median follow-up duration that exceeds 24 months (range, 12+ to 34+ months). Despite induction of complete remission in a high proportion of patients, all-trans RA rarely eradicates molecular evidence of disease in patients with APL; however, subsequent treatment with cytotoxic chemotherapy frequently converts the RT-PCR assay for PML/RAR-alpha to negative. Serial negative tests are associated with prolonged disease-free survival, whereas persistence of a positive test after treatment is highly correlated with subsequent relapse. This test identifies patients in remission at high risk for relapse who may benefit from additional antileukemic therapy.
Characterization of Integrin–Tetraspanin Adhesion Complexes (1999)

Tetraspanins (or proteins from the transmembrane 4 superfamily, TM4SF) form membrane complexes with integrin receptors and are implicated in integrin-mediated cell migration. Here we characterized cellular localization, structural composition, and signaling properties of alpha3beta1-TM4SF adhesion complexes. Double-immunofluorescence staining showed that various TM4SF proteins, including CD9, CD63, CD81, CD82, and CD151 are colocalized within dot-like structures that are particularly abundant at the cell periphery. Differential extraction in conjunction with chemical cross-linking indicated that the cell surface fraction of alpha3beta1-TM4SF protein complexes may not be directly linked to the cytoskeleton. However, in cells treated with cytochalasin B alpha3beta1-TM4SF protein complexes are relocated into intracellular vesicles suggesting that actin cytoskeleton plays an important role in the distribution of tetraspanins into adhesion structures. Talin and MARCKS are partially codistributed with TM4SF proteins, whereas vinculin is not detected within the tetraspanin-containing adhesion structures. Attachment of serum-starved cells to the immobilized anti-TM4SF mAbs induced dephosphorylation of focal adhesion kinase (FAK). On the other hand, clustering of tetraspanins in cells attached to collagen enhanced tyrosine phosphorylation of FAK. Furthermore, ectopic expression of CD9 in fibrosarcoma cells affected adhesion-induced tyrosine phosphorylation of FAK, that correlated with the reorganization of the cortical actin cytoskeleton. These results show that tetraspanins can modulate integrin signaling, and point to a mechanism by which TM4SF proteins regulate cell motility.
25th Anniversary Article: A Soft Future: From Robots and Sensor Skin to Energy Harvesters (2013)

Scientists are exploring elastic and soft forms of robots, electronic skin and energy harvesters, dreaming to mimic nature and to enable novel applications in wide fields, from consumer and mobile appliances to biomedical systems, sports and healthcare. All conceivable classes of materials with a wide range of mechanical, physical and chemical properties are employed, from liquids and gels to organic and inorganic solids. Functionalities never seen before are achieved. In this review we discuss soft robots which allow actuation with several degrees of freedom. We show that different actuation mechanisms lead to similar actuators, capable of complex and smooth movements in 3d space. We introduce latest research examples in sensor skin development and discuss ultraflexible electronic circuits, light emitting diodes and solar cells as examples. Additional functionalities of sensor skin, such as visual sensors inspired by animal eyes, camouflage, self-cleaning and healing and on-skin energy storage and generation are briefly reviewed. Finally, we discuss a paradigm change in energy harvesting, away from hard energy generators to soft ones based on dielectric elastomers. Such systems are shown to work with high energy of conversion, making them potentially interesting for harvesting mechanical energy from human gait, winds and ocean waves.
New asymmetrical limb structured blue emitting material for OLED [Invited] (2014)

New asymmetric limb-structured blue light emitting material, composed of anthracene main core, naphthalene units at 9,10-position of anthracene and m-(di(trifluoromethylphenyl)) units at 2,3-positon of anthracene was designed and developed. And non-doped organic light-emitting diodes have been realized. The maximum efficiency of 1.72 cd/A and the quantum efficiency was around 0.67%.
Surface active fluorosilicone polymers (1994)

Abstract The introduction of low‐intermolecular‐force, aliphatic fluorocarbon groups into siloxane polymers has produced a variety of useful, low surface tension materials including R f (CH 2 ) 2 SiO 3/2 self‐assembled polymer monolayers and silsesquioxane polymers, and [R f (CH 2 ) 2 MeSiO] n siloxanes. The surface tensions of such materials measured by the contact angle approaches of Owens‐Wendt and Girifalco‐Good‐Fowkes‐Young are reviewed and compared with the direct determination from work of adhesion studies based on the Johnson, Kendall and Roberts theory. The lowest surface tension fluorosilicones available are as oleophobic and hydrophobic as any known fluoropolymer. The most efficient, effective incorporation of fluorine in these fluorosilicones is generally achieved with the CF 3 (CF 2 ) 3 (CH 2 ) 2 group, making these nonafluorohexyl‐containing species the most commercially attractive.
PLATINUM-DNA ADDUCT IN HEAD AND NECK-CANCER PATIENTS RECEIVING CISPLATIN AND CARBOPLATIN CHEMOTHERAPY (1993)

Sixteen patients with squamous cell carcinoma of the head and neck region were studied for the formation of platinum-DNA adduct in leukocyte DNA. Every patient received carboplatin and cisplatin, each given intravenously on day 1 of 21-day treatment cycles. Blood was obtained for DNA isolation 24 hours after treatment on cycles 1 and 2; and on the morning before cycle 2 of therapy (21 days after cycle 1 drug delivery). Adduct was measured by atomic absorbance spectrometry with Zeeman background correction. As has been shown in previous studies, adduct persistence and accumulation could be demonstrated in a portion of the cohort. Adduct removal from blood cell DNA during the 21 days of cycle number 1, was determined for 12 patients. In these patients, adduct removal was directly i-elated to clinical resistance to the cisplatin/carboplatin treatment regimen; and adduct removal was inversely related to leukocyte toxicity. These data demonstrate that changes in adduct levels with time may provide valuable information, in the study of the human in vivo biology of platinum-DNA damage and repair.
Influence of the series resistance of on-chip power supply buses on internal device failure after ESD stress (MOS devices) (1993)

Bus wires of on-chip power supplies are resistive because of their limited width. During an ESD event, this resistance initiates a local internal overvoltage through a high discharge current peak, which can cause damage to internal source/drain areas. A detailed description of the mechanism that causes this internal damage and a simple estimation of the minimum width of power supply buses on semiconductor devices is given. Additional protection circuits for improving the ESD resistivity against internal failure are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Real-Time Impedance Monitoring During Electroporation Processes in Vegetal Tissue Using a High-Performance Generator (2020)

Classical application of electroporation is carried out by using fixed protocols that do not clearly assure the complete ablation of the desired tissue. Nowadays, new methods that pursue the control of the treatment by studying the change in impedance during the applied pulses as a function of the electric field are being developed. These types of control seek to carry out the treatment in the fastest way, decreasing undesired effects and treatment time while ensuring the proper tumour ablation. The objective of this research is to determine the state of the treatment by continuously monitoring the impedance by using a novel versatile high-voltage generator and sensor system. To study the impedance dynamics in real time, the use of pulses of reduced voltage, below the threshold of reversible electroporation, is tested to characterise the state-of-the-treatment without interfering with it. With this purpose, a generator that provides both low voltage for sense tissue changes and high voltage for irreversible electroporation (IRE) was developed. In conclusion, the characterisation of the effects of electroporation in vegetal tissue, combined with the real-time monitoring of the state-of-the-treatment, will enable the provision of safer and more effective treatments.
Improved water and lipid suppression for 3D PRESS CSI using rf band selective inversion with gradient dephasing (basing) (1997)

A T1 insensitive solvent suppression technique-band selective inversion with gradient dephasing (BASING)-was developed to suppress water and lipids for 1H magnetic resonance spectroscopy (MRS). BASING, which consists of a frequency selective RF inversion pulse surrounded by spoiler gradient pulses of opposite signs, was used to dephase stopband resonances and minimally impact passband metabolites. Passband phase linearity was achieved with a dual BASING scheme. Using the Shinnar-Le Roux algorithm, a highpass filter was designed to suppress water and rephase the lactate methyl doublet independently of TE, and water/lipid bandstop filters were designed for the brain and prostate. Phantom and in vivo experimental 3D PRESS CSI data were acquired at 1.5 T to compare BASING with CHESS and STIR suppression. With BASING, the measured suppression factor was over 100 times higher than with CHESS or STIR causing baseline distortions to be removed. It was shown that BASING can be incorporated into a variety of sequences to offer improved suppression in the presence of B1 and T1 inhomogeneites.
Photonic Crystals: Molding the Flow of Light (1995)

Since it was first published in 1995, Photonic Crystals has remained the definitive text for both undergraduates and researchers on photonic band-gap materials and their use in controlling the propagation of light. This newly expanded and revised edition covers the latest developments in the field, providing the most up-to-date, concise, and comprehensive book available on these novel materials and their applications. Starting from Maxwell's equations and Fourier analysis, the authors develop the theoretical tools of photonics using principles of linear algebra and symmetry, emphasizing analogies with traditional solid-state physics and quantum theory. They then investigate the unique phenomena that take place within photonic crystals at defect sites and surfaces, from one to three dimensions. This new edition includes entirely new chapters describing important hybrid structures that use band gaps or periodicity only in some directions: periodic waveguides, photonic-crystal slabs, and photonic-crystal fibers. The authors demonstrate how the capabilities of photonic crystals to localize light can be put to work in devices such as filters and splitters. A new appendix provides an overview of computational methods for electromagnetism. Existing chapters have been considerably updated and expanded to include many new three-dimensional photonic crystals, an extensive tutorial on device design using temporal coupled-mode theory, discussions of diffraction and refraction at crystal interfaces, and more. Richly illustrated and accessibly written, Photonic Crystals is an indispensable resource for students and researchers.Extensively revised and expanded Features improved graphics throughout Includes new chapters on photonic-crystal fibers and combined index-and band-gap-guiding Provides an introduction to coupled-mode theory as a powerful tool for device design Covers many new topics, including omnidirectional reflection, anomalous refraction and diffraction, computational photonics, and much more.
Coupling transcriptional and post-transcriptional miRNA regulation in the control of cell fate (2009)

miRNAs function as a critical regulatory layer in development, differentiation, and the maintenance of cell fate. Depletion of miRNAs from embryonic stem cells impairs their differentiation capacity. Total elimination of miRNAs leads to premature senescence in normal cells and tissues through activation of the DNA-damage checkpoint, whereas ablation of miRNAs in cancer cell lines results in an opposite effect, enhancing their tumorigenic potential. Here we compile evidence from the literature that point at miRNAs as key players in the maintenance of genomic integrity and proper cell fate. There is an apparent gap between our understanding of the subtle way by which miRNAs modulate protein levels, and their profound impact on cell fate. We propose that examining miRNAs in the context of the regulatory transcriptional and post-transcriptional networks they are embedded in may provide a broader view of their role in controlling cell fate.
A comparison of enteropathogenic and enterohaemorrhagicEscherichia colipathogenesis (2006)

This review covers enteropathogenic Escherichia coli (EPEC) and enterohaemorrhagic E. coli (EHEC) infections, focusing on differences in their virulence factors and regulation. While Shiga-toxin expression from integrated bacteriophages sets EHEC apart from EPEC, EHEC infections often originate from asymptomatic carriage in ruminants whereas human EPEC are considered to be overt pathogens and more host-restricted. In part, these differences reflect variation in adhesin repertoire, type III-secreted effectors and the way in which these factors are regulated.
Translocon Pores in the Endoplasmic Reticulum Are Permeable to a Neutral, Polar Molecule (2001)

The pore of the translocon complex in the endoplasmic reticulum (ER) is large enough to be permeated by small molecules, but it is generally believed that permeation is prevented by a barrier at the luminal end of the pore. We tested the hypothesis that 4-methylumbelliferyl alpha-d-glucopyranoside (4MalphaG), a small, neutral dye molecule, cannot permeate an empty translocon pore by measuring its activation by an ER resident alpha-glucosidase, which is dependent on entry into the ER. The basal entry of dye into the ER of broken Chinese hamster ovary-S cells was remarkably high, and it was increased by the addition of puromycin, which purges translocon pores of nascent polypeptides, creating additional empty pores. The basal and puromycin-dependent entries of 4MalphaG were mediated by a common, salt-sensitive pathway that was partially blocked by spermine. A similar activation of 4MalphaG was observed in nystatin-perforated cells, indicating that the entry of 4MalphaG into the ER did not result simply from the loss of cytosolic factors in broken cells. We reject the hypothesis and conclude that a small, neutral molecule can permeate the empty pore of a translocon complex, and we propose that translationally inactive, ribosome-bound translocons could provide a pathway for small molecules to cross the ER membrane.
Dicing and slicing (2005)

RNA interference (RNAi) is broadly defined as a gene silencing pathway that is triggered by double-stranded RNA (dsRNA). Many variations have been described on this theme. The dsRNA trigger can be supplied exogenously, as an experimental tool, or can derive from the genome in the form of microRNAs. Gene silencing can be the result of nucleolytic degradation of the mRNA, or by translational suppression. At the heart of the pathway are two ribonuclease machines. The ribonuclease III enzyme Dicer initiates the RNAi pathway by generating the active short interfering RNA trigger. Silencing is effected by the RNA-induced silencing complex and its RNaseH core enzyme Argonaute. This review describes the discovery of these machines and discusses future lines of work on this amazing biochemical pathway.
Asymmetric Catalysis of Intramolecular Cyclopropanation of 5‐Aryl‐1‐diazo‐1‐mesitylsulfonyl‐5‐hexen‐2‐ones (2005)

Abstract We have examined the catalytic asymmetric intramolecular cyclopropanation (IMCP) reactions of 5‐aryl‐1‐diazo‐1‐mesitylsulfonyl‐5‐hexen‐2‐ones, and found that the substituent of the 5‐aryl group dramatically changes the enantioselectivity. That is, no enantioselectivity was observed when the substituent was a methoxy group; however, enantioselectivity was moderate when the substituent was a methylenedioxy group or a tert ‐butyldimethylsilyloxy group, and it dramatically increased when the substituent was lacking (96% ee) or a benzoyloxy group (93% ee).