gebhart/patrepeval huggingface dataset:
Compact designer TALENs for efficient genome engineering (2013)

Transcription activator-like effector nucleases are readily targetable 'molecular scissors' for genome engineering applications. These artificial nucleases offer high specificity coupled with simplicity in design that results from the ability to serially chain transcription activator-like effector repeat arrays to target individual DNA bases. However, these benefits come at the cost of an appreciably large multimeric protein complex, in which DNA cleavage is governed by the nonspecific FokI nuclease domain. Here we report a significant improvement to the standard transcription activator-like effector nuclease architecture by leveraging the partially specific I-TevI catalytic domain to create a new class of monomeric, DNA-cleaving enzymes. In vivo yeast, plant and mammalian cell assays demonstrate that the half-size, single-polypeptide compact transcription activator-like effector nucleases exhibit overall activity and specificity comparable to currently available designer nucleases. In addition, we harness the catalytic mechanism of I-TevI to generate novel compact transcription activator-like effector nuclease-based nicking enzymes that display a greater than 25-fold increase in relative targeted gene correction efficacy.
Death receptor‐induced cell death in prostate cancer (2003)

Prostate cancer mortality results from metastasis and is often coupled with progression from androgen-dependent to androgen-independent growth. Unfortunately, no effective treatment for metastatic prostate cancer increasing patient survival is available. The absence of effective therapies reflects in part a lack of knowledge about the molecular mechanisms involved in the development and progression of this disease. Apoptosis, or programmed cell death, is a cell suicide mechanism that enables multicellular organisms to regulate cell number in tissues. Inhibition of apoptosis appears to be a critical pathophysiological factor contributing to the development and progression of prostate cancer. Understanding the mechanism(s) of apoptosis inhibition may be the basis for developing more effective therapeutic approaches. Our understanding of apoptosis in prostate cancer is relatively limited when compared to other malignancies, in particular, hematopoietic tumors. Thus, a clear need for a better understanding of apoptosis in this malignancy remains. In this review we have focused on what is known about apoptosis in prostate cancer and, more specifically, the receptor/ligand-mediated pathways of apoptosis as potential therapeutic targets.
Monolithic optical phased-array transceiver in a standard SOI CMOS process (2015)

Monolithic microwave phased arrays are turning mainstream in automotive radars and high-speed wireless communications fulfilling Gordon Moores 1965 prophecy to this effect. Optical phased arrays enable imaging, lidar, display, sensing, and holography. Advancements in fabrication technology has led to monolithic nanophotonic phased arrays, albeit without independent phase and amplitude control ability, integration with electronic circuitry, or including receive and transmit functions. We report the first monolithic optical phased array transceiver with independent control of amplitude and phase for each element using electronic circuitry that is tightly integrated with the nanophotonic components on one substrate using a commercial foundry CMOS SOI process. The 8 × 8 phased array chip includes thermo-optical tunable phase shifters and attenuators, nano-photonic antennas, and dedicated control electronics realized using CMOS transistors. The complex chip includes over 300 distinct optical components and over 74,000 distinct electrical components achieving the highest level of integration for any electronic-photonic system.
Oxygen binding to cobalt porphyrins (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOxygen binding to cobalt porphyrinsJames P. Collman, John I. Brauman, Kenneth M. Doxsee, Thomas R. Halbert, Susan E. Hayes, and Kenneth S. SuslickCite this: J. Am. Chem. Soc. 1978, 100, 9, 2761–2766Publication Date (Print):April 1, 1978Publication History Published online1 May 2002Published inissue 1 April 1978https://pubs.acs.org/doi/10.1021/ja00477a031https://doi.org/10.1021/ja00477a031research-articleACS PublicationsRequest reuse permissionsArticle Views1350Altmetric-Citations153LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Anomalous strain relaxation in SiGe thin films and superlattices (1991)

We describe anomalous strain relaxation in graded SiGe superlattices and thin films. This relaxation is characterized by the presence of dislocations in the Si substrate, as well as in the lower part of the film or superlattice, and results in a dislocation-free top layer. This challenges the basic assumption, dating back to Van der Merwe, that the substrate does not participate in the strain-relief process. We show that this phenomenon is due to the paucity of nucleation sites, and controlled by the specific Ge concentration profile in the film. Relaxed, defect-free ${\mathrm{Si}}_{\mathit{x}}$${\mathrm{Ge}}_{1\mathrm{\ensuremath{-}}\mathit{x}}$ films containing up to 60% Ge have been grown in this manner.
Severe Systemic Calciphylaxis in a Young Cat (2014)

alanine aminotransferase Ca 9 P calcium 9 phosphate CK creatine kinase DSH domestic shorthair H&E hematoxylin
Optimizing neurotrophic factor combinations for neurite outgrowth (2006)

Most neurotrophic factors are members of one of three families: the neurotrophins, the glial cell-line derived neurotrophic factor family ligands (GFLs) and the neuropoietic cytokines. Each family activates distinct but overlapping cellular pathways. Several studies have shown additive or synergistic interactions between neurotrophic factors from different families, though generally only a single combination has been studied. Because of possible interactions between the neurotrophic factors, the optimum concentration of a factor in a mixture may differ from the optimum when applied individually. Additionally, the effect of combinations of neurotrophic factors from each of the three families on neurite extension is unclear. This study examines the effects of several combinations of the neurotrophin nerve growth factor (NGF), the GFL glial cell-line derived neurotrophic factor (GDNF) and the neuropoietic cytokine ciliary neurotrophic factor (CNTF) on neurite outgrowth from young rat dorsal root ganglion (DRG) explants. The combination of 50 ng ml(-1) NGF and 10 ng ml(-1) of each GDNF and CNTF induced the highest level of neurite outgrowth at a 752 +/- 53% increase over untreated DRGs and increased the longest neurite length to 2031 +/- 97 microm compared to 916 +/- 64 microm for untreated DRGs. The optimum concentrations of the three factors applied in combination corresponded to the optimum concentration of each factor when applied individually. These results indicate that the efficacy of future therapies for nerve repair would be enhanced by the controlled release of a combination of neurotrophins, GFLs and neuropoietic cytokines at higher concentrations than used in previous conduit designs.
Beginning Java Databases (2001)

Both monetary loss and pain have been studied for decades, but evidence supporting the relationship between them is still lacking. We conducted a meta-analysis to explore the overlapping brain regions between monetary loss and pain, including physical pain and social pain. Regardless of the type of pain experienced, activation of the anterior insula was a shared neural representation of monetary loss and pain. The network representation pattern of monetary loss was more similar to that of social pain than that of physical pain. In conclusion, our research provided evidence of the common neural correlates of monetary loss and pain.
Somatostatin analogue (octreotide) inhibits bile duct epithelial cell proliferation and fibrosis after extrahepatic biliary obstruction. (1993)

Extrahepatic biliary obstruction leads to bile duct epithelial cell proliferation. Somatostatin and its analogue, octreotide, have been shown to inhibit DNA synthesis and proliferation in hepatocytes. We investigated the effect of octreotide on the biliary epithelial cell proliferative responses to biliary obstruction. Male Sprague-Dawley rats underwent common bile duct ligation and subcutaneous injection of either saline or octreotide (6 micrograms/kg) twice daily for 7 days. Morphometric analysis of hepatocytes, bile duct epithelial cells, and periportal connective tissue was performed by computerized point counting. Hepatocyte volume was preserved with octreotide treatment, which also significantly decreased bile duct proliferation and periportal extracellular matrix deposition in response to biliary obstruction compared with saline treated, duct-ligated animals. These results indicate that octreotide prevents the morphological changes that accompany extrahepatic biliary obstruction.
Direct Comparison of Human Mesenchymal Stem Cells Derived from Adipose Tissues and Bone Marrow in Mediating Neovascularization in Response to Vascular Ischemia (2007)

This study showed that hADSC can be an ideal source for therapeutic angiogenesis in ischemic disease in terms of efficacy, accessibility and available tissue amounts.
The Nanos gradient in Drosophila embryos is generated by translational regulation. (1996)

Abdominal segmentation in the Drosophila embryo is governed by a gradient of Nanos (Nos) emanating from the posterior pole. This gradient is derived from translation of the nos mRNA that is localized in the pole plasm; in contrast, unlocalized nos mRNA is translationally repressed. Here we define the essential signals in the 3' untranslated region (UTR) of nos mRNA. Deletion of a 184-nucleotide translational control element (TCE) from the 3' UTR leads to the derepression of nos mRNA in the bulk cytoplasm and the development of lethal anterior defects. Furthermore, a minimal mRNA containing essentially only the TCE in its 3' UTR rescues nos- embryos to adulthood. The TCE is also sufficient to confer on maternal torso mRNA all three aspects of nos mRNA regulation: translational repression in the bulk cytoplasm, localization to the pole plasm, and translational activation at the posterior pole. These three phenomena are coupled intimately, as mutations in a pair of CUGGC pentamers within the TCE simultaneously abrogate all three regulatory events. This coupling suggests a model in which the polarized distribution of nos protein is generated primarily by translational control and that nos mRNA localization is a byproduct of this regulation, at least in part.
Ribotoxic Stress Response: Activation of the Stress-Activated Protein Kinase JNK1 by Inhibitors of the Peptidyl Transferase Reaction and by Sequence-Specific RNA Damage to the α-Sarcin/Ricin Loop in the 28S rRNA (1997)

Inhibition of protein synthesis per se does not potentiate the stress-activated protein kinases (SAPKs; also known as cJun NH2-terminal kinases [JNKs]). The protein synthesis inhibitor anisomycin, however, is a potent activator of SAPKs/JNKs. The mechanism of this activation is unknown. We provide evidence that in order to activate SAPK/JNK1, anisomycin requires ribosomes that are translationally active at the time of contact with the drug, suggesting a ribosomal origin of the anisomycin-induced signaling to SAPK/JNK1. In support of this notion, we have found that aminohexose pyrimidine nucleoside antibiotics, which bind to the same region in the 28S rRNA that is the target site for anisomycin, are also potent activators of SAPK/JNK1. Binding of an antibiotic to the 28S rRNA interferes with the functioning of the molecule by altering the structural interactions of critical regions. We hypothesized, therefore, that such alterations in the 28S rRNA may act as recognition signals to activate SAPK/JNK1. To test this hypothesis, we made use of two ribotoxic enzymes, ricin A chain and alpha-sarcin, both of which catalyze sequence-specific RNA damage in the 28S rRNA. Consistent with our hypothesis, ricin A chain and alpha-sarcin were strong agonists of SAPK/JNK1 and of its activator SEK1/MKK4 and induced the expression of the immediate-early genes c-fos and c-jun. As in the case of anisomycin, ribosomes that were active at the time of exposure to ricin A chain or alpha-sarcin were able to initiate signal transduction from the damaged 28S rRNA to SAPK/JNK1 while inactive ribosomes were not.
Pharmacokinetics of Latanoprost in the Cynomolgus Monkey (2011)

Latanoprost (13,14-dihydro-15(R)-17-phenyl-18,19,20-trinor-PGF2 alpha-isopropyl ester, CAS 130209-82-4, PhXA41, Xalatan), an antiglaucoma drug, labelled with tritium at carbon 13 and 14 (4.8 micrograms, 20.8 MBq/eye) was administered topically on the eyes of cynomolgus monkeys. After 0.5 h the concentration of radioactivity in the cornea was estimated to be about 0.6 ng eq/mg tissue. The elimination half-life of total radioactivity in the cornea was about 4 h. The corneal epithelium contained a higher concentration of radioactivity than the stroma. Cornea seemed to act as a slow release depot to the anterior part of the eye. In the iris, anterior chamber and ciliary body the maximal concentrations were 217.0 +/- 12.9 pg eq/mg, 99.8 +/- 7.4 pg eq/mg and 54.0 +/- 4.9 pg eq/mg, respectively, 1 h after administration. The elimination half-life of total radioactivity from these tissues was 3-4 h. Trace amounts (0.4-9 pg eq/mg) remained in these tissues 24 h after administration. Initially the radioactivity was present in the conjunctiva, sclera and choroid as well as in the general circulation. Radioactivity passed through the lachrymal ducts and high concentrations were observed in the oesophagus, stomach content, small intestine, bile and urine of a monkey administered latanoprost topical on the eye 0.5 and 1 h before sacrifice. In this animal concentrations of radioactivity were found in the kidney, liver, wall of the small intestine and blood. All other tissues in this animal contained lower concentrations of radioiactivity than the blood. In an animal sacrificed 2 h after administration of tritium labelled latanoprost on one eye and 6 h after administration on the other eye the highest concentrations of radioactivity were found in urine, bile and in the stomach content. Low concentration of radioactivity remained in the kidney and the liver. In a monkey administered latanoprost 12 and 24 h before death low concentrations remained in the colon, bile and urine. The anterior parts of the eyes from the monkey sacrificed 0.5 and 1 h after administration of latanoprost were cut out from the tissue sections for HPLC analysis. The predominating peak present corresponded to acid of latanoprost (PhXA85). In the stomach the radioactivity chromatographed as latanoprost and the acid of latanoprost. In the small intestine and in bile the main radioactive peak corresponded to 1,2-dinor-acid of latanoprost and in addition several more polar metabolites were present. In conclusion, latanoprost penetrated the cornea, was hydrolysed and slowly released into the anterior parts of the eye the site of action. The maximum concentration in the eye was reached after 1 h with an elimination half-life of 3-4 h. In the body the distribution was limited mainly to the gastro-intestinal tract, the kidney, the gall- and urinary bladder.
Single-shot ultrafast imaging attaining 70 trillion frames per second (2020)

Real-time imaging of countless femtosecond dynamics requires extreme speeds orders of magnitude beyond the limits of electronic sensors. Existing femtosecond imaging modalities either require event repetition or provide single-shot acquisition with no more than 10<sup>13</sup> frames per second (fps) and 3 × 10<sup>2</sup> frames. Here, we report compressed ultrafast spectral photography (CUSP), which attains several new records in single-shot multi-dimensional imaging speeds. In active mode, CUSP achieves both 7 × 10<sup>13</sup> fps and 10<sup>3</sup> frames simultaneously by synergizing spectral encoding, pulse splitting, temporal shearing, and compressed sensing-enabling unprecedented quantitative imaging of rapid nonlinear light-matter interaction. In passive mode, CUSP provides four-dimensional (4D) spectral imaging at 0.5 × 10<sup>12</sup> fps, allowing the first single-shot spectrally resolved fluorescence lifetime imaging microscopy (SR-FLIM). As a real-time multi-dimensional imaging technology with the highest speeds and most frames, CUSP is envisioned to play instrumental roles in numerous pivotal scientific studies without the need for event repetition.
Carotid Artery Atherosclerosis: Effect of Intensive Lipid Therapy on the Vasa Vasorum—Evaluation by Using Dynamic Contrast-enhanced MR Imaging (2011)

These findings suggest that DCE MR imaging may be a useful imaging method for the assessment of the therapeutic response of the vasa vasorum in patients with atherosclerotic plaque.
TGFβ Signaling and Cardiovascular Diseases (2012)

Transforming growth factor (TGF) family members are involved in a wide range of diverse functions and play key roles in embryogenesis, development and tissue homeostasis. Perturbation of TGF signaling may lead to vascular and other diseases. In vitro studies have provided evidence that TGF family members have a wide range of diverse effects on vascular cells, which are highly dependent on cellular context. Consistent with these observations genetic studies in mice and humans showed that TGF family members have ambiguous effects on the function of the cardiovascular system. In this review we discuss the recent advances on TGF signaling in (cardio)vascular diseases, and describe the value of TGF signaling as both a disease marker and therapeutic target for (cardio)vascular diseases.
Effect of separating bull semen into X and Y chromosome-bearing fractions on the sex ratio of resulting embryos. (1984)

Seventy-six, day 12 to day 15 bovine embryos, collected from 14 donors which had been inseminated with either X or Y chromosome-bearing spermatozoa fractions of semen separated by a thermal convection counterstreaming sedimentation and forced convection galvanization process, were processed for sexing by chromosomal analysis. Fifty-seven embryos were sexed; 20 from Y chromosome-bearing and 37 from X chromosome-bearing fractions of semen. Statistical analysis of the sexing data indicated that there was no significant difference in the male: female ratio for donors receiving male fractions compared to those receiving female fractions. The Y chromosome-bearing fractions produced a male: female ratio that was indistinguishable from the expected 1:1 ratio. However, the X chromosome-bearing fractions of semen produced a highly significant deviation from the expected 1:1 ratio towards the male.
Electron field emission from silicon nanowires (1999)

Silicon nanowires (SiNWs) were synthesized using laser ablation. A continuous SiNW film was prepared by grinding the pieces of sponge-like SiNWs to powder, then dispersing and sticking the powder onto a Si wafer. The field emission characteristics of the SiNW film were studied based on current–voltage measurements and the Fowler–Nordheim equation. The electron field emission increased with decreasing diameter of SiNWs. A hydrogen plasma treatment of the SiNW film aimed at reducing the oxide overlayer improved the emission uniformity of the film.
Expression of apepThomologue fromBacillus subtilis (1996)

We isolated pepT from Bacillus subtilis, a gene with homology to various tripeptidases from different bacterial sources. pepT is preceded by genes encoding a two component regulatory system. Its expression is activated during stationary phase. In minimal medium this activation is boosted in the presence of phosphate. The response regulator is preceded by putative promoter consensus sequences recognized by the stationary phase specific sigma factors sigma H, sigma F, and sigma G. This is in accordance with the initiation of expression at the beginning of stationary phase. Inactivation of pepT causes no obvious phenotype.
Neuroimaging for differentiating vascular from Alzheimer's dementias. (1996)

Recent advances in the clinical and neuroimaging features of vascular dementia (VAD) versus Alzheimer type dementia (DAT) are described. The lacunar type of VAD, which is often accompanied by silent strokes and a progressive course, is easily confused with DAT. Measurements of cerebral blood flow (CBF) and metabolism (CMR) displayed as brain maps, identify VAD from DAT because of the multifocal and often subcortical nature of the infarcts in VAD, which are strikingly different from the diffuse cortical reductions of CBF and CMR in DAT. Thus, neuroimaging is important for establishing the diagnosis in these two most common forms of dementia in the elderly. A dramatic method for separating VAD from DAT is by utilizing the noninvasive acetazolamide test and xenon contrast CT scanning for measuring the cerebral vasomotor capacitance. In DAT the vasodilator reserve is increased due to the law of initial values. In VAD it is absent or severely blunted so that the differences between the two underlying causes of the dementias become readily apparent.
A REVIEW OF INTERACTION OF BENEFICIAL MICROORGANISMS IN PLANTS: Mycorrhizae, Trichoderma spp. and Pseudomonas spp (2011)

Existe una amplia gama de interrelaciones entre especies de microorganismos en los ecosistemas, tales como sinérgicas, antagónicas, de competencia física y bioquímica, moduladas por múltiples y complejos factores bióticos y abióticos. En la rizósfera, uno de los principales sitios donde se presentan microorganismos, específicamente funcionales, como fija-dores de nitrógeno, solubilizadores de fosfatos, promotores del crecimiento vegetal, biocontroladores y especies patogé-nicas, normalmente, compiten por espacio y por nutrientes. Estas interrelaciones entre microorganismos inciden en la interacción suelo-planta-microorganismos-ambiente y re-percuten, de forma directa, en el crecimiento y en el desarro-llo de las especies vegetales. Microorganismos rizosféricos, como los hongos formadores de micorrizas arbusculares (AMf), hongos del género Trichoderma y bacterias del géne-ro Pseudomonas, usualmente, catalogados como agentes de control biológico (BCA) y microorganismos promotores del crecimiento vegetal (PGPM), dependen de los factores mencionados para expresar sus potenciales efectos bené-ficos; sin embargo, en la interacción de estos tres tipos de microorganismos, se pueden presentar efectos sinérgicos, que potencialicen los beneficios o, por el contrario, efectos antagónicos o simplemente que no ocurra ningún efecto en el crecimiento y en el desarrollo de las plantas. De acuerdo a lo anterior, el propósito de esta revisión es brindar informa-ción que permita comprender algunas de las interacciones entre microorganismos y, de esta manera, lograr dilucidar la aplicabilidad de la co-inoculación de BCA y PGPM de dife-rentes especies, con un objetivo común, el control o la regu-lación biológica de fitopatógenos y, como efecto conjunto y paralelo, la estimulación del crecimiento vegetal.