gebhart/patrepeval huggingface dataset:
Comparative Analyses of Arabidopsis <i>complex glycan1</i> Mutants and Genetic Interaction with <i>staurosporin</i>  <i>and temperature sensitive3a</i>   (2008)

We compare three Arabidopsis (Arabidopsis thaliana) complex glycan1 (cgl1) alleles and report on genetic interaction with staurosporin and temperature sensitive3a (stt3a). STT3a encodes a subunit of oligosaccharyltransferase that affects efficiency of N-glycan transfer to nascent secretory proteins in the endoplasmic reticulum; cgl1 mutants lack N-acetyl-glucosaminyltransferase I activity and are unable to form complex N-glycans in the Golgi apparatus. By studying CGL1-green fluorescent protein fusions in transient assays, we show that the extra N-glycosylation site created by a point mutation in cgl1 C5 is used in planta and interferes with folding of full-length membrane-anchored polypeptides in the endoplasmic reticulum. Tunicamycin treatment or expression in the stt3a-2 mutant relieved the folding block, and migration to Golgi stacks resumed. Complementation tests with C5-green fluorescent protein and other N-glycosylation variants of CGL1 demonstrated that suppression of aberrant N-glycosylation restores activity. Interestingly, CGL1 seems to be functional also as nonglycosylated enzyme. Two other cgl1 alleles showed splicing defects of their transcripts. In cgl1 C6, a point mutation affects the 3' splice site of intron 14, resulting in frame shifts; in cgl1-T, intron 11 fails to splice due to insertion of a T-DNA copy. Introgression of stt3a-2 did not restore complex glycan formation in cgl1 C6 or cgl1-T but suppressed the N-acetyl-glucosaminyltransferase I defect in cgl1 C5. Root growth assays revealed synergistic effects in double mutants cgl1 C6 stt3a-2 and cgl1-T stt3a-2 only. Besides demonstrating the conditional nature of cgl1 C5 in planta, our observations with loss-of-function alleles cgl1 C6 and cgl1-T in the stt3a-2 underglycosylation background prove that correct N-glycosylation is important for normal root growth and morphology in Arabidopsis.
The Phytoavailability soil test ‐ PST (1990)

Abstract Current soil tests are based on single and multiple nutrient extractions with a wide range of chemical solutions. For most nutrients this approach provides an “index”; of plant availability, but it may not be accurate on specific soils or in certain regions. Major problems with chemical extraction soil testing cannot be solved because they are inherent in the approach. The Phytoavailability Soil Test (PST) is a simplified soil‐extraction methodology based on ion‐exchange‐resin extraction of nutrients from saturated paste soil samples. The need for drying and grinding soil samples is thus eliminated. PST provides a “universal”; extraction for all nutrients. It mimics nutrient accumulation in plants, thus providing a more theoretically accurate basis for soil testing. PST also provides a system which can be “standardized”; for use in all regions. Factors which influence the rate and amount of resin‐extracted nutrients, including type of resin, shape of resin bag, soil water content, microbial activity, and temperature are presented.
EFFECT OF PASSIVE IMMUNOTHERAPY ON THE RATE OF PROGRESSION OF CEREBRAL AMYLOID ANGIOPATHY (CAA) IN TRANSGENIC MICE (2007)

Cerebral amyloid angiopathy (CAA) is the accumulation of amyloid‐beta peptide (Aβ) in the vessel wall of arteries in the brain. Since CAA is commonly associated with Alzheimer disease (AD), characterized by parenchymal deposition of the same peptide in the form of senile plaques, there is considerable interest in the relationship of the two deposits in generating human disease. The study of CAA is of particularly important for immunotherapeutic approaches to AD, as reports of anti‐Aβ immunotherapy in mice and humans have suggested that, while CAA appeared resistant to clearance, its response to this treatment promoted potential adverse effects, including meningoencephalitis. We used multiphoton microscopy to image CAA in a mouse model of amyloid deposition to evaluate the effects of anti‐Aβ passive immunotherapy. We found detectable clearance of CAA deposits within one week following a single administration of antibody, an effect that was short‐lived. Chronic administration of antibody over 2 weeks led to more robust clearance without evidence of hemorrhage or other destructive changes. We found that the progressive clearance of Aβ from vessels follows distinct kinetics from what has been previously reported for clearance of plaques (parenchymal deposits of Aβ). This quantitative in vivo imaging approach directly demonstrates that CAA can be cleared with an optimized immunotherapy.
Lymphocytic Infiltration and Expression of Intercellular Adhesion Molecule-1 in Photochemically Induced Ischemia of the Rat Cortex (1995)

The contribution of the immune system to the pathogenesis of ischemic lesions is still uncertain. We have analyzed leukocyte infiltration in photochemically induced focal ischemia of the rat parietal cortex by immunocytochemistry. Between 1 and 2 days after photothrombosis, CD5+ T cells adhered to subpial and cortical vessels and infiltrated the ischemic lesion prior to macrophages. By day 3 numerous T cells and some macrophages, whose number increased further between day 3 and day 7, had infiltrated the border zone around the lesion sparing the center. In addition, CD5-/CD8+ lymphocytes that probably represent natural killer cells were found. Intercellular adhesion molecule-1 (ICAM-1) was expressed on endothelial cells on days 1 and 2 and in the border zone on infiltrating leukocytes from day 3 to day 7. Starting on day 7, macrophages infiltrated the core of the lesion to remove debris. When the entire lesion was covered by macrophages at day 14, the number of T cells had decreased and ICAM-1 immunoreactivity was no longer found in or around the infarct. In conclusion, our study shows that ischemic lesions can lead to a local immune reaction in the CNS. Thus, blocking of lymphocyte-derived cytokines or cell adhesion molecules may provide a new approach to confining the sequelae of stroke.
A Comprehensive Panel of Turn‐On Caspase Biosensors for Investigating Caspase Specificity and Caspase Activation Pathways (2011)

Caspases play a central role in apoptosis, differentiation, and proliferation, and represent important therapeutic targets for treating cancer and inflammatory disorders. Toward the goal of developing new tools to probe caspase substrate cleavage specificity as well as to systematically interrogate caspase activation pathways, we have constructed and investigated a comprehensive panel of caspase biosensors with a split-luciferase enabled bioluminescent read out. We first interrogated the panel of caspase biosensors for substrate cleavage specificity of caspase 1-10 in widely utilized in vitro translation systems, namely, rabbit reticulocyte lysate (RRL) and wheat germ extract (WGE). Commercial RRL was found to be unsuitable for investigating caspase specificity, owing to surprising levels of endogenous caspase activity, while specificity profiles of the caspase sensors in WGE agree very well with traditional peptide probes. The full panel of biosensors was utilized for studying caspase activation and inhibition in several mammalian cytosolic extracts, clearly demonstrating that they can be utilized to directly monitor activation or inhibition of procaspase 3/7. Furthermore, the complete panel of caspase biosensors also provided new insights into caspase activation pathways wherein we surprisingly discovered the activation of procaspase 3/7 by caspase 4/5.
AACR: Immunotherapy Antibody Has Activity in Range of Solid Tumors (2013)

The anti-PD-L1 antibody MPDL3280A is effective for several different cancers and was well tolerated. Responses were seen in lung, kidney, colon, and stomach cancer patients. All patients who responded are continuing to respond to the treatment.
Thermal Desorption Spectroscopy of (Ba, Sr)TiO<sub>3</sub> Thin Films Prepared by Chemical Vapor Deposition (1996)

Thermal desorption characteristics of (Ba, Sr)TiO 3 [BST] thin films prepared by metalorganic chemical vapor deposition (CVD) using liguid sources have been studied, together with their crystallinity and electrical properties. Thermal desorption was observed for CO 2 at 400° C and 900° C, and CO at 600° C. The intensities of the CO 2 peaks at 400° C and 900° C increased with the increasing atomic composition ratio of (Ba+Sr)/Ti, in relation to the excess Ba and Sr in the BST films; in particular, the CO 2 peak at 900° C may originate from BaCO 3 and/or SrCO 3 lumps formed in the films, and the CO 2 peak at 400° C may be attributed to gases adsorbed on the sites of contaminants such as BaO x and/or SrO x in films, due to excess Ba and Sr coming from the atmosphere after deposition. On the other hand, the CO peak at 600° C occurred most strongly from BST films with high dielectric constants at (Ba+Sr)/Ti∼1, or perovskite crystalline structures having large grains. Moreover, the desorption of CO at 600° C was also observed from films kept in the atmosphere after annealed above 600° C in vacuum. These results imply that the BST crystalline perovskite grains may have adsorption sites for CO from the atmosphere.
TMemCanal: A VM-oblivious Dynamic Memory Optimization Scheme for Virtual Machines in Cloud Computing (2010)

In current virtualized cloud platforms, resource provisioning strategy is still a big challenge. Provisioning will gain low resource utilization based on peak workload, and provisioning based on average work loads will sacrifice the potential revenue of cloud customers because of bad user experiences. VM-based performance isolation also restrains resource flowing on demand. As to memory, this eventually results in under-loaded memory and over-loaded memory in the same data center. This paper proposes a VM-oblivious dynamic memory optimization scheme, TMemCanal, which leverages under-loaded memory in a data center to accommodate the needs of loaded memory dynamically in a transparent fashion. TMemCanal is able to identify the under-loaded memory located in different VMs and reuse it in a way of memory flowing without any modification to their Guest OSs. We implemented TMemCanal through extending Xen hypervisor and evaluated using SpecWeb 2005 and LinkPack Benchmarks. Our evaluation shows that TMemCanal can efficiently save memory up to 50% with an overhead less than 7%. Our case study of server consolidation also shows TMemCanal can promote the performance of memory-intensive services up to 400%.
A performance management on automobile dealers with applying data envelopment analysis (2010)

This paper analyzes the operating performances of the twenty retailers of two Taiwanese automobile dealers based on the data envelopment analysis combined with the practical experience of the automotive industry. The paper selects important input and output variables to evaluate overall technical efficiency, pure technical efficiency, and scale efficiency for detecting the causes of inefficiency and proposes the improvement comments on project management. The results indicate that there are five retailers presenting relative efficiency at overall technical efficiency during the sample period. The paper looks forward to constructing a complete business operating performance model for enhancing the performances of retailers. The findings can provide useful suggestions for the managers of project management to focus on how to find out and develop the maximum effectiveness by allocating useful human resources fitly for enhancing the operating efficiency on performance management.
Through-substrate coupling elements for silicon-photonics-based short-reach optical interconnects (2019)

Laser integration and photonics chip packaging are the two key challenges that require attention to drive down the cost/bit metric for silicon photonics based optical interconnects. We try to address the latter by demonstrating optical interfaces that fit well in an overall scheme of 2.5D/3D electro-optic integration needed for a high performance computing environment. A through-substrate coupling interface provides the benefit of bonding a silicon photonic chip face-up on a package substrate such that the device-side of the chip remains accessible for die-stacking and fiber-array packaging, thereby offering a promising alternative to flip-chip based packaging. In this paper, we demonstrate three through-substrate coupling elements to enable alignment tolerant and energy-efficient integration of silicon photonics with board-level or package-level optical interconnects : (i) a downward directionality O-band grating coupler with a peak -2.3 dB fiber-to-silicon waveguide coupling efficiency; (ii) polymer microlenses hybrid integrated onto the substrate of a silicon photonic chip to produce an expanded collimated beam at λ=1310 nm for a distance of more than 600 μm; (iii) a ball lens placed in a through-package via to result in a 14 μm chip-to-package 1-dB lateral alignment tolerance for coupling into a 20×24 µm squared cross-section board-level polymer waveguide.
Anthropogenic and biophysical contributions to increasing atmospheric CO <sub>2</sub> growth rate and airborne fraction (2008)

Abstract. We quantify the relative roles of natural and anthropogenic influences on the growth rate of atmospheric CO2 and the CO2 airborne fraction, considering both interdecadal trends and interannual variability. A combined ENSO-Volcanic Index (EVI) relates most (~75%) of the interannual variability in CO2 growth rate to the El-Niño-Southern-Oscillation (ENSO) climate mode and volcanic activity. Analysis of several CO2 data sets with removal of the EVI-correlated component confirms a previous finding of a detectable increasing trend in CO2 airborne fraction (defined using total anthropogenic emissions including fossil fuels and land use change) over the period 1959–2006, at a proportional growth rate 0.24% y−1 with probability ~0.9 of a positive trend. This implies that the atmospheric CO2 growth rate increased slightly faster than total anthropogenic CO2 emissions. To assess the combined roles of the biophysical and anthropogenic drivers of atmospheric CO2 growth, the increase in the CO2 growth rate (1.9% y−1 over 1959–2006) is expressed as the sum of the growth rates of four global driving factors: population (contributing +1.7% y−1); per capita income (+1.8% y−1); the total carbon intensity of the global economy (−1.7% y−1); and airborne fraction (averaging +0.2% y−1 with strong interannual variability). The first three of these factors, the anthropogenic drivers, have therefore dominated the last, biophysical driver as contributors to accelerating CO2 growth. Together, the recent (post-2000) increase in growth of per capita income and decline in the negative growth (improvement) in the carbon intensity of the economy will drive a significant further acceleration in the CO2 growth rate over coming decades, unless these recent trends reverse.
The effect of ionic strength on DNA-tigand unwinding angles for acridine and quinoline derivatives (1980)

We have quantitatively examined the unwinding angles for the complexes of a related series of acridine and quinoline derivatives with DNA. Ethidium bromide was used as a control for determining superhelix densities at different ionic strengths. Relative to ethidium, 9-aminoacridine and quinacrine had an essentially constant unwinding angle of approximately 17 degrees at all ionic strengths tested. The apparent unwinding angle for chloroquine and 9-amino-1,2,3,4-tetrahydroacridine was found to be ionic strength dependent, increasing with increasing ionic strength. This suggests that competitive nonintercalative binding at low ionic strengths causes an apparent lowering of the quinoline unwinding angle. This can also explain why 4-aminoquinaldine, examined at low ionic strength, gives a quite low apparent unwinding angle. Quinacrine along with chloroquinine and 9-aminoacridine approaches a limiting value for their unwinding angle of approximately 17 degrees. 4-aminoquinaldine and 9-amino-1,2,3,4-tetrahydroacridine could not be examined at an ionic strength above 0.03 because of their very low equilibrium binding constants.
In vivo Evidence of γ-Tocotrienol as a Chemosensitizer in the Treatment of Hormone-Refractory Prostate Cancer (2010)

gamma-Tocotrienol (gammaT3) is known to selectively kill prostate cancer (PCa) cells and to sensitize the cells to docetaxel (DTX)-induced apoptosis. In the present study, the pharmacokinetics of gammaT3 and the in vivo cytotoxic response of androgen-independent prostate cancer (AIPCa) tumor following gammaT3 treatment were investigated. Here, we investigated these antitumor effects for PCa tumors in vivo. The pharmacokinetic and tissue distribution of gammaT3 after exogenous gammaT3 supplementation were examined. Meanwhile, the response of the tumor to gammaT3 alone or in combination with DTX were studied by real-time in vivo bioluminescent imaging and by examination of biomarkers associated with cell proliferation and apoptosis. After intraperitoneal injection, gammaT3 rapidly disappeared from the serum and was selectively deposited in the AIPCa tumor cells. Administration of gammaT3 alone for 2 weeks resulted in a significant shrinkage of the AIPCa tumors. Meanwhile, further inhibition of the AIPCa tumor growth was achieved by combined treatment of gammaT3 and DTX (p < 0.002). The in vivo cytotoxic antitumor effects induced by gammaT3 seem to be associated with a decrease in expression of cell proliferation markers (proliferating cell nuclear antigen, Ki-67 and Id1) and an increase in the rate of cancer cell apoptosis [cleaved caspase 3 and poly(ADP-ribose) polymerase]. Additionally, the combined agents may be more effective at suppressing the invasiveness of AIPCa. Overall, our results indicate that gammaT3, either alone or in combination with DTX, may provide a treatment strategy that can improve therapeutic efficacy against AIPCa while reducing the toxicity often seen in patients treated with DTX.
Genomic DNA fingerprinting by pulsed-field gel electrophoresis as an epidemiological marker for study of nosocomial infections caused by methicillin-resistant Staphylococcus aureus (1991)

In this study, we have compared genomic DNA fingerprintings among isolates of methicillin-resistant Staphylococcus aureus (MRSA) by using pulsed-field gel electrophoresis (PFGE). Chromosomal fragments digested with SmaI were most suitable for the PFGE separation. SmaI cut genomic DNA into 15 to 20 fragments whose sizes ranged from about 30 to 1,500 kb. Thirty-one distinctive fragment patterns were identified in 111 infecting and colonizing MRSA isolates from six different hospitals in Japan. On the basis of the genomic typing by PFGE, we performed an epidemiological investigation of an outbreak of nosocomial MRSA infections among inpatients in Nagoya University Hospital. Ten types of chromosomal digestion were identified in the 20 strains isolated from 18 infected patients and 1 from colonized hospital personnel. According to the restriction patterns, we found that four types of these strains had caused epidemic infections among 13 patients in the outbreak. Two types (types 1 and 4) of the strains were involved in the death of five patients. The other infections were sporadic. The clarity and polymorphism of the chromosomal digestion patterns enabled us to discriminate between isolates which could not be differentiated by antibiogram or plasmid analysis. Classification of the genomic DNA fingerprinting patterns by PFGE is therefore proposed as a useful method for investigating the source, transmission, and spread of nosocomial MRSA infections.
Synthesis of 8,8‘-Disubstituted 1,1‘-Binaphthyls Stable to Atropisomerization:  2,2‘-Dimethyl-1,1‘-binaphthalene-8,8‘-diol and 2,2‘-Dimethyl-8,8‘-bis(4-<i>tert</i>-butyloxazolyl)-1,1‘-binaphthyl (1999)

Axially chiral binaphthyls 3a and 3b were synthesized taking, advantage of Ullman coupling of 4a and 4b, respectively. The binaphthyls were shown to be stable to atropisomerization. Binaphthol 3b was resolved with (−)-(1S)-menthyl chloroformate (11). R-axis diastereomer of bisoxazoline 3b was used for enantioselective cyclopropanation of styrene with ethyl diazoacetate.
The role of Rebamipide ophthalmic suspension in management of dry eye disease (2015)

Purpose of review: Review of the drug Rebamipide, an ophthalmic suspension, in the treatment of dry eye and other ocular surface disorders.
Method: An extensive literature search was done on articles published in various ophthalmic journals to review the work on the latest drug rebamipide and its role in treating dry eye and other ocular surface disorders.
Recent Findings: Rebamipide is a novel drug for the treatment of dry eye disorders. It is a mucin-secretogogue, has a cytoprotective, anti-inflammatory effect and also suppresses the detrimental oxygen free radicals and helps in faster healing of epithelium. No major side effect has been noticed apart from dysguesia.
Summary: Rebamipide is the latest drug introduced in the treatment of dry eye. It seems to be a safe and effective treatment in   chronic and severe forms of dry eye particularly due to mucus deficiency.

Key Words: Dry eye, Goblet cell, Microvilli, Rebamipide, Tear film
Effect of Oxidation and Reduction on Potassium Exchange of Biotite (1974)

Abstract The selectivity of K over Ca of Amelia biotite increased sharply upon oxidation by H 2 O 2 at pH 6·0. This increase in K selectivity was only partially reversible upon reduction by Na 2 S 2 O 4 . Oxidation by H 2 O 2 of the Ca-form of this biotite resulted in a loss of no more than 2·8 and 0·4 per cent of the total Fe and Al, respectively, and caused a small and perhaps insignificant decrease in layer charge. Although 95 per cent of the structural Fe 2+ of the Ca-form of this biotite was ozidized by H 2 O 2 , only 17 per cent was reduced again by four treatments with Na 2 S 2 O 4 . The evidence indicates that under the conditions of this experiment the loss of protons from structural hydroxyls was the dominant mechanism by which electroneutrality in the biotite was maintained during oxidation of structural Fe 2+ . Because this mechanism increases the bond strength of interlayer K, it explains the increased K selectivity of biotite upon H 2 O 2 oxidation. The relatively small reduction by Na 2 S 2 O 4 of structural Fe 3+ to Fe 2+ , which implies an equally small reprotonation of structural hydroxyls, explains the incomplete reversibility of K selectivity by Na 2 S 2 O 4 treatment.