gebhart/patrepeval huggingface dataset:
Formation of High-Pressure Silicate Phases in Shock Experiments (2008)

The occurrence of high pressure silicate phases in shocked meteorites allows for estimating the size of their parent bodies: Growth rate and crystallite size of these minerals constrain the high pressure regime during shock. Shock duration is limited by rarefaction of the impact-induced shock wave travelling through the two collided objects. Thus, knowledge of growth rate and determination of crystallite size constrains shock duration and, indirectly, the parent body size at the stage of growth associated with impact velocities needed to generate a given intensity of shock metamorphism. We report growth of high pressure polymorphs of olivine from melt in a shock recovery experiment. This is the first direct observation of formation of high pressure Mg-silicate phases in a shock experiment and enables us to constrain growth rates of silicate phases under dynamic compression or upon shock release to 110 m/s or higher suggesting at least partial control by turbulent mass transport rather than by diffusion. This implies that S5 to S6 level shock events in meteorite parent bodies may have had durations on the order of milliseconds. In the light of our findings, previous estimates of planetesimal size in the early solar system need a careful reevaluation. Our shock recovery experiment was conducted on two doubly polished disks placed face to face in a stainless steel recovery chamber. One disk was a pressed pellet of MgO with 50% porosity and one was fused quartz. A tantalum flyer plate launched at 1.53 km/s imparted shock into the sample chamber. From impedance match we calculate a peak pressure of 26 GPa achieved after multiple reverberations. Based on a recent numerical study [1] we estimate the temperature of MgO at 26 GPa to be between 2000 and 3000 K. A section of the sample was polished for examination. We used EBSD, synchrotron-based micro X-ray diffraction and micro-IR reflectance, and micro-Raman spectroscopy. X-ray diffraction and optical spectroscopy indicated presence of forsterite, wadsleyite and ringwoodite (figure 1) in the sample. Further, by EBSD scanning we could uniquely identify wadsleyite grains, determine their size, and clarify that these grains are embedded in silicate glass rather than forsterite (thus indicating growth from melt rather than solid-solid transformation). The silicate glass has a composition close to enstatite. Grainsize and the duration of the high-pressure regime during the shock experiments constrain the growth rate to be on the order of meters per second or larger. Diffusion-controlled growth is expected to be several orders of magnitude slower.
An importance of diazotrophic cyanobacteria as a primary producer during Cretaceous Oceanic Anoxic Event 2 (2006)

Abstract. In Livello Bonarelli black shale deposited during Cretaceous Oceanic Anoxic Event 2 (OAE-2, ca. 94 Ma), nitrogen isotopic compositions of bulk sediments are in a narrow range from −2.7 to −0.7. We also determined molecular distribution and nitrogen isotopic compositions of geoporphyrins extracted from the black shale. The nitrogen isotopic compositions of C32 Ni deoxophylloerythroetioporphyrin (DPEP) and total Ni porphyrins are −3.5 and −3.3, respectively, leading us to the estimation that the mean nitrogen isotopic composition of photoautotrophic cell was around +1 during the formation of Bonarelli black shale. This value is suggestive of N2-fixation a dominant process for these photoautotrophs when assimilating nitrogen. Furthermore, Ni-chelated C32 DPEP, derived mainly from chlorophyll a was the highest concentration. Based on these evidence, we conclude that diazotrophic cyanobacteria were major primary producers during that time. The cyanobacteria may be key photoautotrophs during the formation of black shale type sediments intermittently observed throughout the later half of the Earth's history, and hence may have played a crucial role in the evolution of geochemical cycles.
E-CADHERIN IMMUNOSTAINING OF BLADDER TRANSITIONAL CELL CARCINOMA, CARCINOMA IN SITU AND LYMPH NODE METASTASES WITH LONG-TERM FOLLOWUP (2001)

In bladder cancer altered E-cadherin expression is associated with the degree of invasiveness, lymph node metastasis and increased risk of death from bladder cancer. Furthermore, E-cadherin status is an independent predictor of disease progression in patients treated with cystectomy for transitional cell carcinoma of the bladder.
Synthesis of Food Effective Constituents toward the Development for Chemical Biology Investigations (2016)

Summarized in this article are the syntheses of food effective constituents catechin and flavone toward the development for chemical biology investigations. Synthesis of (-)-5,7-dideoxy-gallocatechin (21a) was accomplished by 6-endo cyclization of corresponding epoxy-phenol 18. Inspired by the finding that (-)-5,7-dideoxy-epigallocatechin gallate (21b) possessed same biological activity with natural epigallocatechin gallate (1), we designed APDOEGCg (40) as a useful probe precursor. Synthesis of APDOEGCg (40) was accomplished by cationic cyclization utilizing neighboring participation of the gallate carbonyl group. Furthermore, the synthetic APDOEGCg (40) was readily converted to fluorescein probe 42 and immunogen 45 efficiently due to its high reactivity of amine functional group. The synthetic probes were demonstrated the imaging studies and the generation of antibodies. Regioselective synthesis of methylated-EGCgs 46 and 47 was accomplished by employment with the 2-nitrobenzenesulfonyl (Ns) as a novel protecting group of phenols. Additionally utilizing the synthetic 4,4"-diMe-EGCg (54) as an authentic sample, a rapid synthesis of PET probe 55 by incorporation of 11C atom into the EGCg derivative 47 was demonstrated efficiently. Biomimetic synthesis of theaflavin (56) from catechins (3 and 59) was also accomplished by using Ns protecting group to minimize undesired side reactions of electron-rich aromatic rings. Regioselective synthesis of chafurosides A and B (70 and 71) were accomplished from the same intermediate (78a). The both flavone rings were constructed from β-diketone intermediate (72), which was readily obtained by condensation of an acyl donor (79) and ketone (78c). Utilizing our novel flavone synthetic method, practical synthesis of nobiletin (88), a polymethoxylated flavone from citrus, was accomplished in hundred gram-scale. Synthetic nobiletin was readily converted to PET prove (99) by selective demethylation and rapid incorporation of 11C atom.
Regulation of Pulmonary T Cell Responses to Inhaled Antigen: Role in Th1- and Th2-Mediated Inflammation (1999)

DO11.10 transgenic mice, expressing an OVA-specific TCR, were used to study pulmonary T cell responses to inhaled Ags. Before OVA inhalation, the activation of lung parenchymal T cells elicited both strong proliferative responses and IL-2 production. However, following Ag inhalation the proliferative responses of the lung T cells, when restimulated in vitro with OVA323-339 peptide or immobilized anti-CD3, were severely attenuated and associated with a decrease in the level of production of IL-2 but not IFN-gamma. Such immune regulation was tissue-specific, because T cell responses in the lymph nodes and spleens were normal. This dramatic aerosol-induced attenuation of parenchymal T cell proliferation was also observed in BALB/c mice immunized with OVA and in BALB/c mice following adoptive transfer of DO11.10 T cells bearing either a Th1 or Th2 phenotype. In mice that had received Th2 cells, the reduced proliferative responses were associated with a decrease in IL-2 expression but augmented IL-4 and IL-5 production. Invariably, the inhibition of proliferation was a consequence of the action of F4/80+ interstitial macrophages and did not involve alveolar macrophages or their products. These observations demonstrate that clonal expansion of T cells in the lung compartment is prevented following the onset of either Th1- or Th2-mediated inflammation. This form of immune regulation, which appears as a selective defect in IL-2-driven proliferation, may serve to prevent the development of chronic pulmonary lymphoproliferative responses.
Characterization of an unusual tRNA-like sequence found inserted in a Neurospora retroplasmid (2000)

We characterized an unusual tRNA-like sequence that had been found inserted in suppressive variants of the mitochondrial retroplasmid of Neurospora intermedia strain Varkud. We previously identified two forms of the tRNA-like sequence, one of 64 nt (TRL-64) and the other of 78 nt (TRL-78) containing a 14-nt internal insertion in the anticodon stem at a position expected for a nuclear tRNA intron. Here, we show that TRL-78 is encoded in Varkud mitochondrial (mt)DNA within a 7 kb sequence that is not present in Neurospora crassa wild-type 74A mtDNA. This 7-kb insertion also contains a perfectly duplicated tRNATrp gene, segments of several mitochondrial plasmids and numerous GC-rich palindromic sequences that are repeated elsewhere in the mtDNA. The mtDNA-encoded copy of TRL-78 is transcribed and apparently undergoes 5′- and 3′-end processing and 3′ nucleotide addition by tRNA nucleotidyl transferase to yield a discrete tRNA-sized molecule. However, the 14 nt intron-like sequence in TRL-78, which is missing in the TRL-64 form, is not spliced detectably in vivo or in vitro. Our results show that TRL-78 is an unusual tRNA-like species that could be incorporated into suppressive retroplasmids by the same reverse transcription mechanism used to incorporate mt tRNAs. The tRNA-like sequence may have been derived from an intron-containing nuclear tRNA gene or it may serve some function, like tmRNA. Our results suggest that mt tRNAs or tRNA-like species may be integrated into mtDNA via reverse transcription, analogous to SINE elements in animal cells.
Families of islands in InAs/InP self-assembled quantum dots: a census obtained from magneto-photoluminescence (2003)

NRC publication: Yes
Analysis of Long-Term Aerosol Optical Properties Combining AERONET Sunphotometer and Satellite-Based Observations in Hong Kong (2022)

This study analyzes seasonal characteristics and long-term variations in aerosol optical parameters in Hong Kong from 2006 to 2021 using AERONET data and satellite-based observations based on the extreme-point symmetric mode decomposition (ESMD) model. The dominant aerosol types in Hong Kong are mixed aerosols and urban/industrial aerosols with fine-mode sizes, and slightly absorbing or non-absorbing properties. Aerosol optical depth (AOD), Angstrom exponent (AE) and single scattering albedo (SSA) varied seasonally with a lower AOD but higher AE and SSA in summer, and elevated AOD but lower AE and SSA in spring and winter. The long-term variations show the year 2012 to be a turning point, with an upward trend in AOD and AE before 2012 and then downwards after 2012. However, for SSA, a rising trend was exhibited in both pre- and post-2012 periods, but with a larger gradient in the first period. The ESMD analysis shows shorter-term, non-linear fluctuations in aerosol optical parameters, with alternating increasing and declining trends. The examination of the relationships between AOD and meteorological factors based on the extreme gradient boosting (XGBoost) method shows that the effects of weather conditions on AOD are complex and non-monotonic. A lower relative humidity, higher wind speed in southwest directions and lower temperature are beneficial to the abatement of aerosol loads in Hong Kong. In conclusion, the findings of this study enhance the understanding of aerosol properties and the interactions between aerosol loading and meteorological factors.
Cold acclimation, deacclimation and memory in Arabidopsis (2018)

Plants from temperate regions can be cold acclimated by exposure to low, but non-freezing temperatures resulting in improved freezing tolerance. Whereas the molecular and metabolic basis of cold acclimation has been investigated in detail, little is known about the molecular regulation of deacclimation of cold acclimated plants under warm conditions. Transcript profiling identified genes encoding transcription factors that were transiently induced during the first 24 h of deacclimation, constituting potential regulators determining the rate of loss of freezing tolerance under these conditions. We are currently characterizing the mode of action of the first candidates. In addition, after cold acclimation at 4°C and a deacclimation phase at 20°C, a second treatment at 4°C improved the freezing tolerance of Arabidopsis compared to plants that had only received one cold treatment. This indicates that the plants remembered the first cold treatment and reacted more efficiently to the second cold acclimation. To identify transcripts, lipids and metabolites related to this cold memory, we used Illumina-based RNA-Seq, LC-MS-based lipidomics and GC-MS-based metabolite profiling. We are currently analyzing candidate genes with the aim to identify regulators of cold memory in Arabidopsis.
The PPP XNS IDP Control Protocol (XNSCP) (1995)

This document defines the Network Control Protocol for establishing
and configuring the Xerox Network Systems (XNS) Internet Datagram
Protocol (IDP) over PPP. [STANDARDS-TRACK]
The proteasome inhibitor, bortezomib suppresses primary myeloma and stimulates bone formation in myelomatous and nonmyelomatous bones in vivo (2008)

Multiple myeloma (MM), a hematologic malignancy of terminally differentiated plasma cells is closely associated with induction of osteolytic bone disease, induced by stimulation of osteoclastogenesis and suppression of osteoblastogenesis. The ubiquitin-proteasome pathway regulates differentiation of bone cells and MM cell growth. The proteasome inhibitor, bortezomib, is a clinical potent antimyeloma agent. The main goal of this study was to investigate the effect of bortezomib on myeloma-induced bone resorption and tumor growth in SCID-rab mice engrafted with MM cells from 16 patients. Antimyeloma response of bortezomib, which was evident in >50% of 16 experiments and resembled clinical response, was associated with significant increased bone mineral density (BMD) and osteoblast numbers, and reduced osteoclast numbers in myelomatous bones. This bone anabolic effect, which was also visualized on X-ray radiographs and confirmed by static and dynamic histomorphometric analyses, was unique to bortezomib and was not observed in hosts responding to melphalan, a chemotherapeutic drug widely used to treat MM. Bortezomib also increased BMD and osteoblasts number and reduced osteoclasts number in nonmyelomatous implanted bones. In vitro bortezomib directly suppressed human osteoclast formation and promoted maturation of osteoblasts. We conclude that bortezomib promotes bone formation in myelomatous and nonmyelomatous bones by simultaneously inhibiting osteoclastogenesis and stimulating osteoblastogenesis. As clinical and experimental studies indicate that bone disease is both a consequence and necessity of MM progression our results suggest and that bortezomib's effects on bone remodeling contribute to the antimyeloma efficacy of this drug.
QRP05-6: Combined Adaptive Congestion Control Method for Communication-Broadcasting Integrated Services (2006)

This paper proposes a combined adaptive congestion control method for massive and intensive telecommunication traffic expected in communication-broadcasting integrated services. The proposed method adaptively controls data transmissions from viewers by combining transmission restriction and delayed transmission depending on the congestion states, so that the severe congestion can be avoided effectively. Furthermore, it utilizes the broadcasting channel which is not only reliable, but also scalable for controlling the responses from vast numbers of viewers. The performance of the proposed method is evaluated through experiments on a test bed where approximately one million viewers are emulated. The obtained results quantitatively demonstrate the performance of the adaptive control method and its effectiveness under massive and intensive traffic conditions.
LINE-1 activity as molecular basis for genomic instability associated with light exposure at night (2015)

The original hypothesis that exposure to light at night increases risk of breast cancer via suppression of nocturnal melatonin production was proposed over 2 decades ago. In 2007, shift work that involves circadian disruption has been recognized by the World Health Organization as a probable human carcinogen. Our discovery of melatonin-dependent regulation of LINE-1 retrotransposon expression and mobilization is the latest addition to the list of cellular genes and processes that are affected by light exposure at night. This finding establishes an unexpected health relevant connection between this endogenous DNA damaging agent and environmental light exposure. It also offers an appealing hypothesis pertaining to the origin of genomic instability in the genomes of individuals with light at night- or age-associated disruption of melatonin signaling.
Managing Large Multidimensional Array Hydrologic Datasets: A Case Study Comparing NetCDF and SciDB (2016)

Management of large hydrologic datasets including storage, structuring, indexing and query is one of the crucial challenges in the era of big data. This research originates from a specific data query problem: time series extraction at specific locations takes a long time when a large multidimensional dataset is stored in non-chunked NetCDF classic or 64-bit offset format. The essence of this issue lies in the contiguous storage structure adopted by NetCDF. In this research, NetCDF file based solutions and a multidimensional (MD) array database management system (DBMS) applying chunked storage structure are benchmarked to determine the best solution for storing and querying large hydrologic datasets. To achieve this, expert consultancy was conducted to establish benchmark sets. To guarantee a fair benchmark test environment, HydroNET-4 system was utilized and adapters for NetCDF files and SciDB were developed to manage and query data. In final benchmark tests, effect of data storage configurations such as chunk size and compression on query performance is also explored. Results indicate that SciDB arrays utilizing small chunk sizes show favorable performance. However with current implementation of SciDB, large numbers of small chunks cause huge overload of main memory which constraints SciDB's scalability. Compression of SciDB can either have negative or no effect on query performance, while it causes significant query degradation to NetCDF-4 solution. The research illustrates that for big hydrologic array data management, the properly chunked NetCDF-4 solution without compression is in general more efficient than the SciDB DBMS. So under current big data environment, traditionally adopted file-based hydroinformatic solutions can still be applicable after proper updating.
Optimal metabolic route search based on atom mappings (2014)

RouteSearch is accessible at BioCyc.org by using the menu command Metabolism --> Metabolic RouteSearch and by downloading Pathway Tools. Pathway Tools software is freely available to academic users, and for a fee to commercial users. Download from: http://biocyc.org/download.shtml.
Assessment of wind turbines impact on the power quality of autonomous weak grids (2002)

Wind turbines' impact on the power quality of autonomous weak power grids is investigated in terms of variations in the frequency and the voltage, flicker and harmonics. Laboratory measurements on a wind-diesel hardware simulator are presented for various operational scenarios with different characteristics of the wind speed and the wind turbine. In order to assess the effect of the different parameters of a wind power plant to the power quality of an existing diesel powered system the followed methodology was to compare the power system's behaviour operating with and without wind turbines. Results for all scenarios considering all power quality characteristics are presented and discussed.
Ammonia inhibition of interferon synthesis (1981)

Ammonium chloride (NH4Cl) was found to markedly inhibit the ability of cultured human fibroblasts to establish an antiviral state following exposure to poly IC. This antiviral state was diminished by the simultaneous addition of as little as 200 microgram/ml of NH4Cl. The effects of ammonia on the superinduction of human fibroblast interferon (IFN-beta) were also investigated. The titer of IFN dropped from 2600 units/ml in control cultures, to less than 50 units/ml in the presence of 400 microgram/ml of NH4Cl. A critical stage sensitive to ammonia was within the first 15 minutes following addition of poly IC.
Nodular histiocytic lymphoma: an aggressive nodular lymphoma with potential for prolonged disease-free survival (1980)

Nodular histiocytic lymphoma (NH) is uncommon, and its natural history is not well defined. Of 473 patients with non-Hodgkin's lymphoma, we found 16 (3.4%) with NH. Most patients (13/16) presented with pathologic stage (PS) III or IV disease, including 7 with liver involvement. One patient (PS III) was initially treated with cyclophosphamide alone, and 4 patients received only radiotherapy, and none were long-term survivors. Eleven patients received combination chemotherapy, and 8 achieved complete remission. Only one of these patients relapsed and died at 19 mo; the other 7 continue in complete remission without maintenance therapy with a minimum followup of 4.5 yr. The survival of the entire group of patients with NH is intermediate between that of the other nodular lymphomas and diffuse histiocytic lymphoma. Nine of 16 patients had either a repeat lymph node biopsy during the course of their disease or lymph node examination at autopsy. Lymph node histology in the majority converted to a diffuse, less differentiated subtype of lymphoma. NH has a natural history similar to that of diffuse histiocytic lymphoma and should be approached with the same therapeutic strategy.
Induction of a Senescence-Like Phenotype in Bovine Aortic Endothelial Cells by Ionizing Radiation (2001)

Treatment of confluent monolayers of bovine aortic endothelial cells (BAEC) with gamma rays resulted in the delayed appearance of cells with an enlarged surface area that were morphologically similar to senescent cells. The majority of these cells stained positively for senescence-associated beta-galactosidase (SA-beta-gal), indicating that these cells are biochemically similar to senescent cells. The incidence of the senescence-like phenotype increased with dose (5-15 Gy) and time after irradiation. Cells with a senescence-like phenotype began to appear in the monolayer several days after irradiation. The onset of the appearance of this phenotype was accelerated by subculturing 24 h after irradiation. This acceleration was not entirely due to stimulation of progression through the cell cycle, since a high percentage of the senescent-like cells that appeared after subculture were not labeled with BrdUrd during the period after subculture. Prolonged up-regulation of expression of CDKN1A (also known as p21(CIP1/WAF1)) after irradiation was noted by Western blot analysis, again suggesting a similarity to natural senescence. Phenotypically altered endothelial cells were present in the irradiated monolayers as long as 20 weeks after irradiation, suggesting that a subpopulation of altered endothelial cells that might be functionally deficient could persist in the vasculature of irradiated tissue for a prolonged period after irradiation.