gebhart/patrepeval huggingface dataset:
97 Transferability and Reproducibility of Exposed Air-Liquid Interface co-Culture Lung Models (2023)

Abstract The establishment of reliable and robust in vitro models for hazard assessment, moving away from animal testing, requires evaluation of model transferability and reproducibility. Lung models that can be exposed via the air, by means of an air-liquid interface are promising in vitro models for evaluating the safety of nanomaterials (NMs) after inhalation exposure. We performed an inter-laboratory comparison study to evaluate the transferability and reproducibility of a lung model consisting of the human bronchial cell line Calu-3 as monoculture and, to increase the relevance of the model, also as co-culture with macrophages (derived from the THP-1 monocyte cell line or from human blood monocytes). Exposure employed the VITROCELL® Cloud12 system at physiologically relevant doses. Overall, the results of the seven participating laboratories are quite similar. No effects of lipopolysaccharide (LPS), quartz (DQ12) or titanium dioxide (TiO2) NM-105 exposure on cell viability and barrier integrity were seen in the monoculture and co-culture models. Most laboratories showed that LPS induced cytokine release in the co-culture models, but not the monoculture model. Exposure to DQ12 or TiO2 did not increase cytokine release, probably due to too low deposited doses. Interlaboratory variability indicated acceptable variation for cell viability measurements and relatively high variation for cytokine measurements. Based on the transferability and reproducibility of the model and its air exposure we are confident that, based on detailed SOPs, performing a new round of interlaboratory comparison, and increasing the deposited doses of NMs, these models may be taken further towards a possible OECD guideline.
RETRACTED ARTICLE: Association of Ataxia Telangiectasia Mutated (ATM) gene mutation/deletion with Rhabdomyosarcoma (2003)

Rhabdomyosarcoma is a common malignancy in children. There are two major types of rhabdomyosarcomas, the embryonal and the alveolar, differing in cytogenetic and morphologic features. The alveolar type of rhabdomyosarcoma is frequently associated with chromosome translocation t(2, 13) and poor clinical prognosis. Pathogenesis of rhabdomyosarcoma remains obscure, and especially it occurs in the location where skeletal muscle is absent. We report here that there is a high frequency of association of rhabdomyosarcoma with ataxia telangiectasia mutated (ATM) gene mutation/deletion. Totally 17 cases of rhabdomyosarcoma specimens were studied by immunohistochemical or immunofluorescent staining with ATM antibody and revealed that 7 of the 17 cases were negative for ATM expression (41%). Further analyses of rhabdomyosarcoma cell lines with RT-PCR revealed that in Rh30 cells, an alveolar rhabdomyosarcoma cell line, there are three separate deletions/mutations of the ATM mRNA. Western blotting analysis of the Rh30 cellular extract with anti-ATM antibody showed that there is an aberrant form of ATM protein within the Rh30 cells that are smaller than normal control. These results suggest a link of ATM gene deletion/mutation with rhabdomyosarcoma, and since ATM kinase is a crucial regulatory protein in DNA damage repair signaling pathway, and ATM deletion/mutation may contribute to pathogenesis of rhabdomyosarcoma.
Rapamycin Blocks Induction of the Thermogenic Program in White Adipose Tissue (2016)

Rapamycin extends life span in mice, yet paradoxically causes lipid dysregulation and glucose intolerance through mechanisms that remain incompletely understood. Whole-body energy balance can be influenced by beige/brite adipocytes, which are inducible by cold and other stimuli via β-adrenergic signaling in white adipose depots. Induction of beige adipocytes is considered a promising strategy to combat obesity because of their ability to metabolize glucose and lipids, dissipating the resulting energy as heat through uncoupling protein 1. Here, we report that rapamycin blocks the ability of β-adrenergic signaling to induce beige adipocytes and expression of thermogenic genes in white adipose depots. Rapamycin enhanced transcriptional negative feedback on the β3-adrenergic receptor. However, thermogenic gene expression remained impaired even when the receptor was bypassed with a cell-permeable cAMP analog, revealing the existence of a second inhibitory mechanism. Accordingly, rapamycin-treated mice are cold intolerant, failing to maintain body temperature and weight when shifted to 4°C. Adipocyte-specific deletion of the mTORC1 subunit Raptor recapitulated the block in β-adrenergic signaling. Our findings demonstrate a positive role for mTORC1 in the recruitment of beige adipocytes and suggest that inhibition of β-adrenergic signaling by rapamycin may contribute to its physiological effects.
The Effect of Endotoxin on Intestinal Mucosal Permeability to Bacteria In Vitro (1995)

Increased permeability to bacteria at the mucosal level contributes to the bacterial translocation seen in endotoxemia.
ChemInform Abstract: Enantioselective Synthesis of 4‐Hydroxy‐D‐pyroglutamic Acid Derivatives by an Asymmetric 1,3‐Dipolar Cycloaddition. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Role of the intestinal microbiome in low-density polyethylene degradation by caterpillar larvae of the greater wax moth, Galleria mellonella (2020)

Recently, a few insects, including the caterpillar larva of the greater wax moth <i>Galleria mellonella</i>, have been identified as avid 'plastivores'. These caterpillars are able to ingest and metabolize polyethylene at unprecedented rates. While it appears that <i>G. mellonella</i> plays an important role in the biodegradation process, the contribution of its intestinal microbiome remains poorly understood and contested. In a series of experiments, we present strong evidence of an intricate relationship between an intact microbiome, low-density polyethylene (LDPE) biodegradation and the production of glycol as a metabolic by-product. First, we biochemically confirmed that <i>G. mellonella</i> larvae consume and metabolize LDPE, as individual caterpillars fed on polyethylene excreted glycol, but those excretions were reduced by antibiotic treatment. Further, while the gut bacterial communities remained relatively stable regardless of diet, we showed that during the early phases of feeding on LDPE (24-72 h), caterpillars exhibited increased microbial abundance relative to those starved or fed on their natural honeycomb diet. Finally, by isolating and growing gut bacteria with polyethylene as their exclusive carbon source for over 1 year, we identified microorganisms in the genus <i>Acinetobacter</i> that appeared to be involved in this biodegradation process. Taken collectively, our study indicates that during short-term exposure, the intestinal microbiome of <i>G. mellonella</i> is intricately associated with polyethylene biodegradation <i>in vivo</i>.
Pass-them-around (2011)

In this paper we explore shared collocated interactions with mobile phones. We introduce a phone-based application that allows a small group of collocated people to share photos using the metaphor of passing paper photos around. The prototype encourages people to share their devices and use them interchangeably while discussing photos face-to-face. The prototype supports ad-hoc photo sharing in different contexts by taking into account the spatial arrangement of users around a table, measured with sensors embedded in their mobile phones. Our evaluations show that people are willing to share and connect their mobile phones to engage in collaborative interactions. Participants were able to easily share their collections of photos using our proposed interaction techniques.
The Shortage of Protein Concentrates in New South Wales (1951)

Livestock Production/Industries
Butyrylcholinesterase: an enzyme antidote for cocaine intoxication (1998)

Cocaine-associated toxicity is the result of effects on the cardiovascular and central nervous systems. Since the primary route of cocaine inactivation is enzymatic degradation by butyrylcholinesterase (BChE), we sought to determine if the administration of purified human enzyme would ameliorate the lethal effects of cocaine. While the cardiovascular, autonomic or central nervous systems were unaffected by BChE, the enzyme reduced the adverse effects of cocaine including hypertension, hyperactivity and convulsions. BChE decreased both the brain and blood levels of cocaine and shifted the metabolites towards the production of the inactive product ecgonine methyl ester and away from the physiologically active metabolites, norcocaine and benzoylecgonine. We conclude that BChE would appear to be an ideal antidote in the treatment of cocaine intoxication and has potential therapeutic application.
Genome-to-phenome research in rats: progress and perspectives (2020)

Because of their relatively short lifespan (<4 years), rats have become the second most used model organism to study health and diseases in humans who may live for up to 120 years. First-, second- and third-generation sequencing technologies and platforms have produced increasingly greater sequencing depth and accurate reads, leading to significant advancements in the rat genome assembly during the last 20 years. In fact, whole genome sequencing (WGS) of 47 strains have been completed. This has led to the discovery of genome variants in rats, which have been widely used to detect quantitative trait loci underlying complex phenotypes based on gene, haplotype, and sweep association analyses. DNA variants can also reveal strain, chromosome and gene functional evolutions. In parallel, phenome programs have advanced significantly in rats during the last 15 years and more than 10 databases host genome and/or phenome information. In order to discover the bridges between genome and phenome, systems genetics and integrative genomics approaches have been developed. On the other hand, multiple level information transfers from genome to phenome are executed by differential usage of alternative transcriptional start (ATS) and polyadenylation (APA) sites per gene. We used our own experiments to demonstrate how alternative transcriptome analysis can lead to enrichment of phenome-related causal pathways in rats. Development of advanced genome-to-phenome assays will certainly enhance rats as models for human biomedical research.
ChemInform Abstract: EINE KONFORMATIVE UNTERSUCHUNG VON CATECHOLAMIN‐REZEPTOREN 6. MITT. SYNTH. VON D,L‐3‐AMINO‐2‐(3,4‐DIHYDROXYPHENYL)‐TRANS‐2‐DECALINHYDROCHLORIDEN (1971)

Abstract Die Synthesen der vier möglichen D,L‐3‐Amino‐2‐(3,4‐dihydroxyphenyl)‐trans‐2‐decalin‐hydrochloride (I)‐(IV) werden beschrieben und die Ergebnisse der O‐Methylierung dieser Dopaminanaloga (I)‐(IV) durch Catechol‐O‐methyltransferase (COMT) diskutiert.
Generative Multiplane Neural Radiance for 3D-Aware Image Generation (2023)

We present a method to efficiently generate 3D-aware high-resolution images that are view-consistent across multiple target views. The proposed multiplane neural radiance model, named GMNR, consists of a novel α-guided view-dependent representation (α-VdR) module for learning view-dependent information. The α-VdR module, faciliated by an α-guided pixel sampling technique, computes the view-dependent representation efficiently by learning viewing direction and position coefficients. Moreover, we propose a view-consistency loss to enforce photometric similarity across multiple views. The GMNR model can generate 3D-aware high-resolution images that are viewconsistent across multiple camera poses, while maintaining the computational efficiency in terms of both training and inference time. Experiments on three datasets demonstrate the effectiveness of the proposed modules, leading to favorable results in terms of both generation quality and inference time, compared to existing approaches. Our GMNR model generates 3D-aware images of 1024 X 1024 pixels with 17.6 FPS on a single V100. Code : https://github.com/VIROBO-15/GMNR
Adaptive code modulation for 2D optical memories (2003)

Volumetric and page oriented optical storage systems have a great potential for high data density and high speed through page oriented data access (Haichuan Zhang et al, Proc. 18th IEEE Symp. Mass Storage Sys., 2001). However, in order to be practical, they have to maintain data integrity using error correction and modulation codes. The coding comes at a cost of spatial overhead of codeword size over the source data size, and processing time overhead for encoding and decoding. Our proposed adaptive modulation scheme strives to minimize both overheads. It achieves utilization of 74% with constant time complexity, which is competitive with other recently proposed schemes for page-oriented memories.
A New Integrated Assessment Framework for Climate-Smart Nutrition Security in sub-Saharan Africa: The Integrated Future Estimator for Emissions and Diets (iFEED) (2022)

Climate change will put millions more people in Africa at risk of food and nutrition insecurity by 2050. Integrated assessments of food systems tend to be limited by either heavy reliance on models or a lack of information on food and nutrition security. Accordingly, we developed a novel integrated assessment framework that combines models with in-country knowledge and expert academic judgement to explore climate-smart and nutrition-secure food system futures: the integrated Future Estimator for Emissions and Diets (iFEED). Here, we describe iFEED and present its application in Malawi, South Africa, Tanzania and Zambia. The iFEED process begins with a participatory scenario workshop. In-country stakeholders identify two key drivers of food system change, and from these, four possible scenarios are defined. These scenarios provide the underlying narratives of change to the food system. Integrated modeling of climate change, food production and greenhouse gas emissions is then used to explore nutrition security and climate-smart agriculture outcomes for each scenario. Model results are summarized using calibrated statements—quantitative statements of model outcomes and our confidence in them. These include statements about the way in which different trade futures interact with climate change and domestic production in determining nutrition security at the national level. To understand what the model results mean for food systems, the calibrated statements are expanded upon using implication statements. The implications rely on input from a wide range of academic experts—including agro-ecologists and social scientists. A series of workshops are used to incorporate in-country expertise, identifying any gaps in knowledge and summarizing information for country-level recommendations. iFEED stakeholder champions help throughout by providing in-country expertise and disseminating knowledge to policy makers. iFEED has numerous novel aspects that can be used and developed in future work. It provides information to support evidence-based decisions for a climate-smart and nutrition-secure future. In particular, iFEED: (i) employs novel and inclusive reporting of model results and associated in-country food system activities, with comprehensive reporting of uncertainty; (ii) includes climate change mitigation alongside adaptation measures; and (iii) quantifies future population-level nutrition security, as opposed to simply assessing future production and food security implications.
Experimental use of a Dot-Blot Assay to Measure Serologic Responses of Cattle Vaccinated with Brucella Abortus Strain RB51 (1997)

Brucella abortus strain RB51 was recently approved as an official brucellosis calfhood vaccine for cattle by the Animal and Plant Health Inspection Service branch of the United States Department of Agriculture. Currently available serologic surveillance tests for B. abortus do not detect seroconversion following SRB51 vaccination. The purpose of this study was to evaluate a dot-blot assay using γ-irradiated strain RB51 bacteria for its specificity and sensitivity to detect antibody responses of cattle vaccinated with strain RB51. Dot-blot titers of sera at a recommended dosage (10 10 colony-forming units) were similar to those of sera from cattle vaccinated with similar numbers of B. abortus strain 19 and greater ( P &lt; 0.05) than titers of nonvaccinated cattle. In the first 12 weeks after vaccination with 10 10 colony-forming units of strain RB51, the RB51 dot-blot assay had 100% specificity for titers of 80 or less and a 53% sensitivity for titers of 160 or greater. Sensitivity of the RB51 dot-blot assay peaked at 4 weeks after vaccination with 10 10 colony-forming units of strain RB51. Dot-blot responses of sera from cattle vaccinated with a reduced dosage of strain RB51 (10 9 colony-forming units) did not differ ( P &gt; 0.05) from titers of sera from nonvaccinated cattle. Following intraconjunctival challenge with B. abortus strain 2308, titers on the RB51 dot-blot assay did not differ ( P &gt; 0.05) between nonvaccinated cattle and cattle vaccinated at calfhood with strain 19 or strain RB51.
Occurrence of the alpha subunits of G proteins in cerebral cortex synaptic membrane and postsynaptic density fractions: modulation of ADP-ribosylation by Ca2+/calmodulin. (1992)

We have examined the isolated postsynaptic density (PSD) fraction for the presence of a G protein. First, we found specific binding of guanosine 5'-[gamma-[35S]thio]triphosphate to the PSD. Second, pertussis toxin-activated ADP-ribosylation of the isolated PSD fraction resulted in the appearance of a G protein with an apparent molecular mass of 41 kDa, and two G proteins with apparent molecular masses of 41 kDa and 39 kDa in synaptic membrane (SM) fraction and total homogenate (H). The amount of the 41-kDa G protein per unit protein was in the order of SM greater than H greater than PSD. Anti-G(i0 antibodies recognized the 41-kDa G protein in both PSD and SM, whereas anti-G(o) antibodies reacted with the 39-kDa G protein in the SM. The absence of G(o) protein in the PSD suggested that there was no contamination with SM. Moreover, unlabeled PSD incubated with an extract of SM that contained the labeled G proteins resulted in no label in the subsequently reisolated PSD, suggesting that the G protein found in the PSD was not due to adsorption of the G protein onto the PSD during its isolation from the SM. PSD pretreated with EGTA gave an 11-fold increase in the ADP-ribosylation reaction of the G(i) protein; similar effects on the G(i) and G(o) proteins of SM were obtained. Restoration of Ca2+/calmodulin to the PSD, but not of either Ca2+ or calmodulin alone, removed the effect of EGTA, indicating a strong complex formation between G(i) and Ca2+/calmodulin that decreased the ADP-ribosylation reaction. Preincubation with the Ca(2+)-channel blocker nifedipine decreased the ADP-ribosylation reaction in the PSD. We conclude that G(i) is present in the PSD, that it may interact with calmodulin and that it is involved in the regulation of voltage-dependent Ca2+ channel. We present a theory of the involvement of the G protein and calmodulin in postsynaptic neurophysiological events.
The in‐vitro synthesized tomato shikimate kinase precursor is enzymatically active and is imported and processed to the mature enzyme by chloroplasts (1992)

Full-length cDNA clones encoding shikimate kinase (EC 2.7.1.71), an enzyme of the central section of the shikimate pathway, have been isolated from tomato (Lycopersicon esculentum L., cv. UC82b). The open reading frame has the capacity to encode a peptide of 300 amino acids. The in-vitro synthesized peptide catalysed the phosphorylation of shikimate thus confirming the identity of the isolated cDNA clones. The N-terminal portion of the deduced amino acid sequence resembles known chloroplast-specific transit peptides. The existence of such a transit peptide was proven by the uptake of the in-vitro synthesized peptide as well as its processing by isolated chloroplasts. Multiple sites of polyadenylation were observed in shikimate kinase mRNAs. The results of Northern and Southern blot analyses are consistent with the existence of only one shikimate kinase gene per haploid genome in tomato. These results are discussed with respect to the dual pathway hypothesis of the shikimate pathway in higher plants.
ChemInform Abstract: Direct Metalation of Isoprene. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites (2015)

Proteins often exist only as apo structures (unligated) in the Protein Data Bank, with their corresponding holo structures (with ligands) unavailable. However, apoproteins may not represent the amino-acid residue arrangement upon ligand binding well, which is especially problematic for molecular docking. We developed the ProBiS-CHARMMing web interface by connecting the ProBiS ( http://probis.cmm.ki.si ) and CHARMMing ( http://www.charmming.org ) web servers into one functional unit that enables prediction of protein-ligand complexes and allows for their geometry optimization and interaction energy calculation. The ProBiS web server predicts ligands (small compounds, proteins, nucleic acids, and single-atom ligands) that may bind to a query protein. This is achieved by comparing its surface structure against a nonredundant database of protein structures and finding those that have binding sites similar to that of the query protein. Existing ligands found in the similar binding sites are then transposed to the query according to predictions from ProBiS. The CHARMMing web server enables, among other things, minimization and potential energy calculation for a wide variety of biomolecular systems, and it is used here to optimize the geometry of the predicted protein-ligand complex structures using the CHARMM force field and to calculate their interaction energies with the corresponding query proteins. We show how ProBiS-CHARMMing can be used to predict ligands and their poses for a particular binding site, and minimize the predicted protein-ligand complexes to obtain representations of holoproteins. The ProBiS-CHARMMing web interface is freely available for academic users at http://probis.nih.gov.
Supplementary Material from Novel Assay to Detect RNA Polymerase I Activity <i>In Vivo</i> (2023)

&lt;p&gt;Supplementary table ("clinicopathological features of cases on the TMAs") and figures (1; "increased 5'ETS/45S CISH signal in cancer glands", 2; "scatterplot showing correlation between 5ʹETS/45S CISH levels by quantitative image analysis and quantitative real time PCR levels from the experiments shown in Figure 2E") S1. Increased 5ʹETS/45S CISH signals in cancer glands. S2. Scatterplot showing correlation between 5ʹETS/45S CISH levels by quantitative image analysis and quantitative real time PCR levels from the experiments shown in Figure 2E.&lt;/p&gt;
Emergence of half-metallicity in suspended NiO chains:Ab initioelectronic structure and quantum transport calculations (2006)

Contrary to the antiferromagnetic and insulating character of bulk NiO, one-dimensional chains of this material can become half metallic due to the lower coordination of their atoms. Here we present ab initio electronic structure and quantum transport calculations of ideal infinitely long NiO chains and of more realistic short ones suspended between Ni electrodes. While infinite chains are insulating, short suspended chains are half-metallic minority-spin conductors that displays very large magnetoresistance and a spin-valve behavior controlled by a single atom.