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At least 1,081 records · Page 60
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

UPC++ v1.0 Specification (Revision 2021.3.0)

UPC++ is a C++11 library providing classes and functions that support Partitioned Global Address Space (PGAS) programming. The key communication facilities in UPC++ are one-sided Remote Memory Access (RMA) and Remote Procedure Call (RPC). All communication operations are syntactically explicit and default to non-blocking; asynchrony is managed through the use of futures, promises and continuation callbacks, enabling the programmer to construct a graph of operations to execute asynchronously as high-latency dependencies are satisfied. A global pointer abstraction provides system-wide addressability of shared memory, including host and accelerator memories. The parallelism model is primarily process-based, but the interface is thread-safe and designed to allow efficient and expressive use in multi-threaded applications. The interface is designed for extreme scalability throughout, and deliberately avoids design features that could inhibit scalability.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Parallel Runtime Interface for Fortran (PRIF) Specification (Rev. 0.6)

This document specifies an interface to support the multi-image parallelism features of Fortran, named the Parallel Runtime Interface for Fortran (PRIF). PRIF is a solution in which a runtime library is primarily responsible for implementing coarray allocation, deallocation and accesses, image synchronization, atomic operations, events, teams and collective subroutines. The Fortran compiler is responsible for transforming the invocation of Fortran-level multi-image parallelism features into procedure calls to the necessary PRIF subroutines. The interface is designed for portability across shared- and distributed-memory machines, different operating systems, and multiple architectures. Implementations of this interface are intended as an augmentation for the compiler's own runtime library. With an implementation-agnostic interface, alternative parallel runtime libraries may be developed that support the same interface. One benefit of this approach is the ability to vary the communication substrate. A central aim of this document is to define a parallel runtime interface in standard Fortran syntax, which enables us to leverage Fortran to succinctly express various properties of the procedure interfaces, including argument attributes.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

UPC++ v1.0 Specification, Revision 2022.9.0

UPC++ is a C++ library providing classes and functions that support Partitioned Global Address Space (PGAS) programming. The key communication facilities in UPC++ are one-sided Remote Memory Access (RMA) and Remote Procedure Call (RPC). All communication operations are syntactically explicit and default to non-blocking; asynchrony is managed through the use of futures, promises and continuation callbacks, enabling the programmer to construct a graph of operations to execute asynchronously as high-latency dependencies are satisfied. A global pointer abstraction provides system-wide addressability of shared memory, including host and accelerator memories. The parallelism model is primarily process-based, but the interface is thread-safe and designed to allow efficient and expressive use in multi-threaded applications. The interface is designed for extreme scalability throughout, and deliberately avoids design features that could inhibit scalability.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

UPC++ v1.0 Specification, Revision 2020.3.0

UPC++ is a C++11 library providing classes and functions that support Partitioned Global Address Space (PGAS) programming. The key communication facilities in UPC++ are one-sided Remote Memory Access (RMA) and Remote Procedure Call (RPC). All communication operations are syntactically explicit and default to non-blocking; asynchrony is managed through the use of futures, promises and continuation callbacks, enabling the programmer to construct a graph of operations to execute asynchronously as high-latency dependencies are satisfied. A global pointer abstraction provides system-wide addressability of shared memory, including host and accelerator memories. The parallelism model is primarily process-based, but the interface is thread-safe and designed to allow efficient and expressive use in multi-threaded applications. The interface is designed for extreme scalability throughout, and deliberately avoids design features that could inhibit scalability.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Parallel Runtime Interface for Fortran (PRIF) Specification (Rev. 0.4)

This document specifies an interface to support the parallel features of Fortran, named the Parallel Runtime Interface for Fortran (PRIF). PRIF is a proposed solution in which the runtime library is responsible for coarray allocation, deallocation and accesses, image synchronization, atomic operations, events, and teams. In this interface, the compiler is responsible for transforming the invocation of Fortran-level parallel features into procedure calls to the necessary PRIF procedures. The interface is designed for portability across shared- and distributed-memory machines, different operating systems, and multiple architectures. Implementations of this interface are intended as an augmentation for the compiler's own runtime library. With an implementation-agnostic interface, alternative parallel runtime libraries may be developed that support the same interface. One benefit of this approach is the ability to vary the communication substrate. A central aim of this document is to define a parallel runtime interface in standard Fortran syntax, which enables us to leverage Fortran to succinctly express various properties of the procedure interfaces, including argument attributes.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Pyrolysis_Molecular_Beam_Mass_Spectrometry_Analysis_of_Specific_Switchgrass_Genotypes

Select natural variant switchgrass genotypes grown in Tifton, GA were analyzed by Pyrolysis-Molecular Beam Mass Spectrometry (Py-MBMS). Biomass was harvested, milled, several genotypes were analyzed with and without being destarched and extracted with ethanol prior to analysis (indicated with -DE if destarched and extracted). Py-MBMS analysis was conducted using approximately 4 mg of biomass and each sample was analyzed in duplicate. A Frontier PY2020 unit pyrolyzed samples at 500°C for 30 s in 80 µL deactivated stainless steel cups. An Extrel Super-Sonic MBMS Model Max 1000 was used to collect mass spectral data fromm/z30 to 450 at 17 eV and processed using Merlin Automation software (V3). Spectral ion intensities were normalized to the total ion chromatogram signal for each sample for analysis of spectral variance. Lignin content (wt %) was estimated based on relative responses from standards of known Klason lignin content using mean-normalized ion intensities ofm/z120, 124 (G), 137 (G), 138 (G), 150 (G), 152, 154 (S), 164 (G), 167 (S), 168 (S), 178 (G), 180, 181, 182 (S), 194 (S), 208 (S) and 210 (S) where G indicates guaiacyl-derived ions, S indicates syringyl-derived ions, and other ions either derive from other lignin monomers or multiple sources. Ratios of S and G lignin monomer units (S/G) were obtained by dividing the sum of S-based ions by the sum of G-based ions using mean-normalized ion intensities.

CBI↗
DOE OSTI2022

Enhanced Multi-Dimensional Inversion Through Target-Specific Inversion Parameter Bounds With an Application to Crosswell Electromagnetic for Sequestration Monitoring

In geophysical inversions, lower and upper model parameter bounds are a means of solution stabilization. Further, constraints that intend to let only geologically plausible inverse solutions pass are amenable to lower and upper bounds. Reliable prior information is paramount to construct such bound constraints. It is common practice to narrow and widen bound intervals for regions of, respectively, more and less certain prior information. Contrary to this practice, we experiment with widened bound intervals in zones that are poorly resolved by a given survey configuration but where prior information would suggest structural anomalies of interest. The purpose of enlarged parameter bounds that correlate spatially with predefined targets is to let the inversion explore a larger solution space, thus increasing the potential to resolve otherwise hidden anomalies. Application of the method is based on a carbon-sequestration baseline (pre-injection) crosswell electromagnetic (EM) field survey at the Containment and Monitoring Institute Field Research Station (Alberta, Canada), where impeded measurements led to generally reduced sensitivities for the interwell region. Synthetic-data proofs of concept use augmented bounds designed to boost the resolution of artificial plume targets, indicating an enhanced illumination compared to constant bounds. Comparative field data inversions with spatially variable bounds constructed from prior resistivity and velocity information highlight non-horizontal baseline structures.

3-D electrical resistivity imaging↗
DOE OSTI2023

The molecular basis of the neutralization breadth of the RBD-specific antibody CoV11

SARS-CoV-2, the virus behind the COVID-19 pandemic, has changed over time to the extent that the current virus is substantially different from what originally led to the pandemic in 2019–2020. Viral variants have modified the severity and transmissibility of the disease and continue do so. How much of this change is due to viral fitness versus a response to immune pressure is hard to define. One class of antibodies that continues to afford some level of protection from emerging variants are those that closely overlap the binding site for angiotensin-converting enzyme 2 (ACE2) on the receptor binding domain (RBD). Some members of this class that were identified early in the course of the pandemic arose from the VH 3-53 germline gene (IGHV3-53*01) and had short heavy chain complementarity-determining region 3s (CDR H3s). Here, we describe the molecular basis of the SARS-CoV-2 RBD recognition by the anti-RBD monoclonal antibody CoV11 isolated early in the COVID-19 pandemic and show how its unique mode of binding the RBD determines its neutralization breadth. CoV11 utilizes a heavy chain VH 3-53 and a light chain VK 3-20 germline sequence to bind to the RBD. Two of CoV11’s four heavy chain changes from the VH 3-53 germline sequence, $Thr^{28}_{FWRH1}$ to Ile and $Ser^{31}_{CDRH1}$ to Arg, and some unique features in its CDR H3 increase its affinity to the RBD, while the four light chain changes from the VK 3-20 germline sequence sit outside of the RBD binding site. Antibodies of this type can retain significant affinity and neutralization potency against variants of concern (VOCs) that have diverged significantly from original virus lineage such as the prevalent omicron variant. We also discuss the mechanism by which VH 3-53 encoded antibodies recognize spike antigen and show how minimal changes to their sequence, their choice of light chain, and their mode of binding influence their affinity and impact their neutralization breadth.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Sex- and age-specific aspects of human peripheral T-cell dynamics

Background: The diversity of the antigenic T cell receptor (TCR) repertoire clonally expressed on T lymphocytes is a key element of the adaptive immune system protective functions. A decline in diversity in the older adults is associated with health deterioration. This diversity is generated by the rearrangement of TRB genes coding for TCR chains during lymphocyte differentiation in the thymus, but is essentially maintained by peripheral T lymphocytes proliferation for most of life. Deep sequencing of rearranged TRB genes from blood cells allows the monitoring of peripheral T cell repertoire dynamics. We analysed two aspects of rearranged TRB diversity, related to T lymphocyte proliferation and to the distribution of the T cell clone size, in a collection of repertoires obtained from 1 to 74 years-old donors. Results: Our results show that peripheral T lymphocytes expansion differs according to the recombination status of their TRB loci. Their proliferation rate changes with age, with different patterns in men and women. T cell clone size becomes more heterogeneous with time, and, in adults, is always more even in women. Importantly, a longitudinal analysis of TRB repertoires obtained at ten years intervals from individual men and women confirms the findings of this cross-sectional study. Conclusions: Peripheral T lymphocyte proliferation partially depends on their thymic developmental history. The rate of proliferation of T cells differing in their TRB rearrangement status is different in men and women before the age of 18 years old, but similar thereafter.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Personalized, disease-stage specific, rapid identification of immunosuppression in sepsis

Introduction Data overlapping of different biological conditions prevents personalized medical decision-making. For example, when the neutrophil percentages of surviving septic patients overlap with those of non-survivors, no individualized assessment is possible. To ameliorate this problem, an immunological method was explored in the context of sepsis. Methods Blood leukocyte counts and relative percentages as well as the serum concentration of several proteins were investigated with 4072 longitudinal samples collected from 331 hospitalized patients classified as septic (n=286), non-septic (n=43), or not assigned (n=2). Two methodological approaches were evaluated: (i) a reductionist alternative, which analyzed variables in isolation; and (ii) a non-reductionist version, which examined interactions among six (leukocyte-, bacterial-, temporal-, personalized-, population-, and outcome-related) dimensions. Results The reductionist approach did not distinguish outcomes: the leukocyte and serum protein data of survivors and non-survivors overlapped. In contrast, the non-reductionist alternative differentiated several data groups, of which at least one was only composed of survivors (a finding observable since hospitalization day 1). Hence, the non-reductionist approach promoted personalized medical practices: every patient classified within a subset associated with 100% survival subset was likely to survive. The non-reductionist method also revealed five inflammatory or disease-related stages (provisionally named ‘early inflammation, early immunocompetence, intermediary immuno-suppression, late immuno-suppression, or other’). Mortality data validated these labels: both ‘suppression’ subsets revealed 100% mortality, the ‘immunocompetence’ group exhibited 100% survival, while the remaining sets reported two-digit mortality percentages. While the ‘intermediary’ suppression expressed an impaired monocyte-related function, the ‘late’ suppression displayed renal-related dysfunctions, as indicated by high concentrations of urea and creatinine. Discussion The data-driven differentiation of five data groups may foster early and non-overlapping biomedical decision-making, both upon admission and throughout their hospitalization. This approach could evaluate therapies, at personalized level, earlier. To ascertain repeatability and investigate the dynamics of the ‘other’ group, additional studies are recommended.

Immunology↗
DOE OSTI2023

Biochemical basis for the formation of organ-specific volatile blends in mint

Above-ground material of members of the mint family is commercially distilled to extract essential oils, which are then formulated into a myriad of consumer products. Most of the research aimed at characterizing the processes involved in the formation of terpenoid oil constituents has focused on leaves. We now demonstrate, by investigating three mint species, peppermint ( Mentha ˣ piperita L.), spearmint ( Mentha spicata L.) and horsemint ( Mentha longifolia (L.) Huds.; accessions CMEN 585 and CMEN 584), that other organs – namely stems, rhizomes and roots – also emit volatiles and that the terpenoid volatile composition of these organs can vary substantially from that of leaves, supporting the notion that substantial, currently underappreciated, chemical diversity exists. Differences in volatile quantities released by plants whose roots had been dipped in a Verticillium dahliae -spore suspension (experimental) or dipped in water (controls) were evident: increases of some volatiles in the root headspace of mint species that are susceptible to Verticillium wilt disease (peppermint and M. longifolia CMEN 584) were detected, while the quantities of certain volatiles decreased in rhizomes of species that show resistance to the disease (spearmint and M. longifolia CMEN 585). To address the genetic and biochemical basis underlying chemical diversity, we took advantage of the newly sequenced M. longifolia CMEN 585 genome to identify candidate genes putatively coding for monoterpene synthases (MTSs), the enzymes that catalyze the first committed step in the biosynthesis of monoterpenoid volatiles. The functions of these genes were established by heterologous expression in Escherichia coli , purification of the corresponding recombinant proteins, and enzyme assays, thereby establishing the existence of MTSs with activities to convert a common substrate, geranyl diphosphate, to (+)-α-terpineol, 1,8-cineole, γ-terpinene, and (–)-bornyl diphosphate, but were not active with other potential substrates. In conjunction with previously described MTSs that catalyze the formation of (–)-β-pinene and (–)-limonene, the product profiles of the MTSs identified here can explain the generation of all major monoterpene skeletons represented in the volatiles released by different mint organs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A Fully Human IgE Specific for CD38 as a Potential Therapy for Multiple Myeloma

Multiple myeloma (MM) is an incurable malignancy of plasma cells and the second most common hematologic malignancy in the United States. Although antibodies in clinical cancer therapy are generally of the IgG class, antibodies of the IgE class have attractive properties as cancer therapeutics, such as their high affinity for Fc receptors (FcεRs), the low serum levels of endogenous IgE allowing for less competition for FcR occupancy, and the lack of inhibitory FcRs. Importantly, the FcεRs are expressed on immune cells that elicit antibody-dependent cell-mediated cytotoxicity (ADCC), antibody-dependent cell-mediated phagocytosis (ADCP), and/or antigen presentation such as mast cells, eosinophils, macrophages, and dendritic cells. We now report the development of a fully human IgE targeting human CD38 as a potential MM therapy. We targeted CD38 given its high and uniform expression on MM cells. The novel anti-CD38 IgE, expressed in mammalian cells, is properly assembled and secreted, exhibits the correct molecular weight, binds antigen and the high affinity FcεRI, and induces degranulation of FcεRI expressing cells in vitro and also in vivo in transgenic BALB/c mice expressing human FcεRIα. Moreover, the anti-CD38 IgE induces ADCC and ADCP mediated by monocytes/macrophages against human MM cells (MM.1S). Importantly, the anti-CD38 IgE also prolongs survival in a preclinical disseminated xenograft mouse model using SCID-Beige mice and human MM.1S cells when administered with human peripheral blood mononuclear cells (PBMCs) as a source of monocyte effector cells. Our results suggest that anti-CD38 IgE may be effective in humans bearing MM and other malignancies expressing CD38.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2023

Structurally Different Yet Functionally Similar: Aptamers Specific for the Ebola Virus Soluble Glycoprotein and GP1,2 and Their Application in Electrochemical Sensing

The Ebola virus glycoprotein (GP) gene templates several mRNAs that produce either the virion-associated transmembrane protein or one of two secreted glycoproteins. Soluble glycoprotein (sGP) is the predominant product. GP1 and sGP share an amino terminal sequence of 295 amino acids but differ in quaternary structure, with GP1 being a heterohexamer with GP2 and sGP a homodimer. Two structurally different DNA aptamers were selected against sGP that also bound GP1,2. These DNA aptamers were compared with a 2'FY-RNA aptamer for their interactions with the Ebola GP gene products. The three aptamers have almost identical binding isotherms for sGP and GP1,2 in solution and on the virion. They demonstrated high affinity and selectivity for sGP and GP1,2. Furthermore, one aptamer, used as a sensing element in an electrochemical format, detected GP1,2 on pseudotyped virions and sGP with high sensitivity in the presence of serum, including from an Ebola-virus-infected monkey. Our results suggest that the aptamers interact with sGP across the interface between the monomers, which is different from the sites on the protein bound by most antibodies. The remarkable similarity in functional features of three structurally distinct aptamers suggests that aptamers, like antibodies, have preferred binding sites on proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Preliminary Evidence for Sex-Specific Trends in Probiotic Modulation of Gut Saccharibacteria in Familial Mediterranean Fever Patients: Effects of Lactobacillus acidophilus INMIA 9602 Er 317/402 and Escherichia coli M-17

Candidate Phyla Radiation bacteria are emerging members of the human microbiota, particularly in oral and gut environments. Saccharibacteria were previously identified in the gut microbiota of healthy individuals and women diagnosed with familial Mediterranean fever (FMF), a monogenic autoinflammatory disorder prevalent in the eastern Mediterranean region, including Armenia. This study aimed to assess the prevalence and diversity of Saccharibacteria spp. and its basebiont Schaalia odontolytica in FMF patients, explore gender differences, and evaluate the modulation potential of two locally produced probiotics: Lactobacillus acidophilus INMIA9602 Er317/402 (Narine®, VITAMAX-E, Yerevan, Armenia) and Escherichia coli M-17 (Colibacteron®, VITAMAX-E, Yerevan, Armenia). The abundance and behavior of saccharibacteria and S. odontolytica appear to vary depending on health status and sex. Placebo administration caused both quantitative and qualitative shifts, suggesting a possible interaction between Candidatus saccharibacteria spp. and Schaalia odontolytica, though the underlying biological significance remains to be clarified. Narine administration appeared to increase the abundance of Candidatus saccharibacteria operational taxonomic units (OTUs) in FMF women and S. odontolytica OTUs in FMF men, whereas Colibacteron selectively decreased certain OTUs, predominantly in FMF women. These findings underscore the need to further investigate saccharibacteria’s role in systemic inflammation and probiotic-mediated modulation of the gut microbiota.

Biochemistry & Molecular Biology↗
DOE OSTI2022

Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species

The Ganoderma species in Polyporales are ecologically and economically relevant wood decayers used in traditional medicine, but their genomic traits are still poorly documented. In the present study, we carried out a phylogenomic and comparative genomic analyses to better understand the genetic blueprint of this fungal lineage. We investigated seven Ganoderma genomes, including three new genomes, G. australe, G. leucocontextum, and G. lingzhi. The size of the newly sequenced genomes ranged from 60.34 to 84.27 Mb and they encoded 15,007 to 20,460 genes. A total of 58 species, including 40 white-rot fungi, 11 brown-rot fungi, four ectomycorrhizal fungi, one endophyte fungus, and two pathogens in Basidiomycota, were used for phylogenomic analyses based on 143 single-copy genes. It confirmed that Ganoderma species belong to the core polyporoid clade. Comparing to the other selected species, the genomes of the Ganoderma species encoded a larger set of genes involved in terpene metabolism and coding for secreted proteins (CAZymes, lipases, proteases and SSPs). Of note, G. australe has the largest genome size with no obvious genome wide duplication, but showed transposable elements (TEs) expansion and the largest set of terpene gene clusters, suggesting a high ability to produce terpenoids for medicinal treatment. G. australe also encoded the largest set of proteins containing domains for cytochrome P450s, heterokaryon incompatibility and major facilitator families. Besides, the size of G. australe secretome is the largest, including CAZymes (AA9, GH18, A01A), proteases G01, and lipases GGGX, which may enhance the catabolism of cell wall carbohydrates, proteins, and fats during hosts colonization. The current genomic resource will be used to develop further biotechnology and medicinal applications, together with ecological studies of the Ganoderma species.

59 BASIC BIOLOGICAL SCIENCES↗