gebhart/patrepeval huggingface dataset:
Outlier-Aware Training for Improving Group Accuracy Disparities (2022)

Methods addressing spurious correlations such as Just Train Twice (JTT, arXiv:2107.09044v2) involve reweighting a subset of the training set to maximize the worst-group accuracy. However, the reweighted set of examples may potentially contain unlearnable examples that hamper the model's learning. We propose mitigating this by detecting outliers to the training set and removing them before reweighting. Our experiments show that our method achieves competitive or better accuracy compared with JTT and can detect and remove annotation errors in the subset being reweighted in JTT.
Compton Scattering Driven by Quantum Light (2023)

We solve the non-perturbative interaction of free electrons with arbitrary intense quantum electromagnetic fields and exemplify it by predicting extended spectra in Compton scattering driven by non-classical photon statistics.
Stereochemistry at C-1 of geranyl pyrophosphate and neryl pyrophosphate in the cyclization to (+)- and (-)-bornyl pyrophosphate. (1985)

(1R)-1-3H-labeled and (1S)-1-3H-labeled geranyl pyrophosphate and neryl pyrophosphate were prepared from the corresponding 1-3H-labeled aldehydes by a combination of enzymatic and synthetic procedures. Following admixture with the corresponding 2-14C-labeled internal standard, each substrate was converted to (+)-bornyl pyrophosphate and (-)-bornyl pyrophosphate by cell-free enzyme preparations from sage (Salvia officinalis) and tansy (Tanacetum vulgare), respectively. Each pyrophosphate ester was hydrolyzed, and the resulting borneol was oxidized to camphor. The stereochemistry of labeling at C-3 of the derived ketone was determined by base-catalyzed exchange, taking advantage of the known selective exchange of the exo-alpha-protons. By comparison of such exchange rates to those of product generated from (1RS)-2-14C,1-3H2-labeled substrate, it was demonstrated that geranyl pyrophosphate was cyclized to bornyl pyrophosphate with net retention of configuration at C-1 of the acyclic precursor, whereas neryl pyrophosphate was cyclized to product with inversion of configuration at C-1. The observed stereochemistry is consistent with a reaction mechanism whereby geranyl pyrophosphate is first stereospecifically isomerized to linalyl pyrophosphate which, following rotation about C-2-C-3 to the cisoid conformer, cyclizes from the anti-endo configuration. Neryl pyrophosphate cyclizes either directly or via the linalyl intermediate without the attendant rotation.
VTI Media qP-wave Equation Using ONAD Method (2016)

The qP-wave equation is one of extremely important question in seismic exploration, seismology, and so on. However, its poor stability, the traditional finite difference scheme for qP-wave equation modeling suffer instability easily and numerical dispersion seriously. This paper propose a novel difference scheme for qP-wave simulation, named ONAD method. The numerical results demonstrate that, relative to LWC, the ONAD method for qP-wave has obvious advantages. It's suitable for qP-wave modeling.
In-situ gas cleaning technology of hot-wall batch-type reactor for (Ba,Sr)TiO/sub 3/ (2002)

We present a novel approach to gas cleaning technology for Ba/sub x/Sr/sub (1-x)/TiO/sub 2/ (BST) residual coating in hot wall CVD reactors. It consists of two step continuous process. In the first step we use Cl/sub 2/ gas at 800 deg. C to remove Ba and Sr which have low vapor pressure. Second step consists of using ClF/sub 3/ gas to remove Ti at relatively low temperature. Vapor pressures of the chlorine compounds of Ba and Sr are considerably higher than those of their other existing compounds, thus by chlorination, Ba and Sr turn volatile and are easily etched off.
UWB-based sensor networks and the IEEE 802.15.4a standard - a tutorial (2006)

This paper gives a tutorial overview of ultrawide-band communications systems for sensor networks. In particular, we describe the IEEE 802.15.4a standard, which is currently being developed. While most nodes (reduced-function devices) in sensor networks usually have to consume little energy, and are constrained with respect to the complexity of the processing they can perform, some nodes (full-function devices) do not show these restrictions. We describe a hybrid modulation, coding, and multiple access scheme that is particularly suited for heterogeneous networks that contain both FFDs and RFDs. The scheme is a generalization of the well-known time-hopping impulse radio (TH-IR). It employs systematic coding, joint pulse-position modulation and phase shift keying, as well as a combination of polarity scrambling and time-hopping. We also describe two-way ranging algorithms that serve as the basis for geolocation in 802.15.4a, and we discuss the methods for how the ranging information can be kept secret from snoopers.
Characterization of an HSP70 Cognate Gene Family in Arabidopsis (1988)

Analysis of the polypeptide composition of extracts from heat-shocked leaves of Arabidopsis indicated the presence of at least 12 HSP70-related polypeptides, most of which were constitutively expressed. In vitro translation of mRNA from heat-shocked and control leaves indicated that the amount of mRNA encoding four HSP70 polypeptides was increased strongly by heat-shock. Three Arabidopsis genes which exhibit homology to a Drosophila HSP70 gene were cloned. Two of the three genes are arranged in direct orientation approximately 1.5 kilobases apart. The third gene is not closely linked to the other two. Nucleotide sequence analysis of the 5' regions of the two linked genes revealed that both contain a TATA box, the CAAT motif, and several short sequences which are homologous to the Drosophila heat-shock consensus sequence. The deduced partial amino acid sequence of the open reading frames were 79 and 72% homologous to the corresponding regions of the Drosophila HSP70-cognate and HSP70 sequences, respectively. As with the two maize HSP70 genes which have been characterized, and the Drosophila HSP70-cognate genes, the Arabidopsis genes contained a putative intron in the codon specifying amino acid 72. Analysis of mRNA levels with gene-specific oligonucleotide probes indicated that two of the genes were not expressed or were expressed at very low levels in leaves during normal growth or after heat-shock, whereas the other gene was constitutively expressed. By analogy with the results of similar studies of other organisms, it appears that the three cloned genes are members of a small family which are most closely related to the HSP70-cognate genes found in other species.
ChemInform Abstract: Asymmetric Synthesis of Chiral N‐Sulfinyl 3‐Alkyl‐ and 3‐Arylpiperidines by α‐Alkylation of N‐Sulfinyl Imidates with 1‐Chloro‐3‐iodopropane. (2011)

Abstract A new and efficient method to prepare enantiomerically pure 3‐substituted piperidines is reported.
Chemistry and Biology of Terpene Trilactones fromGinkgo Biloba (2004)

Ginkgo biloba, the ginkgo tree, is the oldest living tree, with a long history of use in traditional Chinese medicine. In recent years, the leaf extracts have been widely sold as phytomedicine in Europe and as a dietary supplement worldwide. Effects of Ginkgo biloba extracts have been postulated to include improvement of memory, increased blood circulation, as well as beneficial effects to sufferers of Alzheimer's disease. The most unique components of the extracts are the terpene trilactones, that is, ginkgolides and bilobalide. These structurally complex molecules have been attractive targets for total synthesis. Terpene trilactones are believed to be partly responsible for the neuromodulatory properties of Ginkgo biloba extracts, and several biological effects of the terpene trilactones have been discovered in recent years, making them attractive pharmacological tools that could provide insight into the effects of Ginkgo biloba extracts.
Brake Energy Efficiency (2014)

Electric braking systems for passenger vehicles have become more and more interesting with the recent developments of hybrid electric and electric vehicles (HEVs and EVs). The major issue is the generation of the actuation energy required during the braking maneuver that makes the utilization of electric actuation unfeasible due to the size of electric actuators and to the existence of layout constraints. Self-energizing mechanisms that could be used to reduce both the actuation force and the energy required for braking are presented and compared in terms of the design criteria that are relevant to braking systems, that is, energy adsorption, actuating force, actuating stroke and, last but not least, stability. The derived analytic models are used to identify the driving design quantities and the sensitivity of the presented self-energizing architectures with respect to the caliper stiffness, which is a crucial aspect for traditional hydraulic calipers as well.
Transceivers and Optical Engines for Computer and Datacenter Interconnects (2010)

Technological and manufacturing advances are enabling optical solutions to meet demanding density, bandwidth, and cost metrics. We describe these solutions with respect to different system architectures and applications.
Identification of CDRH3 Loops in the B Cell Receptor Repertoire that Can Be Engaged by Candidate Immunogens (2021)

Abstract A major goal for the development of vaccines against rapidly mutating viruses, such as influenza or HIV, is to elicit antibodies with broad neutralization capacity. However, B cell precursors capable of maturing into broadly neutralizing antibodies (bnAbs) can be rare in the immune repertoire. Due to the stochastic nature of B cell receptor (BCR) rearrangement, a limited number of third heavy chain complementary determining region (CDRH3) sequences are identical between different individuals. Thus, in order to successfully engage broadly neutralizing antibody precursors that rely on their CDRH3 loop for antigen recognition, immunogens must be able to tolerate sequence diversity in the B cell receptor repertoire across an entire vaccinated population. Here, we present a combined experimental and computational approach to identify BCRs in the human repertoire with CDRH3 loops predicted to be engaged by a target immunogen. For a given antibody/antigen pair, deep mutational scanning was first used to measure the effect of CDRH3 loop substitution on binding. BCR sequences, isolated experimentally or generated in silico , were subsequently evaluated to identify CDRH3 loops expected to be bound by the candidate immunogen. We applied this method to characterize two HIV-1 germline-targeting immunogens and found differences in the frequencies with which they are expected to engage target B cells, thus illustrating how this approach can be used to evaluate candidate immunogens towards B cell precursors engagement and to inform immunogen optimization strategies for more effective vaccine design.
Cloud-Controlled Autonomous Mobile Robot Platform (2021)

This paper investigates cloud-based mobile robotics, with a use case focusing on the flexible transportation in modern factories. The feasibility and performance of Autonomous Mobile Robots (AMRs) fully controlled from cloud over wireless connection are studied. We show that completely decoupling the closed-loop control of the robot from the robot’s embedded system and placing it into an edge cloud execution environment while sustaining the necessary KPIs is feasible. Moving the control logic into the cloud benefits from ease of maintenance of the control software and improved resiliency to software and hardware failures. Furthermore, it enables the physical platform and control intelligence to evolve separately from each other.
Chimerism of chrysanthemum stems changes at the nodes during vegetative growth (2020)

The shoot apical meristem (SAM) is typically divided into three cell layers: the outermost epidermal layer (L1), the subepidermal layer (L2) and the inner corpus region (L3). Structures within the cell layers are normally maintained throughout development; however, through vegetative propagation of a periclinal chimeric chrysanthemum expressing a fluorescent protein gene only in the L1 layer, we collected twelve independent shoots that had partially mosaic fluorescent inner cells (L2, L3) in addition to fluorescent epidermal cells (L1). Furthermore, the elongated tissues of nine shoots out of the twelve had no internal fluorescent cells, i.e., they had the original L1 chimerism. Observations of the fluorescence distribution suggested that the change in chimerism occurred at the nodes, indicating previously unnoticed cell layer dynamics occurring at the nodes.
Utilizing a Classification Scheme to Facilitate Rigid-Body Replacement for Compliant Mechanism Design (2010)

The knowledge related to the synthesis and analysis of compliant mechanisms continues to grow and mature. Building on this growth, a classification scheme has been established to categorize compliant elements and mechanisms in a manner that engineers can incorporate compliance into their designs. This paper demonstrates a design approach engineers can use to convert an existing rigid-body mechanism into a compliant mechanism by using an established classification scheme. This approach proposes two possible techniques that use rigid-body replacement synthesis in conjunction with a compliant mechanism classification scheme. One technique replaces rigid-body elements with a respective compliant element. The other technique replaces a complex rigid-body mechanism by decomposing the mechanism into simpler functions and then replacing a respective rigid-body mechanism with a compliant mechanism that has a similar functionality.
IOOC Route to Substituted Chiral Pyrrolidines. Potential Glycosidase Inhibitors (1998)

Branched-chain five-membered ring aza-sugar analogues, synthesized from amino acids by an intramolecular oxime−olefin cycloaddition reaction, the IOOC route, were found to be selective glycosidase inhibitors. The derivative 2,4(S)-di(hydroxymethyl)-3(S)-aminopyrrolidine, obtained from d-serine, was about 1 order of potency more active than its enantiomer obtained from l-serine.
Broadband electromagnetic metamaterials with reconfigurable fluid channels (2014)

We present the design, characterization, and experimental verification of broadband and tunable metamaterials based on reconfigurable fluid channels. We demonstrate through simulation that a finite-height cylinder of water in a background medium behaves as a nonresonant metamaterial. By changing liquid type or adjusting liquid level, we tune the effective material parameters of the metamaterial through altering the composition and amount of water used. We verify the efficacy of the metamaterial through experiment, demonstrating a design procedure for a metamaterial with broadband and tunable properties.
Anti-Tumor Activity of Cytotoxic T Lymphocytes Elicited with Recombinant and Synthetic Forms of a Model Tumor-Associated Antigen (1995)

The recent cloning of tumor-associated antigens (TAAs) recognized by CD8+ T lymphocytes (TCD8+) has made it possible to use recombinant and synthetic forms of TAAs to generate TCD8+ with anti-tumor activity. To explore new therapeutic strategies in a mouse model, we retrovirally transduced the experimental murine tumor CT26(H-2d), with the lacZ gene encoding our model TAA, beta-galactosidase (beta-gal). The transduced cell line, CT26.CL25, grew as rapidly and as lethally as the parental cell line in normal, immunocompetent animals. In an attempt to elicit TCD8+ directed against our model TAA by using purely recombinant and synthetic forms of our model TAA, we synthesized a nine-amino-acid long immunodominant peptide of beta-gal (TPH-PARIGL), corresponding to amino acid residues 876-884, which was known to be presented by the Ld major histocompatibility complex (MHC) class I molecule, and a recombinant vaccinia virus encoding the full-length beta-gal protein (VJS6). Splenocytes obtained from naïve mice and co-cultured with beta-gal peptide could not be expanded in primary ex vivo cultures. However, mice immunized with VJS6, but not with a control recombinant vaccinia virus, yielded splenocytes that were capable of specifically lysing CT26.CL25 in vitro after co-culture with beta-gal peptide. Most significantly, adoptive transfer of these cells could effectively treat mice bearing 3-day-old established pulmonary metastases. These observations show that therapeutic TCD8+ directed against a model TAA could be generated by using purely recombinant and synthetic forms of this antigen. These findings point the way to a potentially useful immunotherapeutic strategy, which has been made possible by the recent cloning of immunogenic TAAs that are expressed by human malignancies.
Transcriptomic Analysis of Intestinal Tissues from Two 90-Day Feeding Studies in Rats Using Genetically Modified MON810 Maize Varieties (2017)

<b>Background:</b> Global as well as specific expression profiles of selected rat tissues were characterized to assess the safety of genetically modified (GM) maize MON810 containing the insecticidal protein Cry1Ab. Gene expression was evaluated by use of Next Generation Sequencing (NGS) as well as RT-qPCR within rat intestinal tissues based on mandatory 90-day rodent feeding studies. In parallel to two 90-day feeding studies, the transcriptional response of rat tissues was assessed as another endpoint to enhance the mechanistic interpretation of GM feeding studies and/or to facilitate the generation of a targeted hypothesis. Rats received diets containing 33% GM maize (MON810) or near-isogenic control maize. As a site of massive exposure to ingested feed the transcriptomic response of ileal and colonic tissue was profiled via RT-qPCR arrays targeting apoptosis, DNA-damage/repair, unfolded protein response (UPR). For global RNA profiling of rat ileal tissue, we applied NGS. <b>Results:</b> No biological response to the GM-diet was observed in male and in female rat tissues. Transcriptome wide analysis of gene expression by RNA-seq confirmed these findings. Nevertheless, gene ontology (GO) analysis clearly associated a set of distinctly regulated transcripts with circadian rhythms. We confirmed differential expression of circadian clock genes using RT-qPCR and immunoassays for selected factors, thereby indicating physiological effects caused by the time point of sampling. <b>Conclusion:</b> Prediction of potential unintended effects of GM-food/feed by transcriptome based profiling of intestinal tissue presents a novel approach to complement classical toxicological testing procedures. Including the detection of alterations in signaling pathways in toxicity testing procedures may enhance the confidence in outcomes of toxicological trials. In this study, no significant GM-related changes in intestinal expression profiles were found in rats fed GM-maize MON810. Relevant alterations of selected cellular pathways (apoptosis, DNA damage and repair, UPR) pointing toward intestinal toxicity of the diets were not observed. Transcriptomic profiles did not reveal perturbations of pathways associated with toxicity, underlining the study results revealed by classical OECD endpoints.
Combined Depth Migration and Constrained Inversion of Low Frequency Electromagnetic Data (2007)

In order to migrate electromagnetic data from a low frequency controlled source, 3D electromagnetic Green functions should be used since the near-fleld efiects may be large. Imaging principles of the correlation type do not have su-cient depth sensitivity to be used in a one-pass migration step. To increase the depth sensitivity, a non-local operator is introduced in the imaging condition. This operator accounts for the lateral propagation of the EM fleld in the high resistivity reservoir. The non-local operator depends on two parameters related to the resistivity and thickness of an assumed resistivity anomaly. We propose to estimate these parameters from a limited set of forward modeling operations. DOI: 10.2529/PIERS060907093858
A Combination of Receptor-Binding Domain and N-Terminal Domain Neutralizing Antibodies Limits the Generation of SARS-CoV-2 Spike Neutralization-Escape Mutants (2021)

Most known SARS-CoV-2 neutralizing antibodies (nAbs), including those approved by the FDA for emergency use, inhibit viral infection by targeting the receptor-binding domain (RBD) of the spike (S) protein. Variants of concern (VOC) carrying mutations in the RBD or other regions of S reduce the effectiveness of many nAbs and vaccines by evading neutralization. Therefore, therapies that are less susceptible to resistance are urgently needed. Here, we characterized the memory B-cell repertoire of COVID-19 convalescent donors and analyzed their RBD and non-RBD nAbs. We found that many of the non-RBD-targeting nAbs were specific to the N-terminal domain (NTD). Using neutralization assays with authentic SARS-CoV-2 and a recombinant vesicular stomatitis virus carrying SARS-CoV-2 S protein (rVSV-SARS2), we defined a panel of potent RBD and NTD nAbs. Next, we used a combination of neutralization-escape rVSV-SARS2 mutants and a yeast display library of RBD mutants to map their epitopes. The most potent RBD nAb competed with hACE2 binding and targeted an epitope that includes residue F490. The most potent NTD nAb epitope included Y145, K150, and W152. As seen with some of the natural VOC, the neutralization potencies of COVID-19 convalescent-phase sera were reduced by 4- to 16-fold against rVSV-SARS2 bearing Y145D, K150E, or W152R spike mutations. Moreover, we found that combining RBD and NTD nAbs did not enhance their neutralization potential. Notably, the same combination of RBD and NTD nAbs limited the development of neutralization-escape mutants <i>in vitro</i>, suggesting such a strategy may have higher efficacy and utility for mitigating the emergence of VOC. <b>IMPORTANCE</b> The U.S. FDA has issued emergency use authorizations (EUAs) for multiple investigational monoclonal antibody (MAb) therapies for the treatment of mild to moderate COVID-19. These MAb therapeutics are solely targeting the receptor-binding domain of the SARS-CoV-2 spike protein. However, the N-terminal domain of the spike protein also carries crucial neutralizing epitopes. Here, we show that key mutations in the N-terminal domain can reduce the neutralizing capacity of convalescent-phase COVID-19 sera. We report that a combination of two neutralizing antibodies targeting the receptor-binding and N-terminal domains may be beneficial to combat the emergence of virus variants.
Effects of Recombinant Bovine Interferons-α and -γ on Some In Vitro Immune Functions of Bovine Intraepithelial and Lamina Propria Leukocytes (1988)

The effects of recombinant bacteria-derived bovine interferon-alpha I1 (rBoIFN-alpha I1) and -gamma (rBoIFN-gamma) on some in vitro immune functions of bovine intestinal leukocytes were studied. The proliferative response of intraepithelial leukocytes (IEL) to concanavalin A (Con A) was significantly inhibited by the addition of 5-1,000 U/ml of either IFN type. In contrast, addition of rBoIFN-alpha I1 to lamina propria leukocytes (LPL) from the same animal, showed significant inhibition only above 500 U/ml, whereas rBoIFN-gamma revealed significant enhancement when added as low as 50 U/ml. The concentration of mitogen and the time of incubation were both critical factors in determining the outcome of IFN-leukocyte interactions. While both IFN types could inhibit DNA synthesis of both leukocyte cultures at suboptimal (0.5 microgram/ml) Con A concentration throughout the time of incubation, their modulatory activities varied significantly at optimal (5.0 micrograms/ml) and supraoptimal (50.0 micrograms/ml) Con A concentrations. Preexposure of cells to IFNs or prestimulation with Con A did not significantly change the kinetics of IFNs with both leukocyte cultures. Pretreatment of leukocyte cultures with either IFN type for 18 h significantly enhanced the expression of MHC surface antigens. These data demonstrate that purified IFNs produced by recombinant DNA technology can significantly alter some in vitro immune functions of cells other than circulating leukocytes and that different IFNs have different capabilities to alter leukocyte functions.