gebhart/patrepeval huggingface dataset:
Contra: Contrarian statistics for controlled variable selection. (2021)

The holdout randomization test (HRT) discovers a set of covariates most predictive of a response. Given the covariate distribution, HRTs can explicitly control the false discovery rate (FDR). However, if this distribution is unknown and must be estimated from data, HRTs can inflate the FDR. To alleviate the inflation of FDR, we propose the contrarian randomization test (CONTRA), which is designed explicitly for scenarios where the covariate distribution must be estimated from data and may even be misspecified. Our key insight is to use an equal mixture of two "contrarian" probabilistic models in determining the importance of a covariate. One model is fit with the real data, while the other is fit using the same data, but with the covariate being tested replaced with samples from an estimate of the covariate distribution. CONTRA is flexible enough to achieve a power of 1 asymptotically, can reduce the FDR compared to state-of-the-art CVS methods when the covariate distribution is misspecified, and is computationally efficient in high dimensions and large sample sizes. We further demonstrate the effectiveness of CONTRA on numerous synthetic benchmarks, and highlight its capabilities on a genetic dataset.
Fusidic acid resistance in Rhodococcus erythropolis due to an inducible extracellular inactivating enzyme (1987)

Fusidic acid is a steroid antibiotic inhibiting Gram-positive microorganisms. The mechanism of resistance previously characterised involves mutation alteration of the target moiety, protein synthesis elongation factor EFG. In the nocardioform bacterium Rhodococcus erythropolis, a novel resistance mechanism to this antibiotic was found, i.e., an inducible extracellular fusidic acid-in-activating enzyme. The presence of this enzyme increased roughly 30-fold the antibiotic concentration at which the organism could grow.
Multimodal multisensor activity annotation tool (2016)

In this paper we describe a multimodal-multisensor annotation tool for physiological computing; for example mobile gesture-based interaction devices or health monitoring devices can be connected. It should be used as an expert authoring tool to annotate multiple video-based sensor streams for domain-specific activities. Resulting datasets can be used as supervised datasets for new machine learning tasks. Our tool provides connectors to commercially available sensor systems (e.g., Intel RealSense F200 3D camera, Leap Motion, and Myo) and a graphical user interface for annotation.
Bulk Niobium Polishing and Electropolishing Steps for Thinfilm Coated Copper SRF Cavities (2015)

Alameda Applied Sciences Corporation (AASC) grows Nb thin films via Coaxial Energetic Deposition (CED) from a cathodic arc plasma. The plasma consists of 60-120eV Nb ions (Nb+ and Nb++) [1] that penetrate a few monolayers into the substrate [2] and enable sufficient surface mobility to ensure that the lowest energy state (crystalline structure with minimal defects) is accessible to the film [3]. One limitation of CED thinfilms is the presence of Nb macroparticles (~0.1-10 microns) that could be deleterious to high field performance of the SRF cavity. One way to remove such macroparticles [4] is to grow a thick film (~3-5 microns), followed by mechanical polishing (MP) using the finest media as might be applied in Centrifugal Barrel Polishing (CBP) to achieve a 0.4 micron surface figure, and an electropolishing (EP) step to remove ~1 micron of Nb that also removes all traces of embedded media in the film. The residual 2-4 micron Nb film should more nearly resemble the surface of a bulk Nb cavity that has been subjected to the same steps. This paper describes experiments conducted on Cu coupons as a prelude to an SRF Cu cavity coating.
Lessons Learned from the Source Physics Experiment (SPE) Near Field Data and Associated Modeling Efforts (2015)

Abstract not provided
The Role of Mitochondria in Apoptosis (2009)

Mitochondria play key roles in activating apoptosis in mammalian cells. Bcl-2 family members regulate the release of proteins from the space between the mitochondrial inner and outer membrane that, once in the cytosol, activate caspase proteases that dismantle cells and signal efficient phagocytosis of cell corpses. Here we review the extensive literature on proteins released from the intermembrane space and consider genetic evidence for and against their roles in apoptosis activation. We also compare and contrast apoptosis pathways in Caenorhabditis elegans, Drosophila melanogaster, and mammals that indicate major mysteries remaining to be solved.
A lagrangian formulation for statistical fluid registration (2009)

We defined a new statistical fluid registration method with Lagrangian mechanics. Although several authors have suggested that empirical statistics on brain variation should be incorporated into the registration problem, few algorithms have included this information and instead use regularizers that guarantee diffeomorphic mappings. Here we combine the advantages of a large-deformation fluid matching approach with empirical statistics on population variability in anatomy. We reformulated the Riemannian fluid algorithm developed in [4], and used a Lagrangian framework to incorporate 0th and 1st order statistics in the regularization process. 92 2D midline corpus callosum traces from a twin MRI database were fluidly registered using the non-statistical version of the algorithm (algorithm 0), giving initial vector fields and deformation tensors. Covariance matrices were computed for both distributions and incorporated either separately (algorithm 1 and algorithm 2) or together (algorithm 3) in the registration. We computed heritability maps and two vector and tensor-based distances to compare the power and the robustness of the algorithms.
Model-free control using time delay estimation and fractional-order nonsingular fast terminal sliding mode for uncertain lower-limb exoskeleton (2018)

A robotic exoskeleton is a nonlinear system, which is subjected to parametric uncertainties and external disturbances. Due to this reason, it is difficult to obtain the exact model of the system, and without knowledge of the system, it cannot be compensated accurately. In this study, time delay estimation (TDE)-based model-free fractional-order nonsingular fast terminal sliding mode control (MFF-TSM) is proposed for the lower-limb robotic exoskeleton in the existence of uncertainties and external disturbance. The main characteristic of the proposed scheme is that it controls the system without relying on the knowledge of exoskeleton dynamics. At first, the fractional-order (FO) with nonsingular fast terminal sliding mode control (NFTSM) is adopted to provide a precise trajectory tracking performance, fast finite-time speed of convergence, singularity-free and chatter-free control inputs. And then, the proposed controller employs TDE, to make the controller model independent, which directly estimates the uncertain exoskeleton dynamics with external disturbances. Later, asymptotical stability analysis of the overall system and finite-time convergence are investigated and ensured using Lyapunov theorem. Finally, the simulation results are conducted to validate the efficacy of the proposed control method.
DNA methylation inhibitor attenuates polyglutamine‐induced neurodegeneration by regulating Hes5 (2019)

Spinal and bulbar muscular atrophy (SBMA) is a polyglutamine-mediated neuromuscular disease caused by a CAG repeat expansion in the <i>androgen receptor</i> (<i>AR</i>) gene. While transcriptional dysregulation is known to play a critical role in the pathogenesis of SBMA, the underlying molecular pathomechanisms remain unclear. DNA methylation is a fundamental epigenetic modification that silences the transcription of various genes that have a CpG-rich promoter. Here, we showed that DNA methyltransferase 1 (Dnmt1) is highly expressed in the spinal motor neurons of an SBMA mouse model and in patients with SBMA. Both genetic <i>Dnmt1</i> depletion and treatment with RG108, a DNA methylation inhibitor, ameliorated the viability of SBMA model cells. Furthermore, a continuous intracerebroventricular injection of RG108 mitigated the phenotype of SBMA mice. DNA methylation array analysis identified <i>hairy and enhancer of split 5</i> (<i>Hes5</i>) as having a CpG island with hyper-methylation in the promoter region, and the Hes5 expression was strongly silenced in SBMA. Moreover, Hes5 over-expression rescued the SBMA cells possibly by inducing Smad2 phosphorylation. Our findings suggest DNA hyper-methylation underlies the neurodegeneration in SBMA.
Multipath TCP (MPTCP) Application Interface Considerations (2013)

Multipath TCP (MPTCP) adds the capability of using multiple paths to a regular TCP session.Even though it is designed to be totally backward compatible to applications, the data transport differs compared to regular TCP, and there are several additional degrees of freedom that applications may wish to exploit.This document summarizes the impact that MPTCP may have on applications, such as changes in performance.Furthermore, it discusses compatibility issues of MPTCP in combination with non-MPTCP-aware applications.Finally, the document describes a basic application interface that is a simple extension of TCP's interface for MPTCP-aware applications.
Multiband spatial angular filtering transmissions through cascade asymmetrical metasurfaces (2021)

Abstract In this paper, a cascade asymmetrical metasurface (CAM) is proposed to generate the functionality of multiband spatial angular filtering transmissions. More specifically, dual‐asymmetrical‐C‐slits printed on the CAM can readily tune the transmission frequencies by controlling the incident angles of electromagnetic waves. In the meanwhile, the CAM with multiple hierarchical structures would be capable of realizing the multiband operative mode with the performance of spatial angular filtering. The proposed method, by using multilayer CAM structures to realize multiband spatial angular filtering transmissions, can offer an efficient way to fulfill reconfigurable radiations of the antennas by tuning the emission frequencies.
Abstract 12157: 4d Flow Mri Demonstrates Hemodynamic Normalization After Coarctation Repair in Pediatric Patients (2022)

Background: Coarctation of the aorta (COA) is a focal aortic narrowing, and intervention is required for patients with severe hemodynamic impairment. Following intervention, patients remain at risk for long-term re-coarctation. We used 4D flow MRI to assess aortic hemodynamics pre- and post- COA repair in children compared to age matched healthy controls. Methods: Aortic 4D flow MRI was performed in 5 pediatric COA patients (baseline age 6-14 yrs, 1F) pre- and post COA repair (4 native COA, 1 re-intervention) and 5 age-matched controls (ages 9-17 yrs, 2 female). Peak systolic velocities were quantified with velocity maximum intensity projections (MIP) ROIs in the ascending aorta (AAo), aortic arch, distal to the coarctation, and descending aorta (DAo) (Figure 1A). For flow quantification, nine 2D planes were placed along the aorta. Regional net flow was determined by averaging the 2D plane flows by region. The ratio between DAo to AAo (DAo/AAo) net flow was used to assess collateral flow. Results: Velocities were generally higher and more consistent across the aorta following surgery (Figure 1A). Plots highlighting changes in DAo/AAo flow ratio are shown in Figure 1B. Compared to controls, DAo/AAo flow ratio was significantly lower prior to COA repair (0.38±0.11 vs 0.61±0.05, p = 0.0004), indicating flow obstruction at the COA and presence of substantial collateral flow. Post COA repair DAo/AAo flow ratio was similar compared to age matched controls (0.59±0.06 vs 0.61±0.05, p = 0.51), indicating normalization of aortic flow. Patient 2, who underwent COA repair via stent placement showed the greatest improvement and normalization of flow consistency (DAo/AAo) across the aorta after intervention. Conclusion: A ortic 4D flow MRI shows normalization of aortic flow velocities, decreased collateral flow following COA repair, and has potential for long term surveillance and quantification of pre- and post-COA repair hemodynamic changes in children.
The effect of sulphide on the anaerobic degradation of propionate (1988)

Abstract The anaerobic degradation of propionate in the presence of excess sulphate was studied in an Upflow Anaerobic Sludge Bed reactor inoculated with granular sludge. A stable and efficient propionate degradation could be achieved (space load 5 kg COD m−3 day−1, VFA removal 96%). Only 23% of the added COD was recovered as sulphide in the effluent and biogas. H2S concentrations above approximately 100 mg 1−1 S caused a sharp drop of the VFA removal efficiency and resulted in process instability, possibly aggravated by propionate inhibition. Recovery took 3–4 weeks. Acetoclastic methanogenesis was not the rate limiting step under sulphide inhibition.
SCAR and RAPD markers associated with 18‐carbon fatty acids in rapeseed, Brassica napus (1999)

Abstract Breeding rapeseed for enhanced oil quality includes the development of varieties with low linolenic acid content. The breeder also aims to develop varieties with a high linoleic acid content because of its nutritional value. Restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD) markers have been developed for linolenic acid content, but they are not best suited for a direct application in marker‐assisted selection. The RFLP technique is too complex and time‐consuming and RAPD markers lack codominance, precluding the distinction of homozygous from heterozygous individuals. In this report the conversion of a RAPD marker to a codominant sequence characterized amplified region (SCAR) marker named L1L9 is described. One of the alleles consisting of an 899 bp fragment (allele A), is associated with low linolenic acid content. The other allele consists of an 641 bp fragment (allele B) and is associated with high linolenic acid content. This marker explains approximately 25% of the genetic variation for this trait. Linkage analysis in the mapping population indicates that the SCAR marker probably tags an ω‐3 desaturase gene in B. napus. Two RAPD markers were found to be associated with oleic/linoleic acid content. Markers M14‐350 and I06‐650 explained approximately 10% and 7% of the genetic variation for linoleic acid content, respectively. These two markers were found linked at 12.3cM in the segregating B. napus F 2 progeny used for mapping. All the markers reported in this paper should be useful in breeding programmes for developing high linoleic and low linolenic acid rapeseed varieties.
Expression of testis angiotensin-converting enzyme is mediated by a cyclic AMP responsive element. (1997)

Testis angiotensin-converting enzyme (testis ACE), an ACE isozyme that plays an important role in male fertility, is transcribed from a unique promotor active only in developing spermatids. In vitro analysis suggests the importance of a cyclic AMP response element (CRE)-like region within the testis ACE promoter, and similar DNA motifs are important in the expression of a variety of testis-specific genes. In the present study, we examined the effects of mutations in the CRE-like element on testis ACE promoter activity in vivo using transgenic mice. Disruption of this element reduced reporter gene expression to near background levels. In contrast, conversion of the CRE-like element to a consensus CRE-binding site resulted in high level expression of the reporter gene specifically in the testis. These experiments prove that the CRE-like element is essential for testis ACE promoter activity, although it does not appear to be responsible for its tissue specificity. These data provide insight into how a phenotypically differentiated tissue, ie, male gem cells, regulate tissue-specific gene expression.
Structure of the guanylyltransferase domain of human mRNA capping enzyme (2011)

The enzyme guanylyltransferase (GTase) plays a central role in the three-step catalytic process of adding an (m7)GpppN cap cotranscriptionally to nascent mRNA (pre-mRNAs). The 5'-mRNA capping process is functionally and evolutionarily conserved from unicellular organisms to human. However, the GTases from viruses and yeast have low amino acid sequence identity (∼25%) with GTases from mammals that, in contrast, are highly conserved (∼98%). We have defined by limited proteolysis of human capping enzyme residues 229-567 as comprising the minimum enzymatically active human GTase (hGTase) domain and have determined the structure by X-ray crystallography. Seven related conformational states of hGTase exist in the crystal. The GTP-binding site is evolutionarily and structurally conserved. The positional variations of the oligonucleotide/oligosaccharide binding fold lid domain over the GTP-binding site provide snapshots of the opening and closing of the active site cleft through a swivel motion. The pattern of conserved surface residues in mammals, but not in yeast, supports the finding that the recognition of the capping apparatus by RNA polymerase II and associated transcription factors is highly conserved in mammals, and the mechanism may differ somewhat from that in yeast. The hGTase structure should help in the design of biochemical and molecular biology experiments to explore the proteinprotein and proteinRNA interactions that ensure regulated transcription of genes in humans and other mammals.
Real time stock price distribution utilising the GSM short messaging service (2002)

The development of value added services based upon the GSM standard is becoming increasingly important to both network operators and the subscriber's to such networks. This paper outlines a prototype system capable of delivering real time stock (share) price information from Internet based stock price servers to mobile subscribers equipped with GSM cellular terminals. The prototype system is based upon a gateway PC system which is connected to both the Internet and also the GSM cellular network. The system allows a subscriber to the service to receive updates on stock prices at desired intervals throughout the day, or on demand, primarily by means of short messages delivered to their GSM mobile phone. In addition to this primary delivery mechanism, a number of enhanced delivery mechanism have also been designed into the system based around a "dial up" interactive voice response (IVR) system on the gateway PC platform. These allow a subscriber to get an immediate update, by a short message or by a spoken prompt, of some/all of his stock portfolio by dialling up and interacting with the IVR functionality in the system server.
Pattern classification using self-organizing feature maps (1990)

The author demonstrates the use of self-organizing feature maps as pattern classifiers. When a set of training patterns is presented to a self-organizing network repeatedly for many iterations, the weight vectors gradually organize themselves to be the cluster centers of these patterns. In the one-dimensional case, they can arrange themselves to satisfy a linear ordering relation. That is, the distance between two weight vectors increases as the physical distance between the two corresponding output nodes increases. However, the latter is true only when an adequate size of neighborhood is used in the network. The author notices a cyclic phenomenon among the distances between weight vectors when the neighborhood size is small
P2‐371: MICROGLIAL ACTIVATION, BUT NOT TAU DEPOSITION, IS INDEPENDENTLY ASSOCIATED WITH AMYLOID POSITIVITY AND MEMORY IMPAIRMENT (2019)

We sought to determine whether amyloid positivity and memory impairment have independent effects on microglial activation and tau deposition. Subjects with either amnestic MCI or mild AD (n = 33) and controls (n = 24) underwent neuropsychological testing and 18F-Florbetaben PET to determine the presence of memory impairment and amyloid (Aβ) positivity.11C-PBR28 and 18F-MK-6240 PET scans were performed to measure microglial activation and tau pathology, respectively. Image data were corrected for partial volume effects and cerebellar grey matter was used as reference to create standardized uptake value ratios. Analyses of variance tested the overall and regional effects of Aβ and memory impairment on 11C-PBR28 and 18F-MK-6240 binding, correcting for age and (for 11C-PBR28) TSPO genotype. Correlation analyses tested the relationships between radioligand binding and Mini Mental State Exam (MMSE) score. For both radioligands, Aβ and impairment had significant overall effects on binding (p < 0.008). There was no interaction between Aβ and impairment in their effect on 11C-PBR28 (p = 0.6722). However, there was significant interaction between amyloid and memory status in their effect on 18F-MK-6240 binding (p = 0.011). Regional effects followed a similar pattern for both radioligands (Fig 1). In amyloid-positive subjects, MMSE negatively correlated with both 18F-MK-6240 (p < 0.02) and 11C-PBR28 (p < 0.03) binding in all regions except medial temporal cortex for 11C-PBR28. In amyloid-negative subjects, MMSE did not correlate with binding of either radioligand in any region.
On iterative equalization, estimation, and decoding (2004)

We consider the problem of coded data transmission over an inter-symbol interference (ISI) channel with unknown and possibly time-varying parameters. We propose a low-complexity algorithm for joint equalization, estimation, and decoding using an estimator, which is separate from the equalizer. Based on existing techniques for analyzing the convergence of iterative decoding algorithms, we show how to find powerful system configurations. This includes the use of recursive precoders in the transmitter. We derive a novel a-posteriori probability equalization algorithm for imprecise knowledge of the channel parameters. We show that the performance loss implied by not knowing the parameters pf the ISI channel is entirely a loss in signal-to-noise ratio for which a suitably designed iterative receiver algorithm converges.
Tomatidine Inhibits Replication of Staphylococcus aureus Small-Colony Variants in Cystic Fibrosis Airway Epithelial Cells (2011)

Small-colony variants (SCVs) often are associated with chronic Staphylococcus aureus infections, such as those encountered by cystic fibrosis (CF) patients. We report here that tomatidine, the aglycon form of the plant secondary metabolite tomatine, has a potent growth inhibitory activity against SCVs (MIC of 0.12 μg/ml), whereas the growth of normal S. aureus strains was not significantly altered by tomatidine (MIC, >16 μg/ml). The specific action of tomatidine was bacteriostatic for SCVs and was clearly associated with their dysfunctional electron transport system, as the presence of the electron transport inhibitor 4-hydroxy-2-heptylquinoline-N-oxide (HQNO) caused normal S. aureus strains to become susceptible to tomatidine. Inversely, the complementation of SCVs' respiratory deficiency conferred resistance to tomatidine. Tomatidine provoked a general reduction of macromolecular biosynthesis but more specifically affected the incorporation of radiolabeled leucine in proteins of HQNO-treated S. aureus at a concentration corresponding to the MIC against SCVs. Furthermore, tomatidine inhibited the intracellular replication of a clinical SCV in polarized CF-like epithelial cells. Our results suggest that tomatidine eventually will find some use in combination therapy with other traditional antibiotics to eliminate persistent forms of S. aureus.