Miracle-dz/UniFAR-FTUs huggingface dataset:
Cyclical Multiple Access in UAV-Aided Communications: A Throughput-Delay Tradeoff

This letter studies a wireless system consisting of distributed ground terminals (GTs) communicating with an unmanned aerial vehicle (UAV) that serves as a mobile base station (BS). The UAV flies cyclically above the GTs at a fixed altitude, which results in a cyclical pattern of the strength of the UAV-GT channels. To exploit such periodic channel variations, we propose a new cyclical multiple access (CMA) scheme to schedule the communications between the UAV and GTs in a cyclical time-division manner based on the flying UAV's position. The time allocations to different GTs are optimized to maximize their minimum throughput. It is revealed that there is a fundamental tradeoff between throughput and access delay in the proposed CMA. Simulation results show significant throughput gains over the case of a static UAV BS in delay-tolerant applications.
Evaluation of niobium as candidate electrode material for dc high voltage photoelectron guns

The field emission characteristics of niobium electrodes were compared to those of stainless steel electrodes using a DC high voltage field emission test apparatus. A total of eight electrodes were evaluated: two 304 stainless steel electrodes polished to mirrorlike finish with diamond grit and six niobium electrodes (two single-crystal, two large-grain, and two fine-grain) that were chemically polished using a buffered-chemical acid solution. Upon the first application of high voltage, the best large-grain and single-crystal niobium electrodes performed better than the best stainless steel electrodes, exhibiting less field emission at comparable voltage and field strength. In all cases, field emission from electrodes (stainless steel and/or niobium) could be significantly reduced and sometimes completely eliminated, by introducing krypton gas into the vacuum chamber while the electrode was biased at high voltage. Of all the electrodes tested, a large-grain niobium electrode performed the best, exhibiting no measurable field emission (< 10 pA) at 225 kV with 20 mm cathode/anode gap, corresponding to a field strength of 18: 7M V=m.
AFM-Based Single Molecule Techniques: Unraveling the Amyloid Pathogenic Species

Background A wide class of human diseases and neurodegenerative disorders, such as Alzheimer’s disease, is due to the failure of a specific peptide or protein to keep its native functional conformational state and to undergo a conformational change into a misfolded state, triggering the formation of fibrillar cross-β sheet amyloid aggregates. During the fibrillization, several coexisting species are formed, giving rise to a highly heterogeneous mixture. Despite its fundamental role in biological function and malfunction, the mechanism of protein self-assembly and the fundamental origins of the connection between aggregation, cellular toxicity and the biochemistry of neurodegeneration remains challenging to elucidate in molecular detail. In particular, the nature of the specific state of proteins that is most prone to cause cytotoxicity is not established. Methods: In the present review, we present the latest advances obtained by Atomic Force Microscopy (AFM) based techniques to unravel the biophysical properties of amyloid aggregates at the nanoscale. Unraveling amyloid single species biophysical properties still represents a formidable experimental challenge, mainly because of their nanoscale dimensions and heterogeneous nature. Bulk techniques, such as circular dichroism or infrared spectroscopy, are not able to characterize the heterogeneity and inner properties of amyloid aggregates at the single species level, preventing a profound investigation of the correlation between the biophysical properties and toxicity of the individual species. Conclusion: The information delivered by AFM based techniques could be central to study the aggregation pathway of proteins and to design molecules that could interfere with amyloid aggregation delaying the onset of misfolding diseases.
Interactive Graphical Representation for Collaborative 3D Virtual Worlds

Abstract: Three‐dimensional (3D) virtual worlds have the potential to make a major impact on global design teams by providing an online place that supports distant design activities without designers being physically present. To accommodate designing in 3D virtual worlds for the architecture, engineering, and construction (AEC) domain, there is an urgent need for the development of a representation system applicable in conceptual design and multi‐disciplinary design. Extended from Qualitative Archi Bond Graphs (QABGs) that are developed as qualitative unified representations for buildings, this article presents and demonstrates an interactive graphical representation for collaborative design in 3D virtual worlds. The representation supports multiple design representation subsystems and their interactions that enable designers to better facilitate design collaboration in 3D virtual worlds.
A Conceptual Framework for Information Retrieval to Support Creativity in Business Processes

Creativity as the prerequisite for innovation is a core competitive factor in contemporary organizations. When creativity happens this involves creative persons who produce creative products in a process that cannot be fully anticipated and predescribed. We introduce the concept of pockets of creativity for those sections of a business process where creativity occurs. These sections are characterized by a high demand for flexibility and knowledge of the involved creative persons. In pockets of creativity previous knowledge is retrieved, transformed and combined into new procedures or artifacts – in short – innovations. Naturally, this raises the question of how pockets of creativity can be supported by information technology. Information retrieval is part of an organizations knowledge processes concerned with the representation, storage, organization, searching and finding of organizational knowledge. Informed by case studies we have conducted with organizations from the Creative Industries and drawing from existing theory, in this paper we introduce a conceptual framework for information retrieval that enables creative persons to access relevant information through a multi-perspective, hierarchical view. Such an approach both appropriately considers different ways of creative thinking and provides stimuli to a person's cognitive network fostering her creativity and thus the development of truly innovative products.
The gain and loss of long noncoding RNA associated-competing endogenous RNAs in prostate cancer

Prostate cancer (PC) is one of the most common solid tumors in men. However, the molecular mechanism of PC remains unclear. Numerous studies have demonstrated that long noncoding RNA (lncRNA) can act as microRNA (miRNA) sponge, one type of competing endogenous RNAs (ceRNAs), which offers a novel viewpoint to elucidate the mechanisms of PC. Here, we proposed an integrative systems biology approach to infer the gain and loss of ceRNAs in PC. First, we re-annotated exon microarray data to obtain lncRNA expression profiles of PC. Second, by integrating mRNA and miRNA expression, as well as miRNA targets, we constructed lncRNA-miRNA-mRNA ceRNA networks in cancer and normal samples. The lncRNAs in these two ceRNA networks tended to have a longer transcript length and cover more exons than the lncRNAs not involved in ceRNA networks. Next, we further extracted the gain and loss ceRNA networks in PC. We found that the gain ceRNAs in PC participated in cell cycle, and the loss ceRNAs in PC were associated with metabolism. We also identified potential prognostic ceRNA pairs such as MALAT1-EGR2 and MEG3-AQP3. Finally, we inferred a novel mechanism of known drugs, such as cisplatin, for the treatment of PC through gain and loss ceRNA networks. The potential drugs such as 1,2,6-tri-O-galloyl-beta-D-glucopyranose (TGGP) could modulate lncRNA-mRNA competing relationships, which may uncover new strategy for treating PC. In summary, we systematically investigated the gain and loss of ceRNAs in PC, which may prove useful for identifying potential biomarkers and therapeutics for PC.
Rapid and noncontaminating sampling system for trace elements in global ocean surveys

A system for the rapid and noncontaminating sampling of trace elements with volumes of up to 36 L per depth and including the dissolved and particulate phases has been developed for ocean sections that are a crucial part of programs such as International GEOTRACES. The system uses commercially available components, including an aluminum Seabird Carousel with all titanium pressure housings for electronics and sensors to eliminate zinc sacrificial anodes and holding twenty‐four 12 L GO‐FLO bottles, and a 7500 m, 14 mm Vectran conducting cable (passing over an A‐frame with nonmetallic sheave) spooled onto a traction winch. The GO‐FLO bottles are stored and processed in a clean lab built into a 20' ISO container. To minimize contamination, the GO‐FLO bottles are triggered when the carousel is moving upward into clean water at 3 m min−1. Analyses of salinity and nutrients in bottle samples from the stopped versus moving carousel show no detectable smearing, whereas the contamination‐prone trace elements show the samples are uncontaminated when compared with other clean sampling methods. Based on the use of this system on three major cruises, the launch‐sample‐recover time for the carousel (2 bottles triggered per depth) is 1 h per 1000 m, and dissolved and particulate sampling time averages 6 h per hydrocast. Thus, the system described here meets all the requirements for ocean basin sampling for trace elements: rapid, good hydrographic fidelity, and noncontaminating.
Why it is time to develop the use of cognitive event-related potentials in the treatment of psychiatric diseases

The relapse rate for many psychiatric disorders is staggeringly high, indicating that treatment methods combining psychotherapy with neuropharmacological interventions are not entirely effective. Therefore, in psychiatry, there is a current push to develop alternatives to psychotherapy and medication-based approaches. Cognitive deficits have gained considerable importance in the field as critical features of mental illness, and it is now believed that they might represent valid therapeutic targets. Indeed, an increase in cognitive skills has been shown to have a long-lasting, positive impact on the patients’ quality of life and their clinical symptoms. We hereby present four principal arguments supporting the use of event-related potentials (ERP) that are derived from electroencephalography, which allow the identification of specific neurocognitive deficiencies in patients. These arguments could assist psychiatrists in the development of individualized, targeted therapy, as well as a follow-up and rehabilitation plan specific to each patient’s deficit. Furthermore, they can be used as a tool to assess the possible benefits of combination therapy, consisting of medication, psychotherapy, and “ERP-oriented cognitive rehabilitation”. Using this strategy, specific cognitive interventions could be planned based on each patient’s needs, for an “individualized” or “personalized” therapy, which may have the potential to reduce relapse rates for many psychiatric disorders. The implementation of such a combined approach would require intense collaboration between psychiatry departments, clinical neurophysiology laboratories, and neuropsychological rehabilitation centers.
Overexpression of Mineralocorticoid Receptors in the Mouse Forebrain Partly Alleviates the Effects of Chronic Early Life Stress on Spatial Memory, Neurogenesis and Synaptic Function in the Dentate Gyrus

Evidence from human studies suggests that high expression of brain mineralocorticoid receptors (MR) may promote resilience against negative consequences of stress exposure, including childhood trauma. We examined, in mice, whether brain MR overexpression can alleviate the effects of chronic early life stress (ELS) on contextual memory formation under low and high stress conditions, and neurogenesis and synaptic function of dentate gyrus granular cells. Male mice were exposed to ELS by housing the dam with limited nesting and bedding material from postnatal day (PND) 2 to 9. We investigated the moderating role of MRs by using forebrain-specific transgenic MR overexpression (MR-tg) mice. Low-stress contextual (i.e., object relocation) memory formation was hampered by ELS in wildtype but not MR-tg mice. Anxiety like behavior and high-stress contextual (i.e., fear) memory formation were unaffected by ELS and/or MR expression level. At the cellular level, an interaction effect was observed between ELS and MR overexpression on the number of doublecortin-positive cells, with a significant difference between the wildtype ELS and MR-tg ELS groups. No interaction was found regarding Ki-67 and BrdU staining. A significant interaction between ELS and MR expression was further observed with regard to mEPSCs and mIPSC frequency. The ratio of evoked EPSC/IPSC or NMDA/AMPA responses was unaffected. Overall, these results suggest that ELS affects contextual memory formation under low stress conditions as well as neurogenesis and synaptic transmission in dentate granule cells, an effect that can be alleviated by MR-overexpression.
Traumatic brain injury and the risk of dementia diagnosis: A nationwide cohort study

Background Traumatic brain injury (TBI) has been associated with dementia. The questions of whether the risk of dementia decreases over time after TBI, whether it is similar for different TBI types, and whether it is influenced by familial aggregation are not well studied. Methods and findings The cohort considered for inclusion comprised all individuals in Sweden aged ≥50 years on December 31, 2005 (n = 3,329,360). Diagnoses of dementia and TBI were tracked through nationwide databases from 1964 until December 31, 2012. In a first cohort, individuals diagnosed with TBI (n = 164,334) were matched with up to two controls. A second cohort consisted of subjects diagnosed with dementia during follow-up (n = 136,233) matched with up to two controls. A third cohort consisted of 46,970 full sibling pairs with discordant TBI status. During a mean follow-up period of 15.3 (range, 0–49) years, 21,963 individuals in the first cohort (6.3% with TBI, 3.6% without TBI) were diagnosed with dementia (adjusted odds ratio [OR], 1.81; 95% confidence interval [CI], 1.75–1.86). The association was strongest in the first year after TBI (OR, 3.52; 95% CI, 3.23–3.84), but the risk remained significant >30 years (OR, 1.25; 95% CI, 1.11–1.41). Single mild TBI showed a weaker association with dementia (OR, 1.63; 95% CI, 1.57–1.70) than did more severe TBI (OR, 2.06; 95% CI, 1.95–2.19) and multiple TBIs (OR, 2.81; 95% CI, 2.51–3.15). These results were in general confirmed in the nested case-control cohort. TBI was also associated with an increased risk of dementia diagnosis in sibling pairs with discordant TBI status (OR, 1.89; 95% CI, 1.62–2.21). A main limitation of the present study is the observational design. Thus, no causal inferences can be made based on the associations found. Conclusions The risk of dementia diagnosis decreased over time after TBI, but it was still evident >30 years after the trauma. The association was stronger for more severe TBI and multiple TBIs, and it persisted after adjustment for familial factors.
Isolation and quantification of episomal expression vectors in human T cells.

This work was supported by an endowment established by the Lombardi Foundation Trust and funding provided by St. Luke’s Medical Center, Milwaukee, WI. T.P.Q. is a graduate student in the Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI. Address correspondence to Katrina T. Trevor, Immunotherapy Research and Treatment Institute, St. Luke’s Medical Center, 2900 W. Oklahoma Ave., Milwaukee, WI 53215, USA. Internet: ktrevor@execpc.com
Probing the dispersion properties of 1D nanophotonic waveguides with far-field Fourier optics

We present an advanced Fourier space imaging technique to probe guided light in nanophotonic structures with an effective numerical aperture of 2.5. This superresolution technique allows us to successfully investigate the dispersive properties of 1D nanowaveguides such as photonic crystal W1 waveguides, photonic wire, slot waveguides, and couplers.
Plasmodium vivax Merozoite Surface Protein-3 (PvMSP3): Expression of an 11 Member Multigene Family in Blood-Stage Parasites

Background Three members of the Plasmodium vivax merozoite surface protein-3 (PvMSP3) family (PvMSP3-α, PvMSP3-β and PvMSP3-γ) were initially characterized and later shown to be part of a larger highly diverse family, encoded by a cluster of genes arranged head-to-tail in chromosome 10. PvMSP3-α and PvMSP3-β have become genetic markers in epidemiological studies, and are being evaluated as vaccine candidates. This research investigates the gene and protein expression of the entire family and pertinent implications. Methodology/Principal Findings A 60 kb multigene locus from chromosome 10 in P. vivax (Salvador 1 strain) was studied to classify the number of pvmsp3 genes present, and compare their transcription, translation and protein localization patterns during blood-stage development. Eleven pvmsp3 paralogs encode an N-terminal NLRNG signature motif, a central domain containing repeated variable heptad sequences, and conserved hydrophilic C-terminal features. One additional ORF in the locus lacks these features and was excluded as a member of the family. Transcripts representing all eleven pvmsp3 genes were detected in trophozoite- and schizont-stage RNA. Quantitative immunoblots using schizont-stage extracts and antibodies specific for each PvMSP3 protein demonstrated that all but PvMSP3.11 could be detected. Homologs were also detected by immunoblot in the closely related simian species, P. cynomolgi and P. knowlesi. Immunofluorescence assays confirmed that eight of the PvMSP3s are present in mature schizonts. Uniquely, PvMSP3.7 was expressed exclusively at the apical end of merozoites. Conclusion/Significance Specific proteins were detected representing the expression of 10 out of 11 genes confirmed as members of the pvmsp3 family. Eight PvMSP3s were visualized surrounding merozoites. In contrast, PvMSP3.7 was detected at the apical end of the merozoites. Pvmsp3.11 transcripts were present, though no corresponding protein was detected. PvMSP3 functions remain unknown. The ten expressed PvMSP3s are predicted to have unique and complementary functions in merozoite biology.
Phylogeography of Three Snubnose Darters (Percidae: Subgenus Ulocentra) Endemic to the Southeastern U.S. Coastal Plain

Abstract The Yazoo Darter, Etheostoma raneyi (Percidae: subgenus Ulocentra), is a narrowly restricted endemic occurring in small tributaries in the Loessial Hills of the upper Yazoo River basin in northern Mississippi. The range of the species is shared between the Little Tallahatchie and adjacent upper Yocona rivers, but populations in the two rivers are separated by unsuitable habitat in the Mississippi Alluvial Plain. The Chickasaw Darter, Etheostoma cervus, and Firebelly Darter, E. pyrrhogaster, show analogous distributions in the Forked Deer and Obion rivers, respectively, of western Tennessee and Kentucky. Phylogenetic analyses of cyt b and control region mtDNA (1497 sites) data from E. raneyi (n = 12), E. cervus (n = 4), and E. pyrrhogaster (n = 5) recovered two clades of E. raneyi with high bootstrap and decay support that are congruent with localities of specimens from the Little Tallahatchie and Yocona drainages, respectively. Divergence between the clades of E. raneyi was 1.3% (SE = 0.3%). Within drainage divergence was 0.3% (SE = 0.1%) for the Little Tallahatchie clade and 0.1% (SE < 0.1%) for the Yocona clade. Etheostoma cervus and E. pyrrhogaster showed interspecific divergence of 1.3% (SE = 0.2%) and intraspecific divergence of 0.7% (SE = 0.2%) and 0.8% (SE = 0.2%), respectively. These results suggest isolation by vicariance as a mode of speciation in fishes restricted to the Upper Coastal Plain. Conservation action may be in order for E. raneyi as populations from the Little Tallahatchie and Yocona rivers should be treated as separate management units with the latter known from only five small streams, some of which are threatened by encroaching development.
Nonlinear Disturbance Observer-Based Dynamic Surface Control for Trajectory Tracking of Pneumatic Muscle System

In this paper, a phenomenological model of pneumatic muscle is established consisting of a contractile element, spring element, and damping element in parallel. To verify the practicability of pneumatic muscle (PM) modeling, dynamic surface control (DSC) characterized by convenient design and good transient performance is employed for realizing PM tracking control. However, parametric uncertainty is inevitable in PM modeling as friction and unknown external disturbances exist in a PM system. These PM modeling errors and unknown variables can undermine and deteriorate the control performance of PM systems. To solve this problem and improve control accuracy, a novel nonlinear disturbance observer-based dynamic surface control (NDOBDSC) is proposed for trajectory tracking of PM system. Through employing the nonlinear disturbance observer, the stated uncertainties can be estimated online and compensated. The proposed novel control scheme therefore integrates the advantages of DSC, while estimating time-varying uncertainties to achieve compensation of inherent uncertainties. The established control law guarantees that the closed-loop system is semiglobally uniformly and ultimately bounded. Both the simulation studies and practical experiments demonstrate the effectiveness of NDOBDSC, showing that the control performance of NDOBDSC is satisfactory in the presence of modeling errors, friction, changing load, and other uncertainties in the PM system.
ACCUSA2: multi-purpose SNV calling enhanced by probabilistic integration of quality scores

SUMMARY Direct comparisons of assembled short-read stacks are one way to identify single-nucleotide variants. Single-nucleotide variant detection is especially challenging across samples with different read depths (e.g. RNA-Seq) and high-background levels (e.g. selection experiments). We present ACCUSA2 to identify variant positions where nucleotide frequency spectra differ between two samples. To this end, ACCUSA2 integrates quality scores for base calling and read mapping into a common framework. Our benchmarks demonstrate that ACCUSA2 is superior to a state-of-the-art SNV caller in situations of diverging read depths and reliably detects subtle differences among sample nucleotide frequency spectra. Additionally, we show that ACCUSA2 is fast and robust against base quality score deviations. AVAILABILITY ACCUSA2 is available free of charge to academic users and may be obtained from https://bbc.mdc-berlin.de/software. CONTACT christoph.dieterich@mdc-berlin.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.