Miracle-dz/UniFAR-FTUs huggingface dataset:
Continuous uncertain interaction

This work describes a novel perspective on the theoretical foundation of human-computer interfaces, framing the problem as a continuous control process. In this view, the system continuously infers a distribution over potential user goals, and provides continuous feedback about its beliefs as it does so. The proper representation and manipulation of uncertainties in interaction – via probability theory – and the explicit inclusion of temporal characteristics – in the form of dynamic systems – are inherent to this framework. The framework is used to derive a novel approach to interaction design, particularly in situations where rich or unusual sensing and display modalities are present. A number of key tools for describing and implementing systems which are consistent with this perspective are presented. The role of system dynamics as a mediating element between sensed state and decision making is described. The work sets out a paradigm for interaction which brings probabilistic models – and thus many of the techniques of modern machine learning – into the interface in a clean and principled manner. The three major techniques for supporting the paradigm outlined in the thesis are: the display of changing probabilistic beliefs; dynamically adjusting system handling qualities according to an inference model; and a general probabilistic selection technique based on the detection of control. Methods are presented for displaying the state of a system with appropriate representation of uncertainty, via Monte Carlo sampling techniques. Specifically, the use of granular synthesis for auditory display of the distributions involved in a period of interaction is described, and it is shown how predictive elements can be introduced into goal directed displays, mitigating delays present in the interaction loop. The use of these techniques in displaying particle filtering processes is illustrated. The process by which the results of goal inference can be fed back into the dynamics that the user directly controlled is presented in general form, and applied specifically to the problem of text entry. It is shown that this inference feedback mechanism unifies a range of conventional techniques, including semantic pointing and bubble pointing. A novel text entry system for mobile devices augmented with inertial sensors is developed to illuminate the inference feedback technique. By viewing human behaviour as a control process, a general, dynamic selection for many possible sensors is developed. This is fully probabilistic and widely applicable in many domains. It provides a sound method for designing the dynamics of an interactive selection system. This is extended to general exploration in high-dimensional spaces via controlled Markov Chain Monte Carlo processes.
A system for processing hyperspectral imagery: application to detecting forest species

Although there are many approaches to hyperspectral data processing, they are typically based on an intuitive search of the appropriate spectral channels to solve the pattern recognition problem. To account for the accuracy of the computational procedures used, optimization techniques are needed to select the most useful spectral channels and to find contextual links for neighbouring pixels within a particular class of observed objects. We describe a system that merges both these types of mathematical formalism using a step-up method to extract the optimal channels from their entire set and to explain the contextual constraints on the images of high spatial resolution. The method is applied to forests of different species and age, which include areas illuminated by the Sun and shaded areas; these are the main classes recognized in this study. The proposed improvements in finding the specific information layers serve to enhance the computational efficiency of the techniques applied. These layers are formed by the sunlit forest canopy, sunlit background, and shaded background for a particular solar zenith angle during an aerial survey. The original system is created based on the relevant construction of the classifier employed, bearing in mind the signal to noise ratio of the hyperspectral device, its calibration, and the elaborated procedures of imagery processing. Results are shown of the related applications using the proposed system, which reveal the higher diversity in mapping forest classes due to the separation of the pixels in accordance with the indicated information layers. The accuracy of the pattern recognition for the processed scenes is shown to increase as the listed procedures are realized.
Morphological analysis and subpopulation characterization of Ripollesa sheep breed

The Ripollesa sheep breed is an important Spanish local breed mainly located in the Mediterranean mountains and cultivated plains of Catalonia, exploited under semi-extensive production systems and currently intended for meat production. The morphological characterization of the Ripollesa breed was carried out from the study of eight flocks representative of different subpopulations. A total of 224 Ripollesa ewes and 17 rams were recorded for their live weight and 12 morphological measures, which were used for calculating 12 zootechnical indexes. Differences (P < 0.05) between flocks and sexes were revealed for several measures. A principal component analysis was performed on the morphological measures and revealed two main principal components accounting for 47.6 and 12.3 percent of the inertia, being related to the frame (body size and live weight) and to withers height and ear length, respectively. The cluster analysis allowed differentiating among four subpopulations with relevant implications to be taken into account for the breed conservation programme. The observed differences could be attributable to geographic location, selective history, flock management and genetics. The estimated zootechnical indexes classified the Ripollesa sheep breed as a medium-sized and long-shaped body frame, with a marked orientation to meat production and with signs of adaptation to the environment.
A new method for describing long‐term changes in total ozone

A new method for describing long‐term changes in total ozone was developed so that variations on time scales greater than that of the QBO may be examined. The technique fits a flexible tendency curve to total ozone data after explained variations have been removed. The derivative of the tendency curve is the growth rate curve. The average along this curve is comparable to total ozone trends reported in the past. Statistical uncertainty of the growth rate is determined using bootstrap techniques. Dobson column ozone measurements with long‐term (30+ years) records from the NOAA/CMDL Cooperative Dobson Network were analyzed. Total ozone decreases ranged from 1‐2%/decade since the 1960s and from 2‐4%/decade since 1979 at all sites except Mauna Loa where results were not significant. The tendency curves indicate that the total ozone decline began in the 1970s and that there are no clear signs of recovery as of the end of 2000.
First southern hemisphere intercomparison of measured solar UV spectra

Three UV spectroradiometers from the National Institute of Water and Atmospheric Research (NIWA) New Zealand, the Fraunhofer Institute (IFU) Germany, and the Australian Radiation Laboratory (ARL) Australia were intercompared at Lauder NZ on 23 February 1993. Over the spectral range 290–400 nm, the agreement between the IFU and NIWA instruments was better than 5%. At noon on this day, the irradiances measured by all three instruments agreed within ±10%, except at wavelengths shorter than 300 nm, where the ARL instrument gave higher readings. At larger solar zenith angles (SZA) the differences at short wavelengths were more pronounced, and at wavelengths above 300 nm the ARL measurements were systematically lower. The reasons for these differences are discussed. Having established the differences between the sets of instrumentation, spectra of maximum clear sky UV irradiances observed by these groups in New Zealand, Australia, and Europe are compared. The erythemally weighted irradiance observed in Melbourne Australia was the highest (0.35 W m−2). Respective maxima for Lauder NZ and for Neuherberg Germany were 85% and 66% of that in Australia. Differences are larger for DNA-weighted UV.
Ion cyclotron waves, pickup ions, and Io's neutral exosphere

During Galileo's December 1995 encounter with Io, the magnetometer observed very strong electromagnetic waves near the SO2+ gyrofrequency. The amplitude of these waves previously has been used to determine the density of SO2+, as well as the production rate near Io. In this paper we examine the details of the interaction between pickup ions and ion cyclotron weaves and use these results to constrain the production rate of O+ and lo's exospheric loss rate. In a sub‐Alfvenic flow we show that ion cyclotron waves scatter pickup ions into a filled, asymmetric distribution, rather than a shell distribution. In addition, the observed waves are strong enough to cause non‐resonant scattering of S+ ions and may result in an asymmetric core population of S+. Because of the absence of waves near the O+ gyrofrequency and the criteria for marginal stability, we find that the O+ production rate was probably under a few times 1026 ions s−1. The amplitude of the observed waves is consistent with an exospheric escape rate of 1–3.5×1027 SO2+ ions s−1, depending on the asymmetry of the loss process.
Identification of modeled ocean plumes in Greenland Gyre ERS-1 SAR data

Oceanic convective plumes modeled with a thermobaric large-eddy simulation and driven by conditions similar to those of the Greenland Sea are compared to observations from ERS-1 Synthetic Aperture Radar (SAR) data from the Greenland Sea for the winter of 1992. In both form and size the two representations are seen to compare favorably. The plume-filled area of the SAR image occupies a region about 20 km by 90 km at the ice edge of the open water in “Nordbukta”, the large seasonal ice retreat, in the “Odden” ice protuberance in the southern Greenland gyre. In the SAR data the plumes appear to be ice covered while the convective-return areas are open.
Unbearability of suffering at the end of life : the development of a new measuring device , the SOS-V

Background: Unbearable suffering is an important issue in end-of-life decisions. However, there has been no systematic, prospective, patient-oriented research which has focused on unbearable suffering, nor is there a suitable measurement instrument. This article describes the methodological development of a quantitative instrument to measure the nature and intensity of unbearable suffering, practical aspects of its use in end-stage cancer patients in general practice, and studies content validity and psychometric properties. Methods: Recognizing the conceptual difference between unbearability of suffering and extent or intensity of suffering, we developed an instrument. The compilation of aspects considered to be of importance was based on a literature search. Psychometric properties were determined on results of the first interviews with 64 end-stage cancer patients that participated in a longitudinal study in the Netherlands. Results: The instrument measures five domains: medical signs and symptoms, loss of function, personal aspects, aspects of environment, and nature and prognosis of the disease. Sixty nine aspects were investigated, and an overall score was asked. In 64 end-stage cancer patients the instrument was used in total 153 times with an average interview time varying from 20-40 minutes. Cronbachs alpha's of the subscales were in majority above 0.7. The sum scores of (sub)scales were correlated strongly to overall measures on suffering. Conclusion: The SOS-V is an instrument for measuring the unbearability of suffering in end-stage cancer patients with good content validity and psychometric properties, which is feasible to be used in practice. This structured instrument makes it possible to identify and study unbearable suffering in a quantitative and patient-oriented way. Background Suffering of patients is inseparably connected with the work of the medical profession. Serious disease can result in serious suffering. At some point, it is possible that patients may consider their suffering unbearable. Some of these patients may request euthanasia. Published: 3 November 2009 BMC Palliative Care 2009, 8:16 doi:10.1186/1472-684X-8-16 Received: 19 December 2008 Accepted: 3 November 2009 This article is available from: http://www.biomedcentral. com/1472-684X/8/16 © 2009 Ruijs et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
A mycobacterial DivIVA domain-containing protein involved in cell length and septation

Mycobacterial cells elongate via polar deposition of cell wall material, similar to the filamentous Streptomyces species, which contain a tip-organizing centre. Coiled-coiled proteins such as DivIVA play an important role in this process. The genome of Mycobacterium tuberculosis , the causative agent of tuberculosis, encodes many coiled-coil proteins that are homologous to DivIVA with a potential role in mycobacterial cell elongation. Here we describe studies on Mycobacterium smegmatis MSMEG_2416, a homologue of M. tuberculosis Rv2927c. Two previous independent studies showed that MSMEG_2416 was involved in septation (subsequently referred to as sepIVA). Contrary to these previous reports, we found sepIVA to be dispensable for growth in laboratory media by generating a viable null mutant. The mutant strain did, however, show a number of differences, including a change in colony morphology and biofilm formation that could be reversed on complementation with sepIVA as well as Rv2927c, the sepIVA homologue from M. tuberculosis . However, analysis of cell wall lipids did not reveal any alterations in lipid profiles of the mutant strain. Microscopic examination of the mutant revealed longer cells with more septa, which occurred at irregular intervals, often generating mini-compartments, a profile similar to that observed in the previous studies following conditional depletion, highlighting a role for sepIVA in mycobacterial growth.
Autonomous detection of indoor and outdoor signs

Most goal-oriented mobile robot tasks involve navigation to one or more known locations. This is generally done using GPS coordinates and landmarks outdoors, or wall-following and fiducial marks indoors. Such approaches ignore the rich source of navigation information that is already in place for human navigation in all man-made environments: signs. A mobile robot capable of detecting and reading arbitrary signs could be tasked using directions that are intuitive to hu-mans, and it could report its location relative to intuitive landmarks (a street corner, a person's office, etc.). Such ability would not require active marking of the environment and would be functional in the absence of GPS. In this paper we present an updated version of a system we call Sign Understanding in Support of Autonomous Navigation (SUSAN). This system relies on cues common to most signs, the presence of text, vivid color, and compact shape. By not relying on templates, SUSAN can detect a wide variety of signs: traffic signs, street signs, store-name signs, building directories, room signs, etc. In this paper we focus on the text detection capability. We present results summarizing probability of detection and false alarm rate across many scenes containing signs of very different designs and in a variety of lighting conditions.
Mammalian Small Nucleolar RNAs Are Mobile Genetic Elements

Small nucleolar RNAs (snoRNAs) of the H/ACA box and C/D box categories guide the pseudouridylation and the 2′-O-ribose methylation of ribosomal RNAs by forming short duplexes with their target. Similarly, small Cajal body–specific RNAs (scaRNAs) guide modifications of spliceosomal RNAs. The vast majority of vertebrate sno/scaRNAs are located in introns of genes transcribed by RNA polymerase II and processed by exonucleolytic trimming after splicing. A bioinformatic search for orthologues of human sno/scaRNAs in sequenced mammalian genomes reveals the presence of species- or lineage-specific sno/scaRNA retroposons (sno/scaRTs) characterized by an A-rich tail and an ∼14-bp target site duplication that corresponds to their insertion site, as determined by interspecific genomic alignments. Three classes of snoRTs are defined based on the extent of intron and exon sequences from the snoRNA parental host gene they contain. SnoRTs frequently insert in gene introns in the sense orientation at genomic hot spots shared with other genetic mobile elements. Previously characterized human snoRNAs are encoded in retroposons whose parental copies can be identified by phylogenic analysis, showing that snoRTs can be faithfully processed. These results identify snoRNAs as a new family of mobile genetic elements. The insertion of new snoRNA copies might constitute a safeguard mechanism by which the biological activity of snoRNAs is maintained in spite of the risk of mutations in the parental copy. I furthermore propose that retroposition followed by genetic drift is a mechanism that increased snoRNA diversity during vertebrate evolution to eventually acquire new RNA-modification functions.
SEQanswers: an open access community for collaboratively decoding genomes

Summary: The affordability of high-throughput sequencing has created an unprecedented surge in the use of genomic data in basic, translational and clinical research. The rapid evolution of sequencing technology, coupled with its broad adoption across biology and medicine, necessitates fast, collaborative interdisciplinary discussion. SEQanswers provides a real-time knowledge-sharing resource to address this need, covering experimental and computational aspects of sequencing and sequence analysis. Developers of popular analysis tools are among the >4000 active members, and ~40 peer-reviewed publications have referenced SEQanswers. Availability: The SEQanswers community is freely accessible at http://SEQanswers.com/ Contact: david.mittelman@vt.edu; ecolivares@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
Seasonal Drought in the Greater Horn of Africa and Its Recent Increase during the March–May Long Rains

AbstractThis paper provides a review of atmospheric circulation and sea surface temperature (SST) conditions that are associated with meteorological drought on the seasonal time scale in the Greater Horn of Africa (the region 10°S–15°N, 30°–52°E). New findings regarding a post-1998 increase in drought frequency during the March–May (MAM) “long rains” are also reported. The period 1950–2010 is emphasized, although rainfall and SST data from 1901–2010 are used to place the recent long rains decline in a multidecadal context. For the latter case, climate model simulations and isolated basin SST experiments are also utilized.Climatologically, rainfall exhibits a unimodal June–August (JJA) maximum in west-central Ethiopia with a generally bimodal [MAM and October–December (OND) maxima] distribution in locations to the south and east. Emphasis will be on these three seasons. SST anomalies in the tropical Pacific and Indian Oceans show the strongest association with drought during OND in locations having a bimod.
Reactive oxygen species inhibit catalytic activity of peptidylarginine deiminase

Abstract Protein citrullination catalysed by peptidylarginine deiminase (PAD) may play an important pathogenic role in several chronic inflammatory diseases and malignancies. PAD2, PAD4, and citrullinated proteins are found in the synovium of rheumatoid arthritis patients. PAD activity is dependent on calcium and reducing conditions. However, reactive oxygen species (ROS) have been shown to induce citrullination of histones in granulocytes. Here we examine the ability of H2O2 and leukocyte-derived ROS to regulate PAD activity using citrullination of fibrinogen as read-out. H2O2 at concentrations above 40 µM inhibited the catalytic activity of PAD2 and PAD4 in a dose-dependent manner. PMA-stimulated leukocytes citrullinated fibrinogen and this citrullination was markedly enhanced when ROS formation was inhibited by the NADPH oxidase inhibitor diphenyleneiodonium (DPI). In contrast, PAD released from stimulated leukocytes was unaffected by exogenously added H2O2 at concentrations up to 1000 µM. The role of ROS in regulating PAD activity may play an important part in preventing hypercitrullination of proteins.
MAPPING GILSONITE VEINS WITH THE ELECTRICAL RESISTIVITY METHOD

Gish‐Rooney type electrical resistivity equipment was employed to map the location and structural attitude of gilsonite veins in the Uinta Basin, southeast of Vernal, Utah. Horizontal profiles at right angles to the strike of the dike‐like gilsonite veins were made using the Wenner electrode configuration. Very sharp anomalies with a peak apparent resistivity value of the order of 20,000–25,000 ohm‐cm were observed. The peak values were measured over the center of the vein, but smaller auxiliary highs were also observed, symmetrically spaced on each side of the vein. The position of the auxiliary high varied as a function of the electrode spacing and was found to occur when the current stake was located in the gilsonite. The observed field profiles were compared with various theoretical profiles computed from theoretical apparent resistivity expressions derived through the use of images. The best correlation was obtained when the theoretical model was assumed to have an infinite resistivity relative to th.
RT-qPCR half-reaction optimization for the detection of SARS-CoV-2

BACKGROUND: The main laboratory test for the diagnosis of COVID-19 is the reverse transcription real-time polymerase chain reaction (RT-qPCR). However, the RT-qPCR is an expensive method due to the number of tests required. OBJECTIVES: To evaluate an alternative RT-qPCR approach for the detection of SARS-CoV-2 sing half of the total volume currently recommended by the US Centers for Disease Control and Prevention. METHODS: The analytical limit of detection (LoD) and the reaction efficiency using half volumes of RT-qPCR assay were evaluated for both the N1 and N2 regions by using a synthetic control RNA. A panel of 76 SARS-CoV-2-positive and 26 SARS-CoV-2-negative clinical samples were evaluated to establish the clinical sensitivity and specificity. FINDINGS: The RT-qPCR assay efficiency was 105% for both the half and standard reactions considering the N2 target and 84% (standard) and 101% (half) for N1. The RT-qPCR half reaction LoD for N1 and N2 were 20 and 80 copies/uL, respectively. Clinical sensitivity and specificity were 100%. The half reaction presented a decrease of up to 5.5 cycle thresholds when compared with the standard RT-qPCR. CONCLUSIONS: The use of RT-qPCR half reaction proved to be a feasible and economic strategy for detection of SARS-CoV-2 RNA.