Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of RNA conformation from circular dichroism and optical rotatory dispersion data

An analysis of optical rotatory dispersion and circular dichroism of RNA is described which leads to an estimate of the degree of base pairing. By the use of new standards for the double‐helical parts of the molecule, based on data for two‐stranded viral RNA species, a good fit between calculated and observed curves can be achieved. Where data are available the results of analyses of optical rotatory dispersion and circular dichroism in general show satisfactory consistency.
Formation and Function of Flavin Anion Radical in Cryptochrome 1 Blue-Light Photoreceptor of Monarch Butterfly*

The monarch butterfly (Danaus plexippus) cryptochrome 1 (DpCry1) belongs in the class of photosensitive insect cryptochromes. Here we purified DpCry1 expressed in a bacterial host and obtained the protein with a stoichiometric amount of the flavin cofactor in the two-electron oxidized, FADox, form. Exposure of the purified protein to light converts the FADox to the \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathrm{FAD}^{{\bar{{\cdot}}}}\) \end{document} flavin anion radical by intraprotein electron transfer from a Trp residue in the apoenzyme. To test whether this novel photoreduction reaction is part of the DpCry1 physiological photocycle, we mutated the Trp residue that acts as the ultimate electron donor in flavin photoreduction. The mutation, W328F, blocked the photoreduction entirely but had no measurable effect on the light-induced degradation of DpCry1 in vivo. In light of this finding and the recently published action spectrum of this class of Crys, we conclude that DpCry1 and similar insect cryptochromes do not contain flavin in the FADox form in vivo and that, most likely, the \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathrm{FAD}_{\mathrm{ox}}{{\rightarrow}^{hv}}\mathrm{FAD}^{{\bar{{\cdot}}}}\) \end{document} photoreduction reaction is not part of the insect cryptochrome photoreaction that results in proteolytic degradation of the photopigment.
Gaining Insight into Exclusive and Common Transcriptomic Features Linked to Drought and Salinity Responses across Fruit Tree Crops

The present study aimed at identifying and mapping key genes expressed in root tissues involved in drought and salinity tolerance/resistance conserved among different fruit tree species. Twenty-six RNA-Seq samples were analyzed from six published studies in five plant species (Olea europaea, Vitis riparia Michx, Prunus mahaleb, Prunus persica, Phoenix dactylifera). This meta-analysis used a bioinformatic pipeline identifying 750 genes that were commonly modulated in three salinity studies and 683 genes that were commonly regulated among three drought studies, implying their conserved role in resistance/tolerance/response to these environmental stresses. A comparison was done on the genes that were in common among both salinity and drought resulted in 82 genes, of which 39 were commonly regulated with the same trend of expression (23 were upregulated and 16 were downregulated). Gene set enrichment and pathway analysis pointed out that pathways encoding regulation of defense response, drug transmembrane transport, and metal ion binding are general key molecular responses to these two abiotic stress responses. Furthermore, hormonal molecular crosstalk plays an essential role in the fine-tuning of plant responses to drought and salinity. Drought and salinity induced a different molecular “hormonal fingerprint”. Dehydration stress specifically enhanced multiple genes responsive to abscisic acid, gibberellin, brassinosteroids, and the ethylene-activated signaling pathway. Salt stress mostly repressed genes encoding for key enzymes in signaling proteins in auxin-, gibberellin-(gibberellin 2 oxidase 8), and abscisic acid-related pathways (aldehyde oxidase 4, abscisic acid-responsive element-binding protein 3). Abiotic stress-related genes were mapped into the chromosome to identify molecular markers usable for the improvement of these complex quantitative traits. This meta-analysis identified genes that serve as potential targets to develop cultivars with enhanced drought and salinity resistance and/or tolerance across different fruit tree crops in a biotechnological sustainable way.
Ethical Issues in Providing Online Psychotherapeutic Interventions

The Internet offers psychotherapists a new communication medium through which they can deliver psychotherapeutic interventions that are appropriate to the medium. Yet online psychotherapy also offers new ethical challenges for therapists interested in providing online psychotherapeutic services. The differences between interactive text-based communication and in-person verbal communication create new ethical challenges not previously encountered in face-to-face therapy. This article will examine the Internet's potential for providing online psychotherapeutic interventions and will review the ethical issues involved with providing interactive text-based psychotherapy.
Unsupervised video object segmentation by supertrajectory labeling

We propose a novel approach to unsupervised video segmentation based on the trajectories of Temporal Super-pixels (TSPs). We cast the segmentation problem as a trajectory-labeling problem and define a Markov random field on a graph in which each node represents a trajectory of TSPs, which we minimize using a new two-stage optimization method we developed. The adaption of the trajectories as basic building blocks brings several advantages over conventional superpixel-based methods, such as more expressive potential functions, temporal coherence of the resulting segmentation, and drastically reduced number of the MRF nodes. The most important effect is, however, that it allows more robust segmentation of the foreground that is static in some frames. The method is evaluated on a subset of the standard SegTrack benchmark and yields competitive results against the state-of-the-art methods.
LOS probability modeling for 5G indoor scenario

Indoor hotspot has been reorganized as an important part of 5G deployments. To satisfied the new requirements on 5G deployment and facilitate the evaluation of 5G candidate technologies, LOS (line of sight) probability model has been studied in this paper. Compared with the existing models, the new model introduced in this paper fits the propagation in indoor hotspot newly defined for 5G best of the four models evaluated. And it can improve the deficiency of ITU model.
Brucellosis. II. Medical aspects of delayed convalescence.

Four clinical types of brucellosis were described by Hughes in his classical monograph on "Mediterranean, Malta, or Undulant Fever. " 1 These were characterized as malignant, undulatory, mild or intermittent, and irregular or mixed, depending largely upon the severity, duration, and course of the infection. Although brucellosis, as studied by Hughes, was probably due almost exclusively to Brucella melitensis, his classification and description of the disease became widely accepted regardless of the species of Brucella causing infection. Cases were included in Hughes' studies only if the evidence was sufficient to "prove" the diagnosis. Hughes' classification of brucellosis has been criticized in that he did not describe cases of chronic disability. 2 Bassett-Smith, in 1903, 3 however, described patients with "chronic brucellosis" who had persistent ill health, with fatigability and inability to carry on normal activities even in the face of a declining or negative agglutinin titer and without physical abnormalities. Acute
SEN1, a positive effector of tRNA-splicing endonuclease in Saccharomyces cerevisiae

The SEN1 gene, which is essential for growth in the yeast Saccharomyces cerevisiae, is required for endonucleolytic cleavage of introns from all 10 families of precursor tRNAs. A mutation in SEN1 conferring temperature-sensitive lethality also causes in vivo accumulation of pre-tRNAs and a deficiency of in vitro endonuclease activity. Biochemical evidence suggests that the gene product may be one of several components of a nuclear-localized splicing complex. We have cloned the SEN1 gene and characterized the SEN1 mRNA, the SEN1 gene product, the temperature-sensitive sen1-1 mutation, and three SEN1 null alleles. The SEN1 gene corresponds to a 6,336-bp open reading frame coding for a 2,112-amino-acid protein (molecular mass, 239 kDa). Using antisera directed against the C-terminal end of SEN1, we detect a protein corresponding to the predicted molecular weight of SEN1. The SEN1 protein contains a leucine zipper motif, consensus elements for nucleoside triphosphate binding, and a potential nuclear localization signal sequence. The carboxy-terminal 1,214 amino acids of the SEN1 protein are essential for growth, whereas the amino-terminal 898 amino acids are dispensable. A sequence of approximately 500 amino acids located in the essential region of SEN1 has significant similarity to the yeast UPF1 gene product, which is involved in mRNA turnover, and the mouse Mov-10 gene product, whose function is unknown. The mutation that creates the temperature-sensitive sen1-1 allele is located within this 500-amino-acid region, and it causes a substitution for an amino acid that is conserved in all three proteins.
New guidelines for the management of the diabetic foot in hospitals: so far so good… but will we get Cinderella to the ball?

The publication in March 2011 of the new National Institute for Health and Clinical Excellence (NICE) short guidelines (CG119) on the management of the diabetic foot in hospitals [1] is hugely welcome. If these guidelines are implemented across the UK, they will have a major impact on the incidence and outcome of limb-threatening disease. In essence, the recommendations—which were triggered by the publication of Putting Feet First by Diabetes UK in 2009 [2]—are simple:
The effect of sympathetic stimulation on mammalian muscle spindles

Several authors have described unmyelinated fibres entering the mammalian spindle (see Barker, 1948). These fibres are reported to degenerate on removal of the appropriate sympathetic ganglia (Hines & Tower, 1928) and are the only fibres to remain intact after complete degeneration of the somatic innervation to the spindle (Hinsey, 1927). Although the characteristics of the discharge from muscle spindle afferent fibres and the influence thereon of motor fibres to the mammalian spindle (fusimotor fibres) have been studied in detail (Matthews, 1933; Leksell, 1945; Kuffler, Hunt & Quilliam, 1951; Hunt & Kuffler, 1951), the physiological role of sympathetic fibres to the spindle has not yet been described. A preliminary report of the present results was presented at the September 1959 meeting of the American Physiological Society (Physiologist, 2, 61-62). In the present experiments the effects of stimulating sympathetic fibres on the discharge frequency in spindle afferent fibres, on the threshold to stretch of spindle receptors, and on the afferent spindle response to fusimotor stimulation, have been studied in the cat. It will be shown that sympathetic stimulation results in significant changes in threshold of spindle afferent endings in the form of an initial facilitation and subsequent depression. These threshold changes are manifest in changes in discharge frequency and in responses to fusimotor stimulation under conditions of constant muscle tension.
California's energy-related greenhouse gas emissions reduction policies

global climate change is expected largely to disrupt physical and biological systems during the second half of the twentyfirst century (Parry et al., 2007). anthropogenic greenhouse gas (gHg) emissions have long been identified as the drivers of such change and, unless societies prove capable of curbing the continual rise in the concentration of those gases in the atmosphere, the costs of adaptation and of the increased risk of catastrophic events occurring will be large.1 in the absence of federal policies to abate gHg emissions, states and regions in the united States of america (uS) started to develop gHg emissions reduction targets. one of the first north american regions to establish a reduction goal was that composed by 11 provinces and states from eastern Canada and the uS in 2001.2 regionally, the goal was established at reducing gHg emissions to a level 10 percent below 1990 emissions by 2020 (ngeeCP, 2001). although several states had since set reduction goals, it was not until 2006 that California became the first subnational uS entity to establish a statewide enforceable target on total gHg emissions.3 Signed into law in September 2006, assembly bill 32 (2006), the California global Warming Solutions act of 2006,4 required the California air resources board (Carb)5 to define strategies to achieve statewide gHg emissions at or below the 1990 levels by 2020 and 80 percent below 1990 levels by 2050. the bill, commonly referred to as ab32, was preceded a year before by a state executive order mandating those reduction targets and directing the California environmental Protection agency to coordinate the efforts of several agencies and secretaries. a Climate action team (Cat), composed of representatives from 17 state agencies, worked on the proposal of gHg emissions reduction strategies. the Cat’s reports (Cat, 2006, 2007) describe such measures, several of which are reflected in the final Scoping Plan (SP) adopted by the Carb (Carb, 2008). aside from the Carb and the 12 subgroups of the Cat, the general public and stakeholders actively participated in the development of the SP through public meetings, workshops and responding to solicitation for ideas.6 Concerns in California regarding climate change are however not that recent and have been reflected in law since 1988, when by assembly bill 4420 (1988) the California energy Commission (CeC) was directed to study the impacts of climate change on the state as well as to develop the first gHg inventory and provide policy recommendations.7 after the establishment of a voluntary registry scheme which started operations in 2002, one of the most important milestones in California climate policy came in 2002 when the passage of assembly bill 1493 (2002) triggered the opposition of automakers and the subsequent involvement of the uS environmental Protection agency (ePa).
Liquid versus dry feeding in weaned piglets: the influence on small intestinal morphology.

Summary Weaning implies to the piglets the transition from a liquid diet (milk) to a dry diet (meal). Therefore the influence of this change on post-weaning intestinal morphology was examined. One group of piglets was weaned on a liquid diet and a second group was weaned conventionally. Bacteriological, virological and light and scanning electron microscopic examination was performed on distal jejunal and ileal samples taken at different days post-weaning. A significant decrease in villus height was found in the piglets weaned on a dry diet on days 8 and 11 post-weaning, whereas in the piglets receiving a liquid diet villus heights remained quite stable. Bacteriological and virological examination did not reveal any differences between the two groups. Zusammenfassung Vergleich von Flussig- und Trockenfutterung bei Absatzferkeln: Einflus auf die Morphologie der Dunndarmschleimhaut Nach dem Absetzen der Ferkel kommt es zu einem Ubergang von Flussigfutter (Milch) auf Trockenfutter (Pellet). Im Rahmen dieser Untersuchungen wurde der Einflus dieses Futterwechsels auf die Darmmorphologie untersucht. Dazu erhielt eine Ferkelgruppe nach dem Absetzen Flussigfutter und eine zweite Vergleichsgruppe konventionelles Trockenfutter. Die Darmproben wurden an verschiedenen Tagen nach dem Absetzen entnommen und bakteriologisch, virologisch sowie licht- und elektronenmikroskopisch untersucht. Am 8. und 11. Tag nach dem Absetzen wiesen Ferkel, die auf Trockenfutter umgestellt wurden, eine deutliche Verkurzung der Darmzotten auf, wahrend sich die Zotten bei den Ferkeln mit Flussigfutterung nicht veranderten. In den bakteriologischen und virologischen Befunden unterschieden sich dagegen die beiden Versuchsgruppen nicht.
Active Therapy for Chronic Low Back Pain: Part 3. Factors Influencing Self-Rated Disability and Its Change Following Therapy

Design. Cross-sectional analysis of the factors influencing self-rated disability associated with chronic low back pain and prospective study of the relationship between changes in each of these factors and in disability following active therapy. Objectives. To examine the relative influences of pain, psychological factors, and physiological factors on self-rated disability. Summary of Background Data. In chronic LBP, the interrelationship between physical impairment, pain, and disability is particularly complicated, due to the influence of various psychological factors and the lack of unequivocal methods for assessing impairment. Investigations using new “belief” questionnaires and “sophisticated” performance tests, which have shown promise as discriminating measures of impairment, may assist in clarifying the situation. Previous studies have rarely investigated all these factors simultaneously. Methods. One hundred forty-eight patients with cLBP completed questionnaires and underwent tests of mobility, strength, muscle activation, and fatigability, and (in a subgroup) erector spinae size and fiber size/type distribution. All measures were repeated after 3 months active therapy. Relationships between each factor and self-rated disability (Roland and Morris questionnaire) at baseline, and between the changes in each factor and changes in disability following therapy, were examined. Results. Stepwise linear regression showed that the most significant predictors of disability at baseline were, in decreasing order of importance: pain; psychological distress; fear-avoidance beliefs; muscle activation levels; lumbar range of motion; gender. Only changes in pain, psychological distress, and fear-avoidance beliefs significantly accounted for the changes in disability following therapy. Conclusion. A combination of pain, psychological and physiological factors was best able to predict baseline disability, although its decrease following therapy was determined only by reductions in pain and psychological variables. The active therapy programm—in addition to improving physical function—appeared capable of modifying important psychological factors, possibly as a result of the positive experience of completing the prescribed exercises without undue harm.
Human-algorithm teaming in face recognition: How algorithm outcomes cognitively bias human decision-making

In face recognition applications, humans often team with algorithms, reviewing algorithm results to make an identity decision. However, few studies have explicitly measured how algorithms influence human face matching performance. One study that did examine this interaction found a concerning deterioration of human accuracy in the presence of algorithm errors. We conducted an experiment to examine how prior face identity decisions influence subsequent human judgements about face similarity. 376 volunteers were asked to rate the similarity of face pairs along a scale. Volunteers performing the task were told that they were reviewing identity decisions made by different sources, either a computer or human, or were told to make their own judgement without prior information. Replicating past results, we found that prior identity decisions, presented as labels, influenced volunteers’ own identity judgements. We extend these results as follows. First, we show that the influence of identity decision labels was independent of indicated decision source (human or computer) despite volunteers’ greater distrust of human identification ability. Second, applying a signal detection theory framework, we show that prior identity decision labels did not reduce volunteers’ attention to the face pair. Discrimination performance was the same with and without the labels. Instead, prior identity decision labels altered volunteers’ internal criterion used to judge a face pair as “matching” or “non-matching”. This shifted volunteers’ face pair similarity judgements by a full step along the response scale. Our work shows how human face matching is affected by prior identity decision labels and we discuss how this may limit the total accuracy of human-algorithm teams performing face matching tasks.
Investigating the Effect of Input Data Uncertainties in Material Balance Calculations for Hydrocarbon Reservoirs

Material balance analysis is an interpretation method used to determine the original oil and gas in place and to predict petroleum reservoir performance based on production and static pressure data analysis, also to evaluate the remaining reserves by applying the principle of material balance to rate-time decline analysis. Material balance techniques are widely used throughout all phase of reservoir development, providing a dynamic measure of hydrocarbon volumes and an estimate of key reservoir parameters. The purpose of this study was the quantification of the uncertainties in the estimation of original hydrocarbon in place. An extensive sensitivity analysis was conducted to provide an insight into the features that must be accurately determined in order to obtain the value of the OGIP. Common tools that are frequently used in the petroleum industry such as Material Balance and Monte Carlo were used in combination to support investment decisions for field development. To deal with this challenge, an automated concept has been developed using Petroleum Experts MBAL software. The results showed that the estimation of OGIP by material balance calculations was very sensitive to the pressure and aquifer models data uncertainties. Therefore, the error in pressure data identified as the most significant source of the uncertainty in material balance estimations. Errors in Porosity distribution and net pay thickness are the main source of uncertainty in the properties of reservoir characteristics. Permeability was the important sources of uncertainty but not significant. Finally, encroachment angel and compressibility were the parameter with less uncertainty on material balance calculations. Therefore, the significant of this study is to investigate the effect of reservoir data uncertainties on material balance calculation.
Covariances between arbitrary relatives with linkage and epistasis in the case of linkage disequilibrium.

In this study the new concept of link relationship is developed for two loci. There is a link relationship between two nonhomologous genes if they derive by descent from the same ancestral gamete belonging to a reference gametic generation. By considering together the link and identity by descent relationships, new coefficients of dependence between genes of one or two zygotes are defined. They are probabilities of having groups of genes at a pair of loci from one or two zygotes such that there are particular link and identity by decent relationships amongst them. Consideration of the states of dependence between the genes of one and of two zygotes at one or two loci leads to new parameters for the expressions of the mean, variance and the covariance under multiallelism and epistjasis limited to a pair of loci. The case of random mating is considered without restriction on epistasis. With second degree statistics for inbred relatives, the epistasis is limited to the additive X additive interaction. Some simplifying assumptions are envisaged, with some applications particularly in the case of biallelism.