Miracle-dz/UniFAR-FTUs huggingface dataset:
A semantics for dynamic ceiling priorities in Ada

Several arguments have been given to justify the exclusion of dynamic ceiling priorities for protected objects in Ada. These arguments center on semantic complexity, the risks that can be derived from an erroneous usage of dynamic ceilings, and efficiency. But dynamic ceilings are very convenient for multi-moded systems and to dynamically adapting existing program libraries containing protected objects to new applications. This paper proposes a semantics for dynamic ceilings that does not add complexity to the language semantics or inefficiency to the run time system.
CLIMATE CHANGE IMPACTS AND ADAPTATION STRATEGIES FOR THE FOREST SECTOR IN CANADA

Impacts on forests will vary regionally across Canada, with continental interior locations likely to experience greater extremes in temperature and precipitation. At the species level there will be short-term physiological responses to climate variability and long-term genetic responses to future climate change. Trees that are adapted to the climate at the time of establishment may be considerably maladapted to the climate at harvest time, displaying reduced productivity and increased frequency of pest attack. Although our ability to pro-actively mitigate possible shortterm impacts to current climate change is limited, we have the opportunity to assist species and populations with migration to climatically-suitable habitats. This is a management activity called “assisted migration”, and represents an important forest management activity to mitigate the negative consequences of climate change. Other possible management interventions to assist the adaptation of tree species include; improved tree breeding, altered silviculture activities, shorter rotation periods, use of exotics and fast-growing species.
Deep Integration of Scripting Languages and Semantic Web Technologies

Python reached out to a wide and diverse audience in the last few years. During its evolution it combined a number of different paradigms under its hood: imperative, object-oriented, functional, listoriented, even aspect-oriented programming paradigms are allowed, but still remain true to the Python way of programming, thus retaining simplicity, readability and fun. OWL is a knowledge representation language for the definition of ontologies, standardised by the W3C. It reaps upon the power of Description Logics and allows both the definition of concepts and their interrelations as well as the description of instances. Being created as part of the notoriously known Semantic Web language stack, its dynamics and openness lends naturally to the ever evolving Python language. We will sketch the idea of an integration of OWL and Python, but not by simply suggesting an OWL library, but rather by introducing and motivating the benefits a really deep integration offers, how it can change programming, and make it even more fun.
Neutralization of Transthyretin Reverses the Neuroprotective Effects of Secreted Amyloid Precursor Protein (APP) in APPSw Mice Resulting in Tau Phosphorylation and Loss of Hippocampal Neurons: Support for the Amyloid Hypothesis

Alzheimer's disease (AD) may be caused by the abnormal processing of the amyloid precursor protein (APP) and the accumulation of β-amyloid (Aβ). The amyloid precursor protein can be proteolytically cleaved into multiple fragments, many of which have distinct biological actions. Although a high level of Aβ can be toxic, the α-secretase cleaved APP (sAPPα) is neuroprotective. However, the mechanism of sAPPα protection is unknown. Here, we show that sAPPα increases the expression levels of several neuroprotective genes and protects organotypic hippocampal cultures from Aβ-induced tau phosphorylation and neuronal death. Antibody interference and small interfering RNA knock-down demonstrate that the sAPPα-driven expression of transthyretin and insulin-like growth factor 2 is necessary for protection against Aβ-induced neuronal death. Mice overexpressing mutant APP possess high levels of sAPPα and transthyretin and do not develop the tau phosphorylation or neuronal loss characteristic of human AD. Chronic infusion of an antibody against transthyretin into the hippocampus of mice overexpressing APP with the Swedish mutation (APPSw) leads to increased Aβ, tau phosphorylation, and neuronal loss and apoptosis within the CA1 neuronal field. Therefore, the elevated expression of transthyretin is mediated by sAPPα and protects APPSw mice from developing many of the neuropathologies observed in AD.
EYE MOVEMENT DESENSITIZATION AND REPROCESSING : ITS CAUTIOUS USE IN THE DISSOCIATIVE DISORDERS

Eye MovementDesensitization and Reprocessing(EMDR) isdescribed in terms of clinical phenomena, the need for appropriate training in EMDR, and the consistency of neural network theory with BASK theory of dissociation. EMDR treatment failures occur in dissociative disorder patients when EMDR is used without making diagnosis of the underlying dissociative condition and without modifying the EMDR procedure to accommodate it. Careful informed consent and the use of the dissociative table technique can allow EMDR to move successfully to completion in a dissociative patient. Certain red flags " contraindicate the use of EMDR for some dissociative patients. A protocol for EMDR with dissociative patients is offered, for crisis intervention (rarely appropriate), abreactive trauma work, and integration/fusion. The safety and effectiveness of EMDR's use in the dissociative disorders requires adequate preparation and skillful trouble-shooting during the EMDR.
The Urge to Decide and Act: Implications for Brain Function and Dysfunction

Humans and other animals are motivated to act so as to maximize their subjective reward rate. Here, we propose that reward rate maximization is accomplished by adjusting a context-dependent “urgency signal,” which influences both the commitment to a developing action choice and the vigor with which the ensuing action is performed. We review behavioral and neurophysiological data suggesting that urgency is controlled by projections from the basal ganglia to cerebral cortical regions, influencing neural activity related to decision making as well as activity related to action execution. We also review evidence suggesting that different individuals possess specific policies for adjusting their urgency signal to particular contextual variables, such that urgency constitutes an individual trait which jointly influences a wide range of behavioral measures commonly related to the overall quality and hastiness of one’s decisions and actions. Consequently, we argue that a central mechanism for reward rate maximization provides a potential link between personality traits such as impulsivity, as well as some of the motivation-related symptomology of clinical disorders such as depression and Parkinson’s disease.
Full-Length Multi-Barcoding: DNA Barcoding from Single Ingredient to Complex Mixtures

DNA barcoding has been used for decades, although it has mostly been applied to some single-species. Traditional Chinese medicine (TCM), which is mainly used in the form of combination-one type of the multi-species, identification is crucial for clinical usage. Next-generation Sequencing (NGS) has been used to address this authentication issue for the past few years, but conventional NGS technology is hampered in application due to its short sequencing reads and systematic errors. Here, a novel method, Full-length multi-barcoding (FLMB) via long-read sequencing, is employed for the identification of biological compositions in herbal compound formulas in adequate and well controlled studies. By directly sequencing the full-length amplicons of ITS2 and psbA-trnH through single-molecule real-time (SMRT) technology, the biological composition of a classical prescription Sheng-Mai-San (SMS) was analyzed. At the same time, clone-dependent Sanger sequencing was carried out as a parallel control. Further, another formula—Sanwei-Jili-San (SJS)—was analyzed with genes of ITS2 and CO1. All the ingredients in the samples of SMS and SJS were successfully authenticated at the species level, and 11 exogenous species were also checked, some of which were considered as common contaminations in these products. Methodology analysis demonstrated that this method was sensitive, accurate and reliable. FLMB, a superior but feasible approach for the identification of biological complex mixture, was established and elucidated, which shows perfect interpretation for DNA barcoding that could lead its application in multi-species mixtures.
Genome-Wide Signatures of Selection Detection in Three South China Indigenous Pigs

South China indigenous pigs are famous for their superior meat quality and crude feed tolerance. Saba and Baoshan pigs without saddleback were located in the high-altitude area of Yunnan Province, while Tunchang and Ding’an pigs with saddleback were located in the low-altitude area of Hainan Province. Although these pigs are different in appearance, the underlying genetic differences have not been investigated. In this study, based on the single-nucleotide polymorphism (SNP) genotypes of 124 samples, both the cross-population extended haplotype homozygosity (XP-EHH) and the fixation index (FST) statistic were used to identify potential signatures of selection in these pig breeds. We found nine potential signatures of selection detected simultaneously by two methods, annotated 22 genes in Hainan pigs, when Baoshan pigs were used as the reference group. In addition, eleven potential signatures of selection detected simultaneously by two methods, annotated 24 genes in Hainan pigs compared with Saba pigs. These candidate genes were most enriched in GO: 0048015~phosphatidylinositol-mediated signaling and ssc00604: Glycosphingolipid biosynthesis—ganglio series. These selection signatures were likely to overlap with quantitative trait loci associated with meat quality traits. Furthermore, one potential selection signature, which was associated with different coat color, was detected in Hainan pigs. These results contribute to a better understanding of the underlying genetic architecture of South China indigenous pigs.
Influence of task duration in text-independent speaker verification

Short duration tasks for text-independent speaker verification have received relatively little attention when compared to that directed at tasks involving many minutes of speech. In this paper we investigate verification performance on a range of durations from a few seconds to a few minutes. We begin with a state-of-the-art GMM-based system operating on a few minutes of speech per person and show that the same system is subop-timal on short (10 seconds) speech recordings. In particular we highlight that optimal frame selection exhibits a dependency on overall duration. This work sheds some light on the difficulties of transposing recent and important techniques such as SVM-NAP to the short duration tasks.
Prevalence of submicroscopic malaria in low transmission state of Punjab: A potential threat to malaria elimination

Background & objectives: Submicroscopic malaria infections with low parasite density serve as a silent reservoir for maintaining residual transmission in the population. These infections should be identified and targeted to be eliminated for sustained malaria control. The conventional methods of diagnosis such as light microscopy and rapid diagnostic kits often fail to detect low density infections. Therefore, the more sensitive molecular techniques should be employed to detect low density infections. The objectives of the study was to explore the prevalence of sub-microscopic infections in low transmission areas of Punjab using highly sensitive molecular tool. Methods: A total of 1114 finger prick blood samples were collected through active surveillance and tested for malaria diagnosis using light microscopy, RDT and PCR. Nested PCR amplification was performed using a pair of Plasmodium genus-specific primers from the 18S rRNA small subunit gene (18S rRNA). The amplified PCR products were analysed using a 2% agarose gel, stained with ethidium bromide and observed under transilluminator. Results: Test positive rate (TPR) by microscopy, RDT and PCR was 4.4, 3.95 and 5.75%, respectively. Microscopy and RDT failed to detect mixed infections whereas 0.26% cases were found to be mixed infection in PCR. Compared to LM and RDT, PCR has detected 1.3% additional positive cases. However, of the total positive cases detected by PCR, 23.4% infections were found to be submicroscopic, which could not be detected by conventional methods of diagnosis. Interpretation & conclusions: The molecular study revealed the existence of submicroscopic malaria cases in the study population which would have remained undetected by conventional methods of diagnosis. This is particularly important because Punjab state is in malaria elimination phase and targeted to achieve elimination in 2021. However, such undetected parasite positive cases may pose bigger problem any time due to continued transmission. Therefore, application of more sensitive diagnostic tools like PCR and LAMP with conventional methods may be much more useful in case detection particularly in low transmission settings for malaria elimination.
Gender differences in chronotype diminish with age: a meta-analysis based on morningness/chronotype questionnaires

ABSTRACT Chronotype is an individual difference trait that is closely linked to biological variables. Usually, men and women differ in their chronotype with men being more evening oriented than women. The aim of the study was to assess gender differences in chronotype based on a systematic review and meta-analysis. In addition, many recent studies do not report gender differences any more although researchers collected data on men and women. This motivated us to contact many researchers directly to obtain and use these additional data. We included 164 studies giving 201 effect size measures in a data set, which only included the most commonly used questionnaires (MEQ, rMEQ and CSM) totaling 186,289 participants in total, of which 75,622 were men and 110,667 were women. We calculated an effect size of the standardized mean difference of −0.072 (95% CI from −0.062 to −0.082) in the fixed effects and of −0.066 (95% CI from −0.043 to- 0.089) in the random effects model. Men were on average more evening oriented than women. Type of questionnaire did not influence the standardized mean difference in chronotype between genders. Mean age, standard deviation of age and publication year (p ≤ 0.05) were found to have significant effects on the standardized mean difference in chronotype between genders. The standardized mean difference in chronotype between genders is predicted to change from negative to positive with increasing mean age (young women were more morning orientated than young men, but older women were less morning orientated than older men). This suggests that the differences between men and women diminish with time. The standardized mean difference in chronotype between genders is decreasing with increasing publication year, as well as with high variation in age of the samples. Abbreviations: CSM: Composite Scale of Morningness (Smith et al. 1989); MEQ: Morningness-Eveningness Questionnaire (Horne and Ostberg, 1976); rMEQ: reduced Morningness-Eveningness Questionnaire (Adan & Almiral, 1991); SMD: standardized mean difference (measure of effect size).
Heegaard Splittings and Bounds for Closed Hyperbolic 3-Manifolds

We will develop a way to Delaunay Triangulate [LL] closed and compact hyperbolic 3-manifolds, and use this method of trianguation to produce Heegaard splittings of such 3-manifolds. This method of triangulating and splitting manifolds will allow us to produce a universal constant K = vol(B5 /4) vol(B /4) , where is half a Margulis constant for H, such that the Heegaard genus of a closed hyperbolic 3-manifold M is at most K vol(M).
The advance of assembly of exopolysaccharide Psl biosynthesis machinery in Pseudomonas aeruginosa

Biofilms are microbial communities embedded in extracellular matrix. Exopolysaccharide Psl (ePsl) is a key biofilm matrix component that initiates attachment, maintains biofilms architecture, and protects bacteria within biofilms of Pseudomonas aeruginosa, an opportunistic pathogen. There are at least 12 Psl proteins involved in the biosynthesis of this exopolysaccharide. However, it remains unclear about the function of each Psl protein and how these proteins work together during the biosynthesis of ePsl. PslG has been characterized as a degrader of ePsl in extracellular or periplasm and PslD is predicted to be a transporter. In this study, we found that PslG and its glycoside hydrolytic activity were also involved in the biosynthesis of ePsl. PslG localized mainly in the inner membrane and some in the periplasm. The inner membrane association of PslG was critical for the biosynthesis of ePsl. The expression of PslA, PslD, and PslE helped PslG remain in the inner membrane. The bacterial two‐hybrid results suggested that PslE could interacted with either PslA, PslD, or PslG. The strongest interaction was found between PslE and PslD. Consistently, PslD was disabled to localize on the outer membrane in the ΔpslE strain, suggesting that the PslE‐PslD interaction affected the localization of PslD. Our results shed light on the assembly of ePsl biosynthesis machinery and suggested that the membrane‐associated PslG was a part of ePsl biosynthesis proteins complex.
Performance bounds for tracking in a multipath environment

Tracking in a multipath environment poses many challenges. It is worth while to quantify the achievable performance bounds in such an environment. However finding the performance bounds could be challenging. This requires calculating derivatives of parameters that are functions of reflection points on walls, with respect to target related quantities. We propose a method to calculate the lower bound for minimum mean squared error (MMSE) in target state estimation in a multipath environment. A novel measurement model is introduced taking into account a general setup with locations of obstacle walls known. Furthermore we model the wall reflectivities as random variables. Simulation results are provided in which we have obtained the bound for various setups.
Older Adult Patients Are at Lower Risk of ARDS Compared to Younger Patients at Risk: Secondary Analysis of a Multicenter Cohort Study

Introduction: Older adult individuals often have acute illnesses predisposing them to developing acute respiratory distress syndrome (ARDS). We aimed to identify the relationship between age and the development of ARDS in a cohort of hospitalized patients. Methods: This was a secondary analysis of a prospective multicenter observational cohort study of hospitalized patients at risk of developing ARDS admitted to 22 hospitals from March 2009 to August 2009. Patients were classified as older adults if their age was 80 or greater. A multivariable logistic regression was performed, adjusting for severity of illness via Acute Physiology and Chronic Health Evaluation (APACHE II) and risk of ARDS via Lung Injury Prediction Score. Results: Of 5584 patients, 377 (6.8%) developed ARDS. Twenty-four (3.5%) of 694 patients aged 80 or older developed ARDS, compared to 353 (7.2%) of 4890 patients aged less than 80 (P < .001). After adjusting for severity of illness and the risk of ARDS development, older adult patients had a lower incidence of ARDS compared to younger individuals (odds ratio: 0.28, 95% confidence interval: 0.18-0.42). Conclusion: Older adult patients aged 80 years or older have a reduced incidence of ARDS compared to younger patients, after adjusting for severity of illness and risk of ARDS development.
Quality improvement project to reduce pediatric clear liquid fasting times prior to anesthesia

Unnecessarily long preprocedural fasting can cause suffering and distress for children and their families. Institutional fasting policies are designed to consistently achieve minimum fasting times, often without regard to the extent to which actual fasting times exceed these minimums. Children at our hospital frequently experienced clear liquid fasting times far in excess of required minimums.
LRRC59 modulates type I interferon signaling by restraining the SQSTM1/p62-mediated autophagic degradation of pattern recognition receptor DDX58/RIG-I

ABSTRACT DDX58/RIG-I, is a critical pattern recognition receptor for viral RNA, which plays an essential role in antiviral immunity. Its posttranslational modifications and stability are tightly regulated to mediate the moderate production of type I IFN to maintain the immune homeostasis. Recently, we reported that macroautophagy/autophagy balances type I IFN signaling through selective degradation of ISG15-associated DDX58 via LRRC25. However, the regulatory mechanism about the autophagic degradation of DDX58 remains largely undefined. Here, we identified LRRC59 as a vital positive regulator of DDX58-mediated type I IFN signaling. Upon virus infection, LRRC59 specifically interacted with ISG15-associated DDX58 and blocked its association with LRRC25, the secondary receptor to deliver DDX58 to autophagosomes for SQSTM1/p62-dependent degradation, leading to the stronger antiviral immune responses. Thus, our study reveals a novel regulatory role of selective autophagy in innate antiviral responses mediated by the cross-regulation of LRRC family members. These data further provide insights into the crosstalk between autophagy and innate immune responses. Abbreviations ATG: Autophagy-related; Baf A1: Bafilomycin A1; DDX58/RIG-I: DEAD [Asp-Glu-Ala-Asp] box polypeptide 58; EV: Empty vector; IC poly[I:C]: Intracellular polyriboinosinic polyribocytidylic acid; IFIH1/MDA5: Interferon induced with helicase C domain 1; IFN: Interferon; ISG15: ISG15 ubiquitin like modifier; IKBKE: Inhibitor of nuclear factor kappa B kinase subunit epsilon; IRF3: Interferon regulatory factor 3; KO: Knockout; LRRC: Leucine rich repeat containing; MAVS: Mitochondrial antiviral signaling protein; CGAS/MB21D1: Cyclic GMP-AMP synthase; SeV: Sendai virus; siRNA: small interfering RNA; SQSTM1/p62: Sequestosome 1; TBK1: TANK binding kinase 1; TLR: Toll like receptor; TMEM173/STING: Transmembrane protein 173; VSV: Vesicular stomatitis virus; WT: Wild type
Dysregulation of gene expression in ABCC6 knockdown HepG2 cells

ABCC6 protein is an ATP-dependent transporter that is mainly found in the basolateral plasma membrane of hepatocytes. ABCC6 deficiency is the primary cause of several forms of ectopic mineralization syndrome. Mutations in the human ABCC6 gene cause pseudoxanthoma elasticum (PXE), an autosomal recessive disease characterized by ectopic calcification of the elastic fibers in dermal, ocular and vascular tissues. Mutations in the mouse ABCC6 gene were also associated with dystrophic cardiac calcification. Reduced levels of ABCC6 protein were found in a β-thalassemic mouse model. Moreover, some cases of generalized arterial calcification in infancy are due to ABCC6 mutations. In order to study the role of ABCC6 in the pathogenesis of ectopic mineralization, the expressions of genes involved in this process were evaluated in HepG2 cells upon stable knockdown of ABCC6 by small hairpin RNA (shRNA) technology. ABCC6 knockdown in HepG2 cells causes a significant upregulation of the genes promoting mineralization, such as TNAP, and a parallel downregulation of genes with anti-mineralization activity, such as NT5E, Fetuin A and Osteopontin. Although the absence of ABCC6 has been already associated with ectopic mineralization syndromes, this study is the first to show a direct relationship between reduced ABCC6 levels and the expression of pro-mineralization genes in hepatocytes.