Miracle-dz/UniFAR-FTUs huggingface dataset:
Formal verification of C systems code Structured types, separation logic and theorem proving

Systems code is almost universally written in the C programming language or a variant. C has a very low level of type and memory abstraction and formal reasoning about C systems code requires a memory model that is able to capture the semantics of C pointers and types. At the same time, proof-based verification demands abstraction, in particular from the aliasing and frame problems. In this paper we present a study in the mechanisation of two proof abstractions for pointer program verification in the Isabelle/HOL theorem prover, based on a low-level memory model for C. The language’s type system presents challenges for the multiple independent typed heaps (Burstall-Bornat) and separation logic proof techniques. In addition to issues arising from explicit value size/alignment, padding, type-unsafe casts and pointer address arithmetic, structured types such as C’s arrays and structs are problematic due to the non-monotonic nature of pointer and lvalue validity in the presence of the unary &-operator. For example, type-safe updates through pointers to fields of a struct break the independence of updates across typed heaps or ∧∗-conjuncts. We provide models and rules that are able to cope with these language features and types, eschewing common over-simplifications and utilising expressive shallow embeddings in higher-order logic. Two case studies are provided that demonstrate the applicability of the mechanised models to real-world systems code; a working of the standard in-place list reversal example and an overview of the verification of the L4 microkernel’s memory allocator.
Characteristics of Phrenic Nerve Injury During Pulmonary Vein Isolation Using a 28‐mm Second‐Generation Cryoballoon and Short Freeze Strategy

Background The reported incidence of phrenic nerve injury (PNI) varies owing to different definitions, balloon generations, balloon size, freezing regimen, and protective maneuvers. We evaluated the incidence, predictors, and outcome of PNI during cryoballoon pulmonary vein isolation in a large population. Methods and Results Five hundred fifty atrial fibrillation patients underwent pulmonary vein isolation using one 28‐mm second‐generation cryoballoon and single 3‐minute freeze strategy under diaphragmatic compound motor action potential (CMAP) monitoring. A total of 34 (6.2%) patients experienced PNI during the right superior and inferior pulmonary vein ablation in 30 and 4 patients, respectively. Applications were interrupted using double‐stop techniques after 136 [104–158] second applications, and a pulmonary vein isolation was already achieved in all but one case. The baseline CMAP amplitude and timing of deflation (CMAP def) were 0.75±0.30 and 0.17±0.17 mV, respectively. Persistent atrial fibrillation, larger right superior pulmonary vein ostia, and deeper balloon positions were associated with higher incidences of PNI. The CMAP def predicted a PNI recovery delay, and the best cutoff value for predicting PNI recovery by the next day was 0.20 mV (sensitivity 57.1%, specificity 100%). Among 6 patients undergoing second procedures 8.5 (6.7–15.0) months later, the right superior pulmonary vein was durable in 3 with >120 second applications. Despite active balloon deflation, no significant pulmonary vein stenosis was observed in 15 right superior pulmonary veins evaluated 6 (5–9) months later. No patients had symptoms, and the PNI recovered 1 day and 1 month postprocedure in 21 and 4 patients, respectively. Conclusions PNI resulting from cryoballoon ablation was reversible. The double‐stop technique is safe, and immediate active deflation following a CMAP decrease appears to be essential for faster PNI recovery.
Natural and Anthropogenic Hybridization in Two Species of Eastern Brazilian Marmosets (Callithrix jacchus and C. penicillata)

Animal hybridization is well documented, but evolutionary outcomes and conservation priorities often differ for natural and anthropogenic hybrids. Among primates, an order with many endangered species, the two contexts can be hard to disentangle from one another, which carries important conservation implications. Callithrix marmosets give us a unique glimpse of genetic hybridization effects under distinct natural and human-induced contexts. Here, we use a 44 autosomal microsatellite marker panel to examine genome-wide admixture levels and introgression at a natural C. jacchus and C. penicillata species border along the São Francisco River in NE Brazil and in an area of Rio de Janeiro state where humans introduced these species exotically. Additionally, we describe for the first time autosomal genetic diversity in wild C. penicillata and expand previous C. jacchus genetic data. We characterize admixture within the natural zone as bimodal where hybrid ancestry is biased toward one parental species or the other. We also show evidence that São Francisco River islands are gateways for bidirectional gene flow across the species border. In the anthropogenic zone, marmosets essentially form a hybrid swarm with intermediate levels of admixture, likely from the absence of strong physical barriers to interspecific breeding. Our data show that while hybridization can occur naturally, the presence of physical, even if leaky, barriers to hybridization is important for maintaining species genetic integrity. Thus, we suggest further study of hybridization under different contexts to set well informed conservation guidelines for hybrid populations that often fit somewhere between “natural” and “man-made. ”
Glucose- but Not Rice-Based Oral Rehydration Therapy Enhances the Production of Virulence Determinants in the Human Pathogen Vibrio cholerae

Despite major attempts to prevent cholera transmission, millions of people worldwide still must address this devastating disease. Cholera research has so far mainly focused on the causative agent, the bacterium Vibrio cholerae, or on disease treatment, but rarely were results from both fields interconnected. Indeed, the treatment of this severe diarrheal disease is mostly accomplished by oral rehydration therapy (ORT), whereby water and electrolytes are replenished. Commonly distributed oral rehydration salts also contain glucose. Here, we analyzed the effects of glucose and alternative carbon sources on the production of virulence determinants in the causative agent of cholera, the bacterium Vibrio cholerae during in vitro experimentation. We demonstrate that virulence gene expression and the production of cholera toxin are enhanced in the presence of glucose or similarly transported sugars in a ToxR-, TcpP- and ToxT-dependent manner. The virulence genes were significantly less expressed if alternative non-PTS carbon sources, including rice-based starch, were utilized. Notably, even though glucose-based ORT is commonly used, field studies indicated that rice-based ORT performs better. We therefore used a spatially explicit epidemiological model to demonstrate that the better performing rice-based ORT could have a significant impact on epidemic progression based on the recent outbreak of cholera in Haiti. Our results strongly support a change of carbon source for the treatment of cholera, especially in epidemic settings.
Vaccinia Protein F12 Has Structural Similarity to Kinesin Light Chain and Contains a Motor Binding Motif Required for Virion Export

Vaccinia virus (VACV) uses microtubules for export of virions to the cell surface and this process requires the viral protein F12. Here we show that F12 has structural similarity to kinesin light chain (KLC), a subunit of the kinesin-1 motor that binds cargo. F12 and KLC share similar size, pI, hydropathy and cargo-binding tetratricopeptide repeats (TPRs). Moreover, molecular modeling of F12 TPRs upon the crystal structure of KLC2 TPRs showed a striking conservation of structure. We also identified multiple TPRs in VACV proteins E2 and A36. Data presented demonstrate that F12 is critical for recruitment of kinesin-1 to virions and that a conserved tryptophan and aspartic acid (WD) motif, which is conserved in the kinesin-1-binding sequence (KBS) of the neuronal protein calsyntenin/alcadein and several other cellular kinesin-1 binding proteins, is essential for kinesin-1 recruitment and virion transport. In contrast, mutation of WD motifs in protein A36 revealed they were not required for kinesin-1 recruitment or IEV transport. This report of a viral KLC-like protein containing a KBS that is conserved in several cellular proteins advances our understanding of how VACV recruits the kinesin motor to virions, and exemplifies how viruses use molecular mimicry of cellular components to their advantage.
Aircraft measurements over Europe of an air pollution plume from Southeast Asia? aerosol and chemical characterization

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. Aircraft measurements over Europe of an air pollution plume from Southeast Asia ? aerosol and chemical characterization A. Stohl, C. Forster, H. Huntrieser, H. Mannstein, W. W. Mcmillan, A. Petzold, H. Schlager, B. Weinzierl
Zinc in attention-deficit/hyperactivity disorder.

OBJECTIVE The aim of this study was to review the published evidence for a role of zinc nutrition in attention-deficit/hyperactivity disorder (ADHD). METHOD A computer literature search was supplemented by the authors' knowledge. RESULTS Numerous controlled studies report cross-sectional evidence of lower zinc tissue levels (serum, red cells, hair, urine, nails) in children who have ADHD, compared to normal controls and population norms. A few studies show correlations of zinc level with either clinical severity or a change thereof in response to stimulant or chemical challenge. Two placebo-controlled trials--one of zinc monotherapy, the other of zinc supplementation of methylphenidate--reported significant benefit. However, diagnostic procedures and sample representativeness were often not clear, and most such reports have come from countries and cultures with different diets and/or socioeconomic realities than are found in the United States (only one American sample in nine published reports). In particular, both positive clinical trials of zinc supplementation came from the Mid-East (Turkey and Iran), an area with suspected endemic zinc deficiency. The largest of these trials used zinc doses above the recommended upper tolerable limit and had a 2 in 3 dropout rate. CONCLUSION It is not clear how well the accumulating evidence for a possible role of zinc in ADHD applies to middle-class American children. However, the evidence appears strong enough to warrant further controlled study in well-diagnosed samples representative of the socioeconomic spectrum. Hypothesis-testing clinical trials are needed of this potential treatment that, if found effective, might become a relatively safe, cheap substitute for, or adjunct to, current treatments in some patients. At present, it should remain an investigational treatment.
ITU-T G.722.1 Annex C: A New Low-Complexity 14 KHZ Audio Coding Standard

This paper describes the low-complexity 14 kHz audio coding algorithm which has been recently standardized by ITU-T as Recommendation G.722. 1 Annex C ("G.722.1C"). The algorithm is an extension to ITU-T Recommendation G.722. 1 and doubles the G.722. 1 algorithm to permit 14 kHz audio bandwidth using a 32 kHz audio sample rate, at 24, 32, and 48 kbit/s. The G.722. 1C codec features very high audio quality and extremely low computational complexity compared to other state-of-the-art audio coding algorithms. This codec is suitable for use in video conferencing and teleconferencing, and Internet streaming applications. Subjective test results from the characterization phase of G.722. 1 C are also presented in the paper
Influence of Absolute Pitch on Music Syntax Processing

Absolute pitch is defined as a unique ability to identify musical tones without external reference. Does pitch relation processing benefit from this ability? Miyazaki (1992, 1993) provided negative evidence suggesting that the poorer performances were observed in transposing musical intervals for absolute pitch possessors relative to the controls. Absolute pitch possessors also had difficulties in perceiving transposed melodies, whereas they performed better in the melodies played in the C major mode as compared to the controls (Miyazaki Rakowski, 2002). It is well known that music syntax highly reflects the relationship of pitch in tonal music. Does music syntax processing benefit from absolute pitch? The question was investigated in two experiments. All the participants were music education undergraduate students, who were recruited by means of advertisements. They were tested in the basic grouping rules of music syntax and segment music phrase structure in the current study. 31 absolute pitch possessors and 31 non-absolute pitch possessors as the controls were selected as the subjects for this study, who were matched in gender and musical background. Experiment 1 involving the basic grouping rules of music syntax focuses on examining the abilities to find tonality and mode, perceiving tendency of melodic pitches and harmonic functional progression. These musical stimuli were played in major keys with C, D, E, Eb, and C minor. Experiment 2 investigated the ability to segment phrase structure, concentrating on segmenting phrase and hierarchy level within phrase structure in four tonal music pieces. The music pieces were mainly played in C major. Results showed that AP possessors scored higher in the tasks of tonality and mode, tendency of melodic pitches and harmonic functional progression compared to the controls in Experiment 1. Furthermore, AP possessors performed better on segmenting phrase and hierarchy level within phrase structures. The findings indicated that the superiority of music syntax processing AP possessors showed may be attributed to their excellent pitch perceptions. In conclusion, absolute pitch may not be perfect in music sense, especially in transposing music processing. However, it goes without saying that AP possessors can identify a specified pitch without external reference due to their long-term pitch memories. For those AP possessors, music syntax processing may benefit from their exceptional memories, thus leading to the superiority of performances on the basic grouping rules of music syntax and segment phrase structure. However, this must be viewed as a tentative study, and more systematic investigation into this question is needed in future.
Learning Structured Outputs from Partial Labels using Forest Ensemble

Learning structured outputs with general structures is computationally challenging, except for tree-structured models. Thus we propose an efficient boosting-based algorithm AdaBoost.MRF for this task. The idea is based on the realization that a graph is a superimposition of trees. Different from most existing work, our algorithm can handle partial labelling, and thus is particularly attractive in practice where reliable labels are often sparsely observed. In addition, our method works exclusively on trees and thus is guaranteed to converge. We apply the AdaBoost.MRF algorithm to an indoor video surveillance scenario, where activities are modelled at multiple levels.
Prevalence and Phylogeny of Kakugo Virus, a Novel Insect Picorna-Like Virus That Infects the Honeybee (Apis mellifera L.), under Various Colony Conditions

ABSTRACT We previously identified a novel insect picorna-like virus, termed Kakugo virus (KV), from the brains of aggressive worker honeybees that had counterattacked a giant hornet. To survey the prevalence of KV in worker populations engaged in various labors, we quantified KV genomic RNA. KV was detected specifically from aggressive workers in some colonies, while it was also detected from other worker populations in other colonies where the amount of KV detected in the workers was relatively high, suggesting that KV can infect various worker populations in the honeybee colonies. To investigate whether the KV strains detected were identical, phylogenetic analysis was performed. There was less than a 2% difference in the RNA-dependent RNA polymerase (RdRp) sequences between KV strains from aggressive workers and those from other worker populations, suggesting that all of the viruses detected were virtually the same KV. We also found that some of the KV-infected colonies were parasitized by Varroa mites, and the sequences of the KV strains detected from the mites were the same as those detected from the workers of the same colonies, suggesting that the mites mediate KV prevalence in the honeybee colonies. KV strains had approximately 6% and 15% sequence differences in the RdRp region from deformed wing virus and Varroa destructor virus 1, respectively, suggesting that KV represents a viral strain closely related to, but distinct from, these two viruses.
Accurate Quantification of Site-specific Acetylation Stoichiometry Reveals the Impact of Sirtuin Deacetylase CobB on the E. coli Acetylome*

Lysine acetylation is a protein posttranslational modification (PTM) that occurs on thousands of lysine residues in diverse organisms from bacteria to humans. Accurate measurement of acetylation stoichiometry on a proteome-wide scale remains challenging. Most methods employ a comparison of chemically acetylated peptides to native acetylated peptides, however, the potentially large differences in abundance between these peptides presents a challenge for accurate quantification. Stable isotope labeling by amino acids in cell culture (SILAC)-based mass spectrometry (MS) is one of the most widely used quantitative proteomic methods. Here we show that serial dilution of SILAC-labeled peptides (SD-SILAC) can be used to identify accurately quantified peptides and to estimate the quantification error rate. We applied SD-SILAC to determine absolute acetylation stoichiometry in exponentially-growing and stationary-phase wild-type and Sirtuin deacetylase CobB-deficient cells. To further analyze CobB-regulated sites under conditions of globally increased or decreased acetylation, we measured stoichiometry in phophotransacetylase (ptaΔ) and acetate kinase (ackAΔ) mutant strains in the presence and absence of the Sirtuin inhibitor nicotinamide. We measured acetylation stoichiometry at 3,669 unique sites and found that the vast majority of acetylation occurred at a low stoichiometry. Manipulations that cause increased nonenzymatic acetylation by acetyl-phosphate (AcP), such as stationary-phase arrest and deletion of ackA, resulted in globally increased acetylation stoichiometry. Comparison to relative quantification under the same conditions validated our stoichiometry estimates at hundreds of sites, demonstrating the accuracy of our method. Similar to Sirtuin deacetylase 3 (SIRT3) in mitochondria, CobB suppressed acetylation to lower than median stoichiometry in WT, ptaΔ, and ackAΔ cells. Together, our results provide a detailed view of acetylation stoichiometry in E. coli and suggest an evolutionarily conserved function of Sirtuin deacetylases in suppressing low stoichiometry acetylation.
Analysis of the history and spread of HIV-1 in Uganda using phylodynamics

HIV prevalence has decreased in Uganda since the 1990s, but remains substantial within high-risk groups. Here, we reconstruct the history and spread of HIV subtypes A1 and D in Uganda and explore the transmission dynamics in high-risk populations. We analysed HIV pol sequences from female sex workers in Kampala (n = 42), Lake Victoria fisher-folk (n = 46) and a rural clinical cohort (n = 74), together with publicly available sequences from adjacent regions in Uganda (n = 412) and newly generated sequences from samples taken in Kampala in 1986 (n = 12). Of the sequences from the three Ugandan populations, 60 (37.1 %) were classified as subtype D, 54 (33.3 %) as subtype A1, 31 (19.1 %) as A1/D recombinants, six (3.7 %) as subtype C, one (0.6 %) as subtype G and 10 (6.2 %) as other recombinants. Among the A1/D recombinants we identified a new candidate circulating recombinant form. Phylodynamic and phylogeographic analyses using BEAST indicated that the Ugandan epidemics originated in 1960 (1950–1968) for subtype A1 and 1973 (1970–1977) for D, in rural south-western Uganda with subsequent spread to Kampala. They also showed extensive interconnection with adjacent countries. The sequence analysis shows both epidemics grew exponentially during the 1970s–1980s and decreased from 1992, which agrees with HIV prevalence reports in Uganda. Inclusion of sequences from the 1980s indicated the origin of both epidemics was more recent than expected and substantially narrowed the confidence intervals in comparison to previous estimates. We identified three transmission clusters and ten pairs, none of them including patients from different populations, suggesting active transmission within a structured transmission network.
A Socioecological Approach to Behavior and Psychological Tendencies on Social Network Sites : The Role of Relational Mobility [an abstract of dissertation and a summary of dissertation review]

Title A Socioecological Approach to Behavior and Psychological Tendencies on Social Network Sites : The Role of Relational Mobility [an abstract of dissertation and a summary of dissertation review] Author(s) THOMSON, Robert John Citation 北海道大学. 博士(文学) 甲第12082号 Issue Date 2016-03-24 Doc URL http://hdl.handle. net/2115/61611 Rights(URL) http://creativecommons.org/licenses/by-nc-sa/2.1/jp/ Type theses (doctoral abstract and summary of review) Additional Information There are other files related to this item in HUSCAP. Check the above URL. File Information Thomson_Robert_John_abstract. pdf (論文内容の要旨)
Temporal Dynamics of Attention during Encoding versus Maintenance of Working Memory: Complementary Views from Event-related Potentials and Alpha-band Oscillations

Working memory (WM) is strongly influenced by attention. In visual WM tasks, recall performance can be improved by an attention-guiding cue presented before encoding (precue) or during maintenance (retrocue). Although precues and retrocues recruit a similar frontoparietal control network, the two are likely to exhibit some processing differences, because precues invite anticipation of upcoming information whereas retrocues may guide prioritization, protection, and selection of information already in mind. Here we explored the behavioral and electrophysiological differences between precueing and retrocueing in a new visual WM task designed to permit a direct comparison between cueing conditions. We found marked differences in ERP profiles between the precue and retrocue conditions. In line with precues primarily generating an anticipatory shift of attention toward the location of an upcoming item, we found a robust lateralization in late cue-evoked potentials associated with target anticipation. Retrocues elicited a different pattern of ERPs that was compatible with an early selection mechanism, but not with stimulus anticipation. In contrast to the distinct ERP patterns, alpha-band (8–14 Hz) lateralization was indistinguishable between cue types (reflecting, in both conditions, the location of the cued item). We speculate that, whereas alpha-band lateralization after a precue is likely to enable anticipatory attention, lateralization after a retrocue may instead enable the controlled spatiotopic access to recently encoded visual information.