Miracle-dz/UniFAR-FTUs huggingface dataset:
TLSim and EVC: a term-level symbolic simulator and an efficient decision procedure for the logic of equality with uninterpreted functions and memories

We present a tool flow for high-level design and formal verification of embedded processors. The tool flow consists of the term-level symbolic simulator TLSim, the decision procedure EVC (Equality Validity Checker) for the logic of Equality with Uninterpreted Functions and Memories (EUFM), and any SAT solver. TLSim accepts high-level models of a pipelined implementation processor and its non-pipelined specification, as well as a command file indicating how to simulate them symbolically, and produces an EUFM formula for the correctness of the implementation. EVC exploits the property of Positive Equality and other optimisations in order to translate the EUFM formula to an equivalent Boolean formula that can be solved with any SAT procedure. An earlier version of our tool flow was used to formally verify a model of the M•CORE processor at Motorola, and detected bugs.
Yates and contingency tables: 75 years later.

Seventy-five years ago, Yates (1934) presented an article introducing his continuity correction to the χ 2 test for independence in contingency tables. The paper also was one of the first introductions to Fisher's exact test. We discuss the histori- cal importance of Yates and his 1934 paper. The development of the exact test and continuity correction are studied in some detail. Subsequent disputes about the exact test and continuity correction are briefly recounted, as we attempt to ascertain the 1934 paper's place in history.
Mismatch repair genes founder mutations and cancer susceptibility in Lynch syndrome

Founder mutations in specific populations are common in several Mendelian disorders. They are shared by apparently unrelated families that inherited them from a common ancestor that existed hundreds to thousands of years ago. They have been proven to impact in molecular diagnostics strategies in specific populations, where they can be assessed as the first screening step and, if positive, avoid further expensive gene scanning. In Lynch syndrome (LS), a dominantly inherited colorectal cancer disease, more than 50 founder pathogenic mutations have been described so far in the mismatch repair (MMR) genes (MLH1, MSH2, MSH6 and PMS2). We here provide a comprehensive summary of the founder mutations found in the MMR genes and an overview of their main characteristics. At a time when high‐throughput strategies are being introduced in the molecular diagnostics of cancer, genetic testing for founder mutations can complement next generation sequencing (NGS) technologies to most efficiently identify MMR gene mutations in any given population. Additionally, special attention is paid to MMR founder mutations with interesting anthropological significance.
ArnR, a Novel Transcriptional Regulator, Represses Expression of the narKGHJI Operon in Corynebacterium glutamicum

ABSTRACT The narKGHJI operon that comprises putative nitrate/nitrite transporter (narK) and nitrate reductase (narGHJI) genes is required for the anaerobic growth of Corynebacterium glutamicum with nitrate as a terminal electron acceptor. In this study, we identified a gene, arnR, which encodes a transcriptional regulator that represses the expression of the narKGHJI operon in C. glutamicum cells under aerobic conditions. Disruption of arnR induced nitrate reductase activities of C. glutamicum cells and increased narKGHJI mRNA levels under aerobic growth conditions. DNA microarray analyses revealed that besides the narKGHJI operon, the hmp gene, which encodes flavohemoglobin, is negatively regulated by ArnR under aerobic conditions. Promoter-reporter assays indicated that arnR gene expression was positively autoregulated by its gene product, ArnR, under both aerobic and anaerobic conditions. Electrophoretic mobility shift assay experiments showed that purified hexahistidyl-tagged ArnR protein specifically binds to promoter regions of the narKGHJI operon and the hmp and arnR genes. A consensus sequence, TA(A/T)TTAA(A/T)TA, found in the promoter regions of these genes was demonstrated to be involved in the binding of ArnR. Effects on LacZ activity by deletion of the ArnR binding sites within the promoter regions fused to the reporter gene were consistent with the view that the expression of the narKGHJI operon is repressed by the ArnR protein under aerobic conditions, whereas the expression of the arnR gene is autoinduced by ArnR.
Industrial application of concolic testing approach: A case study on libexif by using CREST-BV and KLEE

As smartphones become popular, manufacturers such as Samsung Electronics are developing smartphones with rich functionality such as a camera and photo editing quickly, which accelerates the adoption of open source applications in the smartphone platforms. However, developers often do not know the detail of open source applications, because they did not develop the applications themselves. Thus, it is a challenging problem to test open source applications effectively in short time. This paper reports our experience of applying concolic testing technique to test libexif, an open source library to manipulate EXIF information in image files. We have demonstrated that concolic testing technique is effective and efficient at detecting bugs with modest effort in industrial setting. We also compare two concolic testing tools, CREST-BV and KLEE, in this testing project. Furthermore, we compare the concolic testing results with the analysis result of the Coverity Prevent static analyzer. We detected a memory access bug, a null pointer dereference bug, and four divide-by-zero bugs in libexif through concolic testing, none of which were detected by Coverity Prevent.
Infrared Spectral Energy Distributions of Nearby Galaxies

The Spitzer Infrared Nearby Galaxies Survey (SINGS) is carrying out a comprehensive multiwavelength survey on a sample of 75 nearby galaxies. The 1-850 μm spectral energy distributions (SEDs) are presented using broadband imaging data from Spitzer, 2MASS, ISO, IRAS, and SCUBA. The infrared colors derived from the globally integrated Spitzer data are generally consistent with the previous generation of models that were developed using global data for normal star-forming galaxies, although significant deviations are observed. Spitzer's excellent sensitivity and resolution also allow a detailed investigation of the infrared SEDs for various locations within the three large, nearby galaxies NGC 3031 (M81), NGC 5194 (M51), and NGC 7331. A wide variety of spectral shapes is found within each galaxy, especially for NGC 3031, the closest of the three targets and thus the galaxy for which the smallest spatial scales can be explored. Strong correlations exist between the local star formation rate and the infrared colors fν(70 μm)/fν(160 μm) and fν(24 μm)/fν(160 μm), suggesting that the 24 and 70 μm emission are useful tracers of the local star formation activity level. Preliminary evidence indicates that variations in the 24 μm emission, and not variations in the emission from polycyclic aromatic hydrocarbons at 8 μm, drive the variations in the fν(8.0 μm)/fν(24 μm) colors within NGC 3031, NGC 5194, and NGC 7331. If the galaxy-to-galaxy variations in SEDs seen in our sample are representative of the range present at high redshift, then extrapolations of total infrared luminosities and star formation rates from the observed 24 μm flux will be uncertain at the factor of 5 level (total range). The corresponding uncertainties using the redshifted 8.0 μm flux (e.g., observed 24 μm flux for a z = 2 source) are factors of 10-20. Considerable caution should be used when interpreting such extrapolated infrared luminosities.
Identification of an IS711 Element Interrupting the wboA Gene of Brucella abortusVaccine Strain RB51 and a PCR Assay To Distinguish Strain RB51 from Other Brucella Species and Strains

ABSTRACT Brucella abortus vaccine strain RB51 is a natural stable attenuated rough mutant derived from the virulent strain 2308. The genetic mutations that are responsible for the roughness and the attenuation of strain RB51 have not been identified until now. Also, except for an assay based on pulsed-field gel electrophoresis, no other simple method to differentiate strain RB51 from its parent strain 2308 is available. In the present study, we demonstrate that thewboA gene encoding a glycosyltransferase, an enzyme essential for the synthesis of O antigen, is disrupted by an IS711 element in B. abortus vaccine strain RB51. Exploiting this feature, we developed a PCR assay that distinguishes strain RB51 from all other Brucella species and strains tested.
A Study of Internet Routing Stability Using Link Weight

The global Internet routing infrastructure is a large scale distributed system where routing changes occur all the time. While prior work on Internet routing dynamics examined routing stability to individual destinations, in this paper we study the routing stability of the Internet as a whole. We use the observed changes in the number of routes over each AS-AS link as a metric and measure such changes from multiple vantage points over a period of one year. We then apply Principal Component Analysis to identify those AS links that were most involved in routing changes. Our work is the ﬁrst to combine measurement data collected from multiple monitors to gauge the overall routing stability in the Internet. Our results show that very few routing events impact the entire Internet, and those events were due to announcement of new preﬁxes either in the form of route leakages or address space de-aggregation. We also ﬁnd that the impact of most routing events is conﬁned to a small scope, and the existence of unstable AS links over long periods of time. We believe our approach represents a new direction in routing stability measurement and our ﬁndings shed new insight into the routing system performance.
Travelling graphs for the forced mean curvature motion in an arbitrary space dimension

We construct travelling wave graphs of the form $z=-ct+\phi(x)$, $\phi: x \in \mathbb{R}^{N-1} \mapsto \phi(x)\in \mathbb{R}$, $N \geq 2$, solutions to the $N$-dimensional forced mean curvature motion $V_n=-c_0+\kappa$ ($c\geq c_0$) with prescribed asymptotics. For any 1-homogeneous function $\phi_{\infty}$, viscosity solution to the eikonal equation $|D\phi_{\infty}|=\sqrt{(c/c_0)^2-1}$, we exhibit a smooth concave solution to the forced mean curvature motion whose asymptotics is driven by $\phi_{\infty}$. We also describe $\phi_{\infty}$ in terms of a probability measure on $\mathbb{S}^{N-2}$.
Magnetic resonance elastography of frontotemporal dementia

To investigate the feasibility of utilizing brain stiffness as a potential biomarker for behavioral variant frontotemporal dementia (bvFTD) patients. Magnetic resonance elastography (MRE) is a noninvasive technique for evaluating the mechanical properties of brain tissue in vivo. MRE has demonstrated decreased brain stiffness in patients with Alzheimer's disease.
Understanding Interactions between Shoreline Changes and Reef Outer Slope Morphometry on Takapoto Atoll (French Polynesia)

ABSTRACT Collin, A. ; Duvat, V. ; Pillet, V. ; Salvat, B. , and James, D. , 2018. Understanding Interactions between Shoreline Changes and Reef Outer Slope Morphometry on Takapoto Atoll (French Polynesia). In: Shim, J.-S. ; Chun, I. , and Lim, H.S. (eds.), Proceedings from the International Coastal Symposium (ICS) 2018 (Busan, Republic of Korea). Journal of Coastal Research, Special Issue No. 85, pp. 496–500. Coconut Creek (Florida), ISSN 0749-0208. Low-lying atoll reef islands host populations who are highly exposed to increasing ocean-related pressures resulting from accelerated sea-level rise, ocean warming and acidification. Since 2010, changes in the position of atoll reef island shoreline were estimated on more than 400 Pacific islands using multi-date image analysis. These studies have emphasized island persistence and highlighted the major role of local controls, i.e., human activities and tropical cyclones, in shoreline change. However, they provide limited knowledge on the ecological-morphological linkages driving island change. In order to contribute filling this gap, will be studied the statistical relationships between multi-decadal shoreline change and high-resolution outer slope morphometry of the eastern windward coast of Takapoto Atoll (Tuamotu Archipelago, French Polynesia). Shoreline change was estimated using 1969 airborne and 2013 spaceborne imagery, while outer slope morphometry was mapped at 2 m spatial resolution using 2016 spaceborne imagery. Nine classes of shoreline changes (N=1 402), ranging from >50 m accretion to >50 m erosion, were compared with averages of depth and slope metrics, derived from satellite-based bathymetry mapping. A strong positive correlation between shoreline erosion versus (i) depth and (ii) slope averages was obtained (R2=0.93 and R2=0.96, respectively): the deeper/steeper outer transects are, the more eroded shoreline transects are. Those findings suitably match the theory of wave propagation in shallow/gentle waters describing an increase in cross-shore sediment transfer with shallowness, thus explaining spatial variations in shoreline response. The implications of those original results for reef islands' future under climate change will be discussed.
Design and Implementation of a Hypothermic Machine Perfusion Device for Clinical Preservation of Isolated Organs

The imbalance between limited organ supply and huge potential need has hindered the development of organ-graft techniques. In this paper a low-cost hypothermic machine perfusion (HMP) device is designed and implemented to maintain suitable preservation surroundings and extend the survival life of isolated organs. Four necessary elements (the machine perfusion, the physiological parameter monitoring, the thermostatic control and the oxygenation apparatus) involved in this HMP device are introduced. Especially during the thermostatic control process, a modified Bayes estimation, which introduces the concept of improvement factor, is realized to recognize and reduce the possible measurement errors resulting from sensor faults and noise interference. Also, a fuzzy-PID controller contributes to improve the accuracy and reduces the computational load using the DSP. Our experiments indicate that the reliability of the instrument meets the design requirements, thus being appealing for potential clinical preservation applications.
A twin registry study of the relationship between posttraumatic stress disorder and nicotine dependence in men.

CONTEXT Recent studies indicate a strong association between posttraumatic stress disorder (PTSD) and nicotine dependence (ND). However, the explanation for the association remains unclear. OBJECTIVE To test competing explanations for the association between PTSD and ND. DESIGN, SETTING, AND PARTICIPANTS Analysis of data on 6744 members of the Vietnam Era Twin Registry, a national registry of all male-male twin pairs who served in the military during the Vietnam era interviewed in 1991-1992. MAIN OUTCOME MEASURES Risk of PTSD and ND using the Diagnostic Interview Schedule for the DSM-III-R. RESULTS The prevalence of ND was elevated among trauma-exposed individuals (52.0%) and those with PTSD (71.7%) compared with unexposed individuals (40.5%). This association was significant for ND and for trauma without PTSD (odds ratio, 1.31; 95% confidence interval [CI], 1.18-1.45) and for PTSD (odds ratio, 2.34; 95% CI, 1.92-2.84) and was not entirely explained by shared risk factors. Shared genetic effects explained 63% of the PTSD-ND association; the remaining covariance was explained by individual-specific environmental effects. Using survival analysis with time-dependent covariates, ND was associated with a substantially increased risk of PTSD among trauma-exposed men (hazard ratio, 1.98; 95% CI, 1.61-2.42). Trauma (hazard ratio, 1.49; 95% CI, 1.35-1.64) and PTSD (hazard ratio, 1.36; 95% CI, 1.14-1.61) were less strongly but significantly associated with increased risk of ND onset after controlling for shared risk factors. CONCLUSIONS Most of the PTSD-ND association is explained by shared genetic effects. However, there is a substantial, robust PTSD-ND association not explained by shared risk factors. Multiple explanations for the association were supported; however, the strongest association was consistent with preexisting ND increasing the risk of PTSD onset. These data suggest that male veterans with a history of ND may be at increased risk for PTSD. Further research on the biological mechanisms underlying PTSD-ND comorbidity is needed.
Evolution of thermotolerance and the heat-shock response: evidence from inter/intraspecific comparison and interspecific hybridization in the virilis species group of Drosophila. I. Thermal phenotype

SUMMARY Species in the virilis group of Drosophila (fruit flies), which overlap or replace one another along climatic gradients, exhibit corresponding differences in basal thermotolerance, inducible thermotolerance and the heat-shock response. The low-latitude species D. virilis exceeds the high-latitude species D. lummei in these measures of thermotolerance, the temperature threshold for heat-shock factor (HSF) activation and the ability to express hsp70 mRNA and diverse heat-shock proteins (e.g. Hsp70, Hsp83 and small Hsps) after intense heat shock (e.g. 40–41°C). The xeric species D. novamexicana differs from the mesic species D. texana in much the same way for many of these traits. By contrast, intraspecific variation in these traits is small. Because D. virilis and D. lummei can readily be crossed to yield partially fertile progeny, genetic analysis of interspecific differences is possible. Interspecific hybrids are intermediate to the parental species in basal thermotolerance and inducible thermotolerance and resemble D. virilis in Hsp concentrations after intense heat shock and Hsp70 protein electromorphs.
Increased training intensity effects on plasma lactate, ventilatory threshold, and endurance.

The purpose of this study was to determine the effects of increased training intensity (ITI) on VO2max, plasma lactate accumulation, ventilatory threshold (VT), and performance in trained distance runners. Seven trained male distance runners increased their training intensity three d.wk-1 at 90-95% HRmax for eight wk. ITI did not alter VO2max (65.3 +/- 2.3 vs 65.8 +/- 2.4 ml.kg-1.min-1) but improved 10 km race time (means = 63 s decrease) and increased run time to exhaustion on the treadmill at the same speed and grade (means = 3.88 min). Significant decreases in plasma lactate concentration at 85 and 90% of VO2max were observed after ITI. No differences were found in plasma lactate at 65, 70, 75 or 80% of VO2max or VT following ITI. Significant correlations were obtained between 10 km race times and changes in plasma lactate at 85 and 90% of VO2max (r = 0.69 and 0.73, respectively). Lactate accumulation at both 2.5 and 4.0 mM were at a significantly greater percent of VO2max after ITI. Additionally, the changes in plasma lactate were dissociated from alterations in VT after ITI. These data indicate that previously trained runners can increase training intensity to improve endurance performance by lowering lactate at the intensity at which they trained despite no changes in VO2max and VT.
Hardness of the undirected edge-disjoint paths problem with congestion

In the edge-disjoint paths problem with congestion (EDPwC), we are given a graph with n nodes, a set of terminal pairs and an integer c. The objective is to route as many terminal pairs as possible, subject to the constraint that at most c demands can be routed through any edge in the graph. When c = 1, the problem is simply referred to as the edge-disjoint paths (EDP) problem. In this paper, we study the hardness of EDPwC in undirected graphs. We obtain an improved hardness result for EDP, and also show the first polylogarithmic integrality gaps and hardness of approximation results for EDPwC. Specifically, we prove that EDP is (log/sup 1/2 - /spl epsiv// n)-hard to approximate for any constant /spl epsiv/ > 0, unless NP /spl sube/ ZPTIME(n/sup polylog n/). We also show that for any congestion c = o(log log n/log log log n), there is no (log/sup (1-/spl epsiv/)/(c+1)/ n) approximation algorithm for EDPwC, unless NP /spl sube/ ZPTIME(n/sup polylog n/). For larger congestion, where c /spl les/ /spl eta/ log log n/log log log n for some constant /spl eta/, we obtain superconstant inapproximability ratios. All of our hardness results can be converted into integrality gaps for the multicommodity flow relaxation. We also present a separate elementary direct proof of this integrality gap result. Finally, we note that similar results can be obtained for the all-or-nothing flow (ANF) problem, a relaxation of EDP, in which the flow unit routed between the source-sink pairs does not have follow a single path, so the resulting flow is not necessarily integral. Using standard transformations, our results also extend to the node-disjoint versions of these problems as well as to the directed setting.
Fish Diversity Assessment of the Haor Region in Kishoreganj District, Bangladesh

Background and Objective: Fisheries sector play important role in the economy. Diversity status is needed to conserve the fish resources of the haor region. The present study was conducted to assess fish diversity of the Kalai beel and Naoli beel of Karimganj Upazila in Kishoreganj district, Bangladesh. Materials and Methods: Fish samples were collected from the fishermen and local fish market for taxonomic study from December, 2014-November, 2015. Morphometric and meristic characteristics were identified through direct observation and further identification was done following different books. Results: A total of 46 fish species were identified during the study under 17 families. Among 46 fish species, 15 were found belong to Cyprinidae family followed by Bagaridae (4), Channidae (4), Schilbeidae (3), Mastacembelidae (3), Centropomidae (3), Siluridae (2), Anabantidae (2), Palaemonidae (2) and others (8). During the study period, 22 fish species were marked as abundant species, 15 species were marked as rare and 9 species were found as common species. Conclusion: Ecologically, economically and socially haors are playing essential role with its diversified fish resources. Haor fisheries have great impact on the livelihood of the fishermen and provide nutrition to general people. However, the fish diversity is being threatened by anthropogenic activities. Present study emphasized on the conservation of the fish as it is undergone gradual decrease.
Input-output stability with input-to-state stable protocols for quantized and networked control systems

This paper introduces the notion of input-to-state stable (ISS) protocols in the context of scheduling and quantization within networked control systems (NCS) and examines conditions under which a class of continuous-time control systems designed ignoring the network achieves input-to-state stability. Verifiable sufficient conditions for robust stability (ISS) are given for a class of nonlinear systems under the constraint of finite data-rate feedback.