Miracle-dz/UniFAR-FTUs huggingface dataset:
Mining mutation testing simulation traces for security and testbench debugging

Unspecified design functionality can be modified by Hardware Trojans to leak information. Existing methods capable of detecting these Trojans require that unspecified functionality already be characterized, and suggest a manual ad-hoc process to enumerate “don't care” conditions potentially containing security vulnerabilities. Prior work has shown the potential of mutation testing to uncover testbench holes and highlight unspecified functionality, but requires tedious manual analysis of undetected faults to gain useful insight. This work provides the missing link required to fully automate characterization of unspecified functionality and can formally prove the absence of Trojans. Our approach is to mine simulation traces generated during mutation testing to produce assertions characterizing verification holes or unspecified functionality. These assertions can be fed directly to Trojan detection methods making securing unspecified functionality a completely automated process. Our trace mining technique is able to identify unspecified Wishbone bus functionality in a Trojan-free UART core and verify the functionality is benign, while flagging the same functionality in a Trojan-infected version of the design.
A Semantic-Based Framework for Fine Grained Sentiment Analysis

With the explosion of Web 2.0, customers are able to share their opinions and sentiments online. This has led to new opportunities for companies and organizations to understand people's opinions towards their products or services and can serve to improve their products or market strategy more effectively. However, the data on the Web is huge and unstructured, which makes it difficult to analyze automatically and in bulk. This paper proposes a novel (semantic-based) framework for fine-grained sentiment analysis. It also includes a practical implementation of the framework to analyse the sentiments expressed within customer reviews, aiming to provide accuracy of sentiment classification. The framework is able to deal with mixed-opinion reviews and handle contextual information via a sentiment lexicon containing multi-word expressions. Datasets across two domains (phone products and hotel services) were used to evaluate the proposed framework for its reliability and validity. A sizeable performance improvement was noted whereby the proposed methodology yielded a result of 91.3% accuracy in sentiment classification as compared to the baseline (SentiWordNet) which had a result of 71.0%.
New Middle Pleistocene hominin cranium from Gruta da Aroeira (Portugal)

Significance We describe a recently discovered cranium from the Aroeira cave in Portugal dated to around 400 ka. This specimen is the westernmost Middle Pleistocene cranium of Europe and is one of the earliest fossils from this region associated with Acheulean tools. Unlike most other Middle Pleistocene finds, which are of uncertain chronology, the Aroeira 3 cranium is firmly dated to around 400 ka and was in direct association with abundant faunal remains and stone tools. In addition, the presence of burnt bones suggests a controlled use of fire. The Aroeira cranium represents a substantial contribution to the debate on the origin of the Neandertals and the pattern of human evolution in the Middle Pleistocene of Europe. The Middle Pleistocene is a crucial time period for studying human evolution in Europe, because it marks the appearance of both fossil hominins ancestral to the later Neandertals and the Acheulean technology. Nevertheless, European sites containing well-dated human remains associated with an Acheulean toolkit remain scarce. The earliest European hominin crania associated with Acheulean handaxes are at the sites of Arago, Atapuerca Sima de los Huesos (SH), and Swanscombe, dating to 400–500 ka (Marine Isotope Stage 11–12). The Atapuerca (SH) fossils and the Swanscombe cranium belong to the Neandertal clade, whereas the Arago hominins have been attributed to an incipient stage of Neandertal evolution, to Homo heidelbergensis, or to a subspecies of Homo erectus. A recently discovered cranium (Aroeira 3) from the Gruta da Aroeira (Almonda karst system, Portugal) dating to 390–436 ka provides important evidence on the earliest European Acheulean-bearing hominins. This cranium is represented by most of the right half of a calvarium (with the exception of the missing occipital bone) and a fragmentary right maxilla preserving part of the nasal floor and two fragmentary molars. The combination of traits in the Aroeira 3 cranium augments the previously documented diversity in the European Middle Pleistocene fossil record.
Unconventional Layout Techniques for a High Performance, Low Variability Subthreshold Standard Cell Library

A novel subthreshold sizing strategy utilizing the Inverse Narrow Width Effect is demonstrated that has the largest range of propagation delays within the same cell footprint and lowest variability of any subthreshold sizing strategy thus far proposed. Simulation results and ring oscillators implemented in a commercial 65nm low power process confirm a propagation delay improvement of up to 1.95X over the standard superthreshold sizing strategy at 300mV and below. 32 bit multipliers are then synthesized and static timing analysis performed at several subthreshold voltage corners to illustrate applicability to real designs in conventional EDA design flows.
Tumor Resistance against ALK Targeted Therapy-Where It Comes From and Where It Goes

Anaplastic lymphoma kinase (ALK) is a validated molecular target in several ALK-rearranged malignancies, particularly in non-small-cell lung cancer (NSCLC), which has generated considerable interest and effort in developing ALK tyrosine kinase inhibitors (TKI). Crizotinib was the first ALK inhibitor to receive FDA approval for ALK-positive NSCLC patients treatment. However, the clinical benefit observed in targeting ALK in NSCLC is almost universally limited by the emergence of drug resistance with a median of occurrence of approximately 10 months after the initiation of therapy. Thus, to overcome crizotinib resistance, second/third-generation ALK inhibitors have been developed and received, or are close to receiving, FDA approval. However, even when treated with these new inhibitors tumors became resistant, both in vitro and in clinical settings. The elucidation of the diverse mechanisms through which resistance to ALK TKI emerges, has informed the design of novel therapeutic strategies to improve patients disease outcome. This review summarizes the currently available knowledge regarding ALK physiologic function/structure and neoplastic transforming role, as well as an update on ALK inhibitors and resistance mechanisms along with possible therapeutic strategies that may overcome the development of resistance.
A Flexible Pay-per-Device Licensing Scheme for FPGA IP Cores

FPGA based product development companies need third party IP cores to complete the product design time effectively and cost effectively. The one-time payment upfront licensing of IP cores is impractical for FPGA based products, which does not benefit either IP core vendors or product engineering companies. There is a need for good competitive pricing scheme which benefit product development companies and also secure the revenue to IP core vendors. The Pay-per-Device (PPD) pricing model scheme is a suitable pricing scheme. The PPD pricing schemes proposed in the past are complex in terms of communication between different stake holders and inflexible for product development companies to change the FPGA vendor. In this paper, we propose a PPD pricing scheme which overcomes the disadvantages of earlier techniques with better key management and without compromising the security of IP cores. The product development company can change the FPGA vendor at any time in the product life cycle by incorporating the proposed PPD pricing model. The proposed scheme is verified on Xilinx Artix-7 series FPGA.
Coronary pressure and flow relationships in humans: phasic analysis of normal and pathological vessels and the implications for stenosis assessment: a report from the Iberian–Dutch–English (IDEAL) collaborators

Abstract Background Our understanding of human coronary physiological behaviour is derived from animal models. We sought to describe physiological behaviour across a large collection of invasive pressure and flow velocity measurements, to provide a better understanding of the relationships between these physiological parameters and to evaluate the rationale for resting stenosis assessment. Methods and results Five hundred and sixty-seven simultaneous intracoronary pressure and flow velocity assessments from 301 patients were analysed for coronary flow velocity, trans-stenotic pressure gradient (TG), and microvascular resistance (MVR). Measurements were made during baseline and hyperaemic conditions. The whole cardiac cycle and the diastolic wave-free period were assessed. Stenoses were assessed according to fractional flow reserve (FFR) and quantitative coronary angiography DS%. With progressive worsening of stenoses, from unobstructed angiographic normal vessels to those with FFR ≤ 0.50, hyperaemic flow falls significantly from 45 to 19 cm/s, Ptrend < 0.001 in a curvilinear pattern. Resting flow was unaffected by stenosis severity and was consistent across all strata of stenosis ( Ptrend > 0.05 for all). Trans-stenotic pressure gradient rose with stenosis severity for both rest and hyperaemic measures ( Ptrend < 0.001 for both). Microvascular resistance declines with stenosis severity under resting conditions ( Ptrend < 0.001), but was unchanged at hyperaemia (2.3 ± 1.1 mmHg/cm/s; Ptrend = 0.19). Conclusions With progressive stenosis severity, TG rises. However, while hyperaemic flow falls significantly, resting coronary flow is maintained by compensatory reduction of MVR, demonstrating coronary auto-regulation. These data support the translation of coronary physiological concepts derived from animals to patients with coronary artery disease and furthermore, suggest that resting pressure indices can be used to detect the haemodynamic significance of coronary artery stenoses.
Ebola Virus Neutralizing Antibodies Detectable in Survivors of the Yambuku, Zaire Outbreak 40 Years after Infection

Rimoin, Anne W; Lu, Kai; Bramble, Matthew S; Steffen, Imke; Doshi, Reena H; Hoff, Nicole A; Mukadi, Patrick; Nicholson, Bradly P; Alfonso, Vivian H; Olinger, Gerrard; +14 more. Sinai, Cyrus; Yamamoto, Lauren K; Ramirez, Christina M; Okitolonda Wemakoy, Emile; Kebela Illunga, Benoit; Pettitt, James; Logue, James; Bennett, Richard S; Jahrling, Peter; Heymann, David L; Piot, Peter; Muyembe-Tamfum, Jean Jacques; Hensley, Lisa E; Simmons, Graham; (2017) Ebola Virus Neutralizing Antibodies Detectable in Survivors of theYambuku, Zaire Outbreak 40 Years after Infection. The Journal of infectious diseases, 217 (2). pp. 223-231. ISSN 0022-1899 DOI: https://doi.org/10.1093/infdis/jix584
On the Influence of Human Factors for Identifying Code Smells: A Multi-Trial Empirical Study

Context: Code smells are symptoms in the source code that represent poor design choices. Professional developers often perceive several types of code smells as indicators of actual design problems. However, the identification of code smells involves multiple steps that are subjective in nature, requiring the engagement of humans. Human factors are likely to play a key role in the precise identification of code smells in industrial settings. Unfortunately, there is limited knowledge about the influence of human factors on smell identification. Goal: We aim at investigating whether the precision of smell identification is influenced by three key human factors, namely reviewer's professional background, reviewer's module knowledge and collaboration of reviewers during the task. We also aim at deriving recommendations for allocating human resources to smell identification tasks. Method: We performed 19 comparisons among different subsamples from two trials of a controlled experiment conducted in the context of an empirical study on code smell identification. One trial was conducted in industrial settings while the other had involved graduate students. The diversity of the samples allowed us to analyze the influence of the three factors in isolation and in conjunction. Results: We found that (i) reviewers' collaboration significantly increases the precision of smell identification, but (ii) some professional background is required from the reviewers to reach high precision. Surprisingly, we also found that: (iii) having previous knowledge of the reviewed module does not affect the precision of reviewers with higher professional background. However, this factor was influential on successful identification of more complex smells. Conclusion: We expect that our findings are helpful to support researchers in conducting proper experimental procedures in the future. Besides, they may also be useful for supporting project managers in allocating resources for smell identification tasks.
On the Methodological Implications of Extracting Muscle Synergies from Human Locomotion

We investigated the influence of three different high-pass (HP) and low-pass (LP) filtering conditions and a Gaussian (GNMF) and inverse-Gaussian (IGNMF) non-negative matrix factorization algorithm on the extraction of muscle synergies from myoelectric signals during human walking and running. To evaluate the effects of signal recording and processing on the outcomes, we analyzed the intraday and interday computation reliability. Results show that the IGNMF achieved a significantly higher reconstruction quality and on average needs one less synergy to sufficiently reconstruct the original signals compared to the GNMF. For both factorizations, the HP with a cut-off frequency of 250[Formula: see text]Hz significantly reduces the number of synergies. We identified the filter configuration of fourth order, HP 50[Formula: see text]Hz and LP 20[Formula: see text]Hz as the most suitable to minimize the combination of fundamental synergies, providing a higher reliability across all filtering conditions even if HP 250[Formula: see text]Hz is excluded. Defining a fundamental synergy as a single-peaked activation pattern, for walking and running we identified five and six fundamental synergies, respectively using both algorithms. The variability in combined synergies produced by different filtering conditions and factorization methods on the same data set suggests caution when attributing a neurophysiological nature to the combined synergies.
LiREP: Lightweight incremental reprogramming of sensor nodes based on in-situ modification

Energy-efficient consumption of the reprogramming approaches is one of key issues for long-term living wireless sensor networks. Most of the current approaches focus on the power efficiency during data dissemination. However, the program rebuilding phase on target node is rarely considered as another significant part of total reprogramming energy consumed. We propose a novel reprogramming approach-LiREP in two-fold: first, we design an in-situ code modification method which saves more energy compared with traditional way to rebuild program in external flash. Three basic modifying operations are proposed and realized. These operations can reduce the writing/reading operations of flash ROM by producing a modified program with redundant codes in memory. Secondly, we also propose a novel rebuilding method to remove the redundant codes when the available memory is not enough for the in-situ code modification. This rebuilding method totally runs in-chip with least the rebuilding overhead. Experiment results show that LiREP reduces the rebuilding energy overhead by approximately 84% and 74% compared to Deluge and Hermes, and further minimizes the reprogramming energy overhead.
Aquatic hazard assessment of MON 0818, a commercial mixture of alkylamine ethoxylates commonly used in glyphosate‐containing herbicide formulations. Part 2: Roles of sediment, temperature, and capacity for recovery following a pulsed exposure

A series of toxicity tests with MON 0818, a commercial surfactant mixture of polyoxyethylene tallow amines, were performed: 1) in the presence of sediment for benthic invertebrates and fish: 2) to examine the recovery capacity of Daphnia magna and 4 primary producers after a pulsed (24‐h) exposure; and 3) to examine the potential effect of increased water temperature on toxicity of MON 0818 to 2 cold‐water fishes. In the presence of sediment, no acute (24‐h) mortality was observed for 3 of the 5 species up to 10 mg L−1. The median effective concentrations for the other 2 species were significantly greater than for water only tests. The EC50 at 15 °C for Salvelinus alpinus was statistically lower than that at 10 °C. Latent effects of a 24‐h exposure (1 mg L−1) were observed for Rhabdocelis subcapitata and Chlorella vulgaris, as indicated by delayed growth during recovery phase; however, both cultures were able to recover, as indicated by a lack of changes in maximum absolute growth rates. No significant effects of a 24‐h exposure to MON 0818 were observed for Oophila sp. (1.5 mg L−1) or Lemna minor (100 mg L−1). Latent mortality after a 24‐h exposure to 5 mg L−1 was observed during the recovery phase for D. magna; however, reproduction endpoints on surviving individuals were not altered. The results indicate that quick dissipation of MON 0818 in the presence of sediment can reduce the effects on exposed organisms, and that full recovery from 24‐h exposures to concentrations of MON 0818 equal to, or greater than, those expected in the environment is possible. Environ Toxicol Chem 2017;36:512–521. © 2016 SETAC
Microbiota Analysis of an Environmental Slurry and Its Potential Role as a Reservoir of Bovine Digital Dermatitis Pathogens

ABSTRACT At present, very little information exists regarding what role the environmental slurry may play as an infection reservoir and/or route of transmission for bovine digital dermatitis (DD), a disease which is a global problem in dairy herds. To investigate whether DD-related bacteria belong to the indigenous microbiota of the dairy herd environment, we used deep amplicon sequencing of the 16S rRNA gene in 135 slurry samples collected from different sites in 22 dairy farms, with and without DD-infected cows. Both the general bacterial populations and digital dermatitis-associated Treponema were targeted in this study. The results revealed significant differences in the bacterial communities between the herds, with only 12 bacterial taxa shared across at least 80% of all the individual samples. These differences in the herd microbiota appeared to reflect mainly between-herd variation. Not surprisingly, the slurry was dominated by ubiquitous gastrointestinal bacteria, such as Ruminococcaceae and Lachnospiraceae. Despite the low relative abundance of spirochetes, which ranged from 0 to 0.6%, we were able to detect small amounts of bacterial DNA from DD-associated treponemes in the slurry. However, the DD-associated Treponema spp. were detected only in samples from herds with reported DD problems. These data indicate that treponemes involved in the pathogenesis of DD are not part of the normal environmental microflora in dairy herds without clinical DD and, consequently, that slurry is not a primary reservoir of infection. IMPORTANCE Bovine digital dermatitis (DD), a dermal disease which causes lameness in dairy cattle, is a serious problem worldwide. To control this disease, the infection reservoirs and transmission routes of DD pathogens need to be clarified. The dairy herd slurry may be a pathogen reservoir of DD-associated bacteria. The rationale for the present study was, therefore, to examine whether DD-associated bacteria are always present in slurry or if they are found only in DD-afflicted herds. The results strongly indicated that DD Treponema spp. are not part of the indigenous slurry and, therefore, do not comprise an infection reservoir in healthy herds. This study applied next-generation sequencing technology to decipher the microbial compositions of environmental slurry of dairy herds with and without digital dermatitis.
Patterns of coordinated cortical remodeling during adolescence and their associations with functional specialization and evolutionary expansion

Significance During adolescence, the human cortex is morphed under the influence of regionally heterogeneous and heterochronous processes. Accurately mapping these processes and quantifying their effect is essential for understanding brain development, both in order and disorder. Currently, our understanding remains fundamentally “localizational” in nature, while often being limited by small samples. Here, we capitalize on a large cohort of youths and apply advanced multivariate analysis techniques to capture the coordinated growth of structural brain networks during adolescence. Our results delineate a representation of cortical organization that differs markedly from typical anatomical atlases. This representation comprises structural networks that relate closely to functional brain networks, while exhibiting differential developmental effects that are consistent with an evolutionary view of development. During adolescence, the human cortex undergoes substantial remodeling to support a rapid expansion of behavioral repertoire. Accurately quantifying these changes is a prerequisite for understanding normal brain development, as well as the neuropsychiatric disorders that emerge in this vulnerable period. Past accounts have demonstrated substantial regional heterogeneity in patterns of brain development, but frequently have been limited by small samples and analytics that do not evaluate complex multivariate imaging patterns. Capitalizing on recent advances in multivariate analysis methods, we used nonnegative matrix factorization (NMF) to uncover coordinated patterns of cortical development in a sample of 934 youths ages 8–20, who completed structural neuroimaging as part of the Philadelphia Neurodevelopmental Cohort. Patterns of structural covariance (PSCs) derived by NMF were highly reproducible over a range of resolutions, and differed markedly from common gyral-based structural atlases. Moreover, PSCs were largely symmetric and showed correspondence to specific large-scale functional networks. The level of correspondence was ordered according to their functional role and position in the evolutionary hierarchy, being high in lower-order visual and somatomotor networks and diminishing in higher-order association cortex. Furthermore, PSCs showed divergent developmental associations, with PSCs in higher-order association cortex networks showing greater changes with age than primary somatomotor and visual networks. Critically, such developmental changes within PSCs were significantly associated with the degree of evolutionary cortical expansion. Together, our findings delineate a set of structural brain networks that undergo coordinated cortical thinning during adolescence, which is in part governed by evolutionary novelty and functional specialization.