Miracle-dz/UniFAR-FTUs huggingface dataset:
Flowering phenology shifts in response to biodiversity loss

Significance Advanced spring flowering has been described as a fingerprint of climate change—a public, visible display of the detrimental effects of global warming. However, warming experiments fail to account for the full magnitude of observed changes in phenology, suggesting that other factors may play important roles. We show that peak flowering time shifts earlier for most species when we experimentally reduce plant diversity. Additionally, peak flowering times of plant species are more evenly distributed across the season in high-diversity plots. Overall, these results demonstrate the importance of biotic interactions in influencing flowering times and indicate that advancing phenology, one of the most well-described and well-publicized phenomena linking global warming to plant communities, may result equally from biodiversity declines. Observational studies and experimental evidence agree that rising global temperatures have altered plant phenology—the timing of life events, such as flowering, germination, and leaf-out. Other large-scale global environmental changes, such as nitrogen deposition and altered precipitation regimes, have also been linked to changes in flowering times. Despite our increased understanding of how abiotic factors influence plant phenology, we know very little about how biotic interactions can affect flowering times, a significant knowledge gap given ongoing human-caused alteration of biodiversity and plant community structure at the global scale. We experimentally manipulated plant diversity in a California serpentine grassland and found that many plant species flowered earlier in response to reductions in diversity, with peak flowering date advancing an average of 0.6 days per species lost. These changes in phenology were mediated by the effects of plant diversity on soil surface temperature, available soil N, and soil moisture. Peak flowering dates were also more dispersed among species in high-diversity plots than expected based on monocultures. Our findings illustrate that shifts in plant species composition and diversity can alter the timing and distribution of flowering events, and that these changes to phenology are similar in magnitude to effects induced by climate change. Declining diversity could thus contribute to or exacerbate phenological changes attributed to rising global temperatures.
Manifold decoding for neural representations of face viewpoint and gaze direction using magnetoencephalographic data

The main challenge in decoding neural representations lies in linking neural activity to representational content or abstract concepts. The transformation from a neural‐based to a low‐dimensional representation may hold the key to encoding perceptual processes in the human brain. In this study, we developed a novel model by which to represent two changeable features of faces: face viewpoint and gaze direction. These features are embedded in spatiotemporal brain activity derived from magnetoencephalographic data. Our decoding results demonstrate that face viewpoint and gaze direction can be represented by manifold structures constructed from brain responses in the bilateral occipital face area and right superior temporal sulcus, respectively. Our results also show that the superposition of brain activity in the manifold space reveals the viewpoints of faces as well as directions of gazes as perceived by the subject. The proposed manifold representation model provides a novel opportunity to gain further insight into the processing of information in the human brain.
Optimizing virtual reality for all users through gaze-contingent and adaptive focus displays

Significance Wearable displays are becoming increasingly important, but the accessibility, visual comfort, and quality of current generation devices are limited. We study optocomputational display modes and show their potential to improve experiences for users across ages and with common refractive errors. With the presented studies and technologies, we lay the foundations of next generation computational near-eye displays that can be used by everyone. From the desktop to the laptop to the mobile device, personal computing platforms evolve over time. Moving forward, wearable computing is widely expected to be integral to consumer electronics and beyond. The primary interface between a wearable computer and a user is often a near-eye display. However, current generation near-eye displays suffer from multiple limitations: they are unable to provide fully natural visual cues and comfortable viewing experiences for all users. At their core, many of the issues with near-eye displays are caused by limitations in conventional optics. Current displays cannot reproduce the changes in focus that accompany natural vision, and they cannot support users with uncorrected refractive errors. With two prototype near-eye displays, we show how these issues can be overcome using display modes that adapt to the user via computational optics. By using focus-tunable lenses, mechanically actuated displays, and mobile gaze-tracking technology, these displays can be tailored to correct common refractive errors and provide natural focus cues by dynamically updating the system based on where a user looks in a virtual scene. Indeed, the opportunities afforded by recent advances in computational optics open up the possibility of creating a computing platform in which some users may experience better quality vision in the virtual world than in the real one.
Communicating the deadly consequences of global warming for human heat stress

Significance Extremely hot weather can have deadly human consequences. As the climate warms, the frequency and intensity of such conditions are expected to increase—among the most certain negative impacts expected under global warming. Concerns about dangerous climate change have encouraged the international community to commit to limiting global temperature changes to below 2 °C above preindustrial. Although lauded as a great achievement to avoid dangerous climate change, we find that, even if such aspirations are realized, large increases in the frequency of deadly heat should be expected, with more than 350 million more megacity inhabitants afflicted by midcentury. Such conclusions underline the critical role for ambitious adaptation alongside these climate change mitigation targets. In December of 2015, the international community pledged to limit global warming to below 2 °C above preindustrial (PI) to prevent dangerous climate change. However, to what extent, and for whom, is danger avoided if this ambitious target is realized? We address these questions by scrutinizing heat stress, because the frequency of extremely hot weather is expected to continue to rise in the approach to the 2 °C limit. We use analogs and the extreme South Asian heat of 2015 as a focusing event to help interpret the increasing frequency of deadly heat under specified amounts of global warming. Using a large ensemble of climate models, our results confirm that global mean air temperature is nonlinearly related to heat stress, meaning that the same future warming as realized to date could trigger larger increases in societal impacts than historically experienced. This nonlinearity is higher for heat stress metrics that integrate the effect of rising humidity. We show that, even in a climate held to 2 °C above PI, Karachi (Pakistan) and Kolkata (India) could expect conditions equivalent to their deadly 2015 heatwaves every year. With only 1.5 °C of global warming, twice as many megacities (such as Lagos, Nigeria, and Shanghai, China) could become heat stressed, exposing more than 350 million more people to deadly heat by 2050 under a midrange population growth scenario. The results underscore that, even if the Paris targets are realized, there could still be a significant adaptation imperative for vulnerable urban populations.
Videogames for Emotion Regulation: A Systematic Review.

INTRODUCTION Emotion regulation (ER) supports multiple individual functions and promotes mental health and wellbeing. Among the tools that may be used to help people in managing their affective states, videogames are reaching attention and are showing positive effects. Yet, little is known about their effectiveness. OBJECTIVE This study aims to assess the amount and quality of studies investigating the effects and modalities of the use of videogames for ER. MATERIALS AND METHODS A systematic literature search according to PRISMA guidelines was performed. Subsequently, according to expert advice other few studies have been added. RESULTS Twenty-three studies met the inclusion criteria and were included in the review; they can be categorized into three groups, namely (1) cross-sectional and qualitative studies, (2) experimental studies investigating the effects of videogame experience on ER and (3) ER intervention with serious games. DISCUSSION Discussion of the reviewed studies highlights that frequent gaming with commercial games offers more opportunities for ER improvement (related to gameplay and enjoyment of fictional properties) than limited-time experiences, such as those supported by bespoke serious games. This research area is still in its infancy and findings need to be interpreted with caution; furthermore, future reviews are encouraged to include clinical populations. CONCLUSION Videogames offer several opportunities for ER and a challenge for educational and psychological interventions.
Larval aquatic insect responses to cadmium and zinc in experimental streams

To evaluate the risks of metal mixture effects to natural stream communities under ecologically relevant conditions, the authors conducted 30‐d tests with benthic macroinvertebrates exposed to cadmium (Cd) and zinc (Zn) in experimental streams. The simultaneous exposures were with Cd and Zn singly and with Cd+Zn mixtures at environmentally relevant ratios. The tests produced concentration–response patterns that for individual taxa were interpreted in the same manner as classic single‐species toxicity tests and for community metrics such as taxa richness and mayfly (Ephemeroptera) abundance were interpreted in the same manner as with stream survey data. Effect concentrations from the experimental stream exposures were usually 2 to 3 orders of magnitude lower than those from classic single‐species tests. Relative to a response addition model, which assumes that the joint toxicity of the mixtures can be predicted from the product of their responses to individual toxicants, the Cd+Zn mixtures generally showed slightly less than additive toxicity. The authors applied a modeling approach called Tox to explore the mixture toxicity results and to relate the experimental stream results to field data. The approach predicts the accumulation of toxicants (hydrogen, Cd, and Zn) on organisms using a 2‐pKa bidentate model that defines interactions between dissolved cations and biological receptors (biotic ligands) and relates that accumulation through a logistic equation to biological response. The Tox modeling was able to predict Cd+Zn mixture responses from the single‐metal exposures as well as responses from field data. The similarity of response patterns between the 30‐d experimental stream tests and field data supports the environmental relevance of testing aquatic insects in experimental streams. Environ Toxicol Chem 2017;36:749–762. Published 2016 Wiley Periodicals Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America.
Exploring the Hype: Investigating Technology Acceptance Factors of Pokémon Go

We investigate the technology acceptance factors of the AR smart-phone game Pokémon Go with a PLS-SEM approach based on the UTAUT2 model by Venkatesh et al. [1]. Therefore, we conducted an online study in Germany with 683 users of the game. Many other studies rely on the users' imagination of the application's functionality or laboratory environments. In contrast, we asked a relatively large user base already interacting in the natural environment with the application. Not surprisingly, the strongest predictor of behavioral intention to play Pokémon Go is hedonic motivation, i.e. fun and pleasure due to playing the game. Additionally, we find medium-sized effects of effort expectancy on behavioral intention, and of habit on behavioral intention and use behavior. These results imply that AR applications — besides needing to be easily integrable in the users' daily life — should be designed in an intuitive and easily understandable way. We contribute to the understanding of the phenomenon of Pokémon Go by investigating established acceptance factors that potentially fostered the massive adoption of the game.
Investigating the Use of a Hybrid Search Strategy for Systematic Reviews

[Background] Systematic Literature Reviews (SLRs) are one of the important pillars when employing an evidence-based paradigm in Software Engineering. To date most SLRs have been conducted using a search strategy involving several digital libraries. However, significant issues have been reported for digital libraries and applying such search strategy requires substantial effort. On the other hand, snowballing has recently arisen as a potentially more efficient alternative or complementary solution. Nevertheless, it requires a relevant seed set of papers. [Aims] This paper proposes and evaluates a hybrid search strategy combining searching in a specific digital library (Scopus) with backward and forward snowballing. [Method] The proposed hybrid strategy was applied to two previously published SLRs that adopted database searches. We investigate whether it is able to retrieve the same included papers with lower effort in terms of the number of analysed papers. The two selected SLRs relate respectively to elicitation techniques (not confined to Software Engineering (SE)) and to a specific SE topic on cost estimation. [Results] Our results provide preliminary support for the proposed hybrid search strategy as being suitable for SLRs investigating a specific research topic within the SE domain. Furthermore, it helps overcoming existing issues with using digital libraries in SE. [Conclusions] The hybrid search strategy provides competitive results, similar to using several digital libraries. However, further investigation is needed to evaluate the hybrid search strategy.
An efficient and secure scheme for smart home communication using identity-based signcryption

Securing communication between users and devices is an important aspect of Internet of Things applications. Although a number of cryptographic schemes have been proposed for securing communication among IoT devices, the ability to handle such schemes, especially with devices that have constrained computing resources, is difficult. Thus, there is a need for a secure and efficient scheme that will protect connections between devices with limited capabilities. For overcoming such constraints, many symmetric and asymmetric cryptographic techniques have been proposed. However, not all of the available cryptographic mechanisms can satisfy all of the security goals. Fortunately, there is a single mechanism that can provide combined security goals with low cost in terms of computation and communication overhead in addition to memory requirement. This technique, known as signcryption, can more efficiently satisfy authentication, integrity and confidentiality than combining encryption and signature schemes. This paper presents an identity-based signcryption scheme for smart home communication. Analysis and evaluation show that, in addition to efficiently providing authentication, the proposed scheme provides integrity and confidentiality as well as the ability to protect communication between devices against possible attacks.
Core Genome Multilocus Sequence Typing for Identification of Globally Distributed Clonal Groups and Differentiation of Outbreak Strains of Listeria monocytogenes

ABSTRACT Many listeriosis outbreaks are caused by a few globally distributed clonal groups, designated clonal complexes or epidemic clones, of Listeria monocytogenes, several of which have been defined by classic multilocus sequence typing (MLST) schemes targeting 6 to 8 housekeeping or virulence genes. We have developed and evaluated core genome MLST (cgMLST) schemes and applied them to isolates from multiple clonal groups, including those associated with 39 listeriosis outbreaks. The cgMLST clusters were congruent with MLST-defined clonal groups, which had various degrees of diversity at the whole-genome level. Notably, cgMLST could distinguish among outbreak strains and epidemiologically unrelated strains of the same clonal group, which could not be achieved using classic MLST schemes. The precise selection of cgMLST gene targets may not be critical for the general identification of clonal groups and outbreak strains. cgMLST analyses further identified outbreak strains, including those associated with recent outbreaks linked to contaminated French-style cheese, Hispanic-style cheese, stone fruit, caramel apple, ice cream, and packaged leafy green salad, as belonging to major clonal groups. We further developed lineage-specific cgMLST schemes, which can include accessory genes when core genomes do not possess sufficient diversity, and this provided additional resolution over species-specific cgMLST. Analyses of isolates from different common-source listeriosis outbreaks revealed various degrees of diversity, indicating that the numbers of allelic differences should always be combined with cgMLST clustering and epidemiological evidence to define a listeriosis outbreak. IMPORTANCE Classic multilocus sequence typing (MLST) schemes targeting internal fragments of 6 to 8 genes that define clonal complexes or epidemic clones have been widely employed to study L. monocytogenes biodiversity and its relation to pathogenicity potential and epidemiology. We demonstrated that core genome MLST schemes can be used for the simultaneous identification of clonal groups and the differentiation of individual outbreak strains and epidemiologically unrelated strains of the same clonal group. We further developed lineage-specific cgMLST schemes that targeted more genomic regions than the species-specific cgMLST schemes. Our data revealed the genome-level diversity of clonal groups defined by classic MLST schemes. Our identification of U.S. and international outbreaks caused by major clonal groups can contribute to further understanding of the global epidemiology of L. monocytogenes.
High contrast imaging and flexible photomanipulation for quantitative in vivo multiphoton imaging with polygon scanning microscope

In this study, we introduce two key improvements that overcome limitations of existing polygon scanning microscopes while maintaining high spatial and temporal imaging resolution over large field of view (FOV). First, we proposed a simple and straightforward means to control the scanning angle of the polygon mirror to carry out photomanipulation without resorting to high speed optical modulators. Second, we devised a flexible data sampling method directly leading to higher image contrast by over 2‐fold and digital images with 100 megapixels (10 240 × 10 240) per frame at 0.25 Hz. This generates sub‐diffraction limited pixels (60 nm per pixels over the FOV of 512 μm) which increases the degrees of freedom to extract signals computationally. The unique combined optical and digital control recorded fine fluorescence recovery after localized photobleaching (r ~10 μm) within fluorescent giant unilamellar vesicles and micro‐vascular dynamics after laser‐induced injury during thrombus formation in vivo. These new improvements expand the quantitative biological‐imaging capacity of any polygon scanning microscope system.
Effects of the Nitrification Inhibitor 3,4-Dimethylpyrazole Phosphate on Nitrification and Nitrifiers in Two Contrasting Agricultural Soils

ABSTRACT The nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) is a powerful tool that can be used to promote nitrogen (N) use efficiency and reduce N losses from agricultural systems by slowing nitrification. Mounting evidence has confirmed the functional importance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in nitrification and N2O production; however, their responses to DMPP amendment and the microbial mechanisms underlying the variable efficiencies of DMPP across different soils remain largely unknown. Here we compared the impacts of DMPP on nitrification and the dynamics of ammonia oxidizers between an acidic pasture soil and an alkaline vegetable soil using a 15N tracing and 13CO2-DNA–stable-isotope probing (SIP) technique. The results showed that DMPP significantly inhibited nitrification and N2O production in the vegetable soil only, and the transient inhibition was coupled with a significant decrease in AOB abundance. No significant effects on the community structure of ammonia oxidizers or the abundances of total bacteria and denitrifiers were observed in either soil. The 15N tracing experiment revealed that autotrophic nitrification was the predominant form of nitrification in both soils. The 13CO2-DNA–SIP results indicated the involvement of AOB in active nitrification in both soils, but DMPP inhibited the assimilation of 13CO2 into AOB only in the vegetable soil. Our findings provide evidence that DMPP could effectively inhibit nitrification through impeding the abundance and metabolic activity of AOB in the alkaline vegetable soil but not in the acidic pasture soil, possibly due to the low AOB abundance or the adsorption of DMPP by organic matter. IMPORTANCE The combination of the 15N tracing model and 13CO2-DNA–SIP technique provides important evidence that the nitrification inhibitor DMPP could effectively inhibit nitrification and nitrous oxide emission in an alkaline soil through influencing the abundance and metabolic activity of AOB. In contrast, DMPP amendment has no significant effect on nitrification or nitrifiers in an acidic soil, potentially owing to the low abundance of AOB and the possible adsorption of DMPP by organic matter. Our findings have direct implications for improved agricultural practices through utilizing the nitrification inhibitor DMPP in appropriate situations, and they emphasize the importance of microbial communities to the efficacy of DMPP.
Targeted therapies in non-small cell lung cancer: a focus on ALK/ROS1 tyrosine kinase inhibitors

ABSTRACT Introduction: Anaplastic lymphoma kinase (ALK) and ROS1 rearrangements define important molecular subgroups of advanced non-small cell lung cancer (NSCLC). The identification of these genetic driver alterations created new potential for highly active therapeutic interventions. After discovery of ALK rearrangements in NSCLC, it was recognized that these confer sensitivity to ALK inhibition. Areas covered: Crizotinib, the first-in-class ALK/ROS1/MET inhibitor, was initially approved as second-line treatment of ALK-positive advanced NSCLC but after this, it was firmly established as the standard first-line therapy for advanced ALK-positive NSCLC. After initial response to crizotinib, tumors inevitably relapse. Next-generation ALK inhibitors, more potent and brain-penetrable than crizotinib, may be effective in re-inducing remissions when cancers are still addicted to ALK. Ceritinib and alectinib are approved for metastatic ALK positive NSCLC patients, while brigatinib received granted accelerated approval by the United States Food and Drug Administration. Regarding ROS1 rearrangement, to date crizotinib is the only ALK-tyrosine kinase inhibitor receiving indication as treatment of ROS1 positive advanced NSCLC. Expert commentary: Although novel ALK-inhibitors are under clinical investigation compared to crizotinib as front-line treatment for ALK-positive NSCLC, nowadays the current standard first-line therapy for these patients is crizotinib. Further research will clarify the best management of ALK-positive NSCLC, above all who progress on first-line crizotinib.