Miracle-dz/UniFAR-FTUs huggingface dataset:
Disentangling the effects of climate change, landscape heterogeneity, and scale on phenological metrics

Phenology, the study of the timing of cyclical life history events and seasonal changes, is a fundamental aspect of how individual species, communities, and ecosystems will respond to climate change. Both biotic and abiotic phenological patterns are changing rapidly in response to changing seasonal temperatures and other climate-related drivers, and the consequences of these shifts for individual species and entire ecosystems are largely unknown. Landscape-scale simulations can address some of these needs for better predictions by demonstrating how phenology measures can vary with spatial and temporal grain of observations, and how phenological responses can vary with landscape heterogeneity and climate drivers. To explicitly examine the spatial and temporal scale-dependence of multiple phenology measures, we constructed simulated landscapes populated by virtual plant species with realistic phenologies and environmental sensitivities. This enabled us to examine phenology measures and environmental sensitivities along a continuum of spatial and temporal grains, while also controlling other aspects of sampling design. By relating measures of phenology calculated at a given spatiotemporal grain to average environmental conditions at that same grain size, we are able to determine observed environmental sensitivities for multiple phenological metrics at that spatial and temporal scale. We demonstrate that different phenological events change distinctly and predictably with spatial and temporal measurement scale, opening the way to incorporating scaling laws into predictions. Using plant flowering as our example, we identify that the timing of the beginnings or ends of an event (e.g., First Flower date, Last Flower date), can be especially sensitive to the spatial and temporal grain (or resolution) of observations. Our work provides an initial assessment of the role of observation scale in landscape phenology, and a general approach for incorporating scale-dependence into predictions of a variety of phenological time series.
Vertical distribution of deuterium in atmospheric water vapour: problems in application to assess atmospheric condensation models

The paper assesses the use of the author’s data by Rozanski and Sonntag to support a multi-boxmodel of the vertical distribution of deuterium in atmospheric water vapour, in which exchangebetween vapour and falling precipitation produces a steeper deuterium concentration profile thansimpler condensation models. The mean deuterium/altitude profile adopted by Rozanski andSonntag for this purpose is only one of several very different mean profiles obtainable from thedata by arbitrary selection and weighting procedures: although it can be made to match :hespecified multi-box model calculations for deuterium. there is a wide discrepancy between theactual and model mean mixing ratio profiles which cannot be ignored. Taken together. the mixingratio and deuterium profiles indicate that mean vapour of the middle troposphere has beensubjected to condensation at greater heights and lower temperatures than those considered in themodel calculations. When this is taken into account, the data actually fit much better to thesimpler condensation models. But the vapour samples represent meteorological situations tooremote in time from primary precipitation events to permit definite conclusions on cloud systemmechanisms. DOI: 10.1111/j.1600-0889.1984. tb00053.x
Ground cover presence in organic olive orchards affects the interaction of natural enemies against Prays oleae, promoting an effective egg predation

The olive moth, Prays oleae, is one of the most common insects that damages olives in the Mediterranean region. The establishment of ground cover within olive orchards has been promoted in this region in recent years to avoid erosion and soil degradation. Nevertheless, its role as a shelter for natural enemies of pests has been controversial. In this study, we have investigated the effectiveness of the biological control of P. oleae in organic olive orchards with ground cover (mowed) and without ground cover (tilled). For this, (1) we assessed the relationship between predated eggs and the abundance of natural enemies in both types of orchards; (2) we compared both the potential damage of the pest and the egg hatching in the two types of orchards; and (3) we examined the interaction amongst families of natural enemies and P. oleae (as adults and as predated eggs). The results showed that there is a high rate of predation in the studied olive orchards, 81% of the eggs were predated, 12.2% hatched, and 6.9% were live eggs. However, mowed orchards were more effective for controlling P. oleae by means of egg predation rather than tilled orchards, i.e., in mowed orchards, whilst the potential damage of the pest was higher, egg hatching was rather low. The structure of the adult arthropod community, i.e., the composition and abundance of families of natural enemies did not differ between the orchards, but the abundance of the families Anthocoridae, Miridae and Scelionidae was significantly higher in the mowed orchards. Finally, the interaction amongst natural enemies and P. oleae showed that the families that better explained the effects on egg predation were Aeolothripidae, Anthocoridae, Miridae, Chrysopidae (predators), and Formicidae (omnivore). We discuss the results in terms of ecological interactions of trophic guilds and we conclude that the establishment and maintenance of ground cover in organic olive orchards, at least in June and July, is of great significance because it positively affects the egg predation of P. oleae. This effect is especially significant when there is a low abundance of natural enemies in the olive orchards.
Age-related susceptibility to insulin resistance is due to a combination of CPT1B decline and lipid overload

BACKGROUND Advanced age increases the susceptibility to diet-induced insulin resistance (IR). A key driver of this phenomenon is lipid accumulation in the skeletal muscle. It is debated, however, whether this is due to dietary lipid overload or decline of mitochondrial function. To address the interplay of diet and age in the flexibility of muscle lipid and glucose handling, we put young and aged mice on a low- or high-fat diet (HFD). RESULTS As expected, aged mice were more susceptible to IR when given a HFD than young mice. The HFD induced intramuscular lipid accumulation specifically in aged mice, including C18:0-containing ceramides and diacylglycerols. This was reflected by the mitochondrial β-oxidation capacity, which was upregulated by the HFD in young, but not in old mice. Conspicuously, most β-oxidation proteins were upregulated by the HFD in both groups, but carnitine palmitoyltransferase 1B (CPT1B) declined in aged animals. Computational modelling traced the flux control mostly to CPT1B, suggesting a CPT1B-driven loss of flexibility to the HFD with age. Finally, in old animals glycolytic protein levels were reduced and less flexible to the diet. CONCLUSION We conclude that intramuscular lipid accumulation and decreased insulin sensitivity are not due to age-related mitochondrial dysfunction or nutritional overload alone, but rather to their interaction. Moreover, we identify CPT1B as a potential target to counteract age-dependent intramuscular lipid accumulation and thereby IR.
A survey of Aflatoxin M1 in some commercial milk samples and infant formula milk samples in Goa, India

A survey of aflatoxin M1 (AFM1) contamination in packaged milk and infant formula milk samples in the Goan market, India, was conducted using high performance liquid chromatography, association of analytical communities approved commercial kit and a sensitive chemiluminescent sandwich enzyme-linked immunosorbent assay (ELISA). A total of 72 samples of infant formula milk food (18) and packaged milk samples (54) was analysed. One hundred per cent of the analysed samples exceeded the European Communities recommended limits (50 ng/L) and 75% of the samples exceeded Codex Alimentarius, Food Safety and Standards Authority of India (FSSAI) and US Food and Drug Administration recommended limits (500 ng/L). The range of contamination of AFM1 was found lower in infant milk formula (501–713 ng/L) than liquid milk (511–809 ng/L). The methods were also compared for their performance, and ELISA was found to be most suitable for analysis of low-level AFM1 contamination in milk.
Multi-Modal Generative Adversarial Networks Make Realistic and Diverse but Untrustworthy Predictions When Applied to Ill-posed Problems

Ill-posed problems can have a distribution of possible solutions rather than a unique one, where each solution incorporates signiﬁcant features not present in the initial input. We investigate whether cycle-consistent generative neural network models based on generative adversarial networks (GANs) and variational autoencoders (VAEs) can properly sample from this distribution, testing on super-resolution of highly down-sampled images. We are able to produce diverse and plausible predictions, but, looking deeper, we ﬁnd that the statistics of the generated distributions are substantially wrong. This is a critical ﬂaw in applications that require any kind of uncertainty quantiﬁcation. We trace this to the fact that these models cannot easily learn a bijective, invertible map between the latent space and the target distribution. Additionally, we describe a simple method for constraining the distribution of a deterministic encoder’s outputs via the Kullback-Leibler divergence without the reparameterization trick used in VAEs.
Security Analysis of Out-of-Band Device Pairing Protocols: A Survey

Numerous secure device pairing (SDP) protocols have been proposed to establish a secure communication between unidentified IoT devices that have no preshared security parameters due to the scalability requirements imposed by the ubiquitous nature of the IoT devices. In order to provide the most user-friendly IoT services, the usability assessment has become the main requirement. Thus, the complete security analysis has been replaced by a sketch of a proof to partially validate the robustness of the proposal. The few existing formal or computational security verifications on the SDP schemes have been conducted based on the assessment of a wide variety of uniquely defined security properties. Therefore, the security comparison between these protocols is not feasible and there is a lack of a unified security analysis framework to assess these pairing techniques. In this paper, we survey a selection of secure device pairing proposals that have been formally or computationally verified. We present a systematic description of the protocol assumptions, the adopted verification model, and an assessment of the verification results. In addition, we normalize the used taxonomy in order to enhance the understanding of these security validations. Furthermore, we refine the adversary capabilities on the out-of-band channel by redefining the replay capability and by introducing a new notion of delay that is dependent on the protocol structure that is more adequate for the ad hoc pairing context. Also, we propose a classification of a number of out-of-band channels based on their security properties and under our refined adversary model. Our work motivates the future SDP protocol designer to conduct a formal or a computational security assessment to allow the comparability between these pairing techniques. Furthermore, it provides a realistic abstraction of the adversary capabilities on the out-of-band channel which improves the modeling of their security characteristics in the protocol verification tools.
Heterogeneous nuclear ribonucleoprotein K is overexpressed in acute myeloid leukemia

7 Affiliations: 8 Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 9 USA 10 The University of Texas MD Anderson Cancer Center UTHealth Graduate School of 11 Biomedical Sciences, Houston, TX, USA 12 School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, 13 TX, USA 14 Baylor College of Medicine, Houston, TX, USA 15 Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer 16 Center, Houston, TX, USA 17 Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 18 Houston, TX, USA 19 *These authors contributed equally 20 **To whom correspondence should be addressed 21
Diffusion of the disordered E-cadherin tail on β-catenin

Specific protein interactions typically require well-shaped binding interfaces. Here, we report a cunning exception. The disordered tail of the cell-adhesion protein E-cadherin dynamically samples a large surface area of the proto-oncogene β-catenin. Single-molecule experiments and molecular simulations resolve these motions with high resolution in space and time. Contacts break and form within hundreds of microseconds without dissociation of the complex. A few persistent interactions provide specificity whereas unspecific contacts boost affinity. The energy landscape of this complex is rugged with many small barriers (3 – 4 kBT) and reconciles specificity, high affinity, and extreme disorder. Given the roles of β-catenin in cell-adhesion, signalling, and cancer, this Velcro-like design has the potential to tune the stability of the complex without requiring dissociation.
Photosynthesis dynamics and regulation sensed in the frequency domain

Foundations of photosynthesis research have been established mainly by studying the response of plants to changing light, typically to sudden exposure to a constant light intensity after a dark acclimation or light flashes. This approach remains valid and powerful, but can be limited by requiring dark acclimation before time-domain measurements and often assumes that rate constants determining the photosynthetic response do not change between the dark- and light-acclimation. We present experimental data and mathematical models demonstrating that these limits can be overcome by measuring plant responses to sinusoidally modulated light of varying frequency. By its nature, such frequency-domain characterization is performed in light-acclimated plants with no need for prior dark acclimation. Amplitudes, phase shifts, and upper harmonic modulation extracted from the data for a wide range of frequencies can target different kinetic domains and regulatory feedbacks. The occurrence of upper harmonic modulation reflects non-linear phenomena, including photosynthetic regulation. To support these claims, we present a frequency- and time-domain response in chlorophyll fluorescence emission of the green alga Chlorella sorokiniana in the frequency range 1000 – 0.001 Hz. Based on these experimental data and numerical as well as analytical mathematical models, we propose that frequency-domain measurements can become a versatile new tool in plant sensing. One sentence summary It is proposed to characterize photosynthesis in the frequency domain without the need for dark adaptation and, thus, without assumptions about the dark-to-light transition.
Macroscopic quantities of collective brain activity during wakefulness and anesthesia

The study of states of arousal is key to understand the principles of consciousness. Yet, how different brain states emerge from the collective activity of brain regions remains unknown. Here, we studied the fMRI brain activity of monkeys during wakefulness and anesthesia-induced loss of consciousness. Using maximum entropy models, we derived collective, macroscopic properties that quantify the system’s capabilities to produce work, to contain information and to transmit it, and that indicate a phase transition from critical awake dynamics to supercritical anesthetized states. Moreover, information-theoretic measures identified those parameters that impacted the most the network dynamics. We found that changes in brain state and in state of consciousness primarily depended on changes in network couplings of insular, cingulate, and parietal cortices. Our findings suggest that the brain state transition underlying the loss of consciousness is predominantly driven by the uncoupling of specific brain regions from the rest of the network.
The molecular clockwork of the suprachiasmatic nucleus is sufficient to co-ordinate phasing and stabilisation of sleep-wake cycles and enhance memory deficits in a clockless mouse

The timing and quality of sleep-wake cycles are regulated by interacting circadian and homeostatic mechanisms. Although the suprachiasmatic nucleus (SCN) is the principal circadian clock, local clocks are active across the brain and the respective sleep-regulatory roles of SCN and extra-SCN clocks are unclear. To determine the specific contribution(s) of the SCN, we used virally mediated genetic complementation, expressing Cryptochrome1 (Cry1) to restore circadian molecular competence to the SCN of globally clockless Cry1/Cry2-null mice. Under free-running conditions, the rest/activity behaviour of Cry1/Cry2-null controls which received EGFP (SCNCon) was arrhythmic, whereas Cry1-complemented mice (SCNCry1) had circadian behaviour comparable to that of Cry1,2-competent wild-types (WT). In SCNCon mice, sleep-wakefulness, assessed by electroencephalography/electromyography, also lacked circadian organisation. In SCNCry1 mice, however, it was comparable to WT, with consolidated vigilance states (wake, REM and NREM sleep) and rhythms in NREMS delta power and expression of REMS within total sleep. Wakefulness in SCNCon mice was more fragmented than in WT, with more wake-NREMS-wake transitions. This disruption was corrected in SCNCry1 mice. Following sleep deprivation, all mice showed an initial homeostatic increase in NREMS delta power. The SCNCon mice, however, had reduced, non-consolidated NREMS during the inactive phase of the recovery period. In contrast, the dynamics of homeostatic responses in the SCNCry1 mice were equivalent to WT. Finally, SCNCon mice exhibited poor sleep-dependent memory but this was corrected in SCNCry1mice. Therefore, the SCN clock is sufficient for circadian control of sleep-wake, facilitating initiation and maintenance of wake, promoting sleep consolidation, homeostatic dynamics, and sleep-dependent memory. Significance statement The circadian timing system regulates sleep-wake cycles. The hypothalamic suprachiasmatic nucleus (SCN) is the principal circadian clock, but local clocks are also active across the brain and the respective roles of SCN and local clocks in regulating sleep are unclear. To determine, explicitly, the contribution of the SCN, we used virally mediated genetic complementation to restore SCN molecular circadian functions in otherwise genetically clockless mice. This initiated circadian activity-rest cycles, accompanied by circadian sleep-wake cycles, circadian patterning to the intensity of NREM sleep and circadian control of REM sleep as a proportion of total sleep. Consolidation of sleep-wake established normal dynamics of sleep homeostasis and enhanced sleep-dependent memory. Thus, the SCN is the principal and sufficient circadian regulator of sleep-wake.
Defining a Connectome-Based Predictive Model of Attentional Control in Aging

With advancing age, declines in the executive control of attention are accompanied by shifts in the functional topology of brain networks. However, there is increasing recognition of the considerable individual variability in the extent and types of attentional deficits that older adults exhibit, with results from neuroimaging investigations paralleling behavioral heterogeneity. Emerging computational methods leverage whole-brain functional connectivity to predict individual-level behaviors. These approaches are well-suited to the cognitive aging context, as they may elucidate configurations of functional connections that best explain group- and individual-level differences across older adults. Two independent samples of neurologically and psychiatrically healthy older adults were used to separately derive a predictive model of attentional control and test the model’s external validity. Here we show that despite challenges posed by heterogeneity in these aging samples, select functional connections carried meaningful variance, allowing for successful prediction of attention in a novel sample of older individuals.
Genomic analyses of 10,376 individuals provides comprehensive map of genetic variations, structure and reference haplotypes for Chinese population

Here, we initiated the Westlake BioBank for Chinese (WBBC) pilot project with 4,535 whole-genome sequencing individuals and 5,481 high-density genotyping individuals. We identified 80.99 million SNPs and INDELs, of which 38.6% are novel. The genetic evidence of Chinese population structure supported the corresponding geographical boundaries of the Qinling-Huaihe Line and Nanling Mountains. The genetic architecture within North Han was more homogeneous than South Han, and the history of effective population size of Lingnan began to deviate from the other three regions from 6 thousand years ago. In addition, we identified a novel locus (SNX29) under selection pressure and confirmed several loci associated with alcohol metabolism and histocompatibility systems. We observed significant selection of genes on epidermal cell differentiation and skin development only in southern Chinese. Finally, we provided an online imputation server (https://wbbc.westlake.edu.cn/) which could result in higher imputation accuracy compared to the existing panels, especially for lower frequency variants.
Modulating the left inferior frontal cortex by task domain, cognitive challenge and tDCS

The left inferior frontal cortex (LIFC) is a key region for spoken language processing, but its neurocognitive architecture remains controversial. Here we assess the domain-generality vs. domain-specificity of the LIFC from behavioural, functional neuroimaging and neuromodulation data. Using concurrent fMRI and transcranial direct current stimulation (tDCS) delivered to the LIFC, we investigated how brain activity and behavioural performance are modulated by task domain (naming vs. non-naming), cognitive challenge (low vs. high), and tDCS (anodal vs. sham). The data revealed: (1) co-existence of neural signatures both common and distinct across tasks within the LIFC; (2) domain-preferential effects of task (naming); (3) significant tDCS modulations of activity in a LIFC sub-region selectively during high-challenge naming. The presence of both domain-specific and domain-general signals, and the existence of a gradient of activation where naming relied more on sub-regions within the LIFC, may help reconcile both perspectives on spoken language processing.
SSNA1 stabilizes dynamic microtubules and detects microtubule damage

Sjögren’s Syndrome Nuclear Autoantigen 1 (SSNA1/NA14) is a microtubule-associated protein with important functions in cilia, dividing cells and developing neurons. However, the direct effects of SSNA1 on microtubules are not known. We employed in vitro reconstitution with purified proteins and TIRF microscopy to investigate the activity of human SSNA1 on dynamic microtubule ends and lattices. We find that SSNA1 modulates all parameters of microtubule dynamic instability – slowing down the rates of growth, shrinkage and catastrophe, and promoting rescue. SSNA1 accumulation on dynamic microtubule ends correlates with the growth rate slow-down. Furthermore, SSNA1 prevents catastrophe when soluble tubulin is removed or sequestered by Op18/Stathmin. Finally, SSNA1 detects spastin-induced damage and inhibits spastin’s severing activity. Therefore, SSNA1 is both a potent microtubule stabilizing protein and a sensor of microtubule damage; activities that likely underlie SSNA1’s cellular functions.