Miracle-dz/UniFAR-FTUs huggingface dataset:
Light and growth form interact to shape stomatal ratio among British angiosperms

In most plants, stomata are located only on the abaxial leaf surface (hypostomy), but many plants have stomata on both surfaces (amphistomy). High light and herbaceous growth form have been hypothesized to favor amphistomy, but these hypotheses have not been rigourously tested together using phylogenetic comparative methods. I leveraged a large dataset including stomatal ratio, Ellenberg light indicator value, growth form, and phylogenetic relationships for 372 species of British angiosperms. I used phylogenetic comparative methods to test how light and/or growth form influence stomatal ratio and density. High light and herbaceous growth form are correlated with amphistomy, as predicted, but they also interact; the effect of light is pronounced in therophytes (annuals) and perennial herbs, but muted in phanerophytes (shrubs and trees). Furthermore, amphistomy and stomatal density evolve together in response to light. Comparative analyses of British angiosperms reveal two major insights into physiological evolution. First, light and growth form interact to shape variation in stomatal ratio; amphistomy is common under high light, but mostly for herbs. Second, coordinated evolution of adaxial stomatal density and light tolerance indicates that amphistomy is an important adaptation to optimally balance light acquisition with gas exchange. These results advance our understanding of why stomatal ratio evolves and its potential as a functional trait for paleoecology and crop improvement.
Computation is concentrated in rich clubs of local cortical neurons

To understand how neural circuits process information, it is essential to identify the relationship between computation and circuit topology. Rich-clubs, highly interconnected sets of neurons, are known to propagate a disproportionate amount of information within cortical circuits. Here, we test the hypothesis that rich-clubs also perform a disproportionate amount of computation. To do so, we recorded the spiking activity of on average ∼300 well-isolated individual neurons from organotypic cortical cultures. We then constructed weighted, directed networks reflecting the effective connectivity between the neurons. For each neuron, we quantified the amount of computation it performed based on its inputs. We found that rich-club neurons compute ∼200% more information than neurons outside of the rich club. Indeed, the amount of computation performed in the rich-club was proportional to the amount information propagation by the same neurons. This suggests that, in these circuits, information propagation drives computation. Comparing the computation-to-propagation ratio inside versus outside of the rich club showed that rich clubs compute at a slightly, though significantly, reduced level (∼4% lower). In total, our findings indicate that rich club topology in effective cortical circuits supports not only information propagation but also neural computation. AUTHOR SUMMARY Here we answer the question of whether rich club topology in functional cortical circuits supports neural computation as it has been previously shown to do for information propagation. To do so, we combined network analysis with information theoretic tools to analyze the spiking activity of hundreds of neurons recorded from organotypic cultures of mouse somatosensory cortex. We found that neurons in rich clubs computed significantly more than neurons outside of rich clubs, suggesting that rich-clubs do support computation in cortical circuits. Indeed, the amount of computation that we found in the rich club was proportional to the amount of information they propagate suggesting that, in these circuits, information propagation drives computation.
A new proposal for high capacity voice cellular communications

Slotted ALOHA is proposed as a multiple access scheme for high capacity voice cellular communications. In real-world conditions of propagation (fading environment), its performance is evaluated, both on mobile-to-base and on base-to-mobile channels. The analysis shows that the proposed system exhibits remarkable performance when compared with fixed-assignment techniques, and that it can perform even better than code division multiple access (CDMA), which is currently considered to be the most efficient multiple access scheme. <<ETX>>
An ultralight head-mounted camera system integrates detailed behavioral monitoring with multichannel electrophysiology in freely moving mice

Breakthroughs in understanding the neural basis of natural behavior require neural recording and intervention to be paired with high-fidelity multimodal behavioral monitoring. An extensive genetic toolkit for neural circuit dissection, and well-developed neural recording technology, make the mouse a powerful model organism for systems neuroscience. However, methods for high-bandwidth acquisition of behavioral signals in mice remain limited to fixed-position cameras and other off-animal devices, complicating the monitoring of animals freely engaged in natural behaviors. Here, we report the development of an ultralight head-mounted camera system combined with head-movement sensors to simultaneously monitor eye position, pupil dilation, whisking, and pinna movements along with head motion in unrestrained, freely behaving mice. The power of the combined technology is demonstrated by observations linking eye position to head orientation; whisking to non-tactile stimulation; and, in electrophysiological experiments, visual cortical activity to volitional head movements.
Laminar-specific cortical dynamics in human visual and sensorimotor cortices

Lower frequency, feedback, activity in the alpha and beta range is thought to predominantly originate from infragranular cortical layers, whereas feedforward signals in the gamma range stem largely from supragranular layers. Distinct anatomical and spectral channels may therefore play specialized roles in communication within hierarchical cortical networks; however, empirical evidence for this organization in humans is limited. We leverage high precision MEG to test this proposal, directly and non-invasively, in human participants during visually guided actions. Visual alpha activity mapped onto deep cortical laminae, whereas visual gamma activity predominantly arose from superficial laminae. This laminar-specificity was echoed in sensorimotor beta and gamma activity. Visual gamma activity scaled with task demands in a way compatible with feedforward signaling. For sensorimotor activity, we observed a more complex relationship with feedback and feedforward processes. Distinct frequency channels thus operate in a laminar-specific manner, but with dissociable functional roles across sensory and motor cortices.
Gating by induced α-γ asynchrony in selective attention

Visual selective attention operates through top-down mechanisms of signal enhancement and suppression, mediated by α-band oscillations. The effects of such top-down signals on local processing in primary visual cortex (V1) remain poorly understood. In the present work, we characterize the interplay between large-scale interactions and local activity changes in V1 that orchestrates selective attention, using Granger-causality and phase-amplitude coupling (PAC) analysis of EEG source signals. The task required participants to either attend to or ignore oriented gratings. Results from time-varying, directed connectivity analysis revealed frequency specific effects of attentional selection: bottom-up γ-band influences from visual areas increased rapidly in response to attended stimuli while distributed top-down α-band influences originated from parietal cortex in response to ignored stimuli. Importantly, the results revealed a critical interplay between top-down parietal signals and α-γ PAC in visual areas. Parietal α-band influences disrupted the α-γ coupling in visual cortex, which in turn reduced the amount of γ-band outflow from visual areas. Our results are a first demonstration of how directed interactions affect cross-frequency coupling in downstream areas depending on task demands. These findings suggest that parietal cortex realizes selective attention by disrupting cross-frequency coupling at target regions, which prevents them from propagating task-irrelevant information. Significance statement In the present work, we demonstrated how selective attention emerges from the interplay between large-scale brain interactions and local structures of information processing in sensory areas. When visual input is relevant, the visual cortex rapidly propagates attended information through feedforward oscillations in the gamma band. When stimuli are irrelevant, however, the parietal cortex suppresses information processing through inhibitory influences in the alpha band. Importantly, we show that alpha activity from parietal cortex disrupts the coupling between low and high frequencies in visual regions, which in turn, determines their amount of feedforward propagation. Our results provide novel insight into how the brain orchestrates selective attention and reveal how the parietal cortex prevents the processing of irrelevant information in other cortical areas.
Selection and neutral mutations drive pervasive mutability losses in long-lived B cell lineages

High-affinity antibodies arise within weeks of infection from the evolution of B cell receptors under selection to improve antigen recognition. This rapid adaptation is enabled by the frequency and distribution of highly mutable “hotspotx” motifs in B cell receptor genes. High mutability in antigen binding regions (CDRs) creates variation in binding affinity, whereas low mutability in structurally important regions (FRs) may reduce the frequency of destabilizing mutations. During the response, the loss of mutational hotspots and changes in their distribution across CDRs and FRs are predicted to compromise the adaptability of B cell receptors, yet the contributions of different mechanisms to gains and losses of hotspots remain unclear. We reconstructed changes in anti-HIV B cell receptor sequences and show that mutability losses were about 60% more frequent than gains in both CDRs and FRs, with the higher relative mutability of CDRs maintained throughout the response. At least 34% of the mutability losses were caused by synonymous mutations. However, non-synonymous substitutions caused most of the mutability loss in CDRs. Because CDRs also show strong positive selection, this result suggests positive selection contributed to as much as 66% of the mutability loss in those regions. Although recurrent adaptation to the evolving virus could indirectly select for high mutation rates, we found no evidence of indirect selection to increase or retain hotspots. Our results suggest mutability losses are intrinsic to the neutral and adaptive evolution of B cell populations and might constrain their adaptation to rapidly evolving pathogens such as HIV and influenza.
Pivotal roles of PCNA loading and unloading on heterochromatin function

In Saccharomyces cerevisiae, heterochromatin structures required for transcriptional silencing of the HML and HMR loci are duplicated in coordination with passing DNA replication forks. Despite major reorganization of chromatin structure, the heterochromatic, transcriptionally-silent states of HML and HMR are successfully maintained throughout S-phase. Mutations of specific components of the replisome diminish the capacity to maintain silencing of HML and HMR through replication. Similarly, mutations in histone chaperones involved in replication-coupled nucleosome assembly reduce gene silencing. Bridging these observations, we determined that the PCNA unloading activity of Elg1 was important for coordinating DNA replication forks with the process of replication-coupled nucleosome assembly to maintain silencing of HML and HMR through S-phase. Collectively these data identified a mechanism by which chromatin reassembly is coordinated with DNA replication to maintain silencing through S-phase. SIGNIFICANCE STATEMENT DNA replication poses a unique logistical challenge for the cell in that structural features of chromatin and their regulatory functions must be carefully coordinated with passage of replication machinery so faithful duplication of both the genome and its chromatin structures may be achieved. Nucleosome assembly is fundamental to reestablishment of chromatin in the wake of DNA replication, and here a mechanism by which nucleosome assembly is coordinated with DNA replication to maintain silenced chromatin is described.
IMPORTANCE OF WOOD DRYING TO THE FOREST TRANSPORT AND PULP MILL SUPPLY

The forest transportation represents a great proportion of raw material cost for pulp and paper production and, for this reason, the wood moisture content should be low to reduce these cost. The objective was to relate the wood moisture with fuel consumption per kilometer in each vehicle and the number of trips to supply a pulp mill. Three trees of
Synchronization of Digital Telecommunications Networks

From the Publisher: Network synchronization deals with the distribution of time and frequency across a network of clocks often spread over a wide geographical area. The goal is to align (i.e. synchronize) the time and frequency scales of all clocks, by using the communication capacity of their interconnecting links. Network synchronization plays a central role in digital telecommunications as it determines the quality of most services offered by the network operator. However, the importance of network synchronization is often underestimated and how to solve quality-of-service degradation caused by synchronization difficulties can become problematical to all but a synchronization engineer. Systematically covers a wide spectrum of both theoretical and practical topics Features a clear and profound description of synchronous and asynchronous digital multiplexing (PDH, SDH), jitter and timing aspects of SDH networks Expounds synchronization network principles and implementation issues, clock modelling, time and frequency measurement Presents recent advances in telecommunications clock characterization and measurement If you are a system engineer, researcher, designer or postgraduate student searching for both the basics and an insight into more advanced areas currently under discussion then you will find Synchronization of Digital Telecommunications Networks an enlightening read. It will also prove to be a valuable sourcebook for senior undergraduates and technical personnel in telecommunications companies.
Detecting environment-dependent diversification from phylogenies: a simulation study and some empirical illustrations

Understanding the relative influence of various abiotic and biotic variables on diversification dynamics is a major goal of macroevolutionary studies. Recently, phylogenetic approaches have been developed that make it possible to estimate the role of various environmental variables on diversification using time-calibrated species trees, paleoenvironmental data, and maximum-likelihood techniques. These approaches have been effectively employed to estimate how speciation and extinction rates vary with key abiotic variables, such as temperature and sea level, and we can anticipate that they will be increasingly used in the future. Here we compile a series of biotic and abiotic paleodatasets that can be used as explanatory variables in these models and use simulations to assess the statistical properties of the approach when applied to these paleodatasets. We demonstrate that environment-dependent models perform well in recovering environment-dependent speciation and extinction parameters, as well as in correctly identifying the simulated environmental model when speciation isenvironment-dependent. We explore how the strength of the environment-dependency, tree size, missing taxa, and characteristics of the paleoenvironmental curves influence the performance of the models. Finally, using these models, we infer environment-dependent diversification in three empirical phylogenies: temperature-dependence in Cetacea, δ13C-dependence in Ruminantia, and CO2-dependence in Portulacaceae. We illustrate how to evaluate the relative importance of abiotic and biotic variables in these three clades and interpret these results in light of macroevolutionary hypotheses for mammals and plants. Given the important role paleoenvironments are presumed to have played in species evolution, our statistical assessment of how environment-dependent models behave is crucial for their utility in macroevolutionary analysis.
A Randomized Trial to Assess the Effect of Fluoroquinolone Metaphylaxis on the Fecal Prevalence and Quinolone Susceptibilities of Salmonella and Campylobacter in Feedlot Cattle.

Abstract The study objective was to determine effects of fluoroquinolone metaphylaxis on fecal prevalence of Salmonella and Campylobacter and fecal prevalence of quinolone-resistant Salmonella and Campylobacter in feedlot cattle. On Day 0, cattle (n = 288) at risk for bovine respiratory disease (BRD) were randomly assigned to either a nontreated control pen (12 pens) or a fluoroquinolone-treated (enrofloxacin; Baytril® 100) pen (12 pens). Rectal fecal samples were collected from cattle on days 0, 7, 14, 21, and 28. Feces were cultured for Salmonella enterica and Campylobacter spp. using enrichment and selective isolation methods, and confirmed by serology and PCR. Susceptibilities to nalidixic acid and ciprofloxacin were determined using microbroth dilution methods. Data analyses were performed using linear mixed models. Overall, Salmonella sp. and Campylobacter spp. were recovered from 10.2% (139/1,364) and 12.4% (170/1,364) of the fecal samples, respectively. Campylobacter species included hyointestinal.
Response of two wheat cultivars (triticum aestivum l) to amended nitrogen fertilizer on yield and grain quality in halfa elgadidah area

Although, Sudan is considered as a marginal area of wheat production, the wheat crop ranks second after sorghum and now has become a strategic crop due to the shortage of food in the world and to the drastic change in the consumption habit of the people in Sudan.1,2 Wheat is the main crop that provides protein and carbohydrates for many people.3 After cultivars, nitrogenous fertilizer is the second most important input for wheat crop growth and development.4 Although significant achievements have been made in production of wheat yield over the past several decades, requirements for higher-quality wheat have also increased as life styles have improved.5 Wheat production in Sudan is restricted by soil deficiencies in plant nutrients (especially nitrogen). Consequently adequate levels of nitrogen (N) fertilizer are needed.6 Different studies have showed that decreasing N levels decreased grains yield per unit area in wheat. The importance of N fertilization in increasing wheat production has been well documented by many workers7,8 but still it is difficult to determine the quantities to apply with organic manure. On the other hand, application of organic manure has become an important tool used to increase crop yields and grain quality in intensive agricultural systems.9 Thus combined application of organic manure and nitrogen fertilizer can increase crop productivity through improving the chemical, physical and biological properties and nutrient status of the soil. The quantity and quality of cereal yields depend on the interacting numerous factors. One of these factors is the yield potential, which is manifested different areas under various growing conditions, depending on the adaptability of variety to unfavorable climatic conditions. Therefore, the best option for wheat production, yield improvement and yield stability under favorable fertilization is to use specific high yielding wheat cultivars. In view of the above reasons it was imperative to conduct experiment involving different wheat cultivars with regard to their response to low and high N nitrogen levels with or without chicken manure in order to obtain the potential grain yield of these cultivars. These factors interrelate providing an important insight to the study of their interaction on wheat production. Keeping these in view, an experiment was planned to study the effects of cultivars and nitrogen levels with or without chicken manure on yield and grain protein content of wheat.
In vitro transcribed guide RNAs trigger an innate immune response via the RIG-I pathway

CRISPR-Cas9 genome editing is revolutionizing fundamental research and has great potential for the treatment of many diseases. While editing of immortalized cell lines has become relatively easy, editing of therapeutically relevant primary cells and tissues can remain challenging. One recent advancement is the delivery of a Cas9 protein and an in vitro transcribed (IVT) guide RNA (gRNA) as a precomplexed ribonucleoprotein (RNP). This approach allows editing of primary cells such as T cells and hematopoietic stem cells, but the consequences beyond genome editing of introducing foreign Cas9 RNPs into mammalian cells are not fully understood. Here we show that the IVT gRNAs commonly used by many laboratories for RNP editing trigger a potent innate immune response that can be several thousand times stronger than benchmark immune stimulating ligands. IVT gRNAs are recognized in the cytosol through the RIG-I pathway but not the MDA5 pathway, thereby triggering a type I interferon response. Removal of the 5’-triphosphate from gRNAs ameliorates inflammatory signaling and prevents the loss of viability associated with genome editing in hematopoietic stem cells. The potential for Cas9 RNP editing to induce a potent antiviral response indicates that care must be taken when designing therapeutic strategies to edit primary cells. Abbreviations Cas CRISPR-associated CIP calf intestinal alkaline phosphatase CRISPR clustered, regularly interspaced, short palindromic repeat dCas9 nuclease-dead Cas9 HEK293 Human embryonic kidney cells 293 HEK293T Human embryonic kidney cells 293 SV40 large T antigen HeLa Henrietta Lacks cells HSPCs CD34+ human hematopoietic stem and progenitor cells IFNAR1 Interferon Alpha And Beta Receptor Subunit 1 IFNβ/IFNB1 Interferon beta ISG15 Interferon-stimulated gene 15 IVT – in vitro transcribed KO knockout MAVS mitochondrial activator of virus signaling MDA5/IFIH1 melanoma differentiation-associated gene 5/ Interferon Induced with Helicase C Domain 1 PAMP pathogen-associated molecular pattern RIG-I/DDX58 retinoic acid-inducible gene I/ DExD-H-box helicase 58 gRNA guide RNA SPRI solid phase reversible immobilization WT wild type