Miracle-dz/UniFAR-FTUs huggingface dataset:
Trait-trait relationships and tradeoffs vary with genome size in prokaryotes

We report genomic traits that have been associated with the life history of prokaryotes and highlight conflicting findings concerning earlier observed trait correlations and tradeoffs. In order to address possible explanations for these contradictions we examined trait-trait variations of 11 genomic traits from ~ 18,000 sequenced genomes. The studied trait-trait variations suggested: (i) the predominance of two resistance and resilience-related orthogonal axes and (ii) at least in free living species with large effective population sizes whose evolution is little affected by genetic drift an overlap between a resilience axis and an axis of resource usage efficiency. These findings imply that resistance associated traits of prokaryotes are globally decoupled from resilience related traits and in the case of free-living communities also from resource use efficiencies associated traits. However, further inspection of pairwise scatterplots showed that resistance and resilience traits tended to be positively related for genomes up to roughly five million base pairs and negatively for larger genomes. This in turn may preclude a globally consistent assignment of prokaryote genomic traits to the competitor - stress-tolerator - ruderal (CSR) schema that sorts species depending on their location along disturbance and productivity gradients into three ecological strategies and may serve as an explanation for conflicting findings from earlier studies. All reviewed genomic traits featured significant phylogenetic signals and we propose that our trait table can be applied to extrapolate genomic traits from taxonomic marker genes. This will enable to empirically evaluate the assembly of these genomic traits in prokaryotic communities from different habitats and under different productivity and disturbance scenarios as predicted via the resistance-resilience framework formulated here.
Chronic Release of Tailless Phage Particles from Lactococcus lactis

In complex microbial consortia such as fermentation starters, bacteriophages can alter the dynamics and diversity of microbial communities. Bacteriophages infecting Lactococcus lactis are mostly studied for their detrimental impact on industrial dairy fermentation processes. ABSTRACT Lactococcus lactis strains residing in the microbial community of a complex dairy starter culture named “Ur” are hosts to prophages belonging to the family Siphoviridae. L. lactis strains (TIFN1 to TIFN7) showed detectable spontaneous phage production and release (109 to 1010 phage particles/ml) and up to 10-fold increases upon prophage induction, while in both cases we observed no obvious cell lysis typically described for the lytic life cycle of Siphoviridae phages. Intrigued by this phenomenon, we investigated the host-phage interaction using strain TIFN1 (harboring prophage proPhi1) as a representative. We confirmed that during the massive phage release, all bacterial cells remain viable. Further, by monitoring phage replication in vivo, using a green fluorescence protein reporter combined with flow cytometry, we demonstrated that the majority of the bacterial population (over 80%) is actively producing phage particles when induced with mitomycin C. The released tailless phage particles were found to be engulfed in lipid membranes, as evidenced by electron microscopy and lipid staining combined with chemical lipid analysis. Based on the collective observations, we propose a model of phage-host interaction in L. lactis TIFN1 where the phage particles are engulfed in membranes upon release, thereby leaving the producing host intact. Moreover, we discuss possible mechanisms of chronic, or nonlytic, release of LAB Siphoviridae phages and its impact on the bacterial host. IMPORTANCE In complex microbial consortia such as fermentation starters, bacteriophages can alter the dynamics and diversity of microbial communities. Bacteriophages infecting Lactococcus lactis are mostly studied for their detrimental impact on industrial dairy fermentation processes. In this study, we describe a novel form of phage-bacterium interaction in an L. lactis strain isolated from a complex dairy starter culture: when the prophages harbored in the L. lactis genome are activated, the phage particles are engulfed in lipid membranes upon release, leaving the producing host intact. Findings from this study provide additional insights into the diverse manners of phage-bacterium interactions and coevolution, which are essential for understanding the population dynamics in complex microbial communities like fermentation starters.
Temporal course of the sign effect in intertemporal choice

ABSTRACT The sign effect in intertemporal choice means that people typically discount delayed gains more than losses. The lack of a sign effect is associated with problematic behaviours, such as debt, obesity, and smoking. This study investigates the temporal course of the sign effect in intertemporal choice using event-related potentials (ERPs). ERP components were recorded and analysed in the evaluation and choice stages of the intertemporal choice task. Behavioural results found that the sign effect in the loss situation yielded a higher rate of immediate choices than in the gain situation. ERP results found that the gain situation elicited a larger P3. However, the loss situation elicited a larger N400 in the choice stage, indicating that loss situations involve more conflict processing. Gain and loss situations were differentiated in their effects on temporal dynamics of neural activity in intertemporal decision-making, extending the knowledge about sign effect temporal processing in intertemporal choice.
Research of the bending loss of S-shaped waveguides with offsets and trenches

S-shaped polymer waveguides are heavily exploited to connect optical components. Reducing the bending loss of S-shaped polymer waveguides is critical for low-loss and small-size optical circuits. In this paper, the S-shaped waveguide with offsets and trenches (SW-OT) is designed. The dependence of the bending loss on crucial parameters like offsets, trench locations and trench widths is analyzed by the beam propagation method. A comparison of the bending loss among standard S-bend, shifted S-bend, S-bend employing trenches and SW-OT structure is conducted. Results show that the bending loss of the SW-OT with a bending radius of 1000μm is only 0.11dB, reducing by 89.70% compared with the S-shaped waveguide with only shifts. Moreover, a dramatic reduction in the bending loss is obtained by placing trenches properly in the curved region. Therefore, the combination of offsets and trenches can effectively decrease the bending loss of low index contrast polymer S-shaped waveguides.
Transition from axisymmetric to three-dimensional turbulence

In purely axisymmetric turbulence sustained by a linear forcing mechanism, a stable, entirely poloidal flow is observed when the toroidal component of the forcing is below a threshold. We investigate using numerical simulations whether this state persists when toroidal variations of the flow are continuously reintroduced and the forcing is purely poloidal. It is shown how the pressure–strain correlation allows the redistribution of the energy towards the toroidal component. A simple statistical model allows to capture the main physical effects on the level of the global energy balance. This model is then used to investigate the stability of the poloidal state for various toroidal-to-poloidal forcing strengths and different degrees of axisymmetry.
On processing maternal absence, dysfunction and traumatic familial disruption in an early adolescent

ABSTRACT This article describes the course of a psychotherapy with a depressed encopretic boy, using a psychoanalytic approach. The therapy was administered in a public welfare clinic in Israel. Based on an understanding of how the boy’s developmental needs had been neglected, an appropriate intervention programme was constructed and implemented. The principal insights determining the course pursued by the psychotherapist included the understanding acquired of the dysfunction and absences within the mother-child relationship during the boy’s early years, and the need for the therapist to provide corrective and containing maternal emotional experiences, together with insight regarding the repercussions on the boy’s emotional life. Additional understanding was gained about the role of the boy’s encopresis, which comprised a symptom, and seemed to be a response to the repressed, unmodulated regressive anger towards the internal maternal figure, owing to the parents’ difficulties in meeting the boy’s primary developmental needs.
Syntheses, crystal structures, and luminescent properties of three metal coordination polymers based on adipic acid and 2-(pyridine-3-yl)-(1H)-benzimidazole

Three new metal coordination polymers constructed from adipic acid and 2-(pyridin-3-yl)-(1H)-benzimidazole ligands, [M(ADP)(3PBI)2(H2O)2]·2H2O (M = Ni and Co for 1 and 2, respectively) and [Cd(ADP)(3PBI)(H2O)] (3) [ADP = adipic acid dianion; 3PBI = 2-(pyridin-3-yl)-(1H)-benzimidazole], have been synthesized by hydrothermal reactions and were characterized by X-ray single-crystal diffraction, elemental analyses, IR, powder X-ray diffraction, and thermogravimetry. Complexes 1 and 2 are isostructural. Both form a 1-D linear chain structure, which is further assembled into a 3-D supramolecular framework by π⋯π stacking and hydrogen bonding interactions. Complex 3 possesses a binuclear unit and displays a 2-D layer which is further extended to a 3-D supramolecular architecture via hydrogen bonding and other weak packing interactions. The luminescent properties of 3 were investigated in the solid state at room temperature.
Tacit Knowledge and Innovation: Insights from the Public Sector in Delta State, Nigeria

This study empirically investigated the relationship between tacit knowledge and innovation from the public sector context in Delta State, Nigeria. The use of tacit knowledge for innovation has been theoretically analysed in previous studies, but empirical studies in this field have only begun to emerge. Even so, very little research has been conducted in the public sector, even less in developing countries. Using the tacit-linked processes in the Nonaka and Takeuchi’s [Nonaka, I and K Takeuchi (1995). The Knowledge Creating Company. New York: Oxford University Press] knowledge conversion model, the study hypothesised that socialisation, externalisation and internalisation (SEI) relate with each other positively, and all have a significant positive effect on innovation. The study made use of the partial least square method for hypotheses testing with data collected from 169 mid-level health professionals from the Delta State Ministry of Health. Whilst the results show a positive relationship amongst the SEI processes, only socialisation and internalisation were found to have significant positive effects on innovation. However, despite externalisation non-significant effect on innovation, a significant indirect effect was achieved through internalisation. Together, these results provide important implications for public managers and public organisations to utilise the SEI processes in applying the tacit knowledge that has been created and shared to innovation.
The Benefit of Hedgerow Access on the Health and Growth Rate of Pasture Raised Broiler Chickens

Pasture rearing is an increasingly common option for small farms to produce humanely raised poultry products for an expanding market, however profit margins tend to be much lower for pastured poultry producers than for those that opt for conventional indoor rearing. Research into simple methods to optimize the growth and health of pasture-raised poultry can help small farmers maximize meat yields and decrease the morbidity and mortality of their flock, ultimately leading to higher profit margins and improved animal welfare. The objective of this study was to measure how the inclusion of mature, native foliage into pastures can impact the production performance and overall health status of two different popular breeds of commercial broiler chickens; fast-growing Cornish cross and slower growing Red rangers. During the finisher phase (30–78 days old), pastured chickens were separated by breed into either a treatment population with access to a mature bordering hedgerow, or a control population without access to a hedgerow. Weekly weight gain, daily feed intake and basic hematologic values were used to evaluate differences in the production performance and health status between each population. We found that hedge access led to a significant improvement in the rate of gain of the Cornish cross without an associated increase in feed intake, suggesting that the addition of hedges can increase meat yields in fast-growing broilers without increasing feed costs. Red rangers with hedge access demonstrated an improved ability to neutralize bacterial pathogens in whole blood and a lesser degree of hemodilution compared to control populations, suggesting improved immune function and a lower degree of heat stress in these populations. We conclude that the addition of natural environmental enrichment such as mature foliage to grass pastures can lead to improved production performance in fast-growing broilers and improvements in the health and immune function of slower growing broiler chickens.
Assessment of Lentiviral Vector Mediated CFTR Correction in Mice Using an Improved Rapid in vivo Nasal Potential Difference Measurement Protocol

Cystic Fibrosis (CF) is caused by a defect in the CF transmembrane conductance regulator (CFTR) gene responsible for epithelial ion transport. Nasal potential difference (PD) measurement is a well established diagnostic technique for assessing the efficacy of therapies in CF patients and animal models. The aim was to establish a rapid nasal PD protocol in mice and quantify the efficacy of lentiviral (LV) vector-based CFTR gene therapy. Anaesthetised wild-type (WT) and CF mice were non-surgically intubated and nasal PD measurements were made using a range of buffer flow rates. Addition of the cAMP agonist, isoproterenol, to the buffer sequence was then examined. The optimised rapid PD technique was then used to assess CFTR function produced by second and third generation LV-CFTR vectors. V5 epitope tagged-CFTR in nasal tissue was identified by immunohistochemistry. When intubated, mice tolerated higher flow rates. Isoproterenol could discriminate between WT and CF mice. Improved chloride transport was observed for the second and third generation LV-CFTR vectors, with up to 60% correction of the cAMP-driven chloride response towards WT. V5-CFTR was located in ciliated epithelial cells. The rapid PD technique enables improved functional assessment of the bioelectrical ion transport defect for both current and potential CF therapies.
IEEE P7001: A Proposed Standard on Transparency

This paper describes IEEE P7001, a new draft standard on transparency of autonomous systems 1 . In the paper, we outline the development and structure of the draft standard. We present the rationale for transparency as a measurable, testable property. We outline five stakeholder groups: users, the general public and bystanders, safety certification agencies, incident/accident investigators and lawyers/expert witnesses, and explain the thinking behind the normative definitions of “levels” of transparency for each stakeholder group in P7001. The paper illustrates the application of P7001 through worked examples of both specification and assessment of fictional autonomous systems.
Carbon Nanotubes: A Summary of Beneficial and Dangerous Aspects of an Increasingly Popular Group of Nanomaterials

Carbon nanotubes (CNTs) are nanomaterials with broad applications that are produced on a large scale. Animal experiments have shown that exposure to CNTs, especially one type of multi-walled carbon nanotube, MWCNT-7, can lead to malignant transformation. CNTs have characteristics similar to asbestos (size, shape, and biopersistence) and use the same molecular mechanisms and signaling pathways as those involved in asbestos tumorigenesis. Here, a comprehensive review of the characteristics of carbon nanotubes is provided, as well as insights that may assist in the design and production of safer nanomaterials to limit the hazards of currently used CNTs.
A Deep Learning Approach in Optical Inspection to Detect Hidden Hardware Trojans and Secure Cybersecurity in Electronics Manufacturing Supply Chains

Deep learning methods have been extensively studied and have been proven to be very useful in multiple fields of technology. This paper presents a deep learning approach to optically detect hidden hardware trojans in the manufacturing and assembly phase of printed circuit boards to secure electronic supply chains. Trojans can serve as backdoors of accessing on chip data, can potentially alter functioning and in some cases may even deny intended service of the chip. Apart from consumer electronics, printed circuit boards are used in mission critical applications like military and space equipment. Security compromise or data theft can have severe impact and thus demand research attention. The advantage of the proposed method is that it can be implemented in a manufacturing environment with limited training data. It can also provide better coverage in detection of hardware trojans over traditional methods. Image recognition algorithms need to have deeper penetration inside the training layers for recognizing physical variations of image patches. However, traditional network architectures often face vanishing gradient problem when the network layers are added. This hampers the overall accuracy of the network. To solve this a Residual network with multiple layers is used in this article. The ResNet34 algorithm can identify manufacturing tolerances and can differentiate between a manufacturing defect and a hardware trojan. The ResNet operates on the fundamental principle of learning from the residual of the output of preceding layer. In the degradation issue, it is observed that, a shallower network performs better than deeper network. However, this is with the downside of lower accuracy. Thus, a skip connection is made to provide an alternative path for the gradient to skip forward the training of few layers and add in multiple repeating blocks to achieve higher accuracy and lower training times. Implementation of this method can bolster automated optical inspection setup used to detect manufacturing variances on a printed circuit board. The results show a 98.5% accuracy in optically detecting trojans by this method and can help cut down redundancy of physically testing each board. The research results also provide a new consideration of hardware trojan benchmarking and its effect on optical detection.
Determination of Phenolics and Flavonoids of Some Useful Medicinal Plants and Bioassay-Guided Fractionation Substances of Sclerocarya birrea (A. Rich) Hochst Stem (Bark) Extract and Their Efficacy Against Salmonella typhi

Gallic acid and catechin are the most abundant phenolic and flavonoid contents found in all plant extracts. The contents and the bioassay-guided fractionating substances of the Sclerocarya birrea (A. Rich) Hochst (Anacardiaceae) fraction played vital roles. The goals of the study were to determine the contents of some useful medicinal plants and the bioassay-guided fractionation substances of S. birrea fraction compounds capable of acting against Salmonella isolate using LC-MS/LC-HRMS (Dionex ultimate 3000 RS UPLC with Thermo Scientific Q Exactive Orbitrap Hybrid Tandem Mass Spectrometer). The Folin–Ciocalteu reagent procedure and flavonoid content determination were conducted spectrophotometrically. Bioassay-guided fractionation, chronological partitioning, and screening of the antibacterial action against Salmonella typhi were performed. The ethyl acetate fraction extracts of S. birrea stem (bark) extract were analyzed using LC-MS/LC-HRMS. The gallic acid content increased tremendously in Vachellia nilotica (L.) P.J.H. Hurter and Mabb (Fabaceae) pod extracts with curve fitting (R 2 = 0.9958). Catechin content increase was significantly increased in S. birrea stem (bark) extracts followed by that of V. nilotica pod extracts with curve fitting (R 2 = 0.9993); they were all significantly different in the Guiera senegalensis J.F. Gmel. and the Leptadenia lanceolata (Poir.) Goyder leaves extracts at p value <0.0001. Subsequently, 10 mg/ml of S. birrea stem (bark) ethyl acetate fraction extract was the MIC, where no MBC was recorded and susceptible to the positive control with the highest inhibition zone, followed by the ethyl acetate fraction extract at 10 mg/ml (9.7 ± 0.0) at Turkey’s p < 0.0001. Vidarabine is one of the novel compounds, specifically having antimicrobial actions, found in the S. birrea stem (bark). Reasonable amounts of phenolic and flavonoid contents determined the actions of the individual plant extract.
Associations Among Parental Caregiving Quality, Cannabinoid Receptor 1 Expression-Based Polygenic Scores, and Infant-Parent Attachment: Evidence for Differential Genetic Susceptibility?

Attachment is a biological evolutionary system contributing to infant survival. When primary caregivers/parents are sensitive and responsive to their infants’ needs, infants develop a sense of security. Secure infant attachment has been linked to healthy brain and organ-system development. Belsky and colleagues proposed the term differential susceptibility to describe context-dependent associations between genetic variations and behavioral outcomes as a function of parenting environments. Variations in the Cannabinoid Receptor Gene 1 (CNR1) are associated with memory, mood, and reward and connote differential susceptibility to more and less optimal parental caregiving quality in predicting children’s behavioral problems. Aim To determine if parental caregiving quality interacts with children’s expression-based polygenic risk score (ePRS) for the CNR1 gene networks in the prefrontal cortex, striatum, and hippocampus in predicting the probability of attachment security and disorganized attachment. Design Prospective correlational methods examined maternal-infant pairs (n = 142) from which infants provided DNA samples at 3 months. Parental caregiving quality was assessed via the Child Adult Relationship Experiment (CARE)-index at 6 months, and attachment security via the Strange Situation Procedure at a mean age of 22 months. The CNR1 ePRSs include genes co-expressed with the CNR1 genes in the prefrontal cortex, striatum, or hippocampus, and were calculated using the effect size of the association between the individual single nucleotide polymorphisms from those genes and region-specific gene expression (GTEx). Logistic regression was employed (alpha < 0.05, two-tailed) to examine the main and interaction effects between parental caregiving quality and ePRSs in predicting attachment patterns. Interpretation of results was aided by analyses that distinguished between differential susceptibility and diathesis-stress. Results Significant interactions were observed between (1) maternal sensitivity and ePRS in the striatum in predicting attachment security, (2) maternal unresponsiveness with the ePRS in the hippocampus in predicting disorganization, and (3) maternal controlling with the ePRS in the hippocampus in predicting disorganization. Conclusion These findings offer support for genetic differential susceptibility to the quality of maternal sensitivity in the context of the ePRS in the striatum. However, the significant interactions between hippocampal ePRS and maternal unresponsiveness and controlling in predicting the probability of disorganization were more suggestive of the diathesis-stress model.