Miracle-dz/UniFAR-FTUs huggingface dataset:
New insights into food O/W emulsion gels: Strategies of reinforcing mechanical properties and outlook of being applied to food 3D printing

Abstract 3D printing technology has been widely used in food processing with its advantages of customized food design, personalized nutrition design, and simplified food supply chain. Food emulsion gels have application value and prospects in food 3D printing due to their promising properties, including biodegradability, biocompatibility, as well as dual characteristics of emulsions and biopolymer gels. Food emulsion gels with appropriate mechanical properties, as a new type of food inks, expand the types and functions of the inks. However, food emulsion gels without adequate reinforced mechanical properties may suffer from defects in shape, texture, mouthfeel, and functionality during 3D printing and subsequent applications. Therefore, it is necessary to summarize the strategies to improve the mechanical properties of food emulsion gels. According to the methods of characterizing the mechanical properties of emulsion gels, this article summarizes four strategies for improving the mechanical properties of emulsion gels through two ways: inside-out (reinforcement of interface and reinforcement of cross-linking) and outside-in (physical approaches and environmental regulations), as well as their basic mechanisms. The application status and future research trends of emulsion gels in food 3D printing are finally discussed.
Genomic structural variants constrain and facilitate adaptation in natural populations of Theobroma cacao, the chocolate tree

Significance Genomic structural variants (SVs) are frequent contributors to adaptation and speciation, but our understanding of their overall fitness consequences is limited, with data and analyses primarily available for humans and short-lived domesticated species. Here, we use 31 high-quality genome assemblies to study the evolutionary impact of SVs among natural populations of Theobroma cacao. We find that most SVs are deleterious and thus constrain adaptation. These detrimental effects likely arise as a direct result of impaired gene function and as an indirect result of suppressed recombination. Yet we detect several SVs that may contribute to local adaptation mainly through traits involved in pathogen resistance. Overall, we provide important insight into processes underlying the fitness effects of SVs in natural populations. Genomic structural variants (SVs) can play important roles in adaptation and speciation. Yet the overall fitness effects of SVs are poorly understood, partly because accurate population-level identification of SVs requires multiple high-quality genome assemblies. Here, we use 31 chromosome-scale, haplotype-resolved genome assemblies of Theobroma cacao—an outcrossing, long-lived tree species that is the source of chocolate—to investigate the fitness consequences of SVs in natural populations. Among the 31 accessions, we find over 160,000 SVs, which together cover eight times more of the genome than single-nucleotide polymorphisms and short indels (125 versus 15 Mb). Our results indicate that a vast majority of these SVs are deleterious: they segregate at low frequencies and are depleted from functional regions of the genome. We show that SVs influence gene expression, which likely impairs gene function and contributes to the detrimental effects of SVs. We also provide empirical support for a theoretical prediction that SVs, particularly inversions, increase genetic load through the accumulation of deleterious nucleotide variants as a result of suppressed recombination. Despite the overall detrimental effects, we identify individual SVs bearing signatures of local adaptation, several of which are associated with genes differentially expressed between populations. Genes involved in pathogen resistance are strongly enriched among these candidates, highlighting the contribution of SVs to this important local adaptation trait. Beyond revealing empirical evidence for the evolutionary importance of SVs, these 31 de novo assemblies provide a valuable resource for genetic and breeding studies in T. cacao.
Rapid adaptive radiation in a hillstream cyprinid fish in the East African White Nile River basin

Adaptive radiation of freshwater fishes was long thought to be possible only in lacustrine environments. Recently, several studies have shown that riverine and stream environments also provide the ecological opportunity for adaptive radiation. In this study, we report on a riverine adaptive radiation of six ecomorphs of cyprinid hillstream fishes of the genus Garra in a river located in the Ethiopian Highlands in East Africa. Garra are predominantly highly specialized algae‐scrapers with a wide distribution ranging from Southeast Asia to West Africa. However, adaptive phenotypic diversification in mouth type, sucking disc morphology, gut length and body shape have probably been found among these ecomorphs in a single Ethiopian river. Moreover, we found two novel phenotypes of Garra (“thick‐lipped” and “predatory”) that had not been discovered before in this species‐rich genus (>160 species). Mitochondrial and genome‐wide data suggest monophyletic, intrabasin evolution of Garra phenotypic diversity with signatures of gene flow from other local populations. Although sympatric ecomorphs are genetically distinct and can be considered to being young species as suggested by genome‐wide single nucleotide polymorphism data, mitochondrial DNA was unable to identify any genetic structure suggesting recent and rapid speciation events. Some data suggest a hybrid origin of the novel “thick‐lipped” ecomorph. Here we highlight how, driven by ecological opportunity, an ancestral trophically highly specialized lineage is likely to have rapidly radiated in a riverine environment promoted by the evolution of novel feeding strategies.
Fc Galactosylation Promotes Hexamerization of Human IgG1, Leading to Enhanced Classical Complement Activation

Key Points Fc galactosylation enhances complement activity of WT IgG1, but not hexameric IgG. Fc galactosylation improves hexamerization potential of IgG1. Human IgG contains one evolutionarily conserved N-linked glycan in its Fc region at position 297. This glycan is crucial for Fc-mediated functions, including its induction of the classical complement cascade. This is induced after target recognition through the IgG–Fab regions, allowing neighboring IgG–Fc tails to associate through Fc:Fc interaction, ultimately leading to hexamer formation. This hexamerization seems crucial for IgG to enable efficient interaction with the globular heads of the first complement component C1q and subsequent complement activation. In this study, we show that galactose incorporated in the IgG1–Fc enhances C1q binding, C4, C3 deposition, and complement-dependent cellular cytotoxicity in human erythrocytes and Raji cells. IgG1–Fc sialylation slightly enhanced binding of C1q, but had little effect on downstream complement activation. Using various mutations that decrease or increase hexamerization capacity of IgG1, we show that IgG1–Fc galactosylation has no intrinsic effect on C1q binding to IgG1, but enhances IgG1 hexamerization potential and, thereby, complement activation. These data suggest that the therapeutic potential of Abs can be amplified without introducing immunogenic mutations, by relatively simple glycoengineering.
A Novel Occlusion-Aware Vote Cost for Light Field Depth Estimation

Capturing the directions of light by light field cameras powers next-generation immersive multimedia applications. A critical problem in taking advantage of the rich visual information in light field images is depth estimation. Conventional light field depth estimation methods build a cost volume that measures the photo-consistency of pixels refocused to a range of depths, and the highest consistency indicates the correct depth. This strategy works well in most regions but usually generates blurry edges in the estimated depth map due to occlusions. Recent work shows that integrating occlusion models to light field depth estimation can largely reduce blurry edges. However, existing occlusion handling methods rely on complex edge-aided processing and post-refinement, and this reliance limits the resultant depth accuracy and impacts on the computational performance. In this paper, we propose a novel occlusion-aware vote cost (OAVC) which is able to accurately preserve edges in the depth map. Instead of using photo-consistency as an indicator of the correct depth, we construct a novel cost from a new perspective that counts the number of refocused pixels whose deviations from the central-view pixel are less than a small threshold, and utilizes that number to select the correct depth. The pixels from occluders are thus excluded in determining the correct depth. Without the use of any explicit occlusion handling methods, the proposed method can inherently preserve edges and produces high-quality depth estimates. Experimental results show that the proposed OAVC outperforms state-of-the-art light field depth estimation methods in terms of depth estimation accuracy and computational complexity.
De novo generation of dual-target ligands using adversarial training and reinforcement learning

Artificial intelligence, such as deep generative methods, represents a promising solution to de novo design of molecules with the desired properties. However, generating new molecules with biological activities toward two specific targets remains an extremely difficult challenge. In this work, we conceive a novel computational framework, herein called dual-target ligand generative network (DLGN), for the de novo generation of bioactive molecules toward two given objectives. Via adversarial training and reinforcement learning, DLGN treats a sequence-based simplified molecular input line entry system (SMILES) generator as a stochastic policy for exploring chemical spaces. Two discriminators are then used to encourage the generation of molecules that belong to the intersection of two bioactive-compound distributions. In a case study, we employ our methods to design a library of dual-target ligands targeting dopamine receptor D2 and 5-hydroxytryptamine receptor 1A as new antipsychotics. Experimental results demonstrate that the proposed model can generate novel compounds with high similarity to both bioactive datasets in several structure-based metrics. Our model exhibits a performance comparable to that of various state-of-the-art multi-objective molecule generation models. We envision that this framework will become a generally applicable approach for designing dual-target drugs in silico.
The ins and outs of Bacillus proteases: activities, functions and commercial significance

ABSTRACT Because the majority of bacterial species divide by binary fission, and do not have distinguishable somatic and germline cells, they could be considered to be immortal. However, bacteria ‘age’ due to damage to vital cell components such as DNA and proteins. DNA damage can often be repaired using efficient DNA repair mechanisms. However, many proteins have a functional ‘shelf life’; some are short lived, while others are relatively stable. Specific degradation processes are built into the life span of proteins whose activities are required to fulfil a specific function during a prescribed period of time (e.g. cell cycle, differentiation process, stress response). In addition, proteins that are irreparably damaged or that have come to the end of their functional life span need to be removed by quality control proteases. Other proteases are involved in performing a variety of specific functions that can be broadly divided into three categories: processing, regulation and feeding. This review presents a systematic account of the proteases of Bacillus subtilis and their activities. It reviews the proteases found in, or associated with, the cytoplasm, the cell membrane, the cell wall and the external milieu. Where known, the impacts of the deletion of particular proteases are discussed, particularly in relation to industrial applications.
Post-traumatic epilepsy in zebrafish is drug-resistant and impairs cognitive function.

Post-traumatic epilepsy (PTE) is acquired epilepsy after traumatic brain injury (TBI). Despite the availability of more than 20 anti-seizure medications (ASMs), there is no way at present to prevent epileptogenesis in TBI survivors, and many cases of PTE become drug-resistant. Importantly, the adverse effects of ASMs can significantly affect patients' quality of life. Mammalian models are commonly used for studying refractory PTE, but are expensive and laborious. Zebrafish models have become popular for studying epilepsy, but most focus on larvae and there have been no reports to date of pharmacological screening in an adult zebrafish model of acquired epilepsy. Valid animal models are critical for understanding PTE and for developing novel therapeutics. The aim of the present study was to characterize the cognitive impairments of a zebrafish model of TBI that leads to the development of PTE. Using combined behavioural and electrophysiological approaches, we also characterized the pharmacological effects of the most commonly used ASMs to treat PTE (valproate, carbamazepine, and phenytoin). Zebrafish with PTE exhibited impairments in learning and memory, difficulty in decision making, and reduced social preference. Valproate and carbamazepine had a limited protective effect against behavioural seizures, and all three drugs failed to significantly reduce electrographic seizures. The negative impacts of TBI and ASMs in zebrafish parallel those observed in other animals, making the zebrafish model of PTE a promising high-throughput model of refractory and drug-resistant epilepsy.
Impact of sleep‐disordered breathing on behavior and quality of life in children aged 2 to 7 years with non‐syndromic cleft lip and/or palate

Children with cleft are at high risk for sleep‐disordered breathing (SDB). However, little is known about the impact of SDB in this pediatric population. The aim of this study was to investigate whether SDB play a role in behavior and quality of life (QoL) in young children with cleft.
A Behavioral Index for Assessing Bison Stress Level during Handling and Demographic Predictors of Stress Response

ABSTRACT There are an estimated half-a-million Plains Bison (Bison bison) present in North America in commercial and conservation herds. Most bison are rounded up and “worked” annually for parasite control, veterinarian attention, and processing, making it important to understand the impacts of these operations. Research indicates bison generally experience higher levels of stress than cattle during similar handling processes. However, most methods for assessing stress-level during working are invasive, increase handling time, and paradoxically increase stress levels. We designed a behavioral index to assess bison stress level during handling and used it to evaluate various predictors of stress response in a semi-wild bison herd. We examined how sex, age, herd of origin, previous experience, calf rearing, and body condition influenced bison stress response during working operations from 2015 to 2017. Our results indicate that stress level decreased with age and previous experience being worked through a particular facility. Additionally, herd of origin influenced stress level, indicating that stress response may have a genetic or epigenetic component. Our study provides an easily applicable tool for monitoring bison stress levels.
Introduction—First Billion Years: Habitability

The physical processes active during the first billion years (FBY) of Earth's history, such as accretion, differentiation, and impact cratering, provide constraints on the initial conditions that were conducive to the formation and establishment of life on Earth. This motivated the Lunar and Planetary Institute's FBY topical initiative, which was a four-part conference series intended to look at each of these physical processes to study the basic structure and composition of our Solar System that was set during the FBY. The FBY Habitability conference, held in September 2019, was the last in this series and was intended to synthesize the initiative; specifically, to further our understanding of the origins of life, planetary and environmental habitability, and the search for life beyond Earth. The conference included discussions of planetary habitability and the potential emergence of life on bodies within our Solar System, as well as extrasolar systems by applying our knowledge of the Solar System's FBY, and in particular Earth's early history. To introduce this Special Collection, which resulted from work discussed at the conference, we provide a review of the main themes and a synopsis of the FBY Habitability conference.
Moral injury and substance use disorders among US combat veterans: results from the 2019–2020 National Health and Resilience in Veterans Study

Abstract Background Exposure to potentially morally injurious events (PMIEs) is associated with increased risk for substance use disorders (SUDs), although population-based studies remain limited. The goal of this study was to better understand the relationships between PMIE exposure and lifetime and past-year alcohol use disorder (AUD), drug use disorder (DUD), and SUD. Methods Data were analyzed from the 2019–2020 National Health and Resilience in Veterans Study, which surveyed a nationally representative sample of 1321 combat veterans. Multivariable analyses examined associations between three types of PMIE exposure (perpetration, witnessing, and betrayal), and lifetime and past-year AUD, DUD, and SUD, adjusting for sociodemographic variables, combat exposure severity, prior trauma, and lifetime posttraumatic stress disorder and major depressive disorder. Results Perpetration was associated with increased odds of lifetime AUD (OR 1.15; 95% CI 1.01–1.31) and lifetime SUD (OR 1.18; 95% CI 1.03–1.35). Witnessing was associated with greater odds of past-year DUD (OR 1.20; 95% CI 1.04–1.38) and past-year SUD (OR 1.14; 95% CI 1.02–1.28). Betrayal was associated with past-year AUD (OR 1.20; 95% CI 1.03–1.39). A large proportion of the variance in past-year AUD was accounted for by betrayal (38.7%), while witnessing accounted for 25.8% of the variance in past-year DUD. Conclusions Exposure to PMIEs may be a stronger contributor to SUDs among veterans than previously known. These findings highlight the importance of targeted assessment and treatment of moral injury among veterans with SUDs, as well as attending to specific types of morally injurious experiences when conceptualizing and planning care.
Recommendations for Diagnosis and Treatment of Children with Transient Abnormal Myelopoiesis (TAM) and Myeloid Leukemia in Down Syndrome (ML-DS)

Abstract Children with Down syndrome are at a high risk of developing transient abnormal myelopoiesis (TAM; synonym: TMD) or myeloid leukemia (ML-DS). While most patients with TAM are asymptomatic and go into spontaneous remission without a need for therapy, around 20% of patients die within the first six months due to TAM-related complications. Another 20–30% of patients progress from TAM to ML-DS. ML-DS patients are particularly vulnerable to therapy-associated toxicity, but the prognosis of relapsed ML-DS is extremely poor – thus, ML-DS therapy schemata must strive for a balance between appropriate efficacy (to avoid relapses) and treatment-related toxicity. This guideline presents diagnostic and therapeutic strategies for TAM and ML-DS based on the experience and results of previous clinical studies from the BFM working group, which have helped reduce the risk of early death in symptomatic TAM patients using low-dose cytarabine, and which have achieved excellent cure rates for ML-DS using intensity-reduced treatment protocols.
Growth mindset in competency-based medical education

Abstract The ongoing adoption of competency-based medical education (CBME) across health professions training draws focus to learner-centred educational design and the importance of fostering a growth mindset in learners, teachers, and educational programs. An emerging body of literature addresses the instructional practices and features of learning environments that foster the skills and strategies necessary for trainees to be partners in their own learning and progression to competence and to develop skills for lifelong learning. Aligned with this emerging area is an interest in Dweck’s self theory and the concept of the growth mindset. The growth mindset is an implicit belief held by an individual that intelligence and abilities are changeable, rather than fixed and immutable. In this paper, we present an overview of the growth mindset and how it aligns with the goals of CBME. We describe the challenges associated with shifting away from the fixed mindset of most traditional medical education assumptions and practices and discuss potential solutions and strategies at the individual, relational, and systems levels. Finally, we present future directions for research to better understand the growth mindset in the context of CBME.
The role of Bildung in Hegel’s philosophy of history

ABSTRACT The notion of Bildung comes to prominence in the second half of the eighteenth century. It was originally conceived to capture the cultural conditions by which an individual becomes a moral agent. In Hegel’s thought, it develops a much more expansive role; it is at the heart of his socio-historical project. Bildung is Hegel’s theory of culture, but for Hegel, is not just the way in which individuals are cultivated, the process by which individuals internalise the norms of their society, or develop their autonomy. This paper argues that Bildung is key to understanding normative change and has a critical and underappreciated role in the development of world history. It is also at the heart of Hegel’s challenge to the dualism of nature and culture.
Keep climate policy focused on the social cost of carbon

A proposed shift away from the SCC is ill advised In the context of climate change, the application of cost-benefit analysis to inform mitigation policies can help to achieve the best outcomes and avoid the worst: spending trillions of dollars but failing to get the job done (1). The costs of a climate policy are the abatement costs of reducing emissions of carbon dioxide (CO2) (or other greenhouse gases). The standard measure of the benefits of a climate policy is the social cost of carbon (SCC), which measures the avoided economic damages associated with a metric ton of CO2 emissions. Recently, however, there have been calls for an alternative approach to policy evaluation that ignores the benefits of avoided climate damages and instead focuses only on minimizing the compliance costs of a given, politically determined climate objective (2, 3). We argue here that a shift from use of the SCC and cost-benefit analysis to an alternative approach for evaluating policy that focuses on costs alone would be misguided. Rather than advocate for alternative approaches, now is the time to support efforts to update the SCC and its application to official climate policy evaluation.