Miracle-dz/UniFAR-FTUs huggingface dataset:
Neural Representations of Food-Related Attributes in the Human Orbitofrontal Cortex during Choice Deliberation in Anorexia Nervosa

Decisions about what to eat recruit the orbitofrontal cortex (OFC) and involve the evaluation of food-related attributes such as taste and health. These attributes are used differently by healthy individuals and patients with disordered eating behavior, but it is unclear whether these attributes are decodable from activity in the OFC in both groups and whether neural representations of these attributes are differentially related to decisions about food. We used fMRI combined with behavioral tasks to investigate the representation of taste and health attributes in the human OFC and the role of these representations in food choices in healthy women and women with anorexia nervosa (AN). We found that subjective ratings of tastiness and healthiness could be decoded from patterns of activity in the OFC in both groups. However, health-related patterns of activity in the OFC were more related to the magnitude of choice preferences among patients with AN than healthy individuals. These findings suggest that maladaptive decision-making in AN is associated with more consideration of health information represented by the OFC during deliberation about what to eat. SIGNIFICANCE STATEMENT An open question about the OFC is whether it supports the evaluation of food-related attributes during deliberation about what to eat. We found that healthiness and tastiness information was decodable from patterns of neural activity in the OFC in both patients with AN and healthy controls. Critically, neural representations of health were more strongly related to choices in patients with AN, suggesting that maladaptive overconsideration of healthiness during deliberation about what to eat is related to activity in the OFC. More broadly, these results show that activity in the human OFC is associated with the evaluation of relevant attributes during value-based decision-making. These findings may also guide future research into the development of treatments for AN.
Convergence Assessment for Bayesian Phylogenetic Analysis using MCMC simulation

Posterior distributions are commonly approximated by samples produced from a Markov chain Monte Carlo (MCMC) simulation. Every MCMC simulation has to be checked for convergence, i.e., that sufficiently many samples have been obtained and that these samples indeed represent the true posterior distribution. Here we develop and test different approaches for convergence assessment in phylogenetics. We analytically derive a threshold for a minimum effective sample size (ESS) of 625. We observe that only the initial sequence estimator provides robust ESS estimates for common types of MCMC simulations (autocorrelated samples, adaptive MCMC, Metropolis-Coupled MCMC). We show that standard ESS computation can be applied to phylogenetic trees if the tree samples are converted into traces of absence/presence of splits. Convergence in distribution between replicated MCMC runs can be assessed with the Kolmogorov-Smirnov test. The commonly used potential scale reduction factor (PSRF) is biased when applied to skewed posterior distribution. Additionally, we analytically derive the expected difference between split frequencies (EDSF) and show that it depends on the true frequency of a split. Hence, the average standard deviation of split frequencies is too simplistic and the EDSF should be used instead to check for convergence in split frequencies. We implemented the methods described here in the open-source R package Convenience (https://github.com/lfabreti/convenience), which allows users to easily test for convergence using output from standard phylogenetic inference software.
Simple-to-use CRISPR-SpCas9/SaCas9/AsCas12a vector series for genome editing in Saccharomyces cerevisiae

Genome editing using the CRISPR/Cas system has been implemented for various organisms and becomes increasingly popular even in the genetically tractable budding yeast Saccharomyces cerevisiae. Since each CRISPR/Cas system recognizes only the sequences flanked by its unique protospacer adjacent motif (PAM), a certain single system often fails to target a region of interest due to the lack of PAM, thus necessitating the use of another system with a different PAM. Three CRISPR/Cas systems with distinct PAMs, namely SpCas9, SaCas9, and AsCas12a, have been successfully used in yeast genome editing and their combined use should expand the repertoire of editable targets. However, currently available plasmids for these systems were individually developed under different design principles, thus hampering their seamless use in the practice of genome editing. Here we report a series of Golden Gate Assembly-compatible backbone vectors designed under a unified principle to exploit the three CRISPR/Cas systems in yeast genome editing. We also created a software to assist the design of genome-editing plasmids for individual target sequences using the backbone vectors. Genome editing with these plasmids demonstrated practically sufficient efficiency in both insertion of gene fragments to essential genes and complete deletion of an open reading frame. The backbone vectors with the software would thus provide a versatile toolbox to facilitate the seamless use of SpCas9, SaCas9, and AsCas12a in various types of genome manipulation, especially those that are difficult to perform with conventional techniques in yeast genetics.
Comparative meta-proteomic analysis for the identification of novel plasmodesmata proteins and regulatory cues

A major route for cell-to-cell signaling is via cell wall-embedded pores termed plasmodesmata (PD) forming the symplasm. PD regulate many aspects of plant development and responses to the environment however, our understanding of what factors affect their structure and permeability is limited. In this paper, a meta-analysis is presented as a tool for the identification of conditions affecting PD transport and in silico generation of PD proteomes for species of interest. The custom-built pipeline searches the whole genome for protein structural features and conserved domains identified on experimental proteomes and use it to predict PD candidates in 22 compatible plant species. Using the in silico proteome and microarray analysis, interactions between PD genes and conditions affecting PD function are identified. High salinity and osmotic stress affect a significant number of PD candidate genes and we provide evidence that these conditions regulate symplasmic transport of GFP. Using the pipeline, the in silico PD proteome for Medicago truncatula was generated, as an example of a plant in which experimental data is not available. The identification of a candidate receptor like protein was experimentally validated in M. truncatula transgenic roots expressing fluorescently tagged protein fusion. Together the results highlight the power of our newly designed tool in the identification of new factors and proteins influencing PD in diverse plant species.
Creating and Implementing Standardized Management Innovation in a Large Organization

Management innovation represents one of the most important and sustainable sources of competitive advantage due to its context-specific nature. Still, current academic literature on management innovation and standardization is slightly limited. This intensive case study explores management innovation in a large European telecommunications company with the focus on standardization in managerial practices. The research data were gathered through interviews with managers from different levels of the case company. The results show that highly standardized management innovation is effective for reaching a standard level of management in a large company; it is also a prerequisite for further systematic development. Research questions: The purpose of this study is to gain insight into how standardization emerges in management innovation in a large organization by studying the construction and conduction of a managerial toolkit in a European telecommunications company. Links to theory: The theoretical framework is based on a study of management innovations and related processes by Birkinshaw et al. (2008) and a standardization study by Wright, Wylie & Sturdy (2012) in which the tasks of an internal change agent were divided into “standardizing agendas” and “standardizing methods”. Phenomenon studied: Adoption process of a standardized management innovation in a large company. Case context: The case company is a large European telecommunications company which operates in a highly competitive market where organizational excellence is extremely beneficial. The case study focuses on the case company management innovation process for creating a “toolkit” for day-to-day management in the retail sales channel. Research findings: The research findings gathered through systematic combining approach show that standardized management innovation is an effective tool for implementing managerial best practices from management fashions into organizational standards. Through adapting these learnings systematically to managers’ individual work, the good “standard” level of managing can be achieved in a large-size company. Reaching these standards also appears as a prerequisite for a further systematic managerial development in the organization. Discussion: This study contributes to management innovation research by highlighting planning and coordination in introduction and successful adoption of standardized management innovation. Planning communications, setting achievable timeframes and choosing the right implementers are important aspects of implementation. Clear guidelines help employees understand the ideological background of management innovation, and close interaction between change agents and store managers promotes the adoption of management innovation. A standardized management toolkit is an effective tool for putting external leadership ideologies, known as management fashions, into practice in a large organization. However, practical implementation requires comprehensive communication and preferably internal recruitment of change agents.
Repeated ex situ Spawning in Two Highly Disease Susceptible Corals in the Family Meandrinidae

Members of the family Meandrinidae are highly susceptible to stony coral tissue loss disease, resulting in population reductions up to 88% in both Dendrogyra cylindrus and Meandrina meandrites along the Florida Reef Tract. Reductions in abundance on this scale leave these species susceptible to limitations in sexual reproduction and natural recovery without intervention. In response to the ongoing outbreak of the disease across the Caribbean, a variety of genetic rescue projects have been implemented to bring disease susceptible species into ex situ culture and preserve living genetic diversity. In this study, corals being held in a long-term ex situ genetic bank were maintained using artificial lighting and temperature cues programmed to mimic natural cycles in Key Largo, FL, United States. Synchronized broadcast spawning events in both species were documented in aquaria over two annual spawning cycles in 2019 and 2020. Timing of gamete release relative to the perceived date and sunset was highly synchronized with wild observations. Up to 21 unique D. cylindrus genotypes collected from reef locations spanning over 230 km contributed gametes to the larval pool. The majority of these parental colonies are no longer alive in the wild. Repeatable and predictable ex situ spawning events such as these will become an essential tool for managed breeding and assisted fertilization in species suffering from severe population declines. These annual events have the potential to produce thousands of genetically diverse offspring for restoration efforts and offer future hope for the long-term survival of these threatened species.
Fe-Mg mixing in cordierite: Constraints from natural data and implications for cordierite-garnet geothermometry in granulites

From chemicaldata on 108 pairs of naturally occurring garnet and cordierite, the interchange energy of Fe-Mg mixing in cordierite (Wo*-") and the free-energy change of the exchange equilibrium %FerAlrSirO,, -t t/zMgrAIoSirO,, : Y:MgrAlrSirO,, * YzFerAloSirO,, in the temperature range of 700-850 'C have been extracted using standard methods of linear regression analysis. The input thermochemical parameters for multicomponent CaMg-Fe-Mn garnet solid solutions are based on the updated and revised values after Ganguly and Saxena (1984), e.g., Wr"_. ": 2500 cal, W*: W*": 3000 cal calculated on the basis of one-third formula unit. On the basis of the derived values at 710, 760, 800, and 850 "C, Fe-Mg mixing in cordierite has been approximated to a symmetric regular solution. The Fe-Mg substitution shows positive deviation from ideality in cordierite, with tzi:1. , : 9.34 + 4.54kJ/mol of divalent cation. The values derived for the free energy of mixing, at Xi:d : Xi;ds : 0.5, are -3.26 kJ at 700 'C and -4.39 kl at 900 "C. The AG,. value (in joules) for the above equilibrium can be expressed as 15079 8.552. Incorporating these parameters, the geothermometric expression for the exchange equilibrium is
Recent Advances in Protein Homology Detection Propelled by Inter-Residue Interaction Map Threading

Sequence-based protein homology detection has emerged as one of the most sensitive and accurate approaches to protein structure prediction. Despite the success, homology detection remains very challenging for weakly homologous proteins with divergent evolutionary profile. Very recently, deep neural network architectures have shown promising progress in mining the coevolutionary signal encoded in multiple sequence alignments, leading to reasonably accurate estimation of inter-residue interaction maps, which serve as a rich source of additional information for improved homology detection. Here, we summarize the latest developments in protein homology detection driven by inter-residue interaction map threading. We highlight the emerging trends in distant-homology protein threading through the alignment of predicted interaction maps at various granularities ranging from binary contact maps to finer-grained distance and orientation maps as well as their combination. We also discuss some of the current limitations and possible future avenues to further enhance the sensitivity of protein homology detection.
Evidence-based policing in Australia: an examination of the appropriateness and transparency of lineup identification and investigative interviewing practices

Psychological research has been pivotal in influencing the way police forces globally approach and undertake criminal investigations. Increasing psychological research in recent years has led to the development of best-practice guidelines for conducting police investigations, across a number of key areas of criminal investigation. For example, procedures for creating and conducting lineups as recommended by the American Psychology-Law Society, and the UK-developed PEACE model for investigative interviewing, have both been of influence in Australia. However, the extent to which these evidence-based recommendations have been incorporated into policing practice within Australia is unclear. In this article, we conducted an exploratory review of publicly available policing documents within Australian states and territories, to determine the extent to which best practice lineup identification and investigative interviewing procedures have been adopted into police practice. The review revealed that for lineup identification procedures, many of the basic recommendations for conducting lineups were not incorporated into publicly available policing manuals. For investigative interviewing, it appeared on the surface that elements of the PEACE model were implemented within most Australian jurisdictions, albeit this was often not explicitly stated within policing documents. A key issue identified was a lack of (understandable) public transparency of policing procedure, as a number of Australian jurisdictions failed to have publicly available policing manuals or handbooks against which to evaluate their procedures. Therefore, we argue that there is a need for better collaboration between researchers and law enforcement in order to achieve evidence-based, transparent policing within Australia.
Panomics: New Databases for Advancing Cardiology

The multifactorial nature of cardiology makes it challenging to separate noisy signals from confounders and real markers or drivers of disease. Panomics, the combination of various omic methods, provides the deepest insights into the underlying biological mechanisms to develop tools for personalized medicine under a systems biology approach. Questions remain about current findings and anticipated developments of omics. Here, we search for omic databases, investigate the types of data they provide, and give some examples of panomic applications in health care. We identified 104 omic databases, of which 72 met the inclusion criteria: genomic and clinical measurements on a subset of the database population plus one or more omic datasets. Of those, 65 were methylomic, 59 transcriptomic, 41 proteomic, 42 metabolomic, and 22 microbiomic databases. Larger database sample sizes and longer follow-up are often better suited for panomic analyses due to statistical power calculations. They are often more complete, which is important when dealing with large biological variability. Thus, the UK BioBank rises as the most comprehensive panomic resource, at present, but certain study designs may benefit from other databases.
The Role of Trauma in Mothers’ COVID-19 Vaccine Beliefs and Intentions

Abstract Objective Research on COVID-19 vaccine beliefs has focused primarily on adults’ intentions to vaccinate themselves; however, many parents will also face decisions about vaccinating their children. In this study, we examine how maternal posttraumatic stress disorder (PTSD) and trauma history relate to mothers’ beliefs and intentions about the COVID-19 vaccine for themselves and their children. Methods A total of 240 mothers with a mental health history participating in a parenting study answered online survey questions via Prolific. Questions assessed: (a) trauma indictors (past diagnosis, current symptoms, and lifetime exposure to events); (b) vaccine measures (intentions for self and child, COVID-19 vaccine confidence, general vaccine perceived safety, reasoning about vaccine intentions, sources of influence on intentions); and (c) possible explanatory variables (institutional distrust, negative worldviews). ANCOVAs and regression analyses were used. Results When compared with mothers with other mental health diagnoses, mothers with a PTSD history had significantly less confidence in the COVID-19 vaccine and less intent to get the vaccine for themselves or their child. These effects were explained by greater institutional distrust (i.e., significant indirect effects). Mothers with a previous PTSD diagnosis also expressed different reasons for vaccine hesitancy (e.g., less belief in science) and ascribed less influence to healthcare and governmental sources in vaccine decision-making. Conclusion Findings highlight the potential utility of a trauma-informed approach in efforts to reduce COVID-19 vaccine hesitancy. For mothers with a history of PTSD, addressing institutional distrust, including towards the healthcare industry, may be an important element to consider in the content, delivery, and mode of vaccine messaging.
Methamphetamine Use, Syphilis, and Specific Online Sex Partner Meeting Venues Are Associated With HIV Status Among Urban Black Gay and Bisexual Men Who Have Sex Men

A study among urban Black men who have sex men found that methamphetamine use and syphilis positivity were associated with HIV positivity, and specific sex partner meeting venues may provide intervention access points. Supplemental digital content is available in the text. Background In the context of increasing syphilis rates, particularly among Black men who have sex men (MSM), the objectives were to determine the associations between methamphetamine (meth) use and syphilis and HIV positivity, and to identify sex partner meeting venues as potential intervention access points among Black MSM in a mid-Atlantic US city. Methods This study is an ongoing longitudinal cohort study. Participants were recruited from clinical and nonclinical settings and included sexually active MSM aged 18 to 45 years. The baseline visit included a behavioral survey and testing for syphilis, HIV, gonorrhea, and chlamydia. Logistic regression analyses were used for hypothesis testing. Results Among 359 MSM completing baseline, 74.4% (268) Black MSM were included; 31% (84) were aged 24 to 29 years, 43.7% (117) reported unprotected anal intercourse at last sex, and 15.3% (41) reported meth use in the past 3 months. Sixteen percent (43) had syphilis, 46.6% (125) were living with HIV, and 19.0% (51) had gonorrhea and/or chlamydia. Meth use was associated with sexual and drug risk behaviors and HIV, but not syphilis. In adjusted analyses, meth use increased the odds of HIV positivity by 6.43 (95% confidence interval, 2.30–17.98) and syphilis positivity by 2.57 (95% confidence interval, 1.23–5.37). Four online sex partner meeting venues were associated with meth use and HIV, whereas syphilis was associated with one. Conclusions Among Black MSM, meth use and syphilis positivity were associated with more than 6-fold and almost 3-fold increased adjusted odds of HIV positivity, respectively. Four specific sex partner meeting venues may be important access points for HIV/sexually transmitted infection and substance use prevention.
Population genomics of Pocillopora corals: insights from RAD-sequencing

Scleractinian corals are of great ecological interest as ecosystem engineer species. Accordingly, there is a wealth of studies on their adaptive abilities facing climate change. Such studies should rely on precise species and population delimitation. Nevertheless species delimitation in corals can be hindered by the lack of adequate genetic markers, by hybridization, and by morphological plasticity. Here we applied RAD sequencing to the study of species delimitation and genetic structure in populations of Pocillopora spp. from Oman and French Polynesia with the objectives to test primary species hypotheses based on mitochondrial DNA sequencing, and to study the genetic structure among sampling sites inside species. Regarding the varying levels of missing data observed among samples we tested different filtering strategy. The main genetic differentiation was observed between samples from Oman and French Polynesia, which also corresponded to different mitochondrial lineages and species hypotheses. In Oman, we did not observe any clear differentiation according to the main mitochondrial lineages considered here, nor between sampling sites. In French Polynesia where a single mitochondrial lineage was studied, we did not evidence any differentiation according to sampling sites. These results provide an additional example of the importance of using independent nuclear markers for the study of species delimitation. Our analyses also allowed the identification of clonal lineages in our samples, and to take them into account in our interpretations. We used simulations to study the impact of clonal reproduction on the distribution of statistics of genetic diversity and genetic structure among loci.