Miracle-dz/UniFAR-FTUs huggingface dataset:
Post mortem validation of DSI compressed sensing with optical imaging

Compressed sensing (CS) has been used to enhance the feasibility of diffusion spectrum imaging (DSI) by reducing the required acquisition time. CS applied to DSI (CS-DSI) attempts to reconstruct diffusion probability density functions (PDFs) from significantly undersampled q-space data. Dictionary-based CS-DSI using L2-regularized algorithms is an intriguing approach that has demonstrated high fidelity reconstructions, fast computation times and inter-subject generalizability when tested on in vivo data. CS-DSI reconstruction fidelity is typically evaluated using the fully sampled data as ground truth. However, it is difficult to gauge how great an error with respect to the fully sampled PDF we can tolerate, without knowing whether that error also translates to substantial loss of accuracy with respect to the true fiber orientations. Here, we obtain direct measurements of axonal orientations in ex vivo human brain tissue at microscopic resolution with polarization-sensitive optical coherence tomography (PSOCT). We employ dictionary-based CS reconstruction methods to DSI data from the same samples, acquired at high max b-value (40000 s/mm2) and with high spatial resolution. We compare the diffusion orientation estimates from both CS and fully sampled DSI to the ground-truth orientations from PSOCT. This allows us to investigate the conditions under which CS reconstruction preserves the accuracy of diffusion orientation estimates with respect to PSOCT. We find that, for a CS acceleration factor of R=3, CS-DSI preserves the accuracy of the fully sampled DSI data. That acceleration is sufficient to make the acquisition time of DSI comparable to that of state-of-the-art single- or multi-shell acquisitions. We also show that, as the acceleration factor increases further, different CS reconstruction methods degrade in different ways. Finally, we find that the signal-to-noise (SNR) of the training data used to construct the dictionary can have an impact on the accuracy of the CS-DSI, but that there is substantial robustness to loss of SNR in the test data.
A screen for Twist-interacting proteins identifies Twinstar as a regulator of muscle development during embryogenesis

Myogenesis in Drosophila relies on the activity of the transcription factor Twist during several key events of mesoderm differentiation. To identify the mechanism(s) by which Twist establishes a unique gene expression profile in specific spatial and temporal locales, we employed a yeast-based double interaction screen to discover new Twist-interacting proteins (TIPs) at the myocyte enhancer factor 2 (mef2) and tinman (tinB) myogenic enhancers. We identified a number of proteins that interacted with Twist at one or both enhancers, and whose interactions with Twist and roles in muscle development were previously unknown. Through genetic interaction studies, we find that Twinstar (Tsr), and its regulators are required for muscle formation. Loss of function and null mutations in tsr and its regulators result in missing and/or misattached muscles. Our data suggest that the yeast double interaction screen is a worthy approach to investigate spatial-temporal mechanisms of transcriptional regulation in muscle and in other tissues.
Integrating Tactile Feedback Technologies Into Home-Based Telerehabilitation: Opportunities and Challenges in Light of COVID-19 Pandemic

The COVID-19 pandemic has highlighted the need for advancing the development and implementation of novel means for home-based telerehabilitation in order to enable remote assessment and training for individuals with disabling conditions in need of therapy. While somatosensory input is essential for motor function, to date, most telerehabilitation therapies and technologies focus on assessing and training motor impairments, while the somatosensorial aspect is largely neglected. The integration of tactile devices into home-based rehabilitation practice has the potential to enhance the recovery of sensorimotor impairments and to promote functional gains through practice in an enriched environment with augmented tactile feedback and haptic interactions. In the current review, we outline the clinical approaches for stimulating somatosensation in home-based telerehabilitation and review the existing technologies for conveying mechanical tactile feedback (i.e., vibration, stretch, pressure, and mid-air stimulations). We focus on tactile feedback technologies that can be integrated into home-based practice due to their relatively low cost, compact size, and lightweight. The advantages and opportunities, as well as the long-term challenges and gaps with regards to implementing these technologies into home-based telerehabilitation, are discussed.
SARS-CoV-2 variants B.1.351 and B.1.1.248: Escape from therapeutic antibodies and antibodies induced by infection and vaccination

The global spread of SARS-CoV-2/COVID-19 is devastating health systems and economies worldwide. Recombinant or vaccine-induced neutralizing antibodies are used to combat the COVID-19 pandemic. However, recently emerged SARS-CoV-2 variants B.1. 1.7 (UK), B.1. 351 (South Africa) and B.1. 1.248 (Brazil) harbor mutations in the viral spike (S) protein that may alter virus-host cell interactions and confer resistance to inhibitors and antibodies. Here, using pseudoparticles, we show that entry of UK, South Africa and Brazil variant into human cells is susceptible to blockade by entry inhibitors. In contrast, entry of the South Africa and Brazil variant was partially (Casirivimab) or fully (Bamlanivimab) resistant to antibodies used for COVID-19 treatment and was less efficiently inhibited by serum/plasma from convalescent or BNT162b2 vaccinated individuals. These results suggest that SARS-CoV-2 may escape antibody responses, which has important implications for efforts to contain the pandemic.
Beyond fitness: selection and information flow through the constructive steps in lifecycles

The replicator is the fundamental abstraction of evolutionary genetics. Only for replicators do Darwin’s concept of fitness as differential reproductive success, and the formalization by Fisher and Price in terms of apportionment of descendant populations to ancestors, coincide without ambiguity or potential conflict. The organization of the Price equation, causal interpretations of Fisher’s Fundamental Theorem and its relatives, and the abstraction of fitness as the sole channel through which information flows in from environments to form the adapted states of evolving populations, all follow from properties of replicators imposed artificially on the genetics of more complex lifecycles. Here it is shown how to generalize this role of the replicator to the autocatalytic flows in the generators of Stoichiometric Populations Processes, and to generalize from the unique summary statistic of fitness to a class of summary statistics that appear as regression coefficients against the autocatalytic flows associated with reproduction, including replication but also including constructive operations beyond simple copying. Both the statistical construction and the causal interpretation of Fisher’s Theorem and the Price Equation generalize from replicators and fitness to the wider class of regressions. Ad hoc corrections for mis-specified fitness models, which the conventional Price equation groups with “environment” effects, become part of a Fisher covariance on the basis of flows, which takes on a consistent causal interpretation in terms of an expanded concept of selection recognizing distributed information. A measure is derived for the information in the trajectory of a population evolving under a stoichiometric stochastic process, as the large-deviation function for that trajectory from a null model. The interpretation of fitness and other regression coefficients as channels for causation and information flow is derived from their inner product with the gradient of the trajectory entropy.
Study of Symptomatic vs. Silent Brain Infarctions on MRI in Elderly Subjects

Brain infarctions are closely associated with future risk of stroke and dementia. Our goal was to report (i) frequency and characteristics that differentiate symptomatic vs. silent brain infarctions (SBI) on MRI and (ii) frequency and location by vascular distribution (location of stroke by major vascular territories) in a population based sample. From Mayo Clinic Study of Aging, 347 participants (≥50 years) with infarcts detected on their first MRI were included. Infarct information was identified visually on a FLAIR MRI image and a vascular territory atlas was registered to the FLAIR image data in order to identify the arterial territory of infarction. We identified the subset with a clinical history of stroke based on medical chart review and used a logistic regression to evaluate the risk factors associated with greater probability of a symptomatic stroke vs. SBI. We found that 14% of all individuals with infarctions had a history of symptomatic stroke (Silent: n = 300, symptomatic: n = 47). Factors associated with a symptomatic vs. SBI were size which had an odds ratio of 3.07 (p < 0.001), greater frequency of hypertension (odds ratio of 4.12, p = 0.025) and alcohol history (odds ratio of 4.58, p = 0.012). The frequency of infarcts was greater in right hemisphere compared to the left for SBI. This was primarily driven by middle cerebral artery (MCA) infarcts (right = 60%, left = 40%, p = 0.005). While left hemisphere strokes are more common for symptomatic carotid disease and in clinical trials, right hemispheric infarcts may be more frequent in the SBI group.
Adaptive Gene Content and Allele Distribution Variations in the Wild and Domesticated Populations of Saccharomyces cerevisiae

Recent studies on population genomics of Saccharomyces cerevisiae have substantially improved our understanding of the genetic diversity and domestication history of the yeast. However, the origin of the domesticated population of S. cerevisiae and the genomic changes responsible for ecological adaption of different populations and lineages remain to be fully revealed. Here we sequenced 64 African strains from various indigenous fermented foods and forests in different African countries and performed a population genomic analysis on them combined with a set of previously sequenced worldwide S. cerevisiae strains representing the maximum genetic diversity of the species documented so far. The result supports the previous observations that the wild and domesticated populations of S. cerevisiae are clearly separated and that the domesticated population diverges into two distinct groups associated with solid- and liquid-state fermentations from a single ancestor. African strains are mostly located in basal lineages of the two domesticated groups, implying a long domestication history of yeast in Africa. We identified genes that mainly or exclusively occur in specific groups or lineages and genes that exhibit evident group or lineage specific allele distribution patterns. Notably, we show that the homing endonuclease VDE is generally absent in the wild but commonly present in the domesticated lineages of S. cerevisiae. The genes with group specific allele distribution patterns are mostly enriched in functionally similar or related fundamental metabolism processes, including the evolutionary conserved TOR signaling pathway.
Comparative Analyses of Phytochemical Variation Within and Between Congeneric Species of Willow Herb, Epilobium hirsutum and E. parviflorum: Contribution of Environmental Factors

The plants in the Epilobium genus are considered to have several important medicinal properties due to their unique chemical composition. Although metabolic profiles of medicinal plants are mainly controlled by genetic factors, their production is also to some degree influenced by environmental factors, thus, variations in the levels of phytochemicals may represent long-term ecological and evolutionary interactions. In order to depict the magnitude of natural variation in level of chemical compounds among conspecific populations of Epilobium hirsutum (n = 31) and E. parviflorum (n = 16), metabolite profiling of aerial parts of plants was performed with gas chromatography/mass spectrometry analysis. Putative identification and structure annotation revealed the presence of 74 compounds including 46 compounds considered secondary metabolites categorized into flavonoids (n = 8), phenolic acids (n = 26), steroids (n = 3), and terpenes (n = 5) across all populations. Although there was a considerable natural variation among conspecific populations, principal component analysis revealed a clear separation of populations of each species based on the second main principal component which was highly correlated with eight secondary metabolites. The level of secondary metabolites was significantly correlated between species (r = 0.91), suggesting shared metabolic pathways underlying the production of chemical compounds. In addition, redundancy and variance partitioning analyses by including bioclimatic variables and altitude revealed a significant contribution of elevation in explaining the total variation of secondary metabolites in E. hirsutum. Two-thirds of all secondary metabolites were significantly correlated with altitude in E. hirsutum. The large-scale geographic analyses of populations revealed additionally detected flavonoids and terpenes (E. hirsutum and E. parviflorum) and steroids (E. hirsutum) for the first time. This study provides significant information on additional chemical compounds found across the distribution range of the two ecologically important species of willow herb and emphasizes the importance of geographic-wide sampling as a valuable strategy to depict intraspecific and interspecific variability in chemical traits.
Surgical Complexity and Outcome During the Implementation Phase of a Robotic Colorectal Surgery Program—A Retrospective Cohort Study

Background Robotic surgery holds particular promise for complex oncologic colorectal resections, as it can overcome many limitations of the laparoscopic approach. However, similar to the situation in laparoscopic surgery, appropriate case selection (simple vs. complex) with respect to the actual robotic expertise of the team may be a critical determinant of outcome. The present study aimed to analyze the clinical outcome after robotic colorectal surgery over time based on the complexity of the surgical procedure. Methods All robotic colorectal resections (n = 85) performed at the Department of Surgery, Medical University of Vienna, between the beginning of the program in April 2015 until December 2019 were retrospectively analyzed. To compare surgical outcome over time, the cohort was divided into 2 time periods based on case sequence (period 1: patients 1–43, period 2: patients 44–85). Cases were assigned a complexity level (I-IV) according to the type of resection, severity of disease, sex and body mass index (BMI). Postoperative complications were classified using the Clavien-Dindo classification. Results In total, 47 rectal resections (55.3%), 22 partial colectomies (25.8%), 14 abdomino-perineal resections (16.5%) and 2 proctocolectomies (2.4%) were performed. Of these, 69.4% (n = 59) were oncologic cases. The overall rate of major complications (Clavien Dindo III-V) was 16.5%. Complex cases (complexity levels III and IV) were more often followed by major complications than cases with a low to medium complexity level (I and II; 25.0 vs. 5.4%, p = 0.016). Furthermore, the rate of major complications decreased over time from 25.6% (period 1) to 7.1% (period 2, p = 0.038). Of note, the drop in major complications was associated with a learning effect, which was particularly pronounced in complex cases as well as a reduction of case complexity from 67.5% to 45.2% in the second period (p = 0.039). Conclusions The risk of major complications after robotic colorectal surgery increases significantly with escalating case complexity (levels III and IV), particularly during the initial phase of a new colorectal robotic surgery program. Before robotic proficiency has been achieved, it is therefore advisable to limit robotic colorectal resection to cases with complexity levels I and II in order to keep major complication rates at a minimum.
Factors Influencing Pregnancy and Postpartum Weight Management in Women of African and Caribbean Ancestry Living in High Income Countries: Systematic Review and Evidence Synthesis Using a Behavioral Change Theoretical Model

Background: Women of black African heritage living in high income countries (HIC) are at risk of obesity and weight-related complications in pregnancy. This review aimed to synthesize evidence concerning attitudes to weight management-related health behaviors in pregnancy and postpartum, in women of black African ancestry, living in high-income countries. Methods: A systematic review of the literature and thematic evidence synthesis using the Capability-Opportunity-Motivation Behavioral change theoretical model (COM-B). Databases searched included MEDLINE, EMBASE, Web of Science, and Scopus. The CASP tool was used to assess quality. Results: Twenty-four papers met the selection criteria, most of which were from the US. Motivational factors were most commonly described as influencers on behavior. Normative beliefs about “eating for two,” weight gain being good for the baby, the baby itself driving food choice, as well as safety concerns about exercising in pregnancy, were evident and were perpetuated by significant others. These and other social norms, including a cultural acceptance of larger body shapes, and daily fast food, created a challenge for healthy behavior change. Women also had low confidence in their ability to lose weight in the postpartum period. Behavior change techniques, such as provision of social support, use of credible sources, and demonstration may be useful to support change. Conclusions: The women face a range of barriers to engagement in weight-related health behaviors at this life-stage. Using a theoretical behavior change framework can help identify contextual factors that may limit or support behavior change.
Beyond Looking for the Rewarded Target: The Effects of Reward on Attention in Search Tasks

One puzzling result in training-test paradigms is that effects of reward-associated stimuli on attention are often seen in test but not in training. We focus on one study, where reward-related performance benefits occur in the training and which was discussed contentiously. By using a similar design, we conceptually replicated the results. Moreover, we investigated the underlying mechanisms and processes resulting in these reward-related performance benefits. In two experiments, using search tasks and having participants perform the tasks either with or without individually adjusted time pressure, we disentangled the mechanisms and processes contributing to the reward-related benefits. We found evidence that not only search efficiency is increased with increasing reward, but also that non-search factors contribute to the results. By also investigating response time distributions, we were able to show that reward-related performance effects increased as search time increased in demanding tasks but not in less demanding tasks. Theoretical implications of the results regarding how reward influences attentional processing are discussed.
The Late Positive Potential as a Reliable Neural Marker of Cognitive Reappraisal in Children and Youth: A Brief Review of the Research Literature

The mental health of young people is a growing public health concern. With socio-emotional difficulties in youth often resulting in psychiatric disorders later in life and most with mental health conditions rather stabilizing in time, it is essential to support healthy socio-emotional development. With a comprehensive definition of mental health, since emotion regulation (ER) plays a critical role in prevention, it becomes imperative to better understand how children effectively manage their emotions from an early age. Determining effective use of ER skills relies on adequate measurements. Typical methods of data collection in children present consistent shortcomings. This review addresses research findings considering the suitability of the late positive potential measured through electroencephalogram as a neural indicator of ER in children and youth. There is growing evidence, as reported in this review, that indicates that the late positive potential may be a reliable neural indicator of children's cognitive reappraisal abilities more specifically. Results generally suggest that the late positive potential amplitudes are sensitive to directed reappraisal in children. However, given the scant research, questions remain regarding developmental trends, methodology, interindividual variability, reappraisal of various stimuli, and how the late positive potential may relate to more traditional measures of ER. Directions for future research are provided, which are expected to address unanswered research questions and fill literature gaps. Taken together, the findings reviewed indicate that the late positive potential is generally sensitive to directed cognitive reappraisal in children and that there is promise of establishing this neural marker as an indicator of ER.
Regioselective Anodic Monofluorination of Ethers, Lactones, Carbonates, and Esters Using Ionic Liquid Fluoride Salts

Regioselective anodic fluorination of various cyclic and open-chain oxygen compounds like ethers, lactones, carbonates, and esters in ionic liquids, Et 4 NF-nHF and Et 3 N-nHF (n = 4,5) without a solvent was successfully carried out to give the corresponding monofluorinated products in moderate to high yields. It was demonstrated that some fluorinated ethers were isolated simply by distillation of the electrolytic solutions. This is the first example of successful partial anodic fluorination under completely solvent-free conditions.
Wolves, Crows, and Spiders: An eclectic Literature Review inspires a Model explaining Humans’ similar Reactions to ecologically different Wildlife

Coming from the vantage point of managing human relations to potentially problematic wildlife, we bring the following questions: Where do people’s emotionally vigorous and polarized reactions originate? Why do these reactions to different scenarios of human-wildlife conflict appear similar? In this paper we provide the findings from an eclectic review of purposefully sampled literature on human relations to wolves, corvids and spiders. Based on this synthesis, we propose three answers to those questions: 1). The emotional vigor inherent in human-wildlife conflicts is caused by the activation of deep-seated and emotionally loaded factors, specifically worldviews on human-nature relations more broadly, an integral human motivation for seeking control, and symbolic associations to darkness. 2). The opposing attitudes on human-wildlife relations derive from people’s diverging worldviews and different degrees of wanting control in a situation of human-wildlife conflict. 3). Despite ecological specificities, various cases of human-wildlife conflicts may evoke similar mental processes and, accordingly, the same reactions in people. Consequentially, it is possible to develop transferable solutions that may contribute to managing challenges in different instances of human-wildlife encounters.