Miracle-dz/UniFAR-FTUs huggingface dataset:
Convergence of DNA Methylation Profiles of the Reef Coral Porites astreoides in a Novel Environment

Phenotypic acclimatization is an organismal response to environmental change that may be rooted in epigenetic mechanisms. In reef building corals, organisms that are severely threatened by environmental change, some evidence suggests that DNA methylation is an environmentally responsive mediator of acclimatization. We investigated changes in DNA methylation of the reef coral Porites astreoides in response to simulated environmental change. Coral colonies were sampled from a variety of habitats on the Belize Barrier Reef and transplanted to a common garden for 1 year. We used restriction site associated DNA sequencing, including a methylation-sensitive variant, to subsample the genome and assess changes in DNA methylation levels after a year in the common garden. Methylation changes among the 629 CpG loci we recovered were subtle, yet coral methylomes were more similar to each other after a year in the common garden together, indicating convergence of methylation profiles in the common environment. Differentially methylated loci showed matches with both coding and non-coding RNA sequences with putative roles in intracellular signaling, apoptosis, gene regulation, and epigenetic crosstalk. There was a positive and significant relationship between genetic and epigenetic variation, providing evidence of methylation heritability. Altogether, our results suggest that DNA methylation in P. astreoides is at least somewhat responsive to environmental change, reflective of the environment, and heritable, characteristics necessary for methylation to be implicated as part of potential transgenerational acclimatization responses.
Aggressive Behavior, Hostility, and Associated Care Needs in Patients With Psychotic Disorders: A 6-Year Follow-Up Study

Background: Hostility and aggressive behavior in patients with psychotic disorders are associated with demographic and clinical risk factors, as well as with childhood adversity and neglect. Care needs are an essential concept in clinical practice; care needs in the domain of safety for others reflect the actual problem the patient has. Hostility, aggressive behavior, and associated care needs, however, are often studied in retrospect. Method: In a sample of 1,119 patients with non-affective psychotic disorders, who were interviewed three times over a period of 6 years, we calculated the incidence of hostility, self-reported maltreatment to others and care needs associated with safety for other people (safety-to-others). Regression analysis was used to analyze the association between these outcomes and risk factors. The population attributable fraction (PAF) was used to calculate the proportion of the outcome that could potentially be prevented if previous expressions of adverse behavior were eliminated. Results: The yearly incidence of hostility was 2.8%, for safety-to-others 0.8% and for maltreatment this was 1.8%. Safety-to-others was associated with previous hostility and vice versa, but, assuming causality, only 18% of the safety-to-others needs was attributable to previous hostility while 26% was attributable to impulsivity. Hostility, maltreatment and safety-to-others were all associated with number of unmet needs, suicidal ideation and male sex. Hostility and maltreatment, but not safety-to-others, were associated with childhood adversity. Neither safety-to-others, maltreatment nor hostility were associated with premorbid adjustment problems. Conclusion: The incidence of hostility, self-reported aggressive behaviors, and associated care needs is low and linked to childhood adversity. Known risk factors for prevalence also apply to incidence and for care needs associated with safety for other people. Clinical symptoms can index aggressive behaviors years later, providing clinicians with some opportunity for preventing future incidents.
Reaction Time Data in Music Cognition: Comparison of Pilot Data From Lab, Crowdsourced, and Convenience Web Samples

Reaction time (RT) methods have been a mainstay of research in cognitive psychology for over a century. RT methods have been applied in domains as diverse as visual perception (e.g., Ando et al., 2002), personality traits (e.g., Robinson and Tamir, 2005), and social psychology (e.g., Wang et al., 2017). In music cognition, RT methods have been used as an indirect measure of several phenomena such as harmonic expectation (Bharucha and Stoeckig, 1986), melodic expectation (Aarden, 2003) cross modal priming (Goerlich et al., 2012), absolute pitch (Miyazaki, 1989; Bermudez and Zatorre, 2009), and emotional responses (Bishop et al., 2009). Traditionally, reaction time data has been collected in a lab. However, recent years have seen the development of software capable of collecting accurate response time data online, for instance PsyToolkit (Stoet, 2010, 2017), PsychoPy (Peirce et al., 2019), Gorilla (Anwyl-Irvine et al., 2019), and Qualtrics' QRTEngine (Barnhoorn et al., 2015) amongst others. In the early days of web-based reaction time studies, there was considerable skepticism about the viability of RT data collected online. Despite the prevalence of software specifically designed to collect reaction time data online, and the increasing incidence of Web-based data collection, there remains a degree of caution around online reaction time studies. However, recent research (Barnhoorn et al., 2015; de Leeuw and Motz, 2016; Hilbig, 2016) suggests that online reaction time data is perhaps more trustworthy than was previously thought, but these studies have not yet involved music as stimuli. Alongside the developments in software, recruitment of participants in online studies has been made easier by the prevalence of social media and crowdsourcing platforms such as Amazon's MTurk service and Prolific. Not surprisingly, the use of crowdsourced samples by researchers is growing rapidly (Stewart et al., 2017). However, to the authors' knowledge (with the exception of de Leeuw and Motz, 2016) the comparisons of laboratory and online RT data have focused on descriptive measures of the RT distributions, and relatively little attention has been paid to the agreement between the RT distributions as a whole. Moreover, none of these studies considers phenomena associated with music cognition. Given the widespread use of RT methods in music cognition and the growth of crowdsourcing as a recruitment tool, the authors consider there to be a need to test the viability of online RT collection specifically in the case of music cognition. The present data report offers the results of a response time task completed in three different contexts—in a standard lab setting (“Lab”), online recruited via “traditional” online techniques (“Web”) and crowdsourced vis Prolific.ac (“CS”). Below, we present summary data for the three data sets before testing the comparability of the three data sets on an item-by-item basis.
Preservation of Interference Effects in Working Memory After Orbitofrontal Damage

Orbitofrontal cortex (OFC) is implicated in multiple cognitive processes, including inhibitory control, context memory, recency judgment, and choice behavior. Despite an emerging understanding of the role of OFC in memory and executive control, its necessity for core working memory (WM) operations remains undefined. Here, we assessed the impact of OFC damage on interference effects in WM using a Recent Probes task based on the Sternberg item-recognition task (1966). Subjects were asked to memorize a set of letters and then indicate whether a probe letter was presented in a particular set. Four conditions were created according to the forthcoming response (“yes”/“no”) and the recency of the probe (presented in the previous trial set or not). We compared behavioral and electroencephalography (EEG) responses between healthy subjects (n = 14) and patients with bilateral OFC damage (n = 14). Both groups had the same recency pattern of slower reaction time (RT) when the probe was presented in the previous trial but not in the current one, reflecting the proactive interference (PI). The within-group electrophysiological results showed no condition difference during letter encoding and maintenance. In contrast, event-related potentials (ERPs) to probes showed distinct within-group condition effects, and condition by group effects. The response and recency effects for controls occurred within the same time window (300–500 ms after probe onset) and were observed in two distinct spatial groups including right centro-posterior and left frontal electrodes. Both clusters showed ERP differences elicited by the response effect, and one cluster was also sensitive to the recency manipulation. Condition differences for the OFC group involved two different clusters, encompassing only left hemisphere electrodes and occurring during two consecutive time windows (345–463 ms and 565–710 ms). Both clusters were sensitive to the response effect, but no recency effect was found despite the behavioral recency effect. Although the groups had different electrophysiological responses, the maintenance of letters in WM, the evaluation of the context of the probe, and the decision to accept or reject a probed letter were preserved in OFC patients. The results suggest that neural reorganization may contribute to intact recency judgment and response after OFC damage.
Predicting Brain Age of Healthy Adults Based on Structural MRI Parcellation Using Convolutional Neural Networks

Structural magnetic resonance imaging (MRI) studies have demonstrated that the brain undergoes age-related neuroanatomical changes not only regionally but also on the network level during the normal development and aging process. In recent years, many studies have focused on estimating age using structural MRI measurements. However, the age prediction effects on different structural networks remain unclear. In this study, we established age prediction models based on common structural networks using convolutional neural networks (CNN) with data from 1,454 healthy subjects aged 18–90 years. First, based on the reference map of CorticalParcellation_Yeo2011, we obtained structural network images for each subject, including images of the following: the frontoparietal network (FPN), the dorsal attention network (DAN), the default mode network (DMN), the somatomotor network (SMN), the ventral attention network (VAN), the visual network (VN), and the limbic network (LN). Then, we built a 3D CNN model for each structural network using a large training dataset (n = 1,303) and the predicted ages of the subjects in the test dataset (n = 151). Finally, we estimated the age prediction performance of CNN compared with Gaussian process regression (GPR) and relevance vector regression (RVR). The results of CNN showed that the FPN, DAN, and DMN exhibited the optimal age prediction accuracies with mean absolute errors (MAEs) of 5.55 years, 5.77 years, and 6.07 years, respectively, and the other four networks, i.e., the SMN, VAN, VN, and LN, tended to have larger MAEs of more than 8 years. With respect to GPR and RVR, the top three prediction accuracies were still from the FPN, DAN, and DMN; moreover, CNN made more precise predictions than GPR and RVR for these three networks. Our findings suggested that CNN has the optimal age prediction performance, and our age prediction model can be potentially used for brain disorder diagnosis according to age prediction differences.
Applications and Perspectives of Cascade Reactions in Bacterial Infection Control

Cascade reactions integrate two or more reactions, of which each subsequent reaction can only start when the previous reaction step is completed. Employing natural substrates in the human body such as glucose and oxygen, cascade reactions can generate reactive oxygen species (ROS) to kill tumor cells, but cascade reactions may also have potential as a direly needed, novel bacterial infection-control strategy. ROS can disintegrate the EPS matrix of infectious biofilm, disrupt bacterial cell membranes, and damage intra-cellular DNA. Application of cascade reactions producing ROS as a new infection-control strategy is still in its infancy. The main advantages for infection-control cascade reactions include the fact that they are non-antibiotic based and induction of ROS resistance is unlikely. However, the amount of ROS generated is generally low and antimicrobial efficacies reported are still far <3–4 log units necessary for clinical efficacy. Increasing the amounts of ROS generated by adding more substrate bears the risk of collateral damage to tissue surrounding an infection site. Collateral tissue damage upon increasing substrate concentrations may be prevented by locally increasing substrate concentrations, for instance, using smart nanocarriers. Smart, pH-responsive nanocarriers can self-target and accumulate in infectious biofilms from the blood circulation to confine ROS production inside the biofilm to yield long-term presence of ROS, despite the short lifetime (nanoseconds) of individual ROS molecules. Increasing bacterial killing efficacies using cascade reaction components containing nanocarriers constitutes a first, major challenge in the development of infection-control cascade reactions. Nevertheless, their use in combination with clinical antibiotic treatment may already yield synergistic effects, but this remains to be established for cascade reactions. Furthermore, specific patient groups possessing elevated levels of endogenous substrate (for instance, diabetic or cancer patients) may benefit from the use of cascade reaction components containing nanocarriers.
Melatonin Inhibits Formation of Mitochondrial Permeability Transition Pores and Improves Oxidative Phosphorylation of Frozen-Thawed Ram Sperm

Structural and functional damages to mitochondria of frozen-thawed sperm are a typical cryoinjury, with mitochondrial permeability transition pore (MPTP) formation being the hallmark change. Mitochondria are both a primary synthesis site and principle target for melatonin; this compound can directly inhibit MPTP formation and therefore confer protection at a mitochondrial level. The objective was to determine effects of melatonin on MPTP opening, viability, motility, and oxidative phosphorylation (OXPHOS) of frozen-thawed ram sperm. Ram semen was diluted in glucose-egg yolk buffer with 0 or 10−7 M melatonin (frozen and frozen + melatonin groups, respectively) and slow frozen, with fresh semen as Control. In frozen-thawed sperm, melatonin inhibited MPTP opening and lactate concentrations and improved sperm viability, motility, acetyl-CoA concentration and adenosine triphosphate (ATP) production. With regard to the underlying physiological mechanism, melatonin suppressed movement of citrate synthase, isocitrate dehydrogenase, oxoglutarate dehydrogenase complex, and F0F1-ATP synthase permeability from mitochondrial to cytosolic fractions induced by MPTP opening; furthermore, it increased mRNA expressions of respiratory chain complex components and activities of complexes I, II, III, and IV and thereby improved oxygen consumption capacity in frozen-thawed sperm. In conclusion, melatonin improved OXPHOS of frozen-thawed ram sperm, attributed to inhibition of cryopreservation-induced MPTP opening.
A Mobile Phone App for the Generation and Characterization of Motor Habits

Habits are a powerful route to efficiency; the ability to constantly shift between goal-directed and habitual strategies, as well as integrate them into behavioral output, is key to optimal performance in everyday life. When such ability is impaired, it may lead to loss of control and to compulsive behavior. Habits have successfully been induced and investigated in rats using methods such as overtraining stimulus-response associations and outcome devaluation, respectively. However, such methods have ineffectively measured habits in humans because (1) human habits usually involve more complex sequences of actions than in rats and (2) of pragmatic impediments posed by the extensive time (weeks or even months), it may take for routine habits to develop. We present here a novel behavioral paradigm—a mobile-phone app methodology—for inducing and measuring habits in humans during their everyday schedule and environment. It assumes that practice is key to achieve automaticity and proficiency and that the use of a hierarchical sequence of actions is the best strategy for capturing the cognitive mechanisms involved in habit formation (including “chunking”) and consolidation. The task is a gamified self-instructed and self-paced app on a mobile phone that enables subjects to learn and practice two sequences of finger movements, composed of chords and single presses. It involves a step-wise learning procedure in which subjects begin responding to a visual and auditory cued sequence by generating responses on the screen using four fingers. Such cues progressively disappear throughout 1 month of training, enabling the subject ultimately to master the motor skill involved. We present preliminary data for the acquisition of motor sequence learning in 29 healthy individuals, each trained over a month period. We demonstrate an asymptotic improvement in performance, as well as its automatic nature. We also report how people integrate the task into their daily routine, the development of motor precision throughout training, and the effect of intermittent reinforcement and reward extinction in habit preservation. The findings help to validate this “real world” app for measuring human habits.
Whole Slide Imaging and Its Applications to Histopathological Studies of Liver Disorders

Histological analysis of hepatic tissue specimens is essential for evaluating the pathology of several liver disorders such as chronic liver diseases, hepatocellular carcinomas, liver steatosis, and infectious liver diseases. Manual examination of histological slides on the microscope is a classically used method to study these disorders. However, it is considered time-consuming, limited, and associated with intra- and inter-observer variability. Emerging technologies such as whole slide imaging (WSI), also termed virtual microscopy, have increasingly been used to improve the assessment of histological features with applications in both clinical and research laboratories. WSI enables the acquisition of the tissue morphology/pathology from glass slides and translates it into a digital form comparable to a conventional microscope, but with several advantages such as easy image accessibility and storage, portability, sharing, annotation, qualitative and quantitative image analysis, and use for educational purposes. WSI-generated images simultaneously provide high resolution and a wide field of observation that can cover the entire section, extending any single field of view. In this review, we summarize current knowledge on the application of WSI to histopathological analyses of liver disorders as well as to understand liver biology. We address how WSI may improve the assessment and quantification of multiple histological parameters in the liver, and help diagnose several hepatic conditions with important clinical implications. The WSI technical limitations are also discussed.
Effects of Forest Fragment Area on Interactions Between Plants and Their Natural Enemies: Consequences for Plant Diversity at Multiple Spatial Scales

Density-dependent interactions between plants and their natural enemies, including fungal pathogens and insect herbivores, help maintain plant species coexistence and diversity at local scales (α-diversity). However, turnover in plant species composition across space also contributes to biodiversity at larger spatial scales (β-diversity). Despite mounting evidence that enemies can maintain α-diversity, we know little about their contributions to β-diversity. Additionally, in the light of widespread habitat fragmentation and potentially modified insect and pathogen communities in forest fragments, the effects of fragment area on their diversity-maintaining roles are largely unknown. We carried out a field experiment to investigate how natural enemies in impact tree α and β-diversity in a fragmented rainforest landscape in the Western Ghats, India. In 21 rainforest fragments, we suppressed insects and fungi/oomycetes with pesticides, and examined changes in the diversity of tree seedlings. We found that fungicide had no effect on α-diversity, but significantly decreased β-diversity (species turnover among plots). The facilitative effects of fungi and oomycetes on β-diversity, however, weakened as fragments decreased in area, indicating that certain specialized plant-pathogen interactions may be lost when fragments become smaller. Insecticide, in contrast, increased α-diversity but tended to decrease β-diversity between distant plots. In summary, we found that interactions between plants and their natural enemies help maintain β-diversity in large forest fragments but not in small fragments. Small fragments are often viewed as future reservoirs of biodiversity in human-dominated landscapes, but our findings suggest that modified interactions with natural enemies may result in the erosion of this diversity over time.
Sensing the Danger Signals: cis-Jasmone Reduces Aphid Performance on Potato and Modulates the Magnitude of Released Volatiles

In response to herbivory, plants synthesize and release variable mixtures of herbivore-induced plant volatiles (HIPVs) as indirect defense traits. Such induction of indirect plant defense can also be “switched on” by certain chemicals known as priming agents. Preceding work showed that the plant HIPV cis-jasmone (CJ) induced the emission of aphid defense-related volatiles affecting their behavioral response. However, little is known about the extent to which CJ-induced volatiles impacts aphid performance. In the current study, we conducted growth assays of potato aphids, Macrosiphum euphorbiae, observing their reproduction, development, and survival on CJ-primed potato plants. Adult M. euphoribae produced fewer neonates on CJ-treated plants compared to untreated plants. The weight and survival of M. euphorbiae reproduced neonates were significantly lower on CJ-treated plants. Additionally, there was a significant reduction in mean relative growth rate (MRGR) of M. euphoribae nymphs that fed on CJ-treated plants. Furthermore, the intrinsic rate of population increase (rm) of M. euphoribae was significantly reduced on CJ-treated plants. Volatile analysis showed that CJ treatment significantly increased the emission of differently assigned volatile groups that have functional or biosynthetic characteristics, i.e., alcohols, benzenoids, homoterpenes, ketones, and sesquiterpenes at all sampling periods. Such enhanced volatile emissions were persistent over 7 days, suggesting a long-lasting effect of CJ defense priming. A negative correlation was found between volatile emission and MRGR of M. euphoribae. Principal component analysis (PCA) of data for the volatiles showed that (Z)-3-hexen-1-ol, α-pinene, (E)-ocimene, (E)-4,8-dimethyl-1,3,7-nonatriene (DMNT), cis-jasmone, indole, and (E,E)-4,8,12-trimethyl-1,3,7,11-tridecatetraene (TMTT) were the main volatiles contributing to the emitted blends, suggesting possible involvement in the reduced performance of M. euphorbiae. Overall, our findings demonstrate that priming potato with CJ significantly results in elevated emission of known biologically active volatiles, which may negatively impact aphid settling and other performance traits on primed plants.