Miracle-dz/UniFAR-FTUs huggingface dataset:
High Clonality and Geographically Separated Cryptic Lineages in the Threatened Temperate Coral, Acropora pruinosa

Acropora pruinosa is a threatened zooxanthellate scleractinian coral that is distributed in the temperate areas along the coastline of Japan and the northern area of the South China Sea. Since A. pruinosa propagates both asexually and sexually, assessing clonal diversity and genetic connectivity among populations is important for conservation. In addition, high morphological variations in the field create confusion during species identification. To examine the existence of hidden genetic lineages, clonality, and genetic connectivity of A. pruinosa for conservation, we applied microsatellite analysis. Clustering analysis indicated two distinct geographically separated genetic lineages: one is distributed in the west, and the other is distributed in the east. The two lineages co-existed in Nishidomari, Kochi. There was no obvious difference in morphological characteristics between the two lineages. Although the factors influencing the observed distribution patterns remain unknown, there is a possibility that the two lineages might have diverged somewhere in the north-western Kyushu and north-eastern Pacific coast habitats in the past, and then periodically colonized the current habitats. A low clonal diversity was observed in most of the populations, indicating a high rate of asexual reproduction associated with their branching morphologies. In addition, there are strong genetic structuring in this species, indicating weak connectivity among populations. These results indicated a low larval dispersal potential among populations and that populations are basically sustained by a high rate of clone propagation and self-seeding. The existence of cryptic lineages and genetically isolated populations with high clonality emphasized the importance of conservation of A. pruinosa.
DeepOMe: A Web Server for the Prediction of 2′-O-Me Sites Based on the Hybrid CNN and BLSTM Architecture

2′-O-methylations (2′-O-Me or Nm) are one of the most important layers of regulatory control over gene expression. With increasing attentions focused on the characteristics, mechanisms and influences of 2′-O-Me, a revolutionary technique termed Nm-seq were established, allowing the identification of precise 2′-O-Me sites in RNA sequences with high sensitivity. However, as the costs and complexities involved with this new method, the large-scale detection and in-depth study of 2′-O-Me is still largely limited. Therefore, the development of a novel computational method to identify 2′-O-Me sites with adequate reliability is urgently needed at the current stage. To address the above issue, we proposed a hybrid deep-learning algorithm named DeepOMe that combined Convolutional Neural Networks (CNN) and Bidirectional Long Short-term Memory (BLSTM) to accurately predict 2′-O-Me sites in human transcriptome. Validating under 4-, 6-, 8-, and 10-fold cross-validation, we confirmed that our proposed model achieved a high performance (AUC close to 0.998 and AUPR close to 0.880). When testing in the independent data set, DeepOMe was substantially superior to NmSEER V2.0. To facilitate the usage of DeepOMe, a user-friendly web-server was constructed, which can be freely accessed at http://deepome.renlab. org.
Along-Strike Rapid Structural and Geomorphic Transition From Transpression to Strike-Slip to Transtension Related to Active Microplate Rotation, Papua New Guinea

The area of southeastern Papua New Guinea includes three active microplates – the Trobriand, Woodlark, and Solomon Sea plates – that are being deformed by regional convergence between the much larger Pacific and Australian Plates. The landward extent of the plate boundary between the Trobriand and Australian Plates corresponds to the Owen-Stanley Fault Zone (OSFZ), an onland and continuous 510 km-long left-lateral strike-slip fault that forms a linear, intermontane valley within the elongate Owen-Stanley Range (OSR) and continues as a 250 km-long low-angle normal fault along the margins of Goodenough and Woodlark basins. GPS geodesy reveals that the Trobriand microplate has undergone rapid counter-clockwise rotation since the Late Miocene (8.4 Ma) and that this rotation about a nearby pole of rotation predicts transpressional deformation along the 250 km-long northwestern segment of the OSFZ, strike-slip motion along a 100 km-long central segment, and transtension along the 270 km-long ESE-trending southeastern segment of OSFZ. In order to illustrate the along-strike variations in neotectonic uplift resulting from the changing structure of the OSFZ, we delineated 3903 river segments in the northeastern side of the OSR drainage divide and derived river longitudinal profiles along each river segment. Normalized steepness indices (ksn) and knickpoint clusters are the highest and most concentrated, respectively, for the northwestern transpressional segment of the OSR, moderately high and concentrated along the southeastern segment of the OSR, and the lowest and least concentrated along the central strike-slip segment. These geomorphological indices indicate that most of the plate boundary uplift occurs along the transpressional and transtensional segments that are connected by the central strike-slip zone. Within this overall pattern of structural variation, abrupt changes in the azimuth of the OSFZ create more localized anomalies in the geomorphological indices.
Motor Symptom Lateralization Influences Cortico-Striatal Functional Connectivity in Parkinson's Disease

Objective: The striatum is unevenly impaired bilaterally in Parkinson's disease (PD). Because the striatum plays a key role in cortico-striatal circuits, we assume that lateralization affects cortico-striatal functional connectivity in PD. The present study sought to evaluate the effect of lateralization on various cortico-striatal circuits through resting-state functional magnetic resonance imaging (fMRI). Methods: Thirty left-onset Parkinson's disease (LPD) patients, 27 right-onset Parkinson's disease (RPD) patients, and 32 normal controls with satisfactory data were recruited. Their demographic, clinical, and neuropsychological information was collected. Resting-state fMRI was performed, and functional connectivity changes of seven subdivisions of the striatum were explored in the two PD groups. In addition, the associations between altered functional connectivity and various clinical and neuropsychological characteristics were analyzed by Pearson's or Spearman's correlation. Results: Directly comparing the LPD and RPD patients demonstrated that the LPD patients had lower FC between the left dorsal rostral putamen and the left orbitofrontal cortex than the RPD patients. In addition, the LPD patients showed aberrant functional connectivity involving several striatal subdivisions in the right hemisphere. The right dorsal caudate, ventral rostral putamen, and superior ventral striatum had decreased functional connectivity with the cerebellum and parietal and occipital lobes relative to the normal control group. The comparison between RPD patients and the controls did not obtain significant difference in functional connectivity. The functional connectivity between the left dorsal rostral putamen and the left orbitofrontal cortex was associated with contralateral motor symptom severity in PD patients. Conclusions: Our findings provide new insights into the distinct characteristics of cortico-striatal circuits in LPD and RPD patients. Lateralization of motor symptoms is associated with lateralized striatal functional connectivity.
Exploring Strategies to Optimise the Impact of Food-Specific Inhibition Training on Children’s Food Choices

Food-specific inhibition training (FSIT) is a computerised task requiring response inhibition to energy-dense foods within a reaction-time game. Previous work indicates that FSIT can increase the number of healthy foods (relative to energy-dense foods) children choose, and decrease calories consumed from sweets and chocolate. Across two studies, we explored the impact of FSIT variations (e.g., different response signals, different delivery modes) on children’s food choices within a time-limited hypothetical food-choice task. In Study 1, we varied the FSIT Go/No-Go signals to be emotive (happy vs. sad faces) or neutral (green vs. red signs). One-hundred-and-fifty-seven children were randomly allocated to emotive-FSIT, neutral-FSIT, or a non-food control task. Children participated in groups of 4–15. No significant FSIT effects were observed on food choices (all values of p > 0.160). Healthy-food choices decreased over time regardless of condition (p < 0.050). The non-significant effects could be explained by lower accuracy on energy-dense No-Go trials than in previous studies, possibly due to distraction in the group-testing environment. In Study 2, we compared computer-based FSIT (using emotive signals) and app-based FSIT (using neutral signals) against a non-food control with a different sample of 206 children, but this time children worked one-on-one with the experimenter. Children’s accuracy on energy-dense No-Go trials was higher in this study. Children in the FSIT-computer group chose significantly more healthy foods at post-training (M = 2.78, SE = 0.16) compared to the control group (M = 2.02, SE = 0.16, p = 0.001). The FSIT-app group did not differ from either of the other two groups (M = 2.42, SE = 0.16, both comparisons p > 0.050). Healthy choices decreased over time in the control group (p = 0.001) but did not change in the two FSIT groups (both p > 0.300) supporting previous evidence that FSIT may have a beneficial effect on children’s food choices. Ensuring that children perform FSIT with high accuracy (e.g., by using FSIT in quiet environments and avoiding group-testing) may be important for impacts on food choices though. Future research should continue to explore methods of optimising FSIT as a healthy-eating intervention for children.
The Pitfalls of in vivo Cardiac Physiology in Genetically Modified Mice – Lessons Learnt the Hard Way in the Creatine Kinase System

In order to fully understand gene function, at some point, it is necessary to study the effects in an intact organism. The creation of the first knockout mouse in the late 1980’s gave rise to a revolution in the field of integrative physiology that continues to this day. There are many complex choices when selecting a strategy for genetic modification, some of which will be touched on in this review, but the principal focus is to highlight the potential problems and pitfalls arising from the interpretation of in vivo cardiac phenotypes. As an exemplar, we will scrutinize the field of cardiac energetics and the attempts to understand the role of the creatine kinase (CK) energy buffering and transport system in the intact organism. This story highlights the confounding effects of genetic background, sex, and age, as well as the difficulties in interpreting knockout models in light of promiscuous proteins and metabolic redundancy. It will consider the dose-dependent effects and unintended consequences of transgene overexpression, and the need for experimental rigour in the context of in vivo phenotyping techniques. It is intended that this review will not only bring clarity to the field of cardiac energetics, but also aid the non-expert in evaluating and critically assessing data arising from in vivo genetic modification.
Limitations of Only Reporting the Odds Ratio in the Age of Precision Medicine: A Deterministic Simulation Study

Precision medicine aims to tailor healthcare to sub-groups of patients identified by common characteristics instead of a one-approach-fits-all paradigm (1–5). By creating prognostic machine learning models based on patient characteristics, we can stratify patients into multiple risk groups, allowing patients in the low(er) risk group to be treated less aggressively, while high(er) risk groups may be treated more aggressively. When reporting the performance of a binary classifier (such as a machine learning model or a positive/negative lab test with a classification threshold), a pervasive metric in medical literature is the area under the receiver operating characteristic curve (AUROC, or more commonly, AUC) (6, 7), in addition to measures derived from the confusion matrix such as sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). When assessing the association between a binary patient characteristic, say the presence of a comorbidity such as heart disease, and a binary patient outcome, say death within a certain follow-up period, a ubiquitous metric in medical literature is the odds ratio (OR) (8). The odds ratio is defined as the ratio of the odds of the outcome in the presence and the absence of that characteristic. The risk ratio (RR), which is the ratio of the probabilities rather than the odds used in the OR, is arguably a more intuitive and useful metric. If the outcome is rare (<<1%), the OR is approximately equal to the RR (9, 10). Several publications exist explaining the rationale for using OR despite its limitations (11–13). The strongest reasons for using OR are: (1) clinical data often makes it impossible to calculate RR, making OR the practical choice, and (2) OR can be easily calculated when using logistic regression. In this paper, we aim to prove that when using a binary patient characteristic for patient stratification, it is essential to include metrics in addition to OR to provide a complete picture; we do not advocate replacing OR, but supplementing it. While the limitations of OR compared to RR have been discussed in the literature (14–16), in this work, we illustrate their interdependence. Furthermore, using a deterministic simulation, we elucidate the relationship betweenOR and AUC, providing insight into why reporting OR without AUC can be misleading. We do not suggest that AUC is the most important metric. The reason we chose AUC for performing our simulations is that unlike sensitivity/specificity and PPV/NPV, it is not a pairedmetric, and thus easy to use in 2-D figures (i.e., OR and AUC), whereas paired metrics would require 3-D figures (e.g., OR, PPV, NPV).
Porcine Myeloid Antimicrobial Peptides: A Review of the Activity and Latest Advances

Traditional antibiotics have made great contributions to human health and animal husbandry since the discovery of penicillin in 1928, but bacterial resistance and drug residues are growing threats to global public health due to the long-term uncontrolled application of antibiotics. There is a critical need to develop new antimicrobial drugs to replace antibiotics. Antimicrobial peptides (AMPs) are distributed in all kingdoms of life, presenting activity against pathogens as well as anticancer, anti-inflammatory, and immunomodulatory activities; consequently, they have prospects as new potential alternatives to antibiotics. Porcine myeloid antimicrobial peptides (PMAPs), the porcine cathelicidin family of AMPs, have been reported in the literature in recent years. PMAPs have become an important research topic due to their strong antibacterial activity. This review focuses on the universal trends in the biochemical parameters, structural characteristics and biological activities of PMAPs.
Methanotrophs: Discoveries, Environmental Relevance, and a Perspective on Current and Future Applications

Methane is the final product of the anaerobic decomposition of organic matter. The conversion of organic matter to methane (methanogenesis) as a mechanism for energy conservation is exclusively attributed to the archaeal domain. Methane is oxidized by methanotrophic microorganisms using oxygen or alternative terminal electron acceptors. Aerobic methanotrophic bacteria belong to the phyla Proteobacteria and Verrucomicrobia, while anaerobic methane oxidation is also mediated by more recently discovered anaerobic methanotrophs with representatives in both the bacteria and the archaea domains. The anaerobic oxidation of methane is coupled to the reduction of nitrate, nitrite, iron, manganese, sulfate, and organic electron acceptors (e.g., humic substances) as terminal electron acceptors. This review highlights the relevance of methanotrophy in natural and anthropogenically influenced ecosystems, emphasizing the environmental conditions, distribution, function, co-existence, interactions, and the availability of electron acceptors that likely play a key role in regulating their function. A systematic overview of key aspects of ecology, physiology, metabolism, and genomics is crucial to understand the contribution of methanotrophs in the mitigation of methane efflux to the atmosphere. We give significance to the processes under microaerophilic and anaerobic conditions for both aerobic and anaerobic methane oxidizers. In the context of anthropogenically influenced ecosystems, we emphasize the current and potential future applications of methanotrophs from two different angles, namely methane mitigation in wastewater treatment through the application of anaerobic methanotrophs, and the biotechnological applications of aerobic methanotrophs in resource recovery from methane waste streams. Finally, we identify knowledge gaps that may lead to opportunities to harness further the biotechnological benefits of methanotrophs in methane mitigation and for the production of valuable bioproducts enabling a bio-based and circular economy.
Silencing of Long Noncoding RNA Growth Arrest–Specific 5 Alleviates Neuronal Cell Apoptosis and Inflammatory Responses Through Sponging microRNA-93 to Repress PTEN Expression in Spinal Cord Injury

A secondary injury induced by a spinal cord injury (SCI) remains the main cause of devastating neural dysfunction; therefore, it has been the subject of focused research for many years. Long noncoding RNA (lncRNA) has been found to participate in the SCI process, and this finding presents a high potential for diagnosis and treatment; however, the role of lncRNA in a secondary injury induced by SCI remains unclear. The aim of this study was to investigate the regulatory effect of lncRNA growth arrest–specific transcript 5 (GAS5) in secondary injury during SCI. The SCI mice model and hypoxic cellular model were established to research the roles of lncRNA GAS5 during SCI. Reverse transcription quantitative polymerase chain reaction (qRT-PCR) was conducted to determine the expression levels of microR-93 (miR-93) and lncRNA GAS5. Western blot analysis of the apoptosis regulator protein and terminal deoxynucleotidyl transferase dUTP nick end labeling assay was conducted to evaluate neuron cell apoptosis. Basso, Beattie, and Bresnahan (BBB) scores were calculated to assess neurological function. Flow cytometry was used to determine neuron cell apoptosis. The associations among GAS5, miR-93, and the phosphatase and tensin homolog (PTEN) were disclosed using RNA immunoprecipitation (RIP) assay, RNA pulldown assay, and dual-luciferase reporter assay. QRT-PCR demonstrated that GAS5 was significantly upregulated in both the SCI mice and hypoxic cellular models. GAS5 knockdown suppressed neuron cell apoptosis and inflammatory response in the SCI mice model. Further studies have indicated that GAS5 functions as a competing endogenous RNA (ceRNA) by sponging miR-93 in neuronal cells. In addition, PTEN was a target of miR-93, and GAS5 knockdown exhibited its anti-apoptotic and anti-inflammatory effects through the miR-93/PTEN axis. These findings suggest that the GAS5/miR-93/PTEN axis may be a promising therapeutic target for SCI.
Translational Block in Stroke: A Constructive and “Out-of-the-Box” Reappraisal

Why can we still not translate preclinical research to clinical treatments for acute strokes? Despite > 1000 successful preclinical studies, drugs, and concepts for acute stroke, only two have reached clinical translation. This is the translational block. Yet, we continue to routinely model strokes using almost the same concepts we have used for over 30 years. Methodological improvements and criteria from the last decade have shed some light but have not solved the problem. In this conceptual analysis, we review the current status and reappraise it by thinking “out-of-the-box” and over the edges. As such, we query why other scientific fields have also faced the same translational failures, to find common denominators. In parallel, we query how migraine, multiple sclerosis, and hypothermia in hypoxic encephalopathy have achieved significant translation successes. Should we view ischemic stroke as a “chronic, relapsing, vascular” disease, then secondary prevention strategies are also a successful translation. Finally, based on the lessons learned, we propose how stroke should be modeled, and how preclinical and clinical scientists, editors, grant reviewers, and industry should reconsider their routine way of conducting research. Translational success for stroke treatments may eventually require a bold change with solutions that are outside of the box.
Relative Weight of Organic Waste Origin on Compost and Digestate 16S rRNA Gene Bacterial Profilings and Related Functional Inferences

Even though organic waste (OW) recycling via anaerobic digestion (AD) and composting are increasingly used, little is known about the impact of OW origin (fecal matters and food and vegetable wastes) on the end products’ bacterial contents. The hypothesis of a predictable bacterial community structure in the end products according to the OW origin was tested. Nine OW treatment plants were selected to assess the genetic structure of bacterial communities found in raw OW according to their content in agricultural and urban wastes and to estimate their modifications through AD and composting. Two main bacterial community structures among raw OWs were observed and matched a differentiation according to the occurrences of urban chemical pollutants. Composting led to similar 16S rRNA gene OTU profiles whatever the OW origin. With a significant shift of about 140 genera (representing 50% of the bacteria), composting was confirmed to largely shape bacterial communities toward similar structures. The enriched taxa were found to be involved in detoxification and bioremediation activities. This process was found to be highly selective and favorable for bacterial specialists. Digestates showed that OTU profiles differentiated into two groups according to their relative content in agricultural (manure) and urban wastes (mainly activated sludge). About one third of the bacterial taxa was significantly affected by AD. In digestates of urban OW, this sorting led to an enrichment of 32 out of the 50 impacted genera, while for those produced from agricultural or mixed urban/agricultural OW (called central OW), a decay of 54 genera over 60 was observed. Bacteria from activated sludge appeared more fit for AD than those of other origins. Functional inferences showed AD enriched genera from all origins to share similar functional traits, e.g., chemoheterotrophy and fermentation, while being often taxonomically distinct. The main functional traits among the dominant genera in activated sludge supported a role in AD. Raw OW content in activated sludge was found to be a critical factor for predicting digestate bacterial contents. Composting generated highly predictable and specialized community patterns whatever the OW origin. AD and composting bacterial changes were driven by functional traits selected by physicochemical factors such as temperature and chemical pollutants.