Miracle-dz/UniFAR-FTUs huggingface dataset:
Reconstructing the evolutionary history of a functionally diverse gene family reveals complexity at the genetic origins of novelty

Gene duplication is associated with the evolution of many novel biological functions at the molecular level. The dominant view, often referred to as “neofunctionalization”, states that duplications precede many novel gene functions by creating functionally redundant copies which are less constrained than singletons. However, numerous alternative models have been formulated, including some in which novel functions emerge prior to duplication. Unfortunately, few studies have reconstructed the evolutionary history of a functionally diverse gene family sufficiently well to differentiate between these models. Here we examined the evolution of the g2 family of phospholipase A2 (EC 3.1.1.4) in the genomes of 93 species from all major lineages of Vertebrata. This family is evolutionarily important and has been co-opted for a diverse range of functions, including innate immunity and venom. The genomic region in which this family is located is remarkably syntenic. This allowed us to reconstruct all duplication events over hundreds of millions of years of evolutionary history using manual annotation of gene clusters, which enabled the discovery of a large number of previously un-annotated genes. Intriguingly, we found that the same ancestral gene in the phospholipase gene cluster independently acquired novel molecular functions in birds, mammals and snake, and all subsequent expansion of the cluster originates from this locus. This suggests that the locus has a deep ancestral propensity for multiplication, likely conferred by a structural arrangement of genomic material (i.e. the “genomic context” of the locus) that dates back at least the amniote MRCA. These results highlight the underlying complexity of gene family evolution, as well as the historical- and context-dependence of gene family evolution. Graphical abstract
Deformation of road foundations with geogrid reinforcement

The deformation under traffic of crushed rock sub-bases over clay subgrades has been investigated; the experiments included an investigation of the effectiveness of a reinforcing geogrid between the sub-base and the subgrade. Sections with and without reinforcement were trafficked simultaneously by a rigid two-axle lorry with its rear axle loaded to about 80 kn and the number of vehicle passes to cause 40 mm deformation at the sub-base surface was related to the sub-base thickness, subgrade strength and the use of geogrid. Transverse trenching revealed the accumulated deformation in the sub-base and subgrade. The results were compared with existing designs for foundation layers and the performance of the reinforcement was examined over a wide range of test conditions.
Self-Regulation Versus Self-Discipline in Predicting Achievement: A Replication Study With Secondary Data

Self-regulation is one of multiple noncognitive measures that have been found to relate to academic achievement. Zimmerman and Kitsantas (2014) have distinguished self-regulation from the construct of self-discipline and provided evidence that only the former is predictive of high-school GPA, while controlling for the latter. In this brief report we present a preregistered replication study of their finding using secondary data obtained from a published article by Jung et al. (2017). Despite minor differences in the sample, the measures and the analysis approach, the replication supported the original claim that self-regulation was predictive of academic achievement for undergraduate students, while self-discipline was unrelated to the outcome. The positive association for the self-regulation variable with academic achievement was smaller, but in the same direction as in the original study.
Laser Ablation Ionization Mass Spectrometry: A Space Prototype System for In Situ Sulphur Isotope Fractionation Analysis on Planetary Surfaces

The signatures of element isotope fractionation can be used for the indirect identification of extant or extinct life on planetary surfaces or their moons. Element isotope fractionation signatures are very robust against the harsh environmental conditions, such as temperature or irradiation, which typically prevail on solar system bodies. Sulphur is a key element for life as we know it and bacteria exist, such as sulphur reducing bacteria, that can metabolize sulphur resulting in isotope fractionations of up to −70‰ δ34S. Geochemical processes are observed to fractionate up to values of −20‰ δ34S hence, fractionation exceeding that value might be highly indicative for the presence of life. However, the detection of sulphur element isotope fractionation in situ, under the assumption that life has existed or still does exist, is extremely challenging. To date, no instrument developed for space application showed the necessary detection sensitivity or measurement methodology for such an identification. In this contribution, we report a simple measurement protocol for the accurate detection of sulphur fractionation δ34S using our prototype laser ablation ionization mass spectrometer system designed for in situ space exploration missions. The protocol was elaborated based on measurements of five sulphur containing species that were sampled at different Mars analogue field sites, including two cave systems in Romania and the Río Tinto river environment in Spain. Optimising the laser pulse energy of our laser ablation ionization mass spectrometer (LIMS) allowed the identification of a peak-like trend of the 34S/32S ratio, where the maximum, compared to internal standards, allowed to derive isotope fractionation with an estimated δ34S accuracy of ∼2‰. This accuracy is sufficiently precise to differentiate between abiotic and biotic signatures, of which the latter, induced by, e.g., sulphate-reducing microorganism, may fractionate sulphur isotopes by more than −70‰ δ34S. Our miniature LIMS system, including the discussed measurement protocol, is simple and can be applied for life detection on extra-terrestrial surfaces, e.g., Mars or the icy moons like Europa.
Examining Delayed Recall in Cochlear Implant Users Using the Montreal Cognitive Assessment, California Verbal Learning Test, Third Edition, and Item Specific Deficit Approach: Preliminary Results

Purpose: Recent studies using the Montreal Cognitive Assessment (MoCA) suggest delayed recall is challenging for cochlear implant (CI) users. To better understand the underlying processes associated with delayed recall in CI users, we administered the MoCA and the California Verbal Learning Test, Third Edition (CVLT-3), which provides a more comprehensive assessment of delayed recall ability. Methods: The MoCA and CVLT-3 were administered to 18 high-performing CI users. For the CVLT-3, both the traditional scoring and a newer scoring method, the Item-Specific Deficit Approach (ISDA), were employed. Results: The original MoCA score and MoCA delayed recall subtest score did not relate to performance on any CVLT-3 measures regardless of scoring metric applied (i.e., traditional or ISDA). Encoding performance for both the CVLT-3 and ISDA were related. Consolidation, which is only distinctly defined by the ISDA, related to CVLT-3 cued delay recall performance but not free delay recall performance. Lastly, ISDA retrieval only related to CVLT-3 measures when modified. Conclusion: Performance on the MoCA and CVLT-3 in a high performing CI patient population were not related. We demonstrate that the ISDA can be successfully applied to CI users for the quantification and characterization of delayed recall ability; however, future work addressing lower performing CI users, and comparing to normal hearing controls is needed to determine the extent of potential translational applications. Our work also indicates that a modified ISDA retrieval score may be beneficial for evaluating CI users although additional work addressing the clinical relevance of this is still needed.
Clinical Features and Outcomes of 124 Italian Patients With Treatment Resistant Depression: A Real-World, Prospective Study

Introduction: Treatment-resistant depression (TRD) is a debilitating condition affecting 20–30% of patients with major depressive disorders (MDD). Currently, there is no established standard of care for TRD, and wide variation in the clinical approach for disease management has been documented. Real-world data could help describe TRD clinical features, disease burden, and treatment outcome and identify a potential unmet medical need. Methods: We analyzed the Italian data from a European, prospective, multicentric, observational cohort study of patients fulfilling TRD criteria by the European Medicine Agency, with moderate to severe major depressive episode, and starting a new antidepressant treatment according to routinary clinical practice. They were followed up for minimum 6 months. Treatments received throughout the study period, disease severity, health-related quality of life and functioning were prospectively recorded and analyzed. Results: The Italian subcohort included 124 TRD patients (30.2% of patients of the European cohort; mean age 53.2 [sd = 9.8], women: 82, 66.1%). At enrollement, the mean (SD) duration of MDD was 16 years (sd = 11.1) and the mean duration of the ongoing major depressive episode (MDE) was 97.5 weeks (sd = 143.5); low scores of quality of life and functioning were reported. The most frequently antidepressant classes started at baseline (data available for 98 subjects) were selective serotonin reuptake inhibitors (SSRI, 42 patients [42.9%]) and serotonin-norepinephrine reuptake inhibitors (SNRI, 32 patients [32.7%]). In terms of treatment strategies, 50 patients (51%) started augmentation therapies, 18 (18.4%) combination therapies and 24 (24.5%) monoterapies (6 patients [6%] started a non-antidepressant drug only). Fourteen patients (11.3%) were treated with a psychosocial approach, including psychotherapy. After 6 months of treatment, clinical assessments were collected for 89 patients: 64 (71.9%) showed no response, 9 (10.1%) response without remission and 16 (18.0%) were in remission; non-responder patients showed lower quality of life and higher disability scores than responder patients. Conclusions: In our sample of TRD patients, we documented substantial illness burden, low perceived quality of life and poor outcome, suggesting an unmet treatment need in TRD care in Italy. Registration Number: ClinicalTrials.gov, number: NCT03373253.
Stability Analysis of the World Energy Trade Structure by Multiscale Embedding

This study investigates the dynamic trading network structure of the international crude oil and gas market from year 2012 to 2017. We employed the dynamical similarity analysis at different time scales by inducing a multiscale embedding for dimensionality reduction. This analysis quantifies the effect of a global event on the dependencies and correlation stability at both the country and world level, which covers the top 53 countries. The response of China’s trading structure toward events after the unexpected 2014 price drop is compared with other major traders. China, as the world’s largest importing country, lacks strong stability under global events and could be greatly affected by a supply shortage, especially in the gas market. The trend of multi-polarization on the market share gives a chance for China to construct closer relationships with more stable exporters and join in the trade loop of major countries to improve its position in the energy trading networks. The hidden features of trade correlation may provide a deeper understanding of the robustness of relationship and risk resistance.
Influence of wagon structure on the vertical response of freight.

Historically, wagons have been designed according to the American Association of Railroads specifications. These require that wagons be designed to withstand a static load between the couplers of 350 tons. This implies that the structure has a certain stiffness. In order to improve load to tare ratio, there has been talk of reducing the end load specifications. This implies that the stiffness of the wagon will reduce. Using more flexible wagons implies that the freight will probably be exposed to a harsher dynamic environment. There is a trade off between the cost of packaging and the cost of protection devices installed in the vehicle. If handling damage can be prevented then an understanding of the dynamic environment will assist in reducing the packaging requirement. This research looked at the dynamic characteristics of an existing design of wagon using modal analysis. The results from the modal analysis were extended to be inputs to the time domain freight model. Various analytical models of the freight were developed depending on the configuration and dynamic properties. Special consideration was given to a cylinder with its axis transverse to the wagon. The modal model was modified to accommodate the change in mass imposed by the freight. The various sources of dynamic excitation were explored, namely inputs from the coupler and from the bogie. Data from shunting yard simulations were used to generate spectra as input to the wagon model. The objective was to use modal techniques to be able to take individual components, form them into a complete model and make informed decisions about the suitability of a certain configuration for traffic.
Occupational Performance Coaching With Parents to Promote Community Participation of Young Children With Developmental Disabilities: Protocol for a Feasibility and Pilot Randomized Control Trial

Background: High rates of restricted community participation have been reported in young children with developmental disabilities. Occupational performance coaching (OPC), grounded in self-determination theory, aims to facilitate children's participation in life situations through coaching parents. However, there have been limited randomized controlled trials demonstrating the efficacy of OPC, especially with a specific focus on children's community participation. The proposed study is the first step in evaluating the feasibility and acceptability of conducting a pilot randomized controlled trial of OPC in Hong Kong and testing its initial efficacy (in comparison to parent consultation) in promoting children's community participation. Method/Design: A feasibility and pilot double-blind randomized controlled trial will be undertaken. Fifty children aged 6 years or below with developmental disabilities and their parents will be recruited from early intervention centers and/or through social media in Hong Kong. Parents will be randomly assigned to receive OPC or consultation, and will be blinded to group allocation. Outcomes will be assessed by blinded assessors at baseline, pre-intervention, post-intervention, and follow-up. Predetermined success criteria will be used to assess the feasibility of the trial. Qualitative interviews will be conducted with parents to explore the acceptability and perceived impact of OPC. Discussion: This trial will test whether the study protocol and OPC are feasible and acceptable, as well as assess the initial efficacy of OPC to obtain effect size estimates. The results of the trial will inform future preparations for conducting a full-scale efficacy trial of OPC. Trial Registration: ClinicalTrials.gov, U.S. National Library of Medicine, National Institutes of Health (#NCT04796909), Registered on 15th March 2021.
A Dual Marker for Monitoring MDR-TB Treatment: Host-Derived miRNAs and M. tuberculosis-Derived RNA Sequences in Serum

Background In the absence of a late marker of treatment failure or relapse in MDR-TB patients, biomarkers based on host-miRNAs coupled with M. tuberculosis-RNAs evaluated in extracellular vesicles (EVs) are an alternative follow-up for MDR-TB disease. Characterization of EVs cargo to identify differentially expressed miRNAs before and after treatment, and to identify M. tuberculosis-derived RNA in serum EVs from resistant TB patients. Methods EVs were isolated from serum of 26 drug-resistant TB (DR-TB) patients and 16 healthy subjects. Differential expression of miRNAs in pooled exosomes from both untreated and treated patients was assessed and individually validated at different time points during treatment. In addition, M. tuberculosis RNA was amplified in the same samples by qPCR. Results A multivariate analysis using miR-let-7e-5p, -197-3p and -223-3p were found to be a more sensitive discriminator between healthy individuals and those with TB for both DR-TB (AUC= 0.96, 95%, CI=0.907-1) and MDR-TB groups (AUC= 0.95, 95%, CI= 0.89-1). Upregulation of miR-let-7e-5p were observed at the time of M. tuberculosis negative culture T(3-5) for MDR-TB group or for long-term T(9-15) for MDR-TB group without diabetes (T2DM). A second pathogen-based marker based on 30kDa and 5KST sequences was detected in 33% of the MDR-TB patients after the intensive phase of treatment. The miR-let7e-5p is a candidate biomarker for long-term monitoring of treatment for the group of MDR-TB without T2DM. A dual marker of host-derived miR-let7e-5p and M. tuberculosis-derived RNA for monitoring-TB treatment based in serum EVs. Conclusion A dual marker consisting of host-derived miR-let7e-5p and M. tuberculosis-derived RNA, could be an indicator of treatment failure or relapse time after treatment was completed.
Stock Assessment of Hatchery-Released Clam Meretrix meretrix in an Estuary of China From the Perspectives of Population Ecology and Genetic Diversity

In this study, the release effects of the buried clam Meretrix meretrix in a northern estuary of China (Shuangtaizi Estuary) was assessed in terms of population ecology and genetic variability by using longer-term monitoring data from 2011 (used as the baseline data) to 2018. A total of 2.4 × 108 hatchery juveniles were released from 2012 to 2014, and follow-up monitoring survey of the growth, distribution, density, and biomass of M. meretrix population was carried out. Results showed a temporary spike in the population of M. meretrix, and the population underwent considerable year-to-year fluctuations in total abundance and biomass. Meanwhile, the age structure of the populations from 2011 to 2018 is still an unstable expanding type. Genetic analysis based on 10 polymorphic microsatellite markers revealed no significant genetic differentiation and weak genetic structures between years but higher genetic diversities in 2014–2018 than in the initial period (2013) of stock restoration. Our study suggests that effective policies for management and conservation to restore M. meretrix population by local governments are still needed in the long run.
Involvement of Visual Mismatch Negativity in Access Processing to Visual Awareness

Psychophysiological studies with electroencephalography, focusing on the dynamical aspect of neural correlate of consciousness, reported that visual awareness negativity and P3 enhancement are observed at a latency, 200–300 ms after the visual stimulus onset, when the visual stimulus is consciously perceived. However, access processing to visual awareness (APVA) immediately before conscious perception still remains at the earlier stage of visual sensory processing, though there is little known regarding this subject. The present study hypothesized that visual mismatch negativity (vMMN), which reflects automatic change detection at a latency of 130–250 ms, might be involved in the APVA. In a previous study, vMMN was reported to be evoked by the deviant stimulus that is not consciously perceived in binocular rivalry. To clarify whether the visual change detection affects APVA, we conducted a modified experiment of oddball paradigm on binocular rivalry. The results showed a significant correlation between enhancement of vMMN amplitude and facilitation of perceptual alternation when the unconscious deviant was presented. This implies that vMMN is relevant to the APVA, which is a novel role of vMMN. In early visual processing, the attentional mechanism associated with vMMN is suggested to play an important role in unconscious neural processing at an earlier stage of visual awareness.
Comparison of Standard Caribbean Coral Reef Monitoring Protocols and Underwater Digital Photogrammetry to Characterize Hard Coral Species Composition, Abundance and Cover

The precise assessing and monitoring of coral reefs are necessary to address and understand the threats and changes in coral communities. With the development of new technologies and algorithms for image processing, new protocols like underwater photogrammetry are implemented to study these ecosystems. This study compares the main ecological metrics for reef condition assessment, obtained with an underwater digital photogrammetry protocol (UWP) and traditional sampling design simulations in coral reefs of the Cozumel Reefs National Park. Three orthomosaics (380 m2) per reef on six fringing reefs were constructed, and the hard coral community characterized using a Geographic Information System (GIS). The orthomosaics were also used as a basis to simulate transect lines and obtain data on the hard coral community according to the video transect (VT) protocol, point intercept (PIT) protocol, and the Atlantic and Gulf Rapid Reef Assessment (AGRRA) protocol. Higher colony abundance, species richness, and lower coral cover estimates (p < 0.05) were obtained with the UWP. This protocol was also sensitive to small sized species. All the sampling designs showed similar capability to identify dominant species in terms of colony abundance and coral cover. The VT, PIT, and AGGRA showed similar coral cover values (p > 0.05), which seems to indicate that these sampling designs overestimate this important metric. Our results will help to understand and integrate the observations obtained with UWP with long-term data obtained with commonly used monitoring protocols in the Caribbean region.
Fault diagnosis of wind turbines using a set-membership approach

In this paper, the problem of fault diagnosis in wind turbines will be addressed applying a setmembership approach. Fault detection is based on the use of parity equations and unknown but bound description of the noise and modelling errors. Fault detection test is based on checking consistency between measurements and the model by finding if there is parameter in the feasible parameter set (approximated by a zonotope) that is compatible with modelling and noise bounds. The fault isolation algorithm is based on analyzing the observed fault signatures on-line and matching them with the theoretical ones obtained using structural analysis. Finally, the proposed approach will be tested using the wind turbine benchmark proposed in the context of the WT FDI competition.
Investigating the roles of distinct macrophage phenotypes in cardiovascular disease

This thesis examines the role of immune cells in blood vessel diseases such as high cholesterol and high blood pressure. It has identified novel functions of a class of immune cells, known as macrophages, and highlighted new strategies to limit their damaging effects. The information gained may lead to the development of innovative therapies for the treatment of high blood pressure and associated organ damage.