Miracle-dz/UniFAR-FTUs huggingface dataset:
The pro α2(V) collagen gene is evolutionarily related to the major fibrillar-forming collagens

A number of overlapping cDNA clones, covering 5.2 kb of sequences which code for the human pro alpha 2(V) collagen chain, have been isolated. Analysis of the structural data have indicated a close evolutionary kinship between the pro alpha 2(V) chain and the major fibrillar collagen types. Isolation and analysis of an 8 kb genomic fragment has further supported this notion by revealing a homologous arrangement of nine triple-helical domain exons. These studies have therefore provided conclusive evidence which categorizes the Type V collagen as a member of the Group 1 molecules, or fibrillar-forming collagens.
Simulation-Based Airport Capacity Estimation

Airport capacity data are available through many sources such as the FAA Aviation System Performance Metrics (ASPM), the FAA Operational Information System (OIS), and the FAA airport capacity benchmark report. These sources provide departure and arrival capacity data as point values or paretos for some common airport conditions, although capacity varies due to many factors such as runway configuration, meteorological condition, operations mix and other site-specific factors. Analytically modeling the capacity of airports under all these different conditions has limitations. This paper describes a simulation-based approach to estimate airport capacity for any arbitrary set of conditions. This approach uses detailed airport surface operations data to obtain operational characteristics of an airport, such as separation and transit times under different weather conditions and configurations, and uses it in the simulation. In the simulation, we vary the weather condition, runway configuration and operations mix, simulate the operations and compute the maximum throughput an airport can handle under those conditions. Using this approach, we have developed models for 25 major US airports and so far have validated the model for BOS and ATL.
Androgens Profile in Blood Serum and Follicular Fluid of Women With Poor Ovarian Response During Controlled Ovarian Stimulation Reveals Differences Amongst POSEIDON Stratification Groups: A Pilot Study

Patients with poor ovarian response (POR) to exogenous gonadotropins stimulation for assisted reproductive technology (ART) have decreased circulating androgens during spontaneous cycles. The Patient-Oriented Strategies Encompassing Individualized Oocyte Number (POSEIDON) is a 4-tier stratification of women with POR to controlled ovarian stimulation (COH) based on age and biomarkers of ovarian reserve has been proposed to maximize the clinical management of this group for ART. The aim of the present study was to characterize the levels of androgens during COH in follicular fluid (FF) and serum in POSEIDON subgroups and compared them with women of normal ovarian response. Sixty nine consecutive patients undergoing ART were included and testosterone, androstenedione, dehydroepiandrosterone sulfate (DHEA-S), estradiol, sex hormone-binding globulin (SHBG), and insulin-like growth factor 1 (IGF-1) were measured in serum and FF collected at the time of oocyte pick-up. The number of retrieved oocytes was registered for each patient for their allocation to the respective POSEIDON subgroup. The control group comprised 19 women and the POSEIDON group 1 (age < 35, normal ovarian reserve biomarkers) n = 14, group 2 (age ≥ 35, normal ovarian reserve biomarkers) n = 8, group 3 (age < 35, poor ovarian reserve biomarkers) n = 6 and group 4 (age ≥ 35, poor ovarian reserve biomarkers) n = 22. Serum levels of total testosterone, androstenedione and DHEA-S were not different in group 1 vs. control but significantly decreased in group 3 vs. control. DHEA-S in FF was also significantly decreased in group 3 vs. control. In addition, serum testosterone was decreased in groups 2 and 4 vs. control; and serum androstenedione and estradiol were reduced in group 4 vs. control. No differences were observed for estradiol, SHBG and IGF-1 in FF. Finally, a high correlation between serum and FF DHEA-S was observed when data from samples of all groups were pooled. Group 1 did not show hypoandrogenemia however group 3 had low levels of all measured androgens in serum and DHEA-S in FF. Such differences might help to better characterize and/or improve the clinical management of women with POR according to their respective POSEIDON stratification.
Traumatic Pulmonary Pseudocysts in a Young Dog Following Non-penetrating Blunt Thoracic Trauma

Traumatic pulmonary pseudocysts following non-penetrating blunt thoracic trauma is a well-described phenomenon in the human literature, while in veterinary medicine, this disease process is rarely reported and poorly described in the current literature available. This case report describes a 1.5-year-old male castrated Labrador retriever with findings of pulmonary cysts following a road traffic accident. The goal of this report is to expound upon the pathophysiology, diagnosis, and treatment of this disease process in the veterinary field.
Network Diffusion Approach to Predict LncRNA Disease Associations Using Multi-Type Biological Networks: LION

Recently, long-non-coding RNAs (lncRNAs) have attracted attention because of their emerging role in many important biological mechanisms. The accumulating evidence indicates that the dysregulation of lncRNAs is associated with complex diseases. However, only a few lncRNA-disease associations have been experimentally validated and therefore, predicting potential lncRNAs that are associated with diseases become an important task. Current computational approaches often use known lncRNA-disease associations to predict potential lncRNA-disease links. In this work, we exploited the topology of multi-level networks to propose the LncRNA rankIng by NetwOrk DiffusioN (LION) approach to identify lncRNA-disease associations. The multi-level complex network consisted of lncRNA-protein, protein–protein interactions, and protein-disease associations. We applied the network diffusion algorithm of LION to predict the lncRNA-disease associations within the multi-level network. LION achieved an AUC value of 96.8% for cardiovascular diseases, 91.9% for cancer, and 90.2% for neurological diseases by using experimentally verified lncRNAs associated with diseases. Furthermore, compared to a similar approach (TPGLDA), LION performed better for cardiovascular diseases and cancer. Given the versatile role played by lncRNAs in different biological mechanisms that are perturbed in diseases, LION’s accurate prediction of lncRNA-disease associations helps in ranking lncRNAs that could function as potential biomarkers and potential drug targets.
Comparing Free Play and Partly Structured Play in 4-5-Years-Old Children in an Outdoor Playground

The aim of this study was to compare how the organization of a movement session as partly structured play or free play influenced the physical activity engagement in 4–5 years old pre-schoolers. The partly structured playgroup consisted of 46 children and the free playgroup consisted of 33 children. The playground activities consisted of 10 sessions each lasting 1 h, executed once per week in the period Mars to May 2017 at a specific playground setting. The partly structured playgroup conducted a movement activity session that included a combination of both structured- and free play activities. The free playgroup engaged in unstructured play, only. To detect the intensity of the physical activity each child carried an accelerometer 1 h the first week and last week of the intervention. Results indicate a significant difference in physical activity level between the two groups for the 5-year-old in the favor of the partly structured playgroup. There was a significant difference between the four-and 5-year-old in relation to physical activity level. No significant difference between the activity in March and May for the whole group was found.
Phylogeographic Analysis and Genetic Structure of an Endemic Sino-Japanese Disjunctive Genus Diabelia (Caprifoliaceae)

The Sino-Japanese Floristic Region (SJFR) is a key area for plant phylogeographical research, due to its very high species diversity and disjunct distributions of a large number of species and genera. At present, the root cause and temporal origin of the discontinuous distribution of many plants in the Sino-Japanese flora are still unclear. Diabelia (Caprifoliaceae; Linnaeoideae) is a genus endemic to Asia, mostly in Japan, but two recent discoveries in China raised questions over the role of the East China Sea (ECS) in these species' disjunctions. Chloroplast DNA sequence data were generated from 402 population samples for two regions (rpl32-trnL, and trnH-psbA) and 11 nuclear microsatellite loci were screened for 549 individuals. Haplotype, population-level structure, combined analyses of ecological niche modeling, and reconstruction of ancestral state in phylogenies were also performed. During the Last Glacial Maximum (LGM) period after the Tertiary, Diabelia was potentially widely distributed in southeastern China, the continental shelf of the East China Sea and Japan (excluding Hokkaido). After LGM, all populations in China have disappeared except those in Zhejiang which may represent a Glacial refuge. Populations of Diabelia in Japan have not experienced significant bottleneck effects, and populations have maintained a relatively stable state. The observed discontinuous distribution of Diabelia species between China and Japan are interpreted as the result of relatively ancient divergence. The phylogenetic tree of chloroplast fragments shows the characteristics of multi-origin evolution (except for D. sanguinea). STRUCTURE analysis of nuclear Simple Sequence Repeat (nSSR) showed that the plants of the Diabelia were divided into five gene pools: D. serrata, D. spathulata, D. sanguinea, D. ionostachya (D. spathulata var. spathulata-Korea), and populations of D. ionostachya var. ionostachya in Yamagata prefecture, northern Japan. Molecular evidence provides new insights of Diabelia into biogeography, a potential glacial refuge, and population-level genetic structure within species. In the process of species differentiation, ECS acts as a corridor for two-way migration of animals and plants between China and Japan during glacial maxima, providing the possibility of secondary contact for discontinuously distributed species between China and Japan, or as a filter (creating isolation) during glacial minima. The influence of the ECS in speciation and biogeography of Diabelia in the Tertiary remains unresolved in this study. Understanding origins, evolutionary histories, and speciation will provide a framework for the conservation and cultivation of Diabelia.
Effects of Seclusion and Restraint in Adult Psychiatry: A Systematic Review

Background: Determining the clinical effects of coercion is a difficult challenge, raising ethical, legal, and methodological questions. Despite limited scientific evidence on effectiveness, coercive measures are frequently used, especially in psychiatry. This systematic review aims to search for effects of seclusion and restraint on psychiatric inpatients with wider inclusion of outcomes and study designs than former reviews. Methods: A systematic search was conducted following PRISMA guidelines, primarily through Pubmed, Embase, and CENTRAL. Interventional and prospective observational studies on effects of seclusion and restraint on psychiatric inpatients were included. Main search keywords were restraint, seclusion, psychiatry, effect, harm, efficiency, efficacy, effectiveness, and quality of life. Results: Thirty-five articles were included, out of 6,854 records. Studies on the effects of seclusion and restraint in adult psychiatry comprise a wide range of outcomes and designs. The identified literature provides some evidence that seclusion and restraint have deleterious physical or psychological consequences. Estimation of post-traumatic stress disorder incidence after intervention varies from 25% to 47% and, thus, is not negligible, especially for patients with past traumatic experiences. Subjective perception has high interindividual variability, mostly associated with negative emotions. Effectiveness and adverse effects of seclusion and restraint seem to be similar. Compared to other coercive measures (notably forced medication), seclusion seems to be better accepted, while restraint seems to be less tolerated, possibly because of the perception of seclusion as “non-invasive. ” Therapeutic interaction appears to have a positive influence on coercion perception. Conclusion: Heterogeneity of the included studies limited drawing clear conclusions, but the main results identified show negative effects of seclusion and restraint. These interventions should be used with caution and as a last resort. Patients’ preferences should be taken into account when deciding to apply these measures. The therapeutic relationship could be a focus for improvement of effects and subjective perception of coercion. In terms of methodology, studying coercive measures remains difficult but, in the context of current research on coercion reduction, is needed to provide workable baseline data and potential targets for interventions. Well-conducted prospective cohort studies could be more feasible than randomized controlled trials for interventional studies.
Neural Mechanisms Involved in Social Conformity and Psychopathic Traits: Prediction Errors, Reward Processing and Saliency

Aligning behavior in favor of group norms, i.e., social conformity, can help to successfully adapt to uncertain environments and may result in social approval. This may lead to enhanced feelings of belongingness and is found to be associated with reward-related activations in the brain. Individuals high on psychopathic traits violate group norms regularly. Yet, it is unclear how psychopathic traits are related to neural mechanisms involved in social conformity. This functional magnetic resonance imaging (fMRI) study includes 42 healthy females scoring low or high on the Psychopathic Personality Inventory questionnaire (PPI). Participants were asked to rate the trustworthiness of 120 faces while lying in the scanner. After rating each face, participants were presented with the group rating of European students. In an unanticipated second part participants rated all faces again, allowing us to focus on two main contrasts: (1) “Social conflict”: group opinion in conflict with the participant’s rating vs. group opinion aligned with participant rating; and (2) “Conformity”: conflict trials followed by conformity vs. conflict trials followed by non-conformity. Behaviorally, the two groups showed similar conformity behavior. fMRI results showed that both groups activated the nucleus accumbens (NAc) following alignment, suggesting the central role of prediction errors and reward. The data also showed a significant interaction between group and conformity in the amygdala. Following conflicts, females scoring low on psychopathic traits showed a trend in enhanced amygdala activation for conformity relative to non-conformity. Additionally, results showed a trend significant group effect for non-conformity. Females scoring high on psychopathic traits showed more activation for non-conformity compared to females scoring low on psychopathic traits, suggesting altered emotional salience of experiencing conflict depending on psychopathic traits. Taken together, these results support the importance of investigating the role of relevant traits in adaptive behavior when facing uncertain social situations and the neural mechanisms involved in this process.
Perceived Empowering Leadership, Harmonious Passion, and Employee Voice: The Moderating Role of Job Autonomy

Based on self-determination theory, we conceptualized the effect of empowering leadership on employee voice via harmonious passion. This paper further explored the moderating effect of job characteristics in the voice process and proposed a moderated mediation model. Using a sample of 674 supervisor–subordinate dyads, we found that (1) empowering leadership was positively related to employees’ harmonious passion and voice behavior, (2) harmonious passion played a mediating role in the relationship between empowering leadership and employee voice, and (3) job autonomy strengthened the effect of harmonious passion on employee voice, which, in turn, enhanced the mediated relationship between empowering leadership and employee voice via harmonious passion. We discuss the implications of these findings for research and practice.
Toward Highly Dispersed Mesoporous Bioactive Glass Nanoparticles With High Cu Concentration Using Cu/Ascorbic Acid Complex as Precursor

Copper (Cu) ions have a variety of advantageous biological functionalities, such as proangiogenic and bactericidal activities. Given the intrinsic biodegradability and biocompatibility, silicate-based mesoporous bioactive glass nanoparticles (MBGNs) are considered as promising platforms for the delivery of Cu ions. However, effective incorporation of Cu into MBGNs still faces challenges, e.g., particle aggregation, the formation of insoluble crystalline Cu-based nanoparticles, and a low loading amount of Cu. We report a novel method to synthesize chemically homogenous and highly dispersed Cu-containing MBGNs (Cu-MBGNs) with tunable Cu concentration by using ascorbic acid/Cu complexes as the precursor of Cu in a microemulsion-assisted sol-gel approach. Cu-MBGNs exhibited a sphere-like shape with a particle size between 100 and 300 nm while their pore size varied from 2 to 10 nm. The inclusion of Cu, regardless of the incorporated concentration, did not significantly affect the morphology of particles. ICP-AES results indicated that the concentration of Cu in the particles could be conveniently tuned from 0 to ~6 mol% by controlling the amount of ascorbic acid/Cu complexes added, while the formation of crystalline Cu-based nanoparticles was avoided. The amorphous feature of Cu-MBGNs was proved by XRD, while the predominant oxidation state of Cu was evidenced to be Cu2+ by XPS. The incorporation of Cu did not inhibit the apatite-forming ability (bioactivity) of the particles in contact with simulated body fluid. Cu-MBGNs exhibited the capability of releasing Cu, Si, and Ca ions over time in the physiological fluid. The concentration of released Cu ions could be controlled by selecting specific Cu-MBGNs of different Cu contents. The dissolution products of most Cu-MBGNs at the dosage of 1, 0.1, and 0.01 mg/mL did not exhibit cytotoxicity, while only 7Cu-MBGN was cytotoxic at the dosage of 1 mg/mL. This study provided a feasible strategy to synthesize highly dispersed amorphous Cu-MBGNs with high Cu concentrations for biomedical applications. The particles exhibit great potential as building blocks for developing composite 3D scaffolds, coatings, and drug carriers, particularly when a large amount of particles incorporated may compromise the properties of (polymer) matrix materials while a relatively high concentration of released Cu ions is still required.
Regulation of DNA Double Strand Breaks Processing: Focus on Barriers

In all the eukaryotic cells, nucleolytic processing (resection) of a double strand DNA break (DSB) is a key step to channel the repair of the lesion toward the homologous recombination, at the expenses of the non-homologous end joining (NHEJ). The coordinated action of several nucleases and helicases generates 3′ single strand (ss) DNA, which is covered by RPA and recombination factors. Molecular details of the process have been first dissected in the model organism Saccharomyces cerevisiae. When DSB ends are occupied by KU, a central component of the NHEJ, the Mre11-Rad50-Xrs2 (MRX) nuclease complex (MRN in human), aided by the associated factors Sae2 (CTIP in human), initiates the resection process, inducing a nick close to the DSB ends. Then, starting from the nick, the nucleases Mre11, Exo1, Dna2, in cooperation with Sgs1 helicase (BLM in human), degrade DNA strand in both the directions, creating the 3′ ssDNA filament. Multiple levels of regulation of the break processing ensure faithful DSB repair, preventing chromosome rearrangements, and genome instability. Here we review the DSB resection process and its regulation in the context of chromatin. Particularly, we focus on proteins that limit DSB resection, acting as physical barriers toward nucleases and helicases. Moreover, we also take into consideration recent evidence regarding functional interplay between DSB repair and RNA molecules nearby the break site.
A hybrid approach to building gene regulatory networks with Bayesian inference

Gene regulation plays a central role in cell biology. High throughput technologies, such as DNA microarray and next generation sequencing, enable measurement of gene expression at large scale, and this makes it possible to study gene regulation at the network level. Over the past decade, many computational methods have been developed to analyze the colossal amounts of gene expression data to infer gene regulatory network. The recent discovery of microRNA as regulatory elements represents opportunities and challenges to re-examine gene regulation. In this study, we developed a hybrid approach to construct regulatory gene network by incorporating prior knowledge including microRNAs as regulatory elemets. The hybrid approach, with use of Bayesian networks, combines learning without prior knowledge and using a predefined partial network to start the learning process in order to build a well-defined, more complete regulatory network. Existing methods either learn a network from scratch or use a predefined/complete network to just learn networks parameters. We used predefined partial networks and other prior knowledge (protein-protein interactions and transcription factor information) as constraints, and used a Bayesian network to infer new edges for a more complete network. Specifically, we used KEGG pathways as our initial network. With this new approach, we generated gene networks from raw data based on the initial network, and we are expecting to exploit potential cross-talks between pathways. We implemented the system pipeline in Python, which consists of four major steps: parser for KEGG pathways, network initializer, Banjo for bayesian networks, and evaluator. The gene expression data was collected from 10 published studies on breast cancer involving Estrogen receptor ER+ and ER-, and KEGG pathways are signaling pathways downloaded from KEGG database.
Changes in Resting-State Functional Connectivity of the Hippocampus Following Cognitive Effort Predict Memory Decline at Older Age—A Longitudinal fMRI Study

Memory decline is a feature of some, but not all, healthy older adults. The neural patterns of this variability are still largely unknown. We examined the resting-state functional connectivity (RSFC) of older and younger adults before and after cognitive effort as an underlying feature for subsequent memory changes, focusing on the RSFC between the left anterior hippocampus (laHC) and the posterior hippocampi (pHC). Results showed that for younger adults, post-effort increases in laHC–pHC RSFC were related to increases in RSFC between the laHC and the hubs of the default mode network (DMN). However, for older adults, post-effort increases in the RSFC of laHC–pHC were related to decreases in the RSFC of the laHC and right precentral gyrus. Thus, the correlation between intra-HC and inter-HC RSFC was altered with cognitive effort and aging. Importantly, older adults who had lower post-effort RSFC between the laHC and the pHC demonstrated a decline in episodic memory 2 years later. Hence, the change in intra-HC RSFC following cognitive effort was able to predict subsequent memory function with aging in our sample.