Miracle-dz/UniFAR-FTUs huggingface dataset:
The Microbial Landscape of Sea Stars and the Anatomical and Interspecies Variability of Their Microbiome

Sea stars are among the most important predators in benthic ecosystems worldwide which is partly attributed to their unique gastrointestinal features and feeding behaviors. Despite their ecological importance, the microbiome of these animals and its influence on adult host health and development largely remains unknown. To begin to understand such interactions we sought to understand what bacteria are associated with these animals, how the microbiome is partitioned across regions of the body and how seawater influences their microbiome. We analyzed the microbiome composition of a geographically and taxonomically diverse set of sea star taxa by using 16S rRNA gene amplicon sequencing and compared microorganisms associated with different regions of their body and to their local environment. In addition, we estimated the bacterial and coelomocyte abundance in the sea star coelomic fluid and bacterioplankton abundance in the surrounding seawater via epifluorescence microscopy. The average bacterial cell abundance observed in the coelomic fluid was one to two orders of magnitude lower than the bacterioplankton abundance in the surrounding seawater suggesting a selection against the presence of microorganisms in the coelomic fluid. The sea star microbiome was also significantly different from seawater with relatively few shared microbial taxa. Microbial communities were found to be significantly different between the pyloric caeca, gonads, coelomic fluid, and body wall of the animals. The most noticeable difference between anatomical sites was the greater relative abundance of Spirochaetae and Tenericutes found in hard tissues (gonads, pyloric caeca, and body wall) than in the coelomic fluid. The microbiome of sea stars thus appears to be anatomically partitioned, distinct from the microbial community of seawater and contains a relatively low abundance of bacteria within the coelomic cavity.
Differential expression of CCL18 in moderate/severe and mild persistent allergic rhinitis and its correlation with disease parameters

ABSTRACT Background and Aims: This study aimed to assess the level of the expression of CCL-18 on nasal inferior turbinate mucosa in patients with mild (M) and moderate-to-severe (M/S) persistent allergic rhinitis (PAR). Methods: The participants in this case-controlled study were divided into three groups: patients with M/S PAR, patients with M PAR, and the healthy control group. Biopsies of nasal inferior turbinate mucosa were obtained from the participants. Expression of CCL-18 mRNA was evaluated by real-time PCR. The serum levels of CCL-18 were determined by ELISA. Total serum IgE levels and specific serum IgE levels were measured. The clinical manifestations were assessed using the total nasal syndrome score (TNSS). Results: Gene expression and the serum level of CCL-18 in patients with M/S PAR increased significantly compared to the control group and patients with M PAR. The serum level of CCL-18 was found to correlate with TNSS in patients with M/S PAR. There was a statistical correlation between the serum level of CCL-18 and the total serum IgE in the treatment groups. Conclusion: The results of the study indicate that there could be a relationship between the expression of CCL-18 in nasal turbinate mucosa and the severity of allergic rhinitis.
Cultivar-Dependent Responses of Eggplant (Solanum melongena L.) to Simultaneous Verticillium dahliae Infection and Drought

Several studies regarding the imposition of stresses simultaneously in plants have shown that plant responses are different under individual and combined stress. Pathogen infection in combination with drought can act both additively and antagonistically, suggesting a tailored-made plant response to these stresses. The aforementioned combination of stresses can be considered as one of the most important factors affecting global crop production. In the present research we studied eggplant responses to simultaneous Verticillium dahliae infection and drought with respect to the application of the individual stresses alone and investigated the extent to which these responses were cultivar dependent. Two eggplant cultivars (Skoutari and EMI) with intermediate resistance to V. dahliae were subjected to combined stress for a 3-week period. Significant differences in plant growth, several physiological and biochemical parameters (photosynthesis rate, leaf gas exchanges, Malondialdehyde, Proline) and gene expression, were found between plants subjected to combined and individual stresses. Furthermore, plant growth and molecular (lipid peroxidation, hydrogen peroxide, gene expression levels) changes highlight a clear discrimination between the two cultivars in response to simultaneous V. dahliae infection and drought. Our results showed that combined stress affects significantly plants responses compared to the application of individual stresses alone and that these responses are cultivar dependent.
Select Biomarkers on the Day of Anterior Cruciate Ligament Reconstruction Predict Poor Patient-Reported Outcomes at 2-Year Follow-Up: A Pilot Study

Background The majority of patients develop posttraumatic osteoarthritis within 15 years of anterior cruciate ligament (ACL) injury. Inflammatory and chondrodegenerative biomarkers have been associated with both pain and the progression of osteoarthritis; however, it remains unclear if preoperative biomarkers differ for patients with inferior postoperative outcomes. Hypothesis/Purpose The purpose of this pilot study was to compare biomarkers collected on the day of ACL reconstruction between patients with “good” or “poor” 2-year postoperative outcomes. We hypothesized that inflammatory cytokines and chondrodegenerative biomarker concentrations would be significantly greater in patients with poorer outcomes. Study Design Prospective cohort design. Methods 22 patients (9 females, 13 males; age = 19.5 ± 4.1 years; BMI = 24.1 ± 3.6 kg/m2) previously enrolled in a randomized trial evaluating early anti-inflammatory treatment after ACL injury. Biomarkers of chondrodegeneration and inflammation were assessed from synovial fluid (sf) samples collected on the day of ACL reconstruction. Participants completed Knee Injury and Osteoarthritis Outcome Score (KOOS) and International Knee Documentation Committee (IKDC) questionnaires two years following surgery. Patients were then categorized based on whether their KOOS Quality of Life (QOL) score surpassed the Patient Acceptable Symptom State (PASS) threshold of 62.5 points or the IKDC PASS threshold of 75.9 points. Results Patients that failed to reach the QOL PASS threshold after surgery (n = 6, 27%) had significantly greater sf interleukin-1 alpha (IL-1α; p = 0.004), IL-1 receptor antagonist (IL-1ra; p = 0.03), and matrix metalloproteinase-9 (MMP-9; p = 0.01) concentrations on the day of surgery. Patients that failed to reach the IKDC PASS threshold (n = 9, 41%) had significantly greater sf IL-1α (p = 0.02). Conclusion These pilot data suggest that initial biochemical changes after injury may be an indicator of poor outcomes that are not mitigated by surgical stabilization alone. Biological adjuvant treatment in addition to ACL reconstruction may be beneficial; however, these data should be used for hypothesis generation and more definitive randomized clinical trials are necessary.
Caterpillar: A business process execution engine on the Ethereum blockchain

Blockchain platforms, such as Ethereum, allow a set of actors to maintain a ledger of transactions without relying on a central authority and to deploy programs, called smart contracts, that are executed whenever certain transactions occur. These features can be used as basic building blocks for executing collaborative business processes between mutually untrusting parties. However, implementing business processes using the low‐level primitives provided by blockchain platforms is cumbersome and error‐prone. In contrast, established business process management systems (BPMSs), such as those based on the standard Business Process Model and Notation (BPMN), provide convenient abstractions for rapid development of process‐oriented applications. This article demonstrates how to combine the advantages of a BPMS with those of a blockchain platform. The article introduces a blockchain‐based BPMN execution engine, named Caterpillar. Like any BPMN execution engine, Caterpillar supports the creation of instances of a process model and allows users to monitor the state of process instances and to execute tasks thereof. The specificity of Caterpillar is that the state of each process instance is maintained on the (Ethereum) blockchain and the workflow routing is performed by smart contracts generated by a BPMN‐to‐Solidity compiler. The Caterpillar compiler supports a large array of BPMN constructs, including subprocesses, multiple‐instance activities, and event handlers. The paper describes the architecture of Caterpillar and the interfaces it provides to support the monitoring of process instances, the allocation and execution of work items, and the execution of service tasks.
Ecological sorting and character displacement contribute to the structure of communities of Clarkia species

Despite long‐standing interest in the evolutionary ecology of plants that share pollinators, few studies have explored how these interactions may affect communities during both community assembly (ecological sorting) and through ongoing, in situ evolution (character displacement), and how the effects of these interactions may change with community context. To determine if communities display patterns consistent with ecological sorting, we assessed the frequency of co‐occurrence of four species of Clarkia in the southern Sierra foothills (Kern County, CA, USA). To investigate potential character displacement, we measured pollination‐related traits on plants grown in a greenhouse common garden from seed collected in communities with one, two or four Clarkia species. Among the four species of Clarkia in this region, the two species that are often found in multi‐species communities also co‐occur with one another more frequently than expected under a null model. This pattern is consistent with ecological sorting, although further investigation is needed to determine the role of pollinators in shaping community assembly. Patterns of trait variation in a common garden suggest that these two species have diverged in floral traits and converged in flowering time where they co‐occur, which is consistent with character displacement. Trait variation across community types also suggests that the process and outcome of character displacement may vary with community context. Because community context appears to affect both the direction and magnitude of character displacement, change in more species‐rich communities may not be predictable from patterns of change in simpler communities.
Are Dark Energy and Dark Matter Different Aspects of the Same Physical Process?

It is suggested that the apparently disparate cosmological phenomena attributed to so-called 'dark matter' and 'dark energy' arise from the same fundamental physical process: the emergence, from the quantum level, of spacetime itself. This creation of spacetime results in metric expansion around mass points in addition to the usual curvature due to stress-energy sources of the gravitational field. A recent modification of Einstein's theory of general relativity by Chadwick, Hodgkinson, and McDonald incorporating spacetime expansion around mass points, which accounts well for the observed galactic rotation curves, is adduced in support of the proposal. Recent observational evidence corroborates a prediction of the model that the apparent amount of 'dark matter' increases with the age of the universe. In addition, the proposal leads to the same result for the small but nonvanishing cosmological constant, related to 'dark energy, as that of the causet model of Sorkin et al.
A Model for Genome-First Care: Returning Secondary Genomic Findings to Participants and Their Healthcare Providers in a Large Research Cohort

Background Research cohorts with linked genomic data exist, or are being developed, at many research centers. Within any such “sequenced cohort” of more than 100 participants, it is likely that there are participants with previously undisclosed risk for life-threatening monogenic diseases that could be identified with targeted analysis of their existing data. Identification of such disease-associated findings are not usually primary to the enrollment research goals. At Geisinger Health System, MyCode® Community Health Initiative (MyCode) participants represent one such large sequenced cohort. Since 2013, MyCode participants in discovery research have been consented for secondary analysis of their existing research genomic sequences to allow delivery of medically actionable findings to them and their healthcare providers. This return of genomic results program was developed to manage an anticipated 3.5% of MyCode participants who will receive clinically confirmed genomic variants from an approved gene list out of more than 150,000 total participants. Risk-associated DNA sequences alone without any clinical parameter, prompt “genome-first” follow-up encounters. Methods This article describes our process for generating clinical grade results from research-based genomic sequencing data, delivering results to patients and their providers, facilitating targeted clinical evaluations of patients and promoting cascade testing of at-risk relatives. We also summarize our early data about the results generated during this process and our ability to contact patients and their providers to disclose the information. Results This process has been used to generate 343 results on 339 patients. 93% of patients with a result have been successfully contacted about their results as evidenced by direct interaction about their result with the research team or a healthcare provider. 222 healthcare providers have been notified of a result on one or more patient through this result delivery process. Conclusions Here we describe the existing GHS model to deliver genomic data into the electronic medical record and the clinical interactions that are prompted and supported. Elements of this genome-first care model can be applied in other healthcare settings and in national efforts, such as “All of Us”, that wish to establish programs for returning genomic results to research participants.
Cell‐based therapy for Parkinson's disease: A journey through decades toward the light side of the Force

This review describes the history, development, and evolution of cell‐based replacement therapy for Parkinson's disease (PD), from the first pioneering trials with fetal ventral midbrain progenitors to future trials using stem cells as well as reprogrammed cells. In the spirit of Tom Isaacs, the review takes parallels to the storyline of Star Wars, including the temptations from the dark side and the continuous fight for the light side of the Force. It is subdivided into headings based on the original movies, spanning from A New Hope to the Last Jedi.
Host Defense Peptide LL-37-Mediated Chemoattractant Properties, but Not Anti-Inflammatory Cytokine IL-1RA Production, Is Selectively Controlled by Cdc42 Rho GTPase via G Protein-Coupled Receptors and JNK Mitogen-Activated Protein Kinase

The human host defense peptide LL-37 promotes immune activation such as induction of chemokine production and recruitment of leukocytes. Conversely, LL-37 also mediates anti-inflammatory responses such as production of anti-inflammatory cytokines, e.g., IL-1RA, and the control of pro-inflammatory cytokines, e.g., TNF. The mechanisms regulating these disparate immunomodulatory functions of LL-37 are not completely understood. Rho GTPases are GTP-binding proteins that promote fundamental immune functions such as chemokine production and recruitment of leukocytes. However, recent studies have shown that distinct Rho proteins can both negatively and positively regulate inflammation. Therefore, we interrogated the role of Rho GTPases in LL-37-mediated immunomodulation. We demonstrate that LL-37-induced production of chemokines, e.g., GRO-α and IL-8 is largely dependent on Cdc42/Rac1 Rho GTPase, but independent of the Ras pathway. In contrast, LL-37-induced production of the anti-inflammatory cytokine IL-1RA is not dependent on either Cdc42/Rac1 RhoGTPase or Ras GTPase. Functional studies confirmed that LL-37-induced recruitment of leukocytes (monocytes and neutrophils) is also dependent on Cdc42/Rac1 RhoGTPase activity. We demonstrate that Cdc42/Rac1-dependent bioactivity of LL-37 involves G-protein-coupled receptors (GPCR) and JNK mitogen-activated protein kinase (MAPK) signaling, but not p38 or ERK MAPK signaling. We further show that LL-37 specifically enhances the activity of Cdc42 Rho GTPase, and that the knockdown of Cdc42 suppresses LL-37-induced production of chemokines without altering the peptide’s ability to induce IL-1RA. This is the first study to demonstrate the role of Rho GTPases in LL-37-mediated responses. We demonstrate that LL-37 facilitates chemokine production and leukocyte recruitment engaging Cdc42/Rac1 Rho GTPase via GPCR and the JNK MAPK pathway. In contrast, LL-37-mediated anti-inflammatory cytokine IL-1RA production is independent of either Rho or Ras GTPase. The results of this study suggest that Cdc42 Rho GTPase may be the molecular switch that controls the opposing functions of LL-37 in the process of inflammation.
DSM outcomes of psychotic experiences and associated risk factors: 6-year follow-up study in a community-based sample

Abstract Background Psychotic experiences (PEs) may predict a range of common, non-psychotic disorders as well as psychotic disorders. In this representative, general population-based cohort study, both psychotic and non-psychotic disorder outcomes of PE were analysed, as were potential moderators. Methods Addresses were contacted in a multistage clustered probability sampling frame covering 11 districts and 302 neighbourhoods at baseline (n = 4011). Participants were interviewed with the Composite International Diagnostic Interview (CIDI) both at baseline and at 6-year follow-up. Participants with PE at baseline were clinically re-interviewed with the SCID-I at follow-up. The role of socio-demographics, characteristics of PE, co-occurrence of mood disorders and family history of mental disorders were tested in the association between baseline PE and follow-up diagnosis. Results In the participants with baseline PE, the psychotic disorder diagnosis rate at follow up was 7.0% – much lower than the rates of DSM-IV mood disorders without psychotic features (42.8%) and other non-psychotic disorders (24.1%). Within the group with baseline PE, female sex, lower socio-economic status, co-occurrence of mood disorders, family history of a mental disorder and persistence of PE predicted any follow-up DSM diagnosis. Furthermore, onset of psychotic v. non-psychotic disorder was predicted by younger age (15–30 years), co-presence of delusional and hallucinatory PE and family history of severe mental illness. Conclusion The outcome of PE appears to be a consequence of baseline severity of multidimensional psychopathology and familial risk. It may be useful to consider PE as a risk indicator that has trans-diagnostic value.
Performance of a newly developed mineral gel system on erosive and erosive/abrasive enamel loss. An in vitro study

We compared the prevention of erosive and erosive/abrasive enamel loss by a medical minerals gel system (R.O.C.S.) to that by an anti-erosive toothpaste. Seventy-two bovine enamel samples were randomly allocated to six groups (E1–E3 and EA1–EA3; n=12). Per day, samples were eroded (2 min) 9 times using HCl (pH 2.6). Between erosive challenges and over night samples were stored in artificial saliva. Per day, samples were stored (100 s; groups E1–E3) or additionally brushed (20 brushing strokes; groups EA1–EA3) in/with slurries prepared from artificial saliva plus: no additional toothpaste (control groups E1 and EA1), elmex erosion protection toothpaste (groups E2 and EA2), or R.O. C.S. toothpaste (groups E3 and EA3). Once per day, samples of groups E3 and EA3 were additionally treated (40 min) with a slurry prepared from artificial saliva and R.O. C.S. medical minerals gel. After 7, 14 and 21 days enamel loss was measured by surface profilometry and analyzed by Kruskal-Wallis tests and Conover post-hoc tests. Under erosive conditions only (groups E1–E3), at each time point of measurement the significantly lowest enamel loss was observed in group E2. Substance loss in group E3 was significantly higher, but significantly lower compared to that of group E1. Under erosive/abrasive conditions (groups EA1–EA3), at each time point of measurement the significantly lowest enamel wear was observed in group EA2. Wear in group EA3 was significantly higher even compared to that of group EA1. The tested R.O. C.S. medical minerals gel system was able to reduce erosive enamel loss but not erosive/abrasive enamel wear, and it was less effective than the elmex erosion protection toothpaste.
Pulmonary Scedosporium apiospermum Infection with Pulmonary Tumorlet in an Immunocompetent Patient

Scedosporium apiospermum is an opportunistic fungus that can cause various types of infections, including localized infections and life-threatening disseminated infections, particularly in immunocompromised patients. Treatment is especially challenging due to its multidrug resistance. We herein report the case of a 73-year-old woman who was non-immunocompromised but developed S. apiospermum lung infection and a pulmonary tumorlet. To our knowledge, this is the first report of the coexistence of pulmonary S. apiospermum infection and tumorlet. The lung lesion was successfully treated by surgical excision without any antifungal agents, and no recurrence of the tumorlet or S. apiospermum infection has occurred.
Patterns of injuries and predictors of inhospital mortality in trauma patients in Saudi Arabia

Background The aim of this study was to describe the pattern of traumatic injuries and determine the predictors of inhospital mortality in patients admitted to the emergency department. Patients and methods This is a retrospective cohort study of 3,786 patients with traumat injuries admitted to the emergency department of King Abdulaziz Medical City, Riyadh, Saudi Arabia, between January 2012 and December 2014. Data on patient characteristics, trauma characteristics and outcomes were extracted from medical records. A negative binomial regression model was utilized to identify significant predictors of inhospital mortality. Results Of all injured patients, 77.5% were male, 29.8% were aged 15–25 years and 25.7% were aged 26–45 years. Blunt trauma was the main mechanism of injury, including motor vehicle crashes (MVCs) in 52.0% and falls in 25.8% of patients. Most patients had injuries to the extremities (61.3%), followed by the head (32.2%), chest (16.9%) and abdomen (8.9%). Injuries were mild in 49.7% of patients, moderate in 30.2% and severe in 20.1%. The sex of the patients was significantly associated with the mechanism of injury (p<0.001), severity (p<0.001), anatomical site of injury (p<0.001), admission to the intensive care unit (p<0.001), need for trauma team activation (p<0.001) and type of transportation to hospital (p<0.001). The predictors of inhospital mortality were age (rate ratio [RR] for each 10-year increase=1.174; p<0.001), falls and burns (RR=2.337 and 1.728; p<0.001) and moderate and severe injuries (RR=6.438 and 181.780; p<0.001). Conclusion Our results suggest different patterns of trauma injuries according to patient age and sex. MVCs were the leading cause of injuries, but falls and burns had the highest inhospital mortality. This suggests the need for a comprehensive national education and prevention programs that address all causes of injuries.