Miracle-dz/UniFAR-FTUs huggingface dataset:
ResistanceGA: An R package for the optimization of resistance surfaces using genetic algorithms

Understanding how landscape features affect functional connectivity among populations is a cornerstone of landscape genetic analyses. However, parameterization of resistance surfaces that best describe connectivity is largely a subjective process that explores a limited parameter space. ResistanceGA is a new R package that utilizes a genetic algorithm to optimize resistance surfaces based on pairwise genetic distances and either CIRCUITSCAPE resistance distances or cost distances calculated along least cost paths. Functions in this package allow for the optimization of both categorical and continuous resistance surfaces, as well as the simultaneous optimization of multiple resistance surfaces. There is considerable controversy concerning the use of Mantel tests to accurately relate pairwise genetic distances with resistance distances. Optimization in uses linear mixed effects models with the maximum likelihood population effects parameterization to determine AICc, which is the fitness function for the genetic algorithm. ResistanceGA fills a void in the landscape genetic toolbox, allowing for unbiased optimization of resistance surfaces and for the simultaneous optimization of multiple resistance surfaces to create a novel composite resistance surface.
ApPropRiateness of myOcardial revascUlarization assessed by SYNTAX Scores in patients with type 2 diabetes melliTus: the PROUST study*

Introduction Results of currently available trials have shown divergent outcomes in diabetic patients undergoing percutaneous coronary intervention (PCI) or coronary artery bypass grafting (CABG). Current guidelines do not recommend PCI in patients with diabetes and a SYNTAX score ≥ 23. Aim To compare all-cause 4-year mortality after revascularization for complex coronary artery disease (CAD) in diabetics. Material and methods The study group comprised consecutive patients with three-vessel CAD and/or unprotected left main CAD (≥ 50% diameter stenosis) without major hemodynamic instability, who were treated in two institutions with PCI or referred for CABG. Results Out of 342 diabetics, 177 patients underwent PCI and 165 patients were referred for CABG. The incidence of all-cause death was different between diabetics treated with PCI or CABG at 4 years (16/177, 9.0% vs. 26/165, 15.8%, respectively, p = 0.03). The difference was not evident in non-diabetics (PCI: 41/450, 9.1% vs. CABG: 19/249, 7.6%, p = 0.173). In diabetics, there was a higher incidence of all-cause mortality in PCI patients with intermediate-high (≥ 23) SYNTAX scores compared with those with low (0–22) SYNTAX scores (10/56, 17.9% vs. 6/121, 5.0%, respectively, p < 0.01). On the other hand, diabetics who underwent CABG showed similar mortality rates irrespective of the SYNTAX scores (SYNTAX 0–22: 3/29, 10.3%; SYNTAX ≥ 23: 23/136, 11.9%, p = 0.46). In the subgroup analysis, there was no interaction according to presence or absence of left main CAD (p for interaction = 0.12) as well as according to diabetes status (p for interaction = 0.38), whereas gender and SYNTAX scores were differentiators between PCI and CABG with a p for interaction < 0.1. Conclusions Our analysis supports recent evidence that diabetes is not a differentiator between PCI and CABG.
Aspects of Gametogenesis in the Marine Mussel Mytilus Edulis L.

INTRODUCTION Marine bivalve molluscs have in recent years attracted considerable attention for a variety of reasons, not least of which is their importance as a source of food for man. Much of this research has concentrated on studies of reproduction; Mytilus viridis (India: Nagabhushanam & Mane, 1975), M. edulis aoteanus and Aulacomya maoriana (New Zealand: Kennedy, 1977);Choromytilus meridionalis and Aulacomya ater (South Africa: Berry, 1978); Mytilus (= Perna) perna (Brazil: Lunetta, 1969); M. edulis planulatus (Australia: Wilson & Hodgkin, 1967); Mytilus californianus and M. edulis (U.S.A.: Hines, 1979); Mytilus galloprovincialis (France: Lubet, 1959) and M. edulis (U.K.: Chipperfield, 1953; Seed, 1975; Bayne et al. 1978). A review of the literature revealed that in the majority of studies cytology was used as a descriptive tool for the ‘staging’ (Chipperfield, 1953; Lubet, 1957; Seed, 1975, 1976) of the developing gametes and certain anomalies were apparent with regard to the nomenclature of the connective tissue matrix of the mantle lobes.
A Novel GPU-based Fast Monte Carlo Photon Dose Calculating Method for Accurate Radiotherapy Treatment Planning

Background: An accurate and fast radiation dose calculations method is the main part of treatment planning for successful radiation therapy. Objective: This work aimed to create a novel GPU-based fast Monte Carlo Photon Dose Code (MCPDC) as a fast and accurate tool in dose calculation for radiotherapy treatment planning. Materials and Methods: In this analytical study, MCDPC was written to implement photon MC simulation for energies 0.01 to 20 MeV and run on an NVIDIA GTX970. The code was validated using DOSXYZnrc results and experimental measurements, performed by a Mapcheck dosimeter. Using the innovative definition of photon and electron interactions, mean calculation time for the MCPDC was 5.4 sec for 5e7 source particle history, significantly less than that of DOSXYZnrc which was 400 min. Results: Considering the simulations in the anthropomorphic phantom with bone and lung inhomogeneity, more than 96.1% of all significant voxels passed the gamma criteria of 3%-3 mm. Compared to the experimental dosimetry results, 97.6% or more of all significant voxels passed the acceptable clinical gamma index of 3%-3 mm. Conclusion: Very fast calculation speed and high accuracy in dose calculation may allow the MCPDC to be used in radiotherapy as a central component of a treatment plan verification system and also as the dose calculation engine for MC-based planning. MCPDC is currently being developed for electron dose calculation module and graphic user interface. In addition, future work on the applicability of the improved version of the MCPDC in transit dosimetry of megavoltage CT is in process.
Down-Regulation of circNRIP1 Promotes the Apoptosis and Inhibits the Migration and Invasion of Gastric Cancer Cells by miR-182/ROCK1 Axis

Aim Circular RNAs (circRNAs) play important roles in the progression of human cancers. circRNA nuclear receptor interacting protein 1 (circNRIP1) has been reported to play as an oncogene in gastric cancer. However, the mechanism underlying circNRIP1 in gastric cancer progression is far from understood. Patients and Methods Forty-five gastric cancer patients were recruited and overall survival of patients was analyzed. Gastric cancer cell lines MGC-803 and AGS cells were cultured for study in vitro. The expression levels of circNRIP1, microRNA (miR)-182 and rho-associated protein kinase 1 (ROCK1) were detected by quantitative real-time polymerase chain reaction or Western blot. Cell migration, invasion, cell cycle distribution and apoptosis were determined by transwell, flow cytometry and Western blot assays, respectively. The target association between miR-182 and circNRIP1 or ROCK1 was assessed by luciferase reporter assay and RNA immunoprecipitation. Results circNRIP1 expression was enhanced in gastric cancer tissues and cells and high expression of circNRIP1 indicated poor survival of patients. Knockdown of circNRIP1 suppressed cell migration and invasion, arrested cell cycle at G0-G1 phase and promoted apoptosis in gastric cancer cells. miR-182 was a target of circNRIP1 and its deficiency reversed the effect of circNRIP1 silence on cell migration, invasion, cell cycle distribution and apoptosis in gastric cancer cells. Moreover, ROCK1 was validated as a target of miR-182 and competitively regulated by circNRIP1. Conclusion Silence of circNRIP1 inhibited progression of gastric cancer by increasing miR-182 and decreasing ROCK1, providing a novel target for the treatment of gastric cancer.
The proposed mechanism of bactericidal action of eugenol, ∝-terpineol and g-terpinene against Listeria monocytogenes, Streptococcus pyogenes, Proteus vulgaris and Escherichia coli

The mechanism of antimicrobial activity of essential oils components; - terpineol, g-terpinene and eugenol was studied to evaluate their effect on the bacterial membrane against four strains of bacteria: Listeria monocytogenes, Streptococcus pyogenes, Proteus vulgaris and Escherichia coli. The study was done to observe changes in membrane composition by assaying for the leakage of protein and lipid using Bradford and van Handel’s method respectively. The oils components were capable of inducing cell lysis by the leakage of protein and lipid contents. Eugenol at 2 × MIC was highly effective toward protein content leakage after 120 min of exposure. Alpha terpineol and g-terpinene showed similar effect at 2 × MIC under the same condition. Gamma terpinene displayed the highest activity toward lipid content leakage at 2 x MIC while -terpineol and eugenol showed similar effect after 120 min of exposure. The result revealed that both cell wall and membrane of the treated gram negative and gram positive bacteria were significantly damaged.
Evaluating Safety and Efficacy of Follow-up for Patients With Abdominal Pain Using Video Consultation (SAVED Study): Randomized Controlled Trial

Background The benefits of telemedicine include cost savings and decentralized care. Video consultation is one form that enables early detection of deteriorating patients and promotion of self-efficacy in patients who are well but anxious. Abdominal pain is a common symptom presented by patients in emergency departments. These patients could benefit from video consultation, as it enables remote follow-up of patients who do not require admission and facilitates early discharge of patients from overcrowded hospitals. Objective The study aimed to evaluate the safety and efficacy of the use of digital telereview in patients presenting with undifferentiated acute abdominal pain. Methods The SAVED study was a prospective randomized controlled trial in which follow-up using existing telephone-based telereview (control) was compared with digital telereview (intervention). Patients with undifferentiated acute abdominal pain discharged from the emergency department observation ward were studied based on intention-to-treat. The control arm received routine, provider-scheduled telereview with missed reviews actively coordinated and rescheduled by emergency department staff. The intervention arm received access to a platform for digital telereview (asynchronous and synchronous format) that enabled patient-led appointment rescheduling. Patients were followed-up for 2 weeks for outcomes of service utilization, efficacy (compliance with their disposition plan), and safety (re-presentation for the same condition). Results A total of 70 patients participated, with patients randomly assigned to each arm (1:1 ratio). Patients were a mean age of 40.0 (SD 13.8; range 22-71) years, predominantly female (47/70, 67%), and predominantly of Chinese ethnicity (39/70, 56%). The telereview service was used by 32 patients in the control arm (32/35, 91%) and 18 patients in the intervention arm (18/35, 51%). Most patients in control (33/35, 94%; 95% CI 79.5%-99.0%) and intervention (34/35, 97%; 95% CI 83.4%-99.9%) arms were compliant with their final disposition. There was a low rate of re-presentation at 72 hours and 2 weeks for both control (72 hours: 2/35, 6%; 95% CI 1.0%-20.5%; 2 weeks: 2/35, 6%, 95% CI 1.0%-20.5%) and intervention (72 hours: 2/35, 6%; 95% CI 1.0%-20.5%; 2 weeks: 3/35, 9%, 95% CI 2.2%-24.2%) arms. There were no significant differences in safety (P>.99) and efficacy (P>.99) between the two groups. Conclusions The application of digital telereview for the follow-up of patients with abdominal pain may be safe and effective. Future studies are needed to evaluate its cost-effectiveness and usefulness for broader clinical application. Trial Registration ISRCTN Registry ISRCTN28468556; http://www.isrctn. com/ISRCTN28468556.
GRHL2 Upregulation Predicts a Poor Prognosis and Promotes the Resistance of Serous Ovarian Cancer to Cisplatin

Background GRHL2 has been shown to function in ovarian carcinogenesis. However, the relationship between GRHL2 and cisplatin (DDP) resistance in serous ovarian cancer (SOC) is not clear. The purpose of this study was to elucidate the function and mechanism of GRHL2 in DDP resistance of SOC. Materials and Methods Immunohistochemistry (IHC) was utilized to identify GRHL2 protein expression in DDP resistant and sensitive SOC tissues. GRHL2 mRNA and protein levels were identified using quantitative real-time PCR (qRT-PCR) and Western blotting in SKOV3/DDP and SKOV3 cell lines. We conducted loss- and gain-of-function experiments to uncover the consequence of GRHL2 knockdown or overexpression on the sensitivity of ovarian cancer cells to DDP in vitro and in vivo and the underlying mechanism. Results It was observed that expression of GRHL2 was higher in DDP resistant SOC tissues relative to DDP sensitive SOC tissues. In addition, the increased expression of GRHL2 led to shorter progression-free survival (PFS) and overall survival (OS). Meanwhile, the GRHL2 transcript and protein levels in SKOV3/DDP were also higher than SKOV3. Small hairpin RNA (shRNA)-facilitated GRHL2 gene knockdown considerably heightened the sensitivity of SKOV3/DDP cells to DDP by inhibiting proliferation and promoting apoptosis, while up-regulation of GRHL2 significantly reduced the sensitivity of SKOV3 cells to DDP by promoting proliferation and decreasing apoptosis. In addition, GRHL2 promotes DDP resistance of SOC through activation of ERK/MAPK signaling pathways. Conclusion Our results suggest that GRHL2 up-regulation predicts a poor prognosis and promotes the resistance of SOC to DDP. Therefore, GRHL2 may be a possible treatment target for cisplatin-resistant serous ovarian cancer.
Contemporary Management of Clinically Non-functioning Pituitary Adenomas: A Clinical Review

Non-functioning pituitary adenomas (NFPAs) are benign pituitary tumours that constitute about one-third of all pituitary adenomas. They typically present with symptoms of mass effects resulting in hypopituitarism, visual symptoms, or headache. Most NFPAs are macroadenomas (>1 cm in diameter) at diagnosis that can occasionally grow quite large and invade the cavernous sinus causing acute nerve compression and some patients may develop acute haemorrhage due to pituitary apoplexy. The progression from benign to malignant pituitary tumours is not fully understood; however, genetic and epigenetic abnormalities may be involved. Non-functioning pituitary carcinoma is extremely rare accounting for only 0.1% to 0.5 % of all pituitary tumours and presents with cerebrospinal, meningeal, or distant metastasis along with the absence of features of hormonal hypersecretion. Pituitary surgery through trans-sphenoidal approach has been the treatment of choice for symptomatic NFPAs; however, total resection of large macroadenomas is not always possible. Recurrence of tumours is frequent and occurs in 51.5% during 10 years of follow-up and negatively affects the overall prognosis. Adjuvant radiotherapy can decrease and prevent tumour growth but at the cost of significant side effects. The presence of somatostatin receptor types 2 and 3 (SSTR3 and SSTR2) and D2-specific dopaminergic receptors (D2R) within NFPAs has opened a new perspective of medical treatment for such tumours. The effect of dopamine agonist from pooled results on patients with NFPAs has emerged as a very promising treatment modality as it has resulted in reduction of tumour size in 30% of patients and stabilization of the disease in about 58%. Despite the lack of long-term studies on the mortality, the available limited evidence indicates that patients with NFPA have higher standardized mortality ratios (SMR) than the general population, with women particularly having higher SMR than men. Older age at diagnosis and higher doses of glucocorticoid replacement therapy are the only known predictors for increased mortality.
Methods for Measuring the Time of Transfer from Pediatric to Adult Care for Chronic Conditions Using Administrative Data: A Scoping Review

Purpose To describe methods used to identify the timing of transfer from pediatric to adult care within health administrative data and to identify the advantages and limitations of each method to guide future research. Study Design and Settings We conducted a scoping review to identify studies, summarized challenges of identifying the timing of transfer, and proposed methodological approaches for each. Results Studies use the following approaches to capture individuals who transfer from pediatric to adult care by 1) defining the timing of transfer by the last pediatric and first adult care visit last and 2) defining transfer to adult care based on a specific age. Conclusion There are important limitations of administrative data that must be recognized in designing studies examining the transfer to adult care.
EFFECTS OF AGING ON MICROGLIAL ACTIVATION IN RESPONSE TO NEURONAL INJURY

of Dissertation Presented to the Graduate School of the University of Florida in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy EFFECTS OF AGING ON MICROGLIAL ACTIVATION IN RESPONSE TO NEURONAL INJURY By Jessica Renee Conde May, 2005 Chair: Wolfgang J. Streit Major Department: Neuroscience Microglia have been studied extensively in aging-related neurodegenerative diseases, but to a lesser extent in the normally aged central nervous system (CNS), and little is known about how aging affects the ability of microglia to respond to neuronal injury. Microglial activation in response to facial nerve injury is distinguished by proliferation in conjunction with morphological and immunophenotypic changes, followed by turnover to return the microglial cell population to homeostatic levels as the acute phase of the injury subsides. The main goal of this study was to elucidate what changes, if any, occur in the microglial activation program with aging. We found that proliferation of microglia in old (30 m.o.) rats remained significantly higher than in young (3 m.o.) rats 4 days after axotomy, demonstrating that the downregulation of microglial activation is attenuated with aging. We found no agingrelated change in microglial cell death as part of post-mitotic turnover of microglia to balance the prolonged period of proliferation. Because evidence suggests that neuronal-
CCPRD: A Novel Analytical Framework for the Comprehensive Proteomic Reference Database Construction of NonModel Organisms

Protein reference databases are a critical part of producing efficient proteomic analyses. However, the method for constructing clean, efficient, and comprehensive protein reference databases of nonmodel organisms is lacking. Existing methods either do not have contamination control procedures, or these methods rely on a three-frame and/or six-frame translation that sharply increases the search space and the need for computational resources. Herein, we propose a framework for constructing a customized comprehensive proteomic reference database (CCPRD) from draft genomes and deep sequencing transcriptomes. Its effectiveness is demonstrated by incorporating the proteomes of nematocysts from endoparasitic cnidarian: myxozoans. By applying customized contamination removal procedures, contaminations in omic data were successfully identified and removed. This is an effective method that does not result in overdecontamination. This can be shown by comparing the CCPRD MS results with an artificially contaminated database and another database with removed contaminations in genomes and transcriptomes added back. CCPRD outperformed traditional frame-based methods by identifying 35.2–50.7% more peptides and 35.8–43.8% more proteins, with a maximum of 84.6% in size reduction. A BUSCO analysis showed that the CCPRD maintained a relatively high level of completeness compared to traditional methods. These results confirm the superiority of the CCPRD over existing methods in peptide and protein identification numbers, database size, and completeness. By providing a general framework for generating the reference database, the CCPRD, which does not need a high-quality genome, can potentially be applied to nonmodel organisms and significantly contribute to proteomic research.
Overexpression of DGKI in Gastric Cancer Predicts Poor Prognosis

Background: Diacylglycerol kinase iota (DGKI) is overexpressed in a variety of cancers and is associated with poor prognosis in colon cancer. This study evaluated the prognostic value of DGKI in gastric cancer (GC) using data from The Cancer Genome Atlas (TCGA). Methods: RNA sequencing results and clinical data of gastric adenoma and adenocarcinoma samples were obtained from the TCGA database (https://portal.gdc.cancer.gov). The Wilcoxon or Kruskal–Wallis test and logistic regression were used to analyze the relationship between DGKI and the clinicopathological characteristics of GC patients. Univariate Cox regression and Kaplan-Meier analysis were used to analyze the clinicopathological characteristics of GC patients and the relationship between DGKI and overall survival time, and multivariate Cox regression analysis was used to identify independent risk factors affecting the prognosis of GC patients. Gene set enrichment analysis (GSEA) was performed using the TCGA dataset. Results: DGKI was overexpressed in gastric tumors and was related to poor prognosis (p = 0.003). Overexpression of DGKI in GC was significantly correlated with high grade (OR = 1.71 for G3 vs. G2), stage (OR = 2.08 for II vs. I) and T classification (OR = 4.64 for T4 vs. T1; OR = 3.99 for T3 vs. T1; OR = 3.37 for T2 vs. T1) (all p <0.05). DGKI (OR = 7.34; p = 0.000) was an independent risk factor affecting the survival of GC patients. The MAPK signaling pathway was differentially enriched with DGKI overexpression. Conclusion: DGKI overexpression may be a potential molecular marker for poor prognosis in GC. The MAPK signaling pathway may be one of the key pathways related to DGKI regulation in GC.
Three Novel C-Repeat Binding Factor Genes of Dimocarpus longan Regulate Cold Stress Response in Arabidopsis

Longan (Dimocarpus longan) is a typical southern subtropical fruit tree species that is sensitive to cold stress. C-repeat binding factors (CBFs), as transcription factors, are crucial components involved in the molecular regulation of the plant response to cold stress. However, the role of CBF homologs in the cold response regulation of longan remains largely unknown. Here, three novel CBF genes, DlCBF1, DlCBF2, and DlCBF3, were cloned from longan. DlCBF1 and DlCBF2 contain an AP2 domain and PKKPAGR and DSAWR CBF signature motifs, while DlCBF3 has mutations within these conserved signature motifs. DlCBF1/2/3 were mainly localized in the nucleus and specifically bound to CRT/DRE cis-elements, resulting in strong transcriptional activation. DlCBF1/2 exhibited tissue expression specificity, and their expression was induced by low temperature, while DlCBF3 had no tissue specificity and barely responded to low temperature. DlCBF1, DlCBF2, and DlCBF3 overexpression in Arabidopsis-enhanced cold tolerance by increasing proline accumulation and reducing reactive oxygen species (ROS) content, accompanied by upregulated expression of cold-responsive genes (AtRD29A, AtCOR15A, AtCOR47, and AtKIN1) in the CBF cold stress response signaling pathway. In conclusion, the biological functions of DlCBF1/2/3 were somewhat conserved, but slow expression of DlCBF1/2 and low expression of DlCBF3 may partly cause the cold sensitivity of longan. Collectively, these results indicated that differences exist in the expression and function of CBF orthologs in the cold-sensitive plant species longan, and these findings may help to improve the understanding of the cold response regulation mechanism and provide important theoretical support for cold-tolerant breeding of longan.