Miracle-dz/UniFAR-FTUs huggingface dataset:
EPSD: a well-annotated data resource of protein phosphorylation sites in eukaryotes

As an important post-translational modification (PTM), protein phosphorylation is involved in the regulation of almost all of biological processes in eukaryotes. Due to the rapid progress in mass spectrometry-based phosphoproteomics, a large number of phosphorylation sites (p-sites) have been characterized but remain to be curated. Here, we briefly summarized the current progresses in the development of data resources for the collection, curation, integration and annotation of p-sites in eukaryotic proteins. Also, we designed the eukaryotic phosphorylation site database (EPSD), which contained 1 616 804 experimentally identified p-sites in 209 326 phosphoproteins from 68 eukaryotic species. In EPSD, we not only collected 1 451 629 newly identified p-sites from high-throughput (HTP) phosphoproteomic studies, but also integrated known p-sites from 13 additional databases. Moreover, we carefully annotated the phosphoproteins and p-sites of eight model organisms by integrating the knowledge from 100 additional resources that covered 15 aspects, including phosphorylation regulator, genetic variation and mutation, functional annotation, structural annotation, physicochemical property, functional domain, disease-associated information, protein-protein interaction, drug-target relation, orthologous information, biological pathway, transcriptional regulator, mRNA expression, protein expression/proteomics and subcellular localization. We anticipate that the EPSD can serve as a useful resource for further analysis of eukaryotic phosphorylation. With a data volume of 14.1 GB, EPSD is free for all users at http://epsd.biocuckoo. cn/.
Cell Biology International

Hematopoietic stem cell transplantation (HSCT) is the ultimate choice of treatment for patients with hematological diseases and cancer. The success of HSCT is critically dependent on the number and engraftment efficiency of the transplanted donor hematopoietic stem cells (HSCs). Various studies show that bone marrow‐derived mesenchymal stromal cells (MSCs) support hematopoiesis and also promote ex vivo expansion of HSCs. MSCs exert their therapeutic effect through paracrine activity, partially mediated through extracellular vesicles (EVs). Although the physiological function of EVs is not fully understood, inspiring findings indicate that MSC‐derived EVs can reiterate the hematopoiesis, supporting the ability of MSCs by transferring their cargo containing proteins, lipids, and nucleic acids to the HSCs. The activation state of the MSCs or the signaling mechanism that prevails in them also defines the composition of their EVs, thereby influencing the fate of HSCs. Modulating or preconditioning MSCs to achieve a specific composition of the EV cargo for the ex vivo expansion of HSCs is, therefore, a promising strategy that can overcome several challenges associated with the use of naïve/unprimed MSCs. This review aims to speculate upon the potential role of preconditioned/primed MSC‐derived EVs as “cell‐free biologics,” as a novel strategy for expanding HSCs in vitro.
Changes in Stroke Volume After Renal Denervation

Recent trial results support catheter-based renal denervation (RDN) for treatment of hypertension, while the exact mechanisms causing blood pressure to fall remain incompletely understood. Cardiac magnetic resonance imaging was used to assess the effects of RDN on cardiac function in patients with hypertension undergoing RDN and compared with sham treatment. Cardiac magnetic resonance imaging was used to assess stroke volume index, cardiac index, heart rate, systemic vascular resistance index, and stroke work index from aortic flow measurements. Patients with resistant hypertension from a randomized, sham-controlled RDN trial underwent cardiac magnetic resonance imaging before RDN and at follow-up (randomized cohort). Results were then validated in a cohort of patients with resistant hypertension undergoing RDN and cardiac magnetic resonance imaging (validation cohort). In total, 162 patients were included 52 patients in the randomized trial (27 shams) and 110 patients in the validation cohort. In the randomized cohort, stroke volume index was reduced by 4.7±9.8 mL/m2 in the RDN cohort and remained unchanged in the sham cohort (P=0.008 for between-group comparison), while cardiac index and stroke work index tended to be reduced in RDN patients but not in sham patients (−0.10±5.9 versus 0.17±0.51 L/min per m2 and −7.1±12.5 versus −1.4±10.4 g/m2, P=0.08 for both). In contrast, systemic vascular resistance index and heart rate remained unchanged after RDN. In the validation cohort, reduction of stroke volume index was confirmed, and cardiac index and stroke work index were also reduced significantly, whereas systemic vascular resistance index and heart rate remained unchanged at follow-up. In this study of patients with resistant hypertension, RDN resulted in a reduction of stroke volume when compared with sham.
A Replicable Approach to Promoting Best Practices: Translating Cardiovascular Disease Prevention Research

Supplemental Digital Content is Available in the Text. Objective: Significant delays in translating health care–related research into public health programs and medical practice mean that people may not get the best care when they need it. Regarding cardiovascular disease, translation delays can mean lives may be unnecessarily lost each year. To facilitate the translation of knowledge to action, we created a Best Practices Guide for Cardiovascular Disease Prevention Programs. Design: Using the Rapid Synthesis Translation Process and the Best Practices Framework as guiding frameworks, we collected and rated research evidence for hypertension control and cholesterol management strategies. After identifying best practices, we gathered information about programs that were implementing the practices and about resources useful for implementation. Research evidence and supplementary information were consolidated in an informational resource and published online. Web metrics were collected and analyzed to measure use and reach of the guide. Results: The Best Practices Guide was released in January 2018 and included background information and resources on 8 best practice strategies. It was published as an online resource, publicly accessible from the Centers for Disease Control and Prevention Web site in 2 different formats. Web metrics show that in the first year after publication, there were 25 589 Web page views and 2467 downloads. A query of partner use of the guide indicated that it was often shared in partners' own resources, newsletters, and online material. Conclusion: In following a systematic approach to creating the Best Practices Guide and documenting the steps taken in its development, we offer a replicable approach for translating research on health care practices into a resource to facilitate implementation. The success of this approach is attributed to 3 key factors: using a prescribed and documented approach to evidence translation, working closely with stakeholders throughout the process, and prioritizing the content design and accessibility of the final product.
The sludge-based adsorbent from oily sludge and sawdust: preparation and optimization

ABSTRACT Sludge-based adsorbent (S-AB) converted by oily sludge can make full use of the precious resource. In this paper, oily sludge and discarded sawdust are used to prepare adsorbent through chemical activation. The adsorbent prepared is used to adsorb raw petroleum. Firstly, the most reasonable chemical activator ZnCl2 is ascertained through parallel comparative experiments. The characterization results of N2-adsorption are consistent with adsorption experiment results, which shows that higher mesopore surface area and volume are benefitted by the adsorption process. Secondly, the optimization of preparation technology is investigated through orthogonal experiments after parallel comparative experiments. The adsorption capacity of S-AB-ZnCl2 is stronger when the preparation conditions are as follows: an activation temperature of 550°C, an activation time of 3.5 h, a solid–liquid ratio of 1:1.5, a sludge-sawdust ratio of 1:0.5 and the heating rate of 15°C/min. The maximum quantity adsorbed Q 0 = 434.78 mg/g, calculated through the Langmuir adsorption isothermal models, of S-AB-ZnCl2 prepared under optimized condition is higher than that before optimization. In addition, the most reasonable kinetics fits were of the second-order model. GRAPHICAL ABSTRACT
Self-disgust mediates the relationship between childhood adversities and psychosis.

OBJECTIVE Traumatic events in childhood have been implicated in the development of psychosis, but given that trauma is not in itself sufficient to cause psychosis, researchers have started to investigate other psychological constructs potentially involved in explaining this relationship. Given that self-disgust as a transdiagnostic construct plays a role in the development/maintenance of a range of mental health difficulties, the objective of this study was to investigate whether self-disgust mediates the relationship between childhood trauma and psychosis. METHOD A cross-sectional quantitative study design was used. Seventy-eight participants (Mage = 37.64 years, SDage = 11.57 years; 77% women; 88% White Caucasian) who reported experiencing clinical levels of psychosis were recruited using social media. The participants completed online survey measures of childhood trauma, self-disgust, experiences of psychosis, self-esteem, and external shame. The data were analysed using correlation and mediation analyses. RESULTS Significant indirect effects of childhood trauma on both positive (β = .17, BC 95% CI [0.06, 0.30]) and negative symptoms (β = .26, BC 95% CI [0.14, 0.40]) of psychosis via self-disgust were observed. These effects remained despite the inclusion of self-esteem and external shame as control variables in the mediation models. CONCLUSION This study is the first to show a mediating role for self-disgust in the relationship between childhood trauma and later psychosis. Although the findings should be considered preliminary until strengthened by further research, they nevertheless provide corroboration of the potential utility of self-disgust as a transdiagnostic construct not only from a theoretical perspective, but also from its potential to inform formulation and interventions. PRACTITIONER POINTS When assessing individuals with psychosis, especially those with a trauma history explore experiences and feelings related to the construct of self-disgust. Such experiences are likely to centre on feelings of repulsion towards the self/need for distance and might also manifest in the content of their psychotic experiences. Individuals with significant levels or experiences of self-disgust are likely to need specific interventions to address these; while interventions seeking to improve positive aspects of their identity might well be useful, they are unlikely to address the specific maladaptive elements of self-disgust. While self-disgust-focused interventions have not been widely researched, limited current evidence suggests cognitive restructuring and affirmation techniques might be useful.
Implementation and evaluation of a self-directed learning activity for first-year medical students

ABSTRACT Background: It is critical that medical students develop self-directed, life-long learning skills to navigate medical school successfully and to become competent healthcare professionals. Moreover, the Liaison Committee on Medical Education (LCME), the USA medical school accrediting body, requires activities designed to help students develop self-directed learning (SDL) skills in the preclinical years. Objective: We evaluated the feasibility and effectiveness of a self-directed learning activity in a 6-week first-year medical student course. Design: The course director assigned infectious disease case studies to teams of first-year medical students who individually assessed their knowledge gaps of the case, identified scholarly sources to fill their knowledge gaps, shared the information with their teammates, and reflected on their ability to guide their own learning. Students were asked to rate workload, team effort, acquisition of new clinical knowledge, and life-long learning skills. Students were also asked to reflect on how this assignment affected their perception of their SDL skills. Descriptive statistics were used to analyze responses to the Likert scale questions. Thematic analysis was applied to the comments. Results: Survey response rate was 80% (131/163). Students strongly or moderately agreed that 1) they spent an appropriate amount of time on the project (94%), 2) the workload was evenly distributed among their teammates (95%), 3) their teammates made significant and timely contributions to the project (97%), 4) the project contributed to learning new clinical knowledge (92%), and 5) the project contributed to the acquisition of life-long learning skills (85%). The analysis team identified four themes from student reflections on their perception of their self-directed learning skills: self-learning skills, collaboration, application, and meta-cognition, Conclusions: Study results demonstrated that we successfully implemented a case-based SDL activity in a first-year medical school course and that students perceived the activity as a valuable learning experience.
Intratumoral Fibrosis and Tumor Growth Pattern as Prognostic Factors in Optimally Resected Pancreatic Neuroendocrine Neoplasms: An Analysis of 168 Cases.

OBJECTIVES Pancreatic neuroendocrine neoplasms (PanNENs) can recur after curative resection. We sought to establish the significance of tumor fibrosis and tumor growth pattern as predictors of recurrence-free survival and overall survival. METHODS A retrospective query of an institutional surgical database was performed from 2000 to 2018 to identify optimally resected PanNENs. All eligible slides were reviewed by an experienced gastrointestinal pathologist for established histopathologic prognostic factors, as well as fibrosis and tumor growth pattern. We evaluated the effect of the interested variables through Cox proportional hazards models. RESULTS One hundred sixty-eight cases were considered. The majority of patients (90%) had grade 1 or 2 tumors, 46% showed significant fibrosis, and 22% demonstrated an infiltrative growth pattern. Twenty-one percent of patients had a recurrence. In multivariable analysis, lymphovascular invasion with a hazard ratio (HR) of 5.1 and infiltrative growth pattern (HR, 2.8) were significantly associated with increased risk of recurrence and increased risk of death (HR, 3.6 and 2.7, respectively). There was a significant decrease in recurrence-free survival and overall survival for fibrosis and infiltrative growth pattern. CONCLUSIONS In optimally resected PanNENs, the presence of fibrosis and infiltrative growth pattern are significant risk factors for recurrence and/or decreased survival.
Real‐world behavior of CRT pacing using the AdaptivCRT algorithm on patient outcomes: Effect on mortality and atrial fibrillation incidence

The AdaptivCRT (aCRT) algorithm continuously adjusts cardiac resynchronization therapy (CRT) according to intrinsic atrioventricular conduction, providing synchronized left ventricular pacing in patients with normal PR interval and adaptive BiV pacing in patients with prolonged PR interval. Previous analyses demonstrated an association between aCRT and clinical benefit. We evaluated the incidence of patient mortality and atrial fibrillation (AF) with aCRT compared with standard CRT in a real‐world population.
Vietnamese female sex workers in rural cross-border areas of Guangxi, China: migration and HIV/STI risk behaviors

ABSTRACT China’s HIV/AIDS epidemic continues to grow in rural and less developed areas. This consecutive cross-sectional study examines demographic and behavioral factors associated with HIV/STI infection, Hepatitis C (HCV) and other sexually transmitted infections (STIs) among Vietnamese female sex workers (FSW), a vulnerable population who cross into Guangxi, China. This study is a secondary data analysis of 303 Vietnamese and 4,348 Chinese FSWs recruited over seven years from two Chinese counties that border Vietnam. Logistic regression models compared demographics, HIV/STI status, HIV/AIDS-related knowledge, attitudes, and risk behaviors between Vietnamese FSWs and Chinese FSWs. Compared with Chinese FSWs, Vietnamese FSWs were younger, had attained lower education levels, were highly mobile, more likely to report using drugs, and were more vulnerable to HIV/STIs. Younger age, less educational attainment, shorter time in their current working location, no voluntary HIV testing in the last year, greater drug use, and not using condoms for all commercial sex in the last month were associated with higher HIV/STIs. In conclusion, several factors were associated with HIV/STI risk in Vietnamese cross-border FSWs. There is a pressing need to improve support systems for Vietnamese cross-border FSW and health system cooperation across the Chinese/Vietnamese border.
A Matlab toolbox for analyzing repetitive movements: application in gait and tapping experiments

Abstract Coordination and timing in repetitive movements have been intensively investigated in diverse experimental settings for understanding the underlying basic mechanisms in healthy controls. On this basic research side, there are mainly two theoretical models: the Wing-Kristofferson (WK) model and the Haken-Kelso-Bunz (HKB) model. On the clinical side of the research, several efforts have been spent on quantitatively assessing gait and other repetitive movements such as tapping, especially as an outcome measure of clinical trials in diverse neurological disorders. Nevertheless, Parkinson’s disease (PD) remains the predominant disorder in the clinical literature in this context, as the tremor activity and the changes in the gait are both common symptoms in PD. Although there are motion recording systems for data acquisition in clinical settings, the tools for analysis and quantification of the extracted time-series offered by these systems are severely restricted. Therefore, we introduce a toolbox which enables the analysis of repetitive movements within the framework of the two main theoretical models of motor coordination, which explicitly focuses on varying clinical and experimental settings such as self-paced vs. cued or uni-manual vs. bi-manual measurements. The toolbox contains particular pipelines for digital signal processing. Licensed under the GNU General Public License (GNU-GPL), the open source toolbox is freely available and can be downloaded from the Github link: https://github.com/MehmetEylemKirlangic/RepetitiveMovementAnalysis. We illustrate the application of the toolbox on sample experiments of gait and tapping with a control subject, as well as with a Parkinson’s patient. The patient has gone through a brain surgery for deep brain stimulation (DBS); hence, we present the results for both stimulation ON and stimulation OFF modes. Sample data are freely accessible at: https://github.com/MehmetEylemKirlangic/DATA.
Immediate early response protein 2 promotes the migration and invasion of hepatocellular carcinoma cells via regulating the activity of Rho GTPases.

Human immediate early response 2 (IER2) has been implicated in tumor cell motility and metastasis, however, the underlying mechanisms in hepatocellular carcinoma (HCC) metastasis remain to be clarified. In this study, we demonstrate that dysregulation of IER2 was shown in HCC clinical samples, and IER2 expression resulted in promotion of cell migration and invasion in vitro and HCC tumor growth and pulmonary metastasis in vivo. Moreover, we showed that IER2 expression altered assembly of the actin cytoskeleton rearrangement. Furthermore, MAPK and PI3K/Akt signaling pathways induced by IER2 was confirmed to be probably involved in regulating the activity of Rho GTPases, such as RhoA, Rac 1 and Cdc42. Collectively, our results indicated a significant role of IER2 in the HCC cell motility and metastasis through MAPK and PI3K/Akt signaling pathways to regulate the activity of Rho GTPases, thereby modulating actin cytoskeleton rearrangement, unveiling a novel mechanism of cell motility regulation induced by IER2.
So You Want to Image Myelin Using MRI: An Overview and Practical Guide for Myelin Water Imaging

Myelin water imaging (MWI) is an MRI imaging biomarker for myelin. This method can generate an in vivo whole‐brain myelin water fraction map in approximately 10 minutes. It has been applied in various applications including neurodegenerative disease, neurodevelopmental, and neuroplasticity studies. In this review we start with a brief introduction of myelin biology and discuss the contributions of myelin in conventional MRI contrasts. Then the MRI properties of myelin water and four different MWI methods, which are categorized as T2‐, T2*‐, T1‐, and steady‐state‐based MWI, are summarized. After that, we cover more practical issues such as availability, interpretation, and validation of these methods. To illustrate the utility of MWI as a clinical research tool, MWI studies for two diseases, multiple sclerosis and neuromyelitis optica, are introduced. Additional topics about imaging myelin in gray matter and non‐MWI methods for myelin imaging are also included. Although technical and physiological limitations exist, MWI is a potent surrogate biomarker of myelin that carries valuable and useful information of myelin.
Conditions With the Largest Number of Adult Hospital Readmissions by Payer, 2011

Health care reform has pinpointed hospital readmissions as a key area for improving care coordination and achieving potential savings. Stakeholders are using data to devise strategies to reduce readmissions. Two criteria for evaluating potential areas of impact include volume and costs. For example, the Centers for Medicare & Medicaid Services (CMS) Hospital Readmissions Reduction Program has selected acute myocardial infarction, heart failure, and pneumonia as target areas for the Medicare population. CMS chose these conditions, in part, because of their high prevalence and their associated high costs for total admissions and readmissions among Medicare beneficiaries. In 2015, CMS will expand their assessment of readmissions to additional conditions that represent high volume and costs.Identifying conditions that contribute the most to the total number of readmissions and related costs for all payers may aid health care stakeholders in deciding which conditions to target to maximize quality improvement and cost-reduction efforts. This Statistical Brief uses readmissions data from the Healthcare Cost and Utilization Project (HCUP) to present the conditions with the largest number of 30-day all-cause readmissions among U.S. hospitals in 2011 and their associated costs. We limited the study population to Medicare beneficiaries aged 65 years and older and to individuals aged 18–64 years who were privately insured, uninsured, or covered by Medicaid. We display the 10 conditions with the largest number of readmissions for each payer.