Miracle-dz/UniFAR-FTUs huggingface dataset:
Balancing yield, purity and practicality: a modified differential ultracentrifugation protocol for efficient isolation of small extracellular vesicles from human serum

ABSTRACT Ultracentrifugation remains the gold standard for isolation of small extracellular vesicles (sEV), particularly for cancer applications. The objective of this study was to determine if a widely used ultracentrifugation protocol for isolation of serum sEV could be modified to reduce the number of ultracentrifugation cycles and increase efficiency, while maintaining equal or better sample purity and yield. Serum was obtained from two healthy subjects. sEVs were isolated from 1 mL aliquots using three different ultracentrifugation protocols. Co-isolation of RNA carrier protein was assessed by performing Western blots for ApoA-I, ApoB, and Ago2. Small RNA-sequencing was performed on the sEV isolates, and differential detection of small ncRNA was compared across isolation protocols. Reduction from three- to two-ultracentrifuge cycles with no sucrose cushion resulted in a much higher sEV yield but also had the highest levels of lipoprotein and Ago2 contamination. However, the two-ultracentrifugation cycle protocol that incorporated a 30% sucrose cushion into the first cycle resulted in slightly higher sEV yields with lower levels of protein contamination compared to the lengthier three-ultracentrifugation cycle approach, therefore presenting a more efficient alternative approach for isolation of serum sEVs. It was also notable that there were some differences in sEV ncRNA cargo according to protocol, although it was less than expected given the differences in co-isolated RNA carrier proteins. Our results suggest that use of the modified serum sEV isolation protocol with two ultracentrifugation cycles and incorporating a 30% sucrose cushion offers a more efficient approach in terms of efficiency and purity.
Neoadjuvant chemoradiation for patients with advanced oesophageal cancer – which response grading system best impacts prognostic discrimination?

Neoadjuvant chemoradiation reduces tumour volume and improves the R0 resection rate, followed by extended survival for patients with advanced oesophageal cancer. The degree of tumour regression has high prognostic relevance. To date, there is still no generally accepted tumour regression grading system. The aim of this study was to compare the prognostic discrimination power of different histological regression grading systems: (i) the fibrosis/tumour ratio within the primary tumour (Mandard classification), (ii) the percentage of residual vital tumour cells (VTC) compared to the original primary tumour (Cologne Regression) and (iii) the ypT category, in patients with cT3 carcinoma of the oesophagus after neoadjuvant chemoradiation.
Editorial comments for neoadjuvant chemo-radiotherapy in the treatment of locally advanced squamous cell esophageal cancer.

In August 2018 issue of the Journal of Clinical Oncology , Yang and coworker published a well-designed analysis of 451 patients with potentially resectable thoracic esophageal squamous cell carcinoma (SCC), clinically staged as T1-4N1M0/T4N0M0, who were randomly assigned to the neoadjuvant chemoradiotherapy (NCRT) plus surgery, or to surgery alone groups (1). The study was presented as the phase III multicenter, randomized, open-label clinical trial. It was a great honor to be invited to provide editorial comments on this article.
Public self-consciousness, pre-loading and drinking harms among university students

Abstract Background: Social anxiety and self-consciousness are associated with alcohol-related problems in students. The practice of pre-loading is one avenue for exploration regarding this relationship. Individuals may pre-load to reduce social anxiety and feel more confident when socializing, which could lead to the increased harms experienced. The current study aimed to explore reasons for pre-loading, and whether public and private self-consciousness and social anxiety were related to pre-loading, increased drinking, and harms. Objectives: Prospective study with four-week follow up of 325 UK students aged 18-–30 years old. Participants completed measures of private and public self-consciousness, social anxiety, alcohol consumption, alcohol-related harms, and pre-loading. Results: Financial motives and mood-related reasons, such as gaining confidence were reported as reasons for pre-loading. Pre-loading predicted hazardous alcohol consumption, but social anxiety, and public and private self-consciousness did not. However, pre-loading, public self-consciousness, and social anxiety predicted alcohol-related harms. Furthermore, public self-consciousness mediated the relationship between pre-loading and harms in a positive direction and this appeared to be more relevant in high-risk (AUDIT 8+) than low-risk drinkers. Conclusions: Students who scored higher in public self-consciousness appeared to be at greater risk of harms from pre-loading. Further research should examine this relationship with particular attention to high-risk drinkers, and explore which aspects of a night out are related to heightened self-consciousness. Interventions could incorporate measures to reduce public self-consciousness, in order to reduce the negative impacts of pre-loading.
An experimental investigation into the use of eye‐contact in social interactions in women in the acute and recovered stages of anorexia nervosa

OBJECTIVE People with anorexia nervosa (AN) report significant difficulties in social functioning and a growing literature is beginning to explain some of the differences in social skills that might underlie the social challenges experienced by patients. One vital area of social functioning that has been largely neglected to date is how eye-contact is used in the context of social stimuli and in social situations. METHODS This cross-sectional, experimental study used eye-tracking to measure the frequency and duration of eye-contact made with the eye region of interest (ROI) of (1) static social stimuli (man and woman Ekman faces displaying basic emotions); (2) moving social stimuli (a video of two actors conversing); and (3) during a real-life social interaction in 75 women (25 with AN, 25 recovered from AN, and 25 non-AN controls; mean age = 27.18, SD = 6.19). RESULTS Participants showed greater eye-contact during a real-life social interaction than when viewing static social stimuli. Those with AN made contact with the eye ROI of the static and moving social stimuli and during a real-life social interaction significantly less often and for significantly less time than non-AN controls. Those recovered from AN showed greater eye-contact than the acute group but significantly less eye-contact with the eye ROI across the static and moving social stimuli and during the real-life social interaction than non-AN controls. DISCUSSION These findings contribute new knowledge regarding the types of social skills that people with AN may need additional support with to allow them to make greater use of social support in their recovery.
Depression Promotes the Onset of Irritable Bowel Syndrome through Unique Dysbiosis in Rats

Background/Aims Although studies using conventional animal models have shown that specific stressors cause irritable bowel syndrome (IBS), it is unclear whether depression itself causes IBS. Our aim was to establish a rat model to determine if depression itself promotes the onset of IBS and to elucidate the role of gut microbiota in brain-gut axis pathogenesis during coincident depression and IBS. Methods Rat models of depression were induced using our shuttle box method of learned helplessness. Visceral hypersensitivity was evaluated by colorectal distension (CRD) to diagnose IBS. Gut microbiota compositions were analyzed using high-throughput sequencing. In the subanalysis of rats without depression-like symptoms, rats with posttraumatic stress disorder (PTSD) were also examined. Results The threshold value of CRD in depressed rats was significantly lower than that in control rats. Microbial community analysis of cecal microbiota showed that the relative abundance of Clostridiales incertae sedis, the most prevalent microbe, was significantly lower in depressed rats than in control rats. The distribution pattern of the microbiota clearly differed between depressed rats and control rats. Neither visceral hypersensitivity nor the composition of gut microbiota was altered in rats with PTSD-like phenotypes. Conclusions Our rat model of depression is useful for clarifying the effect of depression on IBS and suggests that depression itself, rather than specific stressors, promotes the onset of IBS. Further, we provided evidence that various psychiatric diseases, viz., depression and PTSD, are associated with unique gut microbiota profiles, which could differentially affect the onset and progression of coincident IBS.
Quality Monitoring of a FIT-Based Colorectal Cancer Screening Program.

BACKGROUND Quality assessment is crucial for consistent program performance of colorectal cancer (CRC) screening programs using fecal immunochemical test for hemoglobin (FIT). However, literature on the consistency of FIT performance in laboratory medicine was lacking. This study examined the consistency of FIT in testing positive or detecting advanced neoplasia (AN) for different specimen collection devices, lot reagents, and laboratories. METHODS All participants with a FIT sample with a cutoff concentration of 47 μg Hb/g feces in the Dutch CRC screening program in 2014 and 2015 were included in the analyses. Multivariable logistic regression analyses were performed to estimate the odds ratios of collection devices, reagents, and laboratories on testing positive or detecting AN and positive predictive value (PPV). RESULTS In total, 87519 (6.4%) of the 1371169 participants tested positive. Positivity rates and detection rates of AN differed between collection devices and reagents (all P < 0.01). In contrast, PPVs were not found to vary between collection devices, reagents, or laboratories (all P > 0.05). Positivity rates showed a small difference for laboratories (P = 0.004) but not for detection rates of AN. Size of the population affected by the deviating positivity rates was small (0.1% of the total tested population). CONCLUSIONS Variations were observed in positivity and detection rates between collection devices and reagents, but there was no detected variation in PPV. Although the overall population effect of these variations on the screened population is expected to be modest, there is room for improvement.
Decreased Posterior Tibial Slope Does Not Affect Postoperative Posterior Knee Laxity After Double-Bundle Posterior Cruciate Ligament Reconstruction

Background: Recent clinical studies identified sagittal plane posterior tibial slope as a risk factor for increased postoperative laxity after single-bundle posterior cruciate ligament reconstruction (PCLR). Purpose/Hypothesis: To retrospectively compare the degree of posterior tibial slope and its effect on posterior tibial translation (PTT) after double-bundle (DB) PCLR. Our null hypothesis was that preoperative tibial slope would not be associated with graft laxity. Study Design: Case series; Level of evidence, 4. Methods: Patients who underwent DB PCLR between 2010 and 2017 by a single surgeon were retrospectively analyzed. Measurements of posterior tibial slope were performed on lateral radiographs, and PTT was measured with pre- and postoperative kneeling stress radiographs. Simple and multiple linear regression was performed to estimate the unadjusted and adjusted effect of tibial slope on postoperative graft laxity, respectively. Results: A total of 103 patients with posterior cruciate ligament tears and subsequent reconstructions were included. There was a significant reduction of the mean ± SD side-to-side difference in PTT between stress radiographs (preoperative, 10.6 ± 2.7 mm; postoperative, 1.5 ± 2.6 mm; mean difference, 9.1 mm; 95% CI, 8.4-9.8; P < .001). Linear regression analysis revealed no significant correlation between preoperative posterior tibial slope and the amount of side-to-side difference in PTT on postoperative stress radiographs obtained at a mean 18.5 months (R = −0.115, P = .249). Combined ligament injury (beta = −1.01; 95% CI, −2.00 to −0.01; P = .047) was a significant independent predictor of decreased postoperative side-to-side difference in PTT. Conclusion: Graft laxity, determined by PTT in posterior kneeling stress radiographs, was not influenced by decreased posterior tibial slope after DB PCLRs. The observed results in the current study support the use of DB PCLR. Future studies should be conducted to compare the effect of tibial slope after SB PCLR and DB PCLR at long-term follow-up.
Opportunities for Optimizing Pantoprazole Therapy in Patients with Acute Upper Gastrointestinal Bleeding

Purpose To evaluate the appropriateness of intravenous (IV) pantoprazole in subjects presenting with signs suspicious of acute gastrointestinal bleeding (AGIB) and to identify opportunities for optimizing its use. Methods Retrospective health record review of subjects receiving IV pantoprazole for suspected or confirmed AGIB was conducted at two affiliated teaching hospitals. Results Of the 175 subjects enrolled, 157 (90%) received a diagnostic endoscopy. The median time to endoscopy was 18.5 hours, and the median time to start pantoprazole was 6.9 hours. Thirty-seven subjects (21%) did not receive the appropriate pantoprazole dose of 80 mg bolus followed by 8 mg/h infusion, and 22 high-risk subjects (33%) received less than 60 hours of IV pantoprazole. The median duration of pantoprazole following endoscopy for low-risk subjects was 21.1 hours. Conclusion Opportunities to optimize the use of IV pantoprazole include initiating therapy quickly at the appropriate dosing regimen, continuing the infusion for 72 hours in patients with high-risk bleeds, and discontinuing the infusion promptly once a high-risk AGIB is ruled out.
Two-quartet kit* G-quadruplex is formed via double-stranded pre-folded structure

In the promoter of c-KIT proto-oncogene, whose deregulation has been implicated in many cancers, three G-rich regions (kit1, kit* and kit2) are able to fold into G-quadruplexes. While kit1 and kit2 have been studied in depth, little information is available on kit* folding behavior despite its key role in regulation of c-KIT transcription. Notably, kit* contains consensus sites for SP1 and AP2 transcription factors. Herein, a set of complementary spectroscopic and biophysical methods reveals that kit*, d[GGCGAGGAGGGGCGTGGCCGGC], adopts a chair type antiparallel G-quadruplex with two G-quartets at physiological relevant concentrations of KCl. Heterogeneous ensemble of structures is observed in the presence of Na+ and NH4+ ions, which however stabilize pre-folded structure. In the presence of K+ ions stacking interactions of adenine and thymine residues on the top G-quartet contribute to structural stability together with a G10•C18 base pair and a fold-back motif of the five residues at the 3'-terminal under the bottom G-quartet. The 3'-tail enables formation of a bimolecular pre-folded structure that drives folding of kit* into a single G-quadruplex. Intriguingly, kinetics of kit* G-quadruplex formation matches timescale of transcriptional processes and might demonstrate interplay of kinetic and thermodynamic factors for understanding regulation of c-KIT proto-oncogene expression.
The Pharmacokinetics, Pharmacodynamics, and Mucosal Responses to Maraviroc-Containing PrEP Regimens in Men who have Sex with Men

Objective: HPTN 069/ACTG A5305 was a study of 48-week oral PrEP regimens in MSM and transgender women A rectal substudy was included to evaluate drug concentrations in rectal compartment vs. blood, gut-associated lymphoid tissue (GALT) responses to four antiretroviral (ARV) PrEP regimens (maraviroc (MVC), MVC + emtricitabine (FTC), MVC + tenofovir disoproxil fumarate (TDF), and TDF + FTC), and to determine whether ARV exposure was associated with ex vivo suppression of HIV infection in colorectal explants. Methods: CCR5 genotype was characterized using PCR. At baseline and at weeks 24, 48, and 49, GALT phenotype was characterized by flow cytometry, rectal biopsies were challenged with HIV-1 BaL , and tissue and plasma pharmacokinetics were measured via mass spectrometry. Results: Exposure to MVC was not associated with increased expression of CD4+/CCR5+ HIV target T-cells. Significant ex vivo viral suppression compared to baseline was seen at Weeks 24 and 48, ranging from 1.4 to 1.8 log 10 for all study regimens except the MVC-alone arm which did not show statistically significant viral suppression at Week 48. Tissue concentrations of tenofovir (TFV), TFV-diphosphate (DP), and FTC were correlated with viral suppression. Conclusions: MVC-containing HIV PrEP regimens did not increase GALT CD4+ T-cell activation or the CD4+/CCR5+ phenotype. No virologic suppression was seen with MVC-alone at Week 48 compared to combination regimens, suggesting MVC monotherapy might be less effective than combination ARV PrEP regimens.
Group Maximum Differentiation Competition: Model Comparison with Few Samples

In many science and engineering fields that require computational models to predict certain physical quantities, we are often faced with the selection of the best model under the constraint that only a small sample set can be physically measured. One such example is the prediction of human perception of visual quality, where sample images live in a high dimensional space with enormous content variations. We propose a new methodology for model comparison named group maximum differentiation (gMAD) competition. Given multiple computational models, gMAD maximizes the chances of falsifying a “defender” model using the rest models as “attackers”. It exploits the sample space to find sample pairs that maximally differentiate the attackers while holding the defender fixed. Based on the results of the attacking-defending game, we introduce two measures, aggressiveness and resistance, to summarize the performance of each model at attacking other models and defending attacks from other models, respectively. We demonstrate the gMAD competition using three examples—image quality, image aesthetics, and streaming video quality-of-experience. Although these examples focus on visually discriminable quantities, the gMAD methodology can be extended to many other fields, and is especially useful when the sample space is large, the physical measurement is expensive and the cost of computational prediction is low.
Reduced Right Ventricular Output Reserve in Patients With Systemic Sclerosis and Mildly Elevated Pulmonary Artery Pressure

This prospective study was undertaken to evaluate right ventricular function and pulmonary arterial compliance (PAC; ratio of stroke volume to pulse pressure) at rest and during exercise in patients with systemic sclerosis (SSc) with normal mean pulmonary artery pressure (PAP), patients with SSc with mildly elevated mean PAP, and patients with SSc with manifest pulmonary hypertension (PH).
Does the Effect of a Time Limit for Testing Impair Structural Investigations by Means of Confirmatory Factor Models?

The article reports three simulation studies conducted to find out whether the effect of a time limit for testing impairs model fit in investigations of structural validity, whether the representation of the assumed source of the effect prevents impairment of model fit and whether it is possible to identify and discriminate this method effect from another method effect. Omissions due to the time limit for testing were not considered as missing data but as information on the participants’ processing speed. In simulated data the presence of a time-limit effect impaired comparative fit index and nonnormed fit index whereas normed chi-square, root mean square error of approximation, and standardized root mean square residual indicated good model fit. The explicit consideration of the effect due to the time limit by an additional component of the model improved model fit. Effect-specific assumptions included in the model of measurement enabled the discrimination of the effect due to the time limit from another possible method effect.
Implantation of VEGF‐functionalized cell‐free vascular grafts: regenerative and immunological response

Recently, our group demonstrated that immobilized VEGF can capture flowing endothelial cells (ECs) from the blood in vitro and promote endothelialization and patency of acellular tissue–engineered vessels (A‐TEVs) into the arterial system of an ovine animal model. Here, we demonstrate implantability of submillimeter diameter heparin and VEGF‐decorated A‐TEVs in a mouse model and discuss the cellular and immunologic response. At 1 mo postimplantation, the graft lumen was fully endothelialized, as shown by expression of EC markers such as CD144, eNOS, CD31, and VEGFR2. Interestingly, the same cells coexpressed leukocyte/macrophage (Mϕ) markers CD14, CD16, VEGFR1, CD38, and EGR2. Notably, there was a stark difference in the cellular makeup between grafts containing VEGF and those containing heparin alone. In VEGF‐containing grafts, infiltrating monocytes (MCs) converted into anti‐inflammatory M2‐Mϕs, and the grafts developed well‐demarcated luminal and medial layers resembling those of native arteries. In contrast, in grafts containing only heparin, MCs converted primarily into M1‐Mϕs, and the endothelial and smooth muscle layers were not well defined. Our results indicate that VEGF may play an important role in regulating A‐TEV patency and regeneration, possibly by regulating the inflammatory response to the implants. —Smith, R. J., Jr., Yi, T. , Nasiri, B. , Breuer, C. K. , Andreadis, S. T. Implantation of VEGF‐functionalized cell‐free vascular grafts: regenerative and immunological response. FASEB J. 33, 5089–5100 (2019). www.fasebj. org
Diversity as a Determinant of Attitudes: A Possible Explanation of the Apparent Advantage of Single-Sex Settings

The effects of a single-sex educational setting on girls' computing experience and attitudes were investigated. Questionnaire data were collected from a sample of 231 high school girls (aged approximately 15 years) from three single-sex and two co-educational schools in Victoria, Australia. Girls from single-sex settings were found to have more experience with computers, and more positive attitudes toward computers than girls from co-educational settings. However, once the effects of experience with computers were partialed out, there was no effect of educational setting on computing attitudes. Diversity of computing experience was the strongest predictor of high school girls' attitudes toward computers. The findings indicate the importance of designing computing curricula for girls which emphasize a broad range of computing activities in preference to focusing on skill development in a single area.
A Review on Quantitative Multiplexed Proteomics

Over the last few decades, mass spectrometry‐based proteomics has become an increasingly powerful tool that is now able to routinely detect and quantify thousands of proteins. A major advance for global protein quantification was the introduction of isobaric tags, which, in a single experiment, enabled the global quantification of proteins across multiple samples. Herein, these methods are referred to as multiplexed proteomics. The principles, advantages, and drawbacks of various multiplexed proteomics techniques are discussed and compared with alternative approaches. We also discuss how the emerging combination of multiplexing with targeted proteomics might enable the reliable and high‐quality quantification of very low abundance proteins across multiple conditions. Lastly, we suggest that fusing multiplexed proteomics with data‐independent acquisition approaches might enable the comparison of hundreds of different samples without missing values, while maintaining the superb measurement precision and accuracy obtainable with isobaric tag quantification.