Miracle-dz/UniFAR-FTUs huggingface dataset:
Endoscopic, Single-Session Management of Encrusted, Forgotten Ureteral Stents

Background and Objectives: Remained or forgotten ureteral double-J stents may cause serious complications. Removing of an encrusted, forgotten stent can be challenging. We present our experience with heavily encrusted ureteral stents and discuss the endourologic treatment options as well as their effectivity. Materials and Methods: Eleven men and six women (mean 48.58 ± 14.48 years of age) with 18 encrusted forgotten stents (mean 16.4 ± 13.25 months of indwelling) were treated at our clinic. All patients underwent the operation after negative urine cultures were obtained. Their medical records were retrospectively reviewed and analyzed in terms of number of interventions required to remove the stent, operation time, complications, hospital stay and stone-free rate. Results: According to the Forgotten-Encrusted-Calcified (FECal) classification, the most common form of stent encrustation was grade III (64.7%) and 17.6% of the stents were fragmented. Four of 17 patients were initially treated with extracorporeal shock-wave lithotripsy. The patients required a mean of two endoscopic interventions for removing the encrusted stent and all stents were removed endoscopically in a single session. The mean operating time was 63.3 ± 41.8 minutes. Cystolithotripsy followed by ureteroscopy was the most common intervention (41.1%). Of the 17 patients, peroperative and postoperative complications were Clavien grade I in two, grade II in two and grade IIIb in one. The mean hospital stay was 1.3 ± 0.99 days. All patients were stone-free after a month of stent removal. Conclusions: The endourological removal of the encrusted forgotten stents in a single session is feasible and effective with a minimal morbidity. The treatment strategy should be to minimize the number of interventions.
Dynamic chromosomal rearrangements in Hodgkin’s lymphoma are due to ongoing three-dimensional nuclear remodeling and breakage-bridge-fusion cycles

Background Hodgkin’s lymphoma is characterized by the presence of mono-nucleated Hodgkin cells and bi- to multi-nucleated Reed-Sternberg cells. We have recently shown telomere dysfunction and aberrant synchronous/asynchronous cell divisions during the transition of Hodgkin cells to Reed-Sternberg cells.1 Design and Methods To determine whether overall changes in nuclear architecture affect genomic instability during the transition of Hodgkin cells to Reed-Sternberg cells, we investigated the nuclear organization of chromosomes in these cells. Results Three-dimensional fluorescent in situ hybridization revealed irregular nuclear positioning of individual chromosomes in Hodgkin cells and, more so, in Reed-Sternberg cells. We characterized an increasingly unequal distribution of chromosomes as mono-nucleated cells became multi-nucleated cells, some of which also contained chromosome-poor ‘ghost’ cell nuclei. Measurements of nuclear chromosome positions suggested chromosome overlaps in both types of cells. Spectral karyotyping then revealed both aneuploidy and complex chromosomal rearrangements: multiple breakage-bridge-fusion cycles were at the origin of the multiple rearranged chromosomes. This conclusion was challenged by super resolution three-dimensional structured illumination imaging of Hodgkin and Reed-Sternberg nuclei. Three-dimensional super resolution microscopy data documented inter-nuclear DNA bridges in multi-nucleated cells but not in mono-nucleated cells. These bridges consisted of chromatids and chromosomes shared by two Reed-Sternberg nuclei. The complexity of chromosomal rearrangements increased as Hodgkin cells developed into multi-nucleated cells, thus indicating tumor progression and evolution in Hodgkin’s lymphoma, with Reed-Sternberg cells representing the highest complexity in chromosomal rearrangements in this disease. Conclusions This is the first study to demonstrate nuclear remodeling and associated genomic instability leading to the generation of Reed-Sternberg cells of Hodgkin’s lymphoma. We defined nuclear remodeling as a key feature of Hodgkin’s lymphoma, highlighting the relevance of nuclear architecture in cancer.
In situ 2D maps of pH shifts across brass–lead galvanic joints using microelectrodes

Galvanic corrosion in drinking water distribution systems, such as conditions following partial lead service line replacement, can be a significant source of lead in tap water. The objective of this work was to measure the pH directly near metal surfaces using a novel experimental tool in order to understand the water chemistry at a lead-containing galvanic couple in drinking water. Specifically, pH microprofiles in the proximity of corroding metal surfaces were measured using a microelectrode to construct detailed in situ 2D spatial maps of the pH across a galvanic couple at 100 µm above the metal’s surface under flowing and stagnation conditions. The opposite pH trend was directly observed across the galvanic couple under flow and stagnation conditions. Water stagnation resulted in a pH at the anode (leaded solder) of 1.5 pH units lower than the bulk water pH (9.0) and as much as 2.5 pH units lower than the cathode (brass). These conditions can enhance lead release at the anode, which reflects different anodic–cathodic relationships of coupled metals primarily controlled by water flow. Most importantly, this work has demonstrated the ability to make real pH measurement at the surface of corroding metals using a novel microelectrode approach.
Effect of vaginal douching on vaginal flora and genital infection

Objective: This study aimed at examining the effect of vaginal douching (VD), which is a traditional and cultural application, on the vaginal flora and genital infections. Material and Methods: This descriptive study included 190 women including those who did or did not perform VD. A questionnaire survey and vaginal sampling were employed. The collected samples were transported within 8 h for laboratory testing. Results: There was no significant difference between the two groups in terms of vaginal flora. In the VD group, only a few patients reported a history of Sexually Transmitted disease (STD), but none in the non-VD group had STDs (p<0.05). No significant difference in infections was noted. However, there was a significant relationship between the history of infections and VD (p<0.01). Conclusion: Women who performed VD are at risk for vaginal infections. Further studies are warranted in the future for clinical application.
Classifying the Unclassified: A Phage Classification Method

This work reports the method ClassiPhage to classify phage genomes using sequence derived taxonomic features. ClassiPhage uses a set of phage specific Hidden Markov Models (HMMs) generated from clusters of related proteins. The method was validated on all publicly available genomes of phages that are known to infect Vibrionaceae. The phages belong to the well-described phage families of Myoviridae, Podoviridae, Siphoviridae, and Inoviridae. The achieved classification is consistent with the assignments of the International Committee on Taxonomy of Viruses (ICTV), all tested phages were assigned to the corresponding group of the ICTV-database. In addition, 44 out of 58 genomes of Vibrio phages not yet classified could be assigned to a phage family. The remaining 14 genomes may represent phages of new families or subfamilies. Comparative genomics indicates that the ability of the approach to identify and classify phages is correlated to the conserved genomic organization. ClassiPhage classifies phages exclusively based on genome sequence data and can be applied on distinct phage genomes as well as on prophage regions within host genomes. Possible applications include (a) classifying phages from assembled metagenomes; and (b) the identification and classification of integrated prophages and the splitting of phage families into subfamilies.
Targets, pools, shoulders, and communication – a reflection on the evolution of low-dose radiobiology

Abstract This reflection aims to look at the evolution of thinking about radiation dose response relationships from the early years of the journal when target theory prevailed to the present day when dose response is seen as a more holistic process involving multiple levels of organization and communication. The review is structured to consider how the old ideas evolved leading to apparently abrupt paradigm shifts. The odd data leading to these conceptual shifts are reviewed. Topics, which are currently still not mainstream are considered with a view to how they may change the future of radiobiology. Finally some personal reflections on the insights gained during the writing of the review are presented. The major conclusion from this study is that ideas concerning survival curves and radiation dose responses evolved and (epi)mutated gradually, driven in a large part by the techniques available for studying radiobiological processes. The illusion of abrupt paradigm shifts is not really borne out by the history when primary references are studied rather than textbooks or reviews. The textbooks necessarily simplify and distil complex data to provide a ‘take-home message’ while reviews are usually very personal collations selected among the vast amount of scientific literature. Primary references reveal the context of the discussion and the caveats and uncertainties of the authors.
Selective retransplantation after late hepatic artery thrombosis

Hepatic artery thrombosis (HAT) is a serious and life-threatening complication that can occur any time after liver transplantation. HAT is generally subdivided into 2 categories. Early HAT frequently presents with profound graft dysfunction and sepsis, and requires urgent revascularization or retransplantation. This article is protected by copyright. All rights reserved.
Identifying best practices in interstage care: using a positive deviance approach within the National Pediatric Cardiology Quality Improvement Collaborative

Abstract Introduction To identify interstage best practices associated with lower mortality, we studied National Pediatric Cardiology Quality Improvement Collaborative centres registry using a positive deviance approach. Methods Positive deviant and control centre team members were interviewed to identify potential interstage best practices. Subsequently, all collaborative centres were surveyed on the use of these practices to test their associations with centre mortality. Questionnaires were scored using Likert scales; the overall score was linearly transformed to a 0–100-point scale with higher scores indicating increased use of practices. Mortality was based on patients enrolled after a centre’s first year in the collaborative. Centre mortality rates were divided into tertiles. Survey scores for the low mortality tertile were compared with the other tertiles. Results For this study, seven positive deviant and four control teams were interviewed. A total of 20 potential best practices were identified, including team composition, improvement practices, and parent involvement. Questionnaires were completed by 36/43 eligible centres, providing 1504 patients for analysis. Average survey score was 50.2 (SD 13.4). Average mortality was 6.1% (SD 4.1). There was no correlation between survey scores and mortality (r=0.14, p=0.41). The one practice associated with the low mortality tertile was frequency of discussion of interstage results: 58.3% of low mortality teams discussed results at least monthly versus 8.4% of the middle and high tertile centres (p=0.02). Conclusions Low-mortality centres more frequently discuss interstage results than high-mortality centres. Heightened awareness of outcomes may influence practice; however, further study is needed to understand the variation in outcomes across centres.
Unplanned Return Visits to a Pediatric Emergency Department

Objectives Unplanned return visits (URVs) to emergency departments (EDs) account internationally for 2.5% to 5.2% of all consultations. ED crowding is an increasing challenge, and URVs seem to contribute to this problem. This study aimed to assess factors for URVs at the ED of a tertiary children's hospital to analyze if they are jointly responsible for the steadily rising amount of treated patients. Methods All patients with an URV to a pediatric ED in Switzerland between January and December 2013 were included in the study. Data were taken retrospectively from the electronic patient files, and different variables were defined and analyzed. Results URVs occurred at an incidence of 4.6%, and mostly concerned infants and toddlers (46%). URVs were independent of weekdays and mostly occurred between 10 am and 10 pm. In 84.2% of the cases, the URVs were judged as unnecessary, and in 15.8%, a hospitalization was indicated, mainly for children with a worsening respiratory illness. Conclusions The occurrence of URVs in our ED was within the incidence reported in the literature. While URVs lead to hospitalization in some patients, the majority of URVs were unnecessary from a medical point of view. These results indicate that a correct evaluation of the child's health state by parents is often challenging and requires repeated medical attendance following a first ED visit, especially in infants with airway diseases and infections. Intensive counseling and scheduled short-term follow-up consultation at the pediatrician's office could prevent URVs to the ED.
Recreational use of psychedelics is associated with elevated personality trait openness: Exploration of associations with brain serotonin markers

Background: Recent studies have suggested therapeutic benefits of psychedelics for a variety of mental health conditions. The understanding of how single psychedelic administrations can induce long-lasting effects are, in large, still lacking. However, recent studies in both healthy and clinical populations suggest a role for personality changes. Aim: To test support for some of these plausible mechanisms we evaluated (cross-sectional) associations between recreational use of psychedelics and 3,4-methylene-dioxymethamphetamine (MDMA) and (a) personality measures and (b) key markers of cerebral serotonergic signalling (serotonin transporter and serotonin-2A-receptor binding). Methods: In 10 psychedelic-preferring recreational users, 14 MDMA-preferring users and 21 non-using controls, personality was assessed using the ‘big five‘ instrument Revised NEO Personality Inventory (NEO-PI-R). Frontal serotonin transporter and serotonin-2A-receptor binding potentials were quantified using [11C]DASB and [18F]altanserin positron emission tomography, respectively. Results: Of the five NEO-PI-R traits, only openness to experience scores differed between the three groups; psychedelic-preferring recreational users showing higher openness to experience scores when compared with both MDMA-preferring users and controls. Openness to experience scores were positively associated with lifetime number of psychedelic exposures, and among all MDMA-preferring user/psychedelic-preferring recreational user individuals, frontal serotonin transporter binding – but not frontal serotonin-2A-receptor binding – was positively associated with openness to experience. Conclusion: Our findings from this cross-sectional study support increasing evidence of a positive association between psychedelic experiences and openness to experience, and (a) expands this to the context of ‘recreational’ psychedelics use, and (b) links serotonergic neurotransmission to openness to experience. A modulation of personality induced by psychedelic experiences may have important therapeutic implications via its impact on peoples’ value systems, cognitive flexibility, and individual and social behaviour.
Lack of signal for the impact of conotoxin gene diversity on speciation rates in cone snails.

Understanding why some groups of organisms are more diverse than others is a central goal in macroevolution. Evolvability, or the intrinsic capacity of lineages for evolutionary change, is thought to influence disparities in species diversity across taxa. Over macroevolutionary time scales, clades that exhibit high evolvability are expected to have higher speciation rates. Cone snails (family: Conidae, >900 spp.) provide a unique opportunity to test this prediction because their toxin genes can be used to characterize differences in evolvability between clades. Cone snails are carnivorous, use prey-specific venom (conotoxins) to capture prey, and the genes that encode venom are known and diversify through gene duplication. Theory predicts that higher gene diversity confers a greater potential to generate novel phenotypes for specialization and adaptation. Therefore, if conotoxin gene diversity gives rise to varying levels of evolvability, conotoxin gene diversity should be coupled with macroevolutionary speciation rates. We applied exon capture techniques to recover phylogenetic markers and conotoxin loci across 314 species, the largest venom discovery effort in a single study. We paired a reconstructed timetree using 12 fossil calibrations with species-specific estimates of conotoxin gene diversity and used trait-dependent diversification methods to test the impact of evolvability on diversification patterns. Surprisingly, we did not detect any signal for the relationship between conotoxin gene diversity and speciation rates, suggesting that venom evolution may not be the rate-limiting factor controlling diversification dynamics in Conidae. Comparative analyses showed some signal for the impact of diet and larval dispersal strategy on diversification patterns, though detection of a signal depended on the dataset and the method. If our results remain true with increased taxonomic sampling in future studies, they suggest that the rapid evolution of conid venom may cause other factors to become more critical to diversification, such as ecological opportunity or traits that promote isolation among lineages.
Cone beam computed tomographic evaluation of implants with platform-switched Morse taper connection with the implant-abutment interface at different levels in relation to the alveolar crest.

PURPOSE The aim of this study was to evaluate marginal bone levels, with cone beam computed tomography, on the buccal and lingual aspects of implants placed with the implant-abutment interface (IAI) at different positions in relation to the alveolar crest. MATERIALS AND METHODS Thirty patients in need of single-tooth rehabilitation were randomly assigned to three groups based on the position of the IAI in relation to the buccal aspect of the alveolar crest at the time of implant placement. Patients in groups 0, 1, and 2 had their implants placed level with the buccal crest or 1 or 2 mm apical to the buccal aspect of the alveolar crest, respectively. The implants were restored with screw-retained single crowns after 4 months. Marginal bone levels on the buccal and lingual aspects of the implants were evaluated at 12 months after implant placement. RESULTS All groups of implants demonstrated significantly different crestal positions. Group 2 implants maintained the greatest subcrestal position (1.33 ± 0.86 mm) compared to the implants of group 0 (-0.04 ± 0.18 mm) and group 1 (0.34 ± 0.44 mm). There were no differences between groups in the level of the first bone-to-implant contact relative to the implant platform. Implants of group 0 exhibited less buccal bone remodeling (-0.08 ± 0.25 mm) compared to group 1 (-0.65 ± 0.45 mm) and group 2 (-0.85 ± 0.75 mm) implants. For groups 1 and 2 implants, there was a significant negative correlation between buccal wall thickness following the osteotomy and the amount of buccal bone remodeling. CONCLUSION In this study, different responses were seen in the buccal and lingual peri-implant bone for implants with platform-switched Morse taper connections placed with the IAI at different locations in relation to the alveolar crest.
Prospective Study of Plasma Vitamin B6 and Risk of Colorectal Cancer in Men

Vitamin B6 may lower risk of colorectal cancer by preventing aberrations in one-carbon metabolism or by anti-inflammatory effects. We prospectively evaluated the association between plasma levels of pyridoxal 5′-phosphate (PLP; the active form of vitamin B6) and risk of colorectal cancer in a nested case-control study within the Physicians' Health Study. Among 14,916 men who provided blood specimens in 1982 to 1984, we identified 197 incident colorectal cancer cases through 2000 and individually matched them to 371 controls by age and smoking status. Plasma PLP levels were positively correlated with cold cereal intake and plasma levels of folate and vitamin B12 (age- and smoking-adjusted partial correction r = 0.28-0.48) and slightly inversely correlated with body mass index (r = −0.11) and plasma levels of homocysteine, C-reactive protein, tumor necrosis factor-α receptor 2, and interleukin-6 (r = −0.23 to −0.14). With control for these factors and known risk factors for colorectal cancer, plasma PLP levels were significantly inversely associated with risk of colorectal cancer; compared with men in the lowest quartile, those with PLP in quartiles 2 to 4 had relative risks (95% confidence interval) of 0.92 (0.55-1.56), 0.42 (0.23-0.75), and 0.49 (0.26-0.92; Ptrend = 0.01), respectively. In conclusion, vitamin B6 may protect against colorectal cancer independent of other one-carbon metabolites and inflammatory biomarkers. (Cancer Epidemiol Biomarkers Prev 2009;18(4):1197–202)
Tumor MET Expression and Gene Amplification in Chinese Patients with Locally Advanced or Metastatic Gastric or Gastroesophageal Junction Cancer

MET and its sole ligand, hepatocyte growth factor (HGF), are promising targets in gastric and gastroesophageal junction cancer. We evaluated whether MET protein expression or MET gene amplification is prognostic for overall survival (OS) in Chinese patients with advanced gastric or gastroesophageal junction cancer. Archival formalin-fixed, paraffin-embedded tumor samples from patients with unresectable locally advanced or metastatic gastric or gastroesophageal junction cancer enrolled in clinical trials at Peking University Cancer Hospital from 2008 to 2010 were assessed for MET and phospho-MET (p-MET) expression by immunohistochemistry and MET amplification by FISH. MET-positive expression was defined as membrane protein staining in ≥25% of tumor cells. MET amplification was defined as MET:centromere 7 ratio >2.0. We tested the association of MET status with clinical characteristics and OS, and also evaluated the association between expression and amplification. One hundred sixty-eight patients were eligible. Of the evaluable samples, 53 of 137 (39%) were MET positive, eight of 134 (6%) were p-MET positive, and eight of 113 (7%) were MET amplified. Neither MET expression nor MET amplification were associated with clinical characteristics, except Lauren classification (P = 0.04); MET amplification was associated with diffuse type. No significant OS difference was observed between MET-positive and MET-negative populations, regardless of first-line chemotherapy received. In 95 evaluable patients, MET expression was significantly associated with MET amplification (P < 0.001); all MET-amplified tumor samples showed some MET expression. In 96 evaluable patients, p-MET positivity was significantly associated with MET amplification (P < 0.001). Further evaluation in larger and independent sample sets is warranted to confirm our findings. Mol Cancer Ther; 14(11); 2634–41. ©2015 AACR.