Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of sugammadex on chest radiographic abnormality in the early postoperative period after video-assisted thoracoscopic lobectomy

Background/aim Sugammadex, which offsets the effects of neuromuscular blocking agents (NMBs), has advantages over traditional reversal agents like pyridostigmine, as it enables fast and reliable recovery from neuromuscular blockade. This study compared the incidence of early postoperative chest radiographic abnormalities (CRA) between sugammadex (group S) and pyridostigmine (group P) following video-assisted thoracoscopic (VAT) lobectomy for lung cancer. Materials and methods We performed a retrospective cohort analysis by reviewing the medical records of patients who underwent VAT lobectomy at a single university medical center. We defined the early postoperative CRA as a characteristic appearance on chest radiograph up to 2 days after surgery. Arterial blood gas analysis (ABGA), surgical time, anaesthesia time, extubation time, and the total dose of rocuronium were analysed. Postoperative nausea and vomiting (PONV) and pain scores were observed until 2 days after surgery. Results A total of 257 patients underwent VAT lobectomy during the study period; 159 were included in the final analysis. Ninety patients received sugammadex while 69 received pyridostigmine. The incidence of early postoperative atelectasis was significantly lower in group S than in group P (26.7%, 95% CI: 17.5%‒35.8% and 43.5%, 95% CI: 31.8%‒55.2%, respectively, P = 0.013). The median dose of rocuronium was higher in group S than in group P (120 mg vs. 90 mg, P < 0.001). ABGA, extubation time, and PONV were similar in both groups. Conclusion Sugammadex decreased the incidence of CRA in the early postoperative period despite higher NMB consumption.
A dual-domain deep learning-based reconstruction method for fully 3D sparse data helical CT

Helical CT has been widely used in clinical diagnosis. In this work, we focus on a new prototype of helical CT, equipped with sparsely spaced multidetector and multi-slit collimator (MSC) in the axis direction. This type of system can not only lower radiation dose, and suppress scattering by MSC, but also cuts down the manufacturing cost of the detector. The major problem to overcome with such a system, however, is that of insufficient data for reconstruction. Hence, we propose a deep learning-based function optimization method for this ill-posed inverse problem. By incorporating a Radon inverse operator, and disentangling each slice, we significantly simplify the complexity of our network for 3D reconstruction. The network is composed of three subnetworks. Firstly, a convolutional neural network (CNN) in the projection domain is constructed to estimate missing projection data, and to convert helical projection data to 2D fan-beam projection data. This is follwed by the deployment of an analytical linear operator to transfer the data from the projection domain to the image domain. Finally, an additional CNN in the image domain is added for further image refinement. These three steps work collectively, and can be trained end to end. The overall network is trained on a simulated CT dataset based on eight patients from the American Association of Physicists in Medicine (AAPM) Low Dose CT Grand Challenge. We evaluate the trained network on both simulated datasets and clinical datasets. Extensive experimental studies have yielded very encouraging results, based on both visual examination and quantitative evaluation. These results demonstrate the effectiveness of our method and its potential for clinical usage. The proposed method provides us with a new solution for a fully 3D ill-posed problem.
Middle Ear and Temporal Bone Nonkeratinizing Squamous Cell Carcinomas With DEK-AFF2 Fusion

Primary squamous cell carcinomas (SCCs) of the middle ear and temporal bone are rare and usually keratinizing by morphology. Nonkeratinizing, basaloid SCCs arising in this area are exceedingly rare, and, due to the anatomic proximity to the skull base, nasopharynx, and nasal sinuses, the differential diagnosis is broad. Most tumors with squamous differentiation arising in these subsites are either viral-induced (human papillomavirus/Epstein-Barr virus) or rarely may have specific molecular alterations (BRD4-NUT, EWSR1-FLI translocations). Occasional tumors are negative for these findings, and their pathogenesis is unknown. A recently discovered DEK-AFF2 fusion was clinically detected in a series of 2 cases known to the authors. This fusion has been previously reported in the literature in a patient with a base of skull tumor who was an exceptional responder to programmed cell death protein 1 inhibitor therapy. We examine here the histomorphologic and molecular findings of 2 additional cases of an emerging entity. Two male patients were identified. Each had a primary middle ear/temporal bone mass with locally advanced disease. The histology was reviewed, and immunohistochemistry was performed. RNA-based next-generation sequencing was performed for clinical detection of diagnostic or actionable fusions. Both patients had basaloid/nonkeratinizing tumors on biopsy. They were positive for markers of squamous differentiation (HMWK, CK5, and p40). By RNA sequencing, they demonstrated the presence of a DEK-AFF2 fusion and were negative for EWSR1 and NUT translocations. The DEK-AFF2 fusion may define a novel diagnostic category of middle ear and temporal bone nonkeratinizing/basaloid SCCs. This fusion also may represent a potential avenue for immunotherapy in these patients. Further studies are needed to fully explore whether this fusion defines a location-specific clinicopathologic entity.
Integrated On-Chip 3D Vascular Network Culture under Hypoxia

We developed a portable device made of poly(dimethylsiloxane) (PDMS)/polymethylmethacrylate (PMMA) for long-term 3D cell culture of vascular endothelial cells for the development of a vascular network and evaluated the device under different transitions between normoxia and hypoxia with good optical accessibility. The combination of a nested reservoir device and a bicarbonate/ascorbate buffer system accomplished on-chip incubation with 4.91 ± 0.86% pO2 and 5.19 ± 1.70% pCO2 for up to 10 days. Seventy-two hours of normoxic incubation preceding hypoxic culture increased the cell viability, network formation, and size and stability of the resulting lumens compared with those completely maintained in normoxia for the same total duration. We employed different parameters of the network (e.g., total mesh area, total length, number of branches, among others) for the comparison of different oxygen treatments in the device. The differential effect of hypoxic conditions based on the maturity of the vessels may be used as an external factor to improve vascular development in vitro.
Survival of Patients with Hepatocellular Carcinoma in Renal Insufficiency: Prognostic Role of Albumin-Bilirubin Grade

Renal insufficiency (RI) is commonly seen in patients with hepatocellular carcinoma (HCC). The prognostic role of albumin-bilirubin (ALBI) grade in this special setting is unclear. We aimed to investigate the role of ALBI grade associated with the impact of RI on HCC. A prospective cohort of 3690 HCC patients between 2002 and 2016 were retrospectively analyzed. The Kaplan–Meier method and multivariate Cox proportional hazards model were used to determine survival and independent prognostic predictors. Of all patients, RI was an independent predictor associated with decreased survival. In multivariate Cox analysis for patients with RI, α-fetoprotein level ≥20 ng/mL, tumor size >3 cm, vascular invasion, distant metastasis, presence of ascites, performance status 1–2, performance status 3–4, and ALBI grade 2 and grade 3 were independent predictors of decreased survival (all p < 0.05). In subgroup analysis of patients with RI undergoing curative and non-curative treatments, the ALBI grade remained a significant prognostic predictor associated with decreased survival (p < 0.001). In summary, HCC patients with RI have decreased survival compared to those without RI. The ALBI grade can discriminate the survival in patients with RI independent of treatment strategy and is a feasible prognostic tool in this special patient population.
Early Postoperative Death in Patients Undergoing Emergency High-Risk Surgery: Towards a Better Understanding of Patients for Whom Surgery May not Be Beneficial

The timing, causes, and quality of care for patients who die after emergency laparotomy have not been extensively reported. A large database of 13,953 patients undergoing emergency laparotomy, between July 2014 and March 2017, from 28 hospitals in England was studied. Anonymized data was extracted on day of death, patient demographics, operative details, compliance with standards of care, and 30-day and in-patient mortality. Thirty-day mortality was 8.9%, and overall inpatient mortality was 9.8%. Almost 40% of postoperative deaths occurred within three days of surgery, and 70% of these early deaths occurred on the day of surgery or the first postoperative day. Such early deaths could be considered nonbeneficial surgery. Patients who died within three days of surgery had a significantly higher preoperative lactate, American Society of Anesthesiologists Physical Status (ASA-PS) grade, and Physiological and Operative Severity Score for the enumeration of Mortality and morbidity (P-POSSUM). Compliance with perioperative standards of care based on the Emergency Laparotomy Collaborative care bundle was high overall and better for those patients who died within three days of surgery. Multidisciplinary team involvement from intensive care, care of the elderly physicians, and palliative care may help both the communication and the burden of responsibility in deciding on the risk–benefit of operative versus nonoperative approaches to care.
Diversity of navel microbiome in young adults.

Introduction. Human skin microbial communities represent a tremendous source of genetic diversity that evolves as a function of human age. Microbiota differs between regions of oily and moist skin, and appears to stabilize with age.Aim. We have a minimal understanding of the time frame required for the stabilization of skin microbiota, and the role played by gender. In the current study, we examined the microbiota present in the navel region of college-attending young adults in the age group of 18-25 years and investigated if diversity is associated with gender (male and female). Method. The study involved 16 female and six male subjects. Isolated DNA samples from navel swabs were processed using the Nextera XT library preparation kit and sequenced using the MiSeq platform. Data were analysed using QIIME and statistical analysis performed in R.Results. Microbiota of navel skin is dominated by Corynebacterium and Staphylococcus and includes opportunistic pathogens like Clostridium and Pseudomonas. Also present as the major component of the flora were the organisms normally associated with the gastrointestinal tract such as Acinetobacter, Campylobacter, Klebsiella and organisms from the Enterobacteriaceae and Moraxellaceae families. Comparison of alpha and beta diversity of the microbiota in the male and female navel regions suggests that the flora is not statistically different (P>0.05). However, pairwise comparison suggests that the abundance of 12 specific genera varied with gender, including higher abundance of Klebsiella and Enterobacter in females.Conclusion. Our findings indicate that the navel skin microbiota of young adults has a core microbiota of Corynebacterium and Staphylococcus. We also noted the presence of a significant number of opportunistic pathogens. A minor gender difference in the abundance of individual organisms was also observed.
Effects of Pornography Use and Demographic Parameters on Sexual Response during Masturbation and Partnered Sex in Women

The effect of pornography on sexual response is understudied, particularly among women. A multinational, community-based sample of 2433 women at least 18 years of age completed a 42-item, opt-in questionnaire collecting information on demographic and sexual history characteristics, use of pornography during masturbation, frequency of pornography use, and sexual response parameters. Pornography use and average frequency were compared across demographic variables. We also examined how pornography frequency predicted differences in self-reported arousal difficulty; orgasmic difficulty, latency, and pleasure; and the percent of sexual activities ending in orgasm during both masturbation and partnered sex. On average, women using pornography were younger, and reported more interest in sex. Pornography frequency differed significantly by menopausal status, sexual orientation, anxiety/depression status, number of sexual partners, and origin of data collection. During masturbation, more frequent pornography use predicted lower arousal difficulty and orgasmic difficulty, greater pleasure, and a higher percentage of masturbatory events leading to orgasm. Frequency of pornography use predicted only lower arousal difficulty and longer orgasmic latencies during partnered sex, having no effect on the other outcome variables. Pornography use frequency did not predict overall relationship satisfaction or sexual relationship satisfaction. Overall, more frequent pornography use was generally associated with more favorable sexual response outcomes during masturbation, while not affecting most partnered sex parameters. Several demographic and relationship covariates appear to more consistently and strongly predict orgasmic problems during partnered sexual activity than pornography use.
Dopamine Receptor DRD2 Gene rs1076560, Personality Traits and Anxiety in the Polysubstance Use Disorder

Development of an addiction is conditioned by many factors. The dopaminergic system has been shown to be the key element in this process. In this paper, we analyzed the influence of dopamine receptor 2 polymorphism rs1076560 in two groups—polysubstance-dependent male patients (n = 299) and the controls matched for age (n = 301). In both groups, we applied the same questionnaires for testing—Mini-international neuropsychiatric interview, the NEO Five-Factor Inventory, and the State–Trait Anxiety Inventory. The real-time PCR method was used for genotyping. When we compared the controls with the case group subjects, we observed significantly higher scores in the second group on both the state and trait scales of anxiety, as well as on the Neuroticism and Openness scales of the NEO-FFI; and lower scores on the scales of Extraversion and Agreeability of the NEO-FFI. The model 2 × 3 factorial ANOVA of the addicted subjects and controls was performed, and the DRD2 rs1076560 variant interaction was found for the anxiety state and trait scales, and for the NEO-FFI Neuroticism scale. The observed associations allow noticing that analysis of psychological factors in combination with genetic data opens new possibilities in addiction research.
Ginsenoside Rg1 Acts as a Selective Glucocorticoid Receptor Agonist with Anti-Inflammatory Action without Affecting Tissue Regeneration in Zebrafish Larvae

Glucocorticoids are effective anti-inflammatory drugs, but their clinical use is complicated due to the wide range of side effects they induce. Patients requiring glucocorticoid therapy would benefit from more selective glucocorticoid receptor (GR) agonists, capable of attenuating the immune response without causing these side effects. Ginsenosides, such as the compound Rg1, are natural plant compounds with structural similarity to classical glucocorticoids and well-documented anti-inflammatory effects. Here, we have investigated the activity of the ginsenoside Rg1 using a zebrafish larval model, in which amputation of the tail fin allows us to assess drug effects on inflammation, while the ability to regenerate the wounded tissue serves as a readout for side effects. We found that Rg1 attenuates neutrophilic inflammation at the amputation site, similarly to a classical glucocorticoid, beclomethasone. Mutation of the Gr abolishes this anti-inflammatory effect of Rg1. Rg1 and beclomethasone differentially modulate gene expression, suggesting that Rg1 induces transrepression, but not transactivation, activity of Gr. Interestingly, we found no effect of Rg1 on tissue regeneration, whereas beclomethasone inhibits tissue regeneration entirely. We conclude that Rg1 is a promising candidate for development as a selective glucocorticoid drug, and that zebrafish larvae provide a useful model system for screening of such GR agonists.
Applied scoring of integument and health in laying hens.

Abstract. Different methods for scoring of birds’ integument are often used to describe the effects of various treatments in research on the health and welfare of laying hens. Also in commercial egg production and breeding there is need for having a tool to describe the status of a certain flock of birds or a pure line. Among the main traits to score are plumage and foot condition and pecking wounds on different parts of the body. Scores for these traits may describe problems of feather pecking, perch design and litter condition and cannibalistic or aggressive behaviours respectively. Important characteristics of a scoring system are e.g. the simplicity of the system for users to learn and to use at the same time being descriptive enough in details. The present paper describes a scoring method for six body parts as regards plumage condition and for pecking wounds on comb and rear part of the body and finally, the condition of the foot as regards bumble foot syndrome. The intention is that this system should be easy to use by scorers of different background e.g. scientists, administrators, welfare inspectors, breeders and producer organisations. When used to the system scoring a bird for all characters will not exceed 30 seconds for one person.
In Memoriam / Nécrologie

In 1973, Bill Ricker retired at the age of 65 from his responsibilities with the Fisheries Research Board of Canada. He had worked 27 years for the “Board”, 11 years at Indiana University, and 1 year at the International Pacific Salmon Commission. Over this period and through to his death on 8 September 2001, he produced an amazing array of scientific publications that improved our understanding of nature and helped to found a science needed to manage the developing world fisheries (Fig. 1). It is difficult to know Bill Ricker. With considerable work, it is possible to identify his many and varied scientific accomplishments. In his personal life, he appeared to be a very private individual. Discussions with his sons and grandchildren produce an understanding of his love for his wife Marion, who predeceased him, and of his devotion to his children and their interests. Bill had a partiality towards young people all his life and this kept him young. He particularly enjoyed being part of the adventures of his sons and their friends, which caused Bill to be very active in the Scouting movement in the 1950s. It seems that this spirit of adventure combined with a love of nature guided a young Bill Ricker into a life of discovery. Bill Ricker’s life is an inspiration to any young biologist contemplating a career in aquatic sciences. Few could hope to make as many contributions, but most could learn from his approach to science. He knew the scientific literature, no matter where it was published. He was clear about his assumptions. He was meticulous and applied good common sense and sound logic. He developed his concepts using simple examples. But most importantly, he communicated the results of his studies to his colleagues. A compilation of his publication includes 296 published papers and books, 238 published translations, and 148 scientific or literary manuscripts (K. Ricker 1998; customercare@accutype.net). Among his publications were 38 papers on stoneflies, which described about 88 new species, including some from outside North America as well as one fossil species. To Bill, every day was a good day to discover something new. In fisheries, Bill Ricker focused on issues that were vitally important to Canada’s commercial fisheries and to the science needed to manage them. However, he also found time to become a world authority in the taxonomy of stoneflies. In fact, it has been noted that some scientists believed that there were two W.E. Rickers as the contribution of the entomologist W.E. Ricker was exceptional for any one person. Bill Ricker described 81 of the total of 617 stoneflies now listed in North America. His interests in stoneflies extended into their zoogeography and evolution. Bill recognised distinctions within accepted genera, which he partitioned into subgenera in his classifications. These subgenera were later considered to be distinct genera. In fact, about one-third of the 101 genera currently recognised in North America were originally identified by Bill Ricker. Fellow entomologists iii
Technical Note: Ultra High-Resolution Radiotracer-Specific Digital PET Brain Phantoms based on the BigBrain Atlas.

PURPOSE To introduce a method that allows the generation of ultra high-resolution (sub-millimetre) heterogeneous digital PET brain phantoms and to provide a new publicly available [18 F]FDG phantom as an example. METHOD The radiotracer distribution of the phantom is estimated by minimizing the Kullback-Leibler distance between the parameterised unknown phantom distribution and a radiotracer-specific template used as a reference. The phantom is modelled using the histological and tissue classified volumes of the BigBrain atlas to provide both high resolution and heterogeneity. The Hammersmith brain atlas is also included to allow the estimation of different activity values in different anatomical regions of the brain. Using this method, a realistic [18 F]FDG phantom was produced, where a single real [18 F]FDG scan was used as the reference to match. An MRI T1-weighted image, obtained from the BigBrain atlas, and a pseudo-CT are included to complete the dataset. A full PET-MRI dataset was simulated and reconstructed with MR-guided methods for the new [18 F]FDG phantom. RESULTS An ultra high-resolution (400 µm voxel size) and heterogeneous phantom for [18 F]FDG was obtained. The radiotracer activity follows the patterns observed in the scan used as a reference. The simulated PET-MRI dataset provided a realistic simulation that was able to be reconstructed with MR-guided methods. By visual inspection, the reconstructed images showed similar patterns to the real data and the improvements in contrast and noise with respect to the standard MLEM reconstruction were more modest compared to simulations done with a simpler phantom, which was created from the same MRI image used to assist the reconstruction. CONCLUSIONS A method to create high-resolution heterogeneous digital brain phantoms for different PET radiotracers has been presented and successfully employed to create a new publicly available [18 F]FDG phantom. The generated phantom is high resolution, heterogeneous and simulates the uptake of the radiotracer in the different regions of the brain.
Hepatitis B Immunoglobulin discontinuation in long‐term liver transplant patients

Hepatitis B immunoglobulin (HBIG)—as a monotherapy or combined with nucleos(t)ide analogs (NUCs)—has effectively lowered Hepatitis B virus (HBV) reinfection after liver transplantation. However, it is associated with high costs and viral resistance. HBIG‐free prophylaxis with novel NUCs (tenofovir, entecavir) composes a viable alternative. We evaluated reinfection rate, histological changes, and outcome associated with HBIG discontinuation.