Miracle-dz/UniFAR-FTUs huggingface dataset:
Beyond the bulk: disclosing the life of single microbial cells

Abstract Microbial single cell analysis has led to discoveries that are beyond what can be resolved with population-based studies. It provides a pristine view of the mechanisms that organize cellular physiology, unbiased by population heterogeneity or uncontrollable environmental impacts. A holistic description of cellular functions at the single cell level requires analytical concepts beyond the miniaturization of existing technologies, defined but uncontrolled by the biological system itself. This review provides an overview of the latest advances in single cell technologies and demonstrates their potential. Opportunities and limitations of single cell microbiology are discussed using selected application-related examples.
Improvement of islet function and survival by integration of perfluorodecalin into microcapsules in vivo and in vitro

Hypoxic injury of islets is a major obstacle for encapsulated islet transplantation into the peritoneal cavity. To improve oxygen delivery to encapsulated islets, we integrated 20% of the oxygen carrier material, perfluorodecalin (PFD), in alginate capsules mixed with islets (PFD‐alginate). Integration of PFD clearly improved islet viability and decreased reactive oxygen species production compared to islets encapsulated with alginate only (alginate) and naked islets exposed to hypoxia in vitro. In PFD‐alginate capsules, HIF‐1α expression was minimal, and insulin expression was well maintained. Furthermore, the best islet function represented by glucose‐stimulated insulin secretion was observed for the PFD‐alginate capsules in hypoxic condition. For the in vivo study, the same number of naked islets and encapsulated islets (alginate and PFD‐alginate) was transplanted into streptozotocin‐induced diabetic mice. Nonfasting blood glucose levels and the area under the curve for glucose based on intraperitoneal glucose tolerance tests in the PFD‐alginate group were lower than in the alginate group. The harvested islets stained positive for insulin in all groups, but the ratio of dead cell area was 4 times higher in the alginate group than in the PFD‐alginate group. In conclusion, integration of PFD in alginate microcapsules improved islet function and survival by minimizing the hypoxic damage of islets after intraperitoneal transplantation.
Long-Term Patient-Reported Outcomes following Free Flap Lower Extremity Reconstruction for Traumatic Injuries

Background: Reconstruction of severe lower extremity injuries using free flaps has become a reliable approach. Knowledge of long-term surgical outcomes, limb function, and quality of life is limited. Methods: Two hundred thirty-nine patients undergoing a free flap reconstruction of an open lower extremity fracture between 1993 and 2014 were divided into three groups and studied, as follows: group 1, early free flap reconstruction within 6 weeks; group 2, delayed reconstruction after 6 weeks; and group 3, delayed reconstruction with osteomyelitis. Patient-reported outcomes were assessed with the 36-Item Short-Form Health Survey and the Lower Extremity Functional Scale. Independent variables predicting outcomes were identified using multivariate analyses. Results: Patients in group 3 significantly more often experienced delayed union. Questionnaires were completed by 108 patients (mean follow-up, 9.7 years). The 36-Item Short-Form Health Survey physical component scores were significantly lower in all three groups compared with Dutch norms, as was the mental health score in group 3. There were no significant differences in quality of life and lower limb function among the three groups. Chronic pain was an independent predictor for decreased quality of life and limb function in groups 1 and 2, as was delayed union for decreased limb function in group 3. Conclusions: After free flap reconstruction of severe lower extremity injuries, all patient groups showed significantly lower quality of life compared to the Dutch population; however, there were no significant differences between the groups. Predictors for poorer quality of life and limb function were chronic pain and delayed union.
Microarray analysis reveals Tmub1 as a cell cycle-associated protein in rat hepatocytes

Transmembrane and ubiquitin-like domain containing protein 1 (Tmub1), formerly known as hepatocyte odd protein shuttling (HOPS) has been recognized as a ubiquitously expressed shuttling protein that moves between the nucleus and cytoplasm in hepatocytes. Tmub1 is involved in liver regeneration and functions as a bridging protein in tumor cell proliferation. To investigate the transcriptional profile and potential biological processes affected by Tmub1 expression in normal rat hepatocytes, microarray and bioinformatics experiments were used to identify 127 mRNAs differentially expressed between Tmub1-overexpression, Tmub1-knockdown and normal BRL-3A cells (fold-change ≥2.5). The expression levels of 17 key node genes associated with the cell cycle were confirmed by reverse transcription-quantitative polymerase chain reaction analysis. Flow cytometry, 5-Ethynyl-20-deoxyuridine, Cell Counting Kit-8 and western blotting experiments revealed the effects on the cell cycle and the inhibition of proliferation in BRL-3A cells overexpressing Tmub1. Further co-immunoprecipitation assays demonstrated that Tmub1 interacts with cyclin A2 during the cell cycle and that the overexpression of Tmub1 may postpone cyclin A2 and cyclin B1 degradation in the M phase. The results of the present study indicated that Tmub1 functions as a cell proliferation inhibitor and cell cycle-associated protein.
Revisiting Group Consensus: Collaborative Learning Dynamics During a Problem-Based Learning Activity in Education

Problem-based learning (PBL), especially in conjunction with collaborative learning teams, continues to gain momentum as a popular instructional approach in higher education. In this article, we address three common assumptions about how PBL groups function and report the outcomes of a study in which we examined group dynamics during a computer-assisted PBL module designed to train preservice teachers on the procedures for disciplining students with disabilities. We found that students often do not engage in the constructive dissonance assumed to contribute to strong consensus decisions: groups often defer to an individual or minority opinion with little persuasion or critical thinking. We recommend teaching subject content together with group skills such that future professionals can ensure that all voices are heard, quick answers are scrutinized, and alternative solutions are appropriately vetted by educational teams.
Sleep disordered breathing in spinal cord injury: A systematic review

Context: Spinal cord injury commonly results in neuromuscular weakness that impacts respiratory function. This would be expected to be associated with an increased likelihood of sleep-disordered breathing. Objective: (1) Understand the incidence and prevalence of sleep disordered breathing in spinal cord injury. (2) Understand the relationship between injury and patient characteristics and the incidence of sleep disordered breathing in spinal cord injury. (3) Distinguish between obstructive sleep apnea and central sleep apnea incidence in spinal cord injury. (4) Clarify the relationship between sleep disordered breathing and stroke, myocardial infarction, metabolic dysfunction, injuries, autonomic dysreflexia and spasticity incidence in persons with spinal cord injury. (5) Understand treatment tolerance and outcome in persons with spinal cord injury and sleep disordered breathing. Methods: Extensive database search including PubMed, Cochrane Library, CINAHL and Web of Science. Results: Given the current literature limitations, sleep disordered breathing as currently defined is high in patients with spinal cord injury, approaching 60% in motor complete persons with tetraplegia. Central apnea is more common in patients with tetraplegia than in patients with paraplegia. Conclusion: Early formal sleep study in patients with acute complete tetraplegia is recommended. In patients with incomplete tetraplegia and with paraplegia, the incidence of sleep-disordered breathing is significantly higher than the general population. With the lack of correlation between symptoms and SDB, formal study would be reasonable. There is insufficient evidence in the literature on the impact of treatment on morbidity, mortality and quality of life outcomes.
The Fatty Liver Index (FLI) Relates to Diabetes-Specific Parameters and an Adverse Lipid Profile in a Cohort of Nondiabetic, Dyslipidemic Patients

ABSTRACT Background: Patients with hyperlipidemia are at high risk for developing a fatty liver. The fatty liver index (FLI) is a noninvasive and well-established method for the estimation of a fatty liver. However, little is known about the metabolic characterization of nondiabetic treated patients with hyperlipidemia who have different risk levels for a fatty liver. Methods: In this study, 74 nondiabetic patients with hyperlipidemia were divided into 3 groups according to their fatty liver index. A comparison of metabolic characteristics was done. These characteristics included intima media thickness (IMT) and nutritional habits, which were further divided into FLI subgroups with low, intermediate, and high risk for a fatty liver. Results: Patients with hyperlipidemia, with a high risk for a fatty liver (FLI ≥ 60), had subclinical elevations in parameters of carbohydrate metabolism (insulin, fasting plasma glucose, C-peptide) including a higher insulin resistance (quantitative insulin sensitivity check index, QUICKI) compared to lower FLI groups. These patients also presented a higher risk for a metabolic syndrome (p = 0.018), as well as an adverse lipid profile (e.g., high-density lipoprotein [HDL] cholesterol, triglycerides [TG]–HDL ratio). FLI group 3 was characterized by significantly lower levels of omega-3 fatty acids (p = 0.048). Conclusion: The fatty liver index relates to diabetes-specific parameters and an adverse lipid profile and is an appropriate index for risk evaluation of metabolic syndrome.
Epidemiologic Characteristics of Patients with Inflammatory Bowel Disease in Kermanshah, Iran

BACKGROUND This study was done to define some epidemiological aspects of inflammatory bowel disease (IBD), and to describe its characteristics in west of Iran. METHODS In this descriptive study all patient with the diagnosis of IBD who were visited in universityaffiliated medical centers, between 2014 and 2015 were recruited. Their demographic characteristics, disease-related manifestations, complications, disease course and their chief complaints were analyzed. RESULTS Of 156 referred individuals, 153 patients had ulcerative colitis (UC) and 3 patients had Crohn’s diseases (CD). The mean age of the patients at diagnosis was 35.69±12.35 (range: 17-80) years with the most common age group of 25-35 years and slight female predominance (51.9%). More urban patients were registered (90.4%) and 57% had high school or upper education. Positive family history of the disease was in 25.6% and 66.6% had four or more family members. Furthermore, 51.9% had left sided colitis and 40.4% had pancolitis with bloody diarrhea (79.5%) and abdominal pain (68.6%) as the most common manifestations. 36.5% had other autoimmune diseases. Multiple flare was seen in 47.4%, most commonly due to drug discontinuation (26.28%). Hospital admission was reported in 34.6%. History of contraceptive pill use was in 38.8% of the female patients. CONCLUSION The demographic and clinical manifestations of IBD are usually the same as other developing countries; however, the rarity of CD is eminent. Although the accurate epidemiological characteristic of IBD in Iran is still obscure, it is not a rare disease as previously thought and it seems that gradual reception of a western lifestyle may be linked to the ongoing rise in IBD.
Combining labeled and unlabeled data for biomédical event extraction

In biomédical event extraction domain, there is a small amount of labeled data along with a large pool of unlabeled data. Many supervised learning algorithms for bio-event extraction have been affected by the data sparseness. In this paper, we present a new solution to perform biomédical event extraction from scientific documents, applying a semi-supervised approach to extract features from unlabeled data using labeled data features as a reference. This strategy is evaluated via experiments in which the data from the BioNLP2011 and PubMed are applied. To the best of our knowledge, it is the first time that the combination of labeled and unlabeled data are used for biomédical event extraction and our experimental results demonstrate the state-of-the-art performance in this task.
New Formats and Interfaces for Multi-Document News Summarization and its Evaluation

News production, delivery, and consumption are increasing in ubiquity and speed, spreading over more software and hardware platforms, in particular mobile devices. This has led to an increasing interest in automated methods for multi-document summarization. We start this chapter with discussing several new alternatives for automated news summarization, with a particular focus on temporal text mining, graphbased methods, and graphical interfaces. Then we present automated and user-centric frameworks for cross-evaluating summarization methods that output different summary formats, and describe the challenges associated with each evaluation framework. Based on the results of our user studies, we argue that it is crucial for effective summarization to integrate the user into sense-making through usable, entertaining and ultimately useful interactive summarization-plus-document-search interfaces. In particular, graph-based methods and interfaces may be a better preparation for people to concentrate on what is essential in a collection of texts, and thus may be a key to enhancing the summary evaluation process by replacing the “one gold standard fits all” approach with carefully designed user studies built upon a variety of summary representation formats.
MR Image Segmentation based on Local Information Entropy Geodesic Active Contour Model

In this paper, an improved Geometric Active Contour model is presented. This model introduced a window function to research the mean information of each pixel’s neighbor region, and constructed a novel signed pressure force function based on the entropy to drive the contour towers the boundary. In order to improve the efficiency and stability of the algorithm, this paper adopts two valued level set method to realize the segmentation process. The experimental results show that this method can obtain satisfied result even when the images have intensity inhomogeneity and weak edges.
Predicting Occupancy Distributions of Walking Humans With Convolutional Neural Networks

As robots are increasingly entering human environments, many subtleties of socially compliant navigation are still unsolved. To behave in a socially compliant way, robots need to have an understanding of the natural motion paths of humans in the shared environment. Humans intuitively follow social norms, which allows them to navigate smoothly even in crowded environments. For example, when humans enter a previously unseen building, they are still able to infer from their surroundings where humans would typically walk and use this information to obviate interference. In this letter, we propose an approach to learn such a predictive method. A robot could use this information to find nondisturbing waiting positions, avoid crowded areas, or clean heavily frequented areas more often. We propose the use of convolutional neural networks to predict average occupancy maps of walking humans even in environments where no human trajectory data are available. In experiments, we show that our method transfers from simulation to real-world data and performs better than several baseline methods. We demonstrate the applicability on a real robot to find good waiting positions near narrow passages as well as a planner, which avoids areas where human interference is likely.
Fine-Scale Recombination Maps of Fungal Plant Pathogens Reveal Dynamic Recombination Landscapes and Intragenic Hotspots

Meiotic recombination is an important driver of evolution. Variability in the intensity of recombination across chromosomes can affect sequence composition, nucleotide variation, and rates of adaptation. In many organisms, recombination events are concentrated within short segments termed recombination hotspots. The variation in recombination rate and positions of recombination hotspot can be studied using population genomics data and statistical methods. In this study, we conducted population genomics analyses to address the evolution of recombination in two closely related fungal plant pathogens: the prominent wheat pathogen Zymoseptoria tritici and a sister species infecting wild grasses Z. ardabiliae. We specifically addressed whether recombination landscapes, including hotspot positions, are conserved in the two recently diverged species and if recombination contributes to rapid evolution of pathogenicity traits. We conducted a detailed simulation analysis to assess the performance of methods of recombination rate estimation based on patterns of linkage disequilibrium, in particular in the context of high nucleotide diversity. Our analyses reveal overall high recombination rates, a lack of suppressed recombination in centromeres, and significantly lower recombination rates on chromosomes that are known to be accessory. The comparison of the recombination landscapes of the two species reveals a strong correlation of recombination rate at the megabase scale, but little correlation at smaller scales. The recombination landscapes in both pathogen species are dominated by frequent recombination hotspots across the genome including coding regions, suggesting a strong impact of recombination on gene evolution. A significant but small fraction of these hotspots colocalize between the two species, suggesting that hotspot dynamics contribute to the overall pattern of fast evolving recombination in these species.
Adenovirus Infection of Human Enteroids Reveals Interferon Sensitivity and Preferential Infection of Goblet Cells

ABSTRACT Human adenoviruses (HAdV) are significant human pathogens. Although only a subset of HAdV serotypes commonly cause gastroenteritis in humans, most HAdV species replicate in the gastrointestinal tract. Knowledge of the complex interaction between HAdVs and the human intestinal epithelium has been limited by the lack of a suitable cell culture system containing relevant cell types. Recently, this need has been met by the stable and prolonged cultivation of primary intestinal epithelial cells as enteroids. Human enteroids have been used to reveal novel and interesting aspects of rotavirus, norovirus, and enterovirus replication, prompting us to explore their suitability for HAdV culture. We found that both prototype strains and clinical isolates of enteric and nonenteric HAdVs productively replicate in human enteroids. HAdV-5p, a respiratory pathogen, and HAdV-41p, an enteric pathogen, are both sensitive to type I and III interferons in human enteroid monolayers but not A549 cells. Interestingly, HAdV-5p, but not HAdV-41p, preferentially infected goblet cells. And, HAdV-5p but not HAdV-41p was potently neutralized by the enteric human alpha-defensin HD5. These studies highlight new facets of HAdV biology that are uniquely revealed by primary intestinal epithelial cell culture. IMPORTANCE Enteric adenoviruses are a significant cause of childhood gastroenteritis worldwide, yet our understanding of their unique biology is limited. Here we report robust replication of both prototype and clinical isolates of enteric and respiratory human adenoviruses in enteroids, a primary intestinal cell culture system. Recent studies have shown that other fastidious enteric viruses replicate in human enteroids. Therefore, human enteroids may provide a unified platform for culturing enteric viruses, potentially enabling isolation of a greater diversity of viruses from patients. Moreover, both the ability of interferon to restrict respiratory and enteric adenoviruses and a surprising preference of a respiratory serotype for goblet cells demonstrate the power of this culture system to uncover aspects of adenovirus biology that were previously unattainable with standard cell lines.
C-arm Positioning Is a Significant Source of Radiation in Spine Surgery

Study Design. Prospective chart review. Objective. It is well-known that radiation exposure during minimally invasive spine procedures can be substantial. Less interest has focused on setup radiation exposure before incision, including preoperative images used for surgical approach. The present study seeks to better quantify the significance of setup radiation in the total radiation exposure of minimally invasive spine surgery. Summary of Background Data. Radiographic localization is necessary in minimally invasive spine procedures to visualize anatomy, but increased radiation exposure is associated with health risks. Preoperative imaging for anatomical localization has not been previously analyzed as an appreciable source of radiation. Methods. From an institutional review board–approved database of more than 1100 procedures, the minimally invasive spine cases with recorded set-up radiation were extracted. The total radiation, set-up radiation, and procedure type data were evaluated. Statistics were generated using a chi-squared analysis. Results. Set-up and total radiation data were collected for 270 spine surgeries performed by four surgeons at two locations. There were 30 thoracic and 240 thoracolumbar/lumbar cases; 78 anterior and 192 posterior cases. Average total radiation (set-up and intraoperative) was 8.04 rad, and average setup radiation was 1.90 rad (28%, std 2.97 rad) across all cases. On average for the thoracolumbar/lumbar cases, set-up radiation accounted for almost 25% of total radiation with 1.76 rad from setup out of 8.16 rad total. Thoracic-only cases often necessitated even more images for localization, generating an average set-up/total percentage of 52%. Across all procedures, set-up radiation significantly increased the total radiation exposure because it accounted for more than 25% of the total procedure. Conclusion. Radiation exposure during preoperative localization can be substantial. Operating room personnel should recognize the high percentage of radiation that occurs during set-up, and merit should be given to techniques and technologies that can limit unnecessary radiation exposure during this portion of the procedure. Level of Evidence: 2
Occupational Therapists’ Views of Nussbaum’s Life Capability

Life Capability is the first and most fundamental of Nussbaum’s 10 Central Human Functional Capabilities (CHFCs). This capability refers to a person having a quality life of normal duration. The purpose of this study was to explore the views’ of occupational therapists about Life Capability, specifically, their perspectives of this capability and its perceived relevance to practice. Semi-structured interviews with 14 occupational therapists in British Columbia, Canada, were conducted and thematically analyzed. Within this Canadian context, three themes emerged regarding occupational therapists’ views about Life Capability: basic human right, quality of life, and longevity. Occupational therapists appear to view Life Capability as being consistent with the values of the occupational therapy profession. Nussbaum’s other CHFCs warrant study to explore the degree to which the Capabilities Approach could complement existing occupational therapy theories, science, and practice.