Miracle-dz/UniFAR-FTUs huggingface dataset:
Detecting and phenotyping of aneuploid circulating tumor cells in patients with various malignancies

ABSTRACT Circulating tumor cells (CTCs) have been exclusively studied and served to assess the clinical outcomes of treatments and progression of cancer. Most CTC data have mainly been derived from distinct cohorts or selected tumor types. In the present study, a total of 594 blood samples from 479 cases with 19 different carcinomas and 30 healthy samples were collected and analyzed by Subtraction enrichment method combined with immunostaining-fluorescence in situ hybridization (iFISH). Non-hematopoietic cells with aneuploid chromosome 8 (more than 2 copies) were regarded as positive CTCs. The results showed that none of CTCs was found in all 30 healthy samples. The overall positive rate of CTCs was 89.0% in diagnosed cancer patients (ranging from 75.0% to 100.0%). Average number of 11, 5, 8 and 4 CTCs per 7.5 mL was observed in lung cancer, liver cancer, renal cancer and colorectal cancer, respectively. Among 19 different carcinomas, the total number of CTCs, tetraploid chromosome 8, polyploid chromosome 8, CTM (Circulating tumor microemboli) and large CTCs in patients with stage Ⅲ and Ⅳ were statistically higher than patients with stage Ⅰ and Ⅱ (P < 0.05). Furthermore, EpCAM expression was more frequently found in most CTCs than vimentin expression, confirming that these CTCs were of epithelial origin. In addition, small and large CTCs were also classified, and the expression of vimentin was mostly observed in small CTCs and CTM. Our results revealed that there are higher numbers of CTCs, tetraploid, polyploid and large CTCs in patients with stage Ⅲ and Ⅳ, indicating that the quantification of chromosome ploidy performed by SE-iFISH for CTCs might be a useful tool to predict and evaluate therapeutic efficacy as well as to monitoring disease progression.
Timing of Button Battery Removal From the Upper Gastrointestinal System in Children

Objective The aim of the study was to investigate the appropriate time of removal of button batteries (BB) from the esophagus and stomach in children. Methods This is a retrospective descriptive single-center study reviewing the medical records of all children with BB ingestion seen in the Royal Hospital between January 1, 2011, and December 31, 2014. All children younger than 13 years with a history of BB ingestion were included. Biodemographic data including age and sex were obtained. In addition, time of ingestion of BB, location of BB, time of endoscopic removal, and any complications were recorded. Results Forty-six patients with BB ingestion were identified out of 385 who presented with foreign body ingestion (12%) during the study period. Twenty four (52%) were boys and 22 (48%) were girls. All children had BB of 20 mm in diameter. Two children had the BB in the esophagus, whereas 13 children had the BB in the stomach up on presentation. The mean time of presentation of children with BB in the esophagus was 1.75 hours after ingestion, whereas those with BB in the stomach presented on average 19.4 hours after ingestion (P < 0.035). An endoscopic intervention was done in only 8 of the 46 children. Two children had the BB in the esophagus and 6 children in the stomach. One child required intensive care unit with subsequent esophageal strictures. The mean time of esophageal BB removal was 1.7 hours from ingestion, whereas removal from the stomach was on average 27 hours after ingestion. Endoscopic injuries were noted in 87.5% of the children with BB in the esophagus or the stomach. No mortality occurred during the study period. Conclusions Button batteries ingestion is a common problem with variable time of presentation to the emergency department. Esophageal BB presents the highest risk of injury even in as short time as 2 hours. Gastric mucosal injury can occur within 10 hours of ingestion. Button batteries of 20-mm diameter need to be urgently removed from the esophagus and be considered for removal earlier than 24 hours if in the stomach.
The SNS/HFIR Web Portal System for SANS

The new generation of neutron scattering instruments being built are higher resolution and produce one or more orders of magnitude larger data than the previous generation of instruments. For instance, we have grown out of being able to perform some important tasks with our laptops. The data sizes are too big and the computational time would be too long. These large datasets can be problematic as facility users now begin to struggle with many of the same issues faced by more established computing communities. These issues include data access, management, and movement, data format standards, distributed computing, and collaboration with others. The Neutron Science Portal has been designed, and implemented to provide users with an easy-to-use interface for managing and processing data, while also keeping an eye on meeting modern computer security requirements that are currently being imposed on institutions. Users can browse or search for data which they are allowed to see, run data reduction and analysis applications, perform sample activation calculations and perform McStas simulations. Collaboration is facilitated by providing users a read/writeable common area, shared across all experiment team members. The portal currently has over 370 registered users; almost 7TB of experiment and user data, approximately 1,000,000 files cataloged, and had almost 10,000 unique visits last year. Future directions for enhancing portal robustness include examining how to mirror data and portal services, better facilitation of collaborations via virtual organizations, enhancing disconnected service via "thick client" applications, and better inter-facility connectivity to support cross-cutting research.
A qualitative exploration of the Thai alcohol policy in regulating alcohol industry's marketing strategies and commercial activities

INTRODUCTION AND AIMS The recognition of the association between the use of alcohol and negative health outcomes have led to the endorsement of the World Health Organization's global strategy to reduce the harmful use of alcohol. Given the capacities, capabilities and sociocultural contexts of Thailand, this study aims to examine the Thai alcohol policy against the global strategy's recommended policy measures for marketing control and identify areas for further policy development. DESIGN AND METHODS Semi-structured interviews were conducted with the stakeholders from three sectors: the government, academia and civil society. Their perceptions of the Thai alcohol policy in regulating alcohol industry's commercial strategies and activities were discussed. Audio data were transcribed verbatim, systematically coded and thematically analysed. RESULTS Although the Thai Alcohol Control Act meticulously regulates the content of direct alcohol marketing, the volume of marketing and indirect alcohol marketing have become problematic and difficult for the government to address. The industry has worked to normalise the consumption of alcohol through repetitive brand exposure and their suggestion that drinking was integral for socialisation. The control of alcohol sponsorship was politically sensitive and legally ambiguous because alcohol sponsorship seemed to provide economic and social benefits and further reinforced the industry's positive image. DISCUSSION AND CONCLUSIONS Despite the strict alcohol policy, gaps in the marketing regulations exist. Future policy development should place greater emphasis on alcohol sponsorship and branding through evidenced-based interventions. The interactions between the government and the industry should be monitored and restricted. Rigorous regulations, as seen for tobacco, are encouraged for alcohol marketing.
Assessment of the Immunosuppressive Potential of INF-γ Licensed Adipose Mesenchymal Stem Cells, Their Secretome and Extracellular Vesicles

There is an active search for the ideal strategy to potentialize the effects of Mesenchymal Stem-Cells (MSCs) over the immune system. Also, part of the scientific community is seeking to elucidate the therapeutic potential of MSCs secretome and its extracellular vesicles (EVs), in order to avoid the complexity of a cellular therapy. Here, we investigate the effects of human adipose MSCs (AMSCs) licensing with INF-γ and TLR3 agonist over AMSCs proliferation, migration, as well as the immunomodulatory function. Furthermore, we evaluated how the licensing of AMSCs affected the immunomodulatory function of AMSC derived-secretome, including their EVs. INF-γ licensed-AMSCs presented an elevated expression of indoleamine 2,3-dioxygenase (IDO), accompanied by increased ICAM-1, as well as a higher immunosuppressive potential, compared to unlicensed AMSCs. Interestingly, the conditioned medium obtained from INF-γ licensed-AMSCs also revealed a slightly superior immunosuppressive potential, compared to other licensing strategies. Therefore, unlicensed and INF-γ licensed-AMSCs groups were used to isolate EVs. Interestingly, EVs isolated from both groups displayed similar capacity to inhibit T-cell proliferation. EVs isolated from both groups shared similar TGF-β and Galectin-1 mRNA content but only EVs derived from INF-γ licensed-AMSCs expressed IDO mRNA. In summary, we demonstrated that INF-γ licensing of AMSCs provides an immunosuppressive advantage both from a cell-cell contact-dependent perspective, as well as in a cell-free context. Interestingly, EVs derived from unlicensed and INF-γ licensed-AMSCs have similar ability to control activated T-cell proliferation. These results contribute towards the development of new strategies to control the immune response based on AMSCs or their derived products.
First description of the environmental niche of the epibenthic dinoflagellate species Coolia palmyrensis, C. malayensis, and C. tropicalis (Dinophyceae) from Eastern Australia

Environmental variables such as temperature, salinity, and irradiance are significant drivers of microalgal growth and distribution. Therefore, understanding how these variables influence fitness of potentially toxic microalgal species is particularly important. In this study, strains of the potentially harmful epibenthic dinoflagellate species Coolia palmyrensis, C. malayensis, and C. tropicalis were isolated from coastal shallow water habitats on the east coast of Australia and identified using the D1‐D3 region of the large subunit (LSU) ribosomal DNA (rDNA). To determine the environmental niche of each taxon, growth was measured across a gradient of temperature (15–30°C), salinity (20–38), and irradiance (10–200 μmol photons · m−2 · s−1). Specific growth rates of Coolia tropicalis were highest under warm temperatures (27°C), low salinities (ca. 23), and intermediate irradiance levels (150 μmol photons · m−2 · s−1), while C. malayensis showed the highest growth at moderate temperatures (24°C) and irradiance levels (150 μmol photons · m−2 · s−1) and growth rates were consistent across the range of salinity levels tested (20–38). Coolia palmyrensis had the highest growth rate of all species tested and favored moderate temperatures (24°C), oceanic salinity (35), and high irradiance (>200 μmol photons · m−2 · s−1). This is the first study to characterize the environmental niche of species from the benthic harmful algal bloom genus Coolia and provides important information to help define species distributions and inform risk management.
Frequency Shifts and Depth Dependence of Premotor Beta Band Activity during Perceptual Decision-Making

Neural activity in the premotor and motor cortices shows prominent structure in the beta frequency range (13–30 Hz). Currently, the behavioral relevance of this beta band activity (BBA) is debated. The underlying source of motor BBA and how it changes as a function of cortical depth are also not completely understood. Here, we addressed these unresolved questions by investigating BBA recorded using laminar electrodes in the dorsal premotor cortex of 2 male rhesus macaques performing a visual reaction time (RT) reach discrimination task. We observed robust BBA before and after the onset of the visual stimulus but not during the arm movement. While poststimulus BBA was positively correlated with RT throughout the beta frequency range, prestimulus correlation varied by frequency. Low beta frequencies (∼12–20 Hz) were positively correlated with RT, and high beta frequencies (∼22–30 Hz) were negatively correlated with RT. Analysis and simulations suggested that these frequency-dependent correlations could emerge due to a shift in the component frequencies of the prestimulus BBA as a function of RT, such that faster RTs are accompanied by greater power in high beta frequencies. We also observed a laminar dependence of BBA, with deeper electrodes demonstrating stronger power in low beta frequencies both prestimulus and poststimulus. The heterogeneous nature of BBA and the changing relationship between BBA and RT in different task epochs may be a sign of the differential network dynamics involved in cue expectation, decision-making, motor preparation, and movement execution. SIGNIFICANCE STATEMENT Beta band activity (BBA) has been implicated in motor tasks, in disease states, and as a potential signal for brain–machine interfaces. However, the behavioral relevance of BBA and its laminar organization in premotor cortex have not been completely elucidated. Here we addressed these unresolved issues using simultaneous recordings from multiple cortical layers of the premotor cortex of monkeys performing a decision-making task. Our key finding is that BBA is not a monolithic signal. Instead, BBA consists of at least two frequency bands. The relationship between BBA and eventual behavior, such as reaction time, also dynamically changes depending on task epoch. We also provide further evidence that BBA is laminarly organized, with greater power in deeper electrodes for low beta frequencies.
Lower extremity regional anesthesia: essentials of our current understanding

The advent of ultrasound guidance has led to a renewed interest in regional anesthesia of the lower limb. In keeping with the American Society of Regional Anesthesia and Pain Medicine’s ongoing commitment to provide intensive evidence-based education, this article presents a complete update of the 2005 comprehensive review on lower extremity peripheral nerve blocks. The current review article strives to (1) summarize the pertinent anatomy of the lumbar and sacral plexuses, (2) discuss the optimal approaches and techniques for lower limb regional anesthesia, (3) present evidence to guide the selection of pharmacological agents and adjuvants, (4) describe potential complications associated with lower extremity nerve blocks, and (5) identify informational gaps pertaining to outcomes, which warrant further investigation.
Effect of teriparatide use on bone mineral density and spinal fusion: a narrative review of animal models

Abstract Purpose of the study: Teriparatide (Human recombinant Parathyroid Hormone 1-34) is an anabolic agent that is frequently used in patients with osteoporosis and has been extensively investigated with animal model and clinical studies in current literature. The purpose of the study was to evaluate the impact of teriparatide on bone mineral density and fusion. Materials and methods: The findings from preclinical studies that have investigated the role of teriparatide in animal models are summarized in presented review. Results: Overall, the studies show an improvement in bone mineral density and increased fusion rates for osteoporotic animals undergoing spine fusion with teriparatide use. Conclusion: Further studies should be conducted for unanswered questions, such as teriparatide use before surgery, the effect on cervical fusion and surgery related complications.
Deep Learning Algorithms with Demographic Information Help to Detect Tuberculosis in Chest Radiographs in Annual Workers’ Health Examination Data

We aimed to use deep learning to detect tuberculosis in chest radiographs in annual workers’ health examination data and compare the performances of convolutional neural networks (CNNs) based on images only (I-CNN) and CNNs including demographic variables (D-CNN). The I-CNN and D-CNN models were trained on 1000 chest X-ray images, both positive and negative, for tuberculosis. Feature extraction was conducted using VGG19, InceptionV3, ResNet50, DenseNet121, and InceptionResNetV2. Age, weight, height, and gender were recorded as demographic variables. The area under the receiver operating characteristic (ROC) curve (AUC) was calculated for model comparison. The AUC values of the D-CNN models were greater than that of I-CNN. The AUC values for VGG19 increased by 0.0144 (0.957 to 0.9714) in the training set, and by 0.0138 (0.9075 to 0.9213) in the test set (both p < 0.05). The D-CNN models show greater sensitivity than I-CNN models (0.815 vs. 0.775, respectively) at the same cut-off point for the same specificity of 0.962. The sensitivity of D-CNN does not attenuate as much as that of I-CNN, even when specificity is increased by cut-off points. Conclusion: Our results indicate that machine learning can facilitate the detection of tuberculosis in chest X-rays, and demographic factors can improve this process.
Smooth muscle cell-specific knockout of neuropilin-1 impairs postnatal lung development and pathological vascular smooth muscle cell accumulation

Neuropilin 1 (NRP1) is important for neuronal and cardiovascular development due to its role in conveying class 3 semaphorin and vascular endothelial growth factor signaling, respectively. NRP1 is expressed in smooth muscle cells (SMCs) and mediates their migration and proliferation in cell culture and is implicated in pathological SMC remodeling in vivo. To address the importance of Nrp1 for SMC function during development, we generated conditional inducible Nrp1 SMC-specific knockout mice. Induction of early postnatal SMC-specific Nrp1 knockout led to pulmonary hemorrhage associated with defects in alveogenesis and revealed a specific requirement for Nrp1 in myofibroblast recruitment to the alveolar septae and PDGF-AA-induced migration in vitro. Furthermore, SMC-specific Nrp1 knockout inhibited PDGF-BB-stimulated SMC outgrowth ex vivo in aortic ring assays and reduced pathological arterial neointima formation in vivo. In contrast, we observed little significant effect of SMC-specific Nrp1 knockout on neonatal retinal vascularization. Our results point to a requirement of Nrp1 in vascular smooth muscle and myofibroblast function in vivo, which may have relevance for postnatal lung development and for pathologies characterized by excessive SMC and/or myofibroblast proliferation.
Improved Differential Diagnosis of Alzheimer’s Disease by Integrating ELISA and Mass Spectrometry-Based Cerebrospinal Fluid Biomarkers

Background: Alzheimer’s disease (AD) is diagnosed based on a clinical evaluation as well as analyses of classical biomarkers: Aβ42, total tau (t-tau), and phosphorylated tau (p-tau) in cerebrospinal fluid (CSF). Although the sensitivities and specificities of the classical biomarkers are fairly good for detection of AD, there is still a need to develop novel biochemical markers for early detection of AD. Objective: We explored if integration of novel proteins with classical biomarkers in CSF can better discriminate AD from non-AD subjects. Methods: We applied ELISA, mass spectrometry, and multivariate modeling to investigate classical biomarkers and the CSF proteome in subjects (n = 206) with 76 AD patients, 74 mild cognitive impairment (MCI) patients, 11 frontotemporal dementia (FTD) patients, and 45 non-dementia controls. The MCI patients were followed for 4–9 years and 21 of these converted to AD, whereas 53 remained stable. Results: By combining classical CSF biomarkers with twelve novel markers, the area of the ROC curves (AUROCS) of distinguishing AD and MCI/AD converters from non-AD were 93% and 96%, respectively. The FTDs and non-dementia controls were identified versus all other groups with AUROCS of 96% and 87%, respectively. Conclusions: Integration of new and classical CSF biomarkers in a model-based approach can improve the identification of AD, FTD, and non-dementia control subjects.
Development and Validation of the Real-World Progression in Diabetes (RAPIDS) Model

Introduction. To develop and validate the first real-world data-based type 2 diabetes progression model (RAPIDS) employing econometric techniques that can study the comparative effects of complex dynamic patterns of glucose-lowering drug use. Methods. The US Department of Veterans Affairs (VA) electronic medical record and claims databases were used to identify over 500,000 diabetes patients in 2003 with up to 9-year follow-up. The RAPIDS model contains interdependent first-order Markov processes over quarters for each of the micro- and macrovascular events, hypoglycemia, and death, as well as predictive models for 8 biomarker levels. Model parameters varied by static demographic factors and dynamic factors, such as age, duration of diabetes, 13 possible glucose-lowering treatment combinations, any blood pressure and any cholesterol-lowering medications, and cardiovascular history. To illustrate model capabilities, a simple comparative study was set up to compare observed treatment use patterns to alternate patterns if perfect adherence is assumed following initiating the use of any of these medications. Results. Data were randomly split into 307,288, 105,195, and 105,081 patients to perform estimation, out-of-sample calibration, and validation, respectively. Model predictions in the validation sample closely aligned with the observed longitudinal trajectory of biomarkers and outcomes. Perfect adherence among initiators increased proportion of days covered by only 6 months. Most of this increase came from increased adherence to monotherapies and did not lead to meaningful changes in any of the outcomes over the 9-year period. Conclusion. Future value of increasing medication adherence among VA patients with diabetes may lie among those who never initiate treatment or are late in initiating treatment. The first-of-its-kind real-world data-based model has the potential to carry out many complex comparative-effectiveness research (CER) studies of dynamic glucose-lowering drug regimens.