Miracle-dz/UniFAR-FTUs huggingface dataset:
Illuminating the impact of diel vertical migration on visual gene expression in deep‐sea shrimp

Diel vertical migration (DVM) of marine animals represents one of the largest migrations on our planet. Migrating fauna are subjected to a variety of light fields and environmental conditions that can have notable impacts on sensory mechanisms, including an organism's visual capabilities. Among deep‐sea migrators are oplophorid shrimp that vertically migrate hundreds of metres to feed in shallow waters at night. These species also have bioluminescent light organs that emit light during migrations to aid in camouflage. The organs have recently been shown to contain visual proteins (opsins) and genes that infer light sensitivity. Knowledge regarding the impacts of vertical migratory behaviour, and fluctuating environmental conditions, on sensory system evolution is unknown. In this study, the oplophorid Systellaspis debilis was either collected during the day from deep waters or at night from relatively shallow waters to ensure sampling across the vertical distributional range. De novo transcriptomes of light‐sensitive tissues (eyes/photophores) from the day/night specimens were sequenced and analysed to characterize opsin diversity and visual/light interaction genes. Gene expression analyses were also conducted to quantify expression differences associated with DVM. Our results revealed an expanded opsin repertoire among the shrimp and differential opsin expression that may be linked to spectral tuning during the migratory process. This study sheds light on the sensory systems of a bioluminescent invertebrate and provides additional evidence for extraocular light sensitivity. Our findings further suggest opsin co‐expression and subsequent fluctuations in opsin expression may play an important role in diversifying the visual responses of vertical migrators.
Novel Catheter Multiscope: A Feasibility Study

Open Challenges: Continuous monitoring of fundamental cardiovascular hemodynamic parameters is essential to accomplish critical care diagnostics. Today's standard of care measures these critical parameters using multiple monitoring technologies. These state-of-the-art technologies require expensive instrumentation and complex infrastructure. Therefore, it is challenging to use current technologies to accomplish monitoring in a low resource setting. Objective: In order to address the challenges caused by having to use multiple monitoring systems, a point of care monitoring device was developed in this work to provide multiple critical parameters by uniquely measuring the hemodynamic process. Methods: To demonstrate the usability of this novel catheter multiscope, a feasibility study was performed using an animal model. The developed measurement system first acquires the dynamics of blood flow through a minimally invasive catheter. Then, a signal processing framework was developed to characterize the blood flow dynamics and to obtain critical parameters such as heart rate, respiratory rate, and blood pressure. The framework used to extract the physiological data corresponding to the acoustic field of the blood flow consisted of a noise cancellation method and wavelet-based source separation. Results: The preliminary results of the acoustic pressure field of the blood flow revealed the presence of acoustic heart and respiratory pulses. A unique framework was also developed to extract continuous blood pressure from the acoustic pressure field of the blood flow. Finally, the computed heart and respiratory rates, systolic and diastolic pressures were benchmarked with actual values measured using conventional devices to validate the hypothesis. Conclusion: The results confirm that catheter multiscope can provide multiple critical parameters with clinical reliability. Significance: A novel critical care monitoring system has been developed to accurately measure heart rate, respiratory rate, systolic and diastolic pressures from the blood flow dynamics.
In Vivo Assessment of Lung Ultrasound Features Mimicking Viral Pneumonia Using a Large Animal Model

Lung ultrasound (LUS) is a practical tool for lung diagnosis when computer tomography (CT) is not available. Recent findings suggest that LUS diagnosis is highly advantageous because of its mobility and correlation with radiological findings for viral pneumonia. Simple models for both educational evaluation and technical evaluation are needed. Therefore, this work investigates the usability of a large animal model under aspects of LUS features of viral pneumonia using saline one lung flooding. Six pigs were intubated with a double-lumen tube, and the left lung was instilled with saline. During the instillation of up to 12.5 ml/kg, the sonographic features were assessed. All features present during viral pneumonia were found, such as B-lines, white lung syndrome, pleural thickening, and the formation of pleural consolidations. Sonographic findings correlate well with current LUS scores for COVID19. The scores of 1, 2, and 3 were dominantly present at 1–4-, 4–8-, and 8–12-ml/kg saline instillation, respectively. The noninfective animal model can be used for further investigation of the LUS features and can serve in education, by helping with the appropriate handling of LUS in clinical practice during management of viral pneumonia.
Targeting Colorectal Cancer Stem Cells as an Effective Treatment for Colorectal Cancer

As one of the common cancers that threaten human life, the recurrence and metastasis of colorectal cancer seriously affect the prognosis of patients. Although new drugs and comprehensive treatments have been adopted, the current treatment effect on this tumor, especially in advanced colorectal cancer, is still not satisfactory. More and more evidence shows that tumors are likely to be a stem cell disease. In recent years, the rise of cancer stem cell theory has provided a new way for cancer treatment. Studies have found that a small number of special cells in colorectal cancer tissues that induce tumorigenesis, proliferation, and promote tumor migration and metastasis, namely, colorectal cancer stem cells. Colorectal cancer stem cells are defined with a group of cell-surface markers, such as CD44, CD133, CD24, epithelial cell adhesion factor molecule, LGR5, and acetaldehyde dehydrogenase. They are highly tumorigenic, aggressive, and chemoresistant and thus are critical in the metastasis and recurrence of colorectal cancer. Therefore, targeting colorectal cancer stem cells may become an important research direction for the future cure of colorectal cancer.
Donor‐Transmitted Cancers in Transplanted Livers: Analysis of Clinical Outcomes

The risk of transmission of malignancy from donor to recipient is low. However, this occurrence has dramatic consequences. Many reports of donor‐derived cancers in liver transplant recipients have been published, but they have not been systematically summarized into a lucid and unified analysis. The present study is an attempt to provide clarity to this unusual but clinically important problem. We systematically reviewed all patient reports, patient series, and registries published on cancer transmission events through the end of December 2019. We identified a total of 67 publications with 92 transmission events. The most frequently transmitted cancers were lymphomas (30; 32.6%), melanomas (8; 8.7%), and neuroendocrine tumors (8; 8.7%). Most of the melanomas were metastasizing, whereas most of the lymphomas were localized to the graft. The median time to cancer diagnosis after transplantation was 7 months, with 78.1% of diagnoses established in the first year. Melanoma carried the worst prognosis, with no recipients alive at 1 year after cancer diagnosis. Lymphoma recipients had a better outcome, with more than 75% surviving at 2 years. A metastatic cancer carries a worse prognosis for recipients, and recipients with localized cancer can benefit from the chance to undergo transplantation again. The findings confirm the need to pay attention to donors with a history of melanoma but also suggest the need for a more careful evaluation of groups of donors, such as those dying from cerebral hemorrhage. Finally, recipients of organs from donors with cancer should be carefully followed to detect potential transmission.
The cognitive augmented mobility program (CAMP): feasibility and preliminary efficacy

ABSTRACT Background Best evidence suggests incorporating task-specific training, aerobics, and strengthening to improve mobility and gait in persons with stroke (PWS). Related research suggests incorporating cognitive problem-solving strategy training may lead to better skill maintenance and transfer. The present study examined the feasibility and preliminary outcomes of an evidence-based cognitive augmented mobility program (CAMP) for PWS. Methods A single-arm pre-post and follow-up design was conducted, in two blocks (NCT03683160). Participants completed an exercise intervention with an integrated cognitive strategy component and had weekly 1:1 sessions with a physiotherapist trained in Cognitive Orientation to daily Occupational Performance (CO-OP), focusing on goal practice and cognitive strategy use. CAMP consisted of a pre-intervention education and goal-setting session and 16 90-minute sessions held in a group format, 2x/wk for 8 weeks. Assessments were conducted 1 week prior to beginning the intervention, 1 week post-intervention, and at a 4–5 week follow-up. Results CAMP was found to be feasible with 96% session attendance and strong participant satisfaction. Pre to post-CAMP intervention, a large effect was found for endurance (r = 0.53), balance (r = 0.59), mobility (r = 0.63) and goal attainment (r = 0.63) indicators, and large effects were maintained at follow-up for balance, mobility, and goal attainment. A medium effect was found for functional independence (r = 0.38), gait speed (r = 0.39), and balance confidence (r = 0.38). A small effect was found for participation (r = 0.27) and overall stroke recovery (r = 0.25). Conclusions Preliminary results suggest CAMP is feasible; there may be a beneficial effect of combining best evidence for mobility and fitness with cognitive strategy training. The positive results for skill maintenance and transfer suggest further investigation is warranted.
Experience with Real-Time Continuous Glucose Monitoring in Newborns with Congenital Hyperinsulinemic Hypoglycemia

Abstract Background Effective treatment and close monitoring of hypoglycemia in children with congenital hyperinsulinemic hypoglycemia (CHH) is vital to prevent brain damage. The current use of capillary sampling schedules does not provide a comprehensive assessment of glycemic status and fails to detect asymptomatic hypoglycemia episodes. Aim To investigate the efficacy and accuracy of a real-time continuous glucose monitoring system (RT-CGMS) in neonates with CHH. Methods A sensor connected to RT-CGMS was inserted into the newborn patients and maintained for at least 6 days during their stay in the hospital. We compared the readings of CGMS with capillary blood glucose values using Bland-Altman analysis. Results A total of 110 blood glucose values were compared to readings from the CGMS. All results were calculated and plotted for CGMS values at 0–4, 5–9, 10–14, 15–19, 20–24, and 25–29 min after capillary blood glucose sampling. CGMS readings were highly correlated with blood glucose values, especially during normoglycemia. In case of hypoglycemia, the mean difference between the CGMS and capillary glucose values was higher. Although the false positive rate for hypoglycemia was relatively high in CGMS, RT-CGMS may show some episodes of hypoglycemia earlier than blood measurement. Conclusion RT-CGMS is accurate during normoglycemia, and it can reduce the number of capillary blood samples in children with CHH.
Parallel Computation of 3D Clipped Voronoi Diagrams

Computing the Voronoi diagram of a given set of points in a restricted domain (e.g., inside a 2D polygon, on a 3D surface, or within a volume) has many applications. Although existing algorithms can compute 2D and surface Voronoi diagrams in parallel on graphics hardware, computing clipped Voronoi diagrams within volumes remains a challenge. This article proposes an efficient GPU algorithm to tackle this problem. A preprocessing step discretizes the input volume into a tetrahedral mesh. Then, unlike existing approaches which use the bisecting planes of the Voronoi cells to clip the tetrahedra, we use the four planes of each tetrahedron to clip the Voronoi cells. This strategy drastically simplifies the computation, and as a result, it outperforms state-of-the-art CPU methods up to an order of magnitude.
Bladder Volume Monitoring Using Electrical Impedance Tomography With Simultaneous Multi-Tone Tissue Stimulation and DFT-Based Impedance Calculation Inside an FPGA

In this article, a novel method for measuring the volume of the urinary bladder non-invasively is presented that relies on the principles dictated by Electrical Impedance Tomography (EIT). The electronic prototype responsible for injecting innocuous electrical currents to the lower abdominal region and measuring the developed voltage levels is fully described, as well as the computational models for resolution of the so-called Forward and Inverse Problems in Imaging. The simultaneous multi-tone injection of current provided by a high performance Field Programmable Gate Array (FPGA), combined with impedance estimation by the Discrete Fourier Transform (DFT) constitutes a novelty in Urodynamics with potential to monitor continuously the intravesical volume of patients in a much faster and comfortable way than traditional transurethral catheterization methods. The resolution of the Inverse Problem is performed by the Gauss-Newton method with Laplacian regularization, allowing to obtain a sectional representation of the volume of urine encompassed by the bladder and surrounding body tissues. Experimentation has been carried out with synthetic phantoms and human subjects with results showing a good correlation between the levels of abdominal admittivity acquired by the EIT system and the volume of ingested water.
Analysis of Topologies of Reconfigurable Batteries

Battery packs with flexible connection have drawn growing attention currently as an efficient dynamically reconfigured design solving drawbacks emerged in battery management and cell balancing, enhancing circuit real time reliability and fault tolerance ability. Studies among cell reconfigurable topologies and simulations are carried out in order to reveal the regulations of related topology formation, with existing and proposed topology schemes analyzed for circuit optimization and SOC equalization. A maximum decline of 25% in the number of electronic switches utilization for the same quantity of the batteries is found possible for topologies generated from the proposed method.
Increased HOXC6 mRNA expression is a novel biomarker of gastric cancer

In this study, we aimed to investigate the molecular biomarkers that are pivotal for the development and progression of gastric cancer (GC). We analyzed clinical specimens using RNA sequencing to identify the target genes. We found that the expression of HOXC6 mRNA was upregulated with the progression of cancer, which was validated by quantitative real time PCR and RNA in-situ hybridization. To compare the protein expression of HOXC6, we evaluated GC and normal gastric tissue samples using western blot analysis and immunohistochemistry. We detected significantly higher levels of HOXC6 in the GC tissues than in the normal controls at both mRNA and protein levels. The expression levels of HOXC6 mRNA in patients with advanced gastric cancer (AGC) were significantly higher than those in patients with early gastric cancer (EGC). Kaplan-Meier curves showed that high expression of HOXC6 mRNA is significantly associated with poor clinical prognosis. Our findings suggest that HOXC6 mRNA may be a novel biomarker and can be potentially valuable in predicting the prognosis of GC patients. Especially, HOXC6 mRNA in-situ hybridization may be a diagnostic tool for predicting prognosis of individual GC patients.
Good intentions gone wrong: did conservation management threaten Endangered huemul deer Hippocamelus bisulcus in the future Patagonia National Park?

Abstract Conservation interventions increasingly involve active management of relative species abundances, especially when taxa of conservation concern are threatened by complex food web interactions. Unfortunately, the complexity of such interspecific interactions means that well-meaning management interventions can have unexpected, sometimes detrimental, effects on the species they are intended to protect. Here we report that the abrupt removal of an abundant non-native prey species (domestic sheep) and the cessation of predator control, actions intended to protect huemul deer Hippocamelus bisulcus in the future Patagonia National Park, appear to have had negative effects on this Endangered ungulate. During and following the changes in predator–prey management, predation of huemul fawns and females older than 1 year by native culpeo foxes Lycalopex culpaeus and pumas Puma concolor increased 3- and 5-fold, respectively. Predictions from demographic models suggest that elevated mortality rates of female huemul older than 1 year will, on average, cause this population of huemul to decline. These results highlight risks of unintended consequences when aggressive management actions are taken to protect taxa embedded in complex food webs. They also suggest that careful consideration of both inter- and intra-trophic level effects among all species in a system is warranted before conservation interventions are undertaken.
MHC class II‐mediated apoptosis of mature dendritic cells proceeds by activation of the protein kinase C‐δ isoenzyme

The mature dendritic cell (DC) is considered to be the most potent antigen-presenting cell. Regulation of the DC, particularly its survival, is therefore critical. Mature DC are markedly more sensitive to HLA-DR-mediated apoptosis than immature DC. To further characterize this key survival difference, we compared the intracellular signals initiated via HLA-DR in mature versus immature DC. Apoptosis was unchanged by inhibition of tyrosine kinases or phosphatases. HLADR-mediated re-localization of protein kinase C (PKC)-d to the nucleus was detected in mature DC by confocal microscopy and by immunoblotting. Activation of PKC-d in mature DC was revealed by the detection of the PKC-d catalytic fragment in the nuclear fraction isolated from mature DC which had been stimulated via HLA-DR. The broad-spectrum PKC inhibitor, Calphostin C, as well as the PKC-d-selective inhibitor, Rottlerin, inhibited HLA-DR-mediated apoptosis of mature cells. Taken together, these data reveal a role for the PKC-d isoenzyme in regulating HLA class II-mediated apoptosis of mature DC. Thus, the lifespan of the mature DC could be controlled by signals generated in the course of antigen presentation, and thereby prevent DC persistence and prolonged stimulation of T and B lymphocytes.
Selection of vegetation types and density of bison in an arid ecosystem

Understanding species habitat selection and factors that drive selection are key components for conservation. We report the first resource selection functions (RSFs) for bison inhabiting an arid ecosystem and use them with density estimates of bison to estimate the number of bison that could be supported if the bison range were expanded to federal lands in the San Luis Valley of Colorado. We derived RSFs for vegetation types using locations of plains bison collected weekly over 3 years from 2005 to 2007. Bison selected for wet or mesic grassland habitats in all seasons. Wetland selection by bison was predicted to be 18 times greater than that of rabbitbrush vegetation, the reference category, and selection of meadows was predicted to be 11 times greater than that of the rabbitbrush type. Willow-dominated plant communities were strongly avoided. Cottonwood communities were also avoided, with the exception of some moderate levels of selection in fall. The willow and cottonwood communities have an understory with low biomass of herbaceous species and low productivity in this arid system. Based on the RSFs we predicted that in the San Luis Valley of Colorado up to 2,379 bison could be supported in similar habitats under Fish and Wildlife Service (FWS) jurisdiction, and up to 759 bison could be supported on adjacent National Park Service (NPS) land. This modeling framework provides a conservation tool for the restoration of bison to their historical habitats, and has utility for application to other terrestrial species where assumptions are met. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.
S-MRUT: Sectored-Multiring Ultrasonic Transducer for Selective Powering of Brain Implants

One of the main challenges of the current ultrasonic transducers for powering brain implants is the complexity of focusing ultrasonic waves in various axial and lateral directions. The available transducers usually use electrically controlled phased array for beamforming the ultrasonic waves, which increases the complexity of the system even further. In this article, we propose a straightforward solution for selective powering of brain implants to remove the complexity of conventional phased arrays. Our approach features a Sectored-Multiring Ultrasonic Transducer (S-MRUT) on a single piezoelectric sheet, specifically designed for powering implantable devices for optogenetics in freely moving animals. The proposed unidirectional S-MRUT is capable of focusing the ultrasonic waves on brain implants located at different depths and regions of the brain. The S-MRUT is designed based on Fresnel Zone Plate (FZP) theory, simulated in COMSOL, and fabricated with the microfabrication process. The acoustic profile of the seven different configurations of the S-MRUT was measured using a hydrophone with the total number of 7436 grid points. The measurements show the ability of the proposed S-MRUT to sweep the focus point of the acoustic waves in the axial direction in depths of 1 – 3 mm, which is suitable for powering implants in the striatum of the mouse. Furthermore, the proposed S-MRUT demonstrates a steering area with an average radius of 0.862 mm and 0.678 mm in experiments and simulations, respectively. The S-MRUT is designed with the size of ${3.8}\times {3.8}\times {0.5}$ mm3 and the weight of ${0.054}{gr}$ , showing that it is compact and light enough to be worn by a mouse. Finally, the S-MRUT was tested in our measurement setup, where it successfully transfers sufficient power to a 2.8-mm3 optogentic stimulator to turn on a micro-LED on the stimulator.