Miracle-dz/UniFAR-FTUs huggingface dataset:
Organic Particles: Heterogeneous Hubs for Microbial Interactions in Aquatic Ecosystems

The dynamics and activities of microbes colonizing organic particles (hereafter particles) greatly determine the efficiency of the aquatic carbon pump. Current understanding is that particle composition, structure and surface properties, determined mostly by the forming organisms and organic matter, dictate initial microbial colonization and the subsequent rapid succession events taking place as organic matter lability and nutrient content change with microbial degradation. We applied a transcriptomic approach to assess the role of stochastic events on initial microbial colonization of particles. Furthermore, we asked whether gene expression corroborates rapid changes in carbon-quality. Commonly used size fractionated filtration averages thousands of particles of different sizes, sources, and ages. To overcome this drawback, we used replicate samples consisting each of 3–4 particles of identical source and age and further evaluated the consequences of averaging 10–1000s of particles. Using flow-through rolling tanks we conducted long-term experiments at near in situ conditions minimizing the biasing effects of closed incubation approaches often referred to as “the bottle-effect. ” In our open flow-through rolling tank system, however, active microbial communities were highly heterogeneous despite an identical particle source, suggesting random initial colonization. Contrasting previous reports using closed incubation systems, expression of carbon utilization genes didn’t change after 1 week of incubation. Consequently, we suggest that in nature, changes in particle-associated community related to carbon availability are much slower (days to weeks) due to constant supply of labile, easily degradable organic matter. Initial, random particle colonization seems to be subsequently altered by multiple organismic interactions shaping microbial community interactions and functional dynamics. Comparative analysis of thousands particles pooled togethers as well as pooled samples suggests that mechanistic studies of microbial dynamics should be done on single particles. The observed microbial heterogeneity and inter-organismic interactions may have important implications for evolution and biogeochemistry in aquatic systems.
Understand, Compose and Respond - Answering Visual Questions by a Composition of Abstract Procedures

An image related question defines a specific visual task that is required in order to produce an appropriate answer. The answer may depend on a minor detail in the image and require complex reasoning and use of prior knowledge. When humans perform this task, they are able to do it in a flexible and robust manner, integrating modularly any novel visual capability with diverse options for various elaborations of the task. In contrast, current approaches to solve this problem by a machine are based on casting the problem as an end-to-end learning problem, which lacks such abilities. We present a different approach, inspired by the aforementioned human capabilities. The approach is based on the compositional structure of the question. The underlying idea is that a question has an abstract representation based on its structure, which is compositional in nature. The question can consequently be answered by a composition of procedures corresponding to its substructures. The basic elements of the representation are logical patterns, which are put together to represent the question. These patterns include a parametric representation for object classes, properties and relations. Each basic pattern is mapped into a basic procedure that includes meaningful visual tasks, and the patterns are composed to produce the overall answering procedure. The UnCoRd (Understand Compose and Respond) system, based on this approach, integrates existing detection and classification schemes for a set of object classes, properties and relations. These schemes are incorporated in a modular manner, providing elaborated answers and corrections for negative answers. In addition, an external knowledge base is queried for required common-knowledge. We performed a qualitative analysis of the system, which demonstrates its representation capabilities and provide suggestions for future developments.
Human variation in the shape of the birth canal is significant and geographically structured

The human birth canal shows a tight fit with the size of the neonate, which can lead to obstetric complications. This is not the case in other apes, and has been explained as the outcome of conflicting evolutionary pressures for bipedal locomotion and parturition of a highly encephalized fetus. Despite the suggested evolutionary constraints on the female pelvis, we show that women are, in fact, extremely variable in the shape of the bony birth canal, with human populations having differently shaped pelvic canals. Neutral evolution through genetic drift and differential migration are largely responsible for the observed pattern of morphological diversity, which correlates well with neutral genetic diversity. Climatic adaptation might have played a role, albeit a minor one, with populations from colder regions showing a more transversally oval shape of the canal inlet. The significant extent of canal shape variation among women from different regions of the world has important implications for modern obstetric practice in multi-ethnic societies, as modern medical understanding has been largely developed on studies of European women.
A Tailored Dietary Sodium Intervention Using Technology and Psychosocial Support: A Pilot Study

Background In patients with heart failure (HF), high dietary sodium intake is common and associated with HF symptoms, poor health-related quality of life (HRQOL), and high hospitalization rates. Purpose The aims of this study were to examine the feasibility of a tailored dietary intervention with a practical tool (MyFitnessPal) and to obtain preliminary data about the effects on sodium intake, factors affecting sodium intake (knowledge, skills, experiences, confidence, perceived benefits and barriers, and depressive symptoms), HF symptoms, and HRQOL. Methods A 6-session intervention was delivered to 11 participants. Paired t tests were used to compare the baseline outcomes with those at 3 months. Results Participants completed 98% of intervention sessions, and 91% used MyFitnessPal. Sodium intake was reduced, and factors affecting sodium intake, symptoms, and HRQOL were improved (all P < .05). Conclusion The intervention was feasible and warrants further research to test the effects of the intervention on the outcomes using larger, heterogeneous samples.
Turn-by-turn Intelligent Manoeuvring of Driverless Taxis: A Recursive Value Model Enhanced by Reinforcement Learning

We develop a protocol for constructing intelligent manoeuvring of driverless taxis - especially for empty taxis - with the aim of optimising the efficiency of the taxi system (e.g. minimising the average waiting time of the commuters). The manoeuvring is formulated as a stochastic policy matrix giving optimal choices on which way to go for taxis at any locations, based on the historical patterns of commuter origin and destination distribution. A recursive value (RV) model is formulated for turn-by-turn navigation. The policy matrix is solved by a combination of the RV model and reinforcement learning, together with a comprehensive agent-based microscopic simulation platform we have developed. We show that even for very large road networks, very efficient manoeuvring algorithms can be readily found with reinforcement learning, especially with our RV model as the initial state. Such algorithms are indispensable for the fleet of driverless taxis, and can also give helpful recommendations to human drivers operating taxis. The general framework of our protocol allows the construction of optimal manoeuvring algorithms for a wide range of road networks in a systematic way.
A new invariant of 4-manifolds

Significance All known 4-manifolds invariants cannot distinguish a possible counterexample to the smooth 4-dimensional Poincare Conjecture from the standard 4-sphere. The L invariant, defined in this paper, can do so, for if it vanishes on a homotopy 4-sphere X, then X must be diffeomorphic to the 4-sphere. Unfortunately, it is very hard to calculate. We define an integer invariant LX of a smooth, compact, closed 4-manifold X by minimizing a certain complexity of a trisection of X over all trisections. The good feature of LX is that when LX=0 and X is a homology 4-sphere, then X is diffeomorphic to the 4-sphere. Naturally, L is hard to compute.
Clinical Concept Extraction with Contextual Word Embedding

Automatic extraction of clinical concepts is an essential step for turning the unstructured data within a clinical note into structured and actionable information. In this work, we propose a clinical concept extraction model for automatic annotation of clinical problems, treatments, and tests in clinical notes utilizing domain-specific contextual word embedding. A contextual word embedding model is first trained on a corpus with a mixture of clinical reports and relevant Wikipedia pages in the clinical domain. Next, a bidirectional LSTM-CRF model is trained for clinical concept extraction using the contextual word embedding model. We tested our proposed model on the I2B2 2010 challenge dataset. Our proposed model achieved the best performance among reported baseline models and outperformed the state-of-the-art models by 3.4% in terms of F1-score.
Arrhythmogenic Remodeling of the Left Ventricle in a Porcine Model of Repaired Tetralogy of Fallot

Background Ventricular arrhythmias are frequent in patients with repaired tetralogy of Fallot (rTOF), but their origin and underlying mechanisms remain unclear. In this study, the involvement of left ventricular (LV) electrical and structural remodeling was assessed in an animal model mimicking rTOF sequelae. Methods Piglets underwent a tetralogy of Fallot repair–like surgery (n=6) or were sham operated (Sham, n=5). Twenty-three weeks post-surgery, cardiac function was assessed in vivo by magnetic resonance imaging. Electrophysiological properties were characterized by optical mapping. LV fibrosis and connexin-43 localization were assessed on histological sections and protein expression assessed by Western Blot. Results Right ventricular dysfunction was evident, whereas LV function remained unaltered in rTOF pigs. Optical mapping showed longer action potential duration on the rTOF LV epicardium and endocardium. Epicardial conduction velocity was significantly reduced in the longitudinal direction in rTOF LVs but not in the transverse direction compared with Sham. An elevated collagen content was found in LV basal and apical sections from rTOF pigs. Moreover, a trend for connexin-43 lateralization with no change in protein expression was found in the LV of rTOFs. Finally, rTOF LVs had a lower threshold for arrhythmia induction using incremental pacing protocols. Conclusions We found an arrhythmogenic substrate with prolonged heterogeneous action potential duration and reduced conduction velocity in the LV of rTOF pigs. This remodeling precedes LV dysfunction and is likely to contribute to ventricular arrhythmias and sudden cardiac death in patients with rTOF.
Diffusion kurtosis imaging in the assessment of liver function: Its potential as an effective predictor of liver function.

OBJECTIVES: We aimed to determine whether diffusion kurtosis imaging (DKI) analysis with the breath-hold technique can replace liver function results obtained from laboratory tests. METHODS: Patients (n = 79) suspected of having a hepatobiliary disease, and control group without liver diseases (n = 15) were examined with non-Gaussian diffusion-weighted imaging using a 3.0 T magnetic resonance imaging unit. Based on the findings of DKI, various blood serum parameters, including the indocyanine green (ICG) retention rate 15 min after an intravenous injection of ICG (ICG-R15) and mean kurtosis values and Child-Pugh and albumin-bilirubin (ALBI) scores, were calculated. In total, 17 patients were tested using ICG-R15. For evaluating liver function, correlations between the mean kurtosis value and the Child-Pugh score, ALBI score, and ICG-R15 value as indicators of liver function obtained from blood data were assessed using Spearman's rank correlation. In apparent diffusion coefficient as well, we assessed correlations with these indicators. RESULTS: The mean kurtosis value correlated with the Child-Pugh score (Spearman's rank-correlation coefficient, ρ = 0.3992; p < 0.0001). Moreover, the mean kurtosis value revealed a correlation with the ICG-R15 value (Spearman's rank-correlation coefficient, ρ = 0.5972; p = 0.00114). The correlation between the mean kurtosis value and the ALBI score was the poorest among these (Spearman's rank-correlation coefficient, ρ = 0.3395; p = 0.0008). CONCLUSION: Liver function correlating with the Child-Pugh score and ICG-R15 value can be quantitatively estimated using the mean kurtosis value obtained from DKI analysis. DKI analysis with the breath-hold technique can be used to determine liver function instead of performing laboratory tests. ADVANCES IN KNOWLEDGE: Previous studies have not evaluated liver function in vivo using DKI.
Robust Camera Lidar Sensor Fusion Via Deep Gated Information Fusion Network

In this paper, we introduce a new deep learning architecture for camera and Lidar sensor fusion. The proposed scheme performs 2D object detection using the RGB camera image and the depth, height, and intensity images generated by projecting the 3D Lidar point cloud into camera image plane. The proposed object detector consists of two convolutional neural networks (CNNs) that process the RGB and Lidar images separately as well as the fusion network that combines the feature maps produced at the intermediate layers of the CNNs. We aim to develop a robust object detector that maintains good object detection accuracy even when the quality of the sensor signals is degraded for object detection. Towards this end, we devise the gated fusion unit (GFU) that adjusts the contribution of the feature maps generated by two CNN structures via gating mechanism. Using the GFU, the proposed object detector can fuse the high level feature maps drawn from two modalities with appropriate weights to achieve robust performance. Experiments conducted on the challenging KITTI benchmark show that the proposed camera and Lidar fusion network outperforms the conventional sensor fusion methods even when either of the camera and Lidar sensor signals is corrupted by missing data, occlusion, noise, and illumination change.
EDTA/gelatin zymography method to identify C1s versus activated MMP‐9 in plasma and immune complexes of patients with systemic lupus erythematosus

Gelatin zymography analysis is a sensitive method and commonly used to characterize and quantify the presence of the gelatinases (MMP‐2 and MMP‐9) in biological samples. In human plasma samples from healthy controls and systemic lupus erythematosus (SLE) patients, we observed a gelatinolytic molecule at 80 kDa, suggestive for activated human MMP‐9. However, by developing and using the EDTA/gelatin zymography method and after purification of the 80 kDa entity, we proved that this molecule was the C1s subunit of the complement system. The zymolytic capacity of C1s was validated and found to be enhanced, in the absence of calcium and in the presence of EDTA. Our findings indicate that for correct identification of gelatinolytic proteins in complex biological samples the use of EDTA/gelatin zymography for enzyme development is advised. In addition, by quantification of EDTA/gelatin zymography analysis and ELISA, we observed that the levels of C1s were higher in plasma and immune complexes of SLE patients than of healthy individuals. Therefore, our data imply that C1s may become a marker for the diagnosis of SLE.
Web-Based Self-Management Programs for Bipolar Disorder: Insights From the Online, Recovery-Oriented Bipolar Individualised Tool Project

Background Bipolar disorder (BD) is a complex, relapsing mood disorder characterized by considerable morbidity and mortality. Web-based self-management interventions provide marked opportunities for several chronic mental health conditions. However, Web-based self-management programs targeting BD are underrepresented compared with programs targeting other psychiatric conditions. Objective This paper aims at facilitating future research in the area of self-management of BD and draws insights from the development of one such intervention—the Online, Recovery-Oriented Bipolar Individualised Tool (ORBIT)—that is aimed at improving the quality of life of people with BD. Methods We have discussed the opportunities and challenges in developing an engaging, evidence-based, safe intervention within the context of the following three nested domains: (1) intervention development; (2) scientific testing of the intervention; and (3) ethical framework including risk management. Results We gained the following insights across the three abovementioned overlapping domains: Web-based interventions can be optimized through (1) codesign with consumers with lived experience to ensure relevance and appropriateness to the target audience; (2) novel content development processes that iteratively combine evidence-based information with lived experience perspectives, capitalizing on multimedia (eg, videos) that the digital health space provides; and (3) incorporating Web-based communities to connect end users and promote constructive engagement by access to a Web-based coach. Conclusions Self-management is effective in BD, even for those on the more severe end of the spectrum. While there are challenges to be aware of, guided self-management programs, such as those offered by the ORBIT project, which are specifically developed for Web-based delivery provide highly accessible, engaging, and potentially provocative treatments for chronically ill populations who may otherwise have never engaged with treatment. Key questions about engagement, effectiveness, and cost-effectiveness will be answered by the ORBIT project over the next 18 months.
Exosomes Regulate the Transformation of Cancer Cells in Cancer Stem Cell Homeostasis

In different biological model systems, exosomes are considered mediators of cell-cell communication between different cell populations. Exosomes, as extracellular vesicles, participate in physiological and pathological processes by transmitting signaling molecules such as proteins, nucleic acids, and lipids. The tumor's microenvironment consists of many types of cells, including cancer stem cells and mesenchymal cells. It is well known that these cells communicate with each other and thereby regulate the progression of the tumor. Recent studies have provided evidence that exosomes mediate the interactions between different types of cells in the tumor microenvironment, providing further insight into how these cells interact through exosome signaling. Cancer stem cells are a small kind of heterogeneous cells that existed in tumor tissues or cancer cell lines. These cells possess a stemness phenotype with a self-renewal ability and multipotential differentiation which was considered the reason for the failure of conventional cancer therapies and tumor recurrence. However, a highly dynamic equilibrium was found between cancer stem cells and cancer cells, and this indicates that cancer stem cells are no more special target and blocking the transformation of cancer stem cells and cancer cells seem to be a more significant therapy strategy. Whether exosomes, as an information transforming carrier between cells, regulated cancer cell transformation in cancer stem cell dynamic equilibrium and targeting exosome signaling attenuated the formation of cancer stem cells and finally cure cancers is worthy of further study.
An Automated Vehicle Safety Concept Based on Runtime Restriction of the Operational Design Domain

Automated vehicles need to operate safely in a wide range of environments and hazards. The complex systems that make up an automated vehicle must also ensure safety in the event of system failures. This paper proposes an approach and architectural design for achieving maximum functionality in the case of system failures. The Operational Design Domain (ODD) defines the domain over which the automated vehicle can operate safely. We propose modifying a runtime representation of the ODD based on current system capabilities. This enables the system to react with context-appropriate responses depending on the remaining degraded functionality. In addition to proposing an architectural design, we have implemented the approach to prove its viability. The proof of concept has shown promising directions for future work and moved our automated vehicle research platform closer to achieving level 4 automation.
Prevalence of Sleep Disorders in Adults With Down Syndrome: A Comparative Study of Self-Reported, Actigraphic, and Polysomnographic Findings.

STUDY OBJECTIVES Sleep problems are often undetected in adults with Down syndrome (DS). Our objective was to determine the prevalence of sleep disorders in adults with DS through self-reported and objective sleep measures. METHODS We performed a community-based cross-sectional study of 54 adults with DS not referred for sleep disorders. Two polysomnography (PSG) sleep studies were performed. Sleep quality was evaluated using the Pittsburgh Sleep Quality Index (PSQI); daytime sleepiness was evaluated using the Epworth Sleepiness Scale (ESS) and the risk for the sleep apnea syndrome (OSA) was identified using the Berlin Questionnaire (BQ). Participants' sleep/wake pattern was assessed from sleep diaries and by wrist actigraphy. PSQI, ESS, and PSG measures were compared with 35 sex-, age-, and body mass index-matched patients in the control groups. RESULTS In PSG measures, adults with DS showed lower sleep efficiency (69 ± 17.7 versus 81.6 ± 11; P < .001), less rapid eye movement sleep (9.4 ± 5.8 versus 19.4 ± 5.1; P < .001), a higher prevalence of OSA (78% versus 14%; P < .001), and a higher apnea-hypopnea index (23.5 ± 24.5 versus 3.8 ± 10.5; P < .001) than patients in the control group. In the DS group, the questionnaires (mean PSQI 3.7 ± 2.9; mean ESS 6.3 ± 4.5 and mean BQ 1 ± 0) did not reflect the sleep disturbances detected on the PSG. Actigraphy data recorded daytime sleep that was not self-reported (118.2 ± 104.2 minutes). CONCLUSIONS Adults with DS show severe sleep disruption and a high prevalence of OSA, undetected by self-reported sleep measures. Actigraphy, PSG, and validated simplified devices for screening OSA should be routinely recommended for this population because treatment of sleep disorders can contribute to healthy aging.