Miracle-dz/UniFAR-FTUs huggingface dataset:
Section Plane Effects on Morphometric Values of Microcomputed Tomography

Objectives Histomorphometry is the established gold standard for inspection of trabecular microstructures in biomaterial research. However, microcomputed tomography can provide images from the perspective of various section planes. The aim of the present study was to evaluate the effects of different section planes, which may cause bias in two-dimensional morphometry, on the morphometric values of microcomputed tomography. Methods A socket preservation technique was performed on the extracted premolar area of 4 beagle dogs. After an 8-week healing period, a total of 16 specimens were obtained and analyzed with conventional histomorphometry and microtomographic morphometry. Using the original images of the histologic specimens for comparison, the most similar tomographic image was selected by trial and error. Then, the section plane was then moved with ±79 μm parallel offsets and rotated ±10° around the center from the occlusal view. The images were compared in terms of bone, graft, and noncalcified area, and the concordance correlation coefficient (CCC) was calculated. Results There was a high CCC in the comparison between histomorphometric images and the most similar microtomographic images. However, the CCC value was low in the comparisons with both parallel movement and rotation. Our results demonstrate that the sectioning plane has a significant effect on measurements. Conclusion Two-dimensional morphometric values for biomaterial research should be interpreted with caution, and the simultaneous use of complementary 3-dimensional tools is recommended.
Heat Shock Proteins Can Be Surrogate Autoantigens for Induction of Antigen Specific Therapeutic Tolerance in Rheumatoid Arthritis

Technologies that enable induction of therapeutic tolerance may revolutionize the treatment of autoimmune diseases by their supposed potential to induce drug-free and lasting disease remission. In combination with diagnostic tests that screen for individuals at risk, these approaches may offer chances to halt disease before serious damage in the tissues can occur. In fact, for healthy individuals at risk, this could lead to a preventive form of vaccination. For therapeutic tolerance to re-instate natural self-tolerance it seems essential to induce tolerance for the critical autoantigens involved in disease. However, for most autoimmune diseases such antigens are poorly defined. This is the case for both disease inciting autoantigens and antigens that become involved through epitope spreading. A possible source of surrogate auto-antigens expressed in tissues during inflammation are heat shock proteins (HSP) or stress proteins. In this mini-review we discuss unique characteristics of HSP which provide them with the capacity to inhibit inflammatory processes. Various studies have shown that epitopes of HSP60 and HSP70 molecules can function as vaccines to downregulate a variety of autoimmune inflammatory diseases. Currently, several research groups are developing cell therapies with the intention to reach therapeutic tolerance. In this review, in which we are proposing to ex vivo load tolerant dendritic cells with a Treg inducing HSP70 derived peptide called B29, we are discussing the chances to develop this as an autologous tolDC therapeutic tolerance therapy for rheumatoid arthritis.
Phenotypic and Molecular Selection of a Superior Solanum pennellii Introgression Sub-Line Suitable for Improving Quality Traits of Cultivated Tomatoes

The Solanum pennellii Introgression Line (IL) population can be exploited to identify favorable alleles that can improve yield and fruit quality traits in commercial tomato varieties. Over the past few years, we have selected ILs that exhibit increased content of antioxidant compounds in the fruit compared to the cultivar M82, which represents the genetic background in which the different wild regions of the S. pennellii ILs were included. Recently, we have identified seven sub-lines of the IL7-3 accumulating different amounts of antioxidants in the ripe fruit. Since the wild region carried on chromosome 7 induces a low fruit production in IL7-3, the first aim of the present work was to evaluate yield performances of the selected sub-lines in three experimental fields located in the South of Italy. Another aim was to confirm in the same lines the high levels of antioxidants and evaluate other fruit quality traits. On red ripe fruit, the levels of soluble solids content, firmness, and ascorbic acid (AsA) were highly variable among the sub-lines grown in three environmental conditions, evidencing a significant genotype by environment interaction for soluble solids and AsA content. Only one sub-line (coded R182) exhibited a significantly higher firmness, even though no differences were observed for this trait between the parental lines M82 and IL7-3. The same sub-line showed significantly higher AsA content compared to M82, thus resembling IL7-3. Even though IL7-3 always exhibited a significantly lower yield, all the sub-lines showed yield variability over the three trials. Interestingly, the sub-line R182, selected for its better performances in terms of fruit quality, in all the trials showed a production comparable to that of the control line M82. A group of species-specific molecular markers was tested on R182 and on the parental genotypes in order to better define the wild genomic regions carried by the elite line R182. In these regions three candidate genes that could increase the level of AsA in the fruit were identified. In the future, the line R182 could be used as pre-breeding material in order to obtain new varieties improved for nutritional traits.
A Review of Swine Transportation Research on Priority Welfare Issues: A Canadian Perspective

The purpose of this review is to present the best available scientific knowledge on key animal welfare issues during swine transport, such as transport duration and distance, time off feed and water, rest intervals, environmental conditions, loading density, and transport of young animals, based on their impact on stress, injury, fatigue, dehydration, body temperature, mortality, and carcass and meat quality. The review was limited to this set of priority welfare issues which were identified by the National Farm Animal Care Council (NFACC) Scientific Committee to help with the development of the livestock transportation Codes of Practice. This review focuses primarily on research related to the transport of market pigs (100–135 kg) which is a reflection of the current literature available on pig transportation. This information presented here can be used to support other animal welfare codes, guidelines, standards or legislations regulating the welfare of pigs during transport. Based on the available literature, clear conclusions can be drawn on the impact of vehicle design, pre-transport fasting, control of environmental conditions and loading density on the welfare of pigs during transport and on pork quality. However, the effects of journey duration are still unclear and a recommendation on the maximum transport time cannot be provided. Further studies investigating the impact of factors, such as ambient conditions within the transport vehicle, loading density at extreme ambient conditions, travel distances, maximum travel duration, rest/stop duration, and management of pigs during rest stops are required. More specifically, further research in relation to the welfare of market weight, newly weaned and breeding pigs, and cull sows and boars during transport is needed.
Astrocyte Mechano-Activation by High-Rate Overpressure Involves Alterations in Structural and Junctional Proteins

Primary blast neurotrauma represents a unique injury paradigm characterized by high-rate overpressure effects on brain tissue. One major hallmark of blast neurotrauma is glial reactivity, notably prolonged astrocyte activation. This cellular response has been mainly defined in primary blast neurotrauma by increased intermediate filament expression. Because the intermediate filament networks physically interface with transmembrane proteins for junctional support, it was hypothesized that cell junction regulation is altered in the reactive phenotype as well. This would have implications for downstream transcriptional regulation via signal transduction pathways like nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB). Therefore, a custom high-rate overpressure simulator was built for in vitro testing using mechanical conditions based on intracranial pressure measurements in a rat model of blast neurotrauma. Primary rat astrocytes were exposed to isolated high-rate mechanical stimulation to study cell junction dynamics in relation to their mechano-activation. First, a time course for “classical” features of reactivity was devised by evaluation of glial fibrillary acidic protein (GFAP) and proliferating cell nuclear antigen (PCNA) expression. This was followed by gene and protein expression for both gap junction (connexins) and anchoring junction proteins (integrins and cadherins). Signal transduction analysis was carried out by nuclear localization of two molecules, NF-κB p65 and mitogen-activated protein kinase (MAPK) p38. Results indicated significant increases in connexin-43 expression and PCNA first at 24 h post-overpressure (p < 0.05), followed by structural reactivity (via increased GFAP, p < 0.05) corresponding to increased anchoring junction dynamics at 48 h post-overpressure (p < 0.05). Moreover, increased phosphorylation of focal adhesion kinase (FAK) was observed in addition to increased nuclear localization of both p65 and p38 (p < 0.05) during the period of structural reactivity. To evaluate the transcriptional activity of p65 in the nucleus, electrophoretic mobility shift assay was conducted for a binding site on the promoter region for intracellular adhesion molecule-1 (ICAM-1), an antagonist of tight junctions. A significant increase in the interaction of nuclear proteins with the NF-κB site on the ICAM-1 corresponded to increased gene and protein expression of ICAM-1 (p < 0.05). Altogether, these results indicate multiple targets and corresponding signaling pathways which involve cell junction dynamics in the mechano-activation of astrocytes following high-rate overpressure.
Central Blood Pressure and Pulse Wave Velocity Changes Post Renal Denervation in Patients With Stages 3 and 4 Chronic Kidney Disease: The Regina RDN Study

Background: Central aortic blood pressures and arterial stiffness are better indicators of cardiovascular outcomes than brachial blood pressures. However, their response to renal denervation (RDN) in patients with Stage 3 and Stage 4 chronic kidney disease (CKD) has not yet been examined. Objective: To evaluate the impact of RDN on central blood pressures (CBP), brachial (office and ambulatory) blood pressures, arterial stiffness, glomerular filtration rate (GFR), 24-hour urine protein, and selective cardiac parameters observed on echocardiograms. Design: Single-center, single-arm with pre-/post-RDN follow-up. Setting: Patients were recruited from the multidisciplinary CKD clinic, Regina General Hospital, Canada. Patients: About 25 consecutive patients with Stage 3 or Stage 4 CKD and resistant hypertension, with no radiological or laboratory evidence of secondary causes of hypertension. Measurements: The key measurements were CBP, pulse wave velocity, ambulatory 24-hour blood pressure, office blood pressures on BP Tru, GFR, 24-hour urine protein and sodium, dose and number of blood pressure medication and doses. Methods: The primary outcome measure was the change in CBP from baseline to 6 months post-RDN. Secondary outcome measures included changes in CBP, office blood pressure, 24-hour ambulatory pressures, pulse wave velocity, kidney function (eGFR and 24-hour protein excretion), and the change in the number and dose of medications during the 2-year follow-up period. The primary outcome and the secondary outcomes were evaluated using a Friedman’s analysis of variance (ANOVA) and Wilcoxon signed-rank test for changes from post RDN procedure. Bonferroni correction was used to adjust P values for multiple testing. A two-sided alpha of . 05 was used. Results: Median central blood pressures (mm Hg) were 127/75 at baseline versus 118/70 at 6 months and 118/67 at 24 months (P = .13). Median office blood pressures (mm Hg) were 148/76 at baseline versus 135/75 at 6 months and 133/75 at 24 months (P ≤ .001). Median ambulatory 24-hour day (mm Hg) was 148/64 at baseline and 146/68 at 6 months and 152/67 at 24 months (P = .60). Median pulse wave velocity (m/s) at baseline was 13.8 at baseline versus 13.3 m/s at 6 months and 12.3 at 12 months’ time (P = .62). Estimated glomerular filtration rate (mL/min/1.73m2) at baseline was 37, at 6 months was 36 and 34 at 24 months (P = .33). Limitations: Single-center study, with no sham arm. Conclusions: Our study demonstrates that there was a significant improvement in office blood pressures from baseline to 6 months, maintained to 24 months. There was a numerical improvement in central pressures, and pulse wave velocity at 6 and 24 months, with no sustained changes noted in 24-hour blood pressure. Kidney function remained at or near baseline throughout the 24 months of observation. Trial registration: ClinicalTrials.gov (NCT01832233).
Quadratic Performance Analysis of Switched Affine Time–Varying Systems

Abstract We analyze quadratic performance for switched systems which are composed of a finite set of affine time-varying subsystems, where both subsystem matrices and affine vectors are switched, and no single subsystem has desired quadratic performance. The quadratic performance indexes we deal with include stability, tracking and L2 gain. We show that if a linear convex combination of subsystem matrices is uniformly Hurwitz and another convex combination of affine vectors is zero, then we can design a state-dependent switching law (state feedback) and an output-dependent switching law (output feedback) such that the entire switched affine system is quadratically stable at the origin. In the case where the convex combination of affine vectors is nonzero, we show that the tracking control problem can be posed and solved using a similar switching strategy. Finally, we consider the L2gain analysis problem for the switched affine time-varying systems under state feedback.
CD5-Positive Primary Cutaneous Diffuse Large B-Cell Lymphoma-Leg Type

Most primary cutaneous B-cell lymphomas (PCBCL) are CD5 negative, and only a few cases were found to express CD5. We report the first well-documented CD5+ primary cutaneous diffuse large B-cell lymphoma-leg type (PCDLBCL-LT). A 71-year-old woman with a history of Multiple Sclerosis was admitted because of a nodule at the left thigh. Histological examination of the skin biopsy disclosed a diffuse dermal infiltration by large lymphoid cells. Immunohistochemistry revealed that these large cells were positive for CD5, CD20, CD79a, MUM1/IRF4, Bcl6, Bcl2, and cytoplasmic IgM/λ, whereas CD3, CD56, CD23, CD21, CD10, CD30, cyclin D1, CD68, lysozyme, myeloperoxidase, and CD34 were not detected. Thus, the diagnosis of a CD5+ PCDLBCL-LT was made. Despite treatment, the patient died 11 months after initial diagnosis.
Predicting ConceptNet Path Quality Using Crowdsourced Assessments of Naturalness

In many applications, it is important to characterize the way in which two concepts are semantically related. Knowledge graphs such as ConceptNet provide a rich source of information for such characterizations by encoding relations between concepts as edges in a graph. When two concepts are not directly connected by an edge, their relationship can still be described in terms of the paths that connect them. Unfortunately, many of these paths are uninformative and noisy, which means that the success of applications that use such path features crucially relies on their ability to select high-quality paths. In existing applications, this path selection process is based on relatively simple heuristics. In this paper we instead propose to learn to predict path quality from crowdsourced human assessments. Since we are interested in a generic task-independent notion of quality, we simply ask human participants to rank paths according to their subjective assessment of the paths' naturalness, without attempting to define naturalness or steering the participants towards particular indicators of quality. We show that a neural network model trained on these assessments is able to predict human judgments on unseen paths with near optimal performance. Most notably, we find that the resulting path selection method is substantially better than the current heuristic approaches at identifying meaningful paths.
Stacking with Neural Network for Cryptocurrency investment

Predicting the direction of assets have been an active area of study and difficult task. Machine learning models have been used to build robust models to model the above task. Ensemble methods are one of them resulting better than single supervised method. We have used generative and discriminative classifiers to create the stack, particularly 3 generative and 6 discriminative classifiers and optimized over one-layer Neural Network to model the direction of price cryptocurrencies. Features used are technical indicators not limited to trend, momentum, volume, volatility indicators and sentiment indicators. For Cross validation, Purged Walk forward cross validation has been used. In terms of accuracy, we have done comparative analysis of the performance of Ensemble method with Stacking and individual models. We have also developed methodology for features importance for stacked model. Important indicators are identified based on feature importance.
Hyperbolic Discounting and Learning over Multiple Horizons

Reinforcement learning (RL) typically defines a discount factor as part of the Markov Decision Process. The discount factor values future rewards by an exponential scheme that leads to theoretical convergence guarantees of the Bellman equation. However, evidence from psychology, economics and neuroscience suggests that humans and animals instead have hyperbolic time-preferences. In this work we revisit the fundamentals of discounting in RL and bridge this disconnect by implementing an RL agent that acts via hyperbolic discounting. We demonstrate that a simple approach approximates hyperbolic discount functions while still using familiar temporal-difference learning techniques in RL. Additionally, and independent of hyperbolic discounting, we make a surprising discovery that simultaneously learning value functions over multiple time-horizons is an effective auxiliary task which often improves over a strong value-based RL agent, Rainbow.
LIVE: a manually curated encyclopedia of experimentally validated interactions of lncRNAs

Abstract Advances in studies of long noncoding RNAs (lncRNAs) have provided data regarding the regulatory roles of lncRNAs, which perform functional roles through interactions with other functional elements. To track the underlying relationships among lncRNAs, various databases have been developed as repositories for lncRNA data. However, the ability to comprehensively explore the diverse interactions between lncRNAs and other functional elements is limited. To this end, we developed LIVE (LncRNA Interaction Validated Encyclopaedia), an interactive resource to integrate the diverse interactions of functional elements with lncRNAs. LIVE is a manually curated database of experimentally validated interactions of lncRNAs with genes, proteins and other various functional elements. By mining publications, we constructed LIVE with the following three interaction networks: a binding interaction network, a regulation network and a disease network; then, we combined them to form a comprehensive lncRNA interaction network. The current release of LIVE contains the validated interactions of 572 lncRNAs in humans and mice with 103 proteins, 209 genes, 56 transcription factors and 194 diseases. LIVE provides an interactive interface with charts and figures to aid users in searching and browsing interactions with lncRNAs. LIVE will greatly facilitate further investigation into the regulatory roles of lncRNAs and is freely available.
Customer churn prediction - a case study in retail banking

This work focuses on one of the central topics in customer relationship management (CRM): transfer of valuable customers to a competitor. Customer retention rate has a strong impact on customer lifetime value, and understanding the true value of a possible customer churn will help the company in its customer relationship management. Customer value analysis along with customer churn predictions will help marketing programs target more specific groups of customers. We predict customer churn with logistic regression techniques and analyze the churning and nonchurning customers by using data from a consumer retail banking company. The result of the case study show that using conventional statistical methods to identify possible churners can be successful.
Self-Approach Tendencies: Relations With Explicit and Implicit Self-Evaluations

We used a newly developed Self-Approach-Avoidance Task (Self-AAT) to measure self-approach tendencies in female students. In this task, participants use a joystick to pull portraits of themselves and of others closer or to push them away. In the three studies, we found a significant self-approach tendency: participants were faster to pull mirror-imaged portraits of themselves closer than to push them away. This approach tendency was reduced for non-mirrored self-portraits, and absent for control pictures showing unknown males, unknown females, or empty backgrounds. Moreover, in two out of the three studies, the self-approach tendency was weakly related to explicit self-valuations measured with the Rosenberg Self-Esteem Scale (RSES), and in one out of two studies, it was related to implicit self-evaluations measured with the Implicit Association Task (IAT). Implications and potential applications of the findings are discussed.
After the timber wars: Community-based stewardship

This paper discusses the reasons why community-based stewardship is the solution to proper national forest management. Various groups have diverse goals in terms of promoting sustainable harvest of forest resources, land and forest ownership and restoring ecosystems, but instead of achieving the goal, conflicts arise. Utilizing the knowledge and experience of local communities within national forests could better ameliorate forest ecosystems and provide proper management of these forest.