Miracle-dz/UniFAR-FTUs huggingface dataset:
A worldwide phylogeography of the whiteworm lichens Thamnolia reveals three lineages with distinct habitats and evolutionary histories

Abstract Thamnolia is a lichenized fungus with an extremely wide distribution, being encountered in arctic and alpine environments in most continents. In this study, we used molecular markers to investigate the population structure of the fungal symbiont and the associated photosynthetic partner of Thamnolia. By analyzing molecular, morphological, and chemical variation among 253 specimens covering the species distribution range, we revealed the existence of three mycobiont lineages. One lineage (Lineage A) is confined to the tundra region of Siberia and the Aleutian Islands, a second (Lineage B) is found in the high alpine region of the Alps and the Carpathians Mountains, and a third (Lineage C) has a worldwide distribution and covers both the aforementioned ecosystems. Molecular dating analysis indicated that the split of the three lineages is older than the last glacial maximum, but the distribution ranges and the population genetic analyses suggest an influence of last glacial period on the present‐day population structure of each lineage. We found a very low diversity of Lineage B, but a higher and similar one in Lineages A and C. Demographic analyses suggested that Lineage C has its origin in the Northern Hemisphere, possibly Scandinavia, and that it has passed through a bottleneck followed by a recent population expansion. While all three lineages reproduce clonally, recombination tests suggest rare or past recombination in both Lineages A and C. Moreover, our data showed that Lineage C has a comparatively low photobiont specificity, being found associated with four widespread Trebouxia lineages (three of them also shared with other lichens), while Lineages A and B exclusively harbor T. simplex s. lat. Finally, we did not find support for the recognition of taxa in Thamnolia based on either morphological or chemical characters.
Parasite-Derived MicroRNAs in Host Serum As Novel Biomarkers of Helminth Infection

Background MicroRNAs (miRNAs) are a class of short non-coding RNA that play important roles in disease processes in animals and are present in a highly stable cell-free form in body fluids. Here, we examine the capacity of host and parasite miRNAs to serve as tissue or serum biomarkers of Schistosoma mansoni infection. Methods/Principal Findings We used Exiqon miRNA microarrays to profile miRNA expression in the livers of mice infected with S. mansoni at 7 weeks post-infection. Thirty-three mouse miRNAs were differentially expressed in infected compared to naïve mice (>2 fold change, p<0.05) including miR-199a-3p, miR-199a-5p, miR-214 and miR-21, which have previously been associated with liver fibrosis in other settings. Five of the mouse miRNAs were also significantly elevated in serum by twelve weeks post-infection. Sequencing of small RNAs from serum confirmed the presence of these miRNAs and further revealed eleven parasite-derived miRNAs that were detectable by eight weeks post infection. Analysis of host and parasite miRNA abundance by qRT-PCR was extended to serum of patients from low and high infection sites in Zimbabwe and Uganda. The host-derived miRNAs failed to distinguish uninfected from infected individuals. However, analysis of three of the parasite-derived miRNAs (miR-277, miR-3479-3p and bantam) could detect infected individuals from low and high infection intensity sites with specificity/sensitivity values of 89%/80% and 80%/90%, respectively. Conclusions This work identifies parasite-derived miRNAs as novel markers of S. mansoni infection in both mice and humans, with the potential to be used with existing techniques to improve S. mansoni diagnosis. In contrast, although host miRNAs are differentially expressed in the liver during infection their abundance levels in serum are variable in human patients and may be useful in cases of extreme pathology but likely hold limited value for detecting prevalence of infection.
Gain Modulation as a Mechanism for Coding Depth from Motion Parallax in Macaque Area MT

Observer translation produces differential image motion between objects that are located at different distances from the observer's point of fixation [motion parallax (MP)]. However, MP can be ambiguous with respect to depth sign (near vs far), and this ambiguity can be resolved by combining retinal image motion with signals regarding eye movement relative to the scene. We have previously demonstrated that both extra-retinal and visual signals related to smooth eye movements can modulate the responses of neurons in area MT of macaque monkeys, and that these modulations generate neural selectivity for depth sign. However, the neural mechanisms that govern this selectivity have remained unclear. In this study, we analyze responses of MT neurons as a function of both retinal velocity and direction of eye movement, and we show that smooth eye movements modulate MT responses in a systematic, temporally precise, and directionally specific manner to generate depth-sign selectivity. We demonstrate that depth-sign selectivity is primarily generated by multiplicative modulations of the response gain of MT neurons. Through simulations, we further demonstrate that depth can be estimated reasonably well by a linear decoding of a population of MT neurons with response gains that depend on eye velocity. Together, our findings provide the first mechanistic description of how visual cortical neurons signal depth from MP. SIGNIFICANCE STATEMENT Motion parallax is a monocular cue to depth that commonly arises during observer translation. To compute from motion parallax whether an object appears nearer or farther than the point of fixation requires combining retinal image motion with signals related to eye rotation, but the neurobiological mechanisms have remained unclear. This study provides the first mechanistic account of how this interaction takes place in the responses of cortical neurons. Specifically, we show that smooth eye movements modulate the gain of responses of neurons in area MT in a directionally specific manner to generate selectivity for depth sign from motion parallax. We also show, through simulations, that depth could be estimated from a population of such gain-modulated neurons.
Design and implementation of a spider monkey robot

We report on the development of a spider monkey robot that simulates the arboreal locomotion of a spider monkey, including brachiating on and between the tree-limb-mimicking tubes. The work started from an understanding of the locomotion mechanism of a spider monkey, and then the robot was developed by transforming the bio-inspired information into engineering-feasible solutions. By using the stable motion pattern of its simplified model, the robot can successfully brachiate experimentally.
Optimal dynamic power control for full-duplex bidirectional-channel based wireless networks

We consider the full-duplex transmission over bidirectional channels with imperfect self-interference cancelation in wireless networks. In particular, together using propagation-domain interference suppression, analog-domain interference cancellation, and digital-domain interference cancellation, we develop the optimal dynamic power allocation schemes for the wireless full-duplex sum-rate optimization problem which aims at maximizing the sum-rate of wireless full-duplex bidirectional transmissions. In the high signal-to-interference-plus-noise ratio (SINR) region, the full-duplex sum-rate maximization problem is a convex optimization problem. For interference-dominated wireless full-duplex transmission in the high SINR region, we derive the closed-form expression for the optimal dynamic power allocation scheme. For non-interference-dominated wireless full-duplex transmission in the high SINR region, we obtain the optimal dynamic power allocation scheme by numerically solving the corresponding Karush-Kuhn-Tucker (KKT) conditions. While the full-duplex sum-rate maximization problem is usually not a convex optimization problem, by developing the tightest lower-bound function and using the logarithmic change of variables technique, we convert the full-duplex sum-rate maximization problem to a convex optimization problem. Then, using our proposed iteration algorithm, we can numerically derive the optimal dynamic power allocation scheme for the more generic scenario. Also presented are the numerical results which validate our developed optimal dynamic power allocation schemes.
Deformable HOG-Based Shape Descriptor

In this paper we deal with the problem of recognizing handwritten shapes. We present a new deformable feature extraction method that adapts to the shape to be described, dealing in this way with the variability introduced in the handwriting domain. It consists in a selection of the regions that best define the shape to be described, followed by the computation of histograms of oriented gradients-based features over these points. Our results significantly outperform other descriptors in the literature for the task of hand-drawn shape recognition and handwritten word retrieval.
Development of an automatic reading method and software for pointer instruments

To effectively resolve the automatic recognition of analog pointer measuring instruments, a reading recognition method based on Hough transform is proposed. In order to simplify the following procedure, image graying and binary, mathematical morphology, including dilation and thinning, edge recognition was applied to the system. We proposed the recognition principle for reading recognition of the pointer's angle by using Hough transform. And the reading of the pointer is decided by the linear relationship between the panel's scale and the angle of the instrument's dial revolutionary. Considering that in most practical cases, the panel cannot be horizontal, so the procedure of tilt correction is employed in this paper. Finally, the software is written in MATLAB. The recognition system is achieved in LabVIEW, where the front panel of the reading system is developed. The experimental results demonstrate that our method is feasible for pointer instrument recognition.
Graft Utilization in the Bridging Reconstruction of Irreparable Rotator Cuff Tears: A Systematic Review

Background: Rotator cuff tears are one of the most common conditions affecting the shoulder. Because of the difficulty in managing massive rotator cuff tears and the inability of standard techniques to prevent arthropathy, surgeons have developed several novel techniques to improve outcomes and ideally alter the natural history. Purpose: To systematically review the existing literature and analyze reported outcomes to evaluate the effectiveness of using a bridging graft reconstruction technique to treat large to massive irreparable rotator cuff tears. Study Design: Systematic review. Methods: A systematic search of PubMed, EMBASE, CINAHL, and CENTRAL was employed with the key terms “tear,” “allograft,” and “rotator cuff. ” Eligibility was determined by a 3-phase screening process according to the outlined inclusion/exclusion criteria. Data in relation to the primary and secondary outcomes were summarized. The results were synthesized according to the origin of the graft and the level of evidence. Results: Fifteen studies in total were included in this review: 2 comparative studies and 13 observational case series. Both the biceps tendon and the fascia lata autograft groups had significantly superior structural integrity rates on magnetic resonance imaging at 12-month minimum follow-up when compared with their partial primary repair counterparts (58% vs 26%, P = .036; 79% vs 58%, P < .05), respectively. Multiple noncomparative case series investigating allografts, xenografts, and synthetic materials for bridging reconstruction of large to massive rotator cuff tears demonstrated high structural healing rates (74%-90%, 73%-100%, and 60%-90%, respectively). Additionally, both comparative studies and case series demonstrated a general improvement of patients’ functional outcome scores. Conclusion: Using a graft for an anatomic bridging rotator cuff repair results in improved function on objective testing and may be functionally better than nonanatomic or partial repair of large to massive rotator cuff tears. Allograft or xenograft techniques appear to be favorable options, given demonstrated functional improvement, imaging-supported graft survival, and lack of harvest complication risk. More high-quality randomized controlled studies are needed to further assess this technique.
Control and experimental results of a catheter operating system

In this paper, we developed a novel catheter operating system using force sensors for medical application, which included a highly precise master-slave remote control system. We designed micro force sensors and used them in the system to ensure the operation security in intravascular neurosurgery applications. We carried out the operation simulation experiments and got the force information by force sensors when the catheter contacted the simulator of blood vessel. The experimental results indicated that the proposed force sensors-based catheter operating system works well and can be controlled remotely, and the force feedback can effectively improve operability.
Lipid Targets During Statin Treatment in Dyslipidemic Patients Affected by Nonalcoholic Fatty Liver Disease

Introduction:Nonalcoholic fatty liver disease (NAFLD) is associated with both dyslipidemia and increased risk for cardiovascular disease. Despite the indication to treat in patients affected by both dyslipidemia and NAFLD, an undertreatment in statin therapy due to the potential liver damage is frequently observed. We sought to evaluate retrospectively the impact of statin on the lipid profile and on the achievement of low-density lipoprotein (LDL) cholesterol targets in relation to the National Cholesterol Education Program—Adult Treatment Panel III-cardiovascular risk in dyslipidemic patients presenting with a clinical—diagnosis of NAFLD and elevated liver enzymes before statin prescription. As a secondary endpoint, the authors investigated whether statin could be associated with changes of liver enzymes. Methods:Forty-three patients with dyslipidemic NAFLD presenting with increased values of aspartate aminotransferase and/or alanine aminotransferase and/or &ggr;-glutamyl-transferase at baseline were analyzed retrospectively as regard the lipid profile and liver enzymes (values reported before statin and during statin therapy). Results:Total cholesterol, LDL and triglycerides were significantly reduced at follow-up (5.4 ± 5.4 months). The LDL target was achieved at the second visit in 30 patients (69.8%). The number of patients achieving the LDL target was significantly higher in low-risk group compared with moderate- and high-risk subjects. Liver enzyme levels showed no significant changes between baseline and follow-up. Conclusions:Statin treatment was effective (without changes in liver enzymes) in patients with dyslipidemia and NAFLD and therefore, affected by a profound alteration in lipoprotein metabolism. The number of patients achieving LDL target was related to the Adult Treatment Panel III risk classification, being higher in patients with lower risk.
Redirection of lipid flux toward phospholipids in yeast increases fatty acid turnover and secretion

Significance Replacement of nonrenewable petrochemicals and liquid fuels requires sustainable production of oleochemicals. Free fatty acids (FFAs) are versatile molecules that can be produced by microbial fermentation and are used as precursors for production of these oleochemicals. In the past few years, we have seen major advancements in improving the yeast Saccharomyces cerevisiae for FFA production. Despite these successes, lipid metabolism is highly complex, and the pathways and metabolites involved in the formation of FFAs in yeast remain incompletely understood. In this work, we make important advancements in understanding the dynamics of FFA formation in the cell and explore the role of phospholipids in this process. Bio-based production of fatty acids and fatty acid-derived products can enable sustainable substitution of petroleum-derived fuels and chemicals. However, developing new microbial cell factories for producing high levels of fatty acids requires extensive engineering of lipid metabolism, a complex and tightly regulated metabolic network. Here we generated a Saccharomyces cerevisiae platform strain with a simplified lipid metabolism network with high-level production of free fatty acids (FFAs) due to redirected fatty acid metabolism and reduced feedback regulation. Deletion of the main fatty acid activation genes (the first step in β-oxidation), main storage lipid formation genes, and phosphatidate phosphatase genes resulted in a constrained lipid metabolic network in which fatty acid flux was directed to a large extent toward phospholipids. This resulted in simultaneous increases of phospholipids by up to 2.8-fold and of FFAs by up to 40-fold compared with wild-type levels. Further deletion of phospholipase genes PLB1 and PLB2 resulted in a 46% decrease in FFA levels and 105% increase in phospholipid levels, suggesting that phospholipid hydrolysis plays an important role in FFA production when phospholipid levels are increased. The multiple deletion mutant generated allowed for a study of fatty acid dynamics in lipid metabolism and represents a platform strain with interesting properties that provide insight into the future development of lipid-related cell factories.
Dnmt3a deletion cooperates with the Flt3/ITD mutation to drive leukemogenesis in a murine model

Internal tandem duplications of the juxtamembrane domain of FLT3 (FLT3/ITD) are among the most common mutations in Acute Myeloid Leukemia (AML). Resulting in constitutive activation of the kinase, FLT3/ITD portends a particularly poor prognosis, with reduced overall survival and increased rates of relapse. We previously generated a knock-in mouse, harboring an internal tandem duplication at the endogenous Flt3 locus, which develops a fatal myeloproliferative neoplasm (MPN), but fails to develop acute leukemia, suggesting additional mutations are necessary for transformation. To investigate the potential cooperativity of FLT3/ITD and mutant DNMT3A, we bred a conditional Dnmt3a knockout to a substrain of our Flt3/ITD knock-in mice, and found deletion of Dnmt3a significantly reduced median survival of Flt3ITD/+ mice in a dose dependent manner. As expected, pIpC treated Flt3ITD/+ mice solely developed MPN, while Flt3ITD/+;Dnmt3af/f and Flt3ITD/+;Dnmt3af/+ developed a spectrum of neoplasms, including MPN, T-ALL, and AML. Functionally, FLT3/ITD and DNMT3A deletion cooperate to expand LT-HSCs, which exhibit enhanced self-renewal in serial re-plating assays. These results illustrate that DNMT3A loss cooperates with FLT3/ITD to generate hematopoietic neoplasms, including AML. In combination with FLT3/ITD, homozygous Dnmt3a knock-out results in reduced time to disease onset, LT-HSC expansion, and a higher incidence of T-ALL compared with loss of just one allele. The co-occurrence of FLT3 and DNMT3A mutations in AML, as well as subsets of T-ALL, suggests the Flt3ITD/+;Dnmt3af/f model may serve as a valuable resource for delineating effective therapeutic strategies in two clinically relevant contexts.
Regional Multi-Armed Bandits

We consider a variant of the classic multi-armed bandit problem where the expected reward of each arm is a function of an unknown parameter. The arms are divided into different groups, each of which has a common parameter. Therefore, when the player selects an arm at each time slot, information of other arms in the same group is also revealed. This regional bandit model naturally bridges the non-informative bandit setting where the player can only learn the chosen arm, and the global bandit model where sampling one arms reveals information of all arms. We propose an efficient algorithm, UCB-g, that solves the regional bandit problem by combining the Upper Confidence Bound (UCB) and greedy principles. Both parameter-dependent and parameter-free regret upper bounds are derived. We also establish a matching lower bound, which proves the order-optimality of UCB-g. Moreover, we propose SW-UCB-g, which is an extension of UCB-g for a non-stationary environment where the parameters slowly vary over time.
Linguistic Feature Based Filtering Mechanism for Recommending Posts in a Social Networking Group

Online social networks have spawned myriads of online social groups, where people can interact and exchange their ideas. However, the major issues that interfere with the user security and comfort are privacy breach, groups without opt-in options, clutter created out of numerous groups in which a user is a member of and difficulty in managing group principles. This can be lessened to an extent by an automated filtering mechanism capable of categorizing members within a group based on their pattern of response. In our proposed method, the posts within a group are clustered based on stylistic, thematic, emotional, sentimental, and psycholinguistic aspects. Then the members of the group are categorized based on their response to the posts belonging to different aspects as mentioned above. This results in categories of individuals within a group, who are like minded. The categorization caters to the most important issues related to soft security, such as the clutter associated with irrelevant notifications received from multiple groups, by suggesting the users, posts that are likely to be of interest to them. It also helps to identify the group members intended towards spreading posts that violate group policies. The categorization exhibits satisfiable performance in case of large number of candidate members in a populous group by performing clustering based on linguistic features. The double level of clustering, based on the posts and response of users based on the aspects of the posts, enhances the performance of the system, hence outperforming traditional recommender systems. The system has been tested on Facebook group data, where it offers a significant solution to an unaddressed problem associated with social networking groups.
Spreading of sexually transmitted diseases in heterosexual populations

The spread of sexually transmitted diseases (e.g., chlamydia, syphilis, gonorrhea, HIV, etc.) across populations is a major concern for scientists and health agencies. In this context, both the data collection on sexual contact networks and the modeling of disease spreading are intensive contributions to the search for effective immunization policies. Here, the spreading of sexually transmitted diseases on bipartite scale-free graphs, representing heterosexual contact networks, is considered. We analytically derive the expression for the epidemic threshold and its dependence with the system size in finite populations. We show that the epidemic outbreak in bipartite populations, with number of sexual partners distributed as in empirical observations from national sex surveys, takes place for larger spreading rates than for the case in which the bipartite nature of the network is not taken into account. Numerical simulations confirm the validity of the theoretical results. Our findings indicate that the restriction to crossed infections between the two classes of individuals (males and females) has to be taken into account in the design of efficient immunization strategies for sexually transmitted diseases.