Miracle-dz/UniFAR-FTUs huggingface dataset:
Understory vegetation mediates permafrost active layer dynamics and carbon dioxide fluxes in open-canopy larch forests of northeastern Siberia

Arctic ecosystems are characterized by a broad range of plant functional types that are highly heterogeneous at small (~1–2 m) spatial scales. Climatic changes can impact vegetation distribution directly, and also indirectly via impacts on disturbance regimes. Consequent changes in vegetation structure and function have implications for surface energy dynamics that may alter permafrost thermal dynamics, and are therefore of interest in the context of permafrost related climate feedbacks. In this study we examine small-scale heterogeneity in soil thermal properties and ecosystem carbon and water fluxes associated with varying understory vegetation in open-canopy larch forests in northeastern Siberia. We found that lichen mats comprise 16% of understory vegetation cover on average in open canopy larch forests, and lichen abundance was inversely related to canopy cover. Relative to adjacent areas dominated by shrubs and moss, lichen mats had 2–3 times deeper permafrost thaw depths and surface soils warmer by 1–2°C in summer and less than 1°C in autumn. Despite deeper thaw depths, ecosystem respiration did not differ across vegetation types, indicating that autotrophic respiration likely dominates areas with shrubs and moss. Summertime net ecosystem exchange of CO2 was negative (i.e. net uptake) in areas with high shrub cover, while positive (i.e. net loss) in lichen mats and areas with less shrub cover. Our results highlight relationships between vegetation and soil thermal dynamics in permafrost ecosystems, and underscore the necessity of considering both vegetation and permafrost dynamics in shaping carbon cycling in permafrost ecosystems.
Respiratory, metabolic, and acid-base correlates of aerobic metabolic rate reduction in overwintering frogs.

Aerobic metabolic rates (M˙o 2) and respiratory quotients (RQ = CO2production/M˙o 2) were measured contemporaneously in hibernating frogs Rana temporaria (L.), submerged for 90 days at 3°C. After 3 mo of submergence in fully aerated water,M˙o 2levels were 61% of those seen at the same temperature before hibernation. Over the first 40 days of hibernation, RQ values (≤0.82) favored a lipid-based metabolism that progressively shifted to an exclusively carbohydrate metabolism (RQ = 1.01) by 90 days of hibernation. Liver glycogen concentrations fell by 68% during the first 8 wk of submergence, thereafter exhibiting a less rapid rate of utilization. Conversely, muscle glycogen concentrations remained stable over the first 2 mo of the experiment before falling by 33% over the course of the remaining 2 mo, indicating that the frog was recruiting muscle glycogen reserves to fuel metabolism. Submerged frogs exhibited an extracellular acidosis during the first week of submergence, but over the course of the next 15 wk "extracellular pH" values were not significantly different from the values obtained from the control air-breathing animals. The initial extracellular acidosis was not mirrored in the intracellular compartment, and the acid-base state was not significantly different from the control values for the first 8 wk. However, over the subsequent 8- to 16-wk period, the acid-base status shifted to a lower intracellular pH-[Formula: see text] concentration set point, indicative of a metabolic acidosis. Even so, there was no indication that the acidosis could be attributed to anaerobic metabolism, as both plasma and muscle lactate levels remained low and stable. Muscle adenylate energy charge and lactate-to-pyruvate and creatine-to-phosphocreatine ratios also remained unchanged throughout hibernation. The capacity for profound metabolic rate suppression together with the ability to match substrate use to shifts in aerobic metabolic demands and the ability to fix new acid-base homeostatic set points are highly adaptive, both in terms of survival and reproductive success, to an animal that is often forced to overwinter under the cover of ice.
Extrusion Bioprinting of Shear‐Thinning Gelatin Methacryloyl Bioinks

Bioprinting is an emerging technique for the fabrication of 3D cell‐laden constructs. However, the progress for generating a 3D complex physiological microenvironment has been hampered by a lack of advanced cell‐responsive bioinks that enable bioprinting with high structural fidelity, particularly in the case of extrusion‐based bioprinting. Herein, this paper reports a novel strategy to directly bioprint cell‐laden gelatin methacryloyl (GelMA) constructs using bioinks of GelMA physical gels (GPGs) achieved through a simple cooling process. Attributed to their shear‐thinning and self‐healing properties, the GPG bioinks can retain the shape and form integral structures after deposition, allowing for subsequent UV crosslinking for permanent stabilization. This paper shows the structural fidelity by bioprinting various 3D structures that are typically challenging to fabricate using conventional bioinks under extrusion modes. Moreover, the use of the GPG bioinks enables direct bioprinting of highly porous and soft constructs at relatively low concentrations (down to 3%) of GelMA. It is also demonstrated that the bioprinted constructs not only permit cell survival but also enhance cell proliferation as well as spreading at lower concentrations of the GPG bioinks. It is believed that such a strategy of bioprinting will provide many opportunities in convenient fabrication of 3D cell‐laden constructs for applications in tissue engineering, regenerative medicine, and pharmaceutical screening.
Cyp8b1 ablation prevents Western diet-induced weight gain and hepatic steatosis because of impaired fat absorption.

Bile acids (BAs) are cholesterol derivatives that regulate lipid metabolism, through their dual abilities to promote lipid absorption and activate BA receptors. However, different BA species have varying abilities to perform these functions. Eliminating 12α-hydroxy BAs in mice via Cyp8b1 knockout causes low body weight and improved glucose tolerance. The goal of this study was to determine mechanisms of low body weight in Cyp8b1-/- mice. We challenged Cyp8b1-/- mice with a Western-type diet and assessed body weight and composition. We measured energy expenditure, fecal calories, and lipid absorption and performed lipidomic studies on feces and intestine. We investigated the requirement for dietary fat in the phenotype using a fat-free diet. Cyp8b1-/- mice were resistant to Western diet-induced body weight gain, hepatic steatosis, and insulin resistance. These changes were associated with increased fecal calories, due to malabsorption of hydrolyzed dietary triglycerides. This was reversed by treating the mice with taurocholic acid, the major 12α-hydroxylated BA species. The improvements in body weight and steatosis were normalized by feeding mice a fat-free diet. The effects of BA composition on intestinal lipid handling are important for whole body energy homeostasis. Thus modulating BA composition is a potential tool for obesity or diabetes therapy.
Ultraconformable Temporary Tattoo Electrodes for Electrophysiology

Electrically interfacing the skin for monitoring personal health condition is the basis of skin‐contact electrophysiology. In the clinical practice the use of stiff and bulky pregelled or dry electrodes, in contrast to the soft body tissues, imposes severe restrictions to user comfort and mobility while limiting clinical applications. Here, in this work dry, unperceivable temporary tattoo electrodes are presented. Customized single or multielectrode arrays are readily fabricated by inkjet printing of conducting polymer onto commercial decal transfer paper, which allows for easy transfer on the user's skin. Conformal adhesion to the skin is provided thanks to their ultralow thickness (<1 µm). Tattoo electrode–skin contact impedance is characterized on short‐ (1 h) and long‐term (48 h) and compared with standard pregelled and dry electrodes. The viability in electrophysiology is validated by surface electromyography and electrocardiography recordings on various locations on limbs and face. A novel concept of tattoo as perforable skin‐contact electrode, through which hairs can grow, is demonstrated, thus permitting to envision very long‐term recordings on areas with high hair density. The proposed materials and patterning strategy make this technology amenable for large‐scale production of low‐cost sensing devices.
Mixed Communities of Mucoid and Nonmucoid Pseudomonas aeruginosa Exhibit Enhanced Resistance to Host Antimicrobials

ABSTRACT Pseudomonas aeruginosa causes chronic pulmonary infections in patients with cystic fibrosis (CF). P. aeruginosa mucoid conversion, defined by overproduction of the exopolysaccharide alginate, correlates with accelerated decline in CF patient lung function. Recalcitrance of the mucoid phenotype to clearance by antibiotics and the immune response is well documented. However, despite advantages conferred by mucoidy, mucoid variants often revert to a nonmucoid phenotype both in vitro and in vivo. Mixed populations of mucoid isolates and nonmucoid revertants are recovered from CF lungs, suggesting a selective benefit for coexistence of these variants. In this study, cocultures of mucoid and nonmucoid variants exhibited enhanced resistance to two host antimicrobials: LL-37, a cationic antimicrobial peptide, and hydrogen peroxide (H2O2). Alginate production by mucoid isolates protected nonmucoid variants in consortia from LL-37, as addition of alginate exogenously to nonmucoid variants abrogated LL-37 killing. Conversely, nonmucoid revertants shielded mucoid variants from H2O2 stress via catalase (KatA) production, which was transcriptionally repressed by AlgT and AlgR, central regulators of alginate biosynthesis. Furthermore, extracellular release of KatA by nonmucoid revertants was dependent on lys, encoding an endolysin implicated in autolysis and extracellular DNA (eDNA) release. Overall, these data provide a rationale to study interactions of P. aeruginosa mucoid and nonmucoid variants as contributors to evasion of innate immunity and persistence within the CF lung. IMPORTANCE P. aeruginosa mucoid conversion within lungs of cystic fibrosis (CF) patients is a hallmark of chronic infection and predictive of poor prognosis. The selective benefit of mixed populations of mucoid and nonmucoid variants, often isolated from chronically infected CF patients, has not been explored. Here, we show that mixed-variant communities of P. aeruginosa demonstrate advantages in evasion of innate antimicrobials via production of shared goods: alginate and catalase. These data argue for therapeutically targeting multiple constituents (both mucoid and nonmucoid variants) within diversified P. aeruginosa communities in vivo, as these variants can differentially shield one another from components of the host response. P. aeruginosa mucoid conversion within lungs of cystic fibrosis (CF) patients is a hallmark of chronic infection and predictive of poor prognosis. The selective benefit of mixed populations of mucoid and nonmucoid variants, often isolated from chronically infected CF patients, has not been explored. Here, we show that mixed-variant communities of P. aeruginosa demonstrate advantages in evasion of innate antimicrobials via production of shared goods: alginate and catalase. These data argue for therapeutically targeting multiple constituents (both mucoid and nonmucoid variants) within diversified P. aeruginosa communities in vivo, as these variants can differentially shield one another from components of the host response.
hylogenetic and host – parasite relationship analysis of Henneguya ultiplasmodialis n . sp . infecting Pseudoplatystoma spp . in Brazilian antanal wetland

A new species of the genus Henneguya (Henneguya multiplasmodialis n. sp.) was found infecting the gills of three of 89 specimens (3.3%) of Pseudoplatystoma corruscans and two of 79 specimens (2.6%) of Pseudoplatystoma reticulatum from rivers in the Pantanal wetland, Brazil. Partial sequencing of the 18S rDNA gene of the spores obtained from one plasmodium from the gills of P. corruscans and other one from the gills of P. reticulatum, respectively, resulted in a total of 1560 and 1147 base pairs. As the spores of H. multiplasmodialis n. sp. resemble those of Henneguya corruscans, which is also a parasite of P. corruscans, sequencing of the 18S rDNA gene of the spores of H. corruscans found on P. corruscans caught in the Brazilian Pantanal wetland was also provided to avoid any taxonomic pendency between these two species, resulting in 1913 base pairs. The sequences of H. multiplasmodialis n. sp. parasite of P. corruscans and P. reticulatum and H. corruscans did not match any of the Myxozoa available in the GenBank. The similarity of H. multiplasmodialis n. sp. obtained from P. corruscans to that from P. reticulatum was of 99.7%. Phylogeny revealed a strong tendency among Henneguya species to form clades based on the order and/or family of the host fish. H. multiplasmodialis n. sp. clustered in a clade with Henneguya eirasi and H. corruscans, which are also parasites of siluriforms of the family Pimelodidae and, together Worksupported by FAPESP (Proc. no. 06/59075-6) and CEPTA/ICMBio. ∗ Corresponding author at: Departamento de Ciências Biológicas, Universidade Federal de São Paulo (Unifesp), Rua Professor Artur Riedel, 275, Jardim ldorado, CEP 09972-270 Diadema, SP, Brazil. Tel. : +55 11 3319 3300; fax: +55 11 4043 6428. E-mail address: edapadriano@gmail.com (E.A. Adriano). 1 Research productivity grant from the Brazilian Fostering Agency CNPq. 2 Master’s student supported by FAPESP scholarship. 3 Master’s student supported by CAPES scholarship. oi:10.1016/j.vetpar. 2011.10. 008 © 2011 Elsevier B.V. Open access under the Elsevier OA license. 304-4017 © 2011 Elsevier B.V. Open access under the Elsevier OA license. E.A. Adriano et al. / Veterinary Parasitology 185 (2012) 110– 120 111 with the clade composed of Henneguya spp. parasites of siluriforms of the family Ictaluridae, formed a monophyletic clade of parasites of siluriform hosts. The histological study revealed that the wall of the plasmodia of H. multiplasmodialis n. sp. were covered with a stratified epithelium rich in club cells and supported by a layer of connective tissue. The interior of the plasmodia had a network of septa that divided the plasmodia into numerous compartments. The septa were composed of connective tissue also covered on both sides with a stratified epithelium rich in club cells. Inflammatory infiltrate was found in the tissue surrounding ell as i the plasmodia as w
An agent-based model of cattle grazing toxic Geyer's larkspur

By killing cattle and otherwise complicating management, the many species of larkspur (Delphinium spp.) present a serious, intractable, and complex challenge to livestock grazing management in the western United States. Among the many obstacles to improving our understanding of cattle-larkspur dynamics has been the difficulty of testing different grazing management strategies in the field, as the risk of dead animals is too great. Agent-based models (ABMs) provide an effective method of realistically testing alternate management strategies without risk to livestock. ABMs are especially useful for modeling complex systems such as livestock grazing management, and allow for realistic bottom-up encoding of cattle behavior. Here, we introduce a spatially-explicit, behavior-based ABM of cattle grazing in a pasture with a dangerous amount of Geyer’s larkspur (D. geyeri). This model indicates that herd cohesion and stocking density are key drivers of larkspur-induced toxicosis, and that alteration of these factors within realistic bounds can mitigate risk. Crucially, the model points to herd cohesion, which has received little attention in the discipline, as playing an important role in lethal acute toxicosis. As the first ABM to simulate grazing cattle at realistic scales, this model also demonstrates the tremendous potential of ABMs to illuminate grazing management dynamics, including fundamental aspects of livestock behavior amidst heterogeneity.
Jointly Trained Sequential Labeling and Classification by Sparse Attention Neural Networks

Sentence-level classification and sequential labeling are two fundamental tasks in language understanding. While these two tasks are usually modeled separately, in reality, they are often correlated, for example in intent classification and slot filling, or in topic classification and named-entity recognition. In order to utilize the potential benefits from their correlations, we propose a jointly trained model for learning the two tasks simultaneously via Long Short-Term Memory (LSTM) networks. This model predicts the sentence-level category and the word-level label sequence from the stepwise output hidden representations of LSTM. We also introduce a novel mechanism of "sparse attention" to weigh words differently based on their semantic relevance to sentence-level classification. The proposed method outperforms baseline models on ATIS and TREC datasets.
A general path-based representation for predicting program properties

Predicting program properties such as names or expression types has a wide range of applications. It can ease the task of programming, and increase programmer productivity. A major challenge when learning from programs is how to represent programs in a way that facilitates effective learning. We present a general path-based representation for learning from programs. Our representation is purely syntactic and extracted automatically. The main idea is to represent a program using paths in its abstract syntax tree (AST). This allows a learning model to leverage the structured nature of code rather than treating it as a flat sequence of tokens. We show that this representation is general and can: (i) cover different prediction tasks, (ii) drive different learning algorithms (for both generative and discriminative models), and (iii) work across different programming languages. We evaluate our approach on the tasks of predicting variable names, method names, and full types. We use our representation to drive both CRF-based and word2vec-based learning, for programs of four languages: JavaScript, Java, Python and C#. Our evaluation shows that our approach obtains better results than task-specific handcrafted representations across different tasks and programming languages.
Determinant of successful implementation of Computerized Provider Order Entry (CPOE) system from physicians’ perspective: Feasibility study prior to implementation

Background Health information technology is a solution for medical error reduction through the implementation of Computerized Provider Order Entry (CPOE). Objective The aim of this study was to determine physicians’ attitudes toward the implementation of CPOE. Methods This cross-sectional study was started in March 2017 and completed in June 2017. The study used a questionnaire to collect data from physicians in hospitals affiliated to Urmia University of Medical Sciences. We invited 200 physicians who were not using a CPOE system. Questionnaires were randomly distributed among physicians. In order to understand the physicians’ attitude about implementation the CPOE system, we used the Diffusion of Innovation Theory, developed by E.M. Rogers. Data were analyzed by SPSS version 16.0, using descriptive statistics and one-way ANOVA. A p value <0.05 was considered to be statistically significant. Results Most of the physicians were women (n=54, 60%) and the average age of the physicians was 36.39±8.42 years. About three-quarters of the physicians (76.66%) reported that they found the CPOE system adapted to their specific professional practice. The relative advantage of the CPOE system was estimated to be 42.22% for physicians and the complexity of that was 13.33%. There was no significant relationship between Compatibility, Relative advantages and Complexity with physicians’ experience in HIS use and physicians’ degree of education (p>0.05). Conclusion Since the role of CPOE systems is very important in hospitals in order to reduce medication errors and to improve the quality of care, our results can be used to assist the planning and introduction of CPOE systems.
An Empirical Study of Multi-label Learning Methods for Video Annotation

This paper presents an experimental comparison of different approaches to learning from multi-labeled video data. We compare state-of-the-art multi-label learning methods on the Media mill Challenge dataset. We employ MPEG-7 and SIFT-based global image descriptors independently and in conjunction using variations of the stacking approach for their fusion. We evaluate the results comparing the different classifiers using both MPEG-7 and SIFT-based descriptors and their fusion. A variety of multi-label evaluation measures is used to explore advantages and disadvantages of the examined classifiers. Results give rise to interesting conclusions.
Intersection of endocytic and exocytic systems in Toxoplasma gondii

Host cytosolic proteins are endocytosed by Toxoplasma gondii and degraded in its lysosome‐like compartment, the vacuolar compartment (VAC), but the dynamics and route of endocytic trafficking remain undefined. Conserved endocytic components and plant‐like features suggest T. gondii endocytic trafficking involves transit through early and late endosome‐like compartments (ELCs) and potentially the trans‐Golgi network (TGN) as in plants. However, exocytic trafficking to regulated secretory organelles, micronemes and rhoptries, also proceeds through ELCs and requires classical endocytic components, including a dynamin‐related protein, DrpB. Here, we show that host cytosolic proteins are endocytosed within 7 minutes post‐invasion, trafficked through ELCs en route to the VAC, and degraded within 30 minutes. We could not definitively interpret if ingested protein is trafficked through the TGN. We also found that parasites ingest material from the host cytosol throughout the parasite cell cycle. Ingested host proteins colocalize with immature microneme proteins, proM2AP and proMIC5, in transit to the micronemes, but not with the immature rhoptry protein proRON4, indicating that endocytic trafficking of ingested protein intersects with exocytic trafficking of microneme proteins. Finally, we show that conditional expression of a DrpB dominant negative mutant increases T. gondii ingestion of host‐derived proteins, suggesting that DrpB is not required for parasite endocytosis.