Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional and Phylogenetic Analyses of Phenoloxidases from Brachyuran (Cancer magister) and Branchiopod (Artemia franciscana, Triops longicaudatus) Crustaceans

Arthropod phenoloxidases catalyze the melanization and sclerotization of the new postmolt exoskeleton, and they function in the immune response. Hemocyanin, phylogenetically related to phenoloxidase, can function as a phenoloxidase under certain conditions. We investigated the relative contributions of hemocyte phenoloxidase and hemocyanin in the brachyuran crab Cancer magister, using the physiological ratio at which they occur in the hemolymph, and found that hemocyte phenoloxidase has higher activity. They both convert diphenols to o-quinones, but only the hemocyte phenoloxidase is able to catalyze the conversion of monophenols to diphenols. The quaternary structure of hemocyanin affects its reactivity as phenoloxidase. We suggest that prophenoloxidase is released from hemocytes and moves across epidermis into new exoskeleton during premolt and is activated in early postmolt. In addition to functional studies, we have determined the complete cDNA sequence of C. magister hemocyte prophenoloxidase and partial sequences from the branchiopods Artemia franciscana and Triops longicaudatus. We also sequenced C. magister cryptocyanin 2 and a hemocyanin from the amphipod Cyamus scammoni and used these and other members of the arthropod hemocyanin superfamily for phylogenetic analyses. The phylogenies presented here are consistent with the possibility that a common ancestral molecule had both phenoloxidase and reversible oxygen-binding capabilities.
Uroguanylin Action in the Brain Reduces Weight Gain in Obese Mice via Different Efferent Autonomic Pathways

The gut-brain axis is of great importance in the control of energy homeostasis. The identification of uroguanylin (UGN), a peptide released in the intestines that is regulated by nutritional status and anorectic actions, as the endogenous ligand for the guanylyl cyclase 2C receptor has revealed a new system in the regulation of energy balance. We show that chronic central infusion of UGN reduces weight gain and adiposity in diet-induced obese mice. These effects were independent of food intake and involved specific efferent autonomic pathways. On one hand, brain UGN induces brown adipose tissue thermogenesis, as well as browning and lipid mobilization in white adipose tissue through stimulation of the sympathetic nervous system. On the other hand, brain UGN augments fecal output through the vagus nerve. These findings are of relevance as they suggest that the beneficial metabolic actions of UGN through the sympathetic nervous system do not involve nondesirable gastrointestinal adverse effects, such as diarrhea. The present work provides mechanistic insights into how UGN influences energy homeostasis and suggests that UGN action in the brain represents a feasible pharmacological target in the treatment of obesity.
A Mutual Nonrepudiation Protocol for Cloud Storage with Interchangeable Accesses of a Single Account from Multiple Devices

Obtaining mutual nonrepudiation between the user and service provider is crucial in cloud storage. One of the solutions for mutual nonrepudiation is based on logging attestations, which are signed messages. For every request, clients and service provider exchange attestations. These attestations will be used in an auditing protocol to verify their behavior. The chain-hashing scheme chains attestations and stores them in service provider for supporting write serializability and read freshness of files. However, the chain-hashing scheme is inefficient when files in an account can be accessed by multiple client devices interchangeably. In this paper we first show that the chain-hashing scheme cannot resist roll-back attack from service provider unless client devices keep all the attestations or there exists a way to broadcast the last attestation to all the client devices. We propose a scheme that can guarantee mutual nonrepudiation between the user and service provider without requiring the client devices to exchange any messages, and each client device only has to store the last attestation it received. We also propose how to apply the hash tree to remove accumulated attestations. The results from related experiments demonstrate the feasibility of the proposed scheme. A service provider of cloud storage can use the proposed scheme to provide a mutual nonrepudiation guarantee in their service-level agreement.
High-field fMRI unveils orientation columns in humans

Functional (f)MRI has revolutionized the field of human brain research. fMRI can noninvasively map the spatial architecture of brain function via localized increases in blood flow after sensory or cognitive stimulation. Recent advances in fMRI have led to enhanced sensitivity and spatial accuracy of the measured signals, indicating the possibility of detecting small neuronal ensembles that constitute fundamental computational units in the brain, such as cortical columns. Orientation columns in visual cortex are perhaps the best known example of such a functional organization in the brain. They cannot be discerned via anatomical characteristics, as with ocular dominance columns. Instead, the elucidation of their organization requires functional imaging methods. However, because of insufficient sensitivity, spatial accuracy, and image resolution of the available mapping techniques, thus far, they have not been detected in humans. Here, we demonstrate, by using high-field (7-T) fMRI, the existence and spatial features of orientation- selective columns in humans. Striking similarities were found with the known spatial features of these columns in monkeys. In addition, we found that a larger number of orientation columns are devoted to processing orientations around 90° (vertical stimuli with horizontal motion), whereas relatively similar fMRI signal changes were observed across any given active column. With the current proliferation of high-field MRI systems and constant evolution of fMRI techniques, this study heralds the exciting prospect of exploring unmapped and/or unknown columnar level functional organizations in the human brain.
Matrix-embedded endothelial cells are protected from the uremic milieu.

BACKGROUND Endothelial cells (ECs) embedded in 3D matrices [matrix-embedded endothelial cells (MEECs)] of denatured collagen implanted around vascular access anastomoses preserve luminal patency. MEEC implant efficacy depends on embedded EC health. As the uremic milieu inhibits proliferation and induces apoptosis of ECs, we examined whether uremia might impact MEECs. METHODS ECs grown on 2D gelatin-coated polystyrene tissue culture plates (gTCPS) or in MEEC were treated with sera pooled from 20 healthy control or uremic patients with end-stage renal disease. EC viability was examined using 3-(4,5-dimethylthiazole-2-yl)-2,5-diphenyl tetrazolium bromide assay, cell counting and Trypan blue exclusion. Media conditioned (CM) with 2 and 3D-supported ECs were examined for its potential to inhibit vascular smooth muscle cell (vSMC) proliferation using (3)[H] thymidine incorporation and cyclin D1 expression. ECs grown on gTCPS were treated with uremic serum filtered through matrices to examine if matrices retain uremic toxins or whether EC effects were cell mediated. RESULTS Uremic serum significantly reduced viability and number of live, and increased dead ECs when grown on gTCPS, but not in MEECs. EC survival correlated with vSMC inhibition. While CM from ECs grown in gTCPS with uremic serum inhibited vSMC proliferation no better than uremic serum alone (22 versus 27%), MEEC CM inhibited vSMC proliferation by 47% (P = 0.0004). Cyclin D1 expression tracked with indices of vSMC proliferation. There was no significant difference in EC viability between EC treated with matrix-filtered or unfiltered uremic serum. CONCLUSION The viability, number and efficacy of MEECs were preserved in uremic serum compared to those of ECs on gTCPS. MEECs are protected from uremic toxicity, not from retention of uremic toxins by matrices, but likely from intrinsic changes in EC sensitivity to uremia. MEECs implanted at vascular access sites should inhibit neointimal hyperplasia in uremia. This study underscores the robustness of matrix embedding as a cell protectant, especially in hostile environments like uremia.
Low incidence of infectious complications after nonmyeloablative compared with myeloablative allogeneic stem cell transplantation

Abstract: Allogeneic stem cell transplantation (SCT) using a myeloablative (MA) conditioning regimen is limited to relatively young patients because of increased transplant‐related mortality in elderly patients. Nonmyeloablative (NMA) conditioning regimens have been developed aiming to reduce transplant mortality. In this study, we set out to evaluate the post‐transplant occurrence of infectious complications in recipients of grafts from human leukocyte antigen (HLA)‐identical sibling donors treated with either NMA or MA conditioning regimens. Data of 78 consecutively treated patients were analyzed. An NMA conditioning regimen was used in 40 patients and an MA regimen in 38 patients. A significantly lower rate of episodes of febrile neutropenia (0% vs. 34%, P<0.01) and post‐transplant Epstein–Barr virus reactivations (0% vs. 18%, P<0.05) was found in SCT recipients treated with an NMA conditioning regimen compared with an MA conditioning regimen. Furthermore, fewer invasive fungal infections (2% vs. 12%, not significant) were diagnosed in the NMA group. The incidence of cytomegalovirus (CMV) reactivations and bacterial infections was low in both groups (CMV reactivations: 13% in both groups; bacterial infections: 10% in the NMA group vs. 8% in the MA group), while CMV disease developed in only 1 patient. Overall, compared to our MA regimen, we found a very low rate of infectious complications after NMA SCT.
Chloroquine, an Endocytosis Blocking Agent, Inhibits Zika Virus Infection in Different Cell Models

Zika virus (ZIKV) infection in utero might lead to microcephaly and other congenital defects. Since no specific therapy is available thus far, there is an urgent need for the discovery of agents capable of inhibiting its viral replication and deleterious effects. Chloroquine is widely used as an antimalarial drug, anti-inflammatory agent, and it also shows antiviral activity against several viruses. Here we show that chloroquine exhibits antiviral activity against ZIKV in Vero cells, human brain microvascular endothelial cells, human neural stem cells, and mouse neurospheres. We demonstrate that chloroquine reduces the number of ZIKV-infected cells in vitro, and inhibits virus production and cell death promoted by ZIKV infection without cytotoxic effects. In addition, chloroquine treatment partially reveres morphological changes induced by ZIKV infection in mouse neurospheres.
A Forest Planning Approach with Respect to the Creation of Overmature Reserved Areas in Managed Forests

Abstract: Forest harvest planning to maximize economic benefits also has to consider additional criteria such as the biodiversity functioning of the managed forest. The biodiversity requirements are determined by the size, shapeand distribution of harvest units and forest , stands. A multiple criteria approach is presented where the harvesting volume is maximized while the environmental aspects are also considered. Multiple criteria programming and integer programming techniques are used to find an optimal program of forest harvesting with respect to both economic and environmental requirements. The practicality of the model is shown in a case study for one particular forest management unit. Different optimal solutions are calculated depending on changes made to the criteria weights. This model includes strict spatial constraints, multiple o bjective functions with three objectives , and alternative solutions according to the real manager’s priority. The results show that the spatial pattern and other spatial demands affect the harvest possibilities. It was confirmed that a compromise solution from both forest management and nature conservation could be achieved using the presented harvest scheduling approach.
Viral factors in influenza pandemic risk assessment

The threat of an influenza A virus pandemic stems from continual virus spillovers from reservoir species, a tiny fraction of which spark sustained transmission in humans. To date, no pandemic emergence of a new influenza strain has been preceded by detection of a closely related precursor in an animal or human. Nonetheless, influenza surveillance efforts are expanding, prompting a need for tools to assess the pandemic risk posed by a detected virus. The goal would be to use genetic sequence and/or biological assays of viral traits to identify those non-human influenza viruses with the greatest risk of evolving into pandemic threats, and/or to understand drivers of such evolution, to prioritize pandemic prevention or response measures. We describe such efforts, identify progress and ongoing challenges, and discuss three specific traits of influenza viruses (hemagglutinin receptor binding specificity, hemagglutinin pH of activation, and polymerase complex efficiency) that contribute to pandemic risk. DOI: http://dx.doi. org/10.7554/eLife.18491. 001
The benefits of using multi-objectivization for mining pittsburgh partial classification rules in imbalanced and discrete data

A large number of rule interestingness measures have been used as objectives in multi-objective classification rule mining algorithms. Aggregation or Pareto dominance are commonly used to deal with these multiple objectives. This paper compares these approaches on a partial classification problem over discrete and imbalanced data. After performing a Principal Component Analysis (PCA) to select candidate objectives and find conflictive ones, the two approaches are evaluated. The Pareto dominance-based approach is implemented as a dominance-based local search (DMLS) algorithm using confidence and sensitivity as objectives, while the other is implemented as a single-objective hill climbing using F-Measure as an objective, which combines confidence and sensitivity. Results shows that the dominance-based approach obtains statistically better results than the single-objective approach.
Versatile structural disambiguation for semantic-aware applications

In this paper, we propose a versatile disambiguation approach which can be used to make explicit the meaning of structure based information such as XML schemas, XML document structures, web directories, and ontologies. It can be of support to the semantic-awareness of a wide range of applications, from schema matching and query rewriting to peer data management systems, from XML data clustering to ontology-based automatic annotation of web pages and query expansion. The effectiveness of the achieved results has been experimentally proved and is founded both on a flexible exploitation of the structure context, whose extraction can be tailored on the specific application needs, and of the information provided by commonly available thesauri such as WordNet.
Dynamic Moisture Vapor Transfer through Textiles

Cotton, polyester, and a blend in plain woven, pure finish fabrics were studied to determine their influence on dynamic surface wetness and moisture transfer through textiles. A simulated sweating skin was used, over which were placed test fabrics incorporating a clothing hygrometer to continuously measure dynamic surface wetness. Moisture vapor concentration and its rate of change at both inner and outer fabric surfaces was determined. At the inner fabric surface facing the sweating skin, all-cotton fabric exhibited the slowest buildup of moisture vapor concentration, followed by the cotton/polyester blend. The all-polyester fabric showed the highest rate of change in moisture vapor concentration. These dynamic moisture changes differ from reports of little or no fiber effect when tested at equilibrium moisture transfer conditions. Indeed the equilibrium moisture vapor transfer also showed no significant fiber differences in this work. It is the short time, dynamic moisture vapor transfer that is believed to hold most promise for explaining wetness and moisture-related subjective sensations in human comfort of worn clothing. The newly modified clothing hygrometer provides a sensitive method for ascertaining dynamic surface wetness on both fabrics and clothing as worn.
Guidelines based on validity criteria for the development of multiple choice items.

BACKGROUND Many different guidelines have been presented for the construction of multiple choice items. Those guidelines have been based on the observation of errors when constructing items but not on any clear scientific criterion. Our main objective was to draw up guidelines for the development of multiple choice items based on validity criteria. METHOD We used the properties of adjustment, precision, and differentiation, applying them to three basic phases of instrument construction: the definition of the objective and its context; their expression in the instrument and item stem; and the elaboration of response options. RESULTS We have combined these properties and phases to give nine general guidelines with a firm theoretical footing. CONCLUSIONS Finally, we have written a checklist with twenty-four points to check how far the measurement instruments comply with the proposed guidelines.
The species, sex, and stage specificity of a Caenorhabditis sex pheromone

Four species in the ELEGANS group of subgenus the Caenorhabditis are distinguished by two very different mating systems: androdioecy in C. elegans and Caenorhabditis briggsae with males and self-fertilizing hermaphrodites and dioecy in Caenorhabditis remanei and Caenorhabditis sp. strain CB5161 with males and females. Using chemotaxis assays, we demonstrate that females secrete a potent sex pheromone that attracts males from a distance, whereas hermaphrodites do not. The female sex pheromone is not species-specific, with males of all four species attracted to both the C. remanei and Caenorhabditis sp. female sex pheromones. The pheromone is, however, sex-specific, with only females secreting the pheromone and attracting only males. Furthermore, the sex pheromone is stage-specific, with female secretion and male detection of the pheromone beginning near adulthood. Females lose their attractiveness immediately after mating but regain it several hours after mating ceases. Finally, the female somatic gonad is required for sex-pheromone production, and the male-specific cephalic neurons (CEM) are required for male response.
Evaluation of subgrid-scale models in terms of time correlation

A fitting that is adapted for use between two adjacent frame members that are mechanically isolated from one another. The fitting has two flanged members one fixed to each frame member and a pressurized liquid coolant flow channel with a pair of bellows units on opposite sides of an intermediate ring that is loosely mounted on the outer surface of a spool attached to one member.
Planning with Pattern Databases

Heuristic search planning effectively finds solutions for large planning problems, but since the estimates are either not admissible or too weak, optimal solutions are found in rare cases only. In contrast, heuristic pattern databases are known to significantly improve lower bound estimates for optimally solving challenging single-agent problems like the 24-Puzzle or Rubik’s Cube. This paper studies the effect of pattern databases in the context of deterministic planning. Given a fixed state description based on instantiated predicates, we provide a general abstraction scheme to automatically create admissible domain-independent memory-based heuristics for planning problems, where abstractions are found in factorizing the planning space. We evaluate the impact of pattern database heuristics in A* and hill climbing algorithms for a collection of benchmark domains.
Evaluation of a biphasic medium for blood cultures

A study comparing the recovery of microorganisms from a transiently vented biphasic brain heart infusion medium bottle and a vacuum bottle containing tryptic soy broth demonstrated that growth was initially detected on the slant of the biphasic bottle or on a routine subculture of either broth in nearly 50% of instances. All organisms were isolated equally well in both bottles, with the exception of Staphylococcus aureus, which was isolated significantly more frequently from the biphasic bottle, and anaerobic bacteria, which were isolated significantly more frequently from the tryptic soy broth bottle.
MIB-1 (Ki-67), Estrogen Receptor, Progesterone Receptor, and p53 Expression in Atypical Cells in Uterine Symplastic Leiomyomas

Nine cases of symplastic uterine leiomyomas were chosen from our files using strict criteria. An immunochemical study of the expressions of Ki-67, estrogen receptor, progesterone receptor, and p53 was performed. For each antigen, the percentages of positive atypical (bizarre) cells and nonatypical cells were compared. Both groups had identical and fairly high estrogen receptor and progesterone receptor immunohistochemical profiles and very low levels of p53 expression. The atypical cells had significantly higher percentages of cells expressing Ki-67 compared with nonatypical cells (17±20% vs. 3±3.9%). Therefore, rather than being degenerative in nature, the atypical cells are actively proliferating.
Isolation and Quantification of MicroRNAs from Urinary Exosomes/Microvesicles for Biomarker Discovery

Recent studies indicate that microRNA (miRNA) is contained within exosome. Here we sought to optimize the methodologies for the isolation and quantification of urinary exosomal microRNA as a prelude to biomarker discovery studies. Exosomes were isolated through ultracentrifugation and characterized by immunoelectron microscopy. To determine the RNA was confined inside exosomes, the pellet was treated with RNase before RNA isolation. The minimum urine volume, storage conditions for exosomes and exosomal miRNA was evaluated. The presence of miRNAs in patients with various kidney diseases was validated with real-time PCR. The result shows that miRNAs extracted from the exosomal fraction were resistant to RNase digestion and with high quality confirmed by agarose electrophoresis. 16ml of urine was sufficient for miRNA isolation by absolute quantification with 4.15×105 copies/ul for miR-200c. Exosomes was stable at 4℃ 24h for shipping before stored at -80℃ and was stable in urine when stored at -80°C for 12months. Exosomal miRNA was detectable despite 5 repeat freeze-thaw cycles. The detection of miRNA by quantitative PCR showed high reproducibility (>94% for intra-assay and >76% for inter-assay), high sensitivity (positive call 100% for CKD patients), broad dynamic range (8-log wide) and good linearity for quantification (R2>0.99). miR-29c and miR-200c showed different expression in different types of kidney disease. In summary, the presence of urinary exosomal miRNA was confirmed for patients with a diversity of chronic kidney disease. The conditions of urine collection, storage and miRNA detection determined in this study may be useful for future biomarker discovery efforts.