Miracle-dz/UniFAR-FTUs huggingface dataset:
Terminal investment in the gustatory appeal of nuptial food gifts in crickets

Investment in current versus future reproduction represents a prominent trade‐off in life‐history theory and is likely dependent on an individual's life expectancy. The terminal investment hypothesis posits that a reduction in residual reproductive value (i.e. potential for future offspring) will result in increased investment in current reproduction. We tested the hypothesis that male decorated crickets (Gryllodes sigillatus), when cued to their impending mortality, should increase their reproductive effort by altering the composition of their nuptial food gifts (i.e. spermatophylaxes) to increase their gustatory appeal to females. Using a repeated‐measures design, we analysed the amino acid composition of spermatophylaxes derived from males both before and after injection of either a saline control or a solution of heat‐killed bacteria. The latter, although nonpathogenic, represents an immune challenge that may signal an impending survival threat. One principal component explaining amino acid variation in spermatophylaxes, characterized by a high loading to histidine, was significantly lower in immune‐challenged versus control males. The relevance of this difference for the gustatory appeal of gifts to females was assessed by mapping spermatophylax composition onto a fitness surface derived in an earlier study identifying the amino acid composition of spermatophylaxes preferred by females. We found that immune‐challenged males maintained the level of attractiveness of their gifts post‐treatment, whereas control males produced significantly less attractive gifts post‐injection. These results are consistent with the hypothesis that cues of a survival‐threatening infection stimulate terminal investment in male decorated crickets with respect to the gustatory appeal of their nuptial food gifts.
Hydrodynamic and Phase Wetting Criteria to Assess Corrosion Risk in Two-Phase Oil-Water Pipe Flow

Two-phase oil-water flow is commonly found in the oil industry. The occurrence of water can lead to internal corrosion of the metallic pipes besides other possible degradation phenomena such as environmentally assisted cracking. When water phase is fully entrained into the oil phase, internal corrosion of carbon steel is not likely to occur. Full entrainment of water into oil depends on operating flow conditions, physicochemical properties of both fluids and phase wetting characteristics for the pipe material used. This paper presents a set of hydrodynamic and phase wetting criteria to assess if free water will be in contact with internal pipe walls; and thus, to primarily determine corrosion risk. Experimental data of oil-water pipe flows is shown and compared with theoretical calculations.
Two-Way Shape Memory Behavior of Electrospun Non-Woven Mats Prepared from Sol-Gel Crosslinked Poly(ε-Caprolactone)

Non-woven fibrous mats based on semicrystalline networks were prepared starting from poly(ε-caprolactone) and by combining electrospinning process and sol-gel crosslinking reaction. The mats were subjected to proper thermo-mechanical cycles to investigate their two-way shape memory capabilities (i.e. the possibility to change between two distinguished shapes upon heating and cooling), and an improvement of the two-way behaviour was researched through the application of a training cycle. An ex-situ SEM analysis described the microstructural evolution accompanying the two-way shape memory cyclic response.
cerebroViz: an R package for anatomical visualization of spatiotemporal brain data

Summary: Spatiotemporal transcriptomic profiling has provided valuable insight into the patterning of gene expression throughout the human brain from early fetal development to adulthood. When combined with prior knowledge of a disease's age at onset and region‐specificity, these expression profiles have provided the necessary context to both strengthen putative gene‐disease associations and infer new associations. While a wealth of spatiotemporal expression data exists, there are currently no tools available to visualize this data within the anatomical context of the brain, thus limiting the intuitive interpretation of many such findings. We present cerebroViz, an R package to map spatiotemporal brain data to vector graphic diagrams of the human brain. Our tool allows rapid generation of publication‐quality figures that highlight spatiotemporal trends in the input data, while striking a balance between usability and customization. cerebroViz is generalizable to any data quantifiable at a brain‐regional resolution and currently supports visualization of up to thirty regions of the brain found in databases such as BrainSpan, GTEx and Roadmap Epigenomics. Availability and Implementation: cerebroViz is freely available through GitHub (https://github.com/ethanbahl/cerebroViz). The tutorial is available at http://ethanbahl.github. io/cerebroViz/ Contacts: ethan‐bahl@uiowa.edu or jacob‐michaelson@uiowa.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Succinct Colored de Bruijn Graphs

Iqbal et al. (Nature Genetics, 2012) introduced the colored de Bruijn graph, a variant of the classic de Bruijn graph, which is aimed at “detecting and genotyping simple and complex genetic variants in an individual or population”. Because they are intended to be applied to massive population level data, it is essential that the graphs be represented efficiently. Unfortunately, current succinct de Bruijn graph representations are not directly applicable to the colored de Bruijn graph, which require additional information to be succinctly encoded as well as support for non-standard traversal operations. Our data structure dramatically reduces the amount of memory required to store and use the colored de Bruijn graph, with some penalty to runtime, allowing it to be applied in much larger and more ambitious sequence projects than was previously possible.
M2+ Doping Induced Simultaneous Phase/Size Control and Remarkable Enhanced Upconversion Luminescence of NaLnF4 Probes for Optical‐Guided Tiny Tumor Diagnosis

Doping has played a vital role in constructing desirable hybrid materials with tunable functions and properties via incorporating atoms into host matrix. Herein, a simple strategy for simultaneously modifying the phase, size, and upconversion luminescence (UCL) properties of the NaLnF4 (Ln = Y, Yb) nanocrystals by high‐temperature coprecipitation through nonequivalent M2+ doping (M = Mg2+, Co2+) has been demonstrated. The phase transformation from cubic to hexagonal is readily achieved by doping M2+. Compared with Mg‐free sample, a remarkable enhancement of overall UCL (≈27.5 times) is obtained by doping Mg2+. Interestingly, owing to the efficient UCL, red UCL‐guided tiny tumor (down to 3 mm) diagnosis is demonstrated for the first time. The results open up a new way of designing high efficient UCL probe with combination of hexagonal phase and small size for tiny tumor detection.
Quality Change of Pork Patty Containing Lotus (Nelumbo nucifera) Leaf and Root Powder during Refrigerated Storage

This study was carried out to investigate the effect of lotus root and leaf powder on the quality characteristics of pork patty stored at 3℃ for 9 days. The pork patties were of four types: nothing added(control, T0), 0.5% lotus root powder added (T1), 0.25% lotus root and 0.25% lotus leaf powder added (T2), and 0.5% lotus leaf powder added (T3). The a * value tended to decrease with longer storage period (p＜0.05). The L * and a * value of T3 had the lowest value among the samples, the b * value T2 and T3 were higher than those of T0 and T1 (p＜0.05). Water holding capacity decreased with longer storage period (p＜0.05), the water holding capacity, cooking loss, increase rate of thickness and decrease rate of diameter were not significantly different among the samples. Hardness and chewiness increased and springiness decreased with longer storage period (p＜0.05). The pH creased with longer storage period (p＜0.05), but the VBN content not changed during storage. The TBARS values increased with longer storage period (p＜0.05), and those of T0, T1, T2 and T3 were 4.57, 1.85, 0.43 and 0.41 ㎎ MA/㎏, respectively, after 9 days of the storage. The result suggest that the addition of lotus root and leaf powder at the same time, or addition of lotus leaf powder can be applied to pork patty to its functionality.
mORCA: sailing bioinformatics world with mobile devices

Motivation Nearly 10 years have passed since the first mobile apps appeared. Given the fact that bioinformatics is a web‐based world and that mobile devices are endowed with web‐browsers, it seemed natural that bioinformatics would transit from personal computers to mobile devices but nothing could be further from the truth. The transition demands new paradigms, designs and novel implementations. Results Throughout an in‐depth analysis of requirements of existing bioinformatics applications we designed and deployed an easy‐to‐use web‐based lightweight mobile client. Such client is able to browse, select, compose automatically interface parameters, invoke services and monitor the execution of Web Services using the service's metadata stored in catalogs or repositories. Availability and implementation mORCA is available at http://bitlab‐es.com/morca/app as a web‐app. It is also available in the App store by Apple and Play Store by Google. The software will be available for at least 2 years. Contact ortrelles@uma.es Supplementary information Source code, final web‐app, training material and documentation is available at http://bitlab‐es.com/morca
BlazeIt : An OptimizingQuery Engine for Video at Scale Extended Abstract

Recent advances in deep learning allow us to query the increasing volumes of video data for semantic information. However, these techniques are difficult to deploy in practice and are incredibly computationally expensive. To address these limitations, we propose BlazeIt, a system with a query language and optimizer to accelerate complex queries over video. We demonstrate that BlazeIt can answer a wide range of queries and give significant speed improvements, up to 16×.
Microbial Dark Matter Investigations: How Microbial Studies Transform Biological Knowledge and Empirically Sketch a Logic of Scientific Discovery

Abstract Microbes are the oldest and most widespread, phylogenetically and metabolically diverse life forms on Earth. However, they have been discovered only 334 years ago, and their diversity started to become seriously investigated even later. For these reasons, microbial studies that unveil novel microbial lineages and processes affecting or involving microbes deeply (and repeatedly) transform knowledge in biology. Considering the quantitative prevalence of taxonomically and functionally unassigned sequences in environmental genomics data sets, and that of uncultured microbes on the planet, we propose that unraveling the microbial dark matter should be identified as a central priority for biologists. Based on former empirical findings of microbial studies, we sketch a logic of discovery with the potential to further highlight the microbial unknowns.
Vector Similarity Measures of Simplified Neutrosophic Sets and Their Application in Multicriteria Decision Making

Neutrosophic set is a powerful general formal framework, which generalizes the concept of the classic set, fuzzy set, interval valued fuzzy set, intuitionistic fuzzy set, and interval-valued intuitionistic fuzzy set from philosophical point of view. However, it will be difficult to apply in real science and engineering areas, while a simplified neutrosophic set (SNS) is a subclass of a neutrosophic set and includes the concepts of a single valued neutrosophic set (SVNS) and an interval neutrosophic set (INS), which can be used in real science and engineering applications with the incomplete, indeterminate and inconsistent information which exists commonly in real situations. Therefore, the main purposes of the paper are to present three vector similarity measures between SNSs as a generalization of the Jaccard, Dice, and cosine similarity measures in vector space and to apply them to the multicriteria decision-making problem with simplified neutrosophic information. Through the similarity measure between each alternative and the ideal alternative, the ranking order of all alternatives can be determined and the best alternative can be easily selected as well. Finally, an illustrative example demonstrates the application of the proposed measure methods in the simplified neutrosophic multicriteria decision making.
Read stability and read failure analysis of low voltage Schmitt- Trigger based SRAM bitcell

We analyze Schmitt-Trigger (ST) based differential sensing static random access memory (SRAM) bitcells for ultralow voltage operation. The ST-based SRAM bitcells address the fundamental conflicting design requirement of the read versus write operation of a conventional 6T bitcell. The ST operation gives better read- stability as well as better read-failure probability compared to the standard 6T bitcell. The proposed ST based bitcells incorporate a built-in feedback mechanism. Balancing the trade-offs between small areas, low powers, fast reads/writes are an essential part of any SRAM design. That is, SRAM design requires balancing among various design criteria such as minimizing cell area using smaller transistor, maintaining read/write stability, minimizing power consumption by reducing power supply, minimizing read/write access time, minimizing leakage current, reducing bit-line swing to reduce power consumption. A detailed comparison of 6T bitcell shows that the ST based bitcell can operate at lower supply voltages. Measurement results in 130-nm CMOS technology show that the proposed ST based bitcell gives 1.6 higher read static noise margin and 180mV lower read Vmin compared to the 6T bitcell.
Avian-Type Receptor-Binding Ability Can Increase Influenza Virus Pathogenicity in Macaques

ABSTRACT The first influenza pandemic of the 21st century was caused by novel H1N1 viruses that emerged in early 2009. An Asp-to-Gly change at position 222 of the receptor-binding protein hemagglutinin (HA) correlates with more-severe infections in humans. The amino acid at position 222 of HA contributes to receptor-binding specificity with Asp (typically found in human influenza viruses) and Gly (typically found in avian and classic H1N1 swine influenza viruses), conferring binding to human- and avian-type receptors, respectively. Here, we asked whether binding to avian-type receptors enhances influenza virus pathogenicity. We tested two 2009 pandemic H1N1 viruses possessing HA-222G (isolated from severe cases) and two viruses that possessed HA-222D. In glycan arrays, viruses possessing HA-222D preferentially bound to human-type receptors, while those encoding HA-222G bound to both avian- and human-type receptors. This difference in receptor binding correlated with efficient infection of viruses possessing HA-222G, compared to those possessing HA-222D, in human lung tissue, including alveolar type II pneumocytes, which express avian-type receptors. In a nonhuman primate model, infection with one of the viruses possessing HA-222G caused lung damage more severe than did infection with a virus encoding HA-222D, although these pathological differences were not observed for the other virus pair with either HA-222G or HA-222D. These data demonstrate that the acquisition of avian-type receptor-binding specificity may result in more-efficient infection of human alveolar type II pneumocytes and thus more-severe lung damage. Collectively, these findings suggest a new mechanism by which influenza viruses may become more pathogenic in mammals, including humans.
Analysis and implementation of a power management unit with a multiratio switched capacitor DC–DC converter for a supercapacitor power supply

An energy‐harvesting system requires an energy‐storing device to store the energy retrieved from the surrounding environment. Rechargeable batteries are commonly used to store this energy; however, because of the limited number of charge/discharge cycles, they need to be periodically replaced. A supercapacitor, which has, ideally, a limitless number of charge/discharge cycles, avoids this problem. In this case, it is required for the power management unit to produce a constant output voltage as the supercapacitor discharges. This paper presents a system with a multiratio switched capacitor DC–DC converter, in a 130‐nm technology, with a maximum output power of 2 mW, a maximum efficiency of 79.63% and a maximum output ripple, in the steady state, of 23 mV for an input voltage range of 2.3–0.87 V. The proposed converter has four operation states, to maximize its efficiency, that correspond to the conversion ratios of 1/2, 2/3, 1/1 and 3/2. Its clock frequency is automatically adjusted to produce a stable output voltage of 1 V. These features are implemented through two distinct controller circuits that use two asynchronous time machines to dynamically adjust the clock frequency and to select the active state of the converter. All the theoretical expressions as well as the behaviour of the whole system were verified by using electrical simulations. Copyright © 2016 John Wiley & Sons, Ltd.
Predictive value of CHA2DS2-VASc and CHA2DS2-VASc-HS scores for failed reperfusion after thrombolytic therapy in patients with ST-segment elevation myocardial infarction

Background Thrombolytic therapy is recommended for patients with acute ST-segment elevation myocardial infarction (STEMI) who cannot undergo primary percutaneous coronary intervention within the first 120 min. The aim of this study was to demonstrate the value of CHA2DS2-VASc and CHA2DS2-VASc-HS scores in predicting failed reperfusion in STEMI patients treated with thrombolytic therapy. Methods A total of 537 consecutive patients were enrolled in the study; 139 had failed thrombolysis while the remaining 398 fulfilled the criteria for successful thrombolysis. Thrombolysis failure was defined with the lack of symptom relief, < 50% ST resolution-related electrocardiography within 90 min from initiation of the thrombolytic therapy, presence of hemodynamic or electrical instability or in-hospital mortality. CHA2DS2-VASc and CHA2DS2-VASc-HS scores, which incorporate hyperlipidemia, smoking, switches between female and male gender, were previously shown to be markers of the severity of coronary artery disease (CAD). Results History of hypertension, diabetes mellitus, hyperlipidemia, heart failure, smoking, and CAD were significantly common in failed reperfusion patients (for all; p < 0.05). For prediction of failed reperfusion, the cut-off value of CHA2DS2-VASc score was ≥ 2 with a sensitivity of 80.90% and a specificity of 41.01% (area under curve [AUC] 0.660; 95% confidence interval [CI] 0.618–0.700; p < 0.001) and the cut-off value of CHA2DS2-VASc-HS score was ≥ 3 with a sensitivity of 76.13% and a specificity of 67.63% (AUC 0.764; 95% CI 0.725–0.799; p < 0.001). The CHA2DS2-VASc-HS score was found to be statistically and significantly better than CHA2DS2-VASc score to predict failed reperfusion (p < 0.001). Conclusions The findings suggest that the CHA2DS2-VASc and especially CHA2DS2-VASc-HS scores could be considered as predictors of risk of failed reperfusion in STEMI patients.
Community-Based Peer-Led Diabetes Self-management

Purpose The purpose of this study is to determine the effectiveness of a community-based diabetes self-management program comparing treatment participants to a randomized usual-care control group at 6 months. Methods A total of 345 adults with type 2 diabetes but no criteria for high A1C were randomized to a usual-care control group or 6-week community-based, peer-led diabetes self-management program (DSMP). Randomized participants were compared at 6 months. The DSMP intervention participants were followed for an additional 6 months (12 months total). A1C and body mass index were measured at baseline, 6 months, and 12 months. All other data were collected by self-administered questionnaires. Results At 6 months, DSMP participants did not demonstrate improvements in A1C as compared with controls. Baseline A1C was much lower than in similar trials. Participants did have significant improvements in depression, symptoms of hypoglycemia, communication with physicians, healthy eating, and reading food labels (P < .01). They also had significant improvements in patient activation and self-efficacy. At 12 months, DSMP intervention participants continued to demonstrate improvements in depression, communication with physicians, healthy eating, patient activation, and self-efficacy (P < .01). There were no significant changes in utilization measures. Conclusions These findings suggest that people with diabetes without elevated A1C can benefit from a community-based, peer-led diabetes program. Given the large number of people with diabetes and lack of low-cost diabetes education, the DSMP deserves consideration for implementation.
Stomatal cell wall composition: distinctive structural patterns associated with different phylogenetic groups

Background and Aims Stomatal morphology and function have remained largely conserved throughout ∼400 million years of plant evolution. However, plant cell wall composition has evolved and changed. Here stomatal cell wall composition was investigated in different vascular plant groups in attempt to understand their possible effect on stomatal function. Methods A renewed look at stomatal cell walls was attempted utilizing digitalized polar microscopy, confocal microscopy, histology and a numerical finite-elements simulation. The six species of vascular plants chosen for this study cover a broad structural, ecophysiological and evolutionary spectrum: ferns (Asplenium nidus and Platycerium bifurcatum) and angiosperms (Arabidopsis thaliana and Commelina erecta) with kidney-shaped stomata, and grasses (angiosperms, family Poaceae) with dumbbell-shaped stomata (Sorghum bicolor and Triticum aestivum). Key Results Three distinct patterns of cellulose crystallinity in stomatal cell walls were observed: Type I (kidney-shaped stomata, ferns), Type II (kidney-shaped stomata, angiosperms) and Type III (dumbbell-shaped stomata, grasses). The different stomatal cell wall attributes investigated (cellulose crystallinity, pectins, lignin, phenolics) exhibited taxon-specific patterns, with reciprocal substitution of structural elements in the end-walls of kidney-shaped stomata. According to a numerical bio-mechanical model, the end walls of kidney-shaped stomata develop the highest stresses during opening. Conclusions The data presented demonstrate for the first time the existence of distinct spatial patterns of varying cellulose crystallinity in guard cell walls. It is also highly intriguing that in angiosperms crystalline cellulose appears to have replaced lignin that occurs in the stomatal end-walls of ferns serving a similar wall strengthening function. Such taxon-specific spatial patterns of cell wall components could imply different biomechanical functions, which in turn could be a consequence of differences in environmental selection along the course of plant evolution.