Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamics of nitric oxide controlled by protein complex in bacterial system

Significance Denitrification, a form of microbial anaerobic respiration where nitrate is sequentially reduced (NO3− → NO2− → NO → N2O → N2) is environmentally, biologically, and chemically interesting, as well as being medically significant. Some pathogenic bacteria, including the major opportunistic pathogen Pseudomonas aeruginosa, can survive in oxygen-limited environments such as biofilms and the lungs of cystic fibrosis patients, owing to denitrification. The current proposal of a complex formation of NO-generating nitrite reductase and NO-decomposing nitric oxide reductase for rapid elimination of NO, a cytotoxic intermediate, in denitrification contributes to further understanding of denitrification and to the design of antimicrobial drugs. This paper also provides an idea of how biological systems control the dynamics of cytotoxic diffusible compounds such as NO in cells. Nitric oxide (NO) plays diverse and significant roles in biological processes despite its cytotoxicity, raising the question of how biological systems control the action of NO to minimize its cytotoxicity in cells. As a great example of such a system, we found a possibility that NO-generating nitrite reductase (NiR) forms a complex with NO-decomposing membrane-integrated NO reductase (NOR) to efficiently capture NO immediately after its production by NiR in anaerobic nitrate respiration called denitrification. The 3.2-Å resolution structure of the complex of one NiR functional homodimer and two NOR molecules provides an idea of how these enzymes interact in cells, while the structure may not reflect the one in cells due to the membrane topology. Subsequent all-atom molecular dynamics (MD) simulations of the enzyme complex model in a membrane and structure-guided mutagenesis suggested that a few interenzyme salt bridges and coulombic interactions of NiR with the membrane could stabilize the complex of one NiR homodimer and one NOR molecule and contribute to rapid NO decomposition in cells. The MD trajectories of the NO diffusion in the NiR:NOR complex with the membrane showed that, as a plausible NO transfer mechanism, NO released from NiR rapidly migrates into the membrane, then binds to NOR. These results help us understand the mechanism of the cellular control of the action of cytotoxic NO.
A Design Approach to Maximize the Efficiency vs. Linearity Trade-Off in Fixed and Modulated Load GaN Power Amplifiers

This paper proposes a design method to minimize the phase distortion (AM/PM) in gallium nitride (GaN) power amplifiers (PAs) without significantly worsening other key features such as efficiency, amplitude distortion, and gain. The design strategy consists in the adoption of a smart two-stage architecture, in which the driver stage is devised to act as a sort of “analogue AM/PM predistorter” for the final one. Accounting for the actual trend in PA solutions, the proposed approach has been fine-tuned to implement a two-way class AB PA and a Doherty PA (DPA) for backhaul radio links. Both circuits, realized on the same 0.25- $\mu \text{m}$ GaN technology and in monolithic form, have fully been characterized with continuous wave and modulated signals. At 7 GHz, the DPA shows 38 dBm of saturated output power and less than 3° of phase distortion with a power-added efficiency (PAE) higher than 41% in 6 dB of power back off. The class AB PA achieves almost the same level of saturated output power and maximum PAE, with an inevitable lower efficiency in back-off operation, whereas the registered AM/PM is lower than 1.5°. Moreover, when tested with modulated signals, at 32 dBm of average output power and without any digital predistortion, the DPA shows a spectral regrowth of around 36 dBc and a PAE of 40%, whereas the class AB PA achieves 40 dBc and 30%, respectively.
Cross-layer design for energy efficient communication in wireless sensor networks

There is a plethora of recent research on high performance wireless communications using a cross-layer approach in that adaptive modulation and coding (AMC) schemes at wireless physical layer are used for combating time varying channel fading and enhance link throughput. However, in a wireless sensor network, transmitting packets over deep fading channel can incur excessive energy consumption due to the usage of stronger forwarding error code (FEC) or more robust modulation mode. To avoid such energy inefficient transmission, a straightforward approach is to temporarily buffer packets when the channel is in deep fading, until the channel quality recovers. Unfortunately, packet buffering may lead to communication latency and buffer overflow, which, in turn, can result in severe degradation in communication performance. Specifically, to improve the buffering approach, we need to address two challenging issues: (1) how long should we buffer the packets? and (2) how to choose the optimum channel transmission threshold above which to transmit the buffered packets? In this paper, by using discrete-time queuing model, we analyze the effects of Rayleigh fading over AMC-based communications in a wireless sensor network. We then analytically derive the packet delivery rate and average delay. Guided by these numerical results, we can determine the most energy-efficient operation modes under different transmission environments. Extensive simulation results have validated the analytical results, and indicates that under these modes, we can achieve as much as 40% reduction in energy dissipation. Copyright © 2008 John Wiley & Sons, Ltd.
Multiple Mating and Family Structure of the Western Tent Caterpillar, Malacosoma californicum pluviale: Impact on Disease Resistance

Background Levels of genetic diversity can strongly influence the dynamics and evolutionary changes of natural populations. Survival and disease resistance have been linked to levels of genetic diversity in eusocial insects, yet these relationships remain untested in gregarious insects where disease transmission can be high and selection for resistance is likely to be strong. Methodology/Principal Findings Here we use 8 microsatellite loci to examine genetic variation in 12 families of western tent caterpillars, Malacosoma californicum pluviale from four different island populations to determine the relationship of genetic variability to survival and disease resistance. In addition these genetic markers were used to elucidate the population structure of western tent caterpillars. Multiple paternity was revealed by microsatellite markers, with the number of sires estimated to range from one to three per family (mean ± SE = 1.92±0.23). Observed heterozygosity (HO) of families was not associated to the resistance of families to a nucleopolyhedrovirus (NPV) (r = 0.161, F1,12 = 0.271, P = 0.614), a major cause of mortality in high-density populations, but was positively associated with larval survival (r = 0.635, F1,10 = 5.412, P = 0.048). Genetic differentiation among the families was high (FST = 0.269, P<0.0001), and families from the same island were as differentiated as were families from other islands. Conclusion/Significance We have been able to describe and characterize 8 microsatellite loci, which demonstrate patterns of variation within and between families of western tent caterpillars. We have discovered an association between larval survival and family-level heterozygosity that may be relevant to the population dynamics of this cyclic forest lepidopteran, and this will be the topic of future work.
Benefits for Plants in Ant-Plant Protective Mutualisms: A Meta-Analysis

Costs and benefits for partners in mutualistic interactions can vary greatly, but surprisingly little is known about the factors that drive this variation across systems. We conducted a meta-analysis of ant-plant protective mutualisms to quantify the effects of ant defenders on plant reproductive output, to evaluate if reproductive effects were predicted from reductions in herbivory and to identify characteristics of the plants, ants and environment that explained variation in ant protection. We also compared our approach with two other recent meta-analyses on ant-plant mutualisms, emphasizing differences in our methodology (using a weighted linear mixed effects model) and our focus on plant reproduction rather than herbivore damage. Based on 59 ant and plant species pairs, ant presence increased plant reproductive output by 49% and reduced herbivory by 62%. The effects on herbivory and reproduction within systems were positively correlated, but the slope of this relationship (0.75) indicated that tolerance to foliar herbivory may be a common plant response to absence of ant guards. Furthermore, the relationship between foliar damage and reproduction varied substantially among systems, suggesting that herbivore damage is not a reliable surrogate for fitness consequences of ant protection. Studies that experimentally excluded ants reported a smaller effect of ant protection on plant reproduction than studies that relied upon natural variation in ant presence, suggesting that study methods can affect results in these systems. Of the ecological variables included in our analysis, only plant life history (i.e., annual or perennial) explained variation in the protective benefit of mutualistic ants: presence of ants benefitted reproduction of perennials significantly more than that of annuals. These results contrast with other quantitative reviews of these relationships that did not include plant life history as an explanatory factor and raise several questions to guide future research on ant-plant protection mutualisms.
Exenatide with Metformin Ameliorated Visceral Adiposity and Insulin Resistance

Background To study the effectiveness of exenatide with metformin and sequential treatment with exenatide and glargine added to metformin and their influence on insulin sensitivity and adipose distribution. Methods 20 newly diagnosed obese type 2 diabetic patients were enrolled, and 2-month washout treatment of metformin, 6-month exenatide treatment, and 6-month glargine treatment were administrated sequentially accompanied with previous metformin. Glucolipid metabolic parameters were compared among groups. Adipose distribution was quantified with computerized tomography according to anatomy, dividing into visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT), adding up to total adipose tissue (TAT). Results The 6-month exenatide treatment dramatically ameliorated the glucose and lipid profile, improved insulin sensitivity, and mainly decreased VAT and also the ratio of VAT/SAT (RVS). The following 6-month glargine treatment increased VAT. The whole 12-month sequential treatment with exenatide and glargine added to metformin basically improved the insulin sensitivity and glucolipid control though VAT rebounded at the end, however without deteriorating the other parameters. Conclusion Exenatide is an ideal treatment for obese type 2 diabetic patients in the aspect of adipose tissue distribution. Sequential treatment of exenatide and glargine could be an alternative for low-income patients who cannot afford GLP-1 agonist for long time. This trial is registered with ChiCTR-OOC-17013679.
Overlapping functional modules detection in PPI network with pair‐wise constrained non‐negative matrix tri‐factorisation

A large amount of available protein–protein interaction (PPI) data has been generated by high‐throughput experimental techniques. Uncovering functional modules from PPI networks will help us better understand the underlying mechanisms of cellular functions. Numerous computational algorithms have been designed to identify functional modules automatically in the past decades. However, most community detection methods (non‐overlapping or overlapping types) are unsupervised models, which cannot incorporate the well‐known protein complexes as a priori. The authors propose a novel semi‐supervised model named pairwise constrains nonnegative matrix tri‐factorisation (PCNMTF), which takes full advantage of the well‐known protein complexes to find overlapping functional modules based on protein module indicator matrix and module correlation matrix simultaneously from PPI networks. PCNMTF determinately models and learns the mixed module memberships of each protein by considering the correlation among modules simultaneously based on the non‐negative matrix tri‐factorisation. The experiment results on both synthetic and real‐world biological networks demonstrate that PCNMTF gains more precise functional modules than that of state‐of‐the‐art methods.
The complete nucleotide sequence of the mitochondrial genome of Drosophila formosana (Diptera: Drosophilidae)

Abstract Drosophila formosana (Diptera: Drosophilidae) belongs to the Drosophilidae group of Drosophila. The mitochondrial genome sequence of Drosophila formosana is determined in this study. Mitochondrion of D. formosana is a circular DNA molecule of the 16 100 nucleotide pairs (bp) that contains one encoding region including 37 genes and 1 non-coding A + T-rich region. The similarity and typicality have been showed by the structure and organization analysis. All genes are arranged in the circular DNA molecule. In addition to DN5 that use GTG start codon, all other protein-coding genes (PCGs) start with an ATN start codon. Ten protein-coding genes stop with the termination codon TAN, while other protein-coding genes (PCGs) used incomplete termination codon TA– (cox2, nad5, nad1). The A + T-rich region with a length of 1088 bp is located between rrnS and trnI. The mitochondrial genome of D. formosana has been completely sequenced for the first time in this study.
Membranal and Blood‐Soluble HLA Class II Peptidome Analyses Using Data‐Dependent and Independent Acquisition

The interaction between HLA class II peptide complexes on antigen‐presenting cells and CD4+ T cells is of fundamental importance for anticancer and antipathogen immunity as well as for the maintenance of immunological tolerance. To study CD4+ T cell reactivities, detailed knowledge of the presented peptides is necessary. In recent years, dramatic advances in the characterization of membranal and soluble HLA class I peptidomes could be observed. However, the same is not true for HLA class II peptidomes, where only few studies identify more than hundred peptides. Here we describe a MS‐based workflow for the characterization of membranal and soluble HLA class II DR and DQ peptidomes. Using this workflow, we identify a total of 8595 and 3727 HLA class II peptides from Maver‐1 and DOHH2 cells, respectively. Based on this data, a motif‐based binding predictor is developed and compared to NetMHCIIpan 3.1. We then apply the workflow to human plasma, resulting in the identification of between 34 and 152 HLA‐DR and between 100 and 180 HLA‐DQ peptides, respectively. Finally, we implement a data‐independent acquisition workflow to increase reproducibility and sensitivity of HLA class II peptidome characterizations.
PI 3 Kp 110 α mediates the oncogenic activity induced by loss of the novel tumor suppressor PI 3 Kp 85 α

Mutation or loss of the p85 regulatory subunit of phosphatidylinositol 3-kinase (PI3K) is emerging as a transforming factor in cancer, but the mechanism of transformation has been controversial. Here we find that hemizygous deletion of the PIK3R1 gene encoding p85α is a frequent event in breast cancer, with PIK3R1 expression significantly reduced in breast tumors. PIK3R1 knockdown transforms human mammary epithelial cells, and genetic ablation of Pik3r1 accelerates a mouse model of HER2/neu-driven breast cancer. We demonstrate that partial loss of p85α increases the amount of p110α–p85 heterodimers bound to active receptors, augmenting PI3K signaling and oncogenic transformation. Pan-PI3K and p110αselective pharmacological inhibition effectively blocks transformation driven by partial p85α loss both in vitro and in vivo. Together, our data suggest that p85α plays a tumor-suppressive role in transformation, and suggest that p110α-selective therapeutics may be effective in the treatment of breast cancer patients with PIK3R1 loss.
Outcomes of early parent‐child adrenocortical attunement in the high‐risk offspring of depressed parents

This study examined the impact of parent-child attunement of morning cortisol on parenting and child outcomes in dyads with and without parental depression. Participants included 142 parent-child dyads (3-5 years-old) who provided morning cortisol samples at Wave 1, and 98 dyads returned for the 3-year follow-up at Wave 2. Results indicated that for parents with a history of depression and for female children, stronger attunement predicted increases in parental hostility from Wave 1 to Wave 2. For females only, stronger attunement was related to children's depressive symptoms at Wave 1 and Wave 2. Stronger attunement was also associated with increases in children's depressive symptoms from Wave 1 to Wave 2, poorer psychosocial functioning at Wave 1, and ADHD symptoms at Wave 2. Findings highlight attunement as an important biological process related to parenting and child outcomes and suggest it may play a role in the intergenerational transmission of depression risk.
Modified Ross-Konno procedure in children: subcoronary implantation technique with Konno incision for annular and subannular hypoplasia.

OBJECTIVES The technique of subcoronary autograft implantation for the Ross procedure has shown excellent durability of aortic valve function in adults. However, its use in children with hypoplastic aortic annulus or multilevel left ventricular outflow tract obstruction (LVOTO) was traditionally precluded. We combined this technique with a Konno incision and evaluated LVOTO relief and durability of the autograft function in growing patients. METHODS Between January 2012 and January 2017, 13 patients with severe LVOTO and hypoplastic aortic annulus underwent Ross-Konno procedure with subcoronary autograft implantation. The median age at operation was 14 months. Six were infants. Concomitant procedures included resection of endocardial fibroelastosis (n = 9), mitral valvuloplasty (n = 2) and aortic arch repair (n = 1). The Konno incision was enlarged with a patch. The autograft was implanted beneath the ostia of the coronary arteries, retaining external support by the native aortic annulus. RESULTS A newborn with hypoplastic left heart complex and Turner syndrome died in hospital: early mortality of 7.7%. No residual LVOTO or autograft regurgitation was observed at discharge. At a median follow-up of 20 months, no death had occurred. No catheter or surgical reintervention on the aortic valve or any LVOT site was needed. All peak pressure gradients across the LVOT were <10 mmHg. No autograft regurgitation was detected. CONCLUSIONS The Ross procedure using subcoronary implantation technique combined with LVOT Konno enlargement is feasible even in patients with multilevel LVOTO and marked size discrepancy between the autograft and native aortic annulus. Longer follow-up is indicated to confirm the expected durability of the autograft function.
Software size measurement with use case point for employee application software at STT-PLN

Employee Application (EA) is a system information for realizing the latest personal data and integrated, provide accurate employee information for planning, development, welfare and control of employees. EA in STT-PLN began to be published since 2013. The software size of the EA STT-PLN will be measured with use case point method. Measurement of the software size of EA STT-PLN will be measured with Use Case Point upon use case diagram for EA STT-PLN as shown in the project has small software size where score Use Case Point (UCP) = 70.34. UCP is another alternative implementation method which can be applied to measure application software size whenever needed to deal with time, money and people.
Contributions to objective and subjective visual quality assessment of 3d models. (Contributions à l'évaluation objective et subjective de la qualité visuelle des modèles 3D)

In computer graphics realm, three-dimensional graphical data, generally represented by triangular meshes, have become commonplace, and are deployed in a variety of application processes (e.g., smoothing, compression, remeshing, simplification, rendering, etc.). However, these processes inevitably introduce artifacts, altering the visual quality of the rendered 3D data. Thus, in order to perceptually drive the processing algorithms, there is an increasing need for efficient and effective subjective and objective visual quality assessments to evaluate and predict the visual artifacts. In this thesis, we first present a comprehensive survey on different sources of artifacts in digital graphics, and current objective and subjective visual quality assessments of the artifacts. Then, we introduce a newly designed subjective quality study based on evaluations of the local visibility of geometric artifacts, in which observers were asked to mark areas of 3D meshes that contain noticeable distortions. The collected perceived distortion maps are used to illustrate several perceptual functionalities of the human visual system (HVS), and serve as ground-truth to evaluate the performances of well-known geometric attributes and metrics for predicting the local visibility of distortions. Our second study aims to evaluate the visual quality of texture mapped 3D model subjectively and objectively. To achieve these goals, we introduced 136 processed models with both geometric and texture distortions, conducted a paired-comparison subjective experiment, and invited 101 subjects to evaluate the visual qualities of the models under two rendering protocols. Driven by the collected subjective opinions, we propose two objective visual quality metrics for textured meshes, relying on the optimal combinations of geometry and texture quality measures. These proposed perceptual metrics outperform their counterparts in term of the correlation with the human judgment.
Productivity-Diversity Relationships in Lake Plankton Communities

One of the most intriguing environmental gradients connected with variation in diversity is ecosystem productivity. The role of diversity in ecosystems is pivotal, because species richness can be both a cause and a consequence of primary production. However, the mechanisms behind the varying productivity-diversity relationships (PDR) remain poorly understood. Moreover, large-scale studies on PDR across taxa are urgently needed. Here, we examined the relationships between resource supply and phyto-, bacterio-, and zooplankton richness in 100 small boreal lakes. We studied the PDR locally within the drainage systems and regionally across the systems. Second, we studied the relationships between resource availability, species richness, biomass and resource ratio (N∶P) in phytoplankton communities using Structural Equation Modeling (SEM) for testing the multivariate hypothesis of PDR. At the local scale, the PDR showed variable patterns ranging from positive linear and unimodal to negative linear relationships for all planktonic groups. At the regional scale, PDRs were significantly linear and positive for phyto- and zooplankton. Phytoplankton richness and the amount of chlorophyll a showed a positive linear relationship indicating that communities consisting of higher number of species were able to produce higher levels of biomass. According to the SEM, phytoplankton biomass was largely related to resource availability, yet there was a pathway via community richness. Finally, we found that species richness at all trophic levels was correlated with several environmental factors, and was also related to richness at the other trophic levels. This study showed that the PDRs in freshwaters show scale-dependency. We also documented that the PDR complies with the multivariate model showing that plant biomass is not mirroring merely the resource availability, but is also influenced by richness. This highlights the need for conserving diversity in order to maintain ecosystem processes in freshwaters.