Miracle-dz/UniFAR-FTUs huggingface dataset:
Seasonal variation in the allometry of wing pigmentation in adult males of the territorial damselfly Hetaerina vulnerata (Insecta Odonata)

Several sexually selected traits exhibit positive allometry. One of the explanations for this pattern suggests that positive allometry should be expected only for “pure” threat male signals, whilst isometry and negative allometry should occur in “pure” courtship signals. Wing pigmentation (WP) is a sexually selected trait exhibited by the males of several damselfly taxa (Odonata Zygoptera), which has been the focus of a number of studies of allometry. Whilst WP tends to exhibit positive allometry in many taxa, the pattern is not general. Previous studies have shown that in Hetaerina vulnerata, a territorial species in which WP is used as a “pure” threat signal, positive allometry is common. However, little attention has been paid to the seasonal variation in the allometry of WP in this species. To address this research gap, we collected data from a full reproductive season, from a natural population of H. vulnerata located in Central Mexico. Our results suggest that, first, male WP and body size generally increase throughout the season. Second, WP increases as the end of the season approaches, independently of body size. Finally, WP tends to be either not related to body size, or to exhibit isometry during the first half of the season (April–June), and positive allometry during the second half of the season (July–October). We suggest that our results may be explained by (i) the availability of resources critical to the development of larvae, as well as the duration of development, and (ii) an increase in the number or larger males towards the end of the season, which may favour the exaggeration of WP. Furthermore, the opportunity for sexual selection may vary, so that WP may be more relevant to male mating success towards the end of the reproductive season.
Problems Encountered with the Selection of Cucumber Mosaic Virus (CMV) Isolates for Resistance Breeding Programs

Among the Chili breeding lines from the Asian Vegetable Research Center, two were chosen for the screening of a larger selection of Cucumber mosaic virus (CMV) isolates, mainly from Asian countries. The chili line (VC246) showed a resistance against several CMV-isolates and was compared with chili line VC27a that was susceptible to CMV infection. Among the 28 CMV isolates, five were identified as resistance breaking (AN-like) and non-resistance breaking (P3613-like) for the line VC246, whereas all isolates could establish a systemic infection on VC27a. However, further testing revealed that resistance in VC246 was also dependent on the way of inoculation and the inoculums itself. Graft inoculation could overcome the resistance, and the inoculation with isolated viral RNA resulted in no infection at all on the resistant chili line, independent of the virus isolate. Using a pseudo-recombinant approach, we identified RNA2 of resistance breaking isolates as responsible for systemic infection and confined the area within RNA2 to the 3′ terminal part including the ORF 2b. Sequence alignments of that area revealed eight distinct mutations on amino acid level, which was present either in resistance or non-resistance breaking isolates. A reversion from the P3613-like to the AN-like sequence of two of these mutations induced no effect on Capsicum sp. , but induced symptoms on several tobacco species distinct from those induced by the wild-type virus. However, pseudorecombinants, each generated from sets of two different AN-like isolates, which were expected to infect VC246 systemically, did not indicating that probably RNA2 must be in a specific context to have the effect. In this case, a generalized attribution of functions to single amino acid exchanges might be impossible or at least extremely difficult.
Aquaporin Expression, Regulation and Function in theIntervertebral Disc

Intervertebral disc degeneration-associated low back pain is a debilitating condition with no current treatments directed towards halting or reversing the degenerative cascade at a cellular level. The lack of such treatments is in part due to an incomplete knowledge of the molecular mechanisms that govern IVD function in health and degeneration. Due to the unique location and role of the IVD within the spine, many factors contribute to the microenvironment that cells reside within. The survival and function of cells has been irrefutably linked to their ability to adapt to the microenvironment in which they live. However, it is not completely understood how IVD cells have been able to survive and adapt to their environment. The intervertebral disc is a highly hydrated tissue; the rich proteoglycan matrix imbibes water, enabling the disc to withstand compressive loads. During ageing and degeneration increased matrix degradation leads to dehydration and loss of function. Aquaporins are a family of transmembrane channel proteins that selectively allow the passage of water in and out of cells and are responsible for maintaining water homeostasis in many tissues; hence many AQPs are potentially expressed by cells within the intervertebral disc to enable their adaptation to this highly hydrated tissue. The aim of this thesis was to investigate the expression, regulation and function of AQP transmembrane water channels within the IVD and how they potentially contribute to the adaptation of cells to their environment. Results have highlighted NP cells express many AQP water channels in vivo, whose expression may be altered between disc development and degeneration. AQP1 and 5 were found to be upregulated by TonEBP in hyperosmotic conditions, a transcription factor controlling osmotic adaptation and matrix expression, which may implicate them in the adaptation of NP cells to their environment, which becomes unachievable when AQP1 and 5 are decreased during degeneration. AQP4 and TRPV4 function in NP cells was required for fundamental cellular processes such as cell volume regulation and water permeability, enabling adaptation to their osmotically fluxing environment. Finally, it was identified that other microenvironmental factors also contribute to AQP expression in NP cells, indicating the regulation and function of these water channels is potentially very complex. Together, investigations presented in this thesis have demonstrated many AQPs are expressed by the intervertebral disc and enable NP cells to respond and adapt to their environment, ultimately contributing to the overall function of the tissue. Their regulation by multiple environmental factors may signify that AQPs have diverse roles within the IVD, which remain to be elucidated. Importantly, this body of work has contributed novel findings, increased knowledge and opened new avenues of research in the field of IVD and spine biology.
Genomic signatures of sex, selection and speciation in the microbial world

Understanding the microbial world is key to understanding global biogeochemistry, human health and disease, yet this world is largely inaccessible. Microbial genomes, an increasingly accessible data source, provide an ideal entry point. The genome sequences of different microbes may be compared using the tools of population genetics to infer important genetic changes allowing them to diversify ecologically and adapt to distinct ecological niches. Yet the toolkit of population genetics was developed largely with sexual eukaryotes in mind. In this work, I assess and develop tools for inferring natural selection in microbial genomes. Many tools rely on population genetics theory, and thus require defining distinct populations, or species, of bacteria. Because sex (recombination) is not required for reproduction, some bacteria recombine only rarely, while others are extremely promiscuous, exchanging genes across great genetic distances. This behavior poses a challenge for defining microbial population boundaries. This thesis begins with a discussion of how recombination and positive selection interact to promote ecological adaptation. I then describe a general pipeline for quantifying the impacts of mutation, recombination and selection on microbial genomes, and apply it to two closely related, yet ecologically distinct populations of Vibrio splendidus, each with its own microhabitat preference. I introduce a new tool, STARRInIGHTS, for inferring homologous recombination events. By assessing rates of recombination within and between ecological populations, I conclude that ecological differentiation is driven by small number of habitat-specific alleles, while most loci are shared freely across habitats. The remainder of the thesis focuses on lineage-specific changes in natural selection among anciently diverged species of gamma proteobacteria. I develop two new metrics, selective signatures and slow:fast, for detecting deviations from the expected rate of evolution in 'core' proteins (present in single copy in most species). Because they rely on empirical distributions of evolutionary rates across species, these methods should become increasingly powerful as more and more microbial genomes are sampled. Overall, the methods described here significantly expand the repertoire of tools available for microbial population genomics, both for investigating the process of ecological differentiation at the finest of time scales, and over billions of years of microbial evolution.
2D Simulation of Crimping ProcessFor Electric Vehicle Battery Charge Cable

Turkey Electric and Hybrid Vehicle Platform (TEHAD), according to 2017 data in our country, the first 9 months 2763 Total electric and hybrid vehicles were sold. Worldwide this figure has been 2 million. While the total number of charging stations in our country (open and not yet used) was 1000 in 2016, it reached 1500by the end of 2017.Additionally, it will start the first domestic electric vehicles and Tesla's sales in 2021 also considering entry into the market when Turkey, its development and growth potential of our country in the field of electric vehicle technology can be clearly seen. There is no dependence on imports due to the fact that there is no domestic company producing charge cable in return for the volume of electric vehicle market in our country. In the case of imported charging cables, due to the overheating and burning problems observed due to the crimp area and plug-socket connection designs, there is a need for domestic technology production on this area due to the flexibility problems in the cable parts. In this study, the design of the domestic Electric Vehicle Charging Cable will be implemented in accordance with IEC 62196-2 standards and different from similar products, in which high performance values can be guaranteed in terms of electrical and physical characteristics. Of utmost importance in appliance design and manufacture are the features for protection from fire and for personal safety. Appliance engineers are continually in pursuit of better, longer-life appliances that will provide both lower cost to the consumer and lower energy consumption. Therefore, a 2D simulation of crimping process has been proposed using COMSOL software. Convective and conducting heat analysis results may help engineers decide the optimal crimping shape and process.
Characteristics and Epidemiology of Extended-Spectrum β-Lactamase-Producing Multidrug-Resistant Klebsiella pneumoniae From Red Kangaroo, China

Due to its drug resistant nature, β-lactamase represents a serious challenge for public health. Extended-spectrum β-lactamase (ESBL) producing Klebsiella pneumoniae clones are increasingly reported worldwide. Little is known about the prevalence and biological characteristics of drug-resistant strains in zoos. During routine surveillance at the Zhengzhou Zoo of China, we found Klebsiella pneumoniae isolate in healthy Red Kangaroos (Macropus Rufus) with severe MDR. The Klebsiella pneumoniae were especially resistant to Cefuroxime Sodium (MIC, > 64 μg/mL), Ceftriaxone (MIC, >8 μg/mL) and Cefepime (MIC, >64 μg/mL), and belonged to ST290. Subsequently, whole genome sequencing (WGS) showed that the Chrome Chr-M297-1 harbored blaDHA–3, blaSHV–1, blaCTX–M–14, fosA5, dfrA3, sul3, etc., and pM297-1.1 [222,864 bp, IncFIB(K)], which carried nine antimicrobial genes including blaCTX–M–14, blaTEM–191, aph(3″)-Ib, aph(6)-Id and qnrS1, etc., and pM297-1.2 [225,763 bp, IncFII(K)] carried 22 antimicrobial genes including blaTEM–1, blaCTX–M–3, aph(3′)-Ia, aac(3)-IIa, aac(6′)-Ib-cr, aadA16, qnrB2, qnrS1, qacEΔ1, mphA, sul1, and dfrA27, etc. A traceability analysis then revealed that these two plasmids were highly similar to those recovered from human clinical samples in some southern cities in Sichuan Province, China (>99%), suggesting that these plasmids are spreading in China. Furthermore, two plasmids harboring conjugal transfer genes facilitated the transmission of antimicrobial genes by conjugation with E. coli J53. Our research shows that the transmission and adaptation of Klebsiella pneumoniae producing ESBLs is occurring in zoo environments, suggesting that zoos may be becoming important potential reservoirs for clinically important drug-resistant genes. It is therefore necessary to monitor the emergence and spread of drug-resistant gene strains in captive wild animals held in zoo environments.
Dominance as a New Trusted Computing Primitive for the Internet of Things

The Internet of Things (IoT) is rapidly emerging as one of the dominant computing paradigms of this decade. Applications range from in-home entertainment to large-scale industrial deployments such as controlling assembly lines and monitoring traffic. While IoT devices are in many respects similar to traditional computers, user expectations and deployment scenarios as well as cost and hardware constraints are sufficiently different to create new security challenges as well as new opportunities. This is especially true for large-scale IoT deployments in which a central entity deploys and controls a large number of IoT devices with minimal human interaction. Like traditional computers, IoT devices are subject to attack and compromise. Large IoT deployments consisting of many nearly identical devices are especially attractive targets. At the same time, recovery from root compromise by conventional means becomes costly and slow, even more so if the devices are dispersed over a large geographical area. In the worst case, technicians have to travel to all devices and manually recover them. Data center solutions such as the Intelligent Platform Management Interface (IPMI) which rely on separate service processors and network connections are not only not supported by existing IoT hardware, but are unlikely to be in the foreseeable future due to the cost constraints of mainstream IoT devices. This paper presents Cider, a system that can recover IoT devices within a short amount of time, even if attackers have taken root control of every device in a large deployment. The recovery requires minimal manual intervention. After the administrator has identified the compromise and produced an updated firmware image, he/she can instruct Cider to force the devices to reset and to install the patched firmware on the devices. We demonstrate the universality and practicality of Cider by implementing it on three popular IoT platforms (HummingBoard Edge, Raspberry Pi Compute Module 3 and Nucleo-L476RG) spanning the range from high to low end. Our evaluation shows that the performance overhead of Cider is generally negligible.
A New Genealogy for Critical OA Publishing: Towards a Politics of Intersectional Transnationality

In this article, I suggest opening out from the digital genealogies critical strands within the Open Access (OA) movement usually associate themselves with: I propose a genealogy of OA publishing that takes into consideration feminist and decolonial transnational publishing initiatives that have been active in non-digital realms before, and in parallel to what these critical strands have highlighted as their digital origins. The ways in which these pre-digital initiatives organised and mobilised feminist and decolonial transnational struggle through publishing might offer new insights for contemporary critical OA – specifically, with regards to questions around how to confront uneven hierarchies of place in academia, while holding in tension their intersectional character. By asking “what would the future of critical OA publishing look like, if it BEGAN its formulation from the perspective of feminist, decolonial, anti-capitalist and transnational organising? ”, I would like to sketch critical OA as a practice that moves beyond a liberal academic stance to actively develop a radical transnational and trans-epistemic ethic of resistance against capitalist, colonialist, and patriarchal domination.
Mini Review About Monosodium Glutamate

Monosodium glutamate (MSG) is salt of sodium and glutamic acid. It is most commonly known as a flavouring enhancer in food processing, which provides umami taste that intensifies the meaty, savory flavor of food, as naturally occurring glutamate does in foods such as stews and meat soups. The amino acid glutamic acid it is naturally presents in food. Globally, commercial MSG’s consumption is increasing, markable high in Asia. Likewise, its production has known improvements regarding both method and technical equipment. Although MSG’s safety was evaluated by international organizations (EFSA, FDA) as safe and the limits were set up, there are studies concern about its side effects such as obesity, asthma, migraine headache, etc. The European Union classifies it as a food additive permitted in certain foods and subject to quantitative limits. The increase in commercially MSG use has raised the concern of both scientists and consumers about its safety. Therefore, due to a need of full comprehension about MSG, it is necessary to give more attention in studying it. Advantage in the development of analysis methods and technical equipments should be exploited to obtain higher accuracy result. This review provides a brief and general information about MSG with updates in its research.
State Aggregation for Multiagent Communication over Rate-Limited Channels

A collaborative task is assigned to a multiagent system (MAS) in which agents are allowed to communicate. The MAS runs over an underlying Markov decision process and its task is to maximize the averaged sum of discounted one-stage rewards. Although knowing the global state of the environment is necessary for the optimal action selection of the MAS, agents are limited to individual observations. The inter-agent communication can tackle the issue of local observability, however, the limited rate of the inter-agent communication prevents the agents from acquiring the precise global state information. To overcome this challenge, agents need to communicate their observations in a compact way such that the MAS compromises the minimum possible sum of rewards. We show that this problem is equivalent to a form of rate-distortion problem which we call the task-based information compression. State Aggregation for Information Compression (SAIC) is introduced here to perform the task-based information compression. The SAIC is shown, conditionally, to be capable of achieving the optimal performance in terms of the attained sum of discounted rewards. The proposed algorithm is applied to a rendezvous problem and its performance is compared with two benchmarks; (i) conventional source coding algorithms and the (ii) centralized multiagent control using reinforcement learning. Numerical experiments confirm the superiority and fast convergence of the proposed SAIC.
Robust Differentiable SVD

Eigendecomposition of symmetric matrices is at the heart of many computer vision algorithms. However, the derivatives of the eigenvectors tend to be numerically unstable, whether using the SVD to compute them analytically or using the Power Iteration (PI) method to approximate them. This instability arises in the presence of eigenvalues that are close to each other. This makes integrating eigendecomposition into deep networks difficult and often results in poor convergence, particularly when dealing with large matrices. While this can be mitigated by partitioning the data into small arbitrary groups, doing so has no theoretical basis and makes it impossible to exploit the full power of eigendecomposition. In previous work, we mitigated this using SVD during the forward pass and PI to compute the gradients during the backward pass. However, the iterative deflation procedure required to compute multiple eigenvectors using PI tends to accumulate errors and yield inaccurate gradients. Here, we show that the Taylor expansion of the SVD gradient is theoretically equivalent to the gradient obtained using PI without relying in practice on an iterative process and thus yields more accurate gradients. We demonstrate the benefits of this increased accuracy for image classification and style transfer.
Coding for Mobile Edge Computing Using Luby-Transform codes to lower the latency in edge computing systems

The idea of mobile edge computing (MEC) is to provide external computational and storage resources close to the end user, i.e., close to the network edge. Servers are placed in the vicinity of the users and can be accessed through a direct wireless connection. A typical MEC use case is computation offloading, where the users want some data processed but cannot perform it themselves due to, e.g., not having enough processing capacity or the need to save energy. The users transmit their data to the MEC servers over the wireless channel, the MEC servers process the data and then send the results back to the users. As noted in the research on distributed computing, data servers tend to straggle, i.e., at random occasions require an unacceptable amount of time to finish their assigned tasks. The application of codes has proven to be useful in this regard, enabling recovery of the results from a subset of servers instead of having to wait for all servers to finish. The same principle can be applied in the MEC setting. There is however another dimension to MEC as compared to distributed computing; that of transmitting data over a wireless channel. In particular, it has been shown that computing the same data on multiple servers can introduce diversity in the downlink transmission. The servers that have computed the same data can then collaborate to transmit the data with lower transmission latency than would otherwise be possible. Zhang et al. investigated the use of maximum distance separable (MDS) codes in the context of MEC to protect against straggling servers, and repetition codes to provide a low downlink transmission latency. Their MDS hybrid scheme shows a clear improvement to that of uncoded MEC. In this thesis two coding schemes inspired by the work of Zhang et al. are proposed and evaluated by simulations. The schemes are based on Luby-Transform codes and inactivation decoding. Simulations indicate a lower total latency for one of the proposed schemes as compared to the MDS hybrid. A lower bound on the total latency is also derived and used as a benchmark for the schemes. If the computation latency dominates the total latency, all schemes perform relatively close to the bound. If instead the downlink transmission latency dominates the total latency, the schemes perform somewhat further away.
Separating Climate Signals with Machine Learning

We use machine learning (ML) for the attribution of seasonal and extreme precipitation to different signals in the climate system. We compare ML-based attribution methods to traditional detection and attribution (D&A) techniques. Our project aligns with Focal Area 3 of the AI for Earth System Predictability Call for White Papers: “insight gleaned from complex data (both observed and simulated). ”