Miracle-dz/UniFAR-FTUs huggingface dataset:
Endosymbiosis undone by stepwise elimination of the plastid in a parasitic dinoflagellate

Significance Endosymbiotic organelles are a defining feature of eukaryotes—the last common ancestor and all extant eukaryotes possess at least a mitochondrial derivative. Although mitochondria and plastids are identified with aerobic ATP synthesis and photosynthesis, respectively, their retention by their host cells requires the merging and integration of many, often redundant, metabolic pathways. As a result, complex metabolic interdependencies arise between these formerly independent cells. Complete loss of endosymbiotic organelles, even where aerobic respiration or photosynthesis is lost, is exceedingly difficult, as demonstrated by persistence of organelles throughout secondary anaerobes and parasites. Here, we identify a rare but clear case of plastid loss in a parasitic alga and detail the metabolic disentanglement that was required to achieve this exceptional evolutionary event. Organelle gain through endosymbiosis has been integral to the origin and diversification of eukaryotes, and, once gained, plastids and mitochondria seem seldom lost. Indeed, discovery of nonphotosynthetic plastids in many eukaryotes—notably, the apicoplast in apicomplexan parasites such as the malaria pathogen Plasmodium—highlights the essential metabolic functions performed by plastids beyond photosynthesis. Once a cell becomes reliant on these ancillary functions, organelle dependence is apparently difficult to overcome. Previous examples of endosymbiotic organelle loss (either mitochondria or plastids), which have been invoked to explain the origin of eukaryotic diversity, have subsequently been recognized as organelle reduction to cryptic forms, such as mitosomes and apicoplasts. Integration of these ancient symbionts with their hosts has been too well developed to reverse. Here, we provide evidence that the dinoflagellate Hematodinium sp. , a marine parasite of crustaceans, represents a rare case of endosymbiotic organelle loss by the elimination of the plastid. Extensive RNA and genomic sequencing data provide no evidence for a plastid organelle, but, rather, reveal a metabolic decoupling from known plastid functions that typically impede organelle loss. This independence has been achieved through retention of ancestral anabolic pathways, enzyme relocation from the plastid to the cytosol, and metabolic scavenging from the parasite’s host. Hematodinium sp. thus represents a further dimension of endosymbiosis—life after the organelle.
Soft Tempest { An Opportunity for NATO

NATO countries spend billions of dollars a year on electromagnetic security, of which the Tempest shielding of personal computers, workstations and peripherals is a large component. In the absence of a capable motivated opponent such as the former Soviet Union, this burden on both traditional and new members is increasingly difficult to justify. As a result, many systems at a medium level of sensitivity are migrating from a shielded to a zoned mode of protection. Over the last year, a new technology has emerged which complements zoning in an attractive way. Soft Tempest consists of the use of software techniques to filter, mask or render incomprehensible the information bearing electromagnetic emanations from a computer system. This may give complete protection to some system components, and while the level of protection available for others is only of the order of 10–20 dB, this translates to a difference of about one zone, which can still give a very significant cost saving. It is already available in COTS products; here we discuss its introduction into NATO systems.
British Design and Technology: A Critical Analysis

A great deal of interest has been shown in the British National Design and Technology Curriculum. A number of English Design and Technology education leaders have visited this country and a small group of American technology educators make periodic trips to Britain to observe the curriculum in action. Many of the reports provided to Americans by these individuals suggest that the British have THE answer and that we are years behind the Brits (Bottrill, 1992). However, Americans who question the British model as the utopian answer are often dismissed as unenlightened conservatives trying to protect skill-based programs. This paper is based primarily on a review of Technology in the National Curriculum (National Curriculum Council, 1990) and a trip to England. This trip included discussions with a shire (county) technology leader, an in-service technology teacher trainer, a technology equipment representative, and over 25 technology teachers who work at all educational levels from infant to secondary schools. The teachers covered the spectrum from one person resisting curricular change to a number of groups expending considerable effort to implement the national curriculum. The sample was not a hand-picked group of success stories designed to show the curriculum only at its best, but represented a reasonable cross-section of the teaching and leadership ranks.
The Emergence of an Abstract Grammatical Category in Children’s Early Speech

How do children begin to use language to say things they have never heard before? The origins of linguistic productivity have been a subject of heated debate: Whereas generativist accounts posit that children’s early language reflects the presence of syntactic abstractions, constructivist approaches instead emphasize gradual generalization derived from frequently heard forms. In the present research, we developed a Bayesian statistical model that measures the degree of abstraction implicit in children’s early use of the determiners “a” and “the. ” Our work revealed that many previously used corpora are too small to allow researchers to judge between these theoretical positions. However, several data sets, including the Speechome corpus—a new ultra-dense data set for one child—showed evidence of low initial levels of productivity and higher levels later in development. These findings are consistent with the hypothesis that children lack rich grammatical knowledge at the outset of language learning but rapidly begin to generalize on the basis of structural regularities in their input.
Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces

Many important physiological processes operate at time and space scales far beyond those accessible to atom-realistic simulations, and yet discrete stochastic rather than continuum methods may best represent finite numbers of molecules interacting in complex cellular spaces. We describe and validate new tools and algorithms developed for a new version of the MCell simulation program (MCell3), which supports generalized Monte Carlo modeling of diffusion and chemical reaction in solution, on surfaces representing membranes, and combinations thereof. A new syntax for describing the spatial directionality of surface reactions is introduced, along with optimizations and algorithms that can substantially reduce computational costs (e.g., event scheduling, variable time and space steps). Examples for simple reactions in simple spaces are validated by comparison to analytic solutions. Thus we show how spatially realistic Monte Carlo simulations of biological systems can be far more cost-effective than often is assumed, and provide a level of accuracy and insight beyond that of continuum methods.
Obstructive sleep apnea in combat-related posttraumatic stress disorder: a controlled polysomnography study

Background Obstructive sleep apnea (OSA) may be highly prevalent in posttraumatic stress disorder (PTSD) and may exacerbate PTSD complaints. Objective Our objective was to determine whether the prevalence of OSA was high in a sample of Dutch veterans with PTSD as compared to age- and trauma-matched controls, and whether OSA was associated with more severe PTSD complaints. Methods We determined the apnea hypopnea indices (AHI) with polysomnographic registrations in 20 veterans with PTSD, 24 veterans without PTSD, and 17 healthy controls. PTSD severity and nightmare complaints were assessed with the Clinician-Administered PTSD Scale (CAPS). Results The prevalence of an AHI > 10 was 29% in PTSD, 21% in trauma controls, and 29% in healthy controls (χ2= 0.60, df=2, p=n.s.). The mean CAPS score in patients with OSA (n=6) was significantly higher than in patients without OSA (p<0.05), while nightmare severity was similar in PTSD patients with OSA as compared to PTSD patients without OSA (p=n.s.). Furthermore, there was a significant correlation between AHI and CAPS score in PTSD patients (r=0.46, p<0.05, df=14). Conclusions Our results indicate that PTSD is not necessarily associated with a higher prevalence of OSA. However, PTSD severity was related to OSA, which may possibly mean that comorbid OSA leads to an increase in PTSD complaints. However, future research should indicate whether OSA exerts a negative influence on PTSD, and treatment of OSA alleviates PTSD symptoms. For the abstract or full text in other languages, please see Supplementary files under Reading Tools online
Diversity order in ISI channels with single-carrier frequency-domain equalizers

This paper analyzes the diversity gain achieved by single-carrier frequency-domain equalizers (SC-FDE) in frequency selective channels, and uncovers the interplay between diversity gain d, channel memory length ¿, transmission block length L, and the spectral efficiency R. We specifically show that for the class of minimum mean-square error (MMSE) SCFDE receivers, for rates R ¿ log L/¿ full diversity of d = ¿+ 1 is achievable, while for higher rates the diversity is given by d = [2-R L + 1. In other words, the achievable diversity gain depends not only on the channel memory length, but also on the desired spectral efficiency and the transmission block length. A similar analysis reveals that for zero forcing SC-FDE, the diversity order is always one irrespective of channel memory length and spectral efficiency. These results are supported by simulations.
Store-and-Forward Performance in a DTN

Delay and disruption tolerant networks have been proposed to address data communication challenges in network scenarios where an instantaneous end-to-end path between a source and destination may not exist, and the links between nodes may be opportunistic, predictably connectable, or periodically-(dis)connected. In this paper, we describe the store-and-forward and custody transfer concepts that are used in DTNs. Then, we present simulation results that illustrate the usefulness of the custody transfer feature, and a message ferry in improving the end-to-end message delivery ratio in a multihop scenario where link availability can be as low as 20%. In particular, our results indicate that one can achieve a delivery ratio as high as 90-99% with appropriate buffer allocations. We also provide some preliminary insights on the design factors that influence the end to end delivery ratio, e.g., the link availability patterns and buffer allocation strategies
Outcrossing and recombination in the lichenized fungus Letharia.

We report evidence for recombination in lichenized fungi based on sequenced nuclear DNA markers, judging from the incongruence of their gene genealogies. Recombining population structures were found in two phylogenetic species of Letharia, one species that is observed in nature to produce abundant sexual structures (ascomata) and another species that produces abundant clonal reproductive structures (soredia) and only rarely produces ascomata. To determine whether sexual reproduction was the cause of recombination in both species, we compared several variable loci in the ascomata and maternal tissue for evidence of outcrossing. All ascomata of both species were heterozygous for at least one locus, as would be expected to result from outcrossing and not from selling. Therefore, it appears that even in the sorediate species, rare sexual reproduction results in recombination.
On the Detection of Frequency-Spectra-Based Chipless RFID Using UWB Impulsed Interrogation

A novel approach is presented to accurately estimate the resonant features of a multipatch backscatter-based chipless radio frequency identification (RFID) tag. An ultra-wideband impulse radar (UWB-IR)-based reader interrogates the chipless tag with a UWB pulse, and the received backscatter is analyzed in the time domain. The key components constituting the backscattered signal, the structural mode, and the antenna mode are identified, and their spectral content are analyzed. Analysis shows that the antenna mode backscatter contains the information carrying signal while the structural mode backscatter contains no information about the tag. A semi-analytical model is developed to explain the behavior of the signal backscattered from the chipless RFID tag. Simulation and semi-analytical results are validated by experimental measurements obtained in an anechoic chamber environment using a 4-b multipatch chipless RFID tag. The new method does not rely on calibration tags for operation and has a greater degree of freedom in the orientation of tags with respect to a reader. A novel method, selective spectral interrogation (SSI), that uses a set of interrogation pulses to extract information bits stored in the spectral signature of the chipless tag is also introduced.
Optimal Periodic Testing of Intermittent Faults In Embedded Pipelined Processor Applications

Today's nanometer technology trends have a very negative impact on the reliability of semiconductor products. Intermittent faults constitute the largest part of reliability failures that are manifested in the field during the semiconductor product operation. Since software-based self-test (SBST) has been proposed as an effective strategy for on-line testing of processors integrated in non-safety critical low-cost embedded system applications, optimal test period specification is becoming increasingly challenging. In this paper we first introduce a reliability analysis for optimal periodic testing of intermittent faults that minimizes the test cost incurred based on a two-state Markov model for the probabilistic modeling of intermittent faults. Then, we present for the first time an enhanced SBST strategy for on-line testing of complex pipelined embedded processors. Finally, we demonstrate the effectiveness of the proposed optimal periodic SBST strategy by applying it to a fully-pipelined RISC embedded processor and providing experimental results
Non-Gaussian Distribution and Clustering of Hot and Cold Pixels in the WMAP Five-Year Sky

We present measurements of the clustering of hot and cold patches in the microwave background sky as measured from the Wilkinson Microwave Anisotropy Probe (WMAP) five-year data. These measurements are compared with theoretical predictions which assume that the cosmological signal obeys Gaussian statistics. We find significant differences from the simplest Gaussian-based prediction. However, the measurements are sensitive to the fact that the noise is spatially inhomogeneous (e.g., because different parts of the sky were observed for different lengths of time). We show how to account for this spatial inhomogeneity when making predictions. Differences from the Gaussian-based expectation remain even after this more careful accounting of the noise. In particular, we note that hot and cold pixels cluster differently within the same temperature thresholds at few-degree scales. While these findings may indicate primordial non-Gaussianity, we discuss other plausible explanations for these discrepancies. In addition, we find some deviations from Gaussianity at sub-degree scales, especially in the W band, whose origin may be associated with extragalactic dust emission.
Synthesis of abietic and dehydroabietic acid derivatives to target bacterial biofilms

Sivumäärä/ Sidoantal – Number of pages 61 Tiivistelmä/Referat – Abstract The aim of this study was to synthesize antimicrobial and anti-biofilm agents using abietic (AA) and dehydroabietic acids (DHAA). Bacterial biofilms are formed when bacteria cells cluster together within a self-produced extracellular matrix. This lifestyle makes bacteria highly resilient to different environmental stresses and conventional antibiotics when compared to single-cell bacteria. Currently, there are no approved anti-biofilm agents as drugs and only a few number of compounds can selectively target biofilms and eradicate them at low concentrations. Potent drugs targeting them are needed. AA and DHAA are abietane-type diterpenoids found in the resin of conifer trees. Antibacterial effects of resin acids have been widely studied, specifically against methicillin-resistant Staphylococcus aureus strain (MRSA). Through the combination of DHAA with different amino acids, Manner et al. (2015) discovered a new class of hybrid compounds that target both planktonic and biofilm bacteria in Staphylococcus aureus. The study group also discovered two of the most potent abietane-type anti-biofilm agents reported so far in literature. This thesis followed the work of the research group by designing and synthesizing additional AA and DHAA derivatives to target bacterial biofilms. Rings A, B and C of the diterpenoid core were modified and 24 derivatives were successfully synthesized. Amino acids were attached to the compounds either before or after ring modification. Standard structural elucidation techniques were used to confirm the structure of the synthesized compounds.
Regaining lost cycles with HotCalls: A fast interface for SGX secure enclaves

Intel's SGX secure execution technology allows running computations on secret data using untrusted servers. While recent work showed how to port applications and large-scale computations to run under SGX, the performance implications of using the technology remains an open question. We present the first comprehensive quantitative study to evaluate the performance of SGX. We show that straightforward use of SGX library primitives for calling functions add between 8,200–17,000 cycles overhead, compared to 150 cycles of a typical system call. We quantify the performance impact of these library calls and show that in applications with high system calls frequency, such as memcached, openVPN, and lighttpd, which all have high bandwidth network requirements, the performance degradation may be as high as 79%. We investigate the sources of this performance degradation by leveraging a new set of microbenchmarks for SGX-specific operations such as enclave entry-calls and out-calls, and encrypted memory I/O accesses. We leverage the insights we gain from these analyses to design a new SGX interface framework HotCalls. HotCalls are based on a synchronization spin-lock mechanism and provide a 13–27x speedup over the default interface. It can easily be integrated into existing code, making it a practical solution. Compared to a baseline SGX implementation of memcached, openVPN, and lighttpd — we show that using the new interface boosts the throughput by 2.6–3.7x, and reduces application latency by 62–74%.
Bodhi: Detecting Buffer Overflows with a Game

Buffer overflow is one of the most dangerous and common vulnerabilities in CPS software. Despite static and dynamic analysis, manual analysis is still heavily used which is useful but costly. Human computation harness humans' time and energy in a way of playing games to solve computational problems. In this paper we propose a human computation method to detect buffer overflows that does not ask a person whether there is a potential vulnerability, but rather a random person's idea. We implement this method as a game called Bodhi in which each player is shown a piece of code snippet and asked to choose whether their partner would think there is a buffer overflow vulnerability at a given position in the code. The purpose of the game is to make use of the rich distributed human resource to increase effectiveness of manual detection for buffer overflows. The game has been proven to be efficient and enjoyable in practice.
Transcriptional profiling of a mice plague model: insights into interaction between Yersinia pestis and its host

Despite the importance of pneumonic plague caused by Yersinia pestis, a few is known about the interaction between Y. pestis and its host at the molecular level during the pneumonic plague development. In this study, we employed an intranasally challenged plague model in mice for investigating the kinetics of the disease progression by transcriptional profiling of Y. pestis and mice using qRT‐PCR and microarray, respectively. The increasing transcription of important virulence genes of Y. pestis and of mice genes involving in immune and inflammatory defensive responses, and responses to stimuli, presents an overview of interaction between Y. pestis and mice during development of pneumonic plague. The early and persisting up‐regulation of caf 1, psa A and lcr V in vivo indicated their role in resisting the host innate immune responses. The up‐regulation of fur, ybt A and hms H in vivo reflected the ability of Y. pestis for acquiring iron. The transcription regulators, including pho P, oxy R and omp R, were up‐regulated during plague development, suggesting their roles in interaction between Y. pestis and mice. Many genes encoding cytokines, such as IL2, IL‐1B, CXCL2, CXCL5, CCL20, CD14 and TNFRSF13B, were up‐regulated during the infection, confirming the report that they are important mediators to activate host responses to invading pathogens. The up‐regulation of some genes encoding important virulent factors of Y. pestis and expression alterations of some genes encoding cytokines in the host reflect the interaction between the pathogen and the host, which will help us better understand plague pathogenesis. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Anaerobic Biodegradation of Surfactants – Scientific Review

Abstract The anaerobic biodegradation of surfactants is used as an acceptability criterion in some environmental pieces of legislation (eco-label, risk assessment, etc.), without a proper evaluation of the relevance of such a characteristic. Available screening test methods to assess the anaerobic biodegradation do not simulate the real conditions prevailing in these anaerobic compartments but rather reflect more stringent conditions, due to the high test substance/biomass ratio, possibility of inhibitory effects and limited possibility for adaptation. Therefore positive results are indicative of a similar behaviour under environmental conditions, while a negative result cannot be necessarily interpreted as inherent anaerobic recalcitrance. The majority of surfactants entering the environment will be exposed to and degraded under aerobic conditions, and only less than 20 % will potentially reach temporarily anaerobic environmental compartments. In contrast to the well documented adverse effects observed in the absence of aerobic biodegradation, the lack of anaerobic biodegradation does not seem to be correlated with any apparent environmental problem for most compartments after more than 40 years of widely use of such products. The scientific review concluded that anaerobic biodegradability does not have the same environmental relevance as the aerobic one. Anaerobic biodegradability should not, therefore, be used as a pass/fail property for the environmental acceptability of surfactants which are readily biodegradable under aerobic conditions.