Miracle-dz/UniFAR-FTUs huggingface dataset:
The environmentally tuned transcriptomes of Mytilus mussels

ABSTRACT Transcriptomics is a powerful tool for elucidating the molecular mechanisms that underlie the ability of organisms to survive and thrive in dynamic and changing environments. Here, we review the major contributions in this field, and we focus on studies of mussels in the genus Mytilus, which are well-established models for the study of ecological physiology in fluctuating environments. Our review is organized into four main sections. First, we illustrate how the abiotic forces of the intertidal environment drive the rhythmic coupling of gene expression to diel and tidal cycles in Mytilus californianus. Second, we discuss the challenges and pitfalls of conducting transcriptomic studies in field-acclimatized animals. Third, we examine the link between transcriptomic responses to environmental stress and biogeographic distributions in blue mussels, Mytilus trossulus and Mytilus galloprovincialis. Fourth, we present a comparison of transcriptomic datasets and identify 175 genes that share common responses to heat stress across Mytilus species. Taken together, these studies demonstrate that transcriptomics can provide an informative snapshot of the physiological state of an organism within an environmental context. In a comparative framework, transcriptomics can reveal how natural selection has shaped patterns of transcriptional regulation that may ultimately influence biogeography. Summary: Abiotic factors, such as temperature and the tidal cycle, drive patterns of gene expression in Mytilus mussels that underlie whole-organism physiological states, which, in turn, influence biogeographic distributions.
Do psychobiosocial states mediate the relationship between perceived motivational climate and individual motivation in youngsters?

Abstract Grounded in achievement goal theory and self-determination theory, this cross-sectional study examined the relationship between perceived motivational climate and individuals’ motivation as well as the mediation effect of psychobiosocial states as conceptualised within the individual zones of optimal functioning (IZOF) model. Young students (N = 167, age range 14–15 years) taking part in physical education classes completed measures of teacher-initiated motivational climate, task and ego orientation, motivation and psychobiosocial states. Simple and serial mediation analyses indicated that a perceived mastery climate and individuals’ task orientation were related to intrinsic motivation and identified regulation through the mediation of pleasant/functional psychobiosocial states. In contrast, a perceived performance climate was related to external regulation and amotivation through the mediation of unpleasant/dysfunctional psychobiosocial states. Regression analysis results also showed that discrete psychobiosocial states accounted for a significant proportion of variance in motivational variables. Taken together, findings highlight the role of psychobiosocial states as mediators of the relationship between motivational climate and an individual’s motivation, and suggest that educators should consider a wide range of individual’s functional and dysfunctional reactions deriving from their instructional activity.
Threshold voltage changed by floating gate control in electrolyte-insulator-semiconductor structure

A method for controlling the threshold voltage which has a significant problem in ion-sensitive transistors (IST) with floating gate structures was proposed in this study. Gated lateral pnp-type bipolar junction transistor (BJT) was used in our experiment and was immerged in ionic solution. The experiment results indicated that under a large negative gate bias condition, the threshold voltage can shift in normal state with specific bias. Moreover, we discussed the reasons for the changing phenomenon of threshold voltage in dielectric of gated lateral BJT in electrolyte.
Timed Deletion of Twist1 in the Limb Bud Reveals Age-Specific Impacts on Autopod and Zeugopod Patterning

Twist1 encodes a transcription factor that plays a vital role in limb development. We have used a tamoxifen-inducible Cre transgene, Ubc-CreERT2, to generate time-specific deletions of Twist1 by inducing Cre activity in mouse embryos at different ages from embryonic (E) day 9.5 onwards. A novel forelimb phenotype of supernumerary pre-axial digits and enlargement or partial duplication of the distal radius was observed when Cre activity was induced at E9.5. Gene expression analysis revealed significant upregulation of Hoxd10, Hoxd11 and Grem1 in the anterior half of the forelimb bud at E11.5. There is also localized upregulation of Ptch1, Hand2 and Hoxd13 at the site of ectopic digit formation, indicating a posterior molecular identity for the supernumerary digits. The specific skeletal phenotypes, which include duplication of digits and distal zeugopods but no overt posteriorization, differ from those of other Twist1 conditional knockout mutants. This outcome may be attributed to the deferment of Twist1 ablation to a later time frame of limb morphogenesis, which leads to the ectopic activation of posterior genes in the anterior tissues after the establishment of anterior-posterior anatomical identities in the forelimb bud.
Successive Maximization for Systematic Design of Universally Capacity Approaching Rate-Compatible Sequences of LDPC Code Ensembles over Binary-Input Output-Symmetric Memoryless Channels

A systematic construction of capacity achieving low-density parity-check (LDPC) code ensemble sequences over the Binary Erasure Channel (BEC) has been proposed by Saeedi et al. based on a method, here referred to as Successive Maximization (SM). In SM, the fraction of degree-i nodes are successively maximized starting from i = 2 with the constraint that the ensemble remains convergent over the channel. In this paper, we propose SM to design universally capacity approaching rate-compatible LDPC code ensemble sequences over the general class of Binary-Input Output-Symmetric Memoryless (BIOSM) channels. This is achieved by first generalizing the SM method to other BIOSM channels to design a sequence of capacity approaching ensembles called the parent sequence. The SM principle is then applied to each ensemble within the parent sequence, this time to design rate-compatible puncturing schemes. As part of our results, we extend the stability condition which was previously derived for degree-2 variable nodes to other variable node degrees as well as to the case of rate-compatible codes. Consequently, we prove that using the SM principle, one is able to design universally capacity achieving rate-compatible LDPC code ensemble sequences over the BEC. Unlike the previous results in the literature, the proposed SM approach is naturally extendable to other BIOSM channels. The performance of the rate-compatible schemes designed based on our method is comparable to those designed by optimization.
Prospective phase II study of post-surgical adjuvant chemo-immunotherapy using autologous dendritic cells and activated killer cells from tissue culture of tumor-draining lymph nodes in primary lung cancer patients.

BACKGROUND The efficacy and toxicity of adjuvant chemo-immunotherapy using dendritic cells and activated killer cells are not clear in post-surgical primary lung cancer patients. PATIENTS AND METHODS Pathologically diagnosed N2 lung cancer patients were selected for postsurgical adjuvant chemo-immunotherapy. The activated killer cells and dendritic cells (AKT-DC) obtained from tissue cultures of tumor-draining lymph nodes (TDLN) or from TDLN co-cultured with peripheral blood lymphocytes (TDLN-Pb) were used for the adoptive transfer of immunotherapy. The patients received 4 courses of chemotherapy along with immunotherapy every 2 months for 2 years. RESULTS There were 31 N2 patients eligible for the study. Three cases were excluded because of refusal by the patients after 1-2 courses of immunotherapy. For the 28 cases treated, a total of 313 courses of immunotherapy were administered. The main toxicities were fever (78.0%), chill (83.4%), fatigue (23.0%) and nausea (17.0%) on the day of cell transfer. The 2- and 5-year survival rates were 88.9 % (95.9-81.9; 95% confidence interval, C.I.) and 52.9% (76.4-29.4; C.I.). CONCLUSION Adoptive transfer of activated killer cells and dendritic cells from the tumor-draining lymph nodes of primary lung cancer patients is feasible and safe, and a large-scale multi-institutional study is necessary for evaluation of the efficacy of this treatment.
Complex chronic comorbidities of COPD

Chronic obstructive pulmonary disease (COPD) is defined by fixed airflow limitation associated with an abnormal pulmonary and systemic inflammatory response of the lungs to cigarette smoke. The systemic inflammation induced by smoking may also cause chronic heart failure, metabolic syndrome and other chronic diseases, which may contribute to the clinical manifestations and natural history of COPD. Thus COPD can no longer be considered a disease only of the lungs, as it is often associated with a wide variety of systemic consequences. A better understanding of the origin and consequences of systemic inflammation, and of potential therapies, will most likely lead to better care of patients with COPD. Medical textbooks and clinical guidelines still largely ignore the fact that COPD seldom occurs in isolation. As the diagnosis and assessment of severity of COPD may be greatly affected by the presence of comorbid conditions, the current authors believe that lung function measurement, noninvasive assessment of cardiovascular and metabolic functions, and circulating inflammatory markers (e.g. C-reactive protein) might help to better characterise these patients. Similarly, preventive and therapeutic interventions should address the patient in their complexity.
Seeing or hearing the pianists? A synopsis of an early audiovisual perception experiment and a replication

The visual impact of musicians’ body movements has increasingly attracted research interest over the past twenty years. This article gives an overview of the main findings of this research and introduces and replicates one of the first experiments on visual information in music performance evaluations. In Behne’s study (originally published in German in 1990), a pianist was video-recorded performing compositions by Brahms and Chopin. Using an audiovisual manipulation paradigm, further pianists acted as doubles and pretended to perform the music to the soundtrack of the first pianist. Different groups of ninety-three musicians and non-musicians rated audiovisual presentations of the videos. Only one participant in the whole series of experiments supposed that the musical soundtrack was similar across different performers. Even musically trained participants strongly believed that they perceived differences between performances. Further findings suggest gender effects, such that male interpretations were perceived to be more precise and female interpretations to be more dramatic. The replication generally confirmed the results for a present-day audience. Potential consequences for music evaluations and theories of audiovisual music perception are discussed.
Technique of ultra wideband radar target discrimination using natural frequencies

An aspect independent radar target discrimination method based on the natural frequencies of ultra wideband radar targets is introduced. The sets of points in a multi-dimensional space corresponding to the poles on a complex plane (natural resonances) were offered as signatures of radar targets. This approach allows performing the automated discrimination algorithm of radar targets. The results of experimental research of the signals scattered by scaled aircraft models using the signatures algorithm and cumulant preprocessing are presented.
High Throughput Spectrum-aware Routing for Cognitive Radio Networks

Dynamic spectrum networks enable fast deployment of new wireless technologies by effectively utilizing allo cated yet unused wireless spectrum. By sensing and utilizing availab le wireless channels, cognitive radio devices can provide high thr oughput, low latency communication. Existing schemes for chann el assignment suffer drawbacks in throughput and reachability in the presence of location-dependent channel availability. We p ropose SPEctrum-Aware Routing Protocol (SPEAR), a robust and efficient distributed channel assignment and routing protocol for dynamic spectrum networks based on two principles: integrated spec trum and route discovery for robust multi-hop path formation, and distributed path reservations to minimize interand intra-flow interference. Through simulations and testbed measuremen ts, we show that SPEAR establishes robust paths in diverse spectru m conditions and provides near-optimal throughput and end-t o-end packet delivery latency. SPEAR performs extremely fast flow setup and teardowns, and can maintain interference-free flo ws in the presence of variance in channel availability.
Effectiveness of infection control measures in controlling a nosocomial outbreak of multidrug-resistant tuberculosis among HIV patients in Italy.

SETTING Between October 1992 and February 1994, 33 cases of multidrug-resistant tuberculosis (MDR-TB) were diagnosed among patients infected by the human immunodeficiency virus (HIV) and hospitalised in an HIV ward in Milan, Italy. This outbreak was part of a much larger outbreak, begun in another hospital and probably transferred through a patient. OBJECTIVE To evaluate risk factors for transmission and the effectiveness of infection control measures. DESIGN 1) Active follow-up of exposed patients, 2) cohort study among HIV-infected patients exposed to MDR-TB cases before and after the implementation of control measures, 3) screening of close contacts of MDR-TB cases, and 4) molecular typing by restriction fragment length polymorphism (RFLP) analysis. RESULTS The risk of MDR-TB was higher in patients with lower CD4+ lymphocyte percentages and longer duration of exposure. No difference in the daily risk was observed for in-patients vs day-hospital patients or by room distance from an infectious case. Of the 90 patients exposed before the implementation of infection control measures (i.e., October 1992-June 1993) 26 (28.9%) developed MDR-TB, whereas none of the 44 patients exclusively exposed after implementation developed MDR-TB, despite the continuing presence of infectious MDR-TB cases in the ward. CONCLUSION Simple control measures were effective in significantly reducing nosocomial transmission among patients.
Robust spectrum sensing for cognitive radio based on statistical tests

Spectrum sensing, in particular, detecting the presence of incumbent users in licensed spectrum, is one of the pivotal task for cognitive radios (CRs). In this paper, we provide solutions to the spectrum sensing problem by using statistical test theory, and thus derive novel spectrum sensing approaches. We apply the classical Kolmogorov-Smirnov (KS) test to the problem of spectrum sensing under the assumption that the noise probability distribution is known. In practice, the exact noise distribution is unknown, so a sensing method for Gaussian noise with unknown noise power is proposed. Next it is shown that the proposed sensing scheme is asymptotically robust and can be applied to non-Gaussian noise distributions. We compare the performance of sensing algorithms with the well-known Energy Detector (ED) and Anderson-Darling (AD) sensing proposed in recent literature. Our paper shows that proposed sensing methods outperform both ED and AD based sensing especially for the most important case when the received Signal to Noise Ratio (SNR) is low.
Stable integration and expression of a plant defensin in tomato confers resistance to fusarium wilt

Plant defensins are small cysteine-rich peptides which belong to a group of pathogenasis related defense mechanism proteins. The proteins inhibit the growth of a broad range of microbes and are highly stable under extreme environmental stresses. Tomato cultivation is affected by fungal disease such as Fusarium wilt. In order to overcome fungal damages, transgenic tomato plants expressing the Medicago sativa defensin gene MsDef1 under the control of the CaMV 35S promoter were developed. The Fusarium-susceptible tomato (Lycobersicum esculentum Mill) cultivar CastleRock was used for transformation to acquire fungal resistance. Hypocotyl with a part of cotyledon (hypocotyledonary) for young tomato seedlings were used as an explant material and transformation was performed using the biolistic delivery system. Bombarded shoots were selected on regeneration medium supplemented with hygromycin and suitable concentrations of BA, zeatin ripozide and AgNO3. Putative transgenic plantlets of T0 were confirmed by PCR analysis using primers specific for the transgene and the transformation frequency obtained was 52.3%. Transformation and transcription of transgenes were confirmed in T1 by PCR, Southern hybridizations, and reverse-transcription PCR (RT-PCR). The copy numbers of integrated transgene into tomato genome ranged between 1-3 copies. Greenhouse bioassay was performed on the transgenic T1 and T2 young seedlings and non-transgenic controls by challenging with a vigorous isolate of the fungal pathogen Fusarium oxysporum f. sp. Lycopersici. The level of fungal infectivity was determined using RT-PCR with tomatinase specific primers. Transgenic lines were more resistant to infection by fusarium than the control plants. These results indicated that overexpressing defensins in transgenic plants confer resistance to fungal pathogens.
Design of hair-like appendages and their coordination inspired by water beetles for steady swimming on the water surface

Locomotion of water beetles have been widely studied in biology owing to their remarkable swimming skills. Here, we investigated the coordination between the two pairs of legs to achieve steady swimming with novel hair-like appendages. Some design considerations and a fabrication of the hair-like appendages, which can passively adjust their projected area to obtain net thrust, are proposed. As do water beetles in nature, the coordination between the two pairs of legs were considered to achieve steady swimming without jerky motion by varying the beating frequency and phase of the legs. To verify the functionality of the hair-like appendages and their coordinations, six different types of appendages were fabricated, and two robots (one with single pair and the other with two pairs of legs) were built. Locomotion of the robots were compared through experiments, and steady swimming was achievable by properly coordinating the two-pairs of legs without sacrificing the swmming speed.
Impact of plugins on the security of web applications

Many web applications have evolved into complex software ecosystems, consisting of a core maintained by a set of long term developers and a range of plugins developed by third parties. The security of such applications depends as much on vulnerabilities found in plugins as it does in vulnerabilities in the application core. In this paper, we present a study of vulnerabilities in twelve open source web applications and 13,778 plugins for those applications. We used automated static analysis tools to count vulnerabilities. Plugins made up 93% of the aggregate code base of 10.2 MLOC and contained 92% of the 125,110 vulnerabilities found. Comparing the aggregate plugin source code of each project with its code, we found that four projects had more secure core code than plugin code, as measured by vulnerability density (vulnerabilities per thousand lines of code), while eight projects had plugin code that was more secure than core code. Vulnerability density was significantly correlated with code size for both core code and plugins. We also analyzed the density of individual vulnerability categories, finding plugins to have many more cross-site vulnerabilities and fewer injection vulnerabilities than core code.
Adaptations for nocturnal and diurnal vision in the hawkmoth lamina

Animals use vision over a wide range of light intensities, from dim starlight to bright sunshine. For animals active in very dim light the visual system is challenged by several sources of visual noise. Adaptations in the eyes, as well as in the neural circuitry, have evolved to suppress the noise and enhance the visual signal, thereby improving vision in dim light. Among neural adaptations, spatial summation of visual signals from neighboring processing units is suggested to increase the reliability of signal detection and thus visual sensitivity. In insects, the likely neural candidates for carrying out spatial summation are the lamina monopolar cells (LMCs) of the first visual processing area of the insect brain (the lamina). We have classified LMCs in three species of hawkmoths with considerably different activity periods but very similar ecology—the diurnal Macroglossum stellatarum, the nocturnal Deilephila elpenor and the crepuscular‐nocturnal Manduca sexta. Using this classification, we investigated the anatomical adaptations of hawkmoth LMCs suited for spatial summation. We found that specific types of LMCs have dendrites extending to significantly more neighboring cartridges in the two nocturnal and crepuscular species than in the diurnal species, making these LMC types strong candidates for spatial summation. Moreover, while the absolute number of cartridges visited by the LMCs differed between the two dim‐light species, their dendritic extents were very similar in terms of visual angle, possibly indicating a limiting spatial acuity. The overall size of the lamina neuropil did not correlate with the size of its LMCs. J. Comp. Neurol. 524:160–175, 2016. © 2015 Wiley Periodicals, Inc.
Kinks in dipole chains

It is shown that the topological discrete sine-Gordon system introduced by Speight and Ward models the dynamics of an infinite uniform chain of electric dipoles constrained to rotate in a plane containing the chain. Such a chain admits a novel type of static kink solution which may occupy any position relative to the spatial lattice and experiences no Peierls–Nabarro barrier. Consequently the dynamics of a single kink is highly continuum-like, despite the strongly discrete nature of the model. Static multikinks and kink–antikink pairs are constructed, and it is shown that all such static solutions are unstable. Exact propagating kinks are sought numerically using the pseudo-spectral method, but it is found that none exist, except, perhaps, at very low speed.
Performance assessment of multi user inter cell interference alignment with measured channels

It has been shown that in a multi-user multi-cell network, the Multi User Inter Cell Interference Alignment (MUI-CIA) based transmit precoding outperforms the non-alignment based state of the art precoding schemes. The theory of MUICIA is based on the assumption that the partial and stale inter-cell interference (ICI) information is still useful. This ICI is used by the transmitter to design he precoding such that the ICI and the multi-user interference (MUI) are aligned at the receiver. In this paper, we provide the proof of this concept with the help of measured channels. By using a measurement test-bed, we demonstrate that in slow time variant channels, the partial ICI contains useful information. Our outcomes are based on two different indoor scenarios for a multi user multi cell system with multiple antenna users. We also take into account the impact of training overhead on the performance in order to realize the feasibility of MUICIA with nominal overhead. Moreover, we compare the performance of MUICIA with other non-alignment based multi user precoding schemes. The results show that the concept of MUICIA is valid and it provides higher gains in a multi cell setup than other non-alignment based precodings with high as well as nominal training overhead.