Miracle-dz/UniFAR-FTUs huggingface dataset:
A-Kinase Anchoring Protein 4 Binding Proteins in the Fibrous Sheath of the Sperm Flagellum

Abstract The fibrous sheath is a unique cytoskeletal structure located in the principal piece of the sperm flagellum and is constructed of two longitudinal columns connected by closely spaced circumferential ribs. Cyclic AMP-dependent protein kinases are secured within specific cytoplasmic domains by A-kinase anchoring proteins (AKAPs), and the most abundant protein in the fibrous sheath is AKAP4. Several other fibrous sheath proteins have been identified, but how the fibrous sheath assembles is not understood. Yeast two-hybrid assays and deletion mutagenesis were used to identify AKAP4-binding proteins and to map the binding regions on AKAP4 and on the proteins identified. We found that AKAP4 binds AKAP3 and two novel spermatogenic cell-specific proteins, Fibrous Sheath Interacting Proteins 1 and 2 (FSIP1, FSIP2). Transcription of Akap4, Akap3, and Fsip1 begins in early spermatid development, whereas transcription of Fsip2 begins in late spermatocyte development. AKAP3 is synthesized in round spermatids and incorporated into the fibrous sheath concurrently with formation of the rib precursors. However, AKAP4 is synthesized and incorporated into the nascent fibrous sheath late in spermatid development. The AKAP4 precursor is processed in the flagellum and only the mature form of AKAP4 appears to bind AKAP3. These results suggest that AKAP3 is involved in organizing the basic structure of the fibrous sheath, whereas AKAP4 has a major role in completing fibrous sheath assembly.
Description of activity of living neuronal network by fuzzy bio-indicator

The culture dish describes the small fundamental world resembling human brain function. Multi-site recording system for extracellular action potentials is used for recording the activity of living neuronal networks. The living neuronal network is able to express several patterns independently, and that's meaning that it has fundamental mechanisms for intelligent information processing. In this paper, we propose a model to analyse logicality of signals and connectivity of electrodes in a culture dish of rat hippocampal neurons. We call it "fuzzy bio-indicator". This indicator is a kind of mapping methods to show logicality and connectivity of pulse frequency from active potential of neuronal network. We try to analyze the dynamics of action potentials of neuronal networks by the fuzzy bio-indicator, and identify the logicality and connectivity of neuronal networks through the indicator. We show here the usefulness of fuzzy bio-indicator through numerical examples and action potential detected from the culture neuronal network.
Learning multisensory neural controllers for robot arm tracking

Humans learn multisensory eye-hand coordination starting from infancy without supervision. For an example, they learn to track their hands by exploiting various sensory modalities, such as vision and proprioception. This integration occurs as they learn to perceive the world around them and their relationship to it. Most prior work has focused on the role of vision, as it is a primary sensory source for humans. However, it is interesting to study how vision and proprioception interact. We propose a system which combines visual and proprioceptive information to learn the eye-hand coordination skills that enable a robot to fixate its camera gaze on the end effector of its arm. In our model, visual cues are part of the feedback control loop, whereas proprioceptive cues are part of a feedforward control loop. Both controllers, as well as the sensory transform from raw visual information to a neural sensory representation are learned as the robot performs motor babbling movements. Visual information is encoded by sparse coding. The basis functions that emerge are similar to the receptive fields in the human visual cortex. An actor-critic reinforcement learning algorithm is used to drive eye motor neurons fusing visual and proprioceptive cues. We model and test the system in the iCub simulation environment. Our results suggest that these sensory modalities are capable of jointly learning model parameters to perform the tracking task. The evolved policy has characteristics that are qualitatively similar to the human oculomotor plant.
Exalign: a new method for comparative analysis of exon–intron gene structures

The evolution of genes is usually studied and reconstructed at the sequence level, that is, by comparing and aligning their genomic, transcript or protein sequences. However, including the exon–intron structure of genes in the analysis can provide further and useful information, for example to draw reliable phylogenetic relationships left unsolved by traditional sequence-based evolutionary studies, or to shed further light on patterns of intron gain and loss. In spite of this, no tool especially devised for this task is currently available. In this work we present Exalign, an algorithm designed to retrieve, compare and search for the exon-intron structure of existing gene annotations, that has been implemented in a software tool freely accessible through a web interface as well as available for download. We present different applications of our method, from the reconstruction of the evolutionary history of homologous gene families to the detection of as of today unknown cases of intron loss in human and rodents, and, remarkably, two never reported intron gain events in human and mouse. The web interface for accessing Exalign is available at http://www.pesolelab. it/exalign/ or http://www.beacon. unimi.it/exalign/
Comparison of Thermal Stress during Short-Circuit in Different Types of 1.2 kV SiC Transistors Based on Experiments and Simulations

The temperature evolution during a short-circuit in the die of three different Silicon Carbide1200-V power devices is presented. A transient thermal simulation was performed based on the reconstructedstructure of commercially available devices. The location of the hottest point in the device iscompared. Finally, the analysis supports the necessity to turn off short-circuit events rapidly in orderto protect the device after a fault.
Implications of high energy proportional servers on cluster-wide energy proportionality

Cluster-level packing techniques have long been used to improve the energy proportionality of server clusters by masking the poor energy proportionality of individual servers. With the emergence of high energy proportional servers, we revisit whether cluster-level packing techniques are still the most effective way to achieve high cluster-wide energy proportionality. Our findings indicate that cluster-level packing techniques can eventually limit cluster-wide energy proportionality and it may be more beneficial to depend solely on server-level low power techniques. Server-level low power techniques generally require a high latency slack to be effective due to diminishing idle periods as server core count increases. In order for server-level low power techniques to be a viable alternative, the latency slack required for these techniques must be lowered. We found that server-level active low power modes offer the lowest latency slack, independent of server core count, and propose low power mode switching policies to meet the best-case latency slack under realistic conditions. By overcoming these major issues, we show that server-level low power modes can be a viable alternative to cluster-level packing techniques in providing high cluster-wide energy proportionality.
Typing of urogenital, maternal, and neonatal isolates of Haemophilus influenzae and Haemophilus parainfluenzae in correlation with clinical source of isolation and evidence for a genital specificity of H. influenzae biotype IV

Over a period of 6 years, 114 strains of Haemophilus influenzae and Haemophilus parainfluenzae were isolated from genital, mother-infant, or neonatal infections. Their serotypes, biotypes, antibiotic resistance phenotypes, and outer membrane protein (OMP) electrophoretic patterns were characterized and correlated with the various clinical outcomes. Genital H. influenzae and H. parainfluenzae appeared to behave mostly as opportunistic pathogens; for instance, 62% of the cases of endometritis or pelvic inflammatory disease were related to the presence of an intrauterine device. However, as seen clearly in one case, the strains may be sexually transmitted. The analysis of OMP patterns proved to be a very convenient method to seek evidence for the sexual origin of the infection. H. influenzae was more often involved in complicated genital infections than was H. parainfluenzae. Nontypeable and biotype II H. influenzae strains were the more frequent isolates, except in pelvic inflammatory diseases, in which biotype I prevailed, and in mother-infant infections, in which one-fourth of the cases were due to biotype IV. Characterization of H. influenzae isolates did not support a general concept of specific genital strains. However, strains of biotype IV clearly stood out with two characteristics: (i) a peritrichous fimbriation and (ii) a very peculiar homogeneous OMP pattern comprising an OMP of molecular weight approximately 18,000 unique to this biotype. These characteristics were also found in H. influenzae biotype IV strains isolated from genital infections in the United States and used as controls. H. influenzae biotype IV strains may thus correspond to a group somewhat adapted to the genital tract.
Why Sex Matters: A Darwinian Look at Human Behavior

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A disparity between locomotor economy and territory-holding ability in male house mice

ABSTRACT Both economical locomotion and physical fighting are important performance traits to many species because of their direct influence on components of Darwinian fitness. Locomotion represents a substantial portion of the total daily energy budget of many animals. Fighting performance often determines individual reproductive fitness through the means of resource control, social dominance and access to mates. However, phenotypic traits that improve either locomotor economy or fighting ability may diminish performance in the other. Here, we tested for a predicted disparity between locomotor economy and competitive ability in wild-derived house mice (Mus musculus). We used 8 week social competition trials in semi-natural enclosures to directly measure male competitive ability through territorial control and female occupancy within territories. We also measured oxygen consumption during locomotion for each mouse using running trials in an enclosed treadmill and open-flow respirometry. Our results show that territory-holding males have higher absolute and mass-specific oxygen consumption when running (i.e. reduced locomotor economy) compared with males that do not control territories. This relationship was present both before and after 8 week competition trials in semi-natural enclosures. This disparity between physical competitive ability and economical locomotion may impose viability costs on males in species for which competition over mates is common and may constrain the evolution of behavioral and phenotypic diversity, particularly in natural settings with environmental and resource variability. Summary: Male house mice that control exclusive polygynous territories are less economical runners compared with non-territory-holding males.
The inability to self-evaluate smell performance. How the vividness of mental images outweighs awareness of olfactory performance

To rate one’s individual olfactory performance is difficult and in many cases differs clearly from validated objective olfactory performance measures. This study aimed to investigate the basis for this measurement drift between objective and subjective olfactory performance evaluation. In absence of an actual odor, one may imagine an olfactory stimulus to evaluate his subjective olfactory performance. Therefore, the impact of the vividness of mental images on self-evaluation of smell performance in patients with mild to severe olfactory dysfunction and healthy controls was investigated. Fifty-nine patients with peripheral olfactory dysfunction ranging from reduced olfactory function (hyposmia) to complete loss of olfactory perception (anosmia) and 16 healthy controls were included. Olfactory performance was assessed using the Sniffin’ Sticks battery, the vividness of olfactory mental images was evaluated using the vividness of olfactory imagery questionnaire (VOIQ). Decreased vividness of odor images was obtained for anosmic patients, and a trend of poorer odor imagery was determined in hyposmic patients. Multiple regression analyses revealed the VOIQ score as significant predictor for olfactory self-evaluation for hyposmic patients and healthy controls. In contrast, for anosmic patients, the only significant predictor for self-rating of olfactory performance was the threshold-detection-identification (TDI) score, measuring overall olfactory performance. The results of this study indicate that sensory perception and mental images are closely related to each other. Furthermore, subjects who were able to perceive odors, even to a smaller extent, rely on the vividness of their mental odor images to evaluate their olfactory performance. In contrast, anosmic patients rather trust in their knowledge that they are not able to perceive odors. We are therefore able to subjectively rate our olfactory performance levels, if we are not able to perceive odors, but not if we are able to perceive olfactory input.
Acute hepatitis C in a contemporary US cohort: modes of acquisition and factors influencing viral clearance.

BACKGROUND Acute hepatitis C virus (HCV) infection is often asymptomatic; thus, its epidemiology and natural history are difficult to define. METHODS Acute HCV infection was identified on the basis of HCV seroconversion within 1 year (n=45), new anti-HCV seropositivity with clinical acute hepatitis (n=21), or HCV strain sequencing after an iatrogenic exposure (n=1). Risk factors were assessed with a baseline questionnaire, and participants were followed up prospectively with serial measurement of viral loads. RESULTS Of 67 persons with acute HCV infection, most were asymptomatic (64%) and injection drug users (66%). Thirteen had an unknown mode of transmission; of these, 11 reported high-risk sexual behavior. Ten acquired acute HCV infection within 3 months of an iatrogenic exposure; 3 had confirmed iatrogenic infection, and 4 had no other risk factors identified. The spontaneous viral clearance rate after 6 months of infection was 18% (95% confidence interval, 11%-31%). The rate of viral clearance varied significantly by sex (34% vs. 3% for women vs. men; P<.001). CONCLUSIONS High-risk sexual or iatrogenic exposures may be important contemporary risk factors for HCV infection. The spontaneous viral clearance rate (18%) in this contemporary study was similar to that reported for past studies of transfusion-associated HCV infection. Women were more likely to clear acute HCV infection than men.
Leveraging block decisions and aggregation in the ShareStreams QoS architecture

ShareStreams (Scalable Hardware Architectures for Stream Schedulers) is a canonical architecture for realizing a range of scheduling disciplines. This paper discusses the design choices and tradeoffs made in the development of a endsystem/host-based router realization of the ShareStreams architecture. We evaluate the impact of block decisions and aggregation on the ShareStreams architecture. Using processor resources for queuing and data movement, and FPGA hardware for accelerating stream selection and stream priority updates, ShareStreams can easily meet the wire-speeds of 10 Gbit/s links. This allows provision of customized scheduling solutions and interoperability of scheduling disciplines. Our hardware implemented in the Xilinx Virtex I family easily scales from 4 to 32 stream-slots on a single chip. A host-based router prototype with FPGA PCI card under systems software control, can provide scheduling support for a mix of EDF, static-priority and fair-share streams based on user specifications and meet the temporal bounds and packet-time requirements of multi-gigabit links.
Sexual Desire in Iranian Female University Students: Role of Marital Satisfaction and Sex Guilt

Objective: To determine association between sexual desire and marital satisfaction and sex guilt among a sample of Iranian female university students. Methods: The data presented here were obtained from a total of 192 married Iranian female university students who were selected via a multi-cluster sampling method from universities of Social Welfare and Rehabilitation, Tarbiat Modarres, and Islamic Azad. The subjects' sociodemographic data, marital satisfaction (using ENRICH Marital Satisfaction Questionnaire), sex guilt (using Mosher Revised Sex-Guilt Inventory), and sexual desire (using Hurlbert Index of Sexual Desire) were gathered. Pearson correlation coefficient and regression analysis methods were used to analyse the data. Results: Findings showed there are significant relationships between sexual desire and marital satisfaction (r = 0.51, p < 0.01) and also between sexual desire and sex guilt (r = -0.44, p < 0.01). Also marital satisfaction and sex guilt were able to predict 31 percent of the variance of sexual desire. Conclusion: Marital satisfaction and sex guilt are two factors that significantly affect fluctuations in sexual desire of Iranian female university students.
Dynamics of a Localized Reputation-Based Network Protocol

We consider a type of game theoretic dynamics in a network model where all nodes act selfishly and will forward packets only if it is to their benefit. The model we present assumes that each node receives utility from successfully sending its own flow to its destination(s) and from receiving flow, while it pays a cost (e.g., battery energy) for its transmissions. Each node has to decide whether to relay flow as an intermediate node from other sources, as relaying incurs only costs. To induce nodes into acting as intermediaries, the model implements a reputation-based mechanism which punishes non-cooperative nodes by cutting off links to them, a decision that is made in a very local fashion. In our setting, the nodes know only the state of the network in their local neighborhood, and can only decide on the amount of the flow on their outgoing edges, unlike the previously considered models where users have full knowledge of the network and can also decide the routing of flow originating from them. Given the opportunistic nature of the nodes and their very limited knowledge of the network, our simulations show the rather surprising fact that a non-negligible amount of non-trivial flow (flow over at least two hops) is successfully transmitted.
microRNA Profiling as Tool for Developmental Neurotoxicity Testing (DNT)

microRNAs (miRNAs) are small non‐coding RNA molecules functioning as post‐transcriptional regulators of gene expression. miRNAs play a significant role in organism development, regulating developmental timing, cell differentiation, and specification. In the developing brain, miRNAs regulate neural stem cell differentiation, lineage specification, synaptogenesis, and brain morphogenesis. Temporal and spatial specificity of miRNA expression make them an attractive marker to study cellular responses to toxicant exposure. Neural differentiation of murine embryonic stem cells (mESCs) has been established as an alternative method to study developmental neurotoxicity (DNT) in vitro. This unit will describe a method for miRNA profiling (miRNomics) as a molecular end point to study developmental neurotoxicity. A protocol for neural differentiation of mESC will be described as a cellular model for DNT testing. The miRNomics protocol is versatile and can be used with other DNT cellular systems such as primary cultures, human embryonic stem cells (hESCs), or induced pluripotent stem cells (iPSCs). © 2015 by John Wiley & Sons, Inc.
Biostimulants in Plant Science: A Global Perspective

This review presents a comprehensive and systematic study of the field of plant biostimulants and considers the fundamental and innovative principles underlying this technology. The elucidation of the biological basis of biostimulant function is a prerequisite for the development of science-based biostimulant industry and sound regulations governing these compounds. The task of defining the biological basis of biostimulants as a class of compounds, however, is made more complex by the diverse sources of biostimulants present in the market, which include bacteria, fungi, seaweeds, higher plants, animals and humate-containing raw materials, and the wide diversity of industrial processes utilized in their preparation. To distinguish biostimulants from the existing legislative product categories we propose the following definition of a biostimulant as “a formulated product of biological origin that improves plant productivity as a consequence of the novel or emergent properties of the complex of constituents, and not as a sole consequence of the presence of known essential plant nutrients, plant growth regulators, or plant protective compounds. ” The definition provided here is important as it emphasizes the principle that biological function can be positively modulated through application of molecules, or mixtures of molecules, for which an explicit mode of action has not been defined. Given the difficulty in determining a “mode of action” for a biostimulant, and recognizing the need for the market in biostimulants to attain legitimacy, we suggest that the focus of biostimulant research and validation should be upon proof of efficacy and safety and the determination of a broad mechanism of action, without a requirement for the determination of a specific mode of action. While there is a clear commercial imperative to rationalize biostimulants as a discrete class of products, there is also a compelling biological case for the science-based development of, and experimentation with biostimulants in the expectation that this may lead to the identification of novel biological molecules and phenomenon, pathways and processes, that would not have been discovered if the category of biostimulants did not exist, or was not considered legitimate.