Miracle-dz/UniFAR-FTUs huggingface dataset:
Bioenergetics in human evolution and disease: implications for the origins of biological complexity and the missing genetic variation of common diseases

Two major inconsistencies exist in the current neo-Darwinian evolutionary theory that random chromosomal mutations acted on by natural selection generate new species. First, natural selection does not require the evolution of ever increasing complexity, yet this is the hallmark of biology. Second, human chromosomal DNA sequence variation is predominantly either neutral or deleterious and is insufficient to provide the variation required for speciation or for predilection to common diseases. Complexity is explained by the continuous flow of energy through the biosphere that drives the accumulation of nucleic acids and information. Information then encodes complex forms. In animals, energy flow is primarily mediated by mitochondria whose maternally inherited mitochondrial DNA (mtDNA) codes for key genes for energy metabolism. In mammals, the mtDNA has a very high mutation rate, but the deleterious mutations are removed by an ovarian selection system. Hence, new mutations that subtly alter energy metabolism are continuously introduced into the species, permitting adaptation to regional differences in energy environments. Therefore, the most phenotypically significant gene variants arise in the mtDNA, are regional, and permit animals to occupy peripheral energy environments where rarer nuclear DNA (nDNA) variants can accumulate, leading to speciation. The neutralist–selectionist debate is then a consequence of mammals having two different evolutionary strategies: a fast mtDNA strategy for intra-specific radiation and a slow nDNA strategy for speciation. Furthermore, the missing genetic variation for common human diseases is primarily mtDNA variation plus regional nDNA variants, both of which have been missed by large, inter-population association studies.
A six-stranded double-psi beta barrel is shared by several protein superfamilies.

BACKGROUND Six-stranded beta barrels with a pseudo-twofold axis are found in several proteins. One group comprises a Greek-key structure with all strands antiparallel; an example is the N-terminal domain of ferredoxin reductase. Others involve parallel strands forming two psi structures (the double-psi beta barrel). A recently discovered example of the latter class is aspartate-alpha-decarboxylase (ADC) from Escherichia coli, a pyruvoyl-dependent tetrameric enzyme involved in the synthesis of pantothenate. RESULTS Visual inspection and automated database searches identified the six-stranded double-psi beta barrel in ADC, Rhodobacter sphaeroides dimethylsulfoxide (DMSO) reductase, E. coli formate dehydrogenase H (FDHH), the plant defense protein barwin, Humicola insolens endoglucanase V (EGV) and, with a circular permutation, in the aspartic proteinases. Structure-based sequence alignments revealed several interactions including hydrophobic contacts or sidechain-mainchain hydrogen bonds that position the middle beta strand under a psi loop, which may significantly contribute to stabilizing the fold. The identification of key interactions allowed the filtering of weak sequence similarities to some of these proteins, which had been detected by sequence database searches. This led to the prediction of the double-psi beta-barrel domain in several families of proteins in eukaryotes and archaea. CONCLUSIONS The structure comparison and clustering study of double-psi beta barrels suggests that there could be a common homodimeric ancestor to ADC, FDHH and DMSO reductase, and also to barwin and EGV. There are other protein families with unknown structure that are likely to adopt the same fold. In the known structures, the protein active sites cluster around the psi loop, indicating that its rigidity, protrusion and free mainchain functional groups may be well suited to providing a framework for catalysis.
Cavitation and contrast: The use of bubbles in ultrasound imaging and therapy

Abstract Microbubbles and cavitation are playing an increasingly significant role in both diagnostic and therapeutic applications of ultrasound. Microbubble ultrasound contrast agents have been in clinical use now for more than two decades, stimulating the development of a range of new contrast-specific imaging techniques which offer substantial benefits in echocardiography, microcirculatory imaging, and more recently, quantitative and molecular imaging. In drug delivery and gene therapy, microbubbles are being investigated/developed as vehicles which can be loaded with the required therapeutic agent, traced to the target site using diagnostic ultrasound, and then destroyed with ultrasound of higher intensity energy burst to release the material locally, thus avoiding side effects associated with systemic administration, e.g. of toxic chemotherapy. It has moreover been shown that the motion of the microbubbles increases the permeability of both individual cell membranes and the endothelium, thus enhancing therapeutic uptake, and can locally increase the activity of drugs by enhancing their transport across biologically inaccessible interfaces such as blood clots or solid tumours. In high-intensity focused ultrasound (HIFU) surgery and lithotripsy, controlled cavitation is being investigated as a means of increasing the speed and efficacy of the treatment. The aim of this paper is both to describe the key features of the physical behaviour of acoustically driven bubbles which underlie their effectiveness in biomedical applications and to review the current state of the art.
Complement-Mediated Regulation of Trichomonas vaginalis Infection in Mice

Trichomonas vaginalis is a flagellated protozoan which causes trichomoniasis, a sexually transmitted disease of the human genitourinary tract. The importance of the alternative complement pathway in host defence against T. vaginalis was investigated in vitro. Kinetic studies utilising immunofixation following electrophoresis showed that both a strongly and weakly virulent strain of T. vaginalis activated murine serum C3. In vivo studies with congenic-resistant, C5-deficient, B10.D2/OSn- and C5-sufficient, B10.D2/nSn mice showed that the presence of C5 is a significant factor in the innate host resistance to primary infection with a strongly virulent, but not a weakly virulent trichomonad strain.
Emotions and personality traits as high-level factors in visual attention: a review

The visual sense has outstanding significance for human perception and behavior, and visual attention plays a central role in the processing of the sensory input. Thereby, multiple low- and high-level factors contribute to the guidance of attention. The present review focuses on two neglected high-level factors: emotion and personality. The review starts with an overview of different models of attention, providing a conceptual framework and illustrating the nature of low- and high-level factors in visual attention. Then, the ambiguous concept of emotion is described, and recommendations are made for the experimental practice. In the following, we present several studies showing the influence of emotion on overt attention, whereby the distinction between internally and externally located emotional impacts are emphasized. We also provide evidence showing that emotional stimuli influence perceptual processing outside of the focus of attention, whereby results in this field are mixed. Then, we present some detached studies showing the reversed causal effect: attention can also affect emotional responses. The final section on emotion–attention interactions addresses the interplay on the neuronal level, which has been neglected for a long time in neuroscience. In this context, several conceptual recommendations for future research are made. Finally, based on findings showing inter-individual differences in human sensitivity to emotional items, we introduce the wide range of time-independent personality traits that also influence attention, and in this context we try to raise awareness of the consideration of inter-individual differences in the field of neuroscience.
Selection Bias in Minimum-Wage Research ? A Meta-Regression Analysis

Card and Krueger’s meta-analysis of the employment effects of minimum wages challenged existing theory. Unfortunately, their meta-analysis confused publication selection with the absence of a genuine empirical effect. We apply recently developed meta-analysis methods to 64 US minimum-wage studies and corroborate that Card and Krueger’s findings were nevertheless correct. The minimum-wage effects literature is contaminated by publication selection bias, which we estimate to be slightly larger than the average reported minimumwage effect. Once this publication selection is corrected, little or no evidence of a negative association between minimum wages and employment remains. (P)ublication bias is leading to a new formulation of Gresham’s law — like bad money, bad research drives out good. (Bland 1988: 450)
Icariside II, a natural mTOR inhibitor, disrupts aberrant energy homeostasis via suppressing mTORC1-4E-BP1 axis in sarcoma cells

The aberrant energy homeostasis that characterized by high rate of energy production (glycolysis) and energy consumption (mRNA translation) is associated with the development of cancer. As mammalian target of rapamycin (mTOR) is a critical regulator of aberrant energy homeostasis, it is an attractive target for anti-tumor intervention. The flavonoid compound Icariside II (IS) is a natural mTOR inhibitor derived from Epimedium. Koreanum. Herein, we evaluate the effect of IS on aberrant energy homeostasis. The reduction of glycolysis and mRNA translation in U2OS (osteosarcoma), S180 (fibrosarcoma) and SW1535 (chondrosarcoma) cells observed in our study, indicate that, IS inhibits aberrant energy homeostasis. This inhibition is found to be due to suppression of mammalian target of rapamycin complex 1 (mTORC1)-eukaryotic translation initiation factor 4E-binding protein 1 (4E-BP1) axis through blocking the assembly of mTORC1. Furthermore, IS inhibits the cap-dependent translation of c-myc through mTORC1-4E-BP1 axis which links the relationship between mRNA translation and glycolysis. Inhibition of aberrant energy homeostasis by IS, contributes to its in vitro and in vivo anti-proliferation activity. These data indicate that IS disrupts aberrant energy homeostasis of sarcoma cells through suppression of mTORC1-4E-BP1 axis, providing a novel mechanism of IS to inhibit cell proliferation in sarcoma cells.
Efficient Packet Video Delivery over Heterogeneous Networks

For packet video transmission over heterogeneous networks, a novel Priority-Aware Two Rate Three Color Marker (PATRTCM) method is presented in this paper. PATRTCM introduces three marking probabilities that are calculated according to the importance of the video packet and the network conditions. A video packet is marked red, yellow or green based on the probabilities in the wired DiffServ networks, and mapped to the queues on the IEEE 802.11e MAC layer. Simulation results show that PATRTCM can improve the quality of video streaming over heterogeneous networks.
Evaluating the Appropriateness of College-Age Norms for Use With Adolescents on the NEO Personality Inventory—Revised

The NEO Personality Inventory—Revised (NEO PI-R) measures normal personality characteristics and has demonstrated appropriate score reliability and validity. It is normed for two groups of individuals, college-age individuals 17 to 20 years old and adults 21 and older. Often, personality instruments normed on older individuals have been used with adolescent populations. To examine the appropriateness of this decision, the current study explored the differences between an adolescent sample (n = 79) and a college-age sample (n = 80) on the 30 facets and the five domains of the NEO PI-R. Group differences on the facet and domain scales were analyzed using descriptive discriminant analysis. Results indicated that the adolescent and college groups differed on each of the five domains. As expected, the groups also scored differently using the aggregated domain-level variables as the outcome measures. Suggestions for future research include the development of normative data for the adolescent population.
Auditory-based Acoustic Distinctive Features and Spectral Cues for Robust Automatic Speech Recognition in Low-SNR Car Environments

In this paper, a multi-stream paradigm is proposed to improve the performance of automatic speech recognition (ASR) systems in the presence of highly interfering car noise. It was found that combining the classical MFCCs with some auditory-based acoustic distinctive cues and the main formant frequencies of a speech signal using a multi-stream paradigm leads to an improvement in the recognition performance in noisy car environments.
FPGA-BASED CHIRP GENERATOR FOR HIGH RESOLUTION UAV SAR

This paper discusses the design and development of a FPGA-based chirp generator for high resolution Unmanned Aerial Vehicle (UAV) Synthetic Aperture Radar. The desired bandwidth of the chirp signal is 100MHz (combination of I and Q channels) with a chirp rate of 5MHz/"s. Two algorithms based on the Memory-based architecture and the Direct Digital Synthesizer (DDS) architecture are presented. The measurement results indicate that the DDS chirp generator is a preferred choice for high-resolution SAR application.
CRSN Symposium : Focus on Depression , Part I Symposium du CRSN : le point sur la dépression , première partie Gene – environment interaction and the genetics of depression

Rev Psychiatr Neurosci 2004;29(3) © 2004 Canadian Medical Association Depression is a group of brain disorders with varied origins, complex genetics and obscure neurobiology. Definitions of clinical phenotypes are not rooted in their neurobiology, and animal models of behavioural despair have considerable limitations. Nevertheless, investigation of subtle alterations in gene expression, of correlations between genotype and brain activity, and of environmental variables interacting with genetic variants have advanced research into the genetics of depression. Although the postgenomic era is still in its infancy, several milestones have already been reached: variation in gene expression has been confirmed to play a predominant role in individual differences; gene–environment interactions have been established in humans and in a nonhuman primate model; gene–phenotype correlations have been substantiated by functional neuroimaging; and the notion of gene networks that control brain development is increasingly recognized. Given the etiologic and psychobiologic complexity of mood disorders, it is not surprising that the identification of specific genetic factors is extremely difficult and continues to be among the last frontiers of gene hunting.
A kernel particle filter algorithm for joint tracking and classification

For radar surveillance system, target tracking and classification are two major functions. A kernel particle filter approach with improved information mutual feedback is presented for joint tracking and classification. Delay, Doppler and Radar cross section measurements are used to estimate target state and class respectively. It invokes the kernel particle filter and point model for nonlinear estimation with less amount of calculation. Mutual feedback structure is used to improve the classification probability and estimation accuracy. Simulation results show the efficiency of the proposed method.
L-FABP directly interacts with PPAR&agr; in cultured primary hepatocytes

Although studies with liver type fatty acid binding protein (L-FABP) gene ablated mice demonstrate a physiological role for L-FABP in hepatic fatty acid metabolism, little is known about the mechanisms whereby L-FABP elicits these effects. Studies indicate that L-FABP may function to shuttle lipids to the nucleus, thereby increasing the availability of ligands of nuclear receptors, such as peroxisome proliferator-activated receptor-&agr; (PPAR&agr;). The data herein suggest that such mechanisms involve direct interaction of L-FABP with PPAR&agr;. L-FABP was shown to directly interact with PPAR&agr; in vitro through co-immunoprecipitation (co-IP) of pure proteins, altered circular dichroic (CD) spectra, and altered fluorescence spectra. In vitro fluorescence resonance energy transfer (FRET) between Cy3-labeled PPAR&agr; and Cy5-labeled L-FABP proteins showed that these proteins bound with high affinity (Kd approximately 156 nM) and in close proximity (intermolecular distance of 52Å). This interaction was further substantiated by co-IP of both proteins from liver homogenates of wild-type mice. Moreover, double immunogold electron microscopy and FRET confocal microscopy of cultured primary hepatocytes showed that L-FABP was in close proximity to PPAR&agr; (intermolecular distance 40–49Å) in vivo. Taken together, these studies were consistent with L-FABP regulating PPAR&agr; transcriptional activity in hepatocytes through direct interaction with PPAR&agr;. Our in vitro and imaging experiments demonstrate high affinity, structural molecular interaction of L-FABP with PPAR&agr; and suggest a functional role for L-FABP interaction with PPAR&agr; in long chain fatty acid (LCFA) metabolism.
Soft-switching bidirectional isolated three-phase DC-DC converter with dual phase-shift and variable duty cycle

This paper presents the analysis, design, and experimental results for a soft-switching bidirectional isolated three-phase DC-DC converter with dual phase-shift and variable duty cycle. The topology uses three single H-bridges in the primary side and a three-phase inverter in the secondary side. The high frequency isolation is ensured by using three single-phase transformers connected in open delta-wye configuration. Variation of both phase shift angles between single H-bridge legs and/or primary and secondary side allows the power delivery control. This additional flexibility allows the system to maintain a low reactive power flow. The variable duty cycle is used to ensure a constant voltage bus and ZVS soft switching operation. A detailed analysis is presented considering a model based on fundamental components. Experimental results for a prototype are performed to validate the model used.
THE LIMITS OF COGNITIVE LIBERALISM

The central characteristic of cognitive explanations of behavior is the appeal to inner representations. I examine the grounds which justify representational explanations, seeking the minimum conditions which organisms must meet to be candidates for such explanations. I first discuss Fodor's proposal that representationality be attributed to systems which respond to nonnomic properties, arguing that the distinction between the nomic and nonnomic in perception is fatally ambiguous. Then I turn to an illustrative review of the behavior and neurobiology of Hermissenda crassicornis, a marine mollusk. Concerning this "model system," I compare the representational style of explanation with both behaviorist and neurophysiological explanations. Representational explanation is potentially more comprehensive than its rivals, and thus I conclude that representations are useful posits wherever internal information-bearing states mediate behavior.
Twitter Can Predict Your Next Place of Visit

The present work focuses on predicting users' next place of visit using their past tweets. We hypothesize that tweets of the person have predictive power on his location and therefore can be used to predict his next place of visit. This problem is important for location based advertising and recommender based services. To predict the next place of visit, we calculate the probabilities of visiting different types of places using bank of binary classifiers and Markov models. More specifically, we train bank of binary classifiers on past tweets and calculated the probabilities of visiting next places. Since bank of binary classifiers is based on a bag-of-words model, to account for time of last visited place and place itself, we built Markov models for different time duration to calculate probabilities of visiting next place. Empirical evaluation shows that by combining the probabilities obtained from bank of binary classifiers and Markov models the accuracy of predicting next place increased from 65% to 80%.
eIF3f reduces tumor growth by directly interrupting clusterin with anti-apoptotic property in cancer cells

Clusterin is a secretory heterodimeric glycoprotein and the overexpression of secretory clusterin (sCLU) promotes cancer cell proliferation and reduces chemosensitivity. Therefore, sCLU might be an effective target for anticancer therapy. In the current study, we identified eIF3f as a novel CLU-interacting protein and demonstrated its novel function as a CLU inhibitor. The overexpression of eIF3f retarded cancer cell growth significantly and induced apoptosis. In addition, eIF3f interacted with the α-chain (1–227) of sCLU. This interaction blocked modification of psCLU, thereby decreasing the expression and secretion of α/β CLU. Consequently, the overexpression of eIF3f suppressed Akt and ERK signaling and subsequently depleted CLU expression. In addition, eIF3F stabilized p53, which increased the expression of p21 and Bax. Interestingly, the expression of Bax was increased without the activation of p53. eIF3f injected into a xenograft model of human cervical cancer in nude mice markedly inhibited tumor growth. The identification of this novel function of eIF3f as a sCLU inhibitor might open novel avenues for developing improved strategies for CLU-targeted anti-cancer therapies.
Journal of Ethnobiology and Ethnomedicine Open Access Local Knowledge in Community-based Approaches to Medicinal Plant Conservation: Lessons from India

Background: Community-based approaches to conservation of natural resources, in particular medicinal plants, have attracted attention of governments, non governmental organizations and international funding agencies. This paper highlights the community-based approaches used by an Indian NGO, the Rural Communes Medicinal Plant Conservation Centre (RCMPCC). The RCMPCC recognized and legitimized the role of local medicinal knowledge along with other knowledge systems to a wider audience, i.e. higher levels of government.
Cell-to-cell communication in the anterior pituitary: evidence for gap junction-mediated exchanges between endocrine cells and folliculostellate cells.

The ability of rat anterior pituitary cells to communicate through gap junctions (GJ) was studied using a fluorescent molecule, Lucifer Yellow (LY), which freely passes through GJ channels. The probe was introduced into the cell cytoplasm by using either the cut-end loading method on intact tissue, or cell microinjection on cultured cells. The identification of communicating cells was performed by immunofluorescence labeling of specific hormones in endocrine cells and of S100 protein in folliculostellate (FS) cells. Rat anterior pituitary cells in their physiological organization, i.e. in the intact tissue, exhibited a high level of coupling through GJ. LY-labeled cells were found up to 300-microns apart from its site of introduction. The communicating cells were primarily PRL cells, GH cells, and FS cells. Only a few LH, TSH, and ACTH cells were labeled with LY. Anterior pituitary cells, isolated from the rat tissue by mild protease treatment and cultured for 3 days, reestablished functional GJ as demonstrated by microinjection of LY into individual cells. By immunolabeling of specific hormones and/or S100 protein, we found a GJ coupling between FS cells, and between FS cells and endocrine cells, including PRL cells. The communication between FS cells was by far the most frequent. In conclusion, we demonstrate the presence of functional GJ between anterior pituitary cells of the same type and between anterior pituitary cells having distinct differentiated functions.