Miracle-dz/UniFAR-FTUs huggingface dataset:
Partition of Environmental Chemicals between Maternal and Fetal Blood and Tissues

Passage of environmental chemicals across the placenta has important toxicological consequences, as well as for choosing samples for analysis and for interpreting the results. To obtain systematic data, we collected in 2000 maternal and cord blood, cord tissue, placenta, and milk in connection with births in the Faroe Islands, where exposures to marine contaminants is increased. In 15 sample sets, we measured a total of 87 environmental chemicals, almost all of which were detected both in maternal and fetal tissues. The maternal serum lipid-based concentrations of organohalogen compounds averaged 1.7 times those of cord serum, 2.8 times those of cord tissue and placenta, and 0.7 those of milk. For organohalogen compounds detectable in all matrices, a high degree of correlation between concentrations in maternal serum and the other tissues investigated was generally observed (r2 > 0.5). Greater degree of chlorination resulted in lower transfer from maternal serum into milk. Concentrations of pentachlorbenzene, γ-hexachlorocyclohexane, and several polychlorinated biphenyl congeners with low chlorination were higher in fetal samples and showed poor correlation with maternal levels. Perfluorinated compounds occurred in lower concentrations in cord serum than in maternal serum. Cadmium, lead, mercury, and selenium were all detected in fetal samples, but only mercury showed close correlations among concentrations in different matrices. Although the environmental chemicals examined pass through the placenta and are excreted into milk, partitions between maternal and fetal samples are not uniform.
Laryngeal vibrations: measurements of the glottic wave. I. The normal vibratory cycle.

The student of laryngeal physiology encounters a wealth of diverse information on the subject of voice production: Different theories have been proclaimed and discussed heatedly by laryngeal scientists here and abroad, leaving the impression that many details are still nebulous and open to different interpretations. It is true that numerous important observations have been recorded on the activities of the external and internal laryngeal muscles during phonation, on the behavior of the mucous membrane covering the vocal cords, on the acoustic characteristics of the voice, and even on the sensations experienced during voice production with different laryngeal adjustments or "registers. " Yet detailed quantitative measurements of the fundamental entity of voice production, the vibratory function of the vocal cords in human subjects, have had to await the development of special instruments and their adaptation for these studies. Whereas earlier investigators depended entirely upon anatomical preparations from animals and cadavers for their
Digital Reconstructions of Neuronal Morphology: Three Decades of Research Trends

The importance of neuronal morphology has been recognized from the early days of neuroscience. Elucidating the functional roles of axonal and dendritic arbors in synaptic integration, signal transmission, network connectivity, and circuit dynamics requires quantitative analyses of digital three-dimensional reconstructions. We extensively searched the scientific literature for all original reports describing reconstructions of neuronal morphology since the advent of this technique three decades ago. From almost 50,000 titles, 30,000 abstracts, and more than 10,000 full-text articles, we identified 902 publications describing ∼44,000 digital reconstructions. Reviewing the growth of this field exposed general research trends on specific animal species, brain regions, neuron types, and experimental approaches. The entire bibliography, annotated with relevant metadata and (wherever available) direct links to the underlying digital data, is accessible at NeuroMorpho.Org.
Self-Reported Medical Conditions in Perfluorooctanesulfonyl Fluoride Manufacturing Workers

Objective: To evaluate whether some cancers, other conditions, and pregnancy outcomes were related to occupational perfluorooctane sulfonate (PFOS) exposure. Methods: We surveyed current and former employees of a perfluorooctanesulfonyl fluoride production facility, using a self-administered questionnaire to ascertain several cancers and health conditions. Female cohort members also completed a brief pregnancy history. We requested medical records to validate reported melanoma, breast, prostate, and colon cancers. PFOS exposure was estimated based on a job exposure matrix up to the year of the diagnosis of the condition. Results: Of the 1895 eligible participants, 1400 questionnaires were returned. No association was observed between working in a PFOS-exposed job and the risk of any of the surveyed conditions. Conclusion: We observed no association between working in a PFOS-exposed job and several cancers, common health conditions, and birth weight.
Ecological Correlates of Microfilariae Prevalence in Endangered Galápagos Birds

Abstract This study assesses the ecological factors associated with microfilariae prevalence in wild populations of endangered flightless cormorants (Phalacrocorax harrisi) and Galápagos penguins (Spheniscus mendiculus). Prevalence values were tested for correlation with a large number of environmental variables, as modeled from weather station data and measured by satellite-borne sensors. Predictions were made based on the expected effects of climatic and landscape variables on sustained populations of arthropod vectors required for transmission of microfilariae. In general, findings were consistent with predictions in both cormorants and penguins; prevalence correlated positively with temperature, precipitation, and vegetation density, and negatively with measures of environmental variability. Resulting correlates were used to derive predictive distributions of prevalence values in cormorants throughout the archipelago. Evidence is presented implicating the mosquito Aedes taeniorhynchus as a likely vector. Knowledge of environmental variables that predict risk of disease transmission by arthropod vectors may be useful in control measures should novel pathogens be introduced to the ecosystem.
Development and Validation of SACRAM: A Swiss Approach to the Computational Response of an Ablative Material

Future space exploration missions foresee high-speed entries into planetary atmospheres. The space vehicle is exposed to extreme thermal conditions and requires an appropriate thermal protection system (TPS). A complete set of TPS material properties is not available in open literature. The inter-code comparison exercise proposed by the AF/SNL/NASA Ablation Workshop gives a baseline platform for ablation code calibration, with a complete set of material and gas properties.
SHORT TERM MEMORY IN A NETWORK OF SPIKING NEURONS

A distributed connectionist model of spiking neurons (INFERNET) is used to simulate various aspects of Short Term Memory. In INFERNET, short term memory is the transient activation of long term memory elements. This single store model has a human-like performance in short term memory span tasks, but also displays serial position effects, similarity effects, and double dissociation between short and long term memory which are considered as the main psychological arguments in favor of the multiple-store model.
Large-scale mosaicking with spectral registration based simultaneous localization and mapping (iFMI-SLAM) in the Ligurian Sea

Underwater image mosaicking is an important tool for visual surveys, object detection, and as a means to control the underwater robot if done online. In this paper, novel results of an spectral registration method on image data collected by a remotely operated vehicle in the Ligurian Sea are presented. The registration method computes 2D translation, rotation, and scale, along with a covariance matrix for these parameters. An appearance-based place recognition method is used to detect loops. These methods are embedded in a graph-based Simultaneous Localization and Mapping framework to provide a globally consistent and optimized map of the photographed ground.
Identification of Two Evolutionarily Conserved 5' cis-Elements Involved in Regulating Spatiotemporal Expression of Nolz-1 during Mouse Embryogenesis

Proper development of vertebrate embryos depends not only on the crucial funtions of key evolutionarily conserved transcriptional regulators, but also on the precisely spatiotemporal expression of these transcriptional regulators. The mouse Nolz-1/Znf503/Zfp503 gene is a mammalian member of the conserved zinc-finger containing NET family. The expression pattern of Nolz-1 in mouse embryos is highly correlated with that of its homologues in different species. To study the spatiotemporal regulation of Nolz-1, we first identified two evolutionarily conserved cis-elements, UREA and UREB, in 5′ upstream regions of mouse Nolz-1 locus. We then generated UREA-LacZ and UREB-LacZ transgenic reporter mice to characterize the putative enhancer activity of UREA and UREB. The results indicated that both UREA and UREB contained tissue-specific enhancer activity for directing LacZ expression in selective tissue organs during mouse embryogensis. UREA directed LacZ expression preferentially in selective regions of developing central nervous system, including the forebrain, hindbrain and spinal cord, whereas UREB directed LacZ expression mainly in other developing tissue organs such as the Nolz-1 expressing branchial arches and its derivatives, the apical ectodermal ridge of limb buds and the urogenital tissues. Both UREA and UREB directed strong LacZ expression in the lateral plate mesoderm where endogenous Nolz-1 was also expressed. Despite that the LacZ expression pattern did not full recapitulated the endogenous Nolz-1 expression and some mismatched expression patterns were observed, co-expression of LacZ and Nolz-1 did occur in many cells of selective tissue organs, such as in the ventrolateral cortex and ventral spinal cord of UREA-LacZ embryos, and the urogenital tubes of UREB-LacZ embryos. Taken together, our study suggests that UREA and UREB may function as evolutionarily conserved cis-regulatory elements that coordinate with other cis-elements to regulate spatiotemporal expression of Nolz-1 in different tissue organs during mouse embryogenesis.
Molecular Evolution of HIV-1 CRF01_AE Env in Thai Patients

Background The envelope glycoproteins (Env), gp120 and gp41, are the most variable proteins of human immunodeficiency virus type 1 (HIV-1), and are the major targets of humoral immune responses against HIV-1. A circulating recombinant form of HIV-1, CRF01_AE, is prevalent throughout Southeast Asia; however, only limited information regarding the immunological characteristics of CRF01_AE Env is currently available. In this study, we attempted to examine the evolutionary pattern of CRF01_AE Env under the selection pressure of host immune responses. Methodology/Principal Findings Peripheral blood samples were collected periodically over 3 years from 15 HIV-1-infected individuals residing in northern Thailand, and amplified env genes from the samples were subjected to computational analysis. The V5 region of gp120 showed highest variability in several samples over 3 years, whereas the V1/V2 and/or V4 regions of gp120 also showed high variability in many samples. In addition, the N-terminal part of the C3 region of gp120 showed highest amino acid diversity among the conserved regions of gp120. Chronological changes in the numbers of amino acid residues in gp120 variable regions and potential N-linked glycosylation (PNLG) sites are involved in increasing the variability of Env gp120. Furthermore, the C3 region contained several amino acid residues potentially under positive selection, and APOBEC3 family protein-mediated G to A mutations were frequently detected in such residues. Conclusions/Significance Several factors, including amino acid substitutions particularly in gp120 C3 and V5 regions as well as changes in the number of PNLG sites and in the length of gp120 variable regions, were revealed to be involved in the molecular evolution of CRF01_AE Env. In addition, a similar tendency was observed between CRF01_AE and subtype C Env with regard to the amino acid variation of gp120 V3 and C3 regions. These results may provide important information for understanding the immunological characteristics of CRF01_AE Env.
Transcriptional regulatory circuits controlling mitochondrial biogenesis and function.

We are witnessing a period of renewed interest in the biology of the mitochondrion. The mitochondrion serves a critical function in the maintenance of cellular energy stores, thermogenesis, and apoptosis. Moreover, alterations in mitochondrial function contribute to several inherited and acquired human diseases and the aging process. This review summarizes our understanding of the transcriptional regulatory mechanisms involved in the biogenesis and energy metabolic function of mitochondria in higher organisms.
A 2 DOF predictive control based on evolving fuzzy model

In this paper we present the design of a two degree-of-freedom (2 DOF) control algorithm, developed for a class of single-input multiple-output non-linear systems. The feedforward and feedback control loops are developed based on the known Takagi-Sugeno fuzzy model of the system. The fuzzy model is part of the control law and it is obtained by evolving fuzzy modelling. Although only a single system output is controlled, the clustering in evolving fuzzy model is made on multiple measurable system outputs. The control law is designed in a way that enables clustering in the evolving fuzzy model on multiple outputs. However, every input-output connection is described by a non-linear autoregressive system with exogenous inputs. The purpose of the feed-forward loop is to bring the controlled output close to the desired reference signal, and the feedback loop is used to eliminate the reference tracking error that may occur due to imprecise system modelling, noise or any other disturbances. Linearisation around the reference signal enables the design of an error-model predictive control in the feedback loop. The presented control approach was experimentally validated in simulation environment on a system of three water tanks. The experimental results confirm the applicability of the approach.
A Secure Routing Protocol for Cluster-Based Wireless Sensor Networks Using ID-Based Digital Signature

In this paper, we study the secure routing for cluster-based sensor networks where clusters are formed dynamically and periodically. We point out the deficiency in the secure routing protocols with symmetric key pairing. Along with the investigation of ID-based cryptography for security in WSNs, we propose a new secure routing protocol with ID-based signature scheme for cluster-based WSNs, in which the security relies on the hardness of the Diffie-Hellman problem in the random oracle model. Because of the communication overhead for security, we provide analysis and simulation results in details to illustrate how various parameters act between security and energy efficiency.
Modeling acoustics in virtual environments using the uniform theory of diffraction

Realistic modeling of reverberant sound in 3D virtual worlds provides users with important cues for localizing sound sources and understanding spatial properties of the environment. Unfortunately, current geometric acoustic modeling systems do not accurately simulate reverberant sound. Instead, they model only direct transmission and specular reflection, while diffraction is either ignored or modeled through statistical approximation. However, diffraction is important for correct interpretation of acoustic environments, especially when the direct path between sound source and receiver is occluded. The Uniform Theory of Diffraction (UTD) extends geometrical acoustics with diffraction phenomena: illuminated edges become secondary sources of diffracted rays that in turn may propagate through the environment. In this paper, we propose an efficient way for computing the acoustical effect of diffraction paths using the UTD for deriving secondary diffracted rays and associated diffraction coefficients. Our main contributions are: 1) a beam tracing method for enumerating sequences of diffracting edges efficiently and without aliasing in densely occluded polyhedral environments; 2) a practical approximation to the simulated sound field in which diffraction is considered only in shadow regions; and 3) a real-time auralization system demonstrating that diffraction dramatically improves the quality of spatialized sound in virtual environments.
Control of e2f1 and PCNA by Drosophila transcription factor DREF

DREF (DNA replication‐related element‐binding factor), a zinc finger type transcription factor required for proper cell cycle progression in both mitotic and endocycling cells, is a positive regulator of E2F1, an important transcription factor which regulates genes related to the S‐phase of the cell cycle. DREF and E2F1 regulate similar sets of replication‐related genes, including proliferating cell nuclear antigen (PCNA), and play roles in the G1 to S phase transition. However, the relationships between dref and e2f1 or PCNA during development are poorly understood. Here, we provided evidence for novel control of e2f1 and PCNA involving DREF in endocycling cells. Somatic clone analysis demonstrated that dref knockdown stabilized E2F1 expression at posttranscriptional levels in endocycling salivary gland cells. Similarly, PCNA expression was up‐regulated in the endocycling salivary gland cells. Genetic interaction analysis indicated that the endoreplication defects are partly caused via possible enhancement of E2F1 activity. From these results and previous reports, we conclude that regulation of e2f1 and PCNA by DREF in vivo is complex and the regulation mechanism may differ with the tissue and/or positions in the tissue. genesis 51:741–750. © 2013 Wiley Periodicals, Inc.
Three-Stage Serially Concatenated Codes and Iterative Center-Shifting K-Best Sphere Detection for SDM-OFDM: An EXIT Chart Aided Perspective

Iterative if-best sphere detection (SD) and channel decoding is appealing, since it is capable of achieving a near- maximum-a-posteriori (MAP) performance at a low complexity. However, a potentially excessive computational cost is imposed, especially in a high-throughput Spatial Division Multiplexing (SDM) aided OFDM system employing a large number of transmit antennas and/or high-order modulation schemes. This problem is further aggravated, when the number of transmit antennas exceeds that of the receive antennas, namely in the challenging scenario of rank-deficient systems. In order to further reduce the complexity imposed, we propose a unity-rate-code-aided (URC) three-stage concatenated transceiver constituted by an inner and outer channel encoder/decoder pair as well as the SDM aided OFDM transmitter and K-best SD. We have demonstrated that our proposed three-stage scheme is capable of achieving a substantial performance gain over the classic two-stage scheme. For example, given a target Bit Error Ratio (BER) of 10 5, the three-stage SD-aided receiver is capable of achieving a performance gain of 4 dB over its two-stage counterpart in an (8 x 4)-element SDM/OFDM system. Furthermore, we have also investigated the achievable performance of our novel center- shifting aided SD in the context of this three-stage scheme. Consequently, an additional 0.5 dB performance gain can be attained. Finally, the convergence behavior of the proposed schemes were studied with the aid of 3D Extrinsic Information Transfer (EXIT) charts and their 2D projections.
Improving the Accuracy and Efficiency of Time-Independent Trace Replay

Simulation is a popular approach to obtain objective performance indicators on platforms that are not at one's disposal. It may help the dimensioning of compute clusters in large computing centers. In a previous work, we proposed a framework for the off-line simulation of MPI applications. Its main originality with regard to the literature is to rely on time-independent execution traces. This allows us to completely decouple the acquisition process from the actual replay of the traces in a simulation context. Then we are able to acquire traces for large application instances without being limited to an execution on a single compute cluster. Finally our framework is built on top of a scalable, fast, and validated simulation kernel. In this paper, we detail the performance issues that we encountered with the first implementation of our trace replay framework. We propose several modifications to address these issues and analyze their impact. Results show a clear improvement on the accuracy and efficiency with regard to the initial implementation.
Brain Mapping in Sedated Infants and Young Children with Passive-Functional Magnetic Resonance Imaging

Functional magnetic resonance imaging (fMRI) in pediatric patients presents a unique set of problems due to the need for patient compliance, the frequent need for sedation and an early developmental status. A new method for using fMRI in sedated infants and young children is presented using passive stimuli focused on visual, sensorimotor and language functions. All of these stimuli are presented such that no patient interaction is required. Eight sedated children undergoing diagnostic MRI scans of the brain participated in these passive fMRI procedures. Cortical regions were identified using standard techniques applied to the blood-oxygen-level-dependent signal which is the basis for fMRI. The results support the feasibility of brain mapping in sedated children with passive fMRI techniques. Introduction Recent developments in several imaging modalities have resulted in nonoperative methods for brain mapping. Functional magnetic resonance imaging (fMRI), magnetic source imaging and positron emission tomography have recently been utilized to define regional areas of cerebral function. Relative cost, superior spatial resolution and avoidance of either external or intravenous ionizing radiation are issues that favor fMRI as a superior method for functional imaging. The reliability of this technique has been confirmed through conventional methods of brain mapping [1–9]. Given this level of reliability, fMRI is currently being utilized as an adjunct for assessing surgical risk and tailoring intraoperative strategy in patients with lesions juxtaposed to functional domains. Functional MRI mapping typically requires that a series of specified tasks be performed by the patient being imaged. These tasks are dictated based on the cortical representation area of interest. As an example, object naming is a method used to perform functional imaging of D ow nl oa de d by : Y al e M ed ic al L ib ra ry 13 0. 13 2. 17 3. 17 8 2/ 20 /2 01 4 7: 21 :4 3 P M
Phonetic ignorance is bliss: investigating the effects of phonetic information reduction on ASR performance

Perception studies have long argued that phonetic confusions are more likely to happen across some phonetic features than other (e.g., place of articulation rather than manner) [1]. Similarly, we and others have noted that pronunciation variation occurs more frequently in unstressed syllables, and in syllable codas. This suggests that a phonetic information structure is at play, where for decoding purposes it is important to get phonetic information accurate in stressed syllables, but less so in unstressed syllables. In this work, we explore the role of phonetic information in clean and noisy speech by reducing the phonetic information available to the recognizer. A surprising result is that replacing some phones with manner classes in the dictionary improves recognition in one noise condition.