Miracle-dz/UniFAR-FTUs huggingface dataset:
Higher maternal prenatal cortisol and younger age predict greater infant reactivity to novelty at 4 months: an observation-based study.

Distress-linked activation of the maternal hypothalamic-pituitary-adrenal (HPA)-axis is considered a pathway by which affect regulation impacts the fetal milieu and neurodevelopment. There is little direct evidence for this conceptual model. In 103 women [mean age 27.45 (±5.65) years] at 36-38 weeks gestation, salivary cortisol was measured before/after stress tasks; distress questionnaires were completed. At 18.49 (±1.83) weeks, infants underwent the Harvard Infant Behavioral Reactivity Protocol assessing cry/motor responses to novelty; women reported on infant behavior and postnatal distress. Prenatal cortisol and distress were not significantly correlated (all ps > .10). Proportional odds logistic regressions showed that neither prenatal nor postnatal distress was associated with infant responses to the Harvard Protocol yet pre-stress cortisol and maternal age were: The odds of being classified as High Reactive were 1.60 times higher [95% CI: 1.04, 2.46] for each unit of added cortisol and . 90 times lower [95% CI: . 82, . 99] for every additional year in maternal age. No associations were found between cortisol or prenatal distress and mother-rated infant behavior; postnatal distress was positively associated with mother-rated infant negative behavior (p = .03). Observer and mother-rated infant behavior were not associated (all ps > .05). Based on independent observations of infants in contrast to maternal perceptions, these results lend support to the hypothesis that pregnant women's HPA-axis activity influences infant behavior. The impact of maternal distress was not supported, except in so far as postnatal distress may increase the likelihood of making negative judgments about infant behavior.
Torovirus Non-Discontinuous Transcription: Mutational Analysis of a Subgenomic mRNA Promoter

ABSTRACT Toroviruses (order Nidovirales) are enveloped positive-strand RNA viruses of mammals. The prototype torovirus, equine torovirus strain Berne (Berne virus [BEV]), uses two different transcription strategies to produce a 3′-coterminal nested set of subgenomic (sg) mRNAs. Its mRNA 2 carries a leader sequence derived from the 5′ end of the genome and is produced via discontinuous transcription. The remaining three sg mRNAs, 3 to 5, are colinear with the 3′ end of the genome and are made via non-discontinuous RNA synthesis. Their synthesis is supposedly regulated by short conserved sequence motifs, 5′-ACN3-4CUUUAGA-3′, within the noncoding intergenic regions that precede the M, HE, and N genes (A. L. van Vliet, S. L. Smits, P. J. Rottier, and R. J. de Groot, EMBO J. 21:6571-6580, 2002). We have now studied the—for nidoviruses unusual—non-discontinuous transcription mechanism in further detail by probing the role of the postulated transcription-regulating sequences (TRSs). To this end, we constructed a synthetic defective interfering (DI) RNA, carrying a 24-nucleotide segment of the intergenic region between the HE and N genes. We demonstrate that this DI RNA, when introduced into BEV-infected cells, directs the synthesis of a sg DI RNA species; in fact, a 16-nucleotide cassette containing the TRS already proved sufficient. Synthesis of this sg DI RNA, like that of mRNAs 3 to 5 of the standard virus, initiated at the 5′-most adenylate of the TRS. An extensive mutational analysis of the TRS is presented. Our results provide first and formal experimental evidence that the conserved motifs within the BEV intergenic sequences indeed drive sg RNA synthesis.
Hydrophobic Collapse in Multidomain Protein Folding

We performed molecular dynamics simulations of the collapse of a two-domain protein, the BphC enzyme, into a globular structure to examine how water molecules mediate hydrophobic collapse of proteins. In the interdomain region, liquid water persists with a density 10to 15% lower than in the bulk, even at small domain separations. Water depletion and hydrophobic collapse occur on a nanosecond time scale, which is two orders of magnitude slower than that found in the collapse of idealized paraffin-like plates. When the electrostatic protein-water forces are turned off, a dewetting transition occurs in the interdomain region and the collapse speeds up by more than an order of magnitude. When attractive van der Waals forces are turned off as well, the dewetting in the interdomain region is more profound, and the collapse is even faster.
Melanomacrophage Centers As a Histological Indicator of Immune Function in Fish and Other Poikilotherms

Melanomacrophage centers (MMCs) are aggregates of highly pigmented phagocytes found primarily in the head kidney and spleen, and occasionally the liver of many vertebrates. Preliminary histological analyses suggested that MMCs are structurally similar to the mammalian germinal center (GC), leading to the hypothesis that the MMC plays a role in the humoral adaptive immune response. For this reason, MMCs are frequently described in the literature as “primitive GCs” or the “evolutionary precursors” to the mammalian GC. However, we argue that this designation may be premature, having been pieced together from mainly descriptive studies in numerous distinct species. This review provides a comprehensive overview of the MMC literature, including a phylogenetic analysis of MMC distribution across vertebrate species. Here, we discuss the current understanding of the MMCs function in immunity and lingering questions. We suggest additional experiments needed to confirm that MMCs serve a GC-like role in fish immunity. Finally, we address the utility of the MMC as a broadly applicable histological indicator of the fish (as well as amphibian and reptilian) immune response in both laboratory and wild populations of both model and non-model vertebrates. We highlight the factors (sex, pollution exposure, stress, stocking density, etc.) that should be considered when using MMCs to study immunity in non-model vertebrates in wild populations.
Bayesian Inference of Protein and Domain Interactions Using The Sum-Product Algorithm

In order to fully understand the functions of proteins in living organisms we must study their interactions and construct accurate interaction maps. Each protein can be composed of one or several peptide chains called domains and each protein interaction can be seen as a consequence of an underlying interaction of two domains, one from each protein. Since high-throughput methods of measuring protein interactions, such as yeast two-hybrid assay, have high err o rates, the structural similarities between proteins can beexploited to detect some of the experimental errors and predict new, unmeasured interactions. In this paper we solve the problem of Bayesian inference of protein and domain interactions by computing their probabilities conditioned on the measurement results. We formulate the task of calculating these conditi onal probabilities as a functional marginalization problem, where the multivariate function to be marginalized naturally factor s into simpler local functions, and we demonstrate how this equiva lent problem can be solved using the sum-product algorithm. We note that this task is structurally similar to decoding low density parity check codes using a message passing algorithm. The robustness and accuracy of our approach is demonstrated by predicting protein and domain interactions on both real and artificial measurement data.
Classification of Agarwood Oil Using an Electronic Nose

Presently, the quality assurance of agarwood oil is performed by sensory panels which has significant drawbacks in terms of objectivity and repeatability. In this paper, it is shown how an electronic nose (e-nose) may be successfully utilised for the classification of agarwood oil. Hierarchical Cluster Analysis (HCA) and Principal Component Analysis (PCA), were used to classify different types of oil. The HCA produced a dendrogram showing the separation of e-nose data into three different groups of oils. The PCA scatter plot revealed a distinct separation between the three groups. An Artificial Neural Network (ANN) was used for a better prediction of unknown samples.
The Utility and Management of Vaginal Cytology After Treatment for Endometrial Cancer

OBJECTIVE: To estimate the accuracy of vaginal cytology in postoperative surveillance for detecting recurrent endometrial cancer and to estimate the optimal management of squamous abnormalities detected in this setting. METHODS: This review included women who underwent hysterectomy for endometrial cancer between January 1, 2006, and December 31, 2010, and had at least one postoperative Pap test. Clinical and demographic data were collected and outcomes including abnormal vaginal cytology, results of colposcopic examination, and endometrial cancer recurrence were assessed. A Cox regression model to estimate the risk of abnormal cytology was created. Sensitivity, specificity, and negative and positive predictive values of detecting vaginal recurrences were calculated. RESULTS: Four hundred thirty-three women contributed 2,378 Pap tests. At least one abnormal cytology result was found during follow-up of 55 (13%) women, representing 3% of all Pap tests. No recurrent endometrial cancers were diagnosed on the basis of isolated abnormal cytology. No cases of recurrent cancer were diagnosed in women with atypical squamous cells of undetermined significance or low-grade squamous intraepithelial lesion (LSIL) Pap test results. In multivariable analysis, abnormal cytology was highly associated with prior postoperative radiation therapy (P<.001). The sensitivity, specificity, and positive and negative predictive values of an abnormal Pap test result in detecting a local recurrence are 40%, 87.9%, 7.3%, and 98.4%, respectively. CONCLUSION: Colposcopy is not needed after a Pap test result read as atypical squamous cells of undetermined significance or LSIL. LEVEL OF EVIDENCE: III
Antecedents of Attention-Deficit/Hyperactivity Disorder Symptoms in Children Born Extremely Preterm

Objective: To investigate antecedents of attention-deficit/hyperactivity disorder (ADHD) symptoms in children born extremely preterm (EP; <26-wk gestation). Method: The EPICure study recruited all babies born EP in the United Kingdom and Ireland in March-December 1995. Neurodevelopmental outcomes were assessed at 2.5 (n = 283; 90%), 6 (n = 160; 78%), and 11 (n = 219; 71%) years of age. Parents and teachers completed the DuPaul Rating Scale IV to assess inattention and hyperactivity/impulsivity symptoms at 11 years. Regression analyses were used to explore the association of neonatal, neurodevelopmental, and behavioral outcomes to 6 years with ADHD symptoms at 11 years. Results: Extremely preterm (EP) children had significantly more inattention (mean difference, 1.2 SD; 95% CI, 0.9–1.5) and hyperactivity/impulsivity (mean difference, 0.5 SD; 95% CI, 0.2–0.7) than controls, with a significantly greater effect size for inattention than hyperactivity/impulsivity. Significant independent predictors of inattention at 11 years included smaller head circumference, lower intelligence quotient (IQ), and pervasive peer relationship problems at 6 years, and motor development at 2.5 years. In contrast, significant independent predictors of hyperactivity/impulsivity included lower IQ, pervasive conduct problems and ADHD symptoms at 6 years, externalizing problems at 2.5 years, and non-white maternal ethnicity. Conclusions: Extremely preterm children are at increased risk for ADHD symptoms, predominantly inattention, for which the antecedents differ by symptom domain. Attention deficits after EP birth were associated with poor brain growth and neurological function. Cognitive and behavioral assessments in early and middle childhood to identify neurodevelopmental and peer relationship problems may be beneficial for identifying EP children at risk for inattention.
Smoking and relation to other risk factors in postmenopausal women with coronary artery disease, with particular reference to whole blood viscosity and β‐cell function

Abstract. Os I, Høieggen A, Larsen A, Sandset PM, Djurovic S, Berg K, Os A, Birkeland K, Westheim A (University of Oslo; Ulleval University Hospital; and Aker University Hospital, Oslo, Norway). Smoking and relation to other risk factors in postmenopausal women with coronary artery disease, with particular reference to whole blood viscosity and β‐cell function. J Intern Med 2003; 253: 232–239.
Ghrelin: structure and function.

Small synthetic molecules called growth hormone secretagogues (GHSs) stimulate the release of growth hormone (GH) from the pituitary. They act through the GHS-R, a G protein-coupled receptor whose ligand has only been discovered recently. Using a reverse pharmacology paradigm with a stable cell line expressing GHS-R, we purified an endogenous ligand for GHS-R from rat stomach and named it "ghrelin," after a word root ("ghre") in Proto-Indo-European languages meaning "grow. " Ghrelin is a peptide hormone in which the third amino acid, usually a serine but in some species a threonine, is modified by a fatty acid; this modification is essential for ghrelin's activity. The discovery of ghrelin indicates that the release of GH from the pituitary might be regulated not only by hypothalamic GH-releasing hormone, but also by ghrelin derived from the stomach. In addition, ghrelin stimulates appetite by acting on the hypothalamic arcuate nucleus, a region known to control food intake. Ghrelin is orexigenic; it is secreted from the stomach and circulates in the bloodstream under fasting conditions, indicating that it transmits a hunger signal from the periphery to the central nervous system. Taking into account all these activities, ghrelin plays important roles for maintaining GH release and energy homeostasis in vertebrates.
Signal Processing on Graphs - Contributions to an Emerging Field. (Traitement du signal sur graphes - Contributions à un domaine émergent)

This dissertation introduces in its first part the field of signal processing on graphs. We start by reminding the required elements from linear algebra and spectral graph theory. Then, we define signal processing on graphs and give intuitions on its strengths and weaknesses compared to classical signal processing. In the second part, we introduce our contributions to the field. Chapter 4 aims at the study of structural properties of graphs using classical signal processing through a transformation from graphs to time series. Doing so, we take advantage of a unified method of semi-supervised learning on graphs dedicated to classification to obtain a smooth time series. Finally, we show that we can recognize in our method a smoothing operator on graph signals. Chapter 5 introduces a new translation operator on graphs defined by analogy to the classical time shift operator and verifying the key property of isometry. Our operator is compared to the two operators of the literature and its action is empirically described on several graphs. Chapter 6 describes the use of the operator above to define stationary graph signals. After giving a spectral characterization of these graph signals, we give a method to study and test stationarity on real graph signals. The closing chapter shows the strength of the matlab toolbox developed and used during the course of this PhD.
Generalizations of (U, N)-implications derived from commutative semi-uninorms and pseudo-uninorms

In this paper, two classes of generalized (U, N )−implications derived from commutative semi-uninorms and pseudo- uninorms are investigated, respectively. Then some properties of UI,N operations derived from implications are explored. Last the necessary and sufficient conditions such that a (UCS ,N )−operation (or (UP ,N )−operation) is an implication are given out.
Running on uneven ground: leg adjustment to vertical steps and self-stability

SUMMARY Human running is characterized by comparably simple whole-body dynamics. These dynamics can be modelled with a point mass bouncing on a spring leg. Theoretical studies using such spring–mass models predict that running can be self-stable. In simulations, this self-stability allows for running on uneven ground without paying attention to the ground irregularities. Whether humans actually use this property of the mechanical system in such an irregular environment is, however, unclear. One way to approach this question is to study how the leg stiffness in stance and the leg orientation in flight are changed in response to ground perturbations. Here, for 11 human subjects we studied two consecutive contacts during running on uneven ground with a force plate of adjustable height (step of +5, +10 and +15 cm). We found that runners adjust their leg stiffness to the height of a vertical step. The adjustment is characterized by a 9% increase in leg stiffness in preparation for the perturbation and by a systematic decrease in proportion to the step height. At the highest vertical step (+15 cm), leg stiffness was reduced by about 26%. We also observed that the angle of attack decreased from 68 deg. to 62 deg. with increasing ground height. These leg adjustments are in accordance with the predictions of a stable spring–mass system. Furthermore, we could describe the identified leg forces and leg compressions with a simple spring–mass simulation for a given body mass, leg stiffness, angle of attack and initial conditions. We compared the experimental findings with the self-stabilizing properties of the spring–mass model, and discuss how humans use a combination of strategies that include purely mechanical self-stabilization and active neuromuscular control. Finally, beyond self-stability, we suggest that control may apply to smooth centre of mass kinematics.
Aerobic walking or strengthening exercise for osteoarthritis of the knee? A systematic review

Objective: To compare the efficacy of aerobic walking and home based quadriceps strengthening exercises in patients with knee osteoarthritis. Methods: The Medline, Pubmed, EMBASE, CINAHL, and PEDro databases and the Cochrane controlled trials register were searched for randomised controlled trials (RCTs) of subjects with knee osteoarthritis comparing aerobic walking or home based quadriceps strengthening exercise with a non-exercise control group. Methodological quality of retrieved RCTs was assessed. Outcome data were abstracted for pain and self reported disability and the effect size calculated for each outcome. RCTs were grouped according to exercise mode and the data pooled using both fixed and random effects models. Results: 35 RCTs were identified, 13 of which met inclusion criteria and provided data suitable for further analysis. Pooled effect sizes for pain were 0.52 for aerobic walking and 0.39 for quadriceps strengthening. For self reported disability, pooled effect sizes were 0.46 for aerobic walking and 0.32 for quadriceps strengthening. Conclusions: Both aerobic walking and home based quadriceps strengthening exercise reduce pain and disability from knee osteoarthritis but no difference between them was found on indirect comparison.
Theoretical and experimental research on Ce:YAG crystals for use in blue laser diode illumination

The blue laser diode (LD) illuminator in this study was composed of a cerium doped yttrium aluminum garnet (Ce:YAG) crystal, a 450-nm laser diode and an optical fiber. After a first-principles calculation, the energy gap of the Ce:YAG crystal was found to be 4.71 eV, which was less than that of the YAG. The luminescent properties of the Ce:YAG were determined by the electronic distribution of the Ce (d) and Ce (f) orbits. The Ce:YAG crystal had two characteristic absorption peaks of Ce3+ at 332 nm and 455 nm. Hence, the 450-nm LD excited fluorescence spectra of a Ce:YAG crystal can be used for laser illumination. We discovered that the luminous efficiency of the LD increased with increasing color temperature for 4000 K, 5000 K, 6000 K and 6500 K but not for 3500 K, due to the low light transmittance of the thickest Ce:YAG crystal. The highest color-rendering index was about 70.0. Also, the blue laser without the 430-nm light from spectral radiance was, compared to an LED, a more serious eye hazard. We calculated that the permissible exposure time of the LD was longer than that of an LED. We also discovered that LD illumination is more secure than LED illumination.
VHF radar observation of atmospheric winds, associated shears and C 2 n at a tropical location: interdependence and seasonal pattern

Abstract. The turbulence refractivity structure constant (C 2 n ) is an important parameter of the atmosphere. VHF radars have been used extensively for the measurements of C 2 n . Presently, most of such observations are from mid and high latitudes and only very limited observations are available for equatorial and tropical latitudes. Indian MST radar is an excellent tool for making high-resolution measurements of atmospheric winds, associated shears and turbulence refractivity structure constant (C 2 n ). This radar is located at Gadanki (13.45° N, 79.18° E), a tropical station in India. The objective of this paper is to bring out the height structure of C 2 n for different seasons using the long series of data (September 1995 – August 1999) from Indian MST radar. An attempt is also made to understand such changes in the height structure of C 2 n in relation to background atmospheric parameters such as horizontal winds and associated shears. The height structure of C 2 n , during the summer monsoon and post-monsoon season, shows specific height features that are found to be related to Tropical Easterly Jet (TEJ) winds. It is important to examine the nature of the radar back-scatterers and also to understand the causative mechanism of such scatterers. Aspect sensitivity of the received radar echo is examined for this purpose. It is observed that radar back-scatterers at the upper tropospheric and lower stratospheric heights are more anisotropic, with horizontal correlation length of 10–20 m, as compared to those observed at lower and middle tropospheric heights. Key words. Meteorology and atmospheric dynamics (climatology; tropical meteorology; turbulence)
Shift Work in Nurses: Contribution of Phenotypes and Genotypes to Adaptation

Background Daily cycles of sleep/wake, hormones, and physiological processes are often misaligned with behavioral patterns during shift work, leading to an increased risk of developing cardiovascular/metabolic/gastrointestinal disorders, some types of cancer, and mental disorders including depression and anxiety. It is unclear how sleep timing, chronotype, and circadian clock gene variation contribute to adaptation to shift work. Methods Newly defined sleep strategies, chronotype, and genotype for polymorphisms in circadian clock genes were assessed in 388 hospital day- and night-shift nurses. Results Night-shift nurses who used sleep deprivation as a means to switch to and from diurnal sleep on work days (∼25%) were the most poorly adapted to their work schedule. Chronotype also influenced efficacy of adaptation. In addition, polymorphisms in CLOCK, NPAS2, PER2, and PER3 were significantly associated with outcomes such as alcohol/caffeine consumption and sleepiness, as well as sleep phase, inertia and duration in both single- and multi-locus models. Many of these results were specific to shift type suggesting an interaction between genotype and environment (in this case, shift work). Conclusions Sleep strategy, chronotype, and genotype contribute to the adaptation of the circadian system to an environment that switches frequently and/or irregularly between different schedules of the light-dark cycle and social/workplace time. This study of shift work nurses illustrates how an environmental “stress” to the temporal organization of physiology and metabolism can have behavioral and health-related consequences. Because nurses are a key component of health care, these findings could have important implications for health-care policy.