Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of plasma membrane lipids and luteinizing hormone receptors of ovine corpora lutea during luteolysis and early pregnancy.

Lipid composition of plasma membranes from luteal cells was examined to determine whether changes in this organelle occur during regression and maintenance of the corpus luteum in nonpregnant (NP) and pregnant (P) ewes, respectively. Forty ewes were assigned to be killed on Day 13 or 15 of the estrous cycle (D13-NP and D15-NP) or pregnancy (D13-P and D15-P). Purification of luteal plasma membranes on discontinuous sucrose gradients yielded two fractions, designated F1 and F2, that exhibited the greatest enrichment of 5'-nucleotidase activity (five- and fourfold, respectively) over that of the homogenate. These fractions also yielded the lowest contamination by endoplasmic reticulum as represented by nicotinamide adenine dinucleotide phosphate (NADPH) cytochrome C reductase activity and mitochondrial membranes as indicated by succinate dehydrogenase activity. Predominant phospholipids identified in membranes obtained from all groups were phosphatidylcholine (PC, 48.9 +/- 0.6% of total phospholipid), phosphatidylethanolamine (PE, 33.3 +/- 0.4%), sphingomyelin (SPH, 9.7 +/- 0.3%), phosphatidylserine (PS, 3.5 +/- 0.2%), and phosphatidylinositol (PI, 4.0 +/- 0.5%). No changes in microgram phospholipid/mg membrane protein were observed for any luteal phospholipid on D13 and 15 of the estrous cycle or pregnancy. No significant changes in the relative percentages of major fatty acids present in PC (palmitic [16:0], oleic [18:1]), PE (stearic [18:0], 18:1 and arachidonic [20:4]), or PS (18:0, 18:1, docosatetraenoic [22:4]), nor in the ratios of unsaturated (U) to saturated (S) fatty acids in these phospholipids were observed. Significant differences in unsaturated fatty acids of chain length greater than 20 carbons present in minor quantities in PC, PE, and PS were detected between NP and P ewes as well as between days within reproductive stage. The profile of major fatty acids present in PI revealed decreases in 18:0 and 20:4 in D15-NP and increases in 22:4 and docosapentaenoic acid (22:5) in luteal membranes of both D13- and D15-NP ewes relative to the levels of these fatty acids in PI of corresponding groups of pregnant ewes. There was a general trend for 20:4 levels of PC and PI in membranes of D15-NP ewes to be inversely related to those of D15-P ewes. Collectively, these changes were reflected by an increased U:S fatty acid ratio in luteal membrane PI during the estrous cycle. Specific binding of [125I] iodo-human chorionic gonadotropin to luteal plasma membranes from NP and P ewes on D13 and 15 (6/group) revealed similar affinities and concentrations of unoccupied luteinizing hormone (LH) receptors. (ABSTRACT TRUNCATED AT 400 WORDS)
Broadband ultrasonic attenuation measurements using coded sweep excitations

An experimental method to measure ultrasound attenuation was developed in which the frequency spectrum (FS) of a system consisting of a transmit/receive pair of ultrasonic transducers was broadened from 1.79 MHz to 4.57 MHz. A nonlinear specially designed sweep was employed, which was coded based on the FS of the ultrasonic system. Both coded and linear sweeps were used with the attenuation measurements of a 0.90 glycerol to 0.10 water mixture. Experimental and theoretical results agree with each other to within 0.5 dB. With the proposed method, the frequency range of validated results was improved, since it was possible to enlarge the useful bandwidth of the ultrasonic system without substituting any of the devices from the experimental set up.
Global Genomic Diversity of Human Papillomavirus 6 Based on 724 Isolates and 190 Complete Genome Sequences

ABSTRACT Human papillomavirus type 6 (HPV6) is the major etiological agent of anogenital warts and laryngeal papillomas and has been included in both the quadrivalent and nonavalent prophylactic HPV vaccines. This study investigated the global genomic diversity of HPV6, using 724 isolates and 190 complete genomes from six continents, and the association of HPV6 genomic variants with geographical location, anatomical site of infection/disease, and gender. Initially, a 2,800-bp E5a-E5b-L1-LCR fragment was sequenced from 492/530 (92.8%) HPV6-positive samples collected for this study. Among them, 130 exhibited at least one single nucleotide polymorphism (SNP), indel, or amino acid change in the E5a-E5b-L1-LCR fragment and were sequenced in full. A global alignment and maximum likelihood tree of 190 complete HPV6 genomes (130 fully sequenced in this study and 60 obtained from sequence repositories) revealed two variant lineages, A and B, and five B sublineages: B1, B2, B3, B4, and B5. HPV6 (sub)lineage-specific SNPs and a 960-bp representative region for whole-genome-based phylogenetic clustering within the L2 open reading frame were identified. Multivariate logistic regression analysis revealed that lineage B predominated globally. Sublineage B3 was more common in Africa and North and South America, and lineage A was more common in Asia. Sublineages B1 and B3 were associated with anogenital infections, indicating a potential lesion-specific predilection of some HPV6 sublineages. Females had higher odds for infection with sublineage B3 than males. In conclusion, a global HPV6 phylogenetic analysis revealed the existence of two variant lineages and five sublineages, showing some degree of ethnogeographic, gender, and/or disease predilection in their distribution. IMPORTANCE This study established the largest database of globally circulating HPV6 genomic variants and contributed a total of 130 new, complete HPV6 genome sequences to available sequence repositories. Two HPV6 variant lineages and five sublineages were identified and showed some degree of association with geographical location, anatomical site of infection/disease, and/or gender. We additionally identified several HPV6 lineage- and sublineage-specific SNPs to facilitate the identification of HPV6 variants and determined a representative region within the L2 gene that is suitable for HPV6 whole-genome-based phylogenetic analysis. This study complements and significantly expands the current knowledge of HPV6 genetic diversity and forms a comprehensive basis for future epidemiological, evolutionary, functional, pathogenicity, vaccination, and molecular assay development studies.
Hierarchical Control of Dry Clutch for Engine-Start Process in a Parallel Hybrid Electric Vehicle

Engine start is an important process for a parallel hybrid electric vehicle (HEV), during which the electric motor (EM) must simultaneously provide driver's demand torque and engine-start torque via an engine-disconnect clutch. Therefore, the performance of dynamic and comfort, the engine-start time, and the sliding power of clutch are all supposed to be considered in the control of engine start. This paper introduces a parallel HEV equipped with an automatic dry clutch using an electromechanical actuator, and proposes a hierarchical control method to control the engine start. As upper layer of the controller, a linear quadratic (LQ) optimal control is used to obtain the required torque of EM and clutch based on the current states of the vehicle and engine. As lower layer, a double closed-loop control method is proposed to control the clutch transmitting required torque, which contains a fuzzy controller (FC) as an outer loop and a modified predictive functional controller (mPFC) as an inner loop. Meanwhile, considering the difficulties in measurement of load torque of a running vehicle and actual transmitted torque of a dry clutch, two Kalman filters (KFs) are designed to observe them. Simulations in MATLAB/SIMULINK and hardware-in-loop (HIL) tests were carried out, of which the results show that the hierarchical control method has a satisfying performance.
L'Analyse en Composantes Indépendantes : un outil puissant pour le traitement de l'information

L'analyse en composantes independantes (ACI) est une approche tres generale qui a ete developpee pour resoudre le probleme de separation aveugle de sources (SAS) independantes. Au-dela de ce probleme, l'ACI s'applique a l'etude de la representation parcimonieuse de donnees liees a des phenomenes cognitifs complexes. Cet article est constitue de deux parties. La premiere est une synthese sur les principes de la separation de sources dans laquelle sont abordes la question de la separabilite, les criteres d'independance, et l'utilisation d'informations a priori. La seconde partie presente les approches de la SAS fondees sur des representations parcimonieuses des signaux et montre comment elles permettent de traiter des problemes sous-determines, et comment elles sont liees au codage parcimonieux.
Transcriptional and Translational Regulation of Photosystem I and II Genes in Light-Dark- and Continuous-Light-Grown Cultures of the Unicellular Cyanobacterium Cyanothece sp. Strain ATCC 51142

ABSTRACT Cyanothece sp. strain ATCC 51142, a unicellular, diazotrophic cyanobacterium, demonstrated extensive metabolic periodicities of photosynthesis, respiration, and nitrogen fixation when grown under N2-fixing conditions. This report describes the relationship of the biosynthesis of photosynthesis genes to changes in the oligomerization state of the photosystems. Transcripts of the psbA gene family, encoding the photosystem II (PSII) reaction center protein D1, accumulated primarily during the light period, and net transcription reached a peak between 2 to 6 h in the light in light-dark (LD) growth and between 4 to 10 h in the subjective light when grown under continuous light (LL). The relative amount of the D1 protein (form 1 versus form 2) appeared to change during this diurnal cycle, along with changes in the PSII monomer/dimer ratio. D1 form 1 accumulated at approximately equal levels throughout the 24-h cycle, whereas D1 form 2 accumulated at significantly higher levels at approximately 8 to 10 h in the light or subjective light. The psbD gene, encoding the reaction center protein D2, also demonstrated differences between the two copies of this gene, with one copy transcribed more heavily around 6 to 8 h in the light. Accumulation of the PSI reaction center proteins PsaA and PsaB was maximal in the dark or subjective-dark periods, a period during which PSI was primarily in the trimeric form. We conclude that photosystem organization changes during the diurnal cycle to favor either noncyclic electron flow, which leads to O2 evolution and CO2 fixation, or cyclic electron flow, which favors ATP synthesis.
Maximum number of independent paths and radio connectivity

Methods for determining the network reliability of a multihop packet radio network in the presence of hostile jammers are discussed. A new connectivity parameter called radio connectivity is defined as the maximum number of disjoint communication paths that are still usable between given nodes s and d after the jammer is on or, more generally, the minimum number of jammers needed to disconnect s and d. A lower bound on the radio connectivity is computed by studying the number of jamming independent paths. The time complexity of obtaining the radio connectivity is analyzed and shown to be NP-hard except for some special cases. Greedy heuristics for developing approximate answers for general networks are described. Euclidean networks, in which the nodes and links correspond to points and line segments in the Euclidean geometry and satisfy Euclid's four fundamental axioms, are also discussed. It is found that the maximum number of independent paths between a pair of source and destination nodes that can possibly exist is five. An extension in which there is a protected zone of known size around the sender and receiver is studied. >
Supplemental Information Hierarchical Dysconnectivity in Schizophrenia 1 SUPPLEMENTAL INFORMATION

Figure S1 – Examining Confounding Variables in Schizophrenia: Smoking, Medication and Movement (relates to Figures 1 and 3). Figure S2 – GSR Applied to Significant Connectivity Findings (relates to Figures 1, 3, and 5). Figure S3 – Volumetric Map of Whole-Brain Data-Driven Functional Connectivity Increases in Schizophrenia (relates to Figure 1). Figure S4 – Association and Sensory Network Key (relates to Figure 2-3, 5, 7, S5, S7, S9 and S12). Figure S5 – Symptom Correlations (relates to Figure 3). Figure S6 – Mean Anatomical Connectivity of Association vs. Non-Association Network Regions, Degree-Matched Results (relates to Figure 5 and 7). Figure S7 – Preferential Network-Level Functional Connectivity Changes in Schizophrenia versus Bipolar Disorder Patients (relates to Figure 5). Figure S8 – Relationship Between Movement Characteristics and Covariance in Association Networks (relates to Figure 5). Figure S9 – Preferential Network-Level Variance Changes in Schizophrenia versus Bipolar Disorder Patients (relates to Figure 7). Figure S10 – Examining Effects of Long-term Antipsychotic Treatment on Covariance and Variance Effects in Bipolar Disorder (relates to Figure 3, 5 & 7). Figure S11 – Quantifying Overlap Between Increased Whole-Brain Connectivity in SCZ & Independently Defined Association vs. Sensory Regions (relates to Figure 2). Figure S12 – Within-Network Connectivity and Variance Are Correlated in Association Networks (relates to Figures 5 & 7). Figure S13 – Parameterscape of Homogeneous and Inhomogeneous Model Stable Regimes (relates to Figures 4 & 6).
Port-IO: a Mobile Cloud Platform Supporting Context-Aware Inter-terminal Truck Routing

The role of ports goes far beyond the traditional function of a pure transport node linking sea and landside transportation. Rather, many ports offer value-added logistics and auxiliary services leading to a network of container flows. Moreover, containers may need to be transferred between different areas within the port. Information exchange and optimization is necessary to efficiently coordinate actors and container movements involved in respective inter-terminal transports in order to avoid empty trips and thus high costs, emissions, and additional traffic volume. In this paper, we describe a novel optimization problem for addressing inter-terminal truck routing in ports and propose two greedy heuristics and a hybrid simulated annealing algorithm. The computational results are evaluated in terms of costs, empty trips, and utilized number of trucks and they indicate that the proposed hybrid simulated annealing algorithm is able to report feasible and improved routes within seconds. The optimization component is embedded into a cloud platform integrating truck drivers based on a mobile application. Beyond common functionalities, the proposed platform enables a flexible real-time assignment of truck drivers to container movements by considering the current position of trucks with the objective to better manage and coordinate inter-terminal transports. As such, our approach contributes not only with a valuable approach for vehicle planning in ports, but also presents an accessible, scalable, and multi-tenant system prototype of a mobile cloud platform for handling the interactions with truck drivers in practice, demonstrated with an example for the Port of Hamburg, Germany.
The Development of a Reproducible Immunocytochemical Technique for Demonstrating Colocalized Cutaneous Antigens

A number of double immunocytochemical labeling techniques are available that allow simultaneous identification of two antigens in one tissue section. Those most commonly used are (a) the acid elution method, which uses acid buffer to remove one set of antibodies, thus allowing a second set to be applied; (b) the use of non-cross-reacting combinations of immunoglobulin subclass and subclass-specific antibodies; and (c) application of the diaminobenzidine (DAB) reaction product as an antibody-blocking reagent, preventing cross-reaction of one set of antibodies with those of a second labeling method. We assessed each technique, using a variety of immunoenzyme methods, for the ability to label antigens that are anatomically separate in one tissue section and those that are colocalized on the same cell surface. Acid elution methods increased antibody cross-reaction. The use of immunoglobulin subclass antibodies resulted in inferior staining. The DAB blocking method, using peroxidase antiperoxidase (DAB substrate) and alkaline phosphatase antialkaline phosphatase (APAAP) (fast red substrate) optimally labeled non colocalized antigens. The substitution of fast blue as the APAAP substrate proved optimal for colocalized antigens, producing brown and blue single-labeled and black double-labeled cells.
The dorsal compartment locomotory control system in amphioxus larvae

Amphioxus myotomes consist of separate sets of superficial and deep muscle fibers, each with its own innervation, that are thought to be responsible for slow swimming and escape behavior, respectively. Tracings from serial EM sections of the anterior nerve cord in the larva show that the motoneurons and premotor interneurons controlling the superficial fibers (the dorsal compartment, or DC pathway) are linked by specialized junctions of a previously undescribed type, referred to here as juxta‐reticular (JR) junctions for the characteristic presence of a cisterna of endoplasmic reticulum on each side. JR junctions link the DC motoneurons with each other, with the largest of the anterior paired neurons (LPN3s) and with one class of ipsilateral projection neurons (IPNs), but occur nowhere else. Because of the paucity of synaptic input to the DC system, larval behavior can only be explained if the JR junctions act as functional links between cells. An analysis of the pattern of cell contacts also suggests that the LPN3s are probably pacemakers for both slow and fast locomotion, but act through junctions in the former case and conventional synapses in the latter. The only major synaptic input to the DC system identified in somites 1 and 2 was from four neurons located in the cerebral vesicle, referred to here as Type 2 preinfundibular projection neurons (PPN2s). They have unusually large varicosities, arranged in series, that make periodic contacts with the DC motoneurons. More caudally, the DC motoneurons receive additional input via similar large varicosities from the receptor cells of the first dorsal ocellus, located in somite 5. The overall circuitry of the locomotory control system suggests that the PPN2s may be instrumental in sustaining slow swimming, whereas mechanical stimulation, especially of the rostrum, preferentially activates the fast mode. J. Morphol. 252:227–237, 2002. © 2002 Wiley‐Liss, Inc.
Mixed modeling and multiple imputation for unobservable genotype clusters

Understanding the genetic contributions to complex diseases will require consideration of interaction across multiple genes and environmental factors. At the same time, capturing information on allelic phase, that is, whether alleles within a gene are in cis (on the same chromosome) or in trans (on different chromosomes), is critical when using haplotypic approaches in disease association studies. This paper proposes a combination of mixed modeling and multiple imputation for assessing high‐order genotype–phenotype associations while accounting for the uncertainty in phase inherent in population‐based association studies. This method provides a flexible statistical framework for controlling for potential confounders and assessing gene–environment and gene–gene interactions in studies of unrelated individuals where the haplotypic phase is generally unobservable. The proposed method is applied to a cohort of 626 subjects with human immunodeficiency virus (HIV) to assess the potential contribution of four genes, apolipoprotein‐C‐III, apolipoprotein‐E, endothelial lipase and hepatic lipase in predicting lipid abnormalities. A simulation study is also presented to describe the method performance. Copyright © 2007 John Wiley & Sons, Ltd.
Expression and Production of Human Chorionic Gonadotropin (hCG) in the Normal Secretory Endometrium: Evidence of CGB7 and/or CGB6 Beta hCG Subunit Gene Expression1

ABSTRACT We have previously confirmed glandular cell CGB and CGA subunit mRNA gene expression as well as the expression of their dimeric and single-subunit human chorionic gonadotropin (hCG) proteins in normal secretory transformed endometrium. The objective of this study was to investigate the endometrial epithelial gene locus of the human hCG/LH gene cluster from CGB genes responsible for gene expression. For this study, endometrial specimens were selected from women characterized using our endometrium score and hCG staining index that had normal secretory transformed endometrium and optimal hCG staining. Using full-length CGB mRNA sequence analysis, we found that epithelial CGB is (co)expressed as the product of gene locus CGB7 and CGB6 (48%), as single CGB7 (42%), or to a lower percentage as single CGB6 (10%). In addition to known differences between these genes and CGB5, the nucleotide sequence of the mRNA differs between CGB7 and CGB6 in the untranslated promoter region and in translated exon 2. Immunohistochemical results show that endometrial joint CGB7 and CGB6, single CGB7, and single CGB6 mRNA expression lead to the release of endometrial hCG. Gene-specific antibodies for CGB7 reveal secretory endometrial hCG production, which is not observed for gene-specific CGB5 antibodies, whereas the placenta is positive for CGB5 and negative for CGB7 antibody as revealed by immunohistochemistry and Western blot hCG isoform analysis. Only endometrial CGB7 expression seems to be supported specifically by secretory endometrial transcription factors. In conclusion, epithelial hCG is expressed and produced as CGB7 and/or CGB6 but not CGB5, and it is produced together with CGA as a secretory transformation marker in the normal secretory phase endometrium.
Régulation de la stabilité du cytosquelette microtubulaire : conséquences sur la croissance de la jonction neuromusculaire chez la Drosophile

Lors du developpement du systeme nerveux, de nombreux mecanismes moleculaires sont mis en jeu afin que les axones trouvent leur cible et etablissent des synapses. Une fois ces synapses etablies, elles restent plastiques et peuvent encore etre modifiees d'un point de vue morphologique et fonctionnel en fonction de la taille de la cible ou de l'activite de la synapse. La jonction neuromusculaire (JNM) de la larve de drosophile est un modele ideal pour etudier cette plasticite synaptique developpementale. En effet, la cellule musculaire innervee augmente de taille d'un facteur 50, et la JNM croit en consequence. Cette croissance met en jeu le cystoquelette microtubulaire, composant central de la terminaison synaptique. Dans cette these, nous avons etudie le role de la proteine kinase Shaggy dans la croissance de la JNM et avons montre qu'elle joue un role inhibiteur dependant de la proteine associee aux microtubules (MAP) Futsch. Futsch est le representant d'une des deux familles de MAPs structurales. Ces deux familles comprennent la famille MAP1 (MAP1A, MAP1B et MAP1S) et la famille MAP2/MAP4/Tau. Dans le systeme nerveux, elles stabilisent les microtubules et favorisent la pousse neuritique. Cependant, lors de synaptogenese, leur role est meconnu. Chez la drosophile, il n'existe qu'un membre de chaque famille : Futsch (MAP1) et Tau (MAP2/MAP4/Tau), ce qui simplifie l'etude d'une famille par rapport a l'autre par l'absence de redondance. Nous avons ensuite etudie le role de ces MAPs sur la stabilite des microtubules, ce qu'il en resulte concernant la croissance de la JNM et quels acteurs, notamment ceux de la voie de signalisation Wnt/Wingless, peuvent reguler ces proteines.