Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolution in Four Dimensions

The subtitle of the book is Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life; thus, the four dimensions of the title. ‘‘The challenge [this book] offers is not to Darwin’s theory of evolution through natural se­ lection, but to the prevalent gene-based unidimensional ver­ sion of it. ’’ The audience to which the book is directed is revealed in the Preface in the following sentence: ‘‘We hope that the book can be read not only by professional scientists but also by the many people who are interested in biological ideas, and are fascinated (and sometimes worried) by the current ways of thinking about biology, especially about modern genetics. ’’ The book is divided into three major sections. The first section (Chapters 1, 2, and 3) is devoted to the genetic sys­ tem: how Darwin’s theory became so gene centered; the re­ lation between genes and characters; and evidence that not all genetic changes should be seen as random, chance events. The second section (Chapters 4, 5, and 6) deals individually with three other evolutionary dimensions.
Two NSAIDs, nimesulide and naproxen, can reduce the synthesis of urokinase and IL-6 while increasing PAI-1, in human OA synovial fibroblasts.

OBJECTIVES To evaluate the effect of therapeutic and pharmacologic concentrations of two non-steroidal anti-inflammatory drugs (NSAIDs), nimesulide and naproxen, on the synthesis of urokinase (uPA), plasminogen activator inhibitor (PAI-1) and interleukin-6 (IL-6) in human synovial fibroblasts isolated from osteoarthritis (OA) patients. METHODS Urokinase, PAI-1, and IL-6 production were measured by specific ELISA. RESULTS Nimesulide and naproxen induced a dose-dependent decrease in uPA synthesis. The two drugs, at therapeutic concentrations, exerted a stimulatory effect on the synthesis of PAI-1 whereas the synthesis of IL-6 was significantly reduced by both NSAIDs. CONCLUSION The results of this study indicate some of the mechanisms by which nimesulide and naproxen could exert their effects on the arthritis process. The suppressive action of the two drugs on the synthesis of uPA, while stimulating PAI-1 production, may have a positive impact on the balance of plasminogen activator/inhibitor, which could help reduce cartilage catabolism.
Cladistic Analysis Reveals Brainless Urbilateria

sister groups by any stretch of the imagination. In a very elegant paper, Moroz [2009] reviews the literature, subjects the data to a correct cladistic analysis, and concludes that centralized nervous systems have evolved independently, perhaps as many as seven times. In a particularly striking example, he demonstrates that complex brains have evolved at least three times in molluscans alone. His analysis indicates that Urbilateria did not possess a tripartite brain, or any brain at all. Instead, these animals probably possessed an uncentralized nerve net. It is possible, however, that parts of this nerve net were already concentrated into dorsal, lateral and ventral elements, related to sensory, feeding and locomotory functions, respectively. Moroz appears to pose an evolutionary paradox, however. How can there be homologous genes and molecular mechanisms determining brains that are not homologous? He suggests that modular type molecular mechanisms arose early in metazoan evolution and may be involved in determining many different, complex cellular phenotypes. Hemichordates appear to be a clear example, where many evolutionarily conserved homeodomainrelated transcription factors and morphogens determine the main body axes system Both insects and mammals possess homologous genes and molecular mechanisms that are involved in global body patterning, including the patterning of the central nervous system [reviewed in Hirth and Reichert, 2007]. This has led to the hypothesis that the common ancestor of arthropods and chordates (Urbilateria) possessed a tripartite brain, in which Otx was expressed in the anterior part of the developing brain, and Hox genes in the posterior part, with a Pax -expressing domain positioned between them [Hirth and Reichert, 2007]. Although this hypothesis has been widely cited and has entered textbooks as dogma, it has never been credible, as it is based on an erroneous two-taxon paradigm, in which arthropods and mammals are interpreted as immediate sister groups. Although some strict cladists insist that two-taxon analyses are never valid, this is clearly not the case. When highly similar features are recognized in two immediate sister groups, a cladistic analysis does dictate that these features be interpreted as homologous. Exceptions must certainly exist (due to parallelism, for example), but at present there is no cladistic methodology for recognizing them. In any case, the important point here is not that arthropods and mammals comprise only two taxa, it is that they are not immediate Published online: September 30, 2010
Trends in gastric cancer incidence in a well-defined French population by time period and birth cohort

Epidemiological studies have shown a marked decline in gastric cancer incidence and opposite patterns between proximal and distal sites among different populations. Little is known about trends by histological type. The aim of this study was to analyse the change in gastric cancer incidence patterns by investigating the role of temporal components as determinants of such trends in the population of the Côte d'Or area (France) registered between 1976 and 1995. Gastric cancer incidence decreased over time. There was a decrease in incidence rates for distal cancers (−3.5%P < 0.001 per year in men and −4.6%P < 0.01 in women). In contrast, there was a non-significant increase of proximal cancer incidence in men and in women. Rates of adenocarcinomas decreased, whereas the incidence rates of undifferentiated carcinomas and of other histological types remained quite stable. There was a decrease in cumulative risk throughout the studied cohorts, whereas risk for proximal cancer remained stable and decreased slightly for distal localization. For adenocarcinomas, earlier birth cohorts showed a slight decrease in rates, whereas there was an increase for recent cohorts. Subsite and histological-specific analysis, in revealing different time trends in incidence, suggest, at least partly, different aetiologies for gastric cancer, and future aetiological studies must distinguish proximal and distal cancers.
ASSESSMENT OF INTERATRIAL DYSSYNCHRONY BY TISSUE DOPPLER IMAGING IN MITRAL STENOSIS: EFFECT OF AFTERLOAD REDUCTION AFTER BALLOON MITRAL VALVULOPLASTY.

Abbreviations: A0 wave, peak late annular velocity by TDI; AF, atrial fibrillation; BSA, body surface area; LA, left atrium; LAA, left atrial area; LAD, left atrial dimension; LAEF, left atrial ejection fraction; LAEI, left atrial expansion index; LAV, left atrial volume; MS, mitral stenosis; MV, mitral valve; MVA, mitral valve area; P–A0, the time interval from the initiation of the P wave on the ECG until the beginning of the late diastolic TDI signal at the lateral border of the annulus; PBMV, percutaneous balloon mitral valvuloplasty; P-max, maximum P-wave duration; P-min, minimum P-wave duration; PWD, P-wave dispersion; SPAP, systolic pulmonary artery pressure; TDI, Tissue Doppler Imaging * Corresponding author. Tel. : +2
Creative competence in borrowings : words of Japanese origin in Slovene

Japanese has no category of gender or number. Nouns as well as adjectives have no inflection. The phonological construction of words is syllabic and there is no stress accent but pitch accent. Five vowels have short and long opposition. On the other hand, Slovene has categories of number and gender. Nouns are inflected according to six cases. Phonologically, all nouns carry a stress accent. In this paper, the gender and number assignment to loanwords of Japanese origin in Slovene is discussed on the basis of the morphology and phonology of the source and recipient languages. Assignment rules have certain morphological and semantic foundations. The relative competence of the speakers of the recipient language, Slovene, is particularly noticeable when activating the categories and rules that are specific to their own language. The integration of loanwords may be observed through the additional derivation of adjectives and nouns within the framework of the recipient language.
Distinct Roles for FOXP 3 + and FOXP 3 2 CD 4 + T Cells in Regulating Cellular Immunity to Uncomplicated and Severe Plasmodium falciparum Malaria

Failure to establish an appropriate balance between proand anti-inflammatory immune responses is believed to contribute to pathogenesis of severe malaria. To determine whether this balance is maintained by classical regulatory T cells (CD4 FOXP3 CD127; Tregs) we compared cellular responses between Gambian children (n = 124) with severe Plasmodium falciparum malaria or uncomplicated malaria infections. Although no significant differences in Treg numbers or function were observed between the groups, Treg activity during acute disease was inversely correlated with malaria-specific memory responses detectable 28 days later. Thus, while Tregs may not regulate acute malarial inflammation, they may limit memory responses to levels that subsequently facilitate parasite clearance without causing immunopathology. Importantly, we identified a population of FOXP3, CD45RO CD4 T cells which coproduce IL-10 and IFN-c. These cells are more prevalent in children with uncomplicated malaria than in those with severe disease, suggesting that they may be the regulators of acute malarial inflammation. Citation: Walther M, Jeffries D, Finney OC, Njie M, Ebonyi A, et al. (2009) Distinct Roles for FOXP3 and FOXP3 CD4 T Cells in Regulating Cellular Immunity to Uncomplicated and Severe Plasmodium falciparum Malaria. PLoS Pathog 5(4): e1000364. doi:10.1371/journal.ppat. 1000364 Editor: James W. Kazura, Case Western Reserve University, United States of America Received December 8, 2008; Accepted March 3, 2009; Published April 3, 2009 Copyright: 2009 Walther et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: The project was fully financed by the core budget allocated to the MRC laboratories, Fajara Malaria Programme. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: mwalther@mrc.gm
Epidemiology of Pregnancy Losses and Practical Strategies for Prevention

Pregnancylossesfromfertilizationtoterm� areextensiveinlactatingdairycattle. �Inmany� cases,�theyareunderestimatedbecauseofthe� inabilitytodetermineconceptionearlyafter� insemination. �Formostproducers,�pregnancy� lossesareonlyquantifiedaftertheinitialdi- agnosisisperformedatapproximately�30�to� 45�dofgestation. �Recentstudiesthatprovid- edreliableassessmentsoffertilizationhave� ledtotheconclusionthatmorethan�60%�of� allpregnanciesarelostbeforeterminlactat- ingdairycows. �Thecriticalperiodisfromfer- tilizationuntiltheendofthedifferentiation� phase�(embryonicperiod)�inwhichapproxi- mately�85%�ofthoselossesoccur. �Therefore,� strategiestopreventembryoniclossesshould� resultinthegreatestimprovementinrepro- ductiveperformance. �Nevertheless,�although� fetallossesareminor� (approximately� 15%)� comparedwithembryoniclosses,� thoseare� morecostlythanembryoniclosses;�therefore� theycannotbeoverlooked. �Knownriskfac- torsforpregnancylossincludeprolongedpe- riodsoffolliculardominance,�lowprogester- oneconcentrationduringovulatoryfollicle� development,�heatstress,�postpartumdiseas- esanddisorderssuchasdystocia,� metritis,� endometritis,� mastitis,� fever,� ketosis,� lame-
Preliminary characterization of putative structural cuticular proteins in the malaria vector Anopheles sinensis.

BACKGROUND The insect cuticle protects against environmental stresses such as insecticides, physical injury, dehydration and pathogenic microorganisms. Structural cuticular proteins (CPs) are the primary components of the cuticle, and are of interest for physiology-based pest management methods. Anopheles sinensis CPs are poorly characterised at present, and therefore we performed whole-genome sequence analysis and re-analysed available transcriptome data to identify potential insecticide resistance-associated CPs. RESULTS Genome analysis revealed 238 putative CPs belonging to 11 different families; 136 proteins possessing a Rebers and Riddiford motif (CPR), 12 CPs analogous to peritrophins with a single chitin-binding domain (CPAP1), eight CPs analogous to peritrophins with three chitin-binding domains (CPAP3), four proteins with a 44 amino acid motif (CPF), five CPF-like (CPFL) proteins, nine Tweedle proteins, three proteins of low complexity with alanine residues (CPLCA), 26 proteins of low complexity with conserved glycine residues (CPLCG), seven proteins of low complexity with invariant W residues (CPLCW), 27 proteins of low complexity with proline residues (CPLCP), and one protein with two or three copies of a C-X -C motif (CPCFC). Two CPs belonging to the CPR and CPAP3 families were over-expressed in a deltamethrin-resistant strain. CONCLUSION These results establish an information framework for An. sinensis CPs that provides a basis for further molecular research. © 2017 Society of Chemical Industry.
Projection of pulmonary rapidly adapting receptors to the medulla of the cat: an antidromic mapping study.

The activity of pulmonary rapidly adapting receptor (r.a.r.) neurones was recorded extracellularly in the nodose ganglion of the decerebrate cat. The receptors were identified by their rapid adaptation to 'ramp and hold' hyperinflations of the lung. The antidromic mapping technique was used to determine the sites of projection and branching patterns within the nucleus of the tractus solitarius (n.t.s.) of eleven r.a. r.s. The medulla was explored with a stimulating electrode to activate the r.a. r.s. antidromically. In each penetration, depth‐threshold measurements were made for each antidromic response characterized by a distinct latency. Using the anatomical sites of the minimum threshold points, the locations of central branches of individual r.a. r.s. were determined. The main axons of all of them coursed within the tractus solitarius (t.s.) at levels from 2 mm rostral to 0.5 mm caudal to the obex. The axonal conduction velocities within the t.s. were 6.2‐9.7 m/s, where the peripheral conduction velocities were 11.2‐20.4 m/s (28 degrees C). Different latencies of response evoked in a single penetration were considered to indicate branching. The densest branching was found in the ipsilateral commissural subnucleus of the n.t.s. at levels 0.3‐1.3 mm caudal to the obex and, to a lesser degree, in the contralateral commissural subnucleus. All r.a. r.s. sent a few branches to the medial n.t.s. rostral to the obex. Four r.a. r.s. ramified in the ventrolateral n.t.s. where inspiratory cells are located. Depth‐threshold graphs were interpolated by best fitting parabolic equations: Ith = Ad2 + Bd + C; where Ith is the threshold current, d the corresponding depth of stimulation, and A, B and C are coefficients. Coefficient A is a measure of steepness of the parabola. The A coefficients were inversely related to the conduction velocity (v) of the stimulated branch. An analysis of the data from the present study (v = 5.0‐9.7 m/s) combined with data from the literature (v = 2.2‐85 m/s) led to a simple relationship between the A coefficient and the conduction velocity of the stimulated fibre: A = 6500/v, where A is expressed in microA/mm2 and v is expressed in m/s. Within the range 3‐35 m/s, the formula is useful in predicting the effective current spread when the conduction velocity is known, or to estimate the conduction velocity from the shape of a depth‐threshold curve. Two slowly adapting pulmonary stretch receptors (p.s.r.s) were studied. (ABSTRACT TRUNCATED AT 400 WORDS)
Radial Closing Wedge Osteotomy for Kienböck’s Disease: an Over 10 Year Clinical and Radiographic Follow-Up.

Thirteen patients with Kienböck’s disease who had undergone a radial closing wedge osteotomy were reviewed clinically and radiologically at a follow-up mean of 14 years. Good long-term results were obtained in all patients. Their levels of pain were improved, and significant increases were seen in the range of motion and grip strength. Radiographic stage, as assessed by Lichtman’s classification, improved in one, did not change in four, and advanced in eight patients. The radial inclination angle significantly decreased and the carpal-ulnar distance and lunate covering ratios both increased, demonstrating that radial shift in the alignment of the carpal bones occurs and that the joint contact area of the lunate increases in proportion to the decrease in radial inclination. The preoperative radiolunate and radioscaphoid angles, which were significantly larger than those of the unaffected wrist, did not change postoperatively which shows that this technique was not able to correct the flexion deformity of the lunate and the scaphoid.
Development of NADPH-Diaphorase Activity in the Central Nervous System of the Cichlid Fish, Tilapia mariae

The distribution of nicotinamide adenine dinucleotide phosphate (NADPH)-diaphorase activity was studied in the cichlid fish Tilapia mariae during ontogenesis by the histochemical reaction of NADPH-diaphorase that indicates, in aldehyde-fixed tissue, the presence of nitric oxide synthase, which is the enzyme responsible for nitric oxide production. The first appearance of NADPH-diaphorase-positive neurons has a striking bilateral symmetry and occurs 20 h after fertilization (stage 8) in the olfactory placodes and in the neural tube where two clusters of positive neurons were seen in the diencephalon and in the rhombomere r4 of the hindbrain. Two days after fertilization (stage 10), the clusters of positive neurons showed labeled axons. The two longitudinal fiber bundles that arose from the diencephalic positive neurons ran caudally in the tract of the postoptic commissure. At stage 12 (3.5 days after fertilization), new populations of NADPH-diaphorase-positive neurons appeared in the telencephalon, in some diencephalic nuclei, and in the hypothalamus. Several trigeminal motor neurons showed strong NADPH-diaphorase activity, whereas the optic tectum and cerebellum were completely free of enzymatic activity. In the hindbrain, clusters of positive neurons were seen in the octavolateral region and in the region defined by the exit of the vagus nerve. In the cervical spinal cord, some ventral putative motor neurons were labeled. At stage 14 (5.5 days after fertilization), several periventricular neurons of the optic tectum and some neurons of the cerebellar lamina were labeled. Dorsal neurons, including a few large superficial neurons were also labeled in the cervical spinal cord. NADPH-diaphorase activity was seen in the neuropil area of the telencephalon, the target of olfactory inputs, and in the sensory dorso-lateral area of the spinal cord.
Water sorption and solubility of four self-etching, self-adhesive resin luting agents.

PURPOSE To evaluate and compare the water sorption and water solubility of four self-etching, self-adhesive resin luting agents. MATERIALS AND METHODS Four self-etching, self-adhesive resin luting agents (RelyX Unicem, Maxcem, Biscem, Multilink Sprint) and one classic resin luting agent (Multilink Automix) as a control group were used. Twelve disks (8 mm x 1 mm) of each material were prepared according to ISO 4049. Water sorption and solubility were calculated, using the formulae which the ISO 4049 specification provides. RESULTS Maxcem and Biscem were found to have very high water sorption values. RelyX Unicem and Multilink Sprint exhibited water sorption values only slightly higher than the control group. Regarding water solubility, the greater mass loss was found for Maxcem. Multilink Sprint exhibited no mass change. Biscem was found to have low solubility values, whereas RelyX Unicem and Multilink Automix exhibited negative solubility. CONCLUSION Multilink Sprint and RelyX Unicem were found to comply with the ISO requirements regarding water sorption and solubility, while Maxcem and Biscem did not. Materials of the same group exhibited very different behavior during their interaction with water.
Activation of the IL‐2 gene promoter by HTLV‐I tax involves induction of NF‐AT complexes bound to the CD28‐responsive element.

The tax gene product of the type I human T‐cell leukemia virus (HTLV‐I) is a potent transcriptional activator of various growth‐related cellular genes, including that encoding interleukin‐2 (IL‐2). Tax activation of many of these target genes appears to be mediated by the NF‐kappa B/Rel and CREB/ATF family of cellular transcription factors. However, the mechanism by which Tax transactivates the IL‐2 gene remains unclear. In the present study, we demonstrate that neither NF‐kappa B/Rel nor CREB/ATF is sufficient for Tax‐mediated activation of the IL‐2 promoter. Two novel nuclear protein complexes are induced by Tax and specifically bind to an IL‐2 gene enhancer, the CD28‐responsive element (CD28RE). Immunobiochemical analyses suggest that these DNA binding complexes contain at least two members of the nuclear factor of activated T cells, NF‐ATp and NF‐ATc. However, the CD28 binding NF‐AT complexes do not contain Jun and Fos family proteins that have been proposed to serve as NF‐AT partners in the activation of the IL‐2 NF‐AT motif. Transient transfection studies demonstrate that the in vivo expressed NF‐ATp binds to the CD28RE probe and enhances Tax‐mediated activation of this critical IL‐2 enhancer. We demonstrate further that binding of NF‐AT to CD28RE is critical for Tax activation of the IL‐2 promoter. Together, these results suggest a novel mechanism of Tax‐mediated activation of the IL‐2 gene, which involves the induction of NF‐AT‐containing CD28RE binding complexes.