Miracle-dz/UniFAR-FTUs huggingface dataset:
The osr1 and osr2 genes act in the pronephric anlage downstream of retinoic acid signaling and upstream of wnt2b to maintain pectoral fin development

Vertebrate odd-skipped related genes (Osr) have an essential function during the formation of the intermediate mesoderm (IM) and the kidney structures derived from it. Here, we show that these genes are also crucial for limb bud formation in the adjacent lateral plate mesoderm (LPM). Reduction of zebrafish Osr function impairs fin development by the failure of tbx5a maintenance in the developing pectoral fin bud. Osr morphant embryos show reduced wnt2b expression, and increasing Wnt signaling in Osr morphant embryos partially rescues tbx5a expression. Thus, Osr genes control limb bud development in a non-cell-autonomous manner, probably through the activation of Wnt2b. Finally, we demonstrate that Osr genes are downstream targets of retinoic acid (RA) signaling. Therefore, Osr genes act as a relay within the genetic cascade of fin bud formation: by controlling the expression of the signaling molecule Wnt2ba in the IM they play an essential function transmitting the RA signaling originated in the somites to the LPM.
Wnt9b-dependent FGF signaling is crucial for outgrowth of the nasal and maxillary processes during upper jaw and lip development

Outgrowth and fusion of the lateral and medial nasal processes and of the maxillary process of the first branchial arch are integral to lip and primary palate development. Wnt9b mutations are associated with cleft lip and cleft palate in mice; however, the cause of these defects remains unknown. Here, we report that Wnt9b–/– mice show significantly retarded outgrowth of the nasal and maxillary processes due to reduced proliferation of mesenchymal cells, which subsequently results in a failure of physical contact between the facial processes that leads to cleft lip and cleft palate. These cellular defects in Wnt9b–/– mice are mainly caused by reduced FGF family gene expression and FGF signaling activity resulting from compromised canonical WNT/β-catenin signaling. Our study has identified a previously unknown regulatory link between WNT9B and FGF signaling during lip and upper jaw development.
Clinical Physiology and Functional Imaging

Clinical Physiology started in 1942, when Torgny Sjöstrand became professor in the discipline at the Karolinska Hospital in Stockholm. For several decades it has been a firmly established clinical speciality in Denmark, Finland and Sweden. From its start, the speciality focused on diagnostic examination and functional evaluation of the cardiovascular, the respiratory and the renal systems. While many of the techniques used in the early days of the speciality have become obsolete, technical development has led to new techniques for functional investigations in vivo. This has widened the scope of the speciality. Clinical physiologists are now using several imaging techniques such as ultrasound, nuclear medicine and functional magnetic resonance. Nuclear medicine is often integrated with clinical. The rapid growth in application of imaging techniques in clinical medicine has also led to closer co-operation between clinical physiology and other medical specialities, e.g. diagnostic radiology and cardiology. The Scandinavian Society of Clinical Physiology and Nuclear Medicine was founded in 1979 with the purpose of stimulating research and education in the field of clinical physiology. The journal of the society, Clinical Physiology, started in 1981 and has over its 20 years of existence provided interesting reading for anyone interested in human physiology and pathophysiology. Although medical imaging has been represented in Clinical Physiology from its first volume, the increasing use of imaging techniques for studies of human physiology has prompted the Scandinavian Society of Clinical Physiology and Nuclear Medicine to change the name of its journal to Clinical Physiology and Functional Imaging. This entails not so much a change of scope of the journal as increased emphasis on studies using imaging techniques. Submission of manuscripts based upon the full range of traditional methods and newer imaging techniques is thereby encouraged. As from this issue, there is also a change of the editors of the journal. On behalf of the Scandinavian Society of Clinical Physiology and Nuclear Medicine, we would like to thank Professor Esko Länsimies for his outstanding work during the 4 years he has served as Editor of Clinical Physiology. Professor Länsimies has been working with great enthusiasm for the journal and has made a major contribution to its development. We would also like to thank Professor Anssi Sovijärvi for his excellent work as review articles editor during this period.
Late-life effects on rat reproductive system after developmental exposure to mixtures of endocrine disrupters.

This study examined late-life effects of perinatal exposure of rats to a mixture of endocrine-disrupting contaminants. Four groups of 14 time-mated Wistar rats were exposed by gavage from gestation day 7 to pup day 22 to a mixture of 13 anti-androgenic and estrogenic chemicals including phthalates, pesticides, u.v. -filters, bisphenol A, parabens, and the drug paracetamol. The groups received vehicle (control), a mixture of all 13 chemicals at 150-times (TotalMix150) or 450-times (TotalMix450) high-end human exposure, or 450-times a mixture of nine predominantly anti-androgenic chemicals (AAMix450). Onset of puberty and estrous cyclicity at 9 and 12 months of age were assessed. Few female offspring showed significantly regular estrus cyclicity at 12 months of age in the TotalMix450 and AAMix450 groups compared with controls. In 19-month-old male offspring, epididymal sperm counts were lower than controls, and in ventral prostate an overrepresentation of findings related to hyperplasia was observed in exposed groups compared with controls, particularly in the group dosed with anti-androgens. A higher incidence of pituitary adenoma at 19 months of age was found in males and females in the AAMix450 group. Developmental exposure of rats to the highest dose of a human-relevant mixture of endocrine disrupters induced adverse effects late in life, manifested as earlier female reproductive senescence, reduced sperm counts, higher score for prostate atypical hyperplasia, and higher incidence of pituitary tumors. These delayed effects highlight the need for further studies on the role of endocrine disrupters in hormone-related disorders in aging humans.
Adverse prenatal environment and kidney development: implications for programing of adult disease.

The 'developmental origins of health and disease' hypothesis suggests that many adult-onset diseases can be attributed to altered growth and development during early life. Perturbations during gestation can be detrimental and lead to an increased risk of developing renal, cardiovascular, metabolic, and neurocognitive dysfunction in adulthood. The kidney has emerged as being especially vulnerable to insult at almost any stage of development resulting in a reduction in nephron endowment. In both humans and animal models, a reduction in nephron endowment is strongly associated with an increased risk of hypertension. The focus of this review is twofold: i) to determine the importance of specific periods during development on long-term programing and ii) to examine the effects of maternal perturbations on the developing kidney and how this may program adult-onset disease. Recent evidence has suggested that insults occurring around the time of conception also have the capacity to influence long-term health. Although epigenetic mechanisms are implicated in mediating these outcomes, it is unclear as to how these may impact on kidney development. This presents exciting new challenges and areas for research.
Immature hematopoietic stem cells undergo maturation in the fetal liver

Hematopoietic stem cells (HSCs), which are defined by their capacity to reconstitute adult conventional mice, are first found in the dorsal aorta after 10.5 days post coitus (dpc) and in the fetal liver at 11 dpc. However, lympho-myeloid hematopoietic progenitors are detected in the dorsal aorta from 9 dpc, raising the issue of their role in establishing adult hematopoiesis. Here, we show that these progenitors are endowed with long-term reconstitution capacity, but only engraft natural killer (NK)-deficient Rag2γc–/– mice. This novel population, called here immature HSCs, evolves in culture with thrombopoietin and stromal cells, into HSCs, defined by acquisition of CD45 and MHC-1 expression and by the capacity to reconstitute NK-competent mice. This evolution occurs during ontogeny, as early colonization of fetal liver by immature HSCs precedes that of HSCs. Moreover, organ culture experiments show that immature HSCs acquire, in this environment, the features of HSCs.
FAÇADE: a fast and effective approach to the discovery of dense clusters in noisy spatial data

FAÇADE (Fast and Automatic Clustering Approach to Data Engineering) is a spatial clustering tool that can discover clusters of different sizes, shapes, and densities in noisy spatial data. Compared with the existing clustering methods, FAÇADE has several advantages: first, it separates true data and noise more effectively. Second, most steps of FAÇADE are automatic. Third, it requires only O(nlogn) time. 2D and 3D visualizations are used in FAÇADE to assist parameter selection and result evaluation. More information on FAÇADE is available at: http://viscomp.utdallas. edu/FACADE.
Anterior-posterior differences in HoxD chromatin topology in limb development

A late phase of HoxD activation is crucial for the patterning and growth of distal structures across the anterior-posterior (A-P) limb axis of mammals. Polycomb complexes and chromatin compaction have been shown to regulate Hox loci along the main body axis in embryonic development, but the extent to which they have a role in limb-specific HoxD expression, an evolutionary adaptation defined by the activity of distal enhancer elements that drive expression of 5′ Hoxd genes, has yet to be fully elucidated. We reveal two levels of chromatin topology that differentiate distal limb A-P HoxD activity. Using both immortalised cell lines derived from posterior and anterior regions of distal E10.5 mouse limb buds, and analysis in E10.5 dissected limb buds themselves, we show that there is a loss of polycomb-catalysed H3K27me3 histone modification and a chromatin decompaction over HoxD in the distal posterior limb compared with anterior. Moreover, we show that the global control region (GCR) long-range enhancer spatially colocalises with the 5′ HoxD genomic region specifically in the distal posterior limb. This is consistent with the formation of a chromatin loop between 5′ HoxD and the GCR regulatory module at the time and place of distal limb bud development when the GCR participates in initiating Hoxd gene quantitative collinearity and Hoxd13 expression. This is the first example of A-P differences in chromatin compaction and chromatin looping in the development of the mammalian secondary body axis (limb).
Aesthetic interaction: a pragmatist's aesthetics of interactive systems

There is a growing interest in considering aesthetic aspects in the design of interactive systems. A set of approaches are emerging each representing different applications of the terminology as well as different inherent assumptions on the role of the user, designer and interaction ideals. In this paper, we use the concept of Pragmatist Aesthetics to provide a framework for distinguishing between different approaches to aesthetics. Moreover, we use our own design cases to illustrate how pragmatist aesthetics is a promising path to follow in the context of designing interactive systems, as it promotes aesthetics of use, rather than aesthetics of appearance. We coin this approach in the perspective of aesthetic interaction. Finally we make the point that aesthetics is not re-defining everything known about interactive systems. We provide a framework placing this perspective among other perspectives on interaction.
Endogenous Nodal signaling regulates germ cell potency during mammalian testis development

Germ cells, the embryonic precursors of sperm or oocytes, respond to molecular cues that regulate their sex-specific development in the fetal gonads. In males in particular, the balance between continued proliferation and cell fate commitment is crucial: defects in proliferation result in insufficient spermatogonial stem cells for fertility, but escape from commitment and prolonged pluripotency can cause testicular germ cell tumors. However, the factors that regulate this balance remain unidentified. Here, we show that signaling by the TGFβ morphogen Nodal and its co-receptor Cripto is active during a crucial window of male germ cell development. The Nodal pathway is triggered when somatic signals, including FGF9, induce testicular germ cells to upregulate Cripto. Germ cells of mutant mice with compromised Nodal signaling showed premature differentiation, reduced pluripotency marker expression and a reduced ability to form embryonic germ (EG) cell colonies in vitro. Conversely, human testicular tumors showed upregulation of NODAL and CRIPTO that was proportional to invasiveness and to the number of malignant cells. Thus, Nodal signaling provides a molecular control mechanism that regulates male germ cell potency in normal development and testicular cancer.
Inhibition of zygotic DNA repair: transcriptome analysis of the offspring in trout (Oncorhynchus mykiss).

Zygotic repair of the paternal genome is a key event after fertilization. Spermatozoa accumulate DNA strand breaks during spermatogenesis and can suffer additional damage by different factors, including cryopreservation. Fertilization with DNA-damaged spermatozoa (DDS) is considered to promote implantation failures and abortions, but also long-term effects on the progeny that could be related with a defective repair. Base excision repair (BER) pathway is considered the most active in zygotic DNA repair, but healthy oocytes contain enzymes for all repairing pathways. In this study, the effects of the inhibition of the BER pathway in the zygote were analyzed on the progeny obtained after fertilization with differentially DDS. Massive gene expression (GE; 61 657 unique probes) was analyzed after hatching using microarrays. Trout oocytes are easily fertilized with DDS and the high prolificacy allows live progeny to be obtained even with a high rate of abortions. Nevertheless, the zygotic inhibition of Poly (ADP-ribose) polymerase, upstream of BER pathway, resulted in 810 differentially expressed genes (DEGs) after hatching. DEGs are related with DNA repair, apoptosis, telomere maintenance, or growth and development, revealing a scenario of impaired DNA damage signalization and repair. Downregulation of the apoptotic cascade was noticed, suggesting a selection of embryos tolerant to residual DNA damage during embryo development. Our results reveal changes in the progeny from defective repairing zygotes including higher malformations rate, weight gain, longer telomeres, and lower caspase 3/7 activity, whose long-term consequences should be analyzed in depth.
Technology as experience

In Technology as Experience, John McCarthy and Peter Wright argue that any account of what is often called the user experience must take into consideration the emotional, intellectual, and sensual aspects of our interactions with technology. We don't just use technology, they point out; we live with it. They offer a new approach to understanding human-computer interaction through examining the felt experience of technology. Drawing on the pragmatism of such philosophers as John Dewey and Mikhail Bakhtin, they provide a framework for a clearer analysis of technology as experience. Just as Dewey, in Art as Experience, argued that art is part of everyday lived experience and not isolated in a museum, McCarthy and Wright show how technology is deeply embedded in everyday life. The "zestful integration" or transcendent nature of the aesthetic experience, they say, is a model of what human experience with technology might become. McCarthy and Wright illustrate their theoretical framework with real-world examples that range from online shopping to ambulance dispatch. Their approach to understanding human-computer interactionseeing it as creative, open, and relational, part of felt experienceis a measure of the fullness of technologys potential to be more than merely functional.
Effectiveness of Alkali-Acid Treatment in Enhancement the Adsorption Capacity for Rice Straw: The Removal of Methylene Blue Dye

The effectiveness of alkali-acid modification in enhancement the adsorption capacity of rice straw (RS) for removing a basic dye was studied. The obtained adsorbents were characterized by slurry pH, pHPZC, iodine number, methylene blue number, FTIR, and SEM analyses. Adsorption of methylene blue (MB) was described by the Langmuir, Freundlich, Tempkin, and Redlich-Peterson isotherm models. Effects of contact time, initial concentration of MB dye, pH of solution, adsorbent dose, salt concentration of NaCl, and desorbing agents on the removal of MB were reported. Kinetic studies were analyzed using the pseudo-first-order, pseudo-second-order, and the intraparticle diffusion models and were found to follow closely the pseudo-second-order model. Equilibrium data were best represented by the Langmuir and Redlich-Peterson isotherms. The adsorption capacities were varied between 32.6 and 131.5 mg/g for untreated and treated RS samples with NaOH-1M citric acid (ARS-1C), respectively. Adsorption behavior of the ARS-1C sample was experimented in a binary mixture containing methylene blue (basic) and reactive blue 19 (acidic) dyes which showed its ability to remove MB higher than RB19. Overall, the results indicate that the alkali-acid treatment proved to be potential modification for producing effective low-cost adsorbents for the removal of the basic dyes from wastewater.
The Clinical Significance of Aerobic Exercise Testing and Prescription: From Apparently Healthy to Confirmed Cardiovascular Disease

Aerobic exercise testing clearly provides valuable clinical information in apparently healthy adults as well as a number of patient populations. Maximal aerobic capacity, either estimated from workload or measured directly, is perhaps the most frequently analyzed variable ascertained from such testing. This practice is warranted given the consistent prognostic significance of maximal aerobic capacity. Other variables obtained from the aerobic exercise test, such as the heart rate response during exercise and into recovery, the systolic and diastolic blood pressure responses during exercise, oxygen consumption at anaerobic threshold, and the ventilatory response to exercise, also provide important insight into an individual's health and prognosis. Furthermore, the aerobic exercise test is highly valuable in developing an individualized and safe exercise prescription. Aerobic exercise training goals, with respect to frequency, duration, frequency, and mode of exercise, are well established for the apparently healthy population as well as individuals at risk for or diagnosed with cardiovascular disease. Adherence to these physical activity recommendations clearly provides numerous health benefits, perhaps most important of which is a significant decrease in the risk for cardiovascular events and mortality. This review addresses concepts of aerobic exercise testing and training and discusses their clinical implications.
Swoogle: a search and metadata engine for the semantic web

Swoogle is a crawler-based indexing and retrieval system for the Semantic Web. It extracts metadata for each discovered document, and computes relations between documents. Discovered documents are also indexed by an information retrieval system which can use either character N-Gram or URIrefs as keywords to find relevant documents and to compute the similarity among a set of documents. One of the interesting properties we compute is <i>ontology rank</i>, a measure of the importance of a Semantic Web document.
Reproductive performance primarily depends on the female genotype in a two-factorial breeding experiment using high-fertility mouse lines.

Mouse models showing an improved fertility phenotype are barely described in the literature. In the present study, we further characterized two outbred mouse models that have been selected for the phenotype 'high fertility' for more than 177 generations (fertility lines (FL) 1 and 2). In order to delineate the impact of males and females on fertility parameters, we performed a two-factorial breeding experiment by mating males and females of the three different genotypes (FL1, FL2, unselected control (Ctrl)) in all 9 possible combinations. Reproductive performance, such as number of offspring per litter or total birth weight of the entire pup, mainly depends on the female genotype. Although the reproductive performance of FL1 and FL2 is very similar, their phenotypes differ. FL2 animals of both genders are larger compared to FL1 and control animals. Females of the control line delivered offspring earlier compared to FL1 and FL2 dams. Males of FL1 are the lightest and the only ones who gained weight during the two weeks mating period. To address whether this effect is correlated with differing serum androgen levels, we measured the concentrations of testosterone, dehydroepiandrosterone, 4-androstenedione, androstanediol and dihydrotestosterone in males of all three lines by GC-MS. We measured serum testosterone between 5.0 and 6.4 ng/mL, whereas the concentrations of the other androgens were at least one order of magnitude lower, with no significant differences between the lines. Our data indicate that reproductive outcome largely depends on the genotype of the female in a two-factorial breeding experiment and supports previous findings that the phenotype 'high fertility' is warranted by using different physiological strategies.
Registration of point cloud data from a geometric optimization perspective

We propose a framework for pairwise registration of shapes represented by point cloud data (PCD). We assume that the points are sampled from a surface and formulate the problem of aligning two PCDs as a minimization of the squared distance between the underlying surfaces. Local quadratic approximants of the squared distance function are used to develop a linear system whose solution gives the best aligning rigid transform for the given pair of point clouds. The rigid transform is applied and the linear system corresponding to the new orientation is build. This process is iterated until it converges. The point-to-point and the point-to-plane Iterated Closest Point (ICP) algorithms can be treated as special cases in this framework. Our algorithm can align PCDs even when they are placed far apart, and is experimentally found to be more stable than point-to-plane ICP. We analyze the convergence behavior of our algorithm and of point-to-point and point-to-plane ICP under our proposed framework, and derive bounds on their rate of convergence. We compare the stability and convergence properties of our algorithm with other registration algorithms on a variety of scanned data.