Miracle-dz/UniFAR-FTUs huggingface dataset:
Electron microscopic observation of the primary cilium in the pancreatic islets.

A primary cilium often projected from the Golgi region of pancreatic A, B and D cells. The proximal portion of the cilium was found surrounded by a tubular invagination of the plasmalemma, and then the cilium extended into the intercellular canaliculus. The most proximal portion of the ciliary membrane exhibited periodical densities which might correspond to the ciliary necklace. The axoneme of the cilium was basically of the 9 + 0 pattern, i.e., nine peripheral doublets and no central singlet, though it was modified along the length of the cilium. Although a few appendages were projected from each doublet, it was difficult to identify dynein arms and nexin links. At the most proximal portion of the cilium, a "champagne-glass" structure connected each doublet with the ciliary membrane. The distal and proximal centrioles of the diplosome were connected to each other by a striated band. The proximal centriole, which served as a basal body, had accessory structures, such as alar sheets, basal feet and rootlets. Frequent projections of the primary cilium and its elaborate structure suggest that the cilium is not an aberrant structure but rather one which plays a certain role in the islet cell function.
[cDNA expression array in the differential expression profiles of p53 regulated genes in nasopharyngeal carcinoma and the human normal nasopharynx].

OBJECTIVE To compare the gene expression map of nasopharyngeal carcinoma (NPC) tissue with that of the control tissue by cDNA array and to discuss possible reasons of TP53 accumulation in NPC tissue. METHODS After the hybridization of Atlas human cancer cDNA expression array 7742-1, analysis of Atlas arrays by means of AtlasImage 1.01a was carried out. Then, the results of array were verified by reverse transcription-polymerase chain reaction (RT-PCR). Gene expression alteration on the protein level was verified by immunohistochemistry. RESULTS 134 of 588 tumor-related genes were upregulated and 88 downregulated. Thirteen of 32 p53-regulated genes showed differential expression with 11 upregulated and 2 downregulated. CONCLUSION (1) p53 dysfunction exists in NPC tissues, (2) MDM2, p21 and Bax may be involved in the regulation of nasopharyngeal carcinoma cell growth.
Bayesian Multilevel Models and Medical Applications

BENJAMIN R. SAVILLE: Bayesian Multilevel Models and Medical Applications. (Under the direction of Dr. Amy Herring.) Deciding which predictor effects may vary across subjects is a difficult issue. Standard model selection criteria are often inappropriate for comparing models with different numbers of random effects due to constraints on the parameter space of the variance components. We propose a straightforward approach for testing random effects in the linear mixed model using Bayes factors. We scale the random effects to the residual variance and introduce parameters that control the relative contributions of the random effects. The resulting integrals needed to calculate the Bayes factor are low-dimensional integrals lacking variance components and can be efficiently approximated with Laplace’s method. Our method incorporates default priors and can test multiple random effects simultaneously. We illustrate our method on data from a clinical trial of patients with bipolar disorder and on data from an environmental study of water disinfection by-products and male reproductive outcomes. We extend our method for testing random coefficients to multilevel linear models. A major contribution of our method is the ability to test several variance components from multiple factors simultaneously, and to do so for nested, non-nested, or cross-nested multilevel designs. We illustrate our method on a study investigating significant predictors of infant birth weights in New York City. Random effects are often used for jointly modeling distributions of correlated longitudinal and survival outcomes. These methods generally require strong parametric assumptions and can be difficult to implement. We propose a straightforward approach to evaluate the effect of a treatment or baseline predictor on both longitudinal and survival outcomes simultaneously. We define cutpoints of interest in the longitudinal outcome and time-to-event endpoints based on time to reach a given cutpoint or the survival event, whichever comes first. We use multivariate time-to-event methods on the resulting endpoints to evaluate the effect of the treatment or baseline predictor. The method is particularly attractive in clinical trial settings in which the
Early‐life influences on obesity: from preconception to adolescence

The double burden of under‐ and overnutrition profoundly affects human health globally. According to the World Health Organization, obesity and diabetes rates have almost doubled worldwide since 1980, and, in 2011, more than 40 million children under 5 years of age were overweight. Ecologic factors, parental genetics and fitness, and the intrauterine environment significantly influence the likelihood of offspring developing the dysmetabolic diathesis of obesity. This report examines the effects of these factors, including preconception, intrauterine and postnatal energy balance affecting programming of transgenerational transmission, and development of chronic diseases later in life—in particular, diabesity and its comorbidities.
Myomas and Adenomyosis: Impact on Reproductive Outcome

Among uterine structural abnormalities, myomas and adenomyosis represent two distinct, though frequently coexistent entities, with a remarkable prevalence in women of reproductive age. Various mechanisms have been proposed to explain the impact of each of them on reproductive outcome. In respect to myomas, current evidence implies that submucosal ones have an adverse effect on conception and early pregnancy. A similar effect yet is not quite clear and has been suggested for intramural myomas. Still, it seems reasonable that intramural myomas greater than 4 cm in diameter may negatively impair reproductive outcome. On the contrary, subserosal myomas do not seem to have a significant impact, if any, on reproduction. The presence of submucosal and/or large intramural myomas has also been linked to adverse pregnancy outcomes. In particular increased risk for miscarriage, fetal malpresentation, placenta previa, preterm birth, placenta abruption, postpartum hemorrhage, and cesarean section has been reported. With regard to adenomyosis, besides the tentative coexistence of adenomyosis and infertility, to date a causal relationship among these conditions has not been fully confirmed. Preterm birth and preterm premature rupture of membranes, uterine rupture, postpartum hemorrhage due to uterine atony, and ectopic pregnancy have all been reported in association with adenomyosis. Further research on the impact of adenomyosis on reproductive outcome is welcome.
Group-IV nanosheets with vacancies: a tight-binding extended Hückel study

In this work, we present a theoretical study of the electronic properties of group-IV element nanosheets, namely graphene, silicene, germanene and the corresponding hydrogenated structures for the two latter, silicane and germanane. We compare the results of two different calculation methods, Density Functional Theory (DFT) and Extended Hückel Theory (EHT), for both pristine sheets and sheets of silicene and germanene with a single-atom vacancy. We show that EHT offers a remarkably reliable description of the electronic structure of these materials for all cases, thus offering an affordable way for studying large systems for which DFT calculations would be expensive and lengthy.
A meta-analysis of depression during pregnancy and the risk of preterm birth, low birth weight, and intrauterine growth restriction.

CONTEXT Maternal depressive symptoms during pregnancy have been reported in some, but not all, studies to be associated with an increased risk of preterm birth (PTB), low birth weight (LBW), and intrauterine growth restriction (IUGR). OBJECTIVE To estimate the risk of PTB, LBW, and IUGR associated with antenatal depression. DATA SOURCES AND STUDY SELECTION We searched for English-language and non-English-language articles via the MEDLINE, PsycINFO, CINAHL, Social Work Abstracts, Social Services Abstracts, and Dissertation Abstracts International databases (January 1980 through December 2009). We aimed to include prospective studies reporting data on antenatal depression and at least 1 adverse birth outcome: PTB (<37 weeks' gestation), LBW (<2500 g), or IUGR (<10th percentile for gestational age). Of 862 reviewed studies, 29 US-published and non-US-published studies met the selection criteria. DATA EXTRACTION Information was extracted on study characteristics, antenatal depression measurement, and other biopsychosocial risk factors and was reviewed twice to minimize error. DATA SYNTHESIS Pooled relative risks (RRs) for the effect of antenatal depression on each birth outcome were calculated using random-effects methods. In studies of PTB, LBW, and IUGR that used a categorical depression measure, pooled effect sizes were significantly larger (pooled RR [95% confidence interval] = 1.39 [1.19-1.61], 1.49 [1.25-1.77], and 1.45 [1.05-2.02], respectively) compared with studies that used a continuous depression measure (1.03 [1.00-1.06], 1.04 [0.99-1.09], and 1.02 [1.00-1.04], respectively). The estimates of risk for categorically defined antenatal depression and PTB and LBW remained significant when the trim-and-fill procedure was used to correct for publication bias. The risk of LBW associated with antenatal depression was significantly larger in developing countries (RR = 2.05; 95% confidence interval, 1.43-2.93) compared with the United States (RR = 1.10; 95% confidence interval, 1.01-1.21) or European social democracies (RR = 1.16; 95% confidence interval, 0.92-1.47). Categorically defined antenatal depression tended to be associated with an increased risk of PTB among women of lower socioeconomic status in the United States. CONCLUSIONS Women with depression during pregnancy are at increased risk for PTB and LBW, although the magnitude of the effect varies as a function of depression measurement, country location, and US socioeconomic status. An important implication of these findings is that antenatal depression should be identified through universal screening and treated.
Detection and Feature Extraction of Collective Activity in Human-Computer Interaction

Time-based online media, such as video, has been growing in importance. Still, there is limited research on information retrieval of time-coded media content. This work elaborates on the idea of extracting feature characteristics from time-based online content by means of users' interactions analysis instead of analyzing the content itself. Accordingly, a time series of users’ activity in online media is constructed and shown to exhibit rich temporal dynamics. Additionally it is demonstrated that is also possible to detect characteristic patterns in collective activity while accessing time-based media. Pattern detection of collective activity, as well as feature extraction of the corresponding pattern, is achieved by means of a time series clustering approach. This is demonstrated with the proposed approach featuring information-rich videos. It is shown that the proposed probabilistic algorithm effectively detects distinct shapes of the users’ time series, predicting correctly popularity dynamics, as well as their scale characteristics.
Prognostic value of fetal hemoglobin levels in acquired aplastic anemia.

Abstract Total fetal hemoglobin values (milligrams of fetal hemoglobin per 100 ml of blood) were determined in 30 children with acquired aplastic anemia. Seventeen of 18 patients who died (95 per cent) had less than 400 mg per 100 ml of total fetal hemoglobin whereas 11 of 12 who are alive (92 per cent) and doing well had more than 400 mg per 100 ml of total fetal hemoglobin at the initial examination. The results suggest that the total fetal hemoglobin concentration may reflect the extent of injury to the bone marrow and may be of prognostic value in determining which patients with acquired aplastic anemia are likely to respond to treatment.
Turbulence-induced melting of a nonequilibrium vortex crystal in a forced thin fluid film

To gain a better understanding of recent experiments on the turbulence-induced melting of a periodic array of vortices in a thin fluid film, we perform a direct numerical simulation of the two-dimensional Navier–Stokes equations forced such that, at low Reynolds numbers, the steady state of the film is a square lattice of vortices. We find that as we increase the Reynolds number, this lattice undergoes a series of nonequilibrium phase transitions, first to a crystal with a different reciprocal lattice and then to a sequence of crystals that oscillate in time. Initially, the temporal oscillations are periodic; this periodic behaviour becoming more and more complicated with increasing Reynolds number until the film enters a spatially disordered nonequilibrium statistical steady state that is turbulent. We study this sequence of transitions using fluid-dynamics measures, such as the Okubo–Weiss parameter that distinguishes between vortical and extensional regions in the flow, ideas from nonlinear dynamics, e.g. Poincaré maps, and theoretical methods that have been developed to study the melting of an equilibrium crystal or the freezing of a liquid and that lead to a natural set of order parameters for the crystalline phases and spatial autocorrelation functions that characterize short- and long-range order in the turbulent and crystalline phases, respectively.
Stimulation of DMA Synthesis and Cell Proliferation in the Liver of Rats Fed a Choline-devoid Diet and Their Suppression by PhÃ © nobarbital 1

Feeding of a choline-devoid (CD) diet and dietary administra tion of phÃ©nobarbital (PHB) are efficient promoters of liver carcinogenesis in the rat. Furthermore, inclusion of PHB in a CD diet results in a synergistic effect, inasmuch as the pro moting action of their combination is greater than the sum of those exerted by either agent alone. To investigate the mechanism(s) of action of the two promoters, liver DNA synthesis and liver cell proliferation were studied in rats fed a CD diet, a choline-supplemented diet, or the same diets to which 0.06% PHB was added. DNA synthesis was determined by [3H]thymidine incorporation into DNA and autoradiography, and cell proliferation was determined by mitosis counts. Feeding the CD diet caused an increase of both DNA synthesis and cell proliferation over those present in rats fed the choline-supple mented diet. Inclusion of PHB in the CD diet, on the other hand, inhibited DNA synthesis and cell proliferation. These results indicate that stimulation of cell proliferation per se may not be a sufficient condition for an agent to act as a promoter of liver carcinogenesis.
F plasmid partition depends on interaction of SopA with non‐specific DNA

Bacterial ATPases belonging to the ParA family assure partition of their replicons by forming dynamic assemblies which move replicon copies into the new cell‐halves. The mechanism underlying partition is not understood for the Walker‐box ATPase class, which includes most plasmid and all chromosomal ParAs. The ATPases studied both polymerize and interact with non‐specific DNA in an ATP‐dependent manner. Previous work showed that in vitro, polymerization of one such ATPase, SopA of plasmid F, is inhibited by DNA, suggesting that interaction of SopA with the host nucleoid could regulate partition. In an attempt to identify amino acids in SopA that are needed for interaction with non‐specific DNA, we have found that mutation of codon 340 (lysine to alanine) reduces ATP‐dependent DNA binding > 100‐fold and correspondingly diminishes SopA activities that depend on it: inhibition of polymer formation and persistence, stimulation of basal‐level ATP hydrolysis and localization over the nucleoid. The K340A mutant retained all other SopA properties tested except plasmid stabilization; substitution of the mutant SopA for wild‐type nearly abolished mini‐F partition. The behaviour of this mutant indicates a causal link between interaction with the cell's non‐specific DNA and promotion of the dynamic behaviour that ensures F plasmid partition.
ES cell pluripotency and germ-layer formation require the SWI/SNF chromatin remodeling component BAF250a

ATP-dependent chromatin remodeling complexes are a notable group of epigenetic modifiers that use the energy of ATP hydrolysis to change the structure of chromatin, thereby altering its accessibility to nuclear factors. BAF250a (ARID1a) is a unique and defining subunit of the BAF chromatin remodeling complex with the potential to facilitate chromosome alterations critical during development. Our studies show that ablation of BAF250a in early mouse embryos results in developmental arrest (about embryonic day 6.5) and absence of the mesodermal layer, indicating its critical role in early germ-layer formation. Moreover, BAF250a deficiency compromises ES cell pluripotency, severely inhibits self-renewal, and promotes differentiation into primitive endoderm-like cells under normal feeder-free culture conditions. Interestingly, this phenotype can be partially rescued by the presence of embryonic fibroblast cells. DNA microarray, immunostaining, and RNA analyses revealed that BAF250a-mediated chromatin remodeling contributes to the proper expression of numerous genes involved in ES cell self-renewal, including Sox2, Utf1, and Oct4. Furthermore, the pluripotency defects in BAF250a mutant ES cells appear to be cell lineage-specific. For example, embryoid body-based analyses demonstrated that BAF250a-ablated stem cells are defective in differentiating into fully functional mesoderm-derived cardiomyocytes and adipocytes but are capable of differentiating into ectoderm-derived neurons. Our results suggest that BAF250a is a key component of the gene regulatory machinery in ES cells controlling self-renewal, differentiation, and cell lineage decisions.
Hydroacoustics of a submarine eruption in the Northeast Lau Basin using an acoustic glider

A 1000-m Slocum glider® (Teledyne Webb Research Corporation) with CTD, turbidity, and hydrophone sensors was operated for two days in the Northeast Lau Basin. The survey was conducted near West Mata Volcano, where in November of 2008 the NOAA PMEL Vents program observed an active eruption emanating from near its summit at 1207 m-the deepest submarine activity ever to be witnessed. Our goal was to use the glider as a forensic tool to search for other nearby eruption sites with onboard sensors that detect the chemical and hydroacoustic signatures associated with the volcanic and hydrothermal plumes. The glider was launched on May 6, 2010 at 15° 8'3.60"S-174° 6'15.00"W, approximately 40 km to the west of West Mata. It flew toward West Mata and was recovered near the summit of the volcano after repeating 13 yos during a 41-hour mission. Although the recordings were affected by mechanical noise from the glider's rudder, the data demonstrate that the system can detect the wide-band noises (>1 kHz) associated with submarine volcanic and intense hydrothermal activity. The glider recorded variable acoustic amplitudes based on its distance from West Mata and temporal variations in the volcano's rate of activity, and demonstrated that these geologic processes contribute to the region's high ambient noise levels.
Probing PML body function in ALT cells reveals spatiotemporal requirements for telomere recombination

Promyelocytic leukemia (PML) bodies (also called ND10) are dynamic nuclear structures implicated in a wide variety of cellular processes. ALT-associated PML bodies (APBs) are specialized PML bodies found exclusively in telomerase-negative tumors in which telomeres are maintained by recombination-based alternative (ALT) mechanisms. Although it has been suggested that APBs are directly implicated in telomere metabolism of ALT cells, their precise role and structure have remained elusive. Here we show that PML bodies in ALT cells associate with chromosome ends forming small, spatially well-defined clusters, containing on average 2–5 telomeres. Using an innovative approach that gently enlarges PML bodies in living cells while retaining their overall organization, we show that this physical enlargement of APBs spatially resolves the single telomeres in the cluster, but does not perturb the potential of the APB to recruit chromosome extremities. We show that telomere clustering in PML bodies is cell-cycle regulated and that unique telomeres within a cluster associate with recombination proteins. Enlargement of APBs induced the accumulation of telomere-telomere recombination intermediates visible on metaphase spreads and connecting heterologous chromosomes. The strand composition of these recombination intermediates indicated that this recombination is constrained to a narrow time window in the cell cycle following replication. These data provide strong evidence that PML bodies are not only a marker for ALT cells but play a direct role in telomere recombination, both by bringing together chromosome ends and by promoting telomere-telomere interactions between heterologous chromosomes.
Transmission of Donor Melanoma to Multiple Organ Transplant Recipients

Malignant melanoma represents the most common tumour responsible for donor‐derived post transplantation malignancies. We report the varied presentation and outcome of three graft recipients (two kidney and hepatic) who developed metastatic melanoma following cadaveric organ transplantation from a single multiorgan donor. Two of the recipients presented with symptomatic metastatic lesions and the third patient, despite being carefully monitored, developed evidence of metastatic cutaneous melanoma. Two of the patients died as a direct result of their melanomas. The recipients of corneal and cardiac grafts remain disease‐free. We conclude that despite careful screening, donor‐derived tumours remain a not uncommon clinical entity. The identification of a lesion in one recipient should prompt immediate examination and investigation of the remaining recipients of multiorgan donations.
Evidence is still not informing policy on obesity, conference hears

The government is still not making the best use of evidence in efforts to tackle the UK’s grave obesity problem, a conference of experts heard. Julia Neuberger, who chairs the House of Lords Science and Technology sub-committee, said attempts to change people’s behaviour were not being properly evaluated. She said there was insufficient commitment to implement research and called for more to be done to address environmental impacts on obesity. Baroness Neuberger, a cross-bench peer and former chief executive of the King’s Fund, spoke at the Obesity 2012 seminar, held in London on 7 February by Westminster Food and Nutrition Forum. Last year her committee’s inquiry into behaviour change reported that “nudges” …
The α-proteobacteria: the Darwin finches of the bacterial world

The α-proteobacteria represent one of the most diverse bacterial subdivisions, displaying extreme variations in lifestyle, geographical distribution and genome size. Species for which genome data are available have been classified into a species tree based on a conserved set of vertically inherited core genes. By mapping the variation in gene content onto the species tree, genomic changes can be associated with adaptations to specific growth niches. Genes for adaptive traits are mostly located in ‘plasticity zones’ in the bacterial genome, which also contain mobile elements and are highly variable across strains. By physically separating genes for information processing from genes involved in interactions with the surrounding environment, the rate of evolutionary change can be substantially enhanced for genes underlying adaptation to new growth habitats, possibly explaining the ecological success of the α-proteo-bacterial subdivision.