Miracle-dz/UniFAR-FTUs huggingface dataset:
Food supply and size class depending variations in phytodetritus intake in the benthic foraminifer Ammonia tepida

ABSTRACT Ammonia tepida is a common and abundant benthic foraminifer in intertidal mudflats. Benthic foraminifera are primary consumers and detritivores and act as key players in sediment nutrient fluxes. In this study, laboratory feeding experiments using isotope-labeled phytodetritus were carried out with A. tepida collected at the German Wadden Sea, to investigate the response of A. tepida to varying food supply. Feeding mode (single pulse, constant feeding; different incubation temperatures) caused strong variations in cytoplasmic carbon and nitrogen cycling, suggesting generalistic adaptations to variations in food availability. To study the influence of intraspecific size to foraminiferal carbon and nitrogen cycling, three size fractions (125–250 µm, 250–355 µm, >355 µm) of A. tepida specimens were separated. Small individuals showed higher weight specific intake for phytodetritus, especially for phytodetrital nitrogen, highlighting that size distribution within foraminiferal populations is relevant to interpret foraminiferal carbon and nitrogen cycling. These results were used to extrapolate the data to natural populations of living A. tepida in sediment cores, demonstrating the impact of high abundances of small individuals on phytodetritus processing and nutrient cycling. It is estimated that at high abundances of individuals in the 125–250 µm size fraction, Ammonia populations can account for more than 11% of phytodetritus processing in intertidal benthic communities. Summary: The food intake of Ammonia tepida (marine Protist) is strongly related to food supply and individual size. Specifically, juveniles play a major role in coastal phytodetritus processing.
Structured Factored Inference for Probabilistic Programming

Probabilistic reasoning on complex real-world models is computationally challenging. Inference algorithms have been developed that work well on specific models or on parts of general models, but they require significant handengineering to apply to full-scale problems. Probabilistic programming (PP) enables the expression of rich probabilistic models, but inference remains a bottleneck in many applications. Factored inference is one of the main approaches to inference in graphical models, but has trouble scaling up to some hard problems expressible as probabilistic programs. We present structured factored inference (SFI), a framework that enables factored inference algorithms to scale to significantly more complex programs. Using models encoded in a PP language, SFI provides a sound means to decompose a model into submodels, apply an algorithm to each submodel, and combine results to answer a query. Our results show that SFI successfully reasons on models where standard factored inference algorithms fail due to computational complexity. SFI is nearly as accurate as exact inference and is as fast as approximate inference methods.
Measurement of mother-infant interactions and the home environment in a European setting: preliminary results from a cross-cultural study

Background Infant development is adversely affected in the context of postnatal depression. This relationship may be mediated by both the nature of early mother-infant interactions and the quality of the home environment. Aims To establish the usefulness of the Global Ratings Scales of Mother–Infant Interaction and the Infant–Toddler version of the Home Observation for the Measurement of the Environment (IT–HOME), and to test expected associations of the measures with characteristics of the social context and with major or minor depression. Method Both assessments were administered postnatally in four European centres; 144 mothers were assessed with the Global Ratings Scales and 114 with the IT–HOME. Affective disorder was assessed by means of the Structured Clinical Interview for DSM–IV Disorders. Results Analyses of mother–infant interaction indicated no main effect for depression but maternal sensitivity to infant behaviour was associated with better infant communication, especially for women who were not depressed. Poor overall emotional support also reduced sensitivity scores. Poor support was also related to poorer IT–HOME scores, but there was no effect of depression. Conclusions The Global Ratings Scales were effectively applied but there was less evidence of the usefulness of the IT–HOME.
The General Stress Response Is Conserved in Long-Term Soil-Persistent Strains of Escherichia coli

ABSTRACT Although Escherichia coli is generally considered to be predominantly a commensal of the gastrointestinal tract, a number of recent studies suggest that it is also capable of long-term survival and growth in environments outside the host. As the extraintestinal physical and chemical conditions are often different from those within the host, it is possible that distinct genetic adaptations may be required to enable this transition. Several studies have shown a trade-off between growth and stress resistance in nutrient-poor environments, with lesions in the rpoS locus, which encodes the stress sigma factor RpoS (σS). In this study, we investigated a unique collection of long-term soil-persistent E. coli isolates to determine whether the RpoS-controlled general stress response is altered during adaptation to a nutrient-poor extraintestinal environment. The sequence of the rpoS locus was found to be highly conserved in these isolates, and no nonsense or frameshift mutations were detected. Known RpoS-dependent phenotypes, including glycogen synthesis and γ-aminobutyrate production, were found to be conserved in all strains. All strains expressed the full-length RpoS protein, which was fully functional using the RpoS-dependent promoter reporter fusion PgadX::gfp. RpoS was shown to be essential for long-term soil survival of E. coli, since mutants lacking rpoS lost viability rapidly in soil survival assays. Thus, despite some phenotypic heterogeneity, the soil-persistent strains all retained a fully functional RpoS-regulated general stress response, which we interpret to indicate that the stresses encountered in soil provide a strong selective pressure for maintaining stress resistance, despite limited nutrient availability. IMPORTANCE Escherichia coli has been, and continues to be, used as an important indicator species reflecting potential fecal contamination events in the environment. However, recent studies have questioned the validity of this, since E. coli has been found to be capable of long-term colonization of soils. This study investigated whether long-term soil-persistent E. coli strains have evolved altered stress resistance characteristics. In particular, the study investigated whether the main regulator of genes involved in stress protection, the sigma factor RpoS, has been altered in the soil-persistent strains. The results show that RpoS stress protection is fully conserved in soil-persistent strains of E. coli. They also show that loss of the rpoS gene dramatically reduces the ability of this organism to survive in a soil environment. Overall, the results indicate that soil represents a stressful environment for E. coli, and their survival in it requires that they deploy a full stress protection response.
[Can US-guided vacuum-assisted biopsies be an alternative to diagnostic surgery in cases of non-diagnostic core needle biopsy?].

PURPOSE To assess US-guided vacuum-assisted biopsies in the diagnosis of suspicious sonographic breast lesions after non-diagnostic core needle biopsies (CNB). PATIENTS AND METHODS Retrospective study of 42 females with suspicious breast lesions at US. CNB previously performed were non-diagnostic. Because of the larger sample size, vacuum-assisted biopsies were performed, instead of surgical biopsy. RESULTS Vacuum-assisted biopsies showed 32 benign lesions. Histologic examination of the CNB showed non-specific fibrous tissue in 43% of cases as opposed to 7.1% for vacuum-assisted biopsies. The latter provided a more specific diagnosis (mainly fibrocystic breast disease). From a total of 4 lesions that were suspicious at CNB, 3 were diagnosed as malignancies after vacuum-assisted biopsy and one case was a "borderline" lesion. Three additional malignant and three additional borderline lesions were diagnosed on vacuum-assisted biopsies. In 11 cases, surgical excision was performed, and all diagnoses from vacuum-assisted biopsies were confirmed at microscopy, except in one case where it was underestimated (ADH versus DCIS). CONCLUSION US-guided vacuum-assisted biopsy is a reliable technique. Because it provides more tissue than CNB, it can be an alternative to diagnostic surgery after non-diagnostic CNB. Indeed, it allows confirmation of the diagnosis and provides a more specific diagnosis of benign lesions. With regards to malignant and borderline lesions, it avoids the risk of false-negative CNB and overlooking carcinomas.
Altered Brain Network Segregation in Fragile X Syndrome Revealed by Structural Connectomics

Abstract Fragile X syndrome (FXS), the most common inherited cause of intellectual disability and autism spectrum disorder, is associated with significant behavioral, social, and neurocognitive deficits. Understanding structural brain network topology in FXS provides an important link between neurobiological and behavioral/cognitive symptoms of this disorder. We investigated the connectome via whole‐brain structural networks created from group‐level morphological correlations. Participants included 100 individuals: 50 with FXS and 50 with typical development, age 11‐23 years. Results indicated alterations in topological properties of structural brain networks in individuals with FXS. Significantly reduced small‐world index indicates a shift in the balance between network segregation and integration and significantly reduced clustering coefficient suggests that reduced local segregation shifted this balance. Caudate and amygdala were less interactive in the FXS network further highlighting the importance of subcortical region alterations in the neurobiological signature of FXS. Modularity analysis indicates that FXS and typically developing groups’ networks decompose into different sets of interconnected sub networks, potentially indicative of aberrant local interconnectivity in individuals with FXS. These findings advance our understanding of the effects of fragile X mental retardation protein on large‐scale brain networks and could be used to develop a connectome‐level biological signature for FXS.
Reduced Chronic Lymphocyte Activation following Interferon Alpha Blockade during the Acute Phase of Simian Immunodeficiency Virus Infection in Rhesus Macaques

ABSTRACT Pathogenic human immunodeficiency virus (HIV)/simian immunodeficiency virus (SIV) infection of humans and rhesus macaques (RMs) induces persistently high production of type I interferon (IFN-I), which is thought to contribute to disease progression. To elucidate the specific role of interferon alpha (IFN-α) in SIV pathogenesis, 12 RMs were treated prior to intravenous (i.v.) SIVmac239 infection with a high or a low dose of an antibody (AGS-009) that neutralizes most IFN-α subtypes and were compared with six mock-infused, SIV-infected controls. Plasma viremia was measured postinfection to assess the effect of IFN-α blockade on virus replication, and peripheral blood and lymphoid tissue samples were analyzed by immunophenotypic staining. Consistent with the known antiviral effect of IFN-I, high-dose AGS-009 treatment induced a modest increase in acute-phase viral loads versus controls. Four out of 6 RMs receiving a high dose of AGS-009 also experienced an early decline in CD4+ T cell counts that was associated with progression to AIDS. Interestingly, 50% of the animals treated with AGS-009 (6/12) developed AIDS within 1 year of infection compared with 17% (1/6) of untreated controls. Finally, blockade of IFN-α decreased the levels of activated CD4+ and CD8+ T cells, as well as B cells, as measured by PD-1 and/or Ki67 expression. The lower levels of activated lymphocytes in IFN-α-blockaded animals supports the hypothesis that IFN-α signaling contributes to lymphocyte activation during SIV infection and suggests that this signaling pathway is involved in controlling virus replication during acute infection. The potential anti-inflammatory effect of IFN-α blockade should be explored as a strategy to reduce immune activation in HIV-infected individuals. IMPORTANCE Interferon alpha (IFN-α) is a member of a family of molecules (type I interferons) that prevent or limit virus infections in mammals. However, IFN-α production may contribute to the chronic immune activation that is thought to be the primary cause of immune decline and AIDS in HIV-infected patients. The study presented here attempts to understand the contribution of IFN-α to the natural history and progression of SIV infection of rhesus macaques, the primary nonhuman primate model system for testing hypotheses about HIV infection in humans. Here, we show that blockade of IFN-α action promotes lower chronic immune activation but higher early viral loads, with a trend toward faster disease progression. This study has significant implications for new treatments designed to impact the type I interferon system.
Impact of varicella vaccination on health care utilization.

CONTEXT Since varicella vaccine was first recommended for routine immunization in the United States in 1995, the incidence of disease has dropped substantially. However, national surveillance data are incomplete, and comprehensive data regarding outpatient as well as hospital utilization have not been reported. OBJECTIVE To examine the impact of the varicella vaccination program on medical visits and associated expenditures. DESIGN, SETTING, AND PATIENTS Retrospective population-based study examining the trends in varicella health care utilization, based on data from the MarketScan databases, which include enrollees (children and adults) of more than 100 health insurance plans of approximately 40 large US employers, from 1994 to 2002. MAIN OUTCOME MEASURES Trends in rates of varicella-related hospitalizations and ambulatory visits and direct medical expenditures for hospitalizations and ambulatory visits, analyzed using 1994 and 1995 as the prevaccination baseline. RESULTS From the prevaccination period to 2002, hospitalizations due to varicella declined by 88% (from 2.3 to 0.3 per 100,000 population) and ambulatory visits declined by 59% (from 215 to 89 per 100,000 population). Hospitalizations and ambulatory visits declined in all age groups, with the greatest declines among infants younger than 1 year. Total estimated direct medical expenditures for varicella hospitalizations and ambulatory visits declined by 74%, from an average of 84.9 million dollars in 1994 and 1995 to 22.1 million dollars in 2002. CONCLUSION Since the introduction of the varicella vaccination program, varicella hospitalizations, ambulatory visits, and their associated expenditures have declined dramatically among all age groups in the United States.
Research Data in Core Journals in Biology, Chemistry, Mathematics, and Physics

This study takes a stratified random sample of articles published in 2014 from the top 10 journals in the disciplines of biology, chemistry, mathematics, and physics, as ranked by impact factor. Sampled articles were examined for their reporting of original data or reuse of prior data, and were coded for whether the data was publicly shared or otherwise made available to readers. Other characteristics such as the sharing of software code used for analysis and use of data citation and DOIs for data were examined. The study finds that data sharing practices are still relatively rare in these disciplines’ top journals, but that the disciplines have markedly different practices. Biology top journals share original data at the highest rate, and physics top journals share at the lowest rate. Overall, the study finds that within the top journals, only 13% of articles with original data published in 2014 make the data available to others.
Computational flow cytometry reveals that cryopreservation induces spermptosis but subpopulations of spermatozoa may experience capacitation-like changes.

The reduced lifespan of cryopreserved spermatozoa in the mare reproductive tract has been attributed to both capacitative and apoptotic changes. However, there is a lack of studies investigating both phenomena simultaneously. In order to improve our knowledge in this particular point, we studied in raw and frozen-thawed samples apoptotic and capacitative markers using a wide battery of test based in flow cytometry. Apoptotic markers evaluated were caspase 3 activity, externalization of phosphatidylserine (PS), and mitochondrial membrane potential. Markers of changes resembling capacitation were membrane fluidity, tyrosine phosphorylation, and intracellular sodium. Conventional and computational flow cytometry using nonlinear dimensionally reduction techniques (t-distributed stochastic neighbor embedding (t-SNE)) and automatic classification of cellular expression by nonlinear stochastic embedding (ACCENSE) were used. Most of the changes induced by cryopreservation were apoptotic, with increase in caspase 3 activation (P < 0.01), PS translocation to the outer membrane (P < 0.001), loss of mitochondrial membrane potential (P < 0.05), and increase in intracellular Na+ (P < 0.01). Average values of markers of capacitative changes were not affected by cryopreservation; however, the analysis of the phenotype of individual spermatozoa using computational flow cytometry revealed the presence of subpopulations of spermatozoa experiencing capacitative changes. For the first time advanced computational techniques were applied to the analysis of spermatozoa, and these techniques were able to disclose relevant information of the ejaculate that remained hidden using conventional flow cytometry.
Simultaneous localization and mapping in unmodified environments using stereo vision

In this paper we describe an approach that builds three dimensional maps using visual landmarks extracted from images of an unmodiﬁed environment. We propose a solution to the Simultaneous Localization and Mapping (SLAM) problem for autonomous mobile robots using visual landmarks. Our map is represented by a set of three dimensional landmarks referred to a global reference frame, each landmark contains a visual descriptor that partially differentiates it from others. Signiﬁcant points extracted from stereo images are used as natural landmarks, in particular we employ SIFT features found in the environment. We estimate both the map and the path of the robot using a Rao-Blackwellized particle ﬁlter, thus the problem is decomposed into two parts: one estimation over robot paths using a particle ﬁlter, and N independent estimations over landmark positions, each one conditioned on the path estimate. We actively track visual landmarks at a local neighbourhood and select only those that are more stable. When a visual feature has been observed from a signiﬁcant number of frames it is then integrated in the ﬁlter. By this procedure, the total number of landmarks in the map is reduced, compared to prior approaches. Due to the tracking of each landmark, we obtain different examples that represent the same natural landmark. We use this fact to improve data association. Finally, efficient resampling techniques have been applied, which reduces the number of particles needed and avoids the particle depletion problem.
Mental disorders among college students in the World Health Organization World Mental Health Surveys

Background Although mental disorders are significant predictors of educational attainment throughout the entire educational career, most research on mental disorders among students has focused on the primary and secondary school years. Method The World Health Organization World Mental Health Surveys were used to examine the associations of mental disorders with college entry and attrition by comparing college students (n = 1572) and non-students in the same age range (18–22 years; n = 4178), including non-students who recently left college without graduating (n = 702) based on surveys in 21 countries (four low/lower-middle income, five upper-middle-income, one lower-middle or upper-middle at the times of two different surveys, and 11 high income). Lifetime and 12-month prevalence and age-of-onset of DSM-IV anxiety, mood, behavioral and substance disorders were assessed with the Composite International Diagnostic Interview (CIDI). Results One-fifth (20.3%) of college students had 12-month DSM-IV/CIDI disorders; 83.1% of these cases had pre-matriculation onsets. Disorders with pre-matriculation onsets were more important than those with post-matriculation onsets in predicting subsequent college attrition, with substance disorders and, among women, major depression the most important such disorders. Only 16.4% of students with 12-month disorders received any 12-month healthcare treatment for their mental disorders. Conclusions Mental disorders are common among college students, have onsets that mostly occur prior to college entry, in the case of pre-matriculation disorders are associated with college attrition, and are typically untreated. Detection and effective treatment of these disorders early in the college career might reduce attrition and improve educational and psychosocial functioning.
Pediatric short-bowel syndrome: the cost of comprehensive care.

BACKGROUND Little information is available about the financial charges incurred by patients with short-bowel syndrome (SBS). This is particularly true for pediatric SBS patients who receive some of the most complex medical care. OBJECTIVES The aims of this study were to determine the total cost of care for these patients and to analyze their utilization of home and hospital-based health care services. DESIGN This was a retrospective review of the total charges incurred by 41 children with SBS over the past decade, encompassing both inpatient and home-care charges. RESULTS The mean (+/- SD) total cost of care for pediatric SBS was US$505 250 +/- US$248 398 (corrected for inflation to the year 2005) for the first year of care alone. Inpatient hospitalization accounted for most of these expenses (US$416 818 +/- US$242 689, or 82% of the total), and this was attributable to prolonged requirements for intensive care resources, numerous surgical procedures, and multiple readmissions during the first year of diagnosis. Hospital-based costs steadily declined in subsequent years, but home-care services, in stark contrast, unexpectedly increased every year for the first 5 y of diagnosis-a trend that was highly significant (P < 0.005), reaching US$184 520 +/- US$111 075 for the fifth year of home care. This increasing cost was attributable to increasing complications of parenteral nutrition, especially infectious complications. Although per-patient charges varied widely, the mean total cost of care per child over a 5-y period was US$1 619 851 +/- US$1 028 985. A strong correlation was found between higher charges and infants with <10% of predicted small-bowel length. CONCLUSIONS This study was the first to calculate the total costs for pediatric SBS patients and to provide an in-depth analysis of these patients' actual utilization of health care services. This information may help guide health care providers and families who have children with SBS. The comprehensive care of pediatric SBS patients costs significantly more than has previously been estimated. Contrary to previous views, home care significantly increases each year after diagnosis.