Miracle-dz/UniFAR-FTUs huggingface dataset:
A General Mechanism for Network-Dosage Compensation in Gene Networks

Coping with variations in network dosage is crucial for maintaining optimal function in gene networks. Here we explore how network architecture facilitates network-level dosage compensation. Using the yeast galactose network as a model, we combinatorially deleted one of the two copies of its four regulatory genes and found that network activity was robust to the change in network dosage. A mathematical analysis revealed that a 2-component genetic circuit with elements of opposite regulatory sign (activator and inhibitor) constitutes a minimal requirement for network-dosage invariance. Specific interaction topologies and a 1-to−1 interaction stoichiometry between the activating and inhibiting agents were additional essential elements facilitating dosage invariance. This mechanism of network-dosage invariance could represent a general design for gene network architecture in cells. The number of copies of a gene network in a cell, or network dosage, has a direct effect on cellular phenotypes (1). Network dosage is altered in situations such as the switching of some organisms between haploid and diploid life forms (2), doubling of chromosomes during cell cycle (3), genome-wide duplication of genetic content (4, 5), and global variation (6) in gene expression. Different phenotypes have different levels of sensitivity to such variations and the need for effective compensation mechanisms arises when cells cannot tolerate these alterations. It is believed that in the transition between haploid and diploid forms of life cells utilize a volume-mediated compensation mechanism to keep the concentrations of transcription factors constant as cell volume increases with ploidy (2). However, this mechanism cannot subdue the effects of global expression variation and genome duplication or loss events as they affect cellular phenotypes independently of cell volume. For example, variability in ribosome numbers can cause significant fluctuations in global expression levels. These †To whom correspondence should be addressed: acar@caltech.edu. *These authors contributed equally to this work NIH Public Access
Rural-Urban Migration and Aging in Rural Areas: An Overview of the Last 50 Years

This paper presents a series of rural-urban net migration by age and sex for Brazil as a whole and the five major regions. They refer to the 50s, 60s, 70s, 80s and the first half of the 90s. Based on this, it was possible to analyze the importance of the rural-urban migration of each major region on the Brazilian total migration. Rural-urban migration has been responsible for the reduction of rural population. At the national level, this reduction has continued over the last 50 years. During 1950/80, most of the national rural urban areas were originated in the Southeast and the South regions. In the last two decades, it was the rural areas of the Northeast that were the most important emigration regions. Also in this period, areas of agricultural frontier, such as the Mid-West and the North, became emigration areas. Females predominate the rural-urban migration, but it has varied according to regions and time periods. One consequence is an increase of the rural sex ration and a reduction of the urban ones.
Gastrointestinal microbiota and irritable bowel syndrome

The digestive tract of humans and other mammals is inhabited by millions of microorganisms, especially bacteria. This gastrointestinal microbiota is necessary for the good functioning of the digestive process in the host. Recently, Schmulson et al. published a review article on irritable bowel syndrome (IBS) and its relation to the intestinal microbiota, as well as to other clinical and therapeutic aspects. We would like to make some comments on that article that may be of use to the medical community. First of all, the term «flora» is used on various occasions to refer to methane-producing colonic and fecal microbiota, but this term is incorrect despite its common use in human and veterinary medicine. Second, table 3 not only contains a description of molecular methods for characterizing the intestinal microbiota (the title of the table), but also a description of the 16S subunit of ribosomal RNA and the gene that encodes it, which can be confusing to readers unfamiliar with the subject matter. This same table does not identify what the abbreviation rrs stands for, and the sentence on the use of the variability in 16S for distinguishing proximal and distant organisms is only partially valid, due to the uncertainty in today’s bacterial molecular taxonomy. In addition, table 3 only mentions one (pyrosequencing) of several massive sequencing techniques. This is worth mentioning because this technique will soon disappear from the market and therefore many studies have switched to other techniques, such as that of Ilumina. Third, the clinical heterogeneity of IBS and the different methods employed for the study of the intestinal microbiota are without a doubt some of the reasons behind our incapacity to establish a microbial composition belonging to IBS. However, it is necessary to emphasize that our main problem lies in the
The roles of deep convection and extratropical mixing in the tropical tropopause layer: An in situ measurement perspective

The majority of air which enters the stratosphere passes through the tropical tropopause layer (TTL), where the temperature profile and amount of deep convection set the entry level for stratospheric water vapor. We use simultaneous in situ measurements of ozone, carbon monoxide, carbon dioxide, water vapor, and heavy water vapor (HDO) from the 2006 Costa Rica Aura Validation Experiment and 2007 Tropical Composition, Cloud, and Climate Coupling campaigns in a one‐dimensional mixing model to investigate how different transport pathways in the TTL impact the amount of water vapor which enters the stratosphere. We focused on four main pathways: (1) slow upward ascent, (2) isentropic transport from the midlatitude lowermost stratosphere, (3) convective injection, and (4) descent within the TTL coupled to convection. Each pathway brings air into the TTL with a specific chemical signature, such that anomalies in simultaneously measured tracer concentrations can be used to identify the source of the air mass. We found that isentropic transport from the midlatitude lowermost stratosphere accounted for 20–60% of the air in the lower TTL and 20–40% of air above the tropopause, bringing elevated ozone concentrations which radiatively warm the TTL, impacting the amount of dehydration which takes place. Convective input accounted for on average ~30% of the air measured below 370 K potential temperature, and ~10% of air above the tropopause in both summer and winter, increasing water vapor concentrations above the tropopause by 0.3 ppmv on average and by up to 1.6 ppmv in some air masses.
Associations between Recent Exposure to Ambient Fine Particulate Matter and Blood Pressure in the Multi-Ethnic Study of Atherosclerosis (MESA)

Background Blood pressure (BP) may be implicated in associations observed between ambient particulate matter and cardiovascular morbidity and mortality. This study examined cross-sectional associations between short-term ambient fine particles (particulate matter ≤ 2.5 μm in aerodynamic diameter; PM2.5) and BP: systolic (SBP), diastolic (DBP), mean arterial (MAP), and pulse pressure (PP). Methods The study sample included 5,112 persons 45–84 years of age, free of cardiovascular disease at the Multi-Ethnic Study of Atherosclerosis baseline examination (2000–2002). Data from U.S. Environmental Protection Agency monitors were used to estimate ambient PM2.5 exposures for the preceding 1, 2, 7, 30, and 60 days. Roadway data were used to estimate local exposures to traffic-related particles. Results Results from linear regression found PP and SBP positively associated with PM2.5. For example, a 10-μg/m3 increase in PM2.5 30-day mean was associated with 1.12 mmHg higher pulse pressure [95% confidence interval (CI), 0.28–1.97] and 0.99 mmHg higher systolic BP (95% CI, –0.15 to 2.13), adjusted for age, sex, race/ethnicity, income, education, body mass index, diabetes, cigarette smoking and environmental tobacco smoke, alcohol use, physical activity, medications, atmospheric pressure, and temperature. Results were much weaker and not statistically significant for MAP and DBP. Although traffic-related variables were not themselves associated with BP, the association between PM2.5 and BP was stronger in the presence of higher traffic exposure. Conclusions Higher SBP and PP were associated with ambient levels of PM2.5 and the association was stronger in the presence of roadway traffic, suggesting that impairment of blood pressure regulation may play a role in response to air pollution.
Flash floods in desert rivers: Studying the unexpected

Flash floods in desert ephemeral streams are unpredictable, infrequent, and shortlived. Although some observations of flood bores have been reported [e.g., Hassan, 1990], there is little quantitative data on the hydraulic and sediment transport dynamics of desert flash floods, despite the fact that desert streams pose many problems for river and reservoir management [Tolouie et al., 19937rsqb;. Furthermore, it has been suspected for some time that rates of sediment transfer might differ markedly in ephemeral and perennial rivers [e.g., Reid and Frostick, 1987; Schick et al., 1987]. Today, because of concern over prospective climate change, water resource issues are the subject of lively debate. Since current understanding and models of sediment dynamics derived from perennial streams may not be readily applicable to ephemeral flows, there is an urgent need for improved understanding of the dynamics of dryland rivers.
Stability of neural representations in the auditory midbrain across the lifespan despite age-related brainstem delays

The extent to which aging of the central auditory pathway impairs auditory perception in the elderly independent of peripheral cochlear decline is debated. To cause auditory deficits in normal hearing elderly, central aging needs to degrade neural sound representations at some point along the auditory pathway. However, inaccessible to psychophysical methods, the level of the auditory pathway at which aging starts to effectively degrade neural sound representations remains poorly differentiated. Here we tested how potential age-related changes in the auditory brainstem affect the stability of spatiotemporal multiunit complex speech-like sound representations in the auditory midbrain of old normal hearing CBA/J mice. Although brainstem conduction speed slowed down in old mice, the change was limited to the sub-millisecond range and only minimally affected temporal processing in the midbrain (i.e. gaps-in-noise sensitivity). Importantly, besides the small delay, multiunit complex temporal sound representations in the auditory midbrain did not differ between young and old mice. This shows that although small age-related neural effects in simple sound parameters in the lower brainstem may be present in aging they do not effectively deteriorate complex neural population representations at the level of the auditory midbrain when peripheral hearing remains normal. This result challenges the widespread belief of ‘pure’ central auditory decline as an automatic consequence of aging. However, the stability of midbrain processing in aging emphasizes the role of undetected ‘hidden’ peripheral damage and accumulating effects in higher cortical auditory-cognitive processing explaining perception deficits in ‘normal hearing’ elderly.
Compositional and Isotopic Analytical Methods in Archaeological Micromorphology

Resin‐impregnated sediment blocks are a by‐product of micromorphological sample processing. These blocks can be further studied using a variety of destructive, nondestructive, and minimally destructive geochemical techniques. X‐ray fluorescence microanalyses conducted on sediment blocks yield semiquantitative major and trace elemental abundances that can be used to generate compositional maps, and to illustrate compositional change within or between archaeological strata and features. Sediment blocks can also be drilled to obtain small sediment samples for stable oxygen and carbon isotopic analyses. Both elemental and isotopic analyses can be conducted in conjunction with micromorphological analyses to yield a holistic picture of archaeological sediment composition, source, and depositional processes. The integration of micromorphological, compositional, and isotopic analyses is used here to aid in the differentiation of calcareous ash and lime plasters from the Neolithic site of Asıklı Höyük, Turkey.
Epithelial cells.

Epithelial cells line the surface of the intestine, lung, kidney, and liver and form regulated boundaries between compartments within an organism. By forming a barrier between disparate environments, epithelial cells play a number of important roles in regulating host physiology. They prevent dissipation of concentration gradients between the compartments they separate. They also keep endogenous bacteria, microbial products, and bioactive substances from escaping their internal environment in the gut lumen and lung by acting as a fence preventing translocation of these products into the systemic circulation or lymph. Epithelial cells also have a crucial role in microbial surveillance, communicating with immune cells through cytokines and chemokines. Finally, gut epithelial cells regulate the absorption and secretion of fluids, electrolytes, and nutrients. With the exception of increased apoptosis in the gut, histologic analysis of the epithelium is unremarkable in either human autopsy studies of critical illness (1) or murine models of sepsis (2). Nonetheless, multiple studies suggest that epithelial dysfunction plays a crucial role in the pathogenesis of organ failure (3). This review will focus on how critical illness worsens epithelial barrier function through alterations in the structure and function of tight junctions and how changes in epithelial apoptosis may contribute to organ dysfunction. Epithelial Barrier Dysfunction in Critical Illness
Marine Managers Look Upstream for Connections

The Florida Keys are a heavily managed land-sea reserve, preserved as a National Marine Sanctuary, but fishing and collecting are prohibited in only a small area. Ogden discusses the management of this Sanctuary and how new results on the sources of larvae for marine species in the Caribbean, presented by [ Roberts et al . ][1], will influence future planning. [1]: http://www.sciencemag. org/cgi/content/short/278/5342/1454
Impact melt on lunar crater rims.

The reported study had the objective to determine the origin, distribution, and modes of occurrence of lava-like deposits and the factors responsible for their emplacement. Lava-like deposits around a large number of lunar craters were investigated in order to obtain information on the variation in morphology and the distribution as a function of crater size. The results should have bearing on lunar and terrestrial impact cratering processes and the provenance of the abundant impact melt rocks in the lunar sample collection. Attention is given to the size range of craters with exterior melt deposits, the morphology of deposits as a function of crater size, the factors responsible for melt deposit asymmetry, the time of melt emplacement, and a model for the formation of impact melt deposits on crater rims.
Valores pessoais e percepção de atributos em marcas regionais de café na cidade de Lavras

Regional food brands generate competitive differential because consumer links some desired attributes with a positive image of product's geographical origin. Such image influences the buying decision process, facing their perceptions about brand attributes and desired benefits in consuming products from these brands. On this view, this paper evidences the cognitive structure of consumers of roasted and milled coffee from Lavras' region, Minas Gerais State. Based upon in depth interviews, utilizing the laddering qualitative technique, it was made a hierarchic value map, that shows a connection of the regional brands to the attributes: ‘sensorial characteristics' , ‘from the region', ‘known brand', ‘lower price' and ‘pureness food'. From these attributes, the consumers believe in the possibility to reach personal values as: ‘self achievement', ‘personal and collective wellbeing', ‘happiness', ‘nostalgia', ‘life quality' and ‘longevity'.
Attachment and Mental and Physical Health: Self-compassion and Mattering as Mediators Attachment as a Predictor of Mental and Physical Health

Research shows a strong link between adult attachment and mental and physical health, but little is known about the mechanisms that underlie these relationships. The present study examined self-compassion and mattering, two constructs from positive psychology literature, as potential mediators. Using survey data from a sample of 208 college students, relationships among attachment, self-compassion, mattering, and functional health were explored. Correlational analyses indicated that attachment anxiety and avoidance were strongly related to the mental health component of functional health. Mediation analyses indicated that mattering and self-compassion mediated the relationships between attachment orientation (i.e., levels of avoidance and anxiety) and mental health. These findings suggest that individuals' abilities to be kind toward themselves and their sense of belonging and being important to others are pathways through which attachment orientation relates to mental health. The need for interpersonal attachment is a fundamental human motivation (Baumeister & Leary, 1995), and attachment styles have important implications for mental and physical health (Hunter & Maunder, 2001). Yet, attachment styles are hypothesized to develop early in life and remain relatively stable throughout adulthood (Shaver & Brennan, 1992), making them a difficult target of therapeutic intervention. Understanding how attachment styles affect mental and physical health could help psychologists target those underlying mechanisms in therapy, which may be more amenable to therapeutic change. Self-compassion and mattering, two newly introduced constructs , have been shown to relate to well-being (Elliott, Kao, & Grant, 2004; Neff, 2003b). Self-compassion is characterized by self-kindness, mindfulness, and a sense of common humanity when experiencing suffering (Neff, 2003b), whereas mattering is characterized by the belief that others are aware of, rely on, and care about one's presence (Elliott et al., 2004). These two variables represent positive construal of self and of others, which is a defining characteristic of attachment security. In addition to conceptual links among self-compassion, mattering, and attachment security, research has shown self-compassion to be a fruitful target of clinical intervention (Gilbert & Irons, 2004). Given the need to understand the mechanisms through which attachment affects mental and physical health, and the clinical utility of studying self-compassion and mattering, this study aimed to explore further these associations. Attachment theory (Bowlby, 1969, 1973) explains that early life experiences with primary caregivers strongly influence the formation of internal working models that include self-perceptions of one's own value and worthiness of care, and perceptions of others' ability to provide such care in times of need. …
Experimental investigation into the effects of meteoritic impacts on the spectral properties of phyllosilicates on Mars

Phyllosilicates have been identified in some of the most highly cratered Noachian terrains on Mars. To study the effects of such impacts on the properties of phyllosilicates, we experimentally shocked six phyllosilicate minerals relevant to the Martian surface: montmorillonite, nontronite, kaolinite, prehnite, chlorite, and serpentine. The shock‐treated samples were analyzed with X‐ray diffraction (XRD), near‐ and mid‐infrared (NIR and MIR) spectroscopy, Raman spectroscopy, cathodoluminescence (CL), and the shock pressures and temperatures in some were modeled using Autodyn modeling software. XRD data show that the structure of each mineral, except prehnite, underwent partial structural deformation or amorphization. We also found that while the NIR spectra of shocked samples were very similar to that of the original sample, the MIR spectra changed significantly. This may explain some of the discrepancies between CRISM/OMEGA data (NIR) and TES/THEMIS (MIR) observations of phyllosilicates on Mars. Quartz was identified as a secondary phase in the XRD of shocked chlorite.
VU Research Portal Ethnic differences in survival on dialysis in Europe

patient survival between native Dutch dialysis patients and immigrant dialysis patients, and to explore whether differences could be explained by demographic, clinical and laboratory characteristics at baseline and initial adequacy characteristics. haematocrit, calcium, phosphorus, albumin, and for diabetes mellitus patients HbA1c. Adequacy of initial dialysis treatment was obtained by collecting Kt/Vurea values per week, determined 3 months after the start of dialysis treatment. In addition, we collected date and reason for the end of dialysis treatment.
Converted‐wave imaging in anisotropic media: theory and case studies

Common‐conversion‐point binning associated with converted‐wave (C‐wave) processing complicates the task of parameter estimation, especially in anisotropic media. To overcome this problem, we derive new expressions for converted‐wave prestack time migration (PSTM) in anisotropic media and illustrate their applications using both 2D and 3D data examples.
Numerical simulation and nasal air-conditioning

Heating and humidification of the respiratory air are the main functions of the nasal airways in addition to cleansing and olfaction. Optimal nasal air conditioning is mandatory for an ideal pulmonary gas exchange in order to avoid desiccation and adhesion of the alveolar capillary bed. The complex three-dimensional anatomical structure of the nose makes it impossible to perform detailed in vivo studies on intranasal heating and humidification within the entire nasal airways applying various technical set-ups. The main problem of in vivo temperature and humidity measurements is a poor spatial and time resolution. Therefore, in vivo measurements are feasible only to a restricted extent, solely providing single temperature values as the complete nose is not entirely accessible. Therefore, data on the overall performance of the nose are only based on one single measurement within each nasal segment. In vivo measurements within the entire nose are not feasible. These serious technical issues concerning in vivo measurements led to a large number of numerical simulation projects in the last few years providing novel information about the complex functions of the nasal airways. In general, numerical simulations merely calculate predictions in a computational model, e.g. a realistic nose model, depending on the setting of the boundary conditions. Therefore, numerical simulations achieve only approximations of a possible real situation. The aim of this review is the synopsis of the technical expertise on the field of in vivo nasal air conditioning, the novel information of numerical simulations and the current state of knowledge on the influence of nasal and sinus surgery on nasal air conditioning.