Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic Structure of and Genome-Wide Recombination in the Saccharomyces cerevisiae S288C Progenitor Isolate EM93

The diploid isolate EM93 is the main ancestor to the widely used Saccharomyces cerevisiae haploid laboratory strain, S288C. In this study, we generate a high-resolution overview of the genetic differences between EM93 and S288C. We show that EM93 is heterozygous for >45,000 polymorphisms, including large sequence polymorphisms, such as deletions and a Saccharomyces paradoxus introgression. We also find that many large sequence polymorphisms (LSPs) are associated with Ty-elements and sub-telomeric regions. We identified 2,965 genetic markers, which we then used to genotype 120 EM93 tetrads. In addition to deducing the structures of all EM93 chromosomes, we estimate that the average EM93 meiosis produces 144 detectable recombination events, consisting of 87 crossover and 31 non-crossover gene conversion events. Of the 50 polymorphisms showing the highest levels of non-crossover gene conversions, only three deviated from parity, all of which were near heterozygous LSPs. We find that non-telomeric heterozygous LSPs significantly reduce meiotic recombination in adjacent intervals, while sub-telomeric LSPs have no discernable effect on recombination. We identified 203 recombination hotspots, relatively few of which are hot for both non-crossover gene conversions and crossovers. Strikingly, we find that recombination hotspots show limited conservation. Some novel hotspots are found adjacent to heterozygous LSPs that eliminate other hotspots, suggesting that hotspots may appear and disappear relatively rapidly.
Prediction of Machining Induced Surface Integrity Using Elastic-Viscoplastic Simulations and Temperature-Dependent Flow Softening Material Models in Titanium and Nickel-Based Alloys

In this study, the feasibility of predicting surface integrity and residual stresses by using elasto-viscoplastic finite element simulations and temperature-dependent flow softening constitutive material modeling is investigated. A friction determination method is proposed to identify friction coefficients in presence of tool flank wear. Serrated and cyclical chip formation has been simulated for using tools with and without flank wear. The predicted residual stresses and surface integrity is compared against experimental results from literature. Effect of friction on the residual stress profiles is also investigated. These results are highly essential in predicting machining induced microstructure alterations that are detrimental to fatigue life of nickel and titanium alloy components.
Species Identification and Profiling of Complex Microbial Communities Using Shotgun Illumina Sequencing of 16S rRNA Amplicon Sequences

The high throughput and cost-effectiveness afforded by short-read sequencing technologies, in principle, enable researchers to perform 16S rRNA profiling of complex microbial communities at unprecedented depth and resolution. Existing Illumina sequencing protocols are, however, limited by the fraction of the 16S rRNA gene that is interrogated and therefore limit the resolution and quality of the profiling. To address this, we present the design of a novel protocol for shotgun Illumina sequencing of the bacterial 16S rRNA gene, optimized to amplify more than 90% of sequences in the Greengenes database and with the ability to distinguish nearly twice as many species-level OTUs compared to existing protocols. Using several in silico and experimental datasets, we demonstrate that despite the presence of multiple variable and conserved regions, the resulting shotgun sequences can be used to accurately quantify the constituents of complex microbial communities. The reconstruction of a significant fraction of the 16S rRNA gene also enabled high precision (>90%) in species-level identification thereby opening up potential application of this approach for clinical microbial characterization.
Regulation of Mat Responses by a Differentiation MAPK Pathway in Saccharomyces cerevisiae

Fungal species exhibit diverse behaviors when presented with extracellular challenges. Pathogenic fungi can undergo cell differentiation and biofilm formation in response to fluctuating nutrient levels, and these responses are required for virulence. In the model fungal eukaryote Saccharomyces cerevisiae, nutrient limitation induces filamentous growth and biofilm/mat formation. Both responses require the same signal transduction (MAPK) pathway and the same cell adhesion molecule (Flo11) but have been studied under different conditions. We found that filamentous growth and mat formation are aspects of a related response that is regulated by the MAPK pathway. Cells in yeast-form mats differentiated into pseudohyphae in response to nutrient limitation. The MAPK pathway regulated mat expansion (in the plane of the XY-axis) and substrate invasion (downward in the plane of the Z-axis), which optimized the mat's response to extracellular nutrient levels. The MAPK pathway also regulated an upward growth pattern (in the plane of the Z-axis) in response to nutrient limitation and changes in surface rigidity. Upward growth allowed for another level of mat responsiveness and resembled a type of colonial chemorepulsion. Together our results show that signaling pathways play critical roles in regulating social behaviors in which fungal cells participate. Signaling pathways may regulate similar processes in pathogens, whose highly nuanced responses are required for virulence.
Redes de apoio familiar e desigualdade social: estratégias de classe

As relacoes de parentesco alargado foram por muito tempo consideradas, nas ciencias sociais em geral e na sociologia em particular, algo estritamente caracteristico das sociedades pre-modernas, pensando-se, inversamente, que nas sociedades industrializadas ter-se-ia verificado um esboroamento generalizado da parentela, produto dos processos globais de individualizacao que teriam nuclearizado, conjugalizado e isolado os agregados domesticos. E no trabalho de Durkheim (1975 [1921]) que vamos encontrar a sumula das visoes oitocentistas da familia. Para este autor verificar-se-ia uma lei da contrac
The Theory of Higher Order Lognormal Cascade Distribution and the Origin of Fat Tails in the Fluctuations of Stock Market

This working paper presents the general theory of the higher order "skew lognormal cascade distribution" as a mathematical extension of the previously proposed skew lognormal cascade distribution. In particular, the second order distribution is studied in details, which incorporates the fat tails into the volatility (aka the volatility of volatility). We show that the second order distribution can handle very heavy tails and high kurtosis in the high frequency financial time series. It accurately fi ts the daily log-returns of Dow in 80 years, whose kurtosis is 26. The framework of the higher order lognormal cascade distributions also provides a new way to study the capital distribution (aka firm size distribution), the market index, and the market entropy of the stock market. Such study in the context of stochastic portfolio theory reveals that the origin of the fat tails in the fluctuations of the market index is from the lognormal cascade structure of the capital distribution in the market. We show from a simple stochastic model that the contraction and expansion of the underlying capital distribution is the fundamental driving force of the bull-bear market cycles and the market volatility in the past 20 years. A stochastic equation is derived to establish the relation between the market index and the capital distribution, which is the lognormal cascade equation in our theory. This shows that the fluctuations of the market index are a natural mathematical consequence of the stochastic calculus on the market portfolio in which weights are exponentially distributed. Therefore, we conclude that the phenomena of fat tails should exist everywhere in our financial system.
Macrophage Mitochondrial Oxidative Stress Promotes Atherosclerosis and Nuclear Factor-&kgr;B–Mediated Inflammation in Macrophages

Rationale: Mitochondrial oxidative stress (mitoOS) has been shown to correlate with the progression of human atherosclerosis. However, definitive cell type–specific causation studies in vivo are lacking, and the molecular mechanisms of potential proatherogenic effects remain to be determined. Objective: Our aims were to assess the importance of macrophage mitoOS in atherogenesis and to explore the underlying molecular mechanisms. Methods and Results: We first validated Western diet–fed Ldlr−/− mice as a model of human mitoOS–atherosclerosis association by showing that non-nuclear oxidative DNA damage, a marker of mitoOS in lesional macrophages, correlates with aortic root lesion development. To investigate the importance of macrophage mitoOS, we used a genetic engineering strategy in which the OS suppressor catalase was ectopically expressed in mitochondria (mCAT) in macrophages. MitoOS in lesional macrophages was successfully suppressed in these mice, and this led to a significant reduction in aortic root lesional area. The mCAT lesions had less monocyte-derived cells, less Ly6chi monocyte infiltration into lesions, and lower levels of monocyte chemotactic protein-1. The decrease in lesional monocyte chemotactic protein-1 was associated with the suppression of other markers of inflammation and with decreased phosphorylation of RelA (NF-&kgr;B p65), indicating decreased activation of the proinflammatory NF-&kgr;B pathway. Using models of mitoOS in cultured macrophages, we showed that mCAT suppressed monocyte chemotactic protein-1 expression by decreasing the activation of the I&kgr;B-kinase &bgr;–RelA NF-&kgr;B pathway. Conclusions: MitoOS in lesional macrophages amplifies atherosclerotic lesion development by promoting NF-&kgr;B–mediated entry of monocytes and other inflammatory processes. In view of the mitoOS–atherosclerosis link in human atheromata, these findings reveal a potentially new therapeutic target to prevent the progression of atherosclerosis.
Therapeutic drug monitoring of atypical antipsychotic drugs

Abstract Schizophrenia is a severe psychiatric disorder often associated with cognitive impairment and affective, mainly depressive, symptoms. Antipsychotic medication is the primary intervention for stabilization of acute psychotic episodes and prevention of recurrences and relapses in patients with schizophrenia. Typical antipsychotics, the older class of antipsychotic agents, are currently used much less frequently than newer atypical antipsychotics. Therapeutic drug monitoring (TDM) of antipsychotic drugs is the specific method of clinical pharmacology, which involves measurement of drug serum concentrations followed by interpretation and good cooperation with the clinician. TDM is a powerful tool that allows tailor-made treatment for the specific needs of individual patients. It can help in monitoring adherence, dose adjustment, minimizing the risk of toxicity and in cost-effectiveness in the treatment of psychiatric disorders. The review provides complex knowledge indispensable to clinical pharmacologists, pharmacists and clinicians for interpretation of TDM results.
Copper resistance is essential for virulence of Mycobacterium tuberculosis

Copper (Cu) is essential for many biological processes, but is toxic when present in excessive amounts. In this study, we provide evidence that Cu plays a crucial role in controlling tuberculosis. A Mycobacterium tuberculosis (Mtb) mutant lacking the outer membrane channel protein Rv1698 accumulated 100-fold more Cu and was more susceptible to Cu toxicity than WT Mtb. Similar phenotypes were observed for a M. smegmatis mutant lacking the homolog Ms3747, demonstrating that these mycobacterial copper transport proteins B (MctB) are essential for Cu resistance and maintenance of low intracellular Cu levels. Guinea pigs responded to infection with Mtb by increasing the Cu concentration in lung lesions. Loss of MctB resulted in a 1,000- and 100-fold reduced bacterial burden in lungs and lymph nodes, respectively, in guinea pigs infected with Mtb. In mice, the persistence defect of the Mtb mctB mutant was exacerbated by the addition of Cu to the diet. These experiments provide evidence that Cu is used by the mammalian host to control Mtb infection and that Cu resistance mechanisms are crucial for Mtb virulence. Importantly, Mtb is much more susceptible to Cu than other bacteria and is killed in vitro by Cu concentrations lower than those found in phagosomes of macrophages. Hence, this study reveals an Achilles heel of Mtb that might be a promising target for tuberculosis chemotherapy.
Laminin α5 guides tissue patterning and organogenesis

Laminins (LM) are extracellular matrix molecules that contribute to and are required for the formation of basement membranes. They participate in the modulation of epithelial/mesenchymal interactions and are implicated in organogenesis and maintenance of organ homeostasis. Among the LM molecules, the LM α5 chain (LMα5) is one of the most widely distributed LM in the developing and mature organism. Its presence in some basement membranes during embryogenesis is absolutely required for maintenance of basement membrane integrity and thus for proper organogenesis. LMα5 also regulates the expression of genes important for major biological processes, in part by repressing or activating signaling pathways, depending upon the physiological context.
Facial Action Unit Detection using Probabilistic Actively Learned Support Vector Machines on Tracked Facial Point Data

A system that could enable fast and robust facial expression recognition would have many applications in behavioral science, medicine, security and human-machine interaction. While working toward that goal, we do not attempt to recognize prototypic facial expressions of emotions but analyze subtle changes in facial behavior by recognizing facial muscle action units (AUs, i.e., atomic facial signals) instead. By detecting AUs we can analyse many more facial communicative signals than emotional expressions alone. This paper proposes AU detection by classifying features calculated from tracked ? ducial facial points. We use a Particle Filtering tracking scheme using factorized likelihoods and a novel observation model that combines a rigid and a morphologic model. The AUs displayed in a video are classi? ed using Probabilistic Actively Learned Support VectorMachines (PAL-SVM). When tested on 167 videos from the MMI web-based facial expression database, the proposed method achieved very high recognition rates for 16 different AUs. To ascertain data independency we also performed a validation using another benchmark database. When trained on the MMI-Facial expression database and tested on the Cohn-Kanade database, the proposed method achieved a recognition rate of 84% when detecting 9 AUs occurring alone or in combination in input image sequences.
The Evolution of the US Financial Industry from 1860 to 2007 : Theory and Evidence . ∗

The share of finance in U.S. GDP displays large historical variations. I argue, using evidence and theory, that corporate finance is a key factor behind these evolutions. Corporate demand for intermediation depends crucially on the relative investment opportunities of firms with low cash flows (young firms) and firms with high cash flows (incumbents). A simple general equilibrium model is developed in order to separate demand and supply factors in the market for financial intermediation. The demand parameters accord well with historical evidence on the importance of entrants during technological revolutions. The supply parameters suggest financial regress in the 1930s and progress in the 1990s. The model accounts for much of the variation in the income share of the financial sector from 1860 to 2001. Only the period 2002-2007 appears puzzling.
Does my mouse have Alzheimer's disease?

Small animal models that manifest many of the characteristic neuropathological and behavioral features of Alzheimer's disease (AD) have been developed and have proven of great value for studying the pathogenesis of this disorder at the molecular, cellular and behavioral levels. The great progress made in our understanding of the genetic factors that either cause or contribute to the risk of developing AD has prompted many laboratories to create transgenic (tg) mice that overexpress specific genes which cause familial forms of the disease. Several of these tg mice display neuropathological and behavioral features of AD including amyloid β‐peptide (Aβ) and amyloid deposits, neuritic plaques, gliosis, synaptic alterations and signs of neurodegeneration as well as memory impairment. Despite these similarities, important differences in neuropathology and behavior between these tg mouse models and AD have also been observed, and to date no perfect animal model has emerged. Moreover, ascertaining which elements of the neuropathological and behavioral phenotype of these various strains of tg mice are relevant to that observed in AD continues to be a challenge. Here we provide a critical review of the AD‐like neuropathology and behavioral phenotypes of several well‐known and utilized tg mice that express human APP transgenes.
Acquired resistance in rainbow trout against Gyrodactylus derjavini

Abstract Investigations were conducted on the host response in rainbow trout and the associated changes in mucous cell density during infection with the skin monogenean Gyrodactylus derjavini. Parasite populations increased on all naive hosts and peaked 4–5 weeks p.i. after which infection levels decreased. Introduction of naive fish into responding host populations resulted in heavy infections of the naive fish, whereas parasite expulsion continued in the responding host groups showing an acquired, non-sterile immunity. This non-sterile immunity lasted at least a month as these hosts were refractory to reinfection despite being exposed to a high infection pressure. Mucous cell hyperplasia was seen in some groups during the intermediary phase of infection, but at the termination of the study a significant depletion was evident. Passive immunization of naive host (with sera from immune hosts) did not confer protection. This indicates differences between host responses to G. derjavini compared to responses against other pathogens where such a passive immunity has been described.
Organizational Change Recipients' Beliefs Scale

Based on research conducted by organizational scientists dating to the 1940s, the authors identified five important precursors that determine the degree of buy-in by organizational change recipients. The authors assembled these independent precursors into a framework labeled organizational change recipients' beliefs and developed a psychometrically sound self-report questionnaire that can be used to gauge progress of organizational change efforts. The authors describe a series of four studies used to develop a 24-item assessment tool that can be administered at any stage of the change process. The information obtained can serve as (a) a barometer of the degree of buy-in among change recipients, (b) an assessment of deficiencies in specific beliefs that can adversely impact the success of an organizational change, and (c) a basis for planning and executing actions to enhance buy-in among organizational change recipients.
Mechanisms of angiotensin II natriuresis and antinatriuresis.

The aim of this study was to determine the role of changes in renal arterial pressure (RAP), renal hemodynamics, and tubular reabsorption in mediating the natriuretic and antinatriuretic actions of angiotensin II (ANG II). In seven anesthetized dogs, endogenous ANG II formation was blocked with captopril, and ANG II was infused intravenously at rates of 5-1,215 ng X kg-1 X min-1 while RAP was either servo-controlled at the preinfusion level or permitted to increase. When RAP was servo-controlled, ANG II infusion at all rates from 5-1,215 ng X kg-1 X min-1 decreased urinary sodium excretion (UNaV) and fractional sodium excretion (FENa) while increasing fractional reabsorption of lithium (FRLi) (an index of proximal tubular fractional sodium reabsorption) and causing no change in calculated distal tubule fractional sodium reabsorption (FRDNa). When RAP was permitted to increase, ANG II infusion rates up to 45 ng X kg-1. min-1 also decreased UNaV and FENa while increasing FRLi and causing no change in FRDNa. However, at 135 ng X kg-1 X min-1 and above, UNaV and FENa increased while FRLi and FRDNa decreased when RAP was allowed to rise, even though renal blood flow and filtration fraction were not substantially different from the values observed when RAP was servo-controlled. Filtered sodium load was slightly higher when RAP was permitted to increase during ANG II infusion compared with when RAP was servo-controlled, although the differences were not statistically significant. Thus, even very large doses of ANG II cause antinatriuresis when RAP is prevented from increasing. (ABSTRACT TRUNCATED AT 250 WORDS)
Derivation of Land Surface Albedo at High Resolution by Combining HJ-1A/B Reflectance Observations with MODIS BRDF Products

Land surface albedo is an essential parameter for monitoring global/regional climate and land surface energy balance. Although many studies have been conducted on global or regional land surface albedo using various remote sensing data over the past few decades, land surface albedo product with a high spatio-temporal resolution is currently very scarce. This paper proposes a method for deriving land surface albedo with a high spatio-temporal resolution (space: 30 m and time: 2-4 days). The proposed method works by combining the land surface reflectance data at 30 m spatial resolution obtained from the charge-coupled devices in the Huanjing-1A and -1B (HJ-1A/B) satellites with the Moderate Resolution Imaging Spectroradiometer (MODIS) land surface bidirectional reflectance distribution function (BRDF) parameters product (MCD43A1), which is at a spatial resolution of 500 m. First, the land surface BRDF parameters for HJ-1A/B land surface reflectance with a spatial-temporal resolutions of 30 m and 2-4 day are calculated on the basis of the prior knowledge from the MODIS BRDF product; then, the calculated high resolution BRDF parameters are integrated over the illuminating/viewing hemisphere to produce the white- and black-sky albedos at 30 m resolution. These results form the basis for the final land surface albedo derivation by accounting for the proportion of direct and diffuse solar radiation arriving at the ground. The albedo retrieved by this novel method is compared with MODIS land surface albedo products, as well as with ground