Miracle-dz/UniFAR-FTUs huggingface dataset:
Signature of cryptic sedimentary basin inversion revealed by shale compaction data in the Irish Sea, western British Isles

Inversion is one of the most common modes of intraplate deformation and a primary mechanism of sedimentary basin exhumation. The key criterion for identification of basin inversion is the contractional reactivation of extensional faults. Reverse displacement associated with inversion is focused along the upper segments of faults, so the evidence for inversion may be removed in deeply exhumed basins. We believe this is the case in the Irish Sea, western British Isles. Previous authors have attributed the severe exhumation of this basin to plume‐related uplift and have ruled out inversion as a cause of uplift. We present a method for identifying tectonic inversion in a basin where exhumation has removed evidence of reverse displacement on the upper segments of faults. We utilize compaction‐based mapping of erosion patterns recorded by anomalously high sonic velocities in Upper Triassic shales. We show that the amount of section removed during exhumation in the Irish Sea varies between 1.3 and 3.3 km and that exhumation patterns are markedly heterogeneous. Neither the heterogeneity of exhumation nor its focusing over hanging wall blocks of major faults is consistent with solely plume‐related uplift, and we believe that our results record cryptic basin inversion that is superimposed on epeirogenic exhumation (some of which may be plume related). The direct evidence for this inversion has been removed because erosion has proceeded beneath the null lines of reactivated faults, and we propose erosion of reactivated fault segments as one of the major reasons why shortening is frequently underestimated in inverted basins.
The Neurospora crassa TOB Complex: Analysis of the Topology and Function of Tob38 and Tob37

The TOB or SAM complex is responsible for assembling several proteins into the mitochondrial outer membrane, including all β-barrel proteins. We have identified several forms of the complex in Neurospora crassa. One form contains Tob55, Tob38, and Tob37; another contains these three subunits plus the Mdm10 protein; while additional complexes contain only Tob55. As previously shown for Tob55, both Tob37 and Tob38 are essential for viability of the organism. Mitochondria deficient in Tob37 or Tob38 have reduced ability to assemble β-barrel proteins. The function of two hydrophobic domains in the C-terminal region of the Tob37 protein was investigated. Mutant Tob37 proteins lacking either or both of these regions are able to restore viability to cells lacking the protein. One of the domains was found to anchor the protein to the outer mitochondrial membrane but was not necessary for targeting or association of the protein with mitochondria. Examination of the import properties of mitochondria containing Tob37 with deletions of the hydrophobic domains reveals that the topology of Tob37 may be important for interactions between specific classes of β-barrel precursors and the TOB complex.
Molecular characterization of Chikungunya virus during an outbreak in South India.

INTRODUCTION Re-emergence of Chikungunya is a major public health problem in the southern states of India. OBJECTIVES This study was undertaken to investigate an outbreak of Chikungunya, in June-August 2008 using PCR and determine the prevalent genotypes of Chikungunya virus (CHIKV) associated with the outbreak. MATERIALS AND METHODS Samples of blood were collected (in heparinized vacutainer tubes) from suspected patients of CHIKV infection from both Government Taluk Hospital in Kerala and a tertiary care hospital in Chennai, Tamil Nadu. A one-step RT-PCR was carried out on a block thermo-cycler targeting the E2 gene that codes for the viral envelope protein. The amplicons were verified for 305 bp size by standard agarose gel electrophoresis. The PCR products were purified, sequenced, and compared with other CHIKV strains reported from different geographical regions. A phylogenetic tree was constructed using MEGA 4. RESULTS Altogether 118 samples were collected from patients who presented with sudden onset of fever and/or joint pain, myalgia, and headache. CHIKV infection was confirmed by RT-PCR in 14 patients and all these cases were from Kerala. The positivity correlated with the early stage of the disease as all these patients had fever of less than seven days duration. The study isolates have been allotted the GenBank accession nos. GQ272368-GQ272381. Phylogenetic analysis of recent CHIKV isolates by partial sequencing of E2 region shows that isolates are closely related to strains from neighboring states and the African type. CONCLUSION RT-PCR is a useful technique for the early detection of CHIKV infection during outbreaks. Molecular characterization of the strains indicates that majority of the strains have originated from the Central/East African strains of CHIKV.
Favorable Climate Change Response Explains Non-Native Species' Success in Thoreau's Woods

Invasive species have tremendous detrimental ecological and economic impacts. Climate change may exacerbate species invasions across communities if non-native species are better able to respond to climate changes than native species. Recent evidence indicates that species that respond to climate change by adjusting their phenology (i.e., the timing of seasonal activities, such as flowering) have historically increased in abundance. The extent to which non-native species success is similarly linked to a favorable climate change response, however, remains untested. We analyzed a dataset initiated by the conservationist Henry David Thoreau that documents the long-term phenological response of native and non-native plant species over the last 150 years from Concord, Massachusetts (USA). Our results demonstrate that non-native species, and invasive species in particular, have been far better able to respond to recent climate change by adjusting their flowering time. This demonstrates that climate change has likely played, and may continue to play, an important role in facilitating non-native species naturalization and invasion at the community level.
A Minimum Relative Entropy Principle for Adaptive Control in Linear Quadratic Regulators

The design of optimal adaptive controllers is usually based on heuristics, because solving Bellman’s equations over information states is notoriously intractable. Approximate adaptive controllers often rely on the principle of certainty-equivalence where the control process deals with parameter point estimates as if they represented “true” parameter values. Here we present a stochastic control rule instead where controls are sampled from a posterior distribution over a set of probabilistic input-output models and the true model is identified by Bayesian inference. This allows reformulating the adaptive control problem as an inference and sampling problem derived from a minimum relative entropy principle. Importantly, inference and action sampling both work forward in time and hence such a Bayesian adaptive controller is applicable on-line. We demonstrate the improved performance that can be achieved by such an approach for linear quadratic regulator examples.
A CRISPR/Cas9 Toolbox for Multiplexed Plant Genome Editing and Transcriptional Regulation1[OPEN]

A CRISPR/Cas9 toolbox enables multiplex genome editing and transcriptional regulation of genes in plants. The relative ease, speed, and biological scope of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated Protein9 (Cas9)-based reagents for genomic manipulations are revolutionizing virtually all areas of molecular biosciences, including functional genomics, genetics, applied biomedical research, and agricultural biotechnology. In plant systems, however, a number of hurdles currently exist that limit this technology from reaching its full potential. For example, significant plant molecular biology expertise and effort is still required to generate functional expression constructs that allow simultaneous editing, and especially transcriptional regulation, of multiple different genomic loci or multiplexing, which is a significant advantage of CRISPR/Cas9 versus other genome-editing systems. To streamline and facilitate rapid and wide-scale use of CRISPR/Cas9-based technologies for plant research, we developed and implemented a comprehensive molecular toolbox for multifaceted CRISPR/Cas9 applications in plants. This toolbox provides researchers with a protocol and reagents to quickly and efficiently assemble functional CRISPR/Cas9 transfer DNA constructs for monocots and dicots using Golden Gate and Gateway cloning methods. It comes with a full suite of capabilities, including multiplexed gene editing and transcriptional activation or repression of plant endogenous genes. We report the functionality and effectiveness of this toolbox in model plants such as tobacco (Nicotiana benthamiana), Arabidopsis (Arabidopsis thaliana), and rice (Oryza sativa), demonstrating its utility for basic and applied plant research.
Expression of Large Amino Acid Transporter LAT1 in Rat Brain Endothelium

The expression of the large amino acid transporter, LAT1, was investigated in brain of adult Long-Evans rats. The LAT1 transcript was readily detected in brain microvessels and choroid plexus by reverse transcription polymerase chain reaction analysis using three different gene specific primer pairs. A polyclonal affinity purified antibody against the N-terminus of LAT1 was generated in chickens and used in immunoblot and immunocytochemical analyses of brain tissue sections of adult rats. On immunoblots, the antibody detected a peptide-inhibitable 45 kDa band in a rat brain microvessel membrane preparation. It also identified the same protein band in membrane preparations of different brain structures, as well as in heart and testis, whereas the protein was absent or only faintly detectable in muscle, kidney, and liver. In brain sections, the antibody intensely labeled the luminal and abluminal membranes of brain microvessel endothelial cells in all brain areas examined including cerebral cortex, cerebellum, hippocampus, and in gray and white matter regions. These results suggest that LAT1 is involved in transcellular transport and may play an important role in large, neutral amino acid transfer across the blood–brain barrier.
Multifractality and rainfall extremes: A review

The multifractal representation of rainfall and its use to predict rainfall extremes have advanced significantly in recent years. This paper summarizes this body of work and points at some open questions. The need for a coherent overview comes in part from the use of different terminology, notation, and analysis methods in the literature and in part from the fact that results are dispersed and not always readily available. Two important trends have marked the use of multifractals for rainfall and its extremes. One is the recent shift of focus from asymptotic scaling properties (mainly for the intensity‐duration‐frequency curves and the areal reduction factor) to the exact extreme distribution under nonasymptotic conditions. This shift has made the results more relevant to hydrologic applications. The second trend is a more sparing use of multifractality in modeling, reflecting the limits of scale invariance in space‐time rainfall. This trend has produced models that are more consistent with observed rainfall characteristics, again making the results more suitable for application. Finally, we show that rainfall extremes can be analyzed using rather rough models, provided the parameters are fitted to an appropriate range of large‐deviation statistics.
Submillimeter Array Imaging of the Maser Emission from the H30α Radio Recombination Line in MWC 349A

We used the Submillimeter Array to map the angular distribution of the H30α recombination line (231.9 GHz) in the circumstellar region of the peculiar star MWC 349A. The resolution was 1.2″, but because of high signal-to-noise ratio we measured the positions of all maser components to accuracies better than 0.01″, at a velocity resolution of 1 km s−1. The two strongest maser components (called high-velocity components) at velocities near –14 and 32 km s−1 are separated by 0.048″ ± 0.001″ (60 AU) along a position angle of 102° ± 1°. The distribution of maser emission at velocities between and beyond these two strongest components were also provided. The continuum emission lies at the center of the maser distribution to within 10 mas. The masers appear to trace a nearly edge-on rotating disk structure, reminiscent of the water masers in Keplerian rotation in the nuclear accretion disk of the galaxy NGC 4258. However, the maser components in MWC 349A do not follow a simple Keplerian kinematic prescription with v ∼ r−1/2, but have a larger power-law index. We explore the possibility that the high-velocity masers trace spiral density or shock waves. We also emphasize caution in the interpretation of relative centroid maser positions where the maser is not clearly resolved in position or velocity, and we present simulations that illustrate the range of applicability of the centroiding method.
Isolation, Cloning and Characterization of a Tyrosinase with Improved Activity in Organic Solvents from Bacillus megaterium

A tyrosinase-expressing bacterium was isolated from soil, and extracellular enzymatic activity was induced by the presence of tyrosine and CuSO4. Amplification of the 16S rDNA genes revealed a high similarity with Bacillus megaterium. The enzyme was over-expressed in Escherichia coli BL21 and purified using an affinity column. The tyrosinase was composed of 297 amino acids and was determined to be a monomer with a relative molecular mass of 31 kDa according to gel filtration. The Km values for 3,4-dihydroxy-L-phenylalanine (L-DOPA) and L-tyrosine were 0.35 and 0.075 mM, respectively, and the kcat/Km values were 28.9·103 and 32.9·103 (s–1·M–1). The maximum activity for both monophenolase and diphenolase was observed at 50°C and pH 7.0. Enzymatic activity was enhanced in the presence of 10–50% water-miscible organic solvents, which included ethanol, methanol, 2-propanol and dimethyl sulfoxide (DMSO). The activity in 30% DMSO was 170% of the activity in water and the enantioselectivity towards L-DOPA decreased by 40%. The residual activity following an incubation period of 17 h in 0–70% methanol was constant. This newly isolated and characterized tyrosinase may have potential applications in organic synthesis due to its high activity and stability at typically denaturing conditions.
Role of Primary Sludge Hydrolysis in Energy Recovery from Municipal Wastewater Sludge

Laboratory experiments supported by full-scale operational observations have been utilized to assess the possible yield of methane-rich biogas via decomposition of COD and volatile fatty acids (VFAs) from organic matter trapped and settled in a municipal wastewater treatment plant. The impact of operational conditions (mainly solids' retention time) on VFAs and methane-rich gas generation was estimated by fractionation of COD in sludge and supernatant. Assessment of efficiency of this process was done by steady state measurements of COD solubilization. Full-scale investigations supported by laboratory tests enlightened some specific operational problems that may occur in wastewater treatment plants with an intensive acidic hydrolysis. Relatively high consumption of biodegradable carbon is usually one of adverse and unfavorable effects.
An Omics Perspective on Candida Infections: Toward Next-Generation Diagnosis and Therapy

Candida species can cause severe infections associated with high morbidity and mortality. Therefore, it is essential to gain more insight into the anti-fungal host defense response. The advent of omics technology and development of advanced systems biology tools has permitted to approach this in an unbiased and quantitative manner. This review summarizes the insights gained on anti-Candida immunity from genetic-, transcriptome-, proteome-, metabolome-, microbiome-, mycobiome-, and computational systems biology studies and discusses practical aspects and future perspectives.
Early regulation of brain aromatase (cyp19a1b) by estrogen receptors during zebrafish development

Early expression of estrogen receptors (esr) and their role in regulating early expression of cyp19a1b encoding brain aromatase were examined in the brain of zebrafish. Using in toto hybridization and quantitative reverse transcriptase‐polymerase chain reaction (RT‐PCR), a significant increase in the expression of esr1, esr2a, and esr2b was observed between 24 and 48 hours postfertilization (hpf). In toto hybridization demonstrated that esr2a and esr2b, but not esr1, are found in the hypothalamus. Using real‐time RT‐PCR, an increase in cyp19a1b mRNAs occurs between 24 and 48 hpf, indicating that expression of cyp19a1b is temporally correlated with that of esr. This increase is blocked by the pure anti‐estrogen ICI182,780. Furthermore, E2 treatment of cyp19a1b‐GFP (green fluorescent protein) transgenic embryos results in appearance of GFP expression in the brain as early as 25 hpf. These results indicate that basal expression of cyp19a1b expression in the brain of developing zebrafish most likely relies upon expression of esr that are fully functional before 25 hpf. Developmental Dynamics 238:2641–2651, 2009. © 2009 Wiley‐Liss, Inc.
Learning subgaussian classes : Upper and minimax bounds

We obtain sharp oracle inequalities for the empirical risk minimization procedure in the regression model under the assumption that the target Y and the model F are subgaussian. The bound we obtain is sharp in the minimax sense if F is convex. Moreover, under mild assumptions on F, the error rate of ERM remains optimal even if the procedure is allowed to perform with constant probability. A part of our analysis is a new proof of minimax results for the gaussian regression model.
Reprodutibilidade e validade do Questionrio Internacional de Atividade Fsica em adolescentes

RESUMENReprodutibilidad de la validez de la Encuesta Internacional deActividad Fisica en adolescentes La Encuesta Internacional de Actividad Fisica (IPAQ) se desarro-llo originalmente con proposito de estimar el nivel de practica habi-tual de actividad fisica de poblaciones de paises diferentes. Losobjetivos del estudio fueron analizar al reproducibilidad y la validezde la version corta de IPAQ en adolescentes. La muestra fue cons-tituida por 161 adolescentes (92 muchachas y 69 muchachos) conedades entre 12 y 18 anos. Reproducibilidad se obtuvo a traves delas contestaciones en la aplicacion de la encuesta, con intervalo dedos semanas, involucrando coeficiente de correlacion de Spear-man (Rs) y tecnica de Bland y Altman (B-A). La validacion fue reali-zada por medio de las comparaciones entre el tiempo dispensadoen las actividades periodicas por los adolescentes por medio deIPAQ y para el instrumento del retrospectivo de auto-recordacionde las actividades diarias (R-24h). Para ello, se uso el R
Elevated Soluble Cellular Adhesion Molecules in Subjects With Low HDL-Cholesterol

The purpose of this study was to investigate whether the expression of cellular adhesion molecules (CAMs) is enhanced in individuals with low HDL cholesterol (HDL-C). Plasma levels of soluble vascular cell adhesion molecule-1 (sVCAM-1), intercellular adhesion molecule-1 (sICAM-1), and E-selectin (sE-selectin) were measured in subjects with low (below the 10th percentile for the Italian population), average, or high (above the 90th percentile) HDL-C. Average sICAM-1 and sE-selectin levels were significantly higher in two groups of 65 individuals with low HDL levels, either hyperlipidemic (320.5±16.0 and 61.4±3.5 ng/mL) or normolipidemic (309.6±13.0 and 60.0±2.7 ng/mL), than in subjects with average HDL levels, either hyperlipidemic (267.0±10.1 and 50.4±2.8 ng/mL) or normolipidemic (257.9±5.4 and 51.1±2.4 ng/mL), or with high HDL levels (254.8±10.2 and 52.5±3.2 ng/mL). No significant difference was found in the plasma sVCAM-1 concentration. HDL-C was inversely correlated with sICAM-1 and sE-selectin in the low-HDL subjects (r2=0.087 and 0.035, P =0.0007 and 0.033, respectively), but not in individuals with normal or elevated HDL-C (r2=0.012 and 0.006). A fenofibrate-induced increase of HDL-C in 20 low-HDL subjects was associated with a significant reduction of plasma sICAM-1 and sE-selectin concentrations. An increased CAMs expression may be a mechanism by which a low plasma HDL level promotes atherogenesis and causes acute atherothrombotic events.
What’s with the Attitude? Identifying Sentences with Attitude in Online Discussions

Mining sentiment from user generated content is a very important task in Natural Language Processing. An example of such content is threaded discussions which act as a very important tool for communication and collaboration in the Web. Threaded discussions include e-mails, e-mail lists, bulletin boards, newsgroups, and Internet forums. Most of the work on sentiment analysis has been centered around finding the sentiment toward products or topics. In this work, we present a method to identify the attitude of participants in an online discussion toward one another. This would enable us to build a signed network representation of participant interaction where every edge has a sign that indicates whether the interaction is positive or negative. This is different from most of the research on social networks that has focused almost exclusively on positive links. The method is experimentally tested using a manually labeled set of discussion posts. The results show that the proposed method is capable of identifying attitudinal sentences, and their signs, with high accuracy and that it outperforms several other baselines.
Olfactory dysfunction: common in later life and early warning of neurodegenerative disease.

BACKGROUND Disturbances of smell and taste are common. About 5% of the general population have anosmia (absence of the sense of smell). Olfactory dysfunction can markedly impair the quality of life. METHODS Review of pertinent literature retrieved by a selective search. RESULTS In recent years, simple and reliable tests of the sense of smell have been introduced in otorhinolaryngology. Olfactory testing has become a new focus of attention in neurology as well, mainly because many patients with neurodegenerative diseases-including the majority of those with Parkinson's or Alzheimer's disease-have olfactory loss early on in the course of their disorder. Olfactory dysfunction is thus regarded as an early sign of neurodegenerative disease that may allow a tentative diagnosis to be made years before the motor or cognitive disturbances become evident. As for the treatment of olfactory loss, anti-inflammatory drugs and surgery can help in some cases, and olfactory training can lead to significant improvement of post-viral olfactory deficits. CONCLUSION Olfactory dysfunction is common and becomes more common with advancing age. It is increasingly receiving attention as an important sign for the early diagnosis and the differential diagnosis of neurodegenerative disorders.