Miracle-dz/UniFAR-FTUs huggingface dataset:
Natural Selection and Genetic Constraints on Flowering Phenology in an Invasive Plant

Theory suggests that the contemporary evolution of local adaptation may increase the rate of biological invasion, yet natural selection has rarely been measured in invasive species. A recently published model predicted that latitudinal variation in the strength of stabilizing selection on two correlated traits—flowering time and size—can result in local adaptation during plant invasion but implicitly assumed that population × environment interactions are weak. We tested for stabilizing selection and the effect of growing environment on 13 populations of the invasive plant Lythrum salicaria sampled along a latitudinal gradient. Plants were grown under uniform glasshouse conditions and in a 3-year common garden field experiment at midlatitude. Consistent with model assumptions, the ranking of population means was highly correlated across the 3 years, and with glasshouse measurements, despite significant interannual differences in flowering time and vegetative size. As predicted, the first principal component (PC1) of flowering time and size was under stabilizing selection, and directional selection was detected on PC2, thus favoring plants that flowered earlier at a larger size. Our results demonstrate the value of using a priori models of natural selection to guide hypothesis testing and support the prediction that fitness trade-offs can constrain adaptive evolution in invasive species.
Proteasome inhibition induces reversible impairments in protein synthesis

Proteasome inhibition occurs during normal aging and in a variety of age‐related diseases, with inhibition of proteasome function sufficient to induce physiological and pathological alterations observed in each of these conditions. It is presumed that proteasome inhibition induces cellular alterations by promoting rapid protein accumulation, as the direct result of impairments in protein removal, which assumes protein synthesis remains relatively unchanged during proteasome inhibition. We conducted experimentation using established proteasome inhibitors and primary rat neuron cultures in order to elucidate whether proteasome inhibition had any effect on neuronal protein synthesis. Proteasome inhibition impaired neuronal protein synthesis, with concentrations of inhibitor necessary to significantly inhibit protein synthesis similar to the concentrations necessary to induce subsequent neuron death. The inhibition of protein synthesis was reversible during the first 6h of treatment, with the neurotoxicity of proteasome inhibition reversible during the first 12 h of treatment. These studies are the first to demonstrate a potentially important interplay between the proteasome and protein synthesis in neurons, and the first to identify that some effects of proteasome inhibition are reversible in neurons. Together these findings have important implications for understanding proteasome inhibition as a potential contributor to aging and age‐related disease. —Ding, Q. , Dimayuga, E. , Markesbery, W. R. , Keller, J. N. Proteasome inhibition induces reversible impairments in protein synthesis. FASEB J. 20, 1055–1063 (2006)
Density ripples in expanding low-dimensional gases as a probe of correlations

We investigate theoretically the evolution of the two-point density correlation function of a low-dimensional ultracold Bose gas after release from a tight transverse confinement. In the course of expansion thermal and quantum fluctuations present in the trapped systems transform into density fluctuations. For the case of free ballistic expansion relevant to current experiments, we present simple analytical relations between the spectrum of ``density ripples'' and the correlation functions of the original confined systems. We analyze several physical regimes, including weakly and strongly interacting one-dimensional (1D) Bose gases and two-dimensional (2D) Bose gases below the Berezinskii-Kosterlitz-Thouless (BKT) transition. For weakly interacting 1D Bose gases, we obtain an explicit analytical expression for the spectrum of density ripples which can be used for thermometry. For 2D Bose gases below the BKT transition, we show that for sufficiently long expansion times the spectrum of the density ripples has a self-similar shape controlled only by the exponent of the first-order correlation function. This exponent can be extracted by analyzing the evolution of the spectrum of density ripples as a function of the expansion time.
Staphylococcus aureus Sortase A Transpeptidase

Many virulence factors in Gram-positive bacteria are covalently anchored to the cell-wall peptidoglycan by sortase enzymes, a group of widely distributed cysteine transpeptidases. The Staphylococcus aureus Sortase A protein (SrtA) is the archetypal member of the Sortase family and is activated by Ca2+, an adaptation that may facilitate host colonization as elevated concentrations of this ion are encountered in human tissue. Here we show that a single Ca2+ ion bound to an ordered pocket on SrtA allosterically activates catalysis by modulating both the structure and dynamics of a large active site loop. Detailed nitrogen-15 relaxation measurements indicate that Ca2+ may facilitate the adaptive recognition of the substrate by inducing slow micro- to millisecond time-scale dynamics in the active site. Interestingly, relaxation compensated Carr-Purcell-Meiboom-Gill experiments suggest that the time scale of these motions is directly correlated with ion binding. The results of site-directed mutagenesis indicate that this motional coupling is mediated by the side chain of Glu-171, which is positioned within the β6/β7 loop and shown to contribute to Ca2+ binding. The available structural and dynamics data are compatible with a loop closure model of Ca2+ activation, in which the β6/β7 loop fluctuates between a binding competent closed form that is stabilized by Ca2+, and an open, highly flexible state that removes key substrate contacting residues from the active site.
Spectroscopic Redshifts to z > 2 for Optically Obscured Sources Discovered with the Spitzer Space Telescope

We have surveyed a field covering 9.0 deg2 within the NOAO Deep Wide-Field Survey region in Bootes with the Multiband Imaging Photometer on the Spitzer Space Telescope (SST) to a limiting 24 μm flux density of 0.3 mJy. Thirty-one sources from this survey with F24 μm > 0.75 mJy that are optically very faint (R ≳ 24.5 mag) have been observed with the low-resolution modules of the Infrared Spectrograph on SST (IRS). Redshifts derived primarily from strong silicate absorption features are reported here for 17 of these sources; 10 of these are optically invisible (R ≳ 26 mag), with no counterpart in BW, R, or I. The observed redshifts for 16 sources are 1.7 < z < 2.8. These represent a newly discovered population of highly obscured sources at high redshift with extreme infrared-to-optical ratios. Using IRS spectra of local galaxies as templates, we find that a majority of the sources have mid-infrared spectral shapes most similar to ultraluminous infrared galaxies powered primarily by active galactic nuclei. Assuming that the same templates also apply at longer wavelengths, bolometric luminosities exceed 1013 L☉.
Longitudinal brain imaging in preclinical Alzheimer disease: impact of APOE &egr;4 genotype

While prior work reliably demonstrates that the APOE ɛ4 allele has deleterious group level effects on Alzheimer disease pathology, the homogeneity of its influence across the lifespan and spatially in the brain remains unknown. Further it is unclear what combinations of factors at an individual level lead to observed group level effects of APOE genotype. To evaluate the impact of the APOE genotype on disease trajectories, we examined longitudinal MRI and PET imaging in a cohort of 497 cognitively normal middle and older aged participants. A whole-brain regional approach was used to evaluate the spatial effects of genotype on longitudinal change of amyloid-β pathology and cortical atrophy. Carriers of the ɛ4 allele had increased longitudinal accumulation of amyloid-β pathology diffusely through the cortex, but the emergence of this effect across the lifespan differed greatly by region (e.g. age 49 in precuneus, but 65 in the visual cortex) with the detrimental influence already being evident in some regions in middle age. This increased group level effect on accumulation was due to a greater proportion of ɛ4 carriers developing amyloid-β pathology, on average doing so at an earlier age, and having faster amyloid-β accumulation even after accounting for baseline amyloid-β levels. APOE ɛ4 carriers displayed faster rates of structural loss in primarily constrained to the medial temporal lobe structures at around 50 years, although this increase was modest and proportional to the elevated disease severity in APOE ɛ4 carriers. This work indicates that influence of the APOE gene on pathology can be detected starting in middle age.
Association between HIV-related risk behaviors and HIV testing among high school students in the United States, 2009.

OBJECTIVE To identify the human immunodeficiency virus (HIV)-related risk behaviors associated with HIV testing among US high school students who reported ever having sexual intercourse. DESIGN Secondary analysis of a cross-sectional study. SETTING The 2009 national Youth Risk Behavior Survey. PARTICIPANTS A total of 7591 US high school students who reported ever having sexual intercourse. MAIN EXPOSURES Risk behaviors related to HIV. MAIN OUTCOME MEASURE Having ever been tested for HIV. RESULTS Among the 7591 students who reported ever having sexual intercourse, 22.6% had been tested for HIV. Testing for HIV was most likely to be done among students who had ever injected any illegal drug (41.3%; adjusted odds ratio, 1.70; 95% CI, 1.14-2.56), had ever been physically forced to have sexual intercourse (36.2%; adjusted odds ratio, 1.43; 95% CI, 1.19 -1.72), did not use a condom the last time they had sexual intercourse (28.7%; adjusted odds ratio, 1.28; 95% CI, 1.08-1.51), and had sexual intercourse with 4 or more persons during their life (34.7%; adjusted odds ratio, 2.32; 95% CI, 1.98-2.73). CONCLUSIONS Most sexually active students, even among those who reported high-risk behaviors for HIV, have not been tested for HIV. New strategies for increasing HIV testing among the adolescent population, including encouraging routine voluntary HIV testing among those who are sexually active, are needed.
On skew braces (with an appendix by N. Byott and L. Vendramin)

Braces are generalizations of radical rings, introduced by Rump to study involutive non-degenerate set-theoretical solutions of the Yang-Baxter equation (YBE). Skew braces were also recently introduced as a tool to study not necessarily involutive solutions. Roughly speaking, skew braces provide group-theoretical and ring-theoretical methods to understand solutions of the YBE. It turns out that skew braces appear in many different contexts, such as near-rings, matched pairs of groups, triply factorized groups, bijective 1-cocycles and Hopf-Galois extensions. These connections and some of their consequences are explored in this paper. We produce several new families of solutions related in many different ways with rings, near-rings and groups. We also study the solutions of the YBE that skew braces naturally produce. We prove, for example, that the order of the canonical solution associated with a finite skew brace is even: it is two times the exponent of the additive group modulo its center.
Characterization of subcortical structures during deep brain stimulation utilizing support vector machines

In this paper we discuss an efficient methodology for the characterization of Microelectrode Recordings (MER) obtained during deep brain stimulation surgery for Parkinson's disease using Support Vector Machines and present the results of a preliminary study. The methodology is based in two algorithms: (1) an algorithm extracts multiple computational features from the microelectrode neurophysiology, and (2) integrates them in the support vector machines algorithm for classification. It has been applied to the problem of the recognition of subcortical structures: thalamus nucleus, zona incerta, subthalamic nucleus and substantia nigra. The SVM (support vector machines) algorithm performed quite well achieving 99.4% correct classification. In conclusion, the use of a computer-based system, like the one described in this paper, is intended to avoid human subjectivity in the localization of the subcortical structures and mainly the subthalamic nucleus (STN) for neurostimulation.
Morphometric Analysis of Dose-dependent Effect of Progesterone on Experimental Vasospasm-induced Rat Femoral Arteries

Objective: Our aim of this study was to determine effective doses of progesterone which has a vasodilatory effect during the early stage of vasospasm. Cerebral vasospasm (CV) is a predominant cause of morbidity and mortality which develops following subarachnoidal hemorrhage (SAH). Etiopathogenesis of CV is multifactorial. Despite many previously performed studies on this issue, the mechanism by which blood and blood products in the subarachnoidal space induce CV has not been clarified yet. Materials and Methods: In our study, we used “Rat Femoral Artery Vasospasm Model” introduced by Okada et al. Thanks to easy procurement and maintenance of rats. Rats were divided into four groups as: Group 1 (n = 8; control group), Group 2 (n = 8; vasospasm group), Group 3 (n = 8; vasospasm + 3 mg/kg progesterone group), and Group 4 (n = 8; vasospasm +15 mg/kg progesterone group). Progesterone which is an endogenously synthesized natural steroid was preferred in our study. Progesterone increases the production of vasodilatory epoxyeicosatrienoic acid by acting on its binding sites termed as pregnane X receptor. It decreases the intracellular influx of Ca2+ by blocking the functioning of L-type channels in smooth muscle cells. It manifests another vasodilatory effect by decreasing expression of TxA2 receptor. In our study, at the end of the 7th day, where the most intense vasospasm is seen, 1 cm pieces were excised from the femoral arteries and histopathologically examined under light microscope. Results: Vascular walls of three vasospasm-induced groups were relatively thicker when compared with the control group. Drug-treated groups were not different from each other. Vascular walls of the groups treated with lower and higher doses of the drug were thinner when compared with the vasospasm group without any statistically significant difference between groups (P > 0.05). Luminal cross-sectional areas of the drug-treated groups did not differ from each other. Mean luminal cross-sectional areas of the control and the drug-treated groups were larger than that of the vasospasm group without any statistically significant intergroup difference (P > 0.05). Conclusion: Based on the results of our study, progesterone did not exert protective effects on vascular wall thickness, while histopathological examination of luminal cross-sectional areas revealed its vasodilatory effects without any statistically significant difference between groups. Starting from the study results obtained, we think that its potential use as a preventive agent against the development of post-SAH CV requires conduction of multicentered, placebo-controlled, randomized, and double-blind studies.
Visualization of Biomolecular Structures: State of the Art Revisited

Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three‐dimensional, complex, large and time‐varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The survey concludes with an outlook on promising and important research topics to foster further success in the development of tools that help to reveal molecular secrets.
Resurrecting the Ancestral Enzymatic Role of a Modulatory Subunit*♦

In the post-genomic era, functional prediction of genes is largely based on sequence similarity searches, but sometimes the homologues bear different roles because of evolutionary adaptations. For instance, the existence of enzyme and non-enzyme homologues poses a difficult case for function prediction and the extent of this phenomenon is just starting to be surveyed. Different evolutionary paths are theoretically possible for the loss or acquisition of enzyme function. Here we studied the ancestral role of a model non-catalytic modulatory subunit. With a rational approach, we “resurrected” enzymatic activity from that subunit to experimentally prove that it derived from a catalytic ancestor. We show that this protein (L subunit ADP-glucose pyrophosphorylase) evolved to have a regulatory role, losing catalytic residues more than 130 million years ago, but preserving, possibly as a by-product, the substrate site architecture. Inactivation of catalytic subunits could be the consequence of a general evolutionary strategy to explore new regulatory roles in hetero-oligomers.
Levosulpiride Induced Parkinsonism and Other Movement Disorders

Drug induced Parkinsonism (DIP) is now the second leading cause of Parkinsonism behind idiopathic Parkinson’s disease. DIP can be defined as reversible development of parkinsonian syndrome in patients treated with drugs which impair dopamine function [1]. However some drugs uncover a dormant doparminergic pathway abnormality leading to full blown Parkinsonism. Many commonly prescribed safe drugs for common diseases are being reported to interfere with dopaminergic and cholinergic pathways causing classical parkinsonian manifestations. Movement disorders like tardive dyskinesia, tardive dystonia, akathisia, myoclonus, tremors are the commonly observed disorders with an offending drug as the etiological factor. Failure in identifying the drugs causing Parkinsonism, results in refractory symptoms with frequent outpatient/ inpatient visits forcing an economic burden and untold morbidity on the patient’s part. A community-based survey and a population-based study found DIP prevalence rates of 2.7% and 1.7%, respectively, whereas those of PD were 3.3% and 4.5%, respectively. However, 6.8% of the patients diagnosed with PD were later reclassified as having DIP [2]. This survey, thus reiterates the challenge of identifying the drugs impairing the dopaminergic pathway. The common culprits include neuroleptics such as chlorpromazine and clozapine, anti emetics such as metoclopramide and calcium channel blockers which are properly scrutinized after prescription. However, the repercussions of using Levosulpiride as a prokinetic drug are being brought to light recently. Levosulpiride, a selective dopamine D2-receptor antagonist, though appears as a seemingly harmless adjunct prescribed to a minor complaint, may end up being detrimental to the patient. Abstract
Modulation of Semiconductor Photoluminescence with Intense Terahertz Pulses

Over the last 5 years, tilted pulse-front terahertz (THz) generation has opened the door to new studies of nonlinear dynamics in a variety of materials. With access to strong electric fields that turn on and off over picosecond timescales exciting new possibilities exist to control light-matter interaction. We have developed a new intense THz pulse source, with a peak electric field of 230 kV/cm for exploring nonlinear dynamics in semiconductors. Here, we study the effects of THz pulses on semiconductor photoluminescence (PL). When a femtosecond optical and single-cycle intense THz pulse are simultaneously incident on a direct-gap semiconductor, the THz pulse enhances high energy and quenches low energy PL. However, with time delays larger than 1 ps, no modulation of the PL occurs. We have systematically studied the THz-pulse-induced change in PL (THz∆PL) over a wide range of THz energies and photoexcitation densities in gallium arsenide (GaAs) and indium phosphide (InP) to help understand the mechanism. In most cases, the quenching dominates and there is integrated PL quenching (PLQ). With increasing photoexcited carrier density, the fractional quenching decreases, while the enhancement increases, and less integrated modulation occurs. At high excitation density, by changing
Aerobic and anaerobic enzyme activity in the hake Merluccius gayi gayi related to the Oxygen Minimum Zone off central-southern Chile

El Sistema de Corrientes de Humboldt de la costa de Chile posee una Zona de Minimo Oxigeno (ZMO) entre 30 y 250 m de profundidad, con concentraciones de oxigeno < 0,5 ml L-1. Las mayores densidades de merluza Merluccius gayi gayi se asocian a esta zona, sugiriendo que posee adaptaciones metabolicas para permanecer en ella. Se estimo el potencial aerobico y anaerobico de esta especie demersal mediante la medicion de enzimas metabolicas claves y del sistema de transporte de electrones (ETS) en diferentes tejidos (musculo blanco, corazon, cerebro e higado). La actividad de la enzima citrato sintasa (CS) y de la ETS fueron mayores en el cerebro y corazon, confirmando la predominancia del metabolismo aerobico en los organos vitales diferentes al musculo. La actividad promedio de la enzima anaerobica lactato deshidrogenasa (LDH) fluctuo entre 55 ± 17,5 and 263 ± 79 UI g-1 ww, siendo menor en el corazon y cerebro. Esta baja actividad de LDH y una alta razon MDH/LDH en estos organos vitales indican que ambos serian capaces de lidiar con periodos de acidificacion metabolica producida por hipoxia ambiental. Los niveles de LDH fueron excepcionalmente altos en el higado, lo que podria relacionarse con factores ambientales como la contaminacion ambiental. La baja razon MDH/LDH y la menor actividad de CS y ETS en el musculo, sumado a la alta actividad de LDH en el higado indicarian un perfil metabolico de M. gayi gayi para tolerar condiciones de hipoxia y por lo tanto permanecer en la ZMO, pero disminuyendo su actividad natatoria.