Miracle-dz/UniFAR-FTUs huggingface dataset:
Geographical and Ecological Analysis of Resistance, Coresistance, and Coupled Resistance to Antimicrobials in Respiratory Pathogenic Bacteria in Spain

ABSTRACT A multicenter susceptibility surveillance (the S.A.U.C.E. project) including 2,721 Streptococcus pneumoniae, 3,174 Streptococcus pyogenes, and 2,645 Haemophilus influenzae consecutive isolates was carried out in 25 hospitals all over Spain from November 2001 to October 2002 to evaluate the current epidemiology of resistance of the main bacteria involved in community-acquired respiratory tract infections. Susceptibility testing was performed in a single centralized laboratory by a broth microdilution method. The prevalence of resistant S. pneumoniae strains was 0.4% for cefotaxime, 4.4% for amoxicillin and amoxicillin-clavulanic acid, 25.6% for cefuroxime-axetil, 34.5% for erythromycin, clarithromycin, and azithromycin, and 36.0% for cefaclor. Phenotypes of resistance to erythromycin were MLSB (macrolide-lincosamide-streptogramin B) in 89.9% (gene ermB) and M (macrolide) in 9.7% of cases (gene mefA). No strain harbored both genes simultaneously. Serotypes 19, 6, 23, 14, and 3 were the most prevalent, accounting for 54.6% of the total isolates. Resistance to macrolides seems to be the most alarming point, since among penicillin-susceptible isolates it reached 15.1% compared to 55.8% among penicillin-resistant strains. Geographically, a number of regions had rates of erythromycin resistance above 40% (even higher in children). Resistance to erythromycin was also high in S. pyogenes isolates: mean regional 33.2%, beta-lactamase-producing H. influenzae were 20%, whereas 4.4% had a beta-lactamase-negative, ampicillin-resistant phenotype. We highlight the importance of different geographical frequencies of coresistance (associations of resistance to different drugs within the same species) and coupled resistance (association of resistance between different species) probably resulting from different local coselective events.
Generalized digital waveguide networks

Digital waveguides are generalized to the multivariable case with the goal of maximizing generality while retaining robust numerical properties and simplicity of realization. Multivariable complex power is defined, and conditions for "medium passivity" are presented. Multivariable complex wave impedances, such as those deriving from multivariable lossy waveguides, are used to construct scattering junctions which yield frequency dependent scattering coefficients which can be implemented in practice using digital filters. The general form for the scattering matrix at a junction of multivariable waveguides is derived. An efficient class of loss-modeling filters is derived, including a rule for checking validity of the small-loss assumption. An example application in musical acoustics is given.
A single supply wide bandwidth 4:1 video multiplexer in an 8 GHz dielectrically isolated complementary bipolar process

A high performance monolithic 4:1 analog multiplexer implemented in an 8 GHz dielectrically isolated complementary bipolar process was designed and simulated. It is useful in many general purpose high-speed applications such as driving an 150 Q cable or an analog to digital (A/D) converter. This switched transconductance amplifier 4:1 video multiplexer has a current mode decoder, a voltage feedback amplifier and four PNP-differential-pair input stages. It has a -3 dB small signal bandwidth of 148 MHz and a slew rate of greater than 170 V/us. It has a differential gain and a differential phase error of 0.03% and 0.030. With -113 dB of all-hostile crosstalk and -91 dB of off isolation at 10 MHz, this multiplexer is compatible with a 10 bits A/D converter. It has a channel switching time to 0.1% of 15 ns and consumes less than 6.4 mA on a 5 V single supply voltage. The output voltage swing of this multiplexer extends to within 50 mV of each rail, providing a wide output dynamic range. It offers a high-speed disable feature allowing the output to be put into a high impedance state for multi-stages so that the off channel does not load the output bus. This shutdown feature also reduces the supply current to less than 2.6 mA. Thesis Supervisor: James K. Roberge Title: Professor of Electrical Engineering
Targeting the Large Subunit of Human Ribonucleotide Reductase for Cancer Chemotherapy

Ribonucleotide reductase (RR) is a crucial enzyme in de novo DNA synthesis, where it catalyses the rate determining step of dNTP synthesis. RRs consist of a large subunit called RR1 (α), that contains two allosteric sites and one catalytic site, and a small subunit called RR2 (β), which houses a tyrosyl free radical essential for initiating catalysis. The active form of mammalian RR is an αnβm hetero oligomer. RR inhibitors are cytotoxic to proliferating cancer cells. In this brief review we will discuss the three classes of RR, the catalytic mechanism of RR, the regulation of the dNTP pool, the substrate selection, the allosteric activation, inactivation by ATP and dATP, and the nucleoside drugs that target RR. We will also discuss possible strategies for developing a new class of drugs that disrupts the RR assembly.
Regulation of actions and habits by ventral hippocampal trkB and adolescent corticosteroid exposure

In humans and rodents, stress promotes habit-based behaviors that can interfere with action–outcome decision-making. Further, developmental stressor exposure confers long-term habit biases across rodent–primate species. Despite these homologies, mechanisms remain unclear. We first report that exposure to the primary glucocorticoid corticosterone (CORT) in adolescent mice recapitulates multiple neurobehavioral consequences of stressor exposure, including long-lasting biases towards habit-based responding in a food-reinforced operant conditioning task. In both adolescents and adults, CORT also caused a shift in the balance between full-length tyrosine kinase receptor B (trkB) and a truncated form of this neurotrophin receptor, favoring the inactive form throughout multiple corticolimbic brain regions. In adolescents, phosphorylation of the trkB substrate extracellular signal-regulated kinase 42/44 (ERK42/44) in the ventral hippocampus was also diminished, a long-term effect that persisted for at least 12 wk. Administration of the trkB agonist 7,8-dihydroxyflavone (7,8-DHF) during adolescence at doses that stimulated ERK42/44 corrected long-lasting corticosterone-induced behavioral abnormalities. Meanwhile, viral-mediated overexpression of truncated trkB in the ventral hippocampus reduced local ERK42/44 phosphorylation and was sufficient to induce habit-based and depression-like behaviors. Together, our findings indicate that ventral hippocampal trkB is essential to goal-directed action selection, countering habit-based behavior otherwise facilitated by developmental stress hormone exposure. They also reveal an early-life sensitive period during which trkB–ERK42/44 tone determines long-term behavioral outcomes.
Surface Compaction Estimates and Soil Sensitivity in Aspen Stands of the Great Lakes States

Aspen forests in the Great Lakes States support much of the regional timber industry. Management-induced soil compaction is a concern because it affects forest health and productivity and soil erosion. Soil compaction increases bulk density and soil strength and can also decrease air and water movement into and through the soil profile. Currently, most inventories, and specifically the Forest Inventory and Analysis program, use qualitative estimates of soil compaction. This study compared qualitative estimates with quantitative measurements on aspen clearcuts in five national forests in the Great Lakes States. Research sites were stratified into classes of high and low potential for soil compaction on the basis of soil texture. Qualitative visual assessments of compaction were made according to Forest Inventory and Analysis (FIA) phase 3 protocols and compared with physical measurements of bulk density, soil compression strength, and saturated hydraulic conductivity. No differences in compaction between high- and low-risk soils were detected using visual assessments, but quantitative measurements in high-risk, fine-textured soils indicated greater compaction than low-risk, coarse-textured soils. These results illustrate shortcomings in qualitative estimates of compaction made according to FIA phase 3 field protocols. Inexpensive quantitative measurements, such as those taken with a pocket penetrometer, may be sufficient to quantify compaction levels within the plots.
Mechanism of the Circadian Clock in Physiology Mechanism of the circadian clock in physiology

Richards J, Gumz ML. Mechanism of the circadian clock in physiology. Am J Physiol Regul Integr Comp Physiol 304: R1053–R1064, 2013. First published April 10, 2013; doi:10.1152/ajpregu.00066. 2013. —It has been well established that the circadian clock plays a crucial role in the regulation of almost every physiological process. It also plays a critical role in pathophysiological states including those of obesity and diabetes. Recent evidence has highlighted the potential for targeting the circadian clock as a potential drug target. New studies have also demonstrated the existence of “clock-independent effects” of the circadian proteins, leading to exciting new avenues of research in the circadian clock field in physiology. The goal of this review is to provide an introduction to and overview of the circadian clock in physiology, including mechanisms, targets, and role in disease states. The role of the circadian clocks in the regulation of the cardiovascular system, renal function, metabolism, the endocrine system, immune, and reproductive systems will be discussed.
Landscapes, Learning Costs, and Genetic Assimilation

The evolution of a population can be guided by phenotypic traits acquired by members of that population during their lifetime. This phenomenon, known as the Baldwin effect, can speed the evolutionary process as traits that are initially acquired become genetically specified in later generations. This paper presents conditions under which this genetic assimilation can take place. As well as the benefits that lifetime adaptation can give a population, there may be a cost to be paid for that adaptive ability. It is the evolutionary trade-off between these costs and benefits that provides the selection pressure for acquired traits to become genetically specified. It is also noted that genotypic space, in which evolution operates, and phenotypic space, in which adaptive processes (such as learning) operate, are, in general, of a different nature. To guarantee that an acquired characteristic can become genetically specified, these spaces must have the property of neighborhood correlation, which means that a small distance between two individuals in phenotypic space implies that there is a small distance between the same two individuals in genotypic space.
Rhesus Monkeys' Valuation of Vocalizations during a Free-Choice Task

Adaptive behavior requires that animals integrate current and past information with their decision-making. One important type of information is auditory-communication signals (i.e., species-specific vocalizations). Here, we tested how rhesus monkeys incorporate the opportunity to listen to different species-specific vocalizations into their decision-making processes. In particular, we tested how monkeys value these vocalizations relative to the opportunity to get a juice reward. To test this hypothesis, monkeys chose one of two targets to get a varying juice reward; at one of those targets, in addition to the juice reward, a vocalization was presented. By titrating the juice amounts at the two targets, we quantified the relationship between the monkeys' juice choices relative to the opportunity to listen to a vocalization. We found that, rhesus were not willing to give up a large juice reward to listen to vocalizations indicating that, relative to a juice reward, listening to vocalizations has a low value.
Comparison of mixing properties in convection with the Particle‐Line Method

Spatial resolution in mixing processes is an acute problem. We propose a line method, akin to the contour dynamics technique, which is an extension of the particle method but with the particles redistributed on the line with time. We have used up to 105 particles per line and ten lines to investigate the dynamical and structural properties of mixing for both Newtonian and non‐Newtonian temperature‐dependent viscosity convection in 2D geometry. The spatial structures and the time history of the lines formed in Newtonian convection are different from those produced in non‐Newtonian convection, which has the tendency for producing long‐living horizontal structures. Efficient mixing in the upper mantle would be inhibited by non‐Newtonian rheology.
Three dimensional models of Martian mantle convection with phase transitions

We have employed a three‐dimensional compressible convection model to study the dynamics of phase transitions in the Martian mantle. A large core model with two exothermic phase transitions, the olivine to β‐spinel and the β‐ to γ‐spinel transition, and a small core model including also the endothermic spinel to perovskite transition have been considered. The two exothermic transitions create ‘thermal barriers’ for small upwellings due to the latent heat consumption from the phase change. Upwelling plumes lose part or all of their buoyancy, which causes the formation of one stable area full of plumes. This tendency for the merging of plumes increases with internal heating. This type of convective planform is consistent with the relatively few large volcanic centers. The presence of a 175 km thick perovskite layer above the core‐mantle boundary (CMB) yields a similar flow pattern, albeit with an even smaller number of plumes. However, the excess temperatures of the plumes and the mantle flow velocities in the lower mantle are smaller than those found in models without perovskite layer. The phase transitions cause an increase of temperature near the CMB, which prevents the lower mantle and the core from extensive cooling. A model with a perovskite layer decreasing in thickness with time can account for a peak in volcanic and magnetic activity early in the Martian history.
Texture Classification Using an Invariant Texture Representation and a Tree Matching Kernel

In this paper, an alternative approach for texture classification using an invariant texture representation and a tree matching kernel is proposed. The approach identifies regions of a given texture image using a Speed-Up Robust Feature or SURF descriptor. The regions of all training texture images are then clustered into a tree of non-uniformly shaped regions based on the distribution of them using a hierarchical k-means algorithm. The tree structure forms a tree of keypoints to be used for determining similarities between two texture images. The similarity is computed based on an approximate matching kernel called a tree matching kernel. Finally, Support Vector Machines (SVMs) with the tree matching kernels are constructed to classify textures. The performances of the proposed method are evaluated through experiments performed on textures from the Brodatz and UIUCTex datasets. The experiment results demonstrate that the proposed approach is quite robust to scale, rotation, deformation and viewpoint changes and achieves higher classification rates than some other well known methods.
Modulation of Synaptic Plasticity by Physiological Activation of M1 Muscarinic Acetylcholine Receptors in the Mouse Hippocampus

The muscarinic acetylcholine receptor (mAChR) has been considered one of the neurotransmitter receptors regulating hippocampal synaptic plasticity, which likely plays a critical role in learning and memory. In previous studies, however, muscarinic agonists were used at relatively high concentrations, and the subtype selectivity of muscarinic antagonists was not satisfactory. Thus, it remains to be answered whether physiological levels of ACh are involved in the regulation of synaptic plasticity and which mAChR subtypes are responsible for such effects. We found in this study that a low concentration (50 nm) of carbachol enhanced long-term potentiation (LTP) of excitatory synaptic transmission in mouse hippocampal slices. Notably, this enhancing effect was abolished in M1 mAChR knock-out (KO) but not in M3 mAChR KO mice, although LTP itself was intact in both mutant mice. Furthermore, we found that repetitive stimulation in the stratum oriens, which presumably triggered the release of endogenous ACh from cholinergic terminals, could enhance LTP in wild-type mice but not in M1 mAChR KO mice. These results suggest that physiologically released ACh from cholinergic fibers modulates hippocampal synaptic plasticity through the postsynaptic M1 mAChR activation.
In Vitro Inhibition of Diphtheria Toxin Action by Ammonium Salts and Amines

Kim, K. (University of Washington, Seattle), and N. B. Groman. In vitro inhibition of diphtheria toxin action by ammonium salts and amines. J. Bacteriol. 90:1552–1556. 1965. —An inhibitor for diphtheria toxin action on HeLa cells was demonstrated in the growth supernatant fractions of both toxinogenic and nontoxinogenic strains of Corynebacterium diphtheriae and in the Mueller and Miller medium in which these organisms were grown. The inhibitor in the growth supernatant fractions of the nontoxinogenic strain was dialyzable, stable to autoclaving, and stable on storage in the refrigerator for a period of many months, but was destroyed by ashing. When the components of Mueller and Miller medium were analyzed, only the Casamino Acids proved inhibitory. Further study with artificial mixtures of amino acids revealed that glutamine alone inhibited toxin. It was subsequently shown that ammonium salts and the aliphatic amines, glycamine and prolamine, could also function as inhibitors. Histamine and 16 amino acids tested individually were ineffective. The effectiveness of the amines and the ineffectiveness of sodium or potassium ions indicates that there is a specific requirement for inhibition.
Generating thermotolerant colonies by pairing Beauveria bassiana isolates.

Low thermotolerance in entomopathogenic fungi is the main impediment to their industrialization. This research, for the first time, describes the generation of a thermotolerant colony by pairing and subculturing (cycling) two Beauveria bassiana isolates without sexual reproduction. A mixture of B. bassiana ERL1578 and ERL1576 was inoculated on quarter-strength Sabouraud dextrose agar with yeast extract (¼SDAY). The paired culture (ERL1578 + 1576) was cycled three times to increase the frequency of possible hyphal fusion at the first cycle (c. 5/5 × 10(5) conidia), followed by a heat treatment as a selection pressure. Two non-paired isolates served as controls. Two morphologically different colonies (BbHet1 and BbHet2) were isolated from the pairing. BbHet1 colony had the highest conidial yield. BbHet2 had the most rapid mycelial growth and produced sponge-like mycelial masses (the others were flat), and its conidia were darker than the non-paired colonies under a microscope (400×). BbHet2 conidia had 60.7% germination after exposure to 45 °C for 60 min (the others had < 15%) without significant loss of virulence against Western flower thrips, Frankliniella occidentalis; however, there was a slight decrease in conidial yield. The new phenotypes formed suggested that a genetic variation happened as a result of heterokaryosis and/or recombination, more than environmental adaptation, when mixing different conidia. This methodology seems to be very useful for enhancing thermotolerance in fungi.
The effect of eccentric exercise on position sense and joint reaction angle of the lower limbs

Impaired position sense and impaired joint reaction angle of the lower limbs after muscle‐damaging activities is a serious functional limitation that may lead to an increased risk of injury, particularly in older populations. The purpose of the present study was to examine whether position sense and joint reaction angle to release can be affected by eccentric exercise–induced muscle damage. Twelve women underwent an isokinetic exercise session of the lower limb. Isometric peak torque, delayed‐onset muscle soreness, serum creatine kinase, position sense, and knee joint reaction angle to release were examined before, immediately after, and 24, 48, and 72 h post‐exercise. Due to the effect of eccentric exercise, subjects persistently placed their lower limb at a more extended position, representing a shorter knee extensor muscle. Eccentric exercise increased the knee reaction angle of the lower limb after release from 0° and 15° but not from 30° and 45°. Position sense and joint reaction to release were similarly affected by eccentric exercise and independently of visual feedback. Position sense was impaired only immediately post‐exercise (probably due to muscle fatigue), whereas impairment of the reaction angle to release persisted up to 3 days post‐exercise (probably due to muscle damage). Attenuation of position sense and joint reaction angle of the lower limbs after damaging activities is a serious functional limitation that may lead to an increase risk of injury, particularly in older populations. Muscle Nerve, 2007
Segmentation, categorization, and identification of commercial clips from TV streams using multimodal analysis

TV advertising is ubiquitous, perseverant, and economically vital. Millions of people's living and working habits are affected by TV commercials. In this paper, we present a multimodal ("visual + audio + text") commercial video digest scheme to segment individual commercials and carry out semantic content analysis within a detected commercial segment from TV streams.Two challenging issues are addressed. Firstly, we propose a multimodal approach to robustly detect the boundaries of individual commercials. Secondly, we attempt to classify a commercial with respect to advertised products/services. For the first, the boundary detection of individual commercials is reduced to the problem of binary classification of shot boundaries via the mid-level features derived from two concepts: Image Frames Marked with Product Information (FMPI) and Audio Scene Change Indicator (ASCI). Moreover, the accurate individual boundary enables us to perform commercial identification by clip matching via a spatial-temporal signature. For the second, commercial classification is formulated as the task of text categorization by expanding sparse texts from ASR/OCR with external knowledge. Our boundary detection has achieved a good result of F1 = 93.7% on the dataset comprising 499 individual commercials from TRECVID'05 video corpus. Commercial classification has obtained a promising accuracy of 80.9% on 141 distinct ones. Based on these achievements, various applications such as an intelligent digital TV set-top box can be accomplished to enhance the TV viewer's capabilities in monitoring and managing commercials from TV streams.
Terrestrial tetrapods in Cretaceous Antarctica

Abstract The fossil record of continental vertebrates from Antarctica is practically nonexistent, hence the composition of the supposed Mesozoic terrestrial vertebrate fauna must be inferred indirectly. This may be done using the reconstructed positions of the continents during the Mesozoic. These positions suggest the presence in Antarctica of primitive sauropods, large theropods, hypsilophodontian and iguanodontid ornithopods, ankylosaurs, pterosaurs, crocodilians, lungfish and possibly birds. In the absence of evidence to the contrary, monotremes are considered endemic Australian forms during the Cretaceous. The discovery of hypsilophodontian material in New Zealand corroborates the inference of Antarctic hypsilophodontians from their occurrence in Australia. The existence in the Australian Early Cretaceous of relict taxa and taxa that seem unusual compared to their overseas relatives suggests that the south polar tetrapod fauna was characterized by singular forms.