Miracle-dz/UniFAR-FTUs huggingface dataset:
Archaeal Binding Protein-Dependent ABC Transporter: Molecular and Biochemical Analysis of the Trehalose/Maltose Transport System of the Hyperthermophilic Archaeon Thermococcus litoralis

ABSTRACT We report the cloning and sequencing of a gene cluster encoding a maltose/trehalose transport system of the hyperthermophilic archaeonThermococcus litoralis that is homologous to themalEFG cluster encoding the Escherichia colimaltose transport system. The deduced amino acid sequence of themalE product, the trehalose/maltose-binding protein (TMBP), shows at its N terminus a signal sequence typical for bacterial secreted proteins containing a glyceride lipid modification at the N-terminal cysteine. The T. litoralis malE gene was expressed in E. coli under control of an inducible promoter with and without its natural signal sequence. In addition, in one construct the endogenous signal sequence was replaced by the E. coli MalE signal sequence. The secreted, soluble recombinant protein was analyzed for its binding activity towards trehalose and maltose. The protein bound both sugars at 85°C with aKd of 0.16 μM. Antibodies raised against the recombinant soluble TMBP recognized the detergent-soluble TMBP isolated from T. litoralis membranes as well as the products from all other DNA constructs expressed in E. coli. Transmembrane segments 1 and 2 as well as the N-terminal portion of the large periplasmic loop of the E. coli MalF protein are missing in the T. litoralis MalF. MalG is homologous throughout the entire sequence, including the six transmembrane segments. The conserved EAA loop is present in both proteins. The strong homology found between the components of this archaeal transport system and the bacterial systems is evidence for the evolutionary conservation of the binding protein-dependent ABC transport systems in these two phylogenetic branches.
On the Oxide Trap Density and Profiles of 1-nm EOT Metal-Gate Last CMOS Transistors Assessed by Low-Frequency Noise

The low-frequency noise behavior of replacement metal gate high- k/metal-gate MOSFETs with an equivalent oxide thickness of the SiO2/HfO2 bilayer in the range ~ 1 nm has been investigated. It will be shown that both the average trap density and its profile derived from the frequency exponent γ of the flicker noise spectra are mainly determined by the interfacial layer (IL) oxide processing, with a higher trap density corresponding with a thinner chemical oxide, compared with a ≤ 1-nm thermal SiO2 IL. The thickness of the HfO2 layer and the metal gate fill has only a marginal impact on the noise power spectral density. It will also be shown that for the extraction of the trap density profiles from the 1/fγ noise spectra accurate values for the tunneling effective mass and barrier height are required.
Increased Risks of Coronary Heart Disease and Stroke Among Spousal Caregivers of Cancer Patients

Background— Spousal caregivers of cancer patients suffer psychological and physical burdens that may affect their risk of subsequently developing coronary heart disease and stroke. Methods and Results— Cancer patients were identified in the Swedish Cancer Registry, and information on their spouses was retrieved from the Swedish Multi-Generation Register. Follow-up of caregivers was performed from the date of the first diagnosis of cancer in their spouses through 2008. Standardized incidence ratios were calculated for spousal caregivers of cancer patients compared with those without an affected spouse. After the cancer diagnosis in wives, the risks of coronary heart disease, ischemic stroke, and hemorrhagic stroke in husbands were 1.13 (95% confidence interval [CI], 1.10–1.16), 1.24 (95% CI, 1.21–1.27), and 1.25 (95% CI, 1.18–1.32), respectively. The corresponding risks in wives with an affected husband were 1.13 (95% CI, 1.10–1.16), 1.29 (95% CI, 1.26–1.32), and 1.27 (95% CI, 1.19–1.34). The increases were consistent over time and were more pronounced if the spouse was affected by a cancer with a high mortality rate, such as pancreatic and lung cancers. Conclusions— Spousal caregivers of cancer patients have increased risks of coronary heart disease and stroke that persist over time. Clinical attention should be paid to spousal caregivers, especially those caring for cancer patients with high mortality rates.
Multiscale Analysis of Heterogeneous Media in the Peridynamic Formulation

A methodology is presented for investigating the dynamics of heterogeneous media using the nonlocal continuum model given by the peridynamic formulation. The approach presented here provides the ability to model the macroscopic dynamics while at the same time resolving the dynamics at the length scales of the microstructure. Central to the methodology is a novel two-scale evolution equation. The rescaled solution of this equation is shown to provide a strong approximation to the actual deformation inside the peridynamic material. The two scale evolution can be split into a microscopic component tracking the dynamics at the length scale of the heterogeneities and a macroscopic component tracking the volume averaged (homogenized) dynamics. The interplay between the microscopic and macroscopic dynamics is given by a coupled system of evolution equations. The equations show that the forces generated by the homogenized deformation inside the medium are related to the homogenized deformation through a history dependent constitutive relation
Promotion of Mn(II) Oxidation and Remediation of Coal Mine Drainage in Passive Treatment Systems by Diverse Fungal and Bacterial Communities

ABSTRACT Biologically active, passive treatment systems are commonly employed for removing high concentrations of dissolved Mn(II) from coal mine drainage (CMD). Studies of microbial communities contributing to Mn attenuation through the oxidation of Mn(II) to sparingly soluble Mn(III/IV) oxide minerals, however, have been sparse to date. This study reveals a diverse community of Mn(II)-oxidizing fungi and bacteria existing in several CMD treatment systems.
Using a hybrid neuron in physiologically inspired models of the basal ganglia

Our current understanding of the basal ganglia (BG) has facilitated the creation of computational models that have contributed novel theories, explored new functional anatomy and demonstrated results complementing physiological experiments. However, the utility of these models extends beyond these applications. Particularly in neuromorphic engineering, where the basal ganglia's role in computation is important for applications such as power efficient autonomous agents and model-based control strategies. The neurons used in existing computational models of the BG, however, are not amenable for many low-power hardware implementations. Motivated by a need for more hardware accessible networks, we replicate four published models of the BG, spanning single neuron and small networks, replacing the more computationally expensive neuron models with an Izhikevich hybrid neuron. This begins with a network modeling action-selection, where the basal activity levels and the ability to appropriately select the most salient input is reproduced. A Parkinson's disease model is then explored under normal conditions, Parkinsonian conditions and during subthalamic nucleus deep brain stimulation (DBS). The resulting network is capable of replicating the loss of thalamic relay capabilities in the Parkinsonian state and its return under DBS. This is also demonstrated using a network capable of action-selection. Finally, a study of correlation transfer under different patterns of Parkinsonian activity is presented. These networks successfully captured the significant results of the originals studies. This not only creates a foundation for neuromorphic hardware implementations but may also support the development of large-scale biophysical models. The former potentially providing a way of improving the efficacy of DBS and the latter allowing for the efficient simulation of larger more comprehensive networks.
Toward Testing the Hypothesis that Group B Coxsackieviruses (CVB) Trigger Insulin-Dependent Diabetes: Inoculating Nonobese Diabetic Mice with CVB Markedly Lowers Diabetes Incidence

ABSTRACT Insulin-dependent (type 1) diabetes mellitus (T1D) onset is mediated by individual human genetics as well as undefined environmental influences such as viral infections. The group B coxsackieviruses (CVB) are commonly named as putative T1D-inducing agents. We studied CVB replication in nonobese diabetic (NOD) mice to assess how infection by diverse CVB strains affected T1D incidence in a model of human T1D. Inoculation of 4- or 8-week-old NOD mice with any of nine different CVB strains significantly reduced the incidence of T1D by 2- to 10-fold over a 10-month period relative to T1D incidences in mock-infected control mice. Greater protection was conferred by more-pathogenic CVB strains relative to less-virulent or avirulent strains. Two CVB3 strains were employed to further explore the relationship of CVB virulence phenotypes to T1D onset and incidence: a pathogenic strain (CVB3/M) and a nonvirulent strain (CVB3/GA). CVB3/M replicated to four- to fivefold-higher titers than CVB3/GA in the pancreas and induced widespread pancreatitis, whereas CVB3/GA induced no pancreatitis. Apoptotic nuclei were detected by TUNEL (terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling) assay in CVB3/M-infected pancreata but not in CVB3/GA-infected pancreata. In situ hybridization detected CVB3 RNA in acinar tissue but not in pancreatic islets. Although islets demonstrated inflammatory infiltrates in CVB3-protected mice, insulin remained detectable by immunohistochemistry in these islets but not in those from diabetic mice. Enzyme-linked immunosorbent assay-based examination of murine sera for immunoglobulin G1 (IgG1) and IgG2a immunoreactivity against diabetic autoantigens insulin and HSP60 revealed no statistically significant relationship between CVB3-protected mice or diabetic mice and specific autoimmunity. However, when pooled sera from CVB3/M-protected mice were used to probe a Western blot of pancreatic proteins, numerous proteins were detected, whereas only one band was detected by sera from CVB3/GA-protected mice. No proteins were detected by sera from diabetic or normal mice. Cumulatively, these data do not support the hypothesis that CVB are causative agents of T1D. To the contrary, CVB infections provide significant protection from T1D onset in NOD mice. Possible mechanisms by which this virus-induced protection may occur are discussed.
The spinorial geometry of supersymmetric IIB backgrounds

We investigate the Killing spinor equations of IIB supergravity for one Killing spinor. We show that there are three types of orbits of Spin(9, 1) in the space of Weyl spinors which give rise to Killing spinors with stability subgroups and G2. We solve the Killing spinor equations for the and invariant spinors, give the fluxes in terms of the geometry and determine the conditions on the spacetime geometry imposed by supersymmetry. In both cases, the spacetime admits a null, self-parallel, Killing vector field. We also apply our formalism to examine a class of backgrounds which admit one and two pure spinors as Killing spinors and investigate the geometry of the spacetimes.
Mice with Genetically Altered Glucocorticoid Receptor Expression Show Altered Sensitivity for Stress-Induced Depressive Reactions

Altered glucocorticoid receptor (GR) signaling is a postulated mechanism for the pathogenesis of major depression. To mimic the human situation of altered GR function claimed for depression, we generated mouse strains that underexpress or overexpress GR, but maintain the regulatory genetic context controlling the GR gene. To achieve this goal, we used the following: (1) GR-heterozygous mutant mice (GR+/-) with a 50% GR gene dose reduction, and (2) mice overexpressing GR by a yeast artificial chromosome resulting in a twofold gene dose elevation. GR+/- mice exhibit normal baseline behaviors but demonstrate increased helplessness after stress exposure, a behavioral correlate of depression in mice. Similar to depressed patients, GR+/- mice have a disinhibited hypothalamic-pituitary-adrenal (HPA) system and a pathological dexamethasone/corticotropin-releasing hormone test. Thus, they represent a murine depression model with good face and construct validity. Overexpression of GR in mice evokes reduced helplessness after stress exposure, and an enhanced HPA system feedback regulation. Therefore, they may represent a model for a stress-resistant strain. These mouse models can now be used to study biological changes underlying the pathogenesis of depressive disorders. As a first potential molecular correlate for such changes, we identified a downregulation of BDNF protein content in the hippocampus of GR+/- mice, which is in agreement with the so-called neurotrophin hypothesis of depression.
Comment on Tai Chi for Risk of Falls. A meta‐analysis

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Interleukin‐1 receptor antagonist levels correlate with extent of myocardial loss in patients with acute myocardial infarction

Background: Interleukin‐1 receptor antagonist (IL‐1 Ra) levels are elevated early in patients with acute myocardial infarction (MI) and often precede release of markers of necrosis; however, IL‐1Ra levels did not correlate previously with infarct size and prognosis in such patients.
Fine-Scale Spatial Organization of Face and Object Selectivity in the Temporal Lobe: Do Functional Magnetic Resonance Imaging, Optical Imaging, and Electrophysiology Agree?

The spatial organization of the brain's object and face representations in the temporal lobe is critical for understanding high-level vision and cognition but is poorly understood. Recently, exciting progress has been made using advanced imaging and physiology methods in humans and nonhuman primates, and the combination of such methods may be particularly powerful. Studies applying these methods help us to understand how neuronal activity, optical imaging, and functional magnetic resonance imaging signals are related within the temporal lobe, and to uncover the fine-grained and large-scale spatial organization of object and face representations in the primate brain.
Path following control for a reversing general 2-trailer system

In order to meet the requirements for autonomous systems in real world applications, reliable path following controllers have to be designed to execute planned paths despite the existence of disturbances and model errors. In this paper we propose a Linear Quadratic controller for stabilizing a 2-trailer system with possible off-axle hitching around preplanned paths in backward motion. The controller design is based on a kinematic model of a general 2-trailer system including the possibility for off-axle hitching. Closed-loop stability is proved around a set of paths, typically chosen to represent the possible output from the path planner, using theory from linear differential inclusions. Using convex optimization tools a single quadratic Lyapunov function is computed for the entire set of paths.
Disruption of the Two Digalactosyldiacylglycerol Synthase Genes DGD1 and DGD2 in Arabidopsis Reveals the Existence of an Additional Enzyme of Galactolipid Synthesis Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.016675.

Two genes (DGD1 and DGD2) are involved in the synthesis of the chloroplast lipid digalactosyldiacylglycerol (DGDG). The role of DGD2 for galactolipid synthesis was studied by isolating Arabidopsis T-DNA insertional mutant alleles (dgd2-1 and dgd2-2) and generating the double mutant line dgd1 dgd2. Whereas the growth and lipid composition of dgd2 were not affected, only trace amounts of DGDG were found in dgd1 dgd2. The growth and photosynthesis of dgd1 dgd2 were affected more severely compared with those of dgd1, indicating that the residual amount of DGDG in dgd1 is crucial for normal plant development. DGDG synthesis was increased after phosphate deprivation in the wild type, dgd1, and dgd2 but not in dgd1 dgd2. Therefore, DGD1 and DGD2 are involved in DGDG synthesis during phosphate deprivation. DGD2 was localized to the outer side of chloroplast envelope membranes. Like DGD2, heterologously expressed DGD1 uses UDP-galactose for galactosylation. Galactolipid synthesis activity for monogalactosyldiacylglycerol (MGDG), DGDG, and the unusual oligogalactolipids tri- and tetragalactosyldiacylglycerol was detected in isolated chloroplasts of all mutant lines, including dgd1 dgd2. Because dgd1 and dgd2 carry null mutations, an additional, processive galactolipid synthesis activity independent from DGD1 and DGD2 exists in Arabidopsis. This third activity, which is related to the Arabidopsis galactolipid:galactolipid galactosyltransferase, is localized to chloroplast envelope membranes and is capable of synthesizing DGDG from MGDG in the absence of UDP-galactose in vitro, but it does not contribute to net galactolipid synthesis in planta.
Healthy behaviours, lifestyle patterns and sociodemographic determinants of the metabolic syndrome.

AIM The aim of this study was to examine the influence of healthy behaviours, lifestyle patterns and sociodemographic factors on risk of the metabolic syndrome (MS) in adult residents of rural, small town and large urban areas in Poland. MATERIAL AND METHODS Cross-sectional analysis of randomly selected representative sample of 1,187 men and women aged 20-74 years participating in the nationwide health survey WOBASZ. Metabolic syndrome was defined by AHA/NCEP criteria (2005). Analysed healthy behaviours included nonsmoking, healthy weight, adequate fruits and vegetables consumption, regular leisure-time physical activity. The 4 lifestyle factors were summed to create a lifestyle index (range 0-4). RESULTS Regardless of gender healthy weight, adequate fruits and vegetables consumption and physical activity were associated with lower odds of MS. Non-smoking was significantly related to the lower odds ratio of MS only among men. Following all 4 lifestyle factors was the strongest protective factor against having MS. Being higher educated, in the 20- 34-years-old cohort, living in the rural area were the most important sociodemographic factors reducing risk of MS. CONCLUSIONS The obtained results support the need for effective promotion of healthy behaviors and lifestyle patterns, especially in demonstrated high-risk sub-populations. Due to important differences in metabolic risk between various sociodemographic groups, health promotion interventions should be specific in respect to the targeted subpopulations.
Exploiting Semantic Role Labeling, WordNet and Wikipedia for Coreference Resolution

In this paper we present an extension of a machine learning based coreference resolution system which uses features induced from different semantic knowledge sources. These features represent knowledge mined from WordNet and Wikipedia, as well as information about semantic role labels. We show that semantic features indeed improve the performance on different referring expression types such as pronouns and common nouns.
DNA-binding specificity changes in the evolution of forkhead transcription factors

The evolution of transcriptional regulatory networks entails the expansion and diversification of transcription factor (TF) families. The forkhead family of TFs, defined by a highly conserved winged helix DNA-binding domain (DBD), has diverged into dozens of subfamilies in animals, fungi, and related protists. We have used a combination of maximum-likelihood phylogenetic inference and independent, comprehensive functional assays of DNA-binding capacity to explore the evolution of DNA-binding specificity within the forkhead family. We present converging evidence that similar alternative sequence preferences have arisen repeatedly and independently in the course of forkhead evolution. The vast majority of DNA-binding specificity changes we observed are not explained by alterations in the known DNA-contacting amino acid residues conferring specificity for canonical forkhead binding sites. Intriguingly, we have found forkhead DBDs that retain the ability to bind very specifically to two completely distinct DNA sequence motifs. We propose an alternate specificity-determining mechanism whereby conformational rearrangements of the DBD broaden the spectrum of sequence motifs that a TF can recognize. DNA-binding bispecificity suggests a previously undescribed source of modularity and flexibility in gene regulation and may play an important role in the evolution of transcriptional regulatory networks.
Utilizing Reverse Short-Channel Effect for Optimal Subthreshold Circuit Design

The impact of the reverse short-channel effect (RSCE) on device current is stronger in the subthreshold region due to reduced drain-induced barrier lowering (DIBL) and the exponential dependency of current on threshold voltage. This paper describes a device-size optimization method for subthreshold circuits utilizing RSCE to achieve high drive current, low device capacitance, less sensitivity to random dopant fluctuations, better subthreshold swing, and improved energy dissipation. Simulation results using ISCAS benchmark circuits show that the critical path delay, power consumption, and energy consumption can be improved by up to 10.4%, 34.4%, and 41.2%, respectively.
Mining with rarity: a unifying framework

Rare objects are often of great interest and great value. Until recently, however, rarity has not received much attention in the context of data mining. Now, as increasingly complex real-world problems are addressed, rarity, and the related problem of imbalanced data, are taking center stage. This article discusses the role that rare classes and rare cases play in data mining. The problems that can result from these two forms of rarity are described in detail, as are methods for addressing these problems. These descriptions utilize examples from existing research. So that this article provides a good survey of the literature on rarity in data mining. This article also demonstrates that rare classes and rare cases are very similar phenomena---both forms of rarity are shown to cause similar problems during data mining and benefit from the same remediation methods.