Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional and topological characterization of protein interaction networks

The elucidation of the cell's large‐scale organization is a primary challenge for post‐genomic biology, and understanding the structure of protein interaction networks offers an important starting point for such studies. We compare four available databases that approximate the protein interaction network of the yeast, Saccharomyces cerevisiae, aiming to uncover the network's generic large‐scale properties and the impact of the proteins' function and cellular localization on the network topology. We show how each database supports a scale‐free, topology with hierarchical modularity, indicating that these features represent a robust and generic property of the protein interactions network. We also find strong correlations between the network's structure and the functional role and subcellular localization of its protein constituents, concluding that most functional and/or localization classes appear as relatively segregated subnetworks of the full protein interaction network. The uncovered systematic differences between the four protein interaction databases reflect their relative coverage for different functional and localization classes and provide a guide for their utility in various bioinformatics studies.
A Miniaturized Millimeter-Wave Standing-Wave Filtering Switch With High P1dB

This paper presents the design considerations of a silicon-based transmit/receive (T/R) switch for microwave and millimeter-wave frequencies. Techniques for minimizing switch size and loss while increasing linearity are discussed. With the dedicated idea of the standing-wave concept, a combo design of a bandpass filter and switch, called the filtering switch, is introduced for the front-end system to achieve better performance in terms of low insertion loss, compact size, and good linearity simultaneously. Based on the proposed switchable artificial resonator, a standing-wave single-pole single-throw (SPST) and a single-pole double-throw (SPDT) filtering switches are designed and implemented for demonstration. Fabricated with a 0.18-<formula formulatype="inline"> <tex Notation="TeX">$\mu{\hbox {m}}$</tex></formula> SiGe BiCMOS process, the standing-wave SPST exhibits only 1.9-dB insertion loss and 18-dB isolation with a compact chip area of only 0.027 <formula formulatype="inline"><tex Notation="TeX">${\hbox {mm}}^{2}$</tex></formula> at 50 GHz. The SPDT T/R switch exhibits 3.2-dB insertion loss, good stopband rejection, and 20-dB isolation with only 0.0675 <formula formulatype="inline"><tex Notation="TeX">${\hbox {mm}}^{2}$</tex></formula> active chip area at 60 GHz. With the proposed standing-wave topology, a good linearity with the input 1-dB compression point (P1dB) of 21 dBm is obtained for both switches.
Coordination contracts for a kind of reverse supply chain based on retailer's delivery time guarantee

In this paper, we consider a two-echelon reverse supply chain system with one manufacturer, one retailer and a group of consumers, which offers consumers with perishable products, and consumers are allowed to return products to the retailer after purchasing. Joint decision models of delivery time and ordering quantity as well as refund was established separately in decentralized decision mode and centralized decision mode under the random market demand and delivery time. Further, we also analyze the optimal decisions under the two modes. Results show that centralized decisions not only shorten the delivery time and increase the total profit of the supply chain but increase the ordering quantity. Finally, a sales rebate contract is designed for supply chain coordination and the mechanisms are also discussed.
Foreign Direct Investment and Inequality in Productivity across Countries

Using data for 93 countries for a period from 1970 to 2000, this paper examines the effects of foreign direct investment (FDI) on cross-country differences in productivity. We construct a spatial Gini coefficient of labor productivity across countries, and weighted indices of FDI and gross domestic investment (GDI). We then examine their time series properties to explore the relations of FDI and GDI with productivity. Although we find little evidence of FDI flows – which have increased manifold in last three decades – reducing inequality in productivity for the entire sample, our analysis shows that these three variables are cointegrated for developed, high and middle income developing countries, indicating existence of a long-run equilibrium relationships between FDI, GDI and productivity. FDI seems to reduce inequality in productivity among high and middle income developing countries while it widens productivity gaps among developed countries in the long-run though these effects are statistically significant only for high income developing countries. In middle income developing countries, higher GDI seems to have significant effect in reducing productivity differences. Granger causality tests further suggest that FDI causes productivity differences among petroleum exporting countries. Furthermore, GDI granger causes FDI in high income countries and productivity differences Granger cause FDI into the middle income developing countries.
Evidence for an Additional Heat Source in the Warm Ionized Medium of Galaxies

Spatial variations of the [S II]/Hα and [N II]/Hα line intensity ratios observed in the gaseous halo of the Milky Way and other galaxies are inconsistent with pure photoionization models. They appear to require a supplemental heating mechanism that increases the electron temperature at low densities, ne. This would imply that in addition to photoionization, which has a heating rate per unit volume proportional to n, there is another source of heat with a rate per unit volume proportional to a lower power of ne. One possible mechanism is the dissipation of interstellar plasma turbulence, which, according to Minter & Spangler, heats the ionized interstellar medium in the Milky Way at a rate of ~1 × 10-25ne ergs cm-3 s-1. If such a source were present, it would dominate over photoionization heating in regions where ne ≲ 0.1 cm-3, producing the observed increases in the [S II]/Hα and [N II]/Hα intensity ratios at large distances from the galactic midplane as well as accounting for the constancy of [S II]/[N II], which is not explained by pure photoionization. Other supplemental heating sources, such as magnetic reconnection, cosmic rays, or photoelectric emission from small grains, could also account for these observations, provided they supply ~10-5 ergs s-1 per square centimeter of the Galactic disk to the warm ionized medium.
Active human herpesvirus 6 infection in patients with multiple sclerosis.

CONTEXT Human herpesvirus 6 (HHV-6) has been linked with multiple sclerosis (MS). OBJECTIVES To determine HHV-6 viral load in patients with MS, and to analyze separately its 2 variants, HHV-6A and HHV-6B. PATIENTS AND METHODS We analyzed 149 blood and serum samples; 103 were from patients with relapsing-remitting MS (33 during an MS relapse and 70 during remission), and 46 were from healthy blood donors. To determine whether the HHV-6 genome and its variants were present, we analyzed viral DNA using quantitative real-time polymerase chain reaction, which has a sensitivity of 1 copy. RESULTS We found HHV-6 DNA in the peripheral blood mononuclear cells of 53.4% of patients and 30.4% of healthy blood donors; HHV-6A was found in 20.4% of patients and 4.4% of controls, and HHV-6B was found in 33.0% vs 26.1%, respectively. Mean viral load in both groups was 7.4 copies of HHV-6 per microgram of DNA (range, 1-15 copies). Analysis of serum samples showed that none of the healthy blood donors were positive for HHV-6, although 14.6% of patients were positive for the virus, specifically the HHV-6A variant. There was no difference between patients during remission or relapse. Mean viral load was 26.3 copies/microg microgram of DNA (range, 1-86 copies). CONCLUSIONS Despite the low viral load and the lack of clinical correlation, and given the biological characteristics of the virus, our results suggest that there was active HHV-6A infection in 14.6% of patients with MS. Further quantitative real-time polymerase chain reaction studies will help us understand the clinical significance of such a low viral load.
A Recurrent Network in the Lateral Amygdala: A Mechanism for Coincidence Detection

Synaptic changes at sensory inputs to the dorsal nucleus of the lateral amygdala (LAd) play a key role in the acquisition and storage of associative fear memory. However, neither the temporal nor spatial architecture of the LAd network response to sensory signals is understood. We developed a method for the elucidation of network behavior. Using this approach, temporally patterned polysynaptic recurrent network responses were found in LAd (intra-LA), both in vitro and in vivo, in response to activation of thalamic sensory afferents. Potentiation of thalamic afferents resulted in a depression of intra-LA synaptic activity, indicating a homeostatic response to changes in synaptic strength within the LAd network. Additionally, the latencies of thalamic afferent triggered recurrent network activity within the LAd overlap with known later occurring cortical afferent latencies. Thus, this recurrent network may facilitate temporal coincidence of sensory afferents within LAd during associative learning.
Asymmetry in functional connectivity of the human habenula revealed by high‐resolution cardiac‐gated resting state imaging

The habenula is a hub for cognitive and emotional signals that are relayed to the aminergic centers in the midbrain and, thus, plays an important role in goal‐oriented behaviors. Although it is well described in rodents and non‐human primates, the habenula functional network remains relatively uncharacterized in humans, partly because of the methodological challenges associated with the functional magnetic resonance imaging of small structures in the brain. Using high‐resolution cardiac‐gated resting state imaging in healthy humans and precisely identifying each participants' habenula, we show that the habenula is functionally coupled with the insula, parahippocampus, thalamus, periaqueductal grey, pons, striatum and substantia nigra/ventral tegmental area complex. Furthermore, by separately examining and comparing the functional maps from the left and right habenula, we provide the first evidence of an asymmetry in the functional connectivity of the habenula in humans. Hum Brain Mapp 37:2602–2615, 2016. © 2016 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.
Gluon Tree Amplitudes in Open Twistor String Theory

We show how the link variables of Arkani-Hamed, Cachazo, Cheung and Kaplan (ACCK), can be used to compute general gluon tree amplitudes in the twistor string. They arise from instanton sectors labelled by d, with d=n-1, where n is the number of negative helicities. Read backwards, this shows how the various forms for the tree amplitudes studied by ACCK can be grouped into contour integrals whose structure implies the existence of an underlying string theory.
Alignment between galaxies and large-scale structure

Based on the Sloan Digital Sky Survey DR6 (SDSS) and the Millennium Simulation (MS), we investigate the alignment between galaxies and large-scale structure. For this purpose, we develop two new statistical tools, namely the alignment correlation function and the cos(2θ)-statistic. The former is a two-dimensional extension of the traditional two-point correlation function and the latter is related to the ellipticity correlation function used for cosmic shear measurements. Both are based on the cross correlation between a sample of galaxies with orientations and a reference sample which represents the large-scale structure. We apply the new statistics to the SDSS galaxy catalog. The alignment correlation function reveals an overabundance of reference galaxies along the major axes of red, luminous (L ≥ L ∗ ) galaxies out to projected separations of 60 h - 1 Mpc . The signal increases with central galaxy luminosity. No alignment signal is detected for blue galaxies. The cos(2θ) -statistic yields very similar results. Starting from a MS semi-analytic galaxy catalog, we assign an orientation to each red, luminous and central galaxy, based on that of the central region of the host halo (with size similar to that of the stellar galaxy). As an alternative, we use the orientation of the host halo itself. We find a mean projected misalignment between a halo and its central region of ∼ 25°. The misalignment decreases slightly with increasing luminosity of the central galaxy. Using the orientations and luminosities of the semi-analytic galaxies, we repeat our alignment analysis on mock surveys of the MS. Agreement with the SDSS results is good if the central orientations are used. Predictions using the halo orientations as proxies for central galaxy orientations overestimate the observed alignment by more than a factor of 2. Finally, the large volume of the MS allows us to generate a two-dimensional map of the alignment correlation function, which shows the reference galaxy distribution to be flattened parallel to the orientations of red luminous galaxies with axis ratios of ∼ 0.5 and ∼ 0.75 for halo and central orientations, respectively. These ratios are almost independent of scale out to 60 h - 1 Mpc .
Control point assessment for image registration

Presents several extensions of the basic control point assessment (CPA) algorithm. First, we compare CPA to standard corner detection algorithms and then turn to the question of selecting control points with adequate dispersion, since this is crucial for accurate registration. Two selection methods are proposed. The first consists of clustering the control points via the Lloyd algorithm (S.P. Lloyd, 1957, 1982) followed by selecting the dominant control point in each cluster. This "gold standard" approach produces excellent dispersion but is costly in terms of computational effort. The second selection method consists of subdividing the image and then selecting dominant control points in each subdivision. This is extremely fast and produces results comparable to the Lloyd selection method. The paper concludes with a discussion of how least-squares operator norm information can be coupled with anisotropic diffusion to produce smoothed images without corner degradation.
Atorvastatin, Losartan and Captopril Lead to Upregulation of TGF-β, and Downregulation of IL-6 in Coronary Artery Disease and Hypertension

Introduction Coronary artery disease (CAD) and hypertension are the main reasons of ischemic heart diseases (IHDs). Cytokines as the small glycoproteins are the main arm of immune system and manipulate all of the cardiovascular diseases. The aim of the current study was to examine the effects of treatment of hypertension and CAD on serum levels of IL-6, IL-8, TGF-β and TNF-α. Material and Methods This interventional study was performed on the patients with hypertension without CAD (group 1), hypertension and CAD (group 2), CAD but not hypertension (group 3) and without hypertension and CAD as controls (group 4). The patients received routine treatment for hypertension and CAD. Serum levels of IL-6, IL-8, TGF-β and TNF-α were analyzed in the groups treated with various drugs, using ELISA technique. Results With regard to the medications, Atorvastatin, Losartan and Captopril were administered more in patients (groups 1, 2 and 3) than the patients without hypertension and CAD. The results revealed that serum levels of TGF-β and IL-6 were significantly increased and decreased, respectively, in the groups 1, 2 and 3 when compared to group 4. Serum levels of TGF-β were also increased in females in comparison to males in the group 4. Discussion According to the results it seems that Atorvastatin, Losartan and Captopril have reduced inflammation in in vivo conditions via downregulation of IL-6 and upregulation of TGF-β.
An Existential–Humanistic Perspective on Black Lives Matter and Contemporary Protest Movements

Contemporary protests movements, which are distinguished from historic movements by relying on decentralized leadership and utilizing social media and technology, have a central role in addressing social justice issues. Black Lives Matter represents one of the most influential and controversial of the contemporary protests movements. Much of the controversy is connected to misunderstanding, distorted portrayals, and attempts to discredit the movement. Through an examination of the history of Black Lives Matter, and consideration of issues such as privilege and polarization, it can be recognized that the Black Lives Matter movement is providing a healthy cultural critique and creative use of pain, anger, and suffering to advocate for human dignity and positive cultural change. Furthermore, the principles of existential–humanistic psychology can be used to deepen the understanding of Black Lives Matter and other protest movements, while also offering important guidance on how to avoid various potential risks to the movement’s success.
PolyUbiquitin Chain Linkage Topology Selects the Functions from the Underlying Binding Landscape

Ubiquitin (Ub) can generate versatile molecular signals and lead to different celluar fates. The functional poly-valence of Ub is believed to be resulted from its ability to form distinct polymerized chains with eight linkage types. To provide a full picture of ubiquitin code, we explore the binding landscape of two free Ub monomers and also the functional landscapes of of all eight linkage types by theoretical modeling. Remarkably, we found that most of the compact structures of covalently connected dimeric Ub chains (diUbs) pre-exist on the binding landscape. These compact functional states were subsequently validated by corresponding linkage models. This leads to the proposal that the folding architecture of Ub monomer has encoded all functional states into its binding landscape, which is further selected by different topologies of polymeric Ub chains. Moreover, our results revealed that covalent linkage leads to symmetry breaking of interfacial interactions. We further propose that topological constraint not only limits the conformational space for effective switching between functional states, but also selects the local interactions for realizing the corresponding biological function. Therefore, the topological constraint provides a way for breaking the binding symmetry and reaching the functional specificity. The simulation results also provide several predictions that qualitatively and quantitatively consistent with experiments. Importantly, the K48 linkage model successfully predicted intermediate states. The resulting multi-state energy landscape was further employed to reconcile the seemingly contradictory experimental data on the conformational equilibrium of K48-diUb. Our results further suggest that hydrophobic interactions are dominant in the functional landscapes of K6-, K11-, K33- and K48 diUbs, while electrostatic interactions play a more important role in the functional landscapes of K27, K29, K63 and linear linkages.
Changes of CREB in rat hippocampus, prefrontal cortex and nucleus accumbens during three phases of morphine induced conditioned place preference in rats

Objective: To investigate the changes in CREB (cAMP response element binding protein) in hippocampus, PFC (prefrontal cortex) and NAc (nucleus accumbens) during three phases of morphine induced CPP (conditioned place preference) in rats, and to eluci date the role of CREB during the progress of conditioned place preference. Methods: Morphine induced CPP acquisition, extinction and drug primed reinstatement model was established, and CREB expression in each brain area was measured by Western Blot methods. Results: Eight alternating injections of morphine (10 mg/kg) induced CPP, and 8 d saline extinction training that extinguished CPP. CPP was reinstated following a priming injection of morphine (2.5 mg/kg). During the phases of CPP acquisition and reinstatement, the level of CREB expression was significantly changed in different brain areas. Conclusion: It was proved that CPP model can be used as an effective tool to investigate the mechanisms underlying drug-induced reinstatement of drug seeking after extinction, and that morphine induced CPP and drug primed reinstatement may involve activation of the transcription factor CREB in several brain areas, suggesting that the CREB and its target gene regulation pathway may mediate the basic mechanism underlying opioid dependence and its drug seeking behavior.
Does the Temporal Stability of Behavioral Intentions Moderate Intention-Behavior and Past Behavior-Future Behavior Relations?

This study tested the hypothesis that the temporal stability of behavioral intentions moderates relationships between intentions and behavior and between previous experience and subsequent performance. Respondents (N = 164) completed measures of theory of planned behavior variables, with respect to studying over the winter vacation, at two time points prior to the vacation and subsequently reported their study behavior. Intention stability was computed from within-participants correlations between Time 1 and Time 2 intention items. Intention stability moderated the intention-behavior relation such that stable intentions were more likely to be enacted than unstable intentions. The past behavior-future behavior relation was also moderated by intention stability. When intentions were stable, past behavior was not related to subsequent performance. In contrast, when intentions were unstable, past behavior was the best predictor of future behavior. Findings also revealed that theory of planned behavior variables and past behavior had different associations with stable as compared to unstable intentions.
Feature analysis in early vision: evidence from search asymmetries.

In this article we review some new evidence relating to early visual processing and propose an explanatory framework. A series of search experiments tested detection of targets distinguished from the distractors by differences on a single dimension. Our aim was to use the pattern of search latencies to infer which features are coded automatically in early vision. For each of 12 different dimensions, one or more pairs of contrasting stimuli were tested. Each member of a pair played the role of target in one condition and the role of distractor in the other condition. Many pairs gave rise to a marked asymmetry in search latencies, such that one stimulus in the pair was detected either through parallel processing or with small increases in latency as display size increased, whereas the other gave search functions that increased much more steeply. Targets denned by larger values on the quantitative dimensions of length, number, and contrast, by line curvature, by misaligned orientation, and by values that deviated from a standard or prototypical color or shape were detected easily, whereas targets defined by smaller values on the quantitative dimensions, by straightness, by frame-aligned orientation, and by prototypical colors or shapes required slow and apparently serial search. These values appear to be coded by default, as the absence of the contrasting values. We found no feature of line arrangements that allowed automatic, preattentive detection; nor did connectedness or con-tainment—the two examples of topological features that we tested. We interpret the results as evidence that focused attention to single items or to groups is required to reduce background activity when the Weber fraction distinguishing the pooled feature activity with displays containing a target and with displays containing only distractors is too small to allow reliable discrimination.