Miracle-dz/UniFAR-FTUs huggingface dataset:
The interplay between dynamics and networks: centrality, communities, and cheeger inequality

We study the interplay between a dynamic process and the structure of the network on which it is defined. Specifically, we examine the impact of this interaction on the quality-measure of network clusters and node centrality. This enables us to effectively identify network communities and important nodes participating in the dynamics. As the first step towards this objective, we introduce an umbrella framework for defining and characterizing an ensemble of dynamic processes on a network. This framework generalizes the traditional Laplacian framework to continuous-time biased random walks and also allows us to model some epidemic processes over a network. For each dynamic process in our framework, we can define a function that measures the quality of every subset of nodes as a potential cluster (or community) with respect to this process on a given network. This subset-quality function generalizes the traditional conductance measure for graph partitioning. We partially justify our choice of the quality function by showing that the classic Cheeger's inequality, which relates the conductance of the best cluster in a network with a spectral quantity of its Laplacian matrix, can be extended from the Laplacian-conductance setting to this more general setting.
Strategy shifts in leaf physiology, structure and nutrient content between species of high‐ and low‐rainfall and high‐ and low‐nutrient habitats

Summary 1. Relationships were examined among photosynthetic capacity ( A mass and A area ), foliar dark respiration rate ( R d-mass and R d-area ), stomatal conductance to water ( G s ), specific leaf area (SLA), and leaf nitrogen (N) and phosphorus (P) across 79 perennial species occurring at four sites with contrasting rainfall levels and soil nutrients in eastern Australia. We hypothesized that the slope of log‐log ‘scaling’ relationships between these traits would be positive and would not differ between sites, although slope elevations might shift between habitat types. 2. A mass , R d-mass , SLA, N mass and P mass were positively associated in common slopes fitted across sites or rainfall zones, although rather weakly within individual sites in some cases. The relationships between A mass (and R d-mass ) with each of N mass and SLA were partially independent of each other, with A mass (or R d-mass ) increasing with SLA at a given N mass , or with N mass at a given SLA (only weakly in the case of A mass ). These results improve the quantification and extend the generalization of reported patterns to floras largely unlike those studied previously, with the additional contribution of including phosphorus data. 3. Species from drier sites differed in several important respects. They had (i) higher leaf N and P (per dry mass or area); (ii) lower photosynthetic capacity at a given leaf N or P; (iii) higher R d-mass at a given SLA or A mass ; and (iv) lower G s at a given A area (implying lower internal CO 2 concentration). 4. These trends can be interpreted as part of a previously undocumented water conservation strategy in species from dry habitats. By investing heavily in photosynthetic enzymes, a larger drawdown of internal CO 2 concentration is achieved, and a given photosynthetic rate is possible at a lower stomatal conductance. Transpirational water use is similar, however, due to the lower-humidity air in dry sites. The benefit of the strategy is that dry-site species reduce water loss at a given A area , down to levels similar to wet-site species, despite occurring in lower-humidity environments. The cost of high leaf N is reflected in higher dark respiration rates and, presumably, additional costs incurred by N acquisition and increased herbivory risk.
The Cost of Global Broadcast in Dynamic Radio Networks

We study the single-message broadcast problem in dynamic radio networks. We show that the time complexity of the problem depends on the amount of stability and connectivity of the dynamic network topology and on the adaptiveness of the adversary providing the dynamic topology. More formally, we model communication using the standard graph-based radio network model. To model the dynamic network, we use a generalization of the synchronous dynamic graph model introduced in [Kuhn et al., STOC 2010]. For integer parameters $T\geq 1$ and $k\geq 1$, we call a dynamic graph $T$-interval $k$-connected if for every interval of $T$ consecutive rounds, there exists a $k$-vertex-connected stable subgraph. Further, for an integer parameter $\tau\geq 0$, we say that the adversary providing the dynamic network is $\tau$-oblivious if for constructing the graph of some round $t$, the adversary has access to all the randomness (and states) of the algorithm up to round $t-\tau$. As our main result, we show that for any $T\geq 1$, any $k\geq 1$, and any $\tau\geq 1$, for a $\tau$-oblivious adversary, there is a distributed algorithm to broadcast a single message in time $O\big(\big(1+\frac{n}{k\cdot\min\left\{\tau,T\right\}}\big)\cdot n\log^3 n\big)$. We further show that even for large interval $k$-connectivity, efficient broadcast is not possible for the usual adaptive adversaries. For a $1$-oblivious adversary, we show that even for any $T\leq (n/k)^{1-\varepsilon}$ (for any constant $\varepsilon>0$) and for any $k\geq 1$, global broadcast in $T$-interval $k$-connected networks requires at least $\Omega(n^2/(k^2\log n))$ time. Further, for a $0$ oblivious adversary, broadcast cannot be solved in $T$-interval $k$-connected networks as long as $T
Immunological identification of a 50 kDa Mr FK506-binding immunophilin as a component of the non-DNA binding, hsp90 and hsp70 containing, heterooligomeric form of the chick oviduct progesterone receptor.

p59/HBI, a Heat shock protein (hsp90)-Binding-Immunophilin of approximately 59 kDa, was originally detected in the heterooligomeric, non-DNA binding form of numerous mammalian steroid hormone receptors. P59/HBI belongs to the FKBP family since it binds the immunosuppressants FK506 and Rapamycin. Using immobilized FK506, we purified [3H]Org 2058-progesterone receptor (PR)-hsp90-complexes from chick oviduct cytosol in a species migrating at 9S in density gradient. This led to suppose that a protein present in these complexes is a FK506 binding protein. Following incubation of this FK506-affinity purified 9S-PR with BF4, a specific anti-chick hsp90 monoclonal antibody, a shift of the [3H]Org 2058-PR complexes from 9S to 11S has been observed, indicating the presence of hsp90, hsp70 also is included in the 9S-PR complexes as demonstrated by Western blotting and density gradient experiments. Two lines of evidence support the notion that an immunophilin of 50 kDa also associates to heterooligomeric 9S-PR complexes. Firstly, a shift at 11S of the FK506 eluted 9S-PR occurs in sucrose gradient after incubation with 419, a new polyclonal antibody raised against a peptide corresponding to the Hinge I region [Callebaut I. , Renoir J. M. , Lebeau M. C. , Massol N. , Burny A. , Baulieu E. E. , Mornon J. P. (1992) Proc. Natl. Acad. Sci. USA 89, 6270-6274] of the rabbit p59/HBI (amino acids Phe135 to Gly149). Secondly, in Western blotting experiments, both 419 and another anti-FKBP antibody, raised against purified Streptomyces Crysomallus FKBP12 [Pahl A. and Keller U. (1992) J. Bacteriol. , 3, 325-333], allow detection of the same 50 kDa protein in the affinity purified PR. (ABSTRACT TRUNCATED AT 250 WORDS)
Personality Disorders and the Trimensional Personality Questionnaire Factors in Major Depressive Disorder

We assessed the potential relationship between personality disorder (PD) clusters, as assessed by the SCID-II, and temperamental traits assessed by the Tridimensional Personality Questionnaire (TPQ) among a well-characterized, unmedicated cohort of outpatients with major depressive disorder (MDD). The TPQ and SCID-II were administered to 263 depressed outpatients (mean age= 39.9 ± 10.5 years; women = 139, 53%; initial 17-item Hamilton Rating Scale for Depression = 19.6 ± 3.4) who currently met criteria for MDD and who were enrolled in an 8-week treatment trial. The multiple linear regression method was used to evaluate the relationship between TPQ factors and personality disorder clusters, controlling for age, gender, and initial 17-item Hamilton Rating Scale for Depression score as necessary. Among outpatients with MDD, meeting criteria for a Cluster A PD diagnosis was related to high harm avoidance (HA) scores, as well as low reward dependence and novelty seeking (NS) scores. Additionally, high HA scores were associated with meeting criteria for a Cluster C PD diagnosis, while high NS scores were associated with meeting criteria for a Cluster B PD diagnosis. Certain temperament traits, especially HA and NS, appear to be associated with specific patterns of personality clusters among depressed patients.
Ligand Binding and Structural Properties of Segments of GABAA Receptor α1 Subunit Overexpressed inEscherichia coli *

The γ-aminobutyric acid, type A (GABAA), receptor is the target for numerous therapeutic compounds. In the present study, the Gln28–Leu296, Gln28–Arg276, Gln28–Arg248, and Gln28–Glu165 (numbering of bovine precursor protein) segments of its α1 subunit were overexpressed inEscherichia coli, along with Cys166–Leu296 produced previously, for structural analysis by circular dichroism and ligand binding studies by fluorescence spectroscopy. Results showed that the protein segments were rich in β-sheet structures. Binding of the fluorescent benzodiazepine Bodipy-FL Ro-1986 was evident from fluorescence resonance energy transfer and fluorescence anisotropy measurements. The binding affinity was in the micromolar range. The binding was attributable more to Cys166–Leu296 than to Gln28–Glu165 and was inhibited by known central benzodiazepine site ligands. Three point mutations, Y187A, T234A, and Y237A, were found to perturb protein secondary structures. Studies with the single Trp mutants W198Y and W273Y indicated that Trp273 was closer to the binding site than Trp198.
Incorporating the soil environment and microbial community into plant competition theory

Plants affect microbial communities and abiotic properties of nearby soils, which in turn influence plant growth and interspecific interaction, forming a plant-soil feedback (PSF). PSF is a key determinant influencing plant population dynamics, community structure, and ecosystem functions. Despite accumulating evidence for the importance of PSF and development of specific PSF models, different models are not yet fully integrated. Here, we review the theoretical progress in understanding PSF. When first proposed, PSF was integrated with various mathematical frameworks to discuss its influence on plant competition. Recent theoretical models have advanced PSF research at different levels of ecological organizations by considering multiple species, applying spatially explicit simulations to examine how local-scale predictions apply to larger scales, and assessing the effect of PSF on plant temporal dynamics over the course of succession. We then review two foundational models for microbial- and litter-mediated PSF. We present a theoretical framework to illustrate that although the two models are typically presented separately, their behavior can be understood together by invasibility analysis. We conclude with suggestions for future directions in PSF theoretical studies, which include specifically addressing microbial diversity to integrate litter- and microbial-mediated PSF, and apply PSF to general coexistence theory through a trait-based approach.
Quantitative functional imaging of the brain: towards mapping neuronal activity by BOLD fMRI

Quantitative magnetic resonance imaging (MRI) and spectroscopy (MRS) measurements of energy metabolism (i.e. cerebral metabolic rate of oxygen consumption, CMRO2), blood circulation (i.e. cerebral blood flow, CBF, and volume, CBV), and functional MRI (fMRI) signal over a wide range of neuronal activity and pharmacological treatments are used to interpret the neurophysiologic basis of blood oxygenation level dependent (BOLD) image‐contrast at 7 T in glutamatergic neurons of rat cerebral cortex. Multi‐modal MRI and MRS measurements of CMRO2, CBF, CBV and BOLD signal (both gradient‐echo and spin‐echo) are used to interpret the neuroenergetic basis of BOLD image‐contrast. Since each parameter that can influence the BOLD image‐contrast is measured quantitatively and separately, multi‐modal measurements of changes in CMRO2, CBF, CBV, BOLD fMRI signal allow calibration and validation of the BOLD image‐contrast. Good agreement between changes in CMRO2 calculated from BOLD theory and measured by 13C MRS, reveals that BOLD fMRI signal‐changes at 7 T are closely linked with alterations in neuronal glucose oxidation, both for activation and deactivation paradigms. To determine the neurochemical basis of BOLD, pharmacological treatment with lamotrigine, which is a neuronal voltage‐dependent Na+ channel blocker and neurotransmitter glutamate release inhibitor, is used in a rat forepaw stimulation model. Attenuation of the functional changes in CBF and BOLD with lamotrigine reveals that the fMRI signal is associated with release of glutamate from neurons, which is consistent with a link between neurotransmitter cycling and energy metabolism. Comparisons of CMRO2 and CBF over a wide dynamic range of neuronal activity provide insight into the regulation of energy metabolism and oxygen delivery in the cerebral cortex. The current results reveal the energetic and physiologic components of the BOLD fMRI signal and indicate the required steps towards mapping neuronal activity quantitatively by fMRI at steady‐state. Consequences of these results from rat brain for similar calibrated BOLD fMRI studies in the human brain are discussed. Copyright © 2001 John Wiley & Sons, Ltd.
Correlation between response to cisplatinum‐combination chemotherapy and subsequent radiotherapy in previously untreated patients with advanced squamous cell cancers of the head and neck

Induction chemotherapy, followed by surgery and/or radiotherapy was utilized in patients with advanced squamous cell carcinoma of the head and neck. During these trials, the authors observed that response to chemotherapy predicts further response to subsequent radiotherapy. This study was comprised of 57 patients with 60 separate neoplasms who demonstrated less than complete response (partial or no response) to initial treatment with a combination chemotherapy containing cisplatin. Subsequently radiotherapy, either 5000 rad preoperatively or 6600 rad as definitive therapy, was employed. Forty‐one of the 42 tumors with initial partial response to chemotherapy also responded to radiotherapy (97.6%). Only one of the 18 tumors that initially failed to respond to chemotherapy subsequently responded to radiotherapy (5.5%). This observation suggests that patients with head and neck cancer sensitive to initial chemotherapy share parameters that are also radiation sensitive.
The Costs and Benefits of Extending the Role of the Acute Pain Service on Clinical Outcomes After Major Elective Surgery

BACKGROUND:Acute pain services have received widespread acceptance and formal support from institutions and organizations, but available evidence on their costs and benefits is scarce. Although there is good agreement on the provision of acute pain services after many major surgical procedures, there are other procedures for which the benefits are unclear. Data are required to justify any expansion of acute pain services. In this randomized, controlled clinical trial we compared the costs and effects of acute pain service care on clinical outcomes with conventional pain management on the ward. Patients included in the trial were considered by their anesthesiologist to have either arm be suitable for the procedure. METHODS:Four hundred twenty-three patients undergoing major elective surgery were randomized either to an anesthesiologist-led, nurse-based acute pain service group with patient-controlled analgesia or to a control group with IM or IV boluses of opioid analgesia. Both groups were treated with medications to treat opioid-related adverse effects and received the usual care from health professionals assigned to the ward. The main outcome measures were quality of recovery scores, pain intensity measures, global measure of treatment effectiveness, and overall pain treatment cost. Cost-effectiveness acceptability curves were drawn to detect a difference in the joint cost-effect relationship between groups. RESULTS:There was no difference in quality of recovery score on postoperative day 1 between treatment and control groups (mean difference, 0; 95% confidence interval [CI], −0.7 to 0.7; P = 0.94) or in the rate of improvement in quality of recovery score (mean difference, −0.1; 95% CI, −0.4 to 0.1; P = 0.34). The proportion of patients with 1 or more days of highly effective pain management was higher in the acute pain service group than in the control group (86% vs. 75%; P < 0.01). Costs were higher in the acute pain service group (mean difference, US$46; 95% CI, $44 to $48 per patient; P < 0.001). A cost-effectiveness acceptability curve showed that the acute pain service was more cost effective than was control for providing highly effective pain management if the decision maker was willing to pay more than US$546 per patient per 1 day with highly effective treatment. CONCLUSION:In extending the role of the acute pain service to a specific group of major surgical procedures, the acute pain service was likely to be cost effective.
Next-generation sequencing reveals the biological significance of the N2,3-ethenoguanine lesion in vivo

Etheno DNA adducts are a prevalent type of DNA damage caused by vinyl chloride (VC) exposure and oxidative stress. Etheno adducts are mutagenic and may contribute to the initiation of several pathologies; thus, elucidating the pathways by which they induce cellular transformation is critical. Although N2,3-ethenoguanine (N2,3-εG) is the most abundant etheno adduct, its biological consequences have not been well characterized in cells due to its labile glycosidic bond. Here, a stabilized 2′-fluoro-2′-deoxyribose analog of N2,3-εG was used to quantify directly its genotoxicity and mutagenicity. A multiplex method involving next-generation sequencing enabled a large-scale in vivo analysis, in which both N2,3-εG and its isomer 1,N2-ethenoguanine (1,N2-εG) were evaluated in various repair and replication backgrounds. We found that N2,3-εG potently induces G to A transitions, the same mutation previously observed in VC-associated tumors. By contrast, 1,N2-εG induces various substitutions and frameshifts. We also found that N2,3-εG is the only etheno lesion that cannot be repaired by AlkB, which partially explains its persistence. Both εG lesions are strong replication blocks and DinB, a translesion polymerase, facilitates the mutagenic bypass of both lesions. Collectively, our results indicate that N2,3-εG is a biologically important lesion and may have a functional role in VC-induced or inflammation-driven carcinogenesis.
Hemodynamic, Morphometric and Autonomic Patterns in Hypertensive Rats - Renin-Angiotensin System Modulation

BACKGROUND: Spontaneously hypertensive rats develop left ventricular hypertrophy, increased blood pressure and blood pressure variability, which are important determinants of heart damage, like the activation of renin-angiotensin system. AIMS: To investigate the effects of the time-course of hypertension over 1) hemodynamic and autonomic patterns (blood pressure; blood pressure variability; heart rate); 2) left ventricular hypertrophy; and 3) local and systemic Renin-angiotensin system of the spontaneously hypertensive rats. METHODS: Male spontaneously hypertensive rats were randomized into two groups: young (n=13) and adult (n=12). Hemodynamic signals (blood pressure, heart rate), blood pressure variability (BPV) and spectral analysis of the autonomic components of blood pressure were analyzed. LEFT ventricular hypertrophy was measured by the ratio of LV mass to body weight (mg/g), by myocyte diameter (μm) and by relative fibrosis area (RFA, %). ACE and ACE2 activities were measured by fluorometry (UF/min), and plasma renin activity (PRA) was assessed by a radioimmunoassay (ng/mL/h). Cardiac gene expressions of Agt, Ace and Ace2 were quantified by RT-PCR (AU). RESULTS: The time-course of hypertension in spontaneously hypertensive rats increased BPV and reduced the alpha index in adult spontaneously hypertensive rats. Adult rats showed increases in left ventricular hypertrophy and in RFA. Compared to young spontaneously hypertensive rats, adult spontaneously hypertensive rats had lower cardiac ACE and ACE2 activities, and high levels of PRA. No change was observed in gene expression of Renin-angiotensin system components. CONCLUSIONS: The observed autonomic dysfunction and modulation of Renin-angiotensin system activity are contributing factors to end-organ damage in hypertension and could be interacting. Our findings suggest that the management of hypertensive disease must start before blood pressure reaches the highest stable levels and the consequent established end-organ damage is reached.
Fungal Elicitor MoHrip2 Induces Disease Resistance in Rice Leaves, Triggering Stress-Related Pathways

MoHrip2 Magnaporthe oryzae hypersensitive protein 2 is an elicitor protein of rice blast fungus M. oryzae. Rice seedlings treated with MoHrip2 have shown an induced resistance to rice blast. To elucidate the mechanism underlying this MoHrip2 elicitation in rice, we used differential-display 2-D gel electrophoresis and qRT-PCR to assess the differential expression among the total proteins extracted from rice leaves at 24 h after treatment with MoHrip2 and buffer as a control. Among ~1000 protein spots detected on each gel, 10 proteins were newly induced, 4 were up-regulated, and 3 were down-regulated in MoHrip2-treated samples compared with the buffer control. Seventeen differentially expressed proteins were detected using MS/MS analysis and categorized into six groups according to their putative function: defense-related transcriptional factors, signal transduction-related proteins, reactive oxygen species (ROS) production, programmed cell death (PCD), defense-related proteins, and photosynthesis and energy-related proteins. The qPCR results (relative expression level of genes) further supported the differential expression of proteins in MoHrip2-treated rice leaves identified with 2D-gel, suggesting that MoHrip2 triggers an early defense response in rice leaves via stress-related pathways, and the results provide evidence for elicitor-induced resistance at the protein level.
The prevalence, characteristics and well-being of 'necessity' self-employed and 'latent' entrepreneurs : findings from Sweden

Self-employment is often discussed in terms of 'push' and 'pull' factors. The aim of this article is to assess not only the prevalence of 'necessity' self-employed and 'latent' entrepreneurs in Sweden, but also the characteristics in terms of socio-demography, personality traits, intrinsic work motivation and preference for independence associated with each group. In addition, the article investigates whether 'necessity' self-employment and 'latent' entrepreneurship are related to four measures of well-being. This is done using a nationally representative survey of the self-employed (small-business owners, n = 2,483) and regularly employed (n = 2,642) in Sweden. The main findings indicate that 'necessity' self-employed have characteristics and preferences that differ from other (non-'necessity') self-employed. They display relatively low intrinsic work motivation and preference for independence as well as scores on personality traits typically associated with entrepreneurship. They also report lower levels of work autonomy, job-satisfaction, life satisfaction and family-life satisfaction than other self-employed. 'Latent' entrepreneurs resemble entrepreneurs in many ways but they nevertheless report lower levels of well-being than non-'necessity' self-employed.