What can ecosystems learn? Expanding evolutionary ecology with learning theory

Background: The structure and organisation of ecological interactions within an ecosystem is modified by the evolution and coevolution of the individual species it contains. Understanding how historical conditions have shaped this architecture is vital for understanding system responses to change at scales from the microbial upwards. However, in the absence of a group selection process, the collective behaviours and ecosystem functions exhibited by the whole community cannot be organised or adapted in a Darwinian sense. A long-standing open question thus persists: Are there alternative organising principles that enable us to understand and predict how the coevolution of the component species creates and maintains complex collective behaviours exhibited by the ecosystem as a whole?Results: Here we answer this question by incorporating principles from connectionist learning, a previously unrelated discipline already using well-developed theories on how emergent behaviours arise in simple networks. Specifically, we show conditions where natural selection on ecological interactions is functionally equivalent to a simple type of connectionist learning, ‘unsupervised learning’, well-known in neural-network models of cognitive systems to produce many non-trivial collective behaviours. Accordingly, we find that a community can self-organise in a well-defined and non-trivial sense without selection at the community level; its organisation can be conditioned by past experience in the same sense as connectionist learning models habituate to stimuli. This conditioning drives the community to form a distributed ecological memory of multiple past states, causing the community to: a) converge to these states from any random initial composition; b) accurately restore historical compositions from small fragments; c) recover a state composition following disturbance; and d) to correctly classify ambiguous initial compositions according to their similarity to learned compositions. We examine how the formation of alternative stable states alters the community’s response to changing environmental forcing, and we identify conditions under which the ecosystem exhibits hysteresis with potential for catastrophic regime shifts.Conclusions: This work highlights the potential of connectionist theory to expand our understanding of evo-eco dynamics and collective ecological behaviours. Within this framework we find that, despite not being a Darwinian unit, ecological communities can behave like connectionist learning systems, creating internal conditions that habituate to past environmental conditions and actively recalling those conditions.Theoretical ecology, Communityassembly, Network structures, Ecological memory, Associative learning, Regime shifts, Community matrix*Correspondence

The Grizzly, October 16, 1987

Campus Crackdown Affects All • Police to Halt Under-Age Drinking • Rafuse Paint Crew: Loud, Leering and Surly? • Students Study Abroad • Musser Returns to Dark Ages • Letter: Grizzly Errs • G.E. Attends U.C. Luncheon • The International Job Scene • Commuter Communication Gap • Bears Hope for Winning Season • Soccer Sinks Washington • Athlete of the Week: Walder Forwards Record • Meet the 1987 Homecoming Queen Candidates • Football to Face Gettysburg • Hockey Halted by West Chester • Myrin Catalog System On Line • Busie Body Needs a Bodyhttps://digitalcommons.ursinus.edu/grizzlynews/1196/thumbnail.jp

Exotic foods reveal contact between South Asia and the Near East during the second millennium BCE

Aunque el papel clave del comercio a larga distancia en la transformación de las cocinas en todo el mundo está bien documentado desde al menos la época romana, la prehistoria del comercio de alimentos euroasiático es menos visible. Con el fin de arrojar luz sobre la transformación de las cocinas del Mediterráneo oriental durante la Edad del Bronce y la Edad del Hierro Temprana, analizamos los microrestos y las proteínas conservadas en el cálculo dental de individuos que vivieron durante el segundo milenio a. Nuestros resultados proporcionan evidencia clara del consumo de alimentos básicos esperados, como cereales (Triticeae), sésamo ( Sesamum ) y dátiles ( Phoenix ). Además, informamos evidencia del consumo de soja ( glicina ), probable banano ( Musa ) y cúrcuma (Curcuma ), que hace retroceder la evidencia más antigua de estos alimentos en el Mediterráneo por siglos (cúrcuma) o incluso milenios (soja). Descubrimos que, desde principios del segundo milenio en adelante, al menos algunas personas en el Mediterráneo oriental tuvieron acceso a alimentos de lugares distantes, incluido el sur de Asia, y esos productos probablemente se consumieron en forma de aceites, frutos secos y especias. Estos conocimientos nos obligan a repensar la complejidad y la intensidad del comercio indo-mediterráneo durante la Edad del Bronce, así como el grado de globalización en la cocina del Mediterráneo oriental temprano. Although the key role of long-distance trade in the transformation of cuisines worldwide has been well-documented since at least the Roman era, the prehistory of the Eurasian food trade is less visible. In order to shed light on the transformation of Eastern Mediterranean cuisines during the Bronze Age and Early Iron Age, we analyzed microremains and proteins preserved in the dental calculus of individuals who lived during the second millennium BCE in the Southern Levant. Our results provide clear evidence for the consumption of expected staple foods, such as cereals (Triticeae), sesame (Sesamum), and dates (Phoenix). We additionally report evidence for the consumption of soybean (Glycine), probable banana (Musa), and turmeric (Curcuma), which pushes back the earliest evidence of these foods in the Mediterranean by centuries (turmeric) or even millennia (soybean). We find that, from the early second millennium onwards, at least some people in the Eastern Mediterranean had access to food from distant locations, including South Asia, and such goods were likely consumed as oils, dried fruits, and spices. These insights force us to rethink the complexity and intensity of Indo-Mediterranean trade during the Bronze Age as well as the degree of globalization in early Eastern Mediterranean cuisine

Factors in AIDS Dementia Complex Trial Design: Results and Lessons from the Abacavir Trial

OBJECTIVES: To determine the efficacy of adding abacavir (Ziagen, ABC) to optimal stable background antiretroviral therapy (SBG) to AIDS dementia complex (ADC) patients and address trial design. DESIGN: Phase III randomized, double-blind placebo-controlled trial. SETTING: Tertiary outpatient clinics. PARTICIPANTS: ADC patients on SBG for ≥8 wk. INTERVENTIONS: Participants were randomized to ABC or matched placebo for 12 wk. OUTCOME MEASURES: The primary outcome measure was the change in the summary neuropsychological Z score (NPZ). Secondary measures were HIV RNA and the immune activation markers β-2 microglobulin, soluble tumor necrosis factor (TNF) receptor 2, and quinolinic acid. RESULTS: 105 participants were enrolled. The median change in NPZ at week 12 was +0.76 for the ABC + SBG and +0.63 for the SBG groups (p = 0.735). The lack of efficacy was unlikely related to possible limited antiviral efficacy of ABC: at week 12 more ABC than placebo participants had plasma HIV RNA ≤400 copies/mL (p = 0.002). There were, however, other factors. Two thirds of patients were subsequently found to have had baseline resistance to ABC. Second, there was an unanticipated beneficial effect of SBG that extended beyond 8 wk to 5 mo, thereby rendering some of the patients at baseline unstable. Third, there was an unexpectedly large variability in neuropsychological performance that underpowered the study. Fourth, there was a relative lack of activity of ADC: 56% of all patients had baseline cerebrospinal fluid (CSF) HIV-1 RNA <100 copies/mL and 83% had CSF β-2 microglobulin <3 nmol/L at baseline. CONCLUSIONS: The addition of ABC to SBG for ADC patients was not efficacious, possibly because of the inefficacy of ABC per se, baseline drug resistance, prolonged benefit from existing therapy, difficulties with sample size calculations, and lack of disease activity. Assessment of these trial design factors is critical in the design of future ADC trials

Inhibition of dipeptidyl peptidase IV and xanthine oxidase by amino acids and dipeptides

peer-reviewedXanthine oxidase (XO) and dipeptidyl peptidase IV (DPP-IV) inhibition by amino acids and dipeptides was studied. Trp and Trp-containing dipeptides (Arg-Trp, Trp-Val, Val-Trp, Lys-Trp and Ile-Trp) inhibited XO. Three amino acids (Met, Leu and Trp) and eight dipeptides (Phe-Leu, Trp-Val, His-Leu, Glu-Lys, Ala-Leu, Val-Ala, Ser-Leu and Gly-Leu) inhibited DPP-IV. Trp and Trp-Val were multifunctional inhibitors of XO and DPP-IV. Lineweaver and Burk analysis showed that Trp was a non-competitive inhibitor of XO and a competitive inhibitor of DPP-IV. Molecular docking with Autodock Vina was used to better understand the interaction of the peptides with the active site of the enzyme. Because of the non-competitive inhibition observed, docking of Trp-Val to the secondary binding sites of XO and DPP-IV is required. Trp-Val was predicted to be intestinally neutral (between 25% and 75% peptide remaining after 60 min simulated intestinal digestion). These results are of significance for the reduction of reactive oxygen species (ROS) and the increase of the half-life of incretins by food-derived peptides. (C) 2013 Elsevier Ltd. All rights reserved.ACCEPTEDpeer-reviewe

ASCR/HEP Exascale Requirements Review Report

This draft report summarizes and details the findings, results, and recommendations derived from the ASCR/HEP Exascale Requirements Review meeting held in June, 2015. The main conclusions are as follows. 1) Larger, more capable computing and data facilities are needed to support HEP science goals in all three frontiers: Energy, Intensity, and Cosmic. The expected scale of the demand at the 2025 timescale is at least two orders of magnitude -- and in some cases greater -- than that available currently. 2) The growth rate of data produced by simulations is overwhelming the current ability, of both facilities and researchers, to store and analyze it. Additional resources and new techniques for data analysis are urgently needed. 3) Data rates and volumes from HEP experimental facilities are also straining the ability to store and analyze large and complex data volumes. Appropriately configured leadership-class facilities can play a transformational role in enabling scientific discovery from these datasets. 4) A close integration of HPC simulation and data analysis will aid greatly in interpreting results from HEP experiments. Such an integration will minimize data movement and facilitate interdependent workflows. 5) Long-range planning between HEP and ASCR will be required to meet HEP's research needs. To best use ASCR HPC resources the experimental HEP program needs a) an established long-term plan for access to ASCR computational and data resources, b) an ability to map workflows onto HPC resources, c) the ability for ASCR facilities to accommodate workflows run by collaborations that can have thousands of individual members, d) to transition codes to the next-generation HPC platforms that will be available at ASCR facilities, e) to build up and train a workforce capable of developing and using simulations and analysis to support HEP scientific research on next-generation systems.Comment: 77 pages, 13 Figures; draft report, subject to further revisio

Impact of baryon physics on dark matter structures: a detailed simulation study of halo density profiles

The back-reaction of baryons on the dark matter halo density profile is of great interest, not least because it is an important systematic uncertainty when attempting to detect the dark matter. Here, we draw on a large suite of high resolution cosmological hydrodynamical simulations, to systematically investigate this process and its dependence on the baryonic physics associated with galaxy formation. The inclusion of baryons results in significantly more concentrated density profiles if radiative cooling is efficient and feedback is weak. The dark matter halo concentration can in that case increase by as much as 30 (10) per cent on galaxy (cluster) scales. The most significant effects occur in galaxies at high redshift, where there is a strong anti-correlation between the baryon fraction in the halo centre and the inner slope of both the total and the dark matter density profiles. If feedback is weak, isothermal inner profiles form, in agreement with observations of massive, early-type galaxies. However, we find that AGN feedback, or extremely efficient feedback from massive stars, is necessary to match observed stellar fractions in groups and clusters, as well as to keep the maximum circular velocity similar to the virial velocity as observed for disk galaxies. These strong feedback models reduce the baryon fraction in galaxies by a factor of 3 relative to the case with no feedback. The AGN is even capable of reducing the baryon fraction by a factor of 2 in the inner region of group and cluster haloes. This in turn results in inner density profiles which are typically shallower than isothermal and the halo concentrations tend to be lower than in the absence of baryons.Comment: 20 pages, 14 figures, 1 table. MNRAS in press. Version 2: added a few references

Raltegravir Cerebrospinal Fluid Concentrations in HIV-1 Infection

Raltegravir is an HIV-1 integrase inhibitor currently used in treatment-experienced HIV-1-infected patients resistant to other drug classes. In order to assess its central nervous system penetration, we measured raltegravir concentrations in cerebrospinal fluid (CSF) and plasma in subjects receiving antiretroviral treatment regimens containing this drug.Raltegravir concentrations were determined by liquid chromatography tandem mass spectrometry in 25 paired CSF and plasma samples from 16 HIV-1-infected individuals. The lower limit of quantitation was 2.0 ng/ml for CSF and 10 ng/ml for plasma.Twenty-four of the 25 CSF samples had detectable raltegravir concentrations with a median raltegravir concentration of 18.4 ng/ml (range, <2.0-126.0). The median plasma raltegravir concentration was 448 ng/ml (range, 37-5180). CSF raltegravir concentrations correlated with CSF:plasma albumin ratios and CSF albumin concentrations.Approximately 50% of the CSF specimens exceeded the IC(95) levels reported to inhibit HIV-1 strains without resistance to integrase inhibitors. In addition to contributing to control of systemic HIV-1 infection, raltegravir achieves local inhibitory concentrations in CSF in most, but not all, patients. Blood-brain and blood-CSF barriers likely restrict drug entry, while enhanced permeability of these barriers enhances drug entry

Cidadania mediada : processos de democratização da política municipal no Brasil

This article discusses the notion that the persistence of &ldquo;traditional&rdquo; political practices weakens Brazil&rsquo;s democracy.Drawing on the cases of three Brazilian municipalities administered by the Workers&rsquo; Party (PT), the author examines the space between &ldquo;traditional&rdquo; and &ldquo;modern&rdquo; and argues that successful democratization does not eradicate practices such as clientelism and patronage, but it tends to incorporate and build on these traditional political elements. Moreover, the article maintains that the democratization of municipal politics is inextricably bound up with the eradication of poverty and the construction of a responsive, state-based social safety net.<br /