Pontificia Universidad Católica del Perú

The last few years have witnessed significant changes in Pfam (https://pfam.xfam.org). The number of families has grown substantially to a total of 17,929 in release 32.0. New additions have been coupled with efforts to improve existing families, including refinement of domain boundaries, their classification into Pfam clans, as well as their functional annotation. We recently began to collaborate with the RepeatsDB resource to improve the definition of tandem repeat families within Pfam. We carried out a significant comparison to the structural classification database, namely the Evolutionary Classification of Protein Domains (ECOD) that led to the creation of 825 new families based on their set of uncharacterized families (EUFs). Furthermore, we also connected Pfam entries to the Sequence Ontology (SO) through mapping of the Pfam type definitions to SO terms. Since Pfam has many community contributors, we recently enabled the linking between authorship of all Pfam entries with the corresponding authors' ORCID identifiers. This effectively permits authors to claim credit for their Pfam curation and link them to their ORCID record.

Importance: Application of deep learning algorithms to whole-slide pathology images can potentially improve diagnostic accuracy and efficiency. Objective: Assess the performance of automated deep learning algorithms at detecting metastases in hematoxylin and eosin-stained tissue sections of lymph nodes of women with breast cancer and compare it with pathologists' diagnoses in a diagnostic setting. Design, Setting, and Participants: Researcher challenge competition (CAMELYON16) to develop automated solutions for detecting lymph node metastases (November 2015-November 2016). A training data set of whole-slide images from 2 centers in the Netherlands with (n = 110) and without (n = 160) nodal metastases verified by immunohistochemical staining were provided to challenge participants to build algorithms. Algorithm performance was evaluated in an independent test set of 129 whole-slide images (49 with and 80 without metastases). The same test set of corresponding glass slides was also evaluated by a panel of 11 pathologists with time constraint (WTC) from the Netherlands to ascertain likelihood of nodal metastases for each slide in a flexible 2-hour session, simulating routine pathology workflow, and by 1 pathologist without time constraint (WOTC). Exposures: Deep learning algorithms submitted as part of a challenge competition or pathologist interpretation. Main Outcomes and Measures: The presence of specific metastatic foci and the absence vs presence of lymph node metastasis in a slide or image using receiver operating characteristic curve analysis. The 11 pathologists participating in the simulation exercise rated their diagnostic confidence as definitely normal, probably normal, equivocal, probably tumor, or definitely tumor. Results: The area under the receiver operating characteristic curve (AUC) for the algorithms ranged from 0.556 to 0.994. The top-performing algorithm achieved a lesion-level, true-positive fraction comparable with that of the pathologist WOTC (72.4% [95% CI, 64.3%-80.4%]) at a mean of 0.0125 false-positives per normal whole-slide image. For the whole-slide image classification task, the best algorithm (AUC, 0.994 [95% CI, 0.983-0.999]) performed significantly better than the pathologists WTC in a diagnostic simulation (mean AUC, 0.810 [range, 0.738-0.884]; P < .001). The top 5 algorithms had a mean AUC that was comparable with the pathologist interpreting the slides in the absence of time constraints (mean AUC, 0.960 [range, 0.923-0.994] for the top 5 algorithms vs 0.966 [95% CI, 0.927-0.998] for the pathologist WOTC). Conclusions and Relevance: In the setting of a challenge competition, some deep learning algorithms achieved better diagnostic performance than a panel of 11 pathologists participating in a simulation exercise designed to mimic routine pathology workflow; algorithm performance was comparable with an expert pathologist interpreting whole-slide images without time constraints. Whether this approach has clinical utility will require evaluation in a clinical setting.

With data from 33 nations, we illustrate the differences between cultures that are tight (have many strong norms and a low tolerance of deviant behavior) versus loose (have weak social norms and a high tolerance of deviant behavior). Tightness-looseness is part of a complex, loosely integrated multilevel system that comprises distal ecological and historical threats (e.g., high population density, resource scarcity, a history of territorial conflict, and disease and environmental threats), broad versus narrow socialization in societal institutions (e.g., autocracy, media regulations), the strength of everyday recurring situations, and micro-level psychological affordances (e.g., prevention self-guides, high regulatory strength, need for structure). This research advances knowledge that can foster cross-cultural understanding in a world of increasing global interdependence and has implications for modeling cultural change.

Humans express a wide array of ideal mate preferences. Around the world, people desire romantic partners who are intelligent, healthy, kind, physically attractive, wealthy, and more. In order for these ideal preferences to guide the choice of actual romantic partners, human mating psychology must possess a means to integrate information across these many preference dimensions into summaries of the overall mate value of their potential mates. Here we explore the computational design of this mate preference integration process using a large sample of n = 14,487 people from 45 countries around the world. We combine this large cross-cultural sample with agent-based models to compare eight hypothesized models of human mating markets. Across cultures, people higher in mate value appear to experience greater power of choice on the mating market in that they set higher ideal standards, better fulfill their preferences in choice, and pair with higher mate value partners. Furthermore, we find that this cross-culturally universal pattern of mate choice is most consistent with a Euclidean model of mate preference integration.

We report the first measurement of charged particle elliptic flow in Pb-Pb collisions at $\sqrt{{s}_{NN}}=2.76\text{ }\text{ }\mathrm{TeV}$ with the ALICE detector at the CERN Large Hadron Collider. The measurement is performed in the central pseudorapidity region ($|\ensuremath{\eta}|&lt;0.8$) and transverse momentum range $0.2&lt;{p}_{t}&lt;5.0\text{ }\text{ }\mathrm{GeV}/c$. The elliptic flow signal ${v}_{2}$, measured using the 4-particle correlation method, averaged over transverse momentum and pseudorapidity is $0.087\ifmmode\pm\else\textpm\fi{}0.002(\mathrm{stat})\ifmmode\pm\else\textpm\fi{}0.003(\mathrm{syst})$ in the 40%--50% centrality class. The differential elliptic flow ${v}_{2}({p}_{t})$ reaches a maximum of 0.2 near ${p}_{t}=3\text{ }\text{ }\mathrm{GeV}/c$. Compared to RHIC Au-Au collisions at $\sqrt{{s}_{NN}}=200\text{ }\text{ }\mathrm{GeV}$, the elliptic flow increases by about 30%. Some hydrodynamic model predictions which include viscous corrections are in agreement with the observed increase.

Introduction 1. Houses, gardens, and fences: signs of English possession in the New World 2. Ceremonies: the theatrical rituals of French political possession 3. The requirement: a protocol for conquest 4. 'A New Sky and New Stars': Arabic and Hebrew science, Portuguese seamanship, and the discovery of America 5. Sailing in the wake of the Portuguese Conclusion: the habits of history.

"La reseña no presenta resumen"

Abstract At sufficiently high temperature and energy density, nuclear matter undergoes a transition to a phase in which quarks and gluons are not confined: the quark–gluon plasma (QGP) 1 . Such an exotic state of strongly interacting quantum chromodynamics matter is produced in the laboratory in heavy nuclei high-energy collisions, where an enhanced production of strange hadrons is observed 2,3,4,5,6 . Strangeness enhancement, originally proposed as a signature of QGP formation in nuclear collisions 7 , is more pronounced for multi-strange baryons. Several effects typical of heavy-ion phenomenology have been observed in high-multiplicity proton–proton (pp) collisions 8,9 , but the enhanced production of multi-strange particles has not been reported so far. Here we present the first observation of strangeness enhancement in high-multiplicity proton–proton collisions. We find that the integrated yields of strange and multi-strange particles, relative to pions, increases significantly with the event charged-particle multiplicity. The measurements are in remarkable agreement with the p–Pb collision results 10,11 , indicating that the phenomenon is related to the final system created in the collision. In high-multiplicity events strangeness production reaches values similar to those observed in Pb–Pb collisions, where a QGP is formed.

In this paper measurements are presented of ${\ensuremath{\pi}}^{\ifmmode\pm\else\textpm\fi{}}$, ${K}^{\ifmmode\pm\else\textpm\fi{}}$, $p$, and $\overline{p}$ production at midrapidity ($|y|&lt;0.5$), in Pb-Pb collisions at $\sqrt{{s}_{NN}}=2.76$ TeV as a function of centrality. The measurement covers the transverse-momentum (${p}_{T}$) range from 100, 200, and 300 MeV/$c$ up to 3, 3, and 4.6 GeV/$c$ for $\ensuremath{\pi}$, $K$, and $p$, respectively. The measured ${p}_{T}$ distributions and yields are compared to expectations based on hydrodynamic, thermal and recombination models. The spectral shapes of central collisions show a stronger radial flow than measured at lower energies, which can be described in hydrodynamic models. In peripheral collisions, the ${p}_{T}$ distributions are not well reproduced by hydrodynamic models. Ratios of integrated particle yields are found to be nearly independent of centrality. The yield of protons normalized to pions is a factor $\ensuremath{\sim}$1.5 lower than the expectation from thermal models.

We report on the first measurement of the triangular v3, quadrangular v4, and pentagonal v5 charged particle flow in Pb-Pb collisions at sqrt(s(NN)) = 2.76 TeV measured with the ALICE detector at the CERN Large Hadron Collider. We show that the triangular flow can be described in terms of the initial spatial anisotropy and its fluctuations, which provides strong constraints on its origin. In the most central events, where the elliptic flow v2 and v3 have similar magnitude, a double peaked structure in the two-particle azimuthal correlations is observed, which is often interpreted as a Mach cone response to fast partons. We show that this structure can be naturally explained from the measured anisotropic flow Fourier coefficients.

The centrality dependence of the charged-particle multiplicity density at midrapidity in Pb-Pb collisions at sqrt[s_{NN}]=2.76 TeV is presented. The charged-particle density normalized per participating nucleon pair increases by about a factor of 2 from peripheral (70%-80%) to central (0%-5%) collisions. The centrality dependence is found to be similar to that observed at lower collision energies. The data are compared with models based on different mechanisms for particle production in nuclear collisions.

Very few demographic surveys in developing countries have gathered information on household incomes or consumption expenditures. Researchers interested in living standards therefore have had little alternative but to rely on simple proxy indicators. The properties of these proxies have not been analyzed systematically. We ask what hypotheses can be tested using proxies, and compare these indicators with consumption expenditures per adult, our preferred measure of living standards. We find that the proxies employed in much demographic research are very weak predictors of consumption per adult. Nevertheless, hypothesis tests based on proxies are likely to be powerful enough to warrant consideration.

Markus and Kitayama's (1991) theory of independent and interdependent self-construals had a major influence on social, personality, and developmental psychology by highlighting the role of culture in psychological processes. However, research has relied excessively on contrasts between North American and East Asian samples, and commonly used self-report measures of independence and interdependence frequently fail to show predicted cultural differences. We revisited the conceptualization and measurement of independent and interdependent self-construals in 2 large-scale multinational surveys, using improved methods for cross-cultural research. We developed (Study 1: N = 2924 students in 16 nations) and validated across cultures (Study 2: N = 7279 adults from 55 cultural groups in 33 nations) a new 7-dimensional model of self-reported ways of being independent or interdependent. Patterns of global variation support some of Markus and Kitayama's predictions, but a simple contrast between independence and interdependence does not adequately capture the diverse models of selfhood that prevail in different world regions. Cultural groups emphasize different ways of being both independent and interdependent, depending on individualism-collectivism, national socioeconomic development, and religious heritage. Our 7-dimensional model will allow future researchers to test more accurately the implications of cultural models of selfhood for psychological processes in diverse ecocultural contexts. (PsycINFO Database Record

In the original version of this manuscript, an error was introduced on pp352. '2.7nb:1.6nb' has been corrected to '2.4nb:1.3nb' in the current online and printed version. doi:10.1093/ptep/ptz106.

Inclusive transverse momentum spectra of primary charged particles in Pb–Pb collisions at sNN=2.76TeV have been measured by the ALICE Collaboration at the LHC. The data are presented for central and peripheral collisions, corresponding to 0–5% and 70–80% of the hadronic Pb–Pb cross section. The measured charged particle spectra in |η|<0.8 and 0.3<pT<20GeV/c are compared to the expectation in pp collisions at the same sNN, scaled by the number of underlying nucleon–nucleon collisions. The comparison is expressed in terms of the nuclear modification factor RAA. The result indicates only weak medium effects (RAA≈0.7) in peripheral collisions. In central collisions, RAA reaches a minimum of about 0.14 at pT=6–7GeV/c and increases significantly at larger pT. The measured suppression of high-pT particles is stronger than that observed at lower collision energies, indicating that a very dense medium is formed in central Pb–Pb collisions at the LHC.

Human spatial behavior has been the focus of hundreds of previous research studies. However, the conclusions and generalizability of previous studies on interpersonal distance preferences were limited by some important methodological and sampling issues. The objective of the present study was to compare preferred interpersonal distances across the world and to overcome the problems observed in previous studies. We present an extensive analysis of interpersonal distances over a large data set ( N = 8,943 participants from 42 countries). We attempted to relate the preferred social, personal, and intimate distances observed in each country to a set of individual characteristics of the participants, and some attributes of their cultures. Our study indicates that individual characteristics (age and gender) influence interpersonal space preferences and that some variation in results can be explained by temperature in a given region. We also present objective values of preferred interpersonal distances in different regions, which might be used as a reference data point in future studies.

Leaf dark respiration (Rdark ) is an important yet poorly quantified component of the global carbon cycle. Given this, we analyzed a new global database of Rdark and associated leaf traits. Data for 899 species were compiled from 100 sites (from the Arctic to the tropics). Several woody and nonwoody plant functional types (PFTs) were represented. Mixed-effects models were used to disentangle sources of variation in Rdark . Area-based Rdark at the prevailing average daily growth temperature (T) of each site increased only twofold from the Arctic to the tropics, despite a 20°C increase in growing T (8-28°C). By contrast, Rdark at a standard T (25°C, Rdark (25) ) was threefold higher in the Arctic than in the tropics, and twofold higher at arid than at mesic sites. Species and PFTs at cold sites exhibited higher Rdark (25) at a given photosynthetic capacity (Vcmax (25) ) or leaf nitrogen concentration ([N]) than species at warmer sites. Rdark (25) values at any given Vcmax (25) or [N] were higher in herbs than in woody plants. The results highlight variation in Rdark among species and across global gradients in T and aridity. In addition to their ecological significance, the results provide a framework for improving representation of Rdark in terrestrial biosphere models (TBMs) and associated land-surface components of Earth system models (ESMs).

This publication describes the methods used to measure the centrality of inelastic Pb-Pb collisions at a center-of-mass energy of 2.76 TeV per colliding nucleon pair with ALICE. The centrality is a key parameter in the study of the properties of QCD matter at extreme temperature and energy density, because it is directly related to the initial overlap region of the colliding nuclei. Geometrical properties of the collision, such as the number of participating nucleons and the number of binary nucleon-nucleon collisions, are deduced from a Glauber model with a sharp impact parameter selection and shown to be consistent with those extracted from the data. The centrality determination provides a tool to compare ALICE measurements with those of other experiments and with theoretical calculations.

In this Letter, comprehensive results on π ± , K ± , K S 0 , p( p ¯ ) and Λ ( Λ ¯ ) production at mid-rapidity ( 0 < y CMS < 0.5 ) in p–Pb collisions at s NN = 5.02 TeV , measured by the ALICE detector at the LHC, are reported. The transverse momentum distributions exhibit a hardening as a function of event multiplicity, which is stronger for heavier particles. This behavior is similar to what has been observed in pp and Pb–Pb collisions at the LHC. The measured p T distributions are compared to d–Au, Au–Au and Pb–Pb results at lower energy and with predictions based on QCD-inspired and hydrodynamic models .

The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native Americans. We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally calibrated reconstruction of the peopling of the Americas in a Bayesian coalescent analysis. The data suggest that a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages.