bluuebunny/crossref_metadata_2025 huggingface dataset:
Defects in ZnO
Authors: McCluskey M. D. , Jokela S. J.
Published: October 2009

Zinc oxide (ZnO) is a wide band gap semiconductor with potential applications in optoelectronics, transparent electronics, and spintronics. The high efficiency of UV emission in this material could be harnessed in solid-state white lighting devices. The problem of defects, in particular, acceptor dopants, remains a key challenge. In this review, defects in ZnO are discussed, with an emphasis on the physical properties of point defects in bulk crystals. As grown, ZnO is usually n-type, a property that was historically ascribed to native defects. However, experiments and theory have shown that O vacancies are deep donors, while Zn interstitials are too mobile to be stable at room temperature. Group-III (B, Al, Ga, and In) and H impurities account for most of the n-type conductivity in ZnO samples. Interstitial H donors have been observed with IR spectroscopy, while substitutional H donors have been predicted from first-principles calculations but not observed directly. Despite numerous reports, reliable p-type conductivity has not been achieved. Ferromagnetism is complicated by the presence of secondary phases, grain boundaries, and native defects. The famous green luminescence has several possible origins, including Cu impurities and Zn vacancies. The properties of group-I (Cu, Li, and Na) and group-V (N, P, As, and Sb) acceptors, and their complexes with H, are discussed. In the future, doping of ZnO nanocrystals will rely on an understanding of these fundamental properties.
The velocity, refractive index, and equation of state of liquid ammonia at high temperatures and high pressures
Authors: Li Fangfei , Li Min , Cui Qiliang , Cui Tian , He Zhi , Zhou Qiang , Zou Guangtian
Published: October 2009

The high temperature and high pressure Brillouin scattering studies of liquid ammonia have been performed in a diamond anvil cell. Acoustic velocity, refractive index, adiabatic bulk modulus, and the equation of state of liquid ammonia were determined at temperatures up to 410 K and at pressures up to the solidification point. Velocity and refractive index increase smoothly with increasing pressure along isothermals but decrease slightly with the temperature increase. The bulk modulus increases linearly with pressure and its slope dB/dP decreases slightly with increasing temperature from 6.67 at 297 K to 5.94 at 410 K.
Defect structure of Ge(111)/cubic Pr2O3(111)/Si(111) heterostructures: Thickness and annealing dependence
Authors: Giussani A. , Zaumseil P. , Rodenbach P. , Weidner G. , Schubert M. A. , Geiger D. , Lichte H. , Storck P. , Wollschläger J. , Schroeder T.
Published: October 2009

The defect structure of Ge(111) epilayers grown by molecular beam epitaxy on cubic Pr2O3(111)/Si(111) support systems was investigated by means of transmission electron microscopy and laboratory-based x-ray diffraction techniques. Three main types of defects were identified, namely, rotation twins, microtwins, and stacking faults, and studied as a function of Ge film thickness and after annealing at 825 °C in ultrahigh vacuum. Rotation twins were found to be localized at the Ge(111)/cubic Pr2O3(111) interface and their amount could be lowered by the thermal treatment. Microtwins across {111¯} were detected only in closed Ge films, after Ge island coalescence. The fraction of Ge film volume affected by microtwinning is constant within the thickness range of ∼20–260 nm. Beyond 260 nm, the density of microtwins is clearly reduced, resulting in thick layers with a top part of higher crystalline quality. Microtwins resulted insensitive to the postdeposition annealing. Instead, the density of stacking faults across {111¯} planes decreases with the thermal treatment. In conclusion, the defect density was proved to diminish with increasing Ge thickness and after annealing. Moreover, it is noteworthy that the annealing generates a tetragonal distortion in the Ge films, which get in-plane tensely strained, probably due to thermal mismatch between Ge and Si.
Discrete instability in the DNA double helix
Authors: Tabi Conrad Bertrand , Mohamadou Alidou , Kofané Timoléon Crépin
Published: October 2009

Modulational instability (MI) is explored in the framework of the base-rotor model of DNA dynamics. We show, in fact, that the helicoidal coupling introduced in the spin model of DNA reduces the system to a modified discrete sine-Gordon (sG) equation. The MI criterion is thus modified and displays interesting features because of the helicoidal coupling. In the simulations, we have found that a train of pulses is generated when the lattice is subjected to MI, in agreement with analytical results obtained in a modified discrete sG equation. Also, the competitive effects of the harmonic longitudinal and helicoidal constants on the dynamics of the system are notably pointed out. In the same way, it is shown that MI can lead to energy localization which becomes high for some values of the helicoidal coupling constant.
Equation of state for gadolinium gallium garnet crystals: Experimental and computational study
Authors: Durygin A. , Drozd V. , Paszkowicz W. , Werner-Malento E. , Buczko R. , Kaminska A. , Saxena S. , Suchocki A.
Published: October 2009

Experimentally and theoretically determined elastic properties of gadolinium gallium garnet, Gd3Ga5O12, under high-pressure are reported. The x-ray diffraction part of the study was performed using a diamond-anvil cell at pressures up to 25 GPa, at conditions ascertaining hydrostatic compression up to about 10 GPa. The experimental bulk modulus, K0=169(15) GPa, and its first derivative, K0′=3.6(2.9), were derived from the diffraction data collected in pressure range limited to 10.2 GPa, assuming the Birch–Murnaghan equation of state. Ab initio calculations yielded K0=161(8) GPa and K0′=5.4(0.6) being in excellent agreement with the experiment.
Homogeneous nucleation with magic numbers: Aluminum
Authors: Girshick Steven L. , Agarwal Pulkit , Truhlar Donald G.
Published: October 2009

Homogeneous nucleation of clusters that exhibit magic numbers is studied numerically, using as an example aluminum at 2000 K, based on recent calculations of free energies [Li et al., J. Phys. Chem. C 111, 16227 (2007)] and condensation rate constants [Li and Truhlar, J. Phys. Chem. C 112, 11109 (2008)] that provide a database for Ali up to i=60. The nucleation behavior for saturation ratios greater than about 4.5 is found to be dominated by a peak in the free energy change associated with the reaction iAl→Ali at i=55, making it the critical size over a wide range of saturation ratios. Calculated steady-state nucleation rates are many orders of magnitude lower than predicted by classical nucleation theory (CNT). The onset of nucleation is predicted to occur at a saturation ratio of about 13.3, compared to about 5.1 in CNT, while for saturation ratios greater than about 25 the abundance of magic-numbered clusters becomes high enough to invalidate the assumption that cluster growth occurs solely by monomer addition. Transient nucleation is also predicted to be substantially different than predicted by CNT, with a much longer time required to reach steady state: about 10−4 s at a saturation ratio of 20, compared to about 10−7 s from CNT. Magic numbers are seen to play an important role in transient nucleation, as the nucleation currents for clusters of adjacent sizes become equal to each other in temporally successive groups, where the largest cluster in each group is the magic-numbered one.
Optical emission spectroscopy for simultaneous measurement of plasma electron density and temperature in a low-pressure microwave induced plasma
Authors: Konjević N. , Jovićević S. , Ivković M.
Published: October 2009

The simple optical emission spectroscopy technique for diagnostics of low pressure microwave induced plasma (MIP) in hydrogen or in MIP seeded with hydrogen is described and tested. This technique uses the Boltzmann plot of relative line intensities along Balmer spectral series in conjunction with the criterion for partial local thermodynamic equilibrium for low electron density (Ne) plasma diagnostics. The proposed technique is tested in a low pressure MIP discharge for simultaneous determination of electron density Ne (1017–1018 m−3) and temperature Te.
Kinetic theory for the ion humps at the foot of the Earth’s bow shock
Authors: Jovanović D. , Krasnoselskikh V. V.
Published: October 2009

The nonlinear kinetic theory is presented for the ion acoustic perturbations at the foot of the Earth’s quasiperpendicular bow shock, that is characterized by weakly magnetized electrons and unmagnetized ions. The streaming ions, due to the reflection of the solar wind ions from the shock, provide the free energy source for the linear instability of the acoustic wave. In the fully nonlinear regime, a coherent localized solution is found in the form of a stationary ion hump, which is traveling with the velocity close to the phase velocity of the linear mode. The structure is supported by the nonlinearities coming from the increased population of the resonant beam ions, trapped in the self-consistent potential. As their size in the direction perpendicular to the local magnetic field is somewhat smaller that the electron Larmor radius and much larger that the Debye length, their spatial properties are determined by the effects of the magnetic field on weakly magnetized electrons. These coherent structures provide a theoretical explanation for the bipolar electric pulses, observed upstream of the shock by Polar and Cluster satellite missions.
Physical analysis of thermal effects on the optimization of GaN Gunn diodes
Authors: Tang X. , Rousseau M. , Dalle C. , De Jaeger J. C.
Published: October 2009

This letter describes the analysis of GaN Gunn oscillations by means of a physical-thermal modeling based on the coupling of an energy-balance model for the description of electron transport in the active area with a thermal model for the description of the lattice temperature everywhere in the device. The most important aspect of the model is the possibility to take into account the local temperature at each point of the device and its influence on transport properties. Electric behaviors (static and microwave characterizations), as well as thermal behaviors are described, thus making it possible to optimize the device.
Production of monodispersed micron-sized bubbles at high rates in a microfluidic device
Authors: Chen Chuanpin , Zhu Yonggang , Leech Patrick W. , Manasseh Richard
Published: October 2009

A polydimethylsiloxane microchip consisting of a T-junction microchannel network and a thin glass capillary has been developed for the generation of microbubbles. The glass capillary is used to produce an ultrathin gas jet and to controllably block the straight liquid channel, thereby increasing the local liquid velocity near the intersection. Liquid flow rate, liquid viscosity, gas pressure, and inner diameter of the gas jet are varied to investigate the effect on bubble generation. Bubbles with a diameter down to 4.5 μm can be produced at a high rate of 7.5 kHz using a capillary with an inner diameter of 2 μm.
Broadband downconversion based infrared quantum cutting by cooperative energy transfer from Eu2+ to Yb3+ in glasses
Authors: Zhou Jiajia , Zhuang Yixi , Ye Song , Teng Yu , Lin Geng , Zhu Bin , Xie Junhua , Qiu Jianrong
Published: October 2009

Near-infrared quantum cutting involving the emission of near-infrared photons by downconversion cooperative energy transfer from Eu2+ to Yb3+ in borate glasses was reported. Electron spin resonance spectra and absorption spectra were measured to prove the existence of Eu2+ in borate glasses. Excitation, emission, and fluorescence decay measurements were performed to examine the occurrence of cooperative energy transfer from Eu2+ to Yb3+ ions. Yb3+ concentration dependent quantum efficiency was calculated and the maximum efficiency approaches 164.19%.
Demonstration of extreme ultraviolet supercontinuum at the high harmonic plateau with a 6.5 fs/800 nm driving laser pulse
Authors: Zheng Yinghui , Zeng Zhinan , Xiong Hui , Li Ruxin , Xu Zhizhan , Peng Yan , Yang Xuan , Zeng Heping
Published: October 2009

We demonstrate experimentally the extreme ultraviolet supercontinuum in the plateau of high-order harmonic emission from the argon gas cell driven by a 6.5 fs, 800 nm phase-stabilized laser pulse. The result is interpreted as a selection of single quantum path of the returning electrons due to the propagation process in the gas cell. Moreover we predict the possibility to generate isolated 100 as pulses using a driving laser pulse longer than 2 cycles.
Study of quantum confinement effects on hole mobility in silicon and germanium double gate metal-oxide-semiconductor field-effect transistors
Authors: Tang Chun-Jung , Wang Tahui , Chang Chih-Sheng
Published: October 2009

Quantum confinement effects on hole mobility in silicon and germanium double gate p-channel metal-oxide-semiconductor field-effect transistors (MOSFETs) are studied by using a Monte Carlo method. Uniaxial stress and channel/substrate orientation effects are considered. Our result shows that the hole mobility in a (100)/[110] silicon well decreases with a decreasing well thickness, which is in agreement with the experimental result. The hole mobility in a germanium channel MOSFET, however, exhibits a peak in a sub-20 nm well because of the interplay between intrasubband and intersubband scatterings.
Relative contributions of chromatin and kinetochores to mitotic spindle assembly
Authors: O'Connell Christopher B. , Lončarek Jadranka , Kaláb Petr , Khodjakov Alexey
Published: October 2009

During mitosis and meiosis in animal cells, chromosomes actively participate in spindle assembly by generating a gradient of Ran guanosine triphosphate (RanGTP). A high concentration of RanGTP promotes microtubule nucleation and stabilization in the vicinity of chromatin. However, the relative contributions of chromosome arms and centromeres/kinetochores in this process are not known. In this study, we address this issue using cells undergoing mitosis with unreplicated genomes (MUG). During MUG, chromatin is rapidly separated from the forming spindle, and both centrosomal and noncentrosomal spindle assembly pathways are active. MUG chromatin is coated with RCC1 and establishes a RanGTP gradient. However, a robust spindle forms around kinetochores/centromeres outside of the gradient peak. When stable kinetochore microtubule attachment is prevented by Nuf2 depletion in both MUG and normal mitosis, chromatin attracts astral microtubules but cannot induce spindle assembly. These results support a model in which kinetochores play the dominant role in the chromosome-mediated pathway of mitotic spindle assembly.
Glyburide inhibits the Cryopyrin/Nalp3 inflammasome
Authors: Lamkanfi Mohamed , Mueller James L. , Vitari Alberto C. , Misaghi Shahram , Fedorova Anna , Deshayes Kurt , Lee Wyne P. , Hoffman Hal M. , Dixit Vishva M.
Published: October 2009

Inflammasomes activate caspase-1 for processing and secretion of the cytokines interleukin-1β (IL-1β) and IL-18. Cryopyrin/NALP3/NLRP3 is an essential component of inflammasomes triggered by microbial ligands, danger-associated molecular patterns (DAMPs), and crystals. Inappropriate Cryopyrin activity has been incriminated in the pathogenesis of gouty arthritis, Alzheimer's, and silicosis. Therefore, inhibitors of the Nalp3 inflammasome offer considerable therapeutic promise. In this study, we show that the type 2 diabetes drug glyburide prevented activation of the Cryopyrin inflammasome. Glyburide's cyclohexylurea group, which binds to adenosine triphosphatase (ATP)–sensitive K+ (KATP) channels for insulin secretion, is dispensable for inflammasome inhibition. Macrophages lacking KATP subunits or ATP-binding cassette transporters also activate the Cryopyrin inflammasome normally. Glyburide analogues inhibit ATP- but not hypothermia-induced IL-1β secretion from human monocytes expressing familial cold-associated autoinflammatory syndrome–associated Cryopyrin mutations, thus suggesting that inhibition occurs upstream of Cryopyrin. Concurrent with the role of Cryopyrin in endotoxemia, glyburide significantly delays lipopolysaccharide-induced lethality in mice. Therefore, glyburide is the first identified compound to prevent Cryopyrin activation and microbial ligand-, DAMP-, and crystal-induced IL-1β secretion.
Electron-tomographic analysis of intraflagellar transport particle trains in situ
Authors: Pigino Gaia , Geimer Stefan , Lanzavecchia Salvatore , Paccagnini Eugenio , Cantele Francesca , Diener Dennis R. , Rosenbaum Joel L. , Lupetti Pietro
Published: October 2009

Intraflagellar transport (IFT) is the bidirectional movement of multipolypeptide particles between the ciliary membrane and the axonemal microtubules, and is required for the assembly, maintenance, and sensory function of cilia and flagella. In this paper, we present the first high-resolution ultrastructural analysis of trains of flagellar IFT particles, using transmission electron microscopy and electron-tomographic analysis of sections from flat-embedded Chlamydomonas reinhardtii cells. Using wild-type and mutant cells with defects in IFT, we identified two different types of IFT trains: long, narrow trains responsible for anterograde transport; and short, compact trains underlying retrograde IFT. Both types of trains have characteristic repeats and patterns that vary as one sections longitudinally through the trains of particles. The individual IFT particles are highly complex, bridged to each other and to the outer doublet microtubules, and are closely apposed to the inner surface of the flagellar membrane.
Empirical Antimicrobial Therapy for Bloodstream Infection Due to Methicillin-Resistant Staphylococcus aureus: No Better than a Coin Toss
Authors: Herzke Carrie A. , Chen Luke F. , Anderson Deverick J. , Choi Yong , Sexton Daniel J. , Kaye Keith S.
Published: October 2009

Background.

Despite the high prevalence of methicillin-resistant Staphylococcus aureus (MRSA) infection in the hospital, the proportion of patients with MRSA bacteremia who receive appropriate empirical therapy remains suboptimal.

Objective.

To investigate the proportion of patients with MRSA bloodstream infection (BSI) who received appropriate empirical antibiotic therapy and to identify risk factors associated with receipt of appropriate empirical therapy.

Methods.

We studied a cohort of patients from 10 hospitals. The primary outcome was the proportion of patients who received appropriate empirical antibiotic therapy for MRSA BSI. Appropriate therapy was defined as receipt of daptomycin, linezolid, quinupristin-dalfopristin, or vancomycin within 1 calendar day after the first blood culture result positive for S. aureus (ie, before antimicrobial susceptibilities were known). Multivariable logistic regression was used to determine variables associated with receipt of appropriate empirical therapy.

Results.

The study included 562 patients with MRSA BSI. The mean (± standard deviation) age of the patients was 64 ± 16 years, and 288 (51.2%) were male. Only 291 (51.8%) patients received appropriate empirical therapy. Patients were more likely to receive appropriate therapy if they required hemodialysis (odds ratio [OR], 1.36 [95% confidence interval {CI}, 1.00–1.85]), had undergone knee or hip arthroplasty (OR, 3.04 [95% CI, 1.21–7.6]), had a central venous catheter at admission (OR, 1.72 [95% CI, 1.01–2.93]), or had a McCabe score of 1 at admission (OR, 1.83 [95% CI, 1.16–2.83]). Bowel incontinence (OR, 0.41 [95% CI, 0.19–0.92]) and BSIs categorized as primary (OR, 0.41 [95% CI, 0.27–0.63]) were associated with a decreased likelihood of receiving appropriate empirical therapy.

Conclusions.

Only half of patients with MRSA BSI received appropriate empirical therapy. Factors associated with receiving appropriate empirical antibiotics included the presence of a central venous catheter at admission and a history of joint arthroplasty. Surprisingly, prior MRSA infection was not predictive of receipt of appropriate antimicrobial therapy.
Use of International Classification of Diseases, Ninth Revision Clinical Modification Codes and Medication Use Data to Identify Nosocomial Clostridium difficile Infection
Authors: Schmiedeskamp Mia , Harpe Spencer , Polk Ronald , Oinonen Michael , Pakyz Amy
Published: October 2009

Objective.

The International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) code for Clostridium difficile infection (CDI) is used for surveillance of CDI. However, the ICD-9-CM code alone cannot separate nosocomial cases from cases acquired outside the institution. The purpose of this study was to determine whether combining the ICD-9-CM code with medication treatment data for CDI in hospitalized patients could enable us to distinguish between patients with nosocomial CDI and patients who were admitted with CDI. The primary objective was to compare the sensitivity, specificity, and predictive value of using the combination of ICD-9-CM code for CDI and CDI treatment records to identify cases of nosocomial CDI with the sensitivity, specificity, and predictive value of using the ICD-9-CM code alone.

Design.

Validation sample cross-sectional study.

Setting.

Academic health center.

Methods.

Administrative claims data from July 1, 2004, to June 30, 2005, were queried to identify adults discharged with an ICD-9-CM code for CDI and to find documentation of CDI therapy with oral vancomycin or metronidazole. Laboratory and medical records were queried to identify symptomatic CDI toxin-positive adult patients with nosocomial CDI and were compared with records of patients whose cases were predicted to be nosocomial by means of ICD-9-CM code and CDI therapy data.

Results.

Of 23,920 adult patients discharged from the hospital, 62 had nosocomial CDI according to symptoms and toxin assay. The sensitivity of the ICD-9-CM code alone for identifying nosocomial CDI was 96.8%, the specificity was 99.6%, the positive predictive value was 40.8%, and the negative predictive value was 100%. When CDI drug therapy was included with the ICD-9-CM code, the sensitivity ranged from 58.1% to 85.5%, specificity was virtually unchanged, and the range in positive predictive value was 37.9%–80.0%.

Conclusion.

Combining the ICD-9-CM code for CDI with drug therapy information increased the positive predictive value for nosocomial CDI but decreased the sensitivity.
Developing a Risk Stratification Model for Surgical Site Infection after Abdominal Hysterectomy
Authors: Olsen Margaret A. , Higham-Kessler James , Yokoe Deborah S. , Butler Anne M. , Vostok Johanna , Stevenson Kurt B. , Khan Yosef , Fraser Victoria J. ,   Prevention Epicenter Program, Centers for Disease Control and Prevention
Published: October 2009

Objective.

The incidence of surgical site infection (SSI) after hysterectomy ranges widely from 2% to 21%. A specific risk stratification index could help to predict more accurately the risk of incisional SSI following abdominal hysterectomy and would help determine the reasons for the wide range of reported SSI rates in individual studies. To increase our understanding of the risk factors needed to build a specific risk stratification index, we performed a retrospective multihospital analysis of risk factors for SSI after abdominal hysterectomy.

Methods.

Retrospective case-control study of 545 abdominal and 275 vaginal hysterectomies from July 1, 2003, to June 30, 2005, at 4 institutions. SSIs were defined by using Centers for Disease Control and Prevention/National Nosocomial Infections Surveillance criteria. Independent risk factors for abdominal hysterectomy were identified by using logistic regression.

Results.

There were 13 deep incisional, 53 superficial incisional, and 18 organ-space SSIs after abdominal hysterectomy and 14 organ-space SSIs after vaginal hysterectomy. Because risk factors for organ-space SSI were different according to univariate analysis, we focused further analyses on incisional SSI after abdominal hysterectomy. The maximum serum glucose level within 5 days after operation was highest in patients with deep incisional SSI, lower in patients with superficial incisional SSI, and lowest in uninfected patients (median, 189, 156, and 141 mg/dL, respectively; P = .005). Independent risk factors for incisional SSI included blood transfusion (odds ratio [OR], 2.4) and morbid obesity (body mass index [BMI], >35; OR, 5.7). Duration of operation greater than the 75th percentile (OR, 1.7), obesity (BMI, 30–35; OR, 3.0), and lack of private health insurance (OR, 1.7) were marginally associated with increased odds of SSI.

Conclusions.

Incisional SSI after abdominal hysterectomy was associated with increased BMI and blood transfusion. Longer duration of operation and lack of private health insurance were marginally associated with SSI.
Sufficient dimension reduction and prediction in regression
Authors: Adragni Kofi P. , Cook R. Dennis
Published: October 2009

Dimension reduction for regression is a prominent issue today because technological advances now allow scientists to routinely formulate regressions in which the number of predictors is considerably larger than in the past. While several methods have been proposed to deal with such regressions, principal components (PCs) still seem to be the most widely used across the applied sciences. We give a broad overview of ideas underlying a particular class of methods for dimension reduction that includes PCs, along with an introduction to the corresponding methodology. New methods are proposed for prediction in regressions with many predictors.
Cherry-picking for complex data: robust structure discovery
Authors: Banks David L. , House Leanna , Killourhy Kevin
Published: October 2009

Complex data often arise as a superposition of data generated from several simpler models. The traditional strategy for such cases is to use mixture modelling, but it can be problematic, especially in higher dimensions. This paper considers an alternative approach, emphasizing data exploration and robustness to model misspecification. The strategy is applied to problems in regression, cluster analysis and multidimensional scaling. The approach is illustrated through simulation and the analysis of several datasets.
Statistical inference for exploratory data analysis and model diagnostics
Authors: Buja Andreas , Cook Dianne , Hofmann Heike , Lawrence Michael , Lee Eun-Kyung , Swayne Deborah F. , Wickham Hadley
Published: October 2009

We propose to furnish visual statistical methods with an inferential framework and protocol, modelled on confirmatory statistical testing. In this framework, plots take on the role of test statistics, and human cognition the role of statistical tests. Statistical significance of ‘discoveries’ is measured by having the human viewer compare the plot of the real dataset with collections of plots of simulated datasets. A simple but rigorous protocol that provides inferential validity is modelled after the ‘lineup’ popular from criminal legal procedures. Another protocol modelled after the ‘Rorschach’ inkblot test, well known from (pop-)psychology, will help analysts acclimatize to random variability before being exposed to the plot of the real data. The proposed protocols will be useful for exploratory data analysis, with reference datasets simulated by using a null assumption that structure is absent. The framework is also useful for model diagnostics in which case reference datasets are simulated from the model in question. This latter point follows up on previous proposals. Adopting the protocols will mean an adjustment in working procedures for data analysts, adding more rigour, and teachers might find that incorporating these protocols into the curriculum improves their students’ statistical thinking.
Feature selection by higher criticism thresholding achieves the optimal phase diagram
Authors: Donoho David , Jin Jiashun
Published: October 2009

We consider two-class linear classification in a high-dimensional, small-sample-size setting. Only a small fraction of the features are useful, these being unknown to us, and each useful feature contributes weakly to the classification decision. This was called the rare/weak (RW) model in our previous study (Donoho, D. & Jin, J. 2008Proc. Natl Acad. Sci. USA105, 14 790–14 795). We select features by thresholding featureZ-scores. The threshold is set byhigher criticism(HC). For 1≤i≤N, let πidenote thep-value associated with theithZ-score and π(i)denote theith order statistic of the collection ofp-values. The HC threshold (HCT) is the order statistic of theZ-score corresponding to indeximaximizing. The ideal threshold optimizes the classification error. In that previous study, we showed that HCT was numerically close to the ideal threshold.

We formalize an asymptotic framework for studying the RW model, considering a sequence of problems with increasingly many features and relatively fewer observations. We show that, along this sequence, the limiting performance of ideal HCT is essentially just as good as the limiting performance of ideal thresholding. Our results describe two-dimensionalphase space, a two-dimensional diagram with coordinates quantifying ‘rare’ and ‘weak’ in the RW model. The phase space can be partitioned into two regions—one where ideal threshold classification is successful, and one where the features are so weak and so rare that it must fail. Surprisingly, the regions where ideal HCT succeeds and fails make exactly the same partition of the phase diagram. Other threshold methods, such as false (feature) discovery rate (FDR) threshold selection, are successful in a substantially smaller region of the phase space than either HCT or ideal thresholding. The FDR and local FDR of the ideal and HC threshold selectors have surprising phase diagrams, which are also described. Results showing the asymptotic equivalence of HCT with ideal HCT can be found in a forthcoming paper (Donoho, D. & Jin, J. In preparation).
On landmark selection and sampling in high-dimensional data analysis
Authors: Belabbas Mohamed-Ali , Wolfe Patrick J.
Published: October 2009

In recent years, the spectral analysis of appropriately defined kernel matrices has emerged as a principled way to extract the low-dimensional structure often prevalent in high-dimensional data. Here, we provide an introduction to spectral methods for linear and nonlinear dimension reduction, emphasizing ways to overcome the computational limitations currently faced by practitioners with massive datasets. In particular, a data subsampling or landmark selection process is often employed to construct a kernel based on partial information, followed by an approximate spectral analysis termed the Nyström extension. We provide a quantitative framework to analyse this procedure, and use it to demonstrate algorithmic performance bounds on a range of practical approaches designed to optimize the landmark selection process. We compare the practical implications of these bounds by way of real-world examples drawn from the field of computer vision, whereby low-dimensional manifold structure is shown to emerge from high-dimensional video data streams.
An overview of recent developments in genomics and associated statistical methods
Authors: Bickel Peter J. , Brown James B. , Huang Haiyan , Li Qunhua
Published: October 2009

The landscape of genomics has changed drastically in the last two decades. Increasingly inexpensive sequencing has shifted the primary focus from the acquisition of biological sequences to the study of biological function. Assays have been developed to study many intricacies of biological systems, and publicly available databases have given rise to integrative analyses that combine information from many sources to draw complex conclusions. Such research was the focus of the recent workshop at the Isaac Newton Institute, ‘High dimensional statistics in biology’. Many computational methods from modern genomics and related disciplines were presented and discussed. Using, as much as possible, the material from these talks, we give an overview of modern genomics: from the essential assays that make data-generation possible, to the statistical methods that yield meaningful inference. We point to current analytical challenges, where novel methods, or novel applications of extant methods, are presently needed.
Social evolution in micro-organisms and a Trojan horse approach to medical intervention strategies
Authors: Brown Sam P. , West Stuart A. , Diggle Stephen P. , Griffin Ashleigh S.
Published: October 2009

Medical science is typically pitted against the evolutionary forces acting upon infective populations of bacteria. As an alternative strategy, we could exploit our growing understanding of population dynamics of social traits in bacteria to help treat bacterial disease. In particular, population dynamics of social traits could be exploited to introduce less virulent strains of bacteria, or medically beneficial alleles into infective populations. We discuss how bacterial strains adopting different social strategies can invade a population of cooperative wild-type, considering public good cheats, cheats carrying medically beneficial alleles (Trojan horses) and cheats carrying allelopathic traits (anti-competitor chemical bacteriocins or temperate bacteriophage viruses). We suggest that exploitation of the ability of cheats to invade cooperative, wild-type populations is a potential new strategy for treating bacterial disease.
Lifetime monogamy and the evolution of eusociality
Authors: Boomsma Jacobus J.
Published: October 2009

All evidence currently available indicates that obligatory sterile eusocial castes only arose via the association of lifetime monogamous parents and offspring. This is consistent with Hamilton's rule (brs>roc), but implies that relatedness cancels out of the equation because average relatedness to siblings (rs) and offspring (ro) are both predictably 0.5. This equality implies that any infinitesimally small benefit of helping at the maternal nest (b), relative to the cost in personal reproduction (c) that persists throughout the lifespan of entire cohorts of helpers suffices to establish permanent eusociality, so that group benefits can increase gradually during, but mostly after the transition. The monogamy window can be conceptualized as a singularity comparable with the single zygote commitment of gametes in eukaryotes. The increase of colony size in ants, bees, wasps and termites is thus analogous to the evolution of multicellularity. Focusing on lifetime monogamy as a universal precondition for the evolution of obligate eusociality simplifies the theory and may help to resolve controversies about levels of selection and targets of adaptation. The monogamy window underlines that cooperative breeding and eusociality are different domains of social evolution, characterized by different sectors of parameter space for Hamilton's rule.
Adaptation and the genetics of social behaviour
Authors: Keller Laurent
Published: October 2009

In recent years much progress has been made towards understanding the selective forces involved in the evolution of social behaviour including conflicts over reproduction among group members. Here, I argue that an important additional step necessary for advancing our understanding of the resolution of potential conflicts within insect societies is to consider the genetics of the behaviours involved. First, I discuss how epigenetic modifications of behaviour may affect conflict resolution within groups. Second, I review known natural polymorphisms of social organization to demonstrate that a lack of consideration of the genetic mechanisms involved may lead to erroneous explanations of the adaptive significance of behaviour. Third, I suggest that, on the basis of recent genetic studies of sexual conflict in
Drosophila
, it is necessary to reconsider the possibility of within-group manipulation by means of chemical substances (i.e. pheromones). Fourth, I address the issue of direct versus indirect genetic effects, which is of particular importance for the study of behaviour in social groups. Fifth, I discuss the issue of how a genetic influence on dominance hierarchies and reproductive division of labour can have secondary effects, for example in the evolution of promiscuity. Finally, because the same sets of genes (e.g. those implicated in chemical signalling and the responses that are triggered) may be used even in species as divergent as ants, cooperative breeding birds and primates, an integration of genetic mechanisms into the field of social evolution may also provide unifying ideas.
The evolution of cooperative breeding in birds: kinship, dispersal and life history
Authors: Hatchwell Ben J.
Published: October 2009

The evolution of cooperation among animals has posed a major problem for evolutionary biologists, and despite decades of research into avian cooperative breeding systems, many questions about the evolution of their societies remain unresolved. A review of the kin structure of avian societies shows that a large majority live in kin-based groups. This is consistent with the proposed evolutionary routes to cooperative breeding via delayed dispersal leading to family formation, or limited dispersal leading to kin neighbourhoods. Hypotheses proposed to explain the evolution of cooperative breeding systems have focused on the role of population viscosity, induced by ecological/demographic constraints or benefits of philopatry, in generating this kin structure. However, comparative analyses have failed to generate robust predictions about the nature of those constraints, nor differentiated between the viscosity of social and non-social populations, except at a coarse level. I consider deficiencies in our understanding of how avian dispersal strategies differ between social and non-social species, and suggest that research has focused too narrowly on population viscosity and that a broader perspective that encompasses life history and demographic processes may provide fresh insights into the evolution of avian societies.
Social stability and helping in small animal societies
Authors: Field Jeremy , Cant Michael A.
Published: October 2009

In primitively eusocial societies, all individuals can potentially reproduce independently. The key fact that we focus on in this paper is that individuals in such societies instead often queue to inherit breeding positions. Queuing leads to systematic differences in expected future fitness. We first discuss the implications this has for variation in behaviour. For example, because helpers nearer to the front of the queue have more to lose, they should work less hard to rear the dominant's offspring. However, higher rankers may be more aggressive than low rankers, even if they risk injury in the process, if aggression functions to maintain or enhance queue position. Second, we discuss how queuing rules may be enforced through hidden threats that rarely have to be carried out. In fishes, rule breakers face the threat of eviction from the group. In contrast, subordinate paper wasps are not injured or evicted during escalated challenges against the dominant, perhaps because they are more valuable to the dominant. We discuss evidence that paper-wasp dominants avoid escalated conflicts by ceding reproduction to subordinates. Queuing rules appear usually to be enforced by individuals adjacent in the queue rather than by dominants. Further manipulative studies are required to reveal mechanisms underlying queue stability and to elucidate what determines queue position in the first place.
The evolutionary and ecological roots of human social organization
Authors: Kaplan Hillard S. , Hooper Paul L. , Gurven Michael
Published: October 2009

Social organization among human foragers is characterized by a three-generational system of resource provisioning within families, long-term pair-bonding between men and women, high levels of cooperation between kin and non-kin, and relatively egalitarian social relationships. In this paper, we suggest that these core features of human sociality result from the learning- and skill-intensive human foraging niche, which is distinguished by a late age-peak in caloric production, high complementarity between male and female inputs to offspring viability, high gains to cooperation in production and risk-reduction, and a lack of economically defensible resources. We present an explanatory framework for understanding variation in social organization across human societies, highlighting the interactive effects of four key ecological and economic variables: (i) the role of skill in resource production; (ii) the degree of complementarity in male and female inputs into production; (iii) economies of scale in cooperative production and competition; and (iv) the economic defensibility of physical inputs into production. Finally, we apply this framework to understanding variation in social and political organization across foraging, horticulturalist, pastoralist and agriculturalist societies.
Nepotistic cooperation in non-human primate groups
Authors: Silk Joan B.
Published: October 2009

Darwin was struck by the many similarities between humans and other primates and believed that these similarities were the product of common ancestry. He would be even more impressed by the similarities if he had known what we have learned about primates over the last 50 years. Genetic kinship has emerged as the primary organizing force in the evolution of primate social organization and the patterning of social behaviour in non-human primate groups. There are pronounced nepotistic biases across the primate order, from tiny grey mouse lemurs (Microcebus murinus) that forage alone at night but cluster with relatives to sleep during the day, to cooperatively breeding marmosets that rely on closely related helpers to rear their young, rhesus macaque (Macaca mulatta) females who acquire their mother's rank and form strict matrilineal dominance hierarchies, male howler monkeys that help their sons maintain access to groups of females and male chimpanzees (Pan troglodytes) that form lasting relationships with their brothers. As more evidence of nepotism has accumulated, important questions about the evolutionary processes underlying these kin biases have been raised. Although kin selection predicts that altruism will be biased in favour of relatives, it is difficult to assess whether primates actually conform to predictions derived from Hamilton's rule:br>c. In addition, other mechanisms, including contingent reciprocity and mutualism, could contribute to the nepotistic biases observed in non-human primate groups. There are good reasons to suspect that these processes may complement the effects of kin selection and amplify the extent of nepotistic biases in behaviour.
Trust and cooperation among economic agents
Authors: Dasgupta Partha
Published: October 2009

The units that are subject to selection pressure in evolutionary biology are ‘strategies’, which are conditional actions (‘Do P if X occurs, otherwise do Q’). In contrast, the units in economics select strategies from available menus so as to further their projects and purposes. As economic agents do not live in isolation, each agent's optimum choice, in general, depends on the choices made by others. Because their projects and purposes involve the future, not just the present, each agent reasons about the likely present and future consequences of their respective choices. That is why
beliefs
, about what others may do and what the consequences of those choices could be, are at the basis of strategy selection. A catalogue of social environments is constructed in which agents not only promise each other's cooperation, but also rationally believe that the promises will be kept. Unfortunately, non-cooperation arising from mistrust can be the outcome in those same environments: societies harbour multiple ‘equilibria’ and can skid from cooperation to non-cooperation. Moreover, a pre-occupation among analysts with the Prisoners' Dilemma game has obscured the fact that cooperative arrangements can harbour not only inequality, but also exploitation. The analysis is used to discuss why international cooperation over the use of global public goods has proved to be so elusive.
The evolution of extreme altruism and inequality in insect societies
Authors: Ratnieks Francis L. W. , Helanterä Heikki
Published: October 2009

In eusocial organisms, some individuals specialize in reproduction and others in altruistic helping. The evolution of eusociality is, therefore, also the evolution of remarkable inequality. For example, a colony of honeybees (Apis mellifera) may contain 50 000 females all of whom can lay eggs. But 100 per cent of the females and 99.9 per cent of the males are offspring of the queen. How did such extremes evolve? Phylogenetic analyses show that high relatedness was almost certainly necessary for the origin of eusociality. However, even the highest family levels of kinship are insufficient to cause the extreme inequality seen in e.g. honeybees via ‘voluntary altruism’. ‘Enforced altruism’ is needed, i.e. social pressures that deter individuals from attempting to reproduce. Coercion acts at two stages in an individual's life cycle. Queens are typically larger so larvae can be coerced into developing into workers by being given less food. Workers are coerced into working by ‘policing’, in which workers or the queen eat worker-laid eggs or aggress fertile workers. In some cases, individuals rebel, such as when stingless bee larvae develop into dwarf queens. The incentive to rebel is strong as an individual is the most closely related to its own offspring. However, because individuals gain inclusive fitness by rearing relatives, there is also a strong incentive to ‘acquiesce’ to social coercion. In a queenright honeybee colony, the policing of worker-laid eggs is very effective, which results in most workers working instead of attempting to reproduce. Thus, extreme altruism is due to both kinship and coercion. Altruism is frequently seen as a Darwinian puzzle but was not a puzzle that troubled Darwin. Darwin saw his difficulty in explaining how individuals that did not reproduce could evolve, given that natural selection was based on the accumulation of small heritable changes. The recognition that altruism is an evolutionary puzzle, and the solution was to wait another 100 years for William Hamilton.
The ecology of social transitions in human evolution
Authors: Foley Robert , Gamble Clive
Published: October 2009

We know that there are fundamental differences between humans and living apes, and also between living humans and their extinct relatives. It is also probably the case that the most significant and divergent of these differences relate to our social behaviour and its underlying cognition, as much as to fundamental differences in physiology, biochemistry or anatomy. In this paper, we first attempt to demarcate what are the principal differences between human and other societies in terms of social structure, organization and relationships, so that we can identify what derived features require explanation. We then consider the evidence of the archaeological and fossil record, to determine the most probable context in time and taxonomy, of these evolutionary trends. Finally, we attempt to link five major transitional points in hominin evolution to the selective context in which they occurred, and to use the principles of behavioural ecology to understand their ecological basis. Critical changes in human social organization relate to the development of a larger scale of fission and fusion; the development of a greater degree of nested substructures within the human community; and the development of intercommunity networks. The underlying model that we develop is that the evolution of ‘human society’ is underpinned by ecological factors, but these are influenced as much by technological and behavioural innovations as external environmental change.