bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of protein assembly prediction in CASP12
Authors: Lafita Aleix , Bliven Spencer , Kryshtafovych Andriy , Bertoni Martino , Monastyrskyy Bohdan , Duarte Jose M. , Schwede Torsten , Capitani Guido 
Published: October 2017

AbstractWe present the results of the first independent assessment of protein assemblies in CASP. A total of 1624 oligomeric models were submitted by 108 predictor groups for the 30 oligomeric targets in the CASP12 edition. We evaluated the accuracy of oligomeric predictions by comparison to their reference structures at the interface patch and residue contact levels. We find that interface patches are more reliably predicted than the specific residue contacts. Whereas none of the 15 hard oligomeric targets have successful predictions for the residue contacts at the interface, six have models with resemblance in the interface patch. Successful predictions of interface patch and contacts exist for all targets suitable for homology modeling, with at least one group improving over the best available template for each target. However, the participation in protein assembly prediction is low and uneven. Three human groups are closely ranked at the top by overall performance, but a server outperforms all other predictors for targets suitable for homology modeling. The state of the art of protein assembly prediction methods is in development and has apparent room for improvement, especially for assemblies without templates.
Assessment of the model refinement category in CASP12
Authors: Hovan Ladislav , Oleinikovas Vladimiras , Yalinca Havva , Kryshtafovych Andriy , Saladino Giorgio , Gervasio Francesco Luigi 
Published: October 2017

AbstractWe here report on the assessment of the model refinement predictions submitted to the 12th Experiment on the Critical Assessment of Protein Structure Prediction (CASP12). This is the fifth refinement experiment since CASP8 (2008) and, as with the previous experiments, the predictors were invited to refine selected server models received in the regular (nonrefinement) stage of the CASP experiment. We assessed the submitted models using a combination of standard CASP measures. The coefficients for the linear combination of Z‐scores (the CASP12 score) have been obtained by a machine learning algorithm trained on the results of visual inspection. We identified eight groups that improve both the backbone conformation and the side chain positioning for the majority of targets. Albeit the top methods adopted distinctively different approaches, their overall performance was almost indistinguishable, with each of them excelling in different scores or target subsets. What is more, there were a few novel approaches that, while doing worse than average in most cases, provided the best refinements for a few targets, showing significant latitude for further innovation in the field.
Designing Phase I Shewhart X¯charts: Extended tables and software
Authors: Yao Y. , Hilton C.W. , Chakraborti S. 
Published: October 2017

AbstractControl charts play an important role in Phase I studies, which are conducted to establish process control and generate reference data for parameter estimation and calculation of prospective (Phase II) control limits. Researchers have tabulated the necessary charting constants for the normal theory–based Phase I Shewhart
chart for the process mean to achieve a desired nominal false alarm probability given the number of Phase I subgroups, m, up to 15. However, in practice, when parameters are estimated, the currently recommended number of Phase I subgroups is much larger than covered by their tables. Recognizing the need and taking advantage of some recently available software and computing resources, an extension to these tables is provided for m = 3(1)10 , 15(5)30 , 50(25)300 and n = 3 , 5 , 7 , 10. In addition to the tables, an R program is provided to calculate the charting constant, on demand, for user‐given values of nominal false alarm probability, m, and n. An appendix shows the details of how the program should be used.
Immune profiling of human prostate epithelial cells determined by expression of p38/TRAF‐6/ERK MAP kinases pathways
Authors: Bouraoui Yosra , Achour Mongia , Royuela Mar , Oueslati Ridha 
Published: October 2017

AbstractThe aim of the present work was to study the immune profiling of prostate epithelial cells by the expression of ASK‐1/p38 and Raf‐1/ERK MAP Kinases signaling pathways mediated by TRAF‐6. Immunohistochemical and Western blot analyses for TRAF‐6, ASK‐1, MEK‐6, p38, Raf‐1, MEK‐1, ERK‐1, ERK‐2 and PSA were carried out in 5 samples of normal prostate gland, 24 samples of BPH and 19 samples of PC. Immunoreaction to TRAF‐6 was found in the cytoplasm of epithelial cells of BPH and tumor cells of PC samples. For patients with the profile (TRAF‐6+), optical densities revealed a weak immunoexpression of ASK‐1 in PC compared to BPH patients. Whereas, immunoexpression to Raf‐1 was higher in PC than in BPH. According to the expression of ASK‐1 and Raf‐1, two main profiles were identified: (TRAF‐6+, ASK‐1+, Raf‐1+) and (TRAF‐6+, ASK‐1+, RAF‐1−) in both BPH and PC. In addition, ASK‐1/p38 axis expression was increased in BPH. Raf‐1/ERK signaling pathway was increased in PC samples. On the other hand, representing of individual signaling protein expression enclosing each of p38 and ERK MAP Kinases according to TRAF‐6+ showed a qualitative behavior of ASK61/p38 and Raf‐1/ERK signaling pathways and a dynamic expression of PSA associated with immune and inflammatory process. These findings suggest that prostate epithelial cell could able an immune and inflammatory setting.
Greek Historical Influence on Early Roman History
Authors: Trundle Matthew 
Published: October 2017

AbstractThis study employs a comparative approach using Greek models of historical enquiry, especially those of Herodotus, to illustrate how Romans prior to the Punic Wars, and indeed as early as the fifth and fourth centuriesBC, might have developed their own historical consciousness and historical traditions concerning their early past in much the same way as we know the Greeks had done by the fifth centuryBC. What follows is not at all new. Many have identified Roman historical and historiographical roots, connections, and even parallels with Greek history and historians.1What follows reiterates those connections, explicitly by assessing how Herodotus presented his inquiries to his Greek audience, laying the foundations for the discipline ofhistoria, and then by examining specifically the story of the Fabii at the Cremera in Livy, Dionysius and Diodorus. Through this one historical example, I hope to show that the roots of genuine historical thought can be found in the sources of our sources for early Roman traditions. Despite the fact that these traditions appear in works written much later than the events they describe, the nature of the stories preserved in our extant accounts suggests similar historiographical roots and interest as those preserved by Herodotus for the Greeks in the stories he told in hisHistories.
Politics, Power, and the Divine: TheRex Sacrorumand the Transition from Monarchy to Republic at Rome
Authors: Glinister Fay 
Published: October 2017

AbstractWhether the result of internal revolution or external factors, in the late sixth centuryBCRome underwent regime change. A king, or at least a sole ruler of some sort, was replaced by a governmental system in which power was distributed amongst a wider aristocratic group. Just what that elite group comprised at that point in time remains open to question, and the institutional reality is certainly more complicated than the simple shift from monarchy to consulship portrayed in the later literary sources;1but as part of that change, according to Roman tradition, a priesthood was instituted to perform the deposed king’s sacred duties. This priesthood provides us with an opportunity to reappraise the role of religion in the development of the Roman state, and a useful locus from which to assess changes in religious and political power in the transition from monarchy to Republic at Rome.
The South Dakota Model: Health Care Professions Student Disaster Preparedness and Deployment Training
Authors: Owens Matt P. , Buffington Cheri , Frost Michael P. , Waldner Randall J. 
Published: October 2017

ABSTRACTObjectiveThe Association of American Medical Colleges recommended an increase in medical education for public health emergencies, bioterrorism, and weapons of mass destruction in 2003. The University of South Dakota Sanford School of Medicine (USD SSOM) implemented a 1-day training event to provide disaster preparedness training and deployment organization for health professions students called Disaster Training Day (DTD).MethodsHospital staff and emergency medical services personnel provided the lecture portion of DTD using Core Disaster Life Support (CDLS; National Disaster Life Support Foundation) as the framework. Pre-test and post-test analyses were presented to the students. Small group activities covered leadership, anaphylaxis, mass fatality, points of dispensing deployment training, psychological first aid, triage, and personal protective equipment. Students were given the option to sign up for statewide deployment through the South Dakota Statewide Emergency Registry of Volunteers (SERV SD). DTD data and student satisfaction surveys from 2009 to 2016 were reviewed.ResultsSince 2004, DTD has provided disaster preparedness training to 2246 students across 13 health professions. Significant improvement was shown on CDLS post-test performance with a t-score of −14.24 and a resulting P value of <0.00001. Students showed high levels of satisfaction on a 5-level Likert scale with overall training, small group sessions, and perceived self-competency relating to disaster response. SERV SD registration increased in 2015, and 77.5% of the participants registered in 2016.ConclusionDTD at the USD SSOM provides for an effective 1-day disaster training course for health professions students. Resources from around the state were coordinated to provide training, liability coverage, and deployment organization for hundreds of students representing multiple health professions. (Disaster Med Public Health Preparedness. 2017;11:735–740)
Hegel and Marx on the Necessity of the Reign of Terror
Authors: James David 
Published: October 2017

AbstractBoth Hegel and Marx appear committed to the idea that the Reign of Terror was in some sense necessary. I argue that Hegel explains this necessity in terms of the concept of ‘absolute freedom’, together with the associated self-conception and normative picture of the world. It will be argued that Marx also views the Reign of Terror as necessary because of an abstract conception of political freedom and the citizen which conflicts with a determinate individuality that is characterized by particular interests and identities. In connection with Marx’s critique of Hegel’s theory of the modern state I draw attention to a puzzle, the discussion of which will lead to a brief account of how Marx’s attempt to overcome the opposition between the state and civil society differs from Hegel’s.
Evaluating the Relationship Between Hospital Antibiotic Use and Antibiotic Resistance in Common Nosocomial Pathogens
Authors: Wang Annie , Daneman Nick , Tan Charlie , Brownstein John S. , MacFadden Derek R. 
Published: October 2017

OBJECTIVEThe relationship between hospital antibiotic use and antibiotic resistance is poorly understood. We evaluated the association between antibiotic utilization and resistance in academic and community hospitals in Ontario, Canada.METHODSWe conducted a multicenter observational ecological study of 37 hospitals in 2014. Hospital antibiotic purchasing data were used as an indicator of antibiotic use, whereas antibiotic resistance data were extracted from hospital indexes of resistance. Multivariate regression was performed, with antibiotic susceptibility as the primary outcome, antibiotic consumption as the main predictor, and additional covariates of interest (ie, hospital type, laboratory standards, and patient days).RESULTSWith resistance data representing more than 90,000 isolates, we found the increased antibiotic consumption in defined daily doses per 1,000 patient days (DDDs/1,000 PD) was associated with decreased antibiotic susceptibility forPseudomonas aeruginosa(−0.162% per DDD/1,000 PD;P=.119). However, increased antibiotic consumption predicted increased antibiotic susceptibility significantly forEscherichia coli(0.173% per DDD/1,000 PD;P=.005),Klebsiellaspp (0.124% per DDD/1,000 PD;P=.004),Enterobacterspp (0.194% per DDD/1,000 PD;P=.003), andEnterococcusspp (0.309% per DDD/1,000 PD;P=.001), and nonsignificantly forStaphylococcus aureus(0.012% per DDD/1,000 PD;P=.878). Hospital type (P=.797) and laboratory standard (P=.394) did not significantly predict antibiotic susceptibility, while increased hospital patient days generally predicted increased organism susceptibility (0.728% per 10,000 PD;P<.001).CONCLUSIONSWe found that hospital-specific antibiotic usage was generally associated with increased, rather than decreased hospital antibiotic susceptibility. These findings may be explained by community origins for many hospital-diagnosed infections and practitioners choosing agents based on local antibiotic resistance patterns.Infect Control Hosp Epidemiol2017;38:1457–1463
Continuum theory for rapid cohesive-particle flows: general balance equations and discrete-element-method-based closure of cohesion-specific quantities
Authors: Kellogg Kevin M. , Liu Peiyuan , LaMarche Casey Q. , Hrenya Christine M. 
Published: October 2017

The continuum description of rapid cohesive-particle flows comprises the population balance, which tracks various agglomerate sizes in space and time, and kinetic-theory-based balances for momentum and granular energy. Here, fundamental closures are provided in their most general form. In previous population balances, the probability (‘success factor’) that a given collision results in agglomeration or breakage has been set to a constant even though it is well established that the outcome of a collision depends on the impact (relative) velocity. Here, physically based closures that relate the success factors to the granular temperature, a (continuum) measure of the impact velocity, are derived. A key aspect of this derivation is the recognition that the normal component of the impact velocity dictates whether agglomeration occurs. With regard to the kinetic-theory balances, cohesion between particles makes the collisions more dissipative, thereby decreasing the granular temperature. The extra dissipation due to cohesion is accounted for using an effective coefficient of restitution, again determined using the derived distribution of normal impact velocities. This collective treatment of the population and kinetic-theory balances results in a general set of equations that contain several parameters (e.g. critical velocities of agglomeration) that are cohesion-specific (van der Waals, liquid bridging, etc.). The determination of these cohesion-specific quantities using simple discrete element method simulations, as well as validation of the resulting theory, is also presented.
Thermosolutal convection in an evolving soluble porous medium
Authors: Corson Lindsey T. , Pritchard David 
Published: October 2017

We describe a mathematical model of double-diffusive (thermosolutal) convection in a saturated porous layer, when the solubility of the solute depends on the temperature, and the porosity and permeability of the porous medium evolve through dissolution and precipitation. We present the results of linear and weakly nonlinear stability analyses and explore the longer-term development of the system numerically. When the solutal concentration gradient is destabilising, the dynamics are somewhat similar to those previously found for single-species convection (Ritchie & Pritchard, J. Fluid Mech., vol. 673, 2011, pp. 286–317), including the occurrence of subcritical instabilities driven by a reaction–diffusion mechanism. However, when the solutal concentration gradient is stabilising and the thermal gradient is destabilising, novel dynamics emerge. These include a vertical segregation of circulation cells and porosity perturbations near the onset of convection, and over longer time scales the formation of a low-permeability region in the middle of the layer, pierced by occasional high-permeability channels. Under these conditions, convection may die away to nearly zero for extended periods before resuming vigorously in localised regions at later times.
Vortex-dipole collapse induced by droplet inertia and phase change
Authors: Ravichandran S. , Govindarajan Rama 
Published: October 2017

Droplet-laden flows with phase change are common. This study brings to light a mechanism by which droplet inertial dynamics and local phase change, taking place at sub-Kolmogorov scales, affect vortex dynamics in the inertial range of turbulence. To do this we consider vortices placed in a supersaturated ambient initially at constant temperature, homogeneous vapour concentration and uniformly distributed droplets. The droplets also act as sites of phase change. This allows the time scales associated with particle inertia and phase change, which could be significantly different from each other and from the time scale of the flow, to become coupled, and for their combined dynamics to govern the flow. The thermodynamics of condensation and evaporation have a characteristic time scale $\unicode[STIX]{x1D70F}_{s}$. The water droplets are treated as Stokesian inertial particles with a characteristic time scale $\unicode[STIX]{x1D70F}_{p}$, whose behaviour we approximate using an $O(\unicode[STIX]{x1D70F}_{p})$ truncation of the Maxey–Riley equation for heavy particles. This inertia leads the water droplets to vacate the vicinity of vortices, leaving no nuclei for the vapour to condense. The condensation process is thus spatially inhomogeneous, and leaves vortices in the flow colder than their surroundings. The combination of buoyancy and vorticity generates a lift force on the vortices perpendicular to their velocity relative to the fluid around them. In the case of a vortex dipole, this lift force can propel the vortices towards each other and undergo collapse, a phenomenon studied by Ravichandran et al. (Phys. Rev. Fluids, vol. 2, 2017, 034702). We find, spanning the space of the two time scales, $\unicode[STIX]{x1D70F}_{p}$ and $\unicode[STIX]{x1D70F}_{s}$, the region in which lift-induced dipole collapse can occur, and show numerically that the product of the time scales is the determining parameter. Our findings agree with our results from scaling arguments. We also study the influence of varying the initial supersaturation, and find that the strength of the lift-induced mechanism has a power-law dependence on the phase-change time scale $\unicode[STIX]{x1D70F}_{s}$. We then study systems of many vortices and show that the same coupling between the two time scales alters the dynamics of such systems, by energising the smaller scales. We show that this effect is significantly more pronounced at higher Reynolds numbers. Finally, we discuss how this effect could be relevant in conditions typical of clouds.
The aeroacoustics of finite wall-mounted square cylinders
Authors: Porteous Ric , Moreau Danielle J. , Doolan Con J. 
Published: October 2017

This paper presents the results of an experimental study that relates the flow structures in the wake of a square finite wall-mounted cylinder with the radiated noise. Acoustic and hot-wire measurements were taken in an anechoic wind tunnel. The cylinder was immersed in a near-zero-pressure gradient boundary layer whose thickness was 130 % of the cylinder width,$W$. Aspect ratios were in the range$0.29\leqslant L/W\leqslant 22.9$(where$L$is the cylinder span), and the Reynolds number, based on width, was$1.4\times 10^{4}$. Four shedding regimes were identified, namely R0 ($L/W<2$), RI ($2<L/W<10$), RII ($10<L/W<18$) and RIII ($L/W>18$), with each shedding regime displaying an additional acoustic tone as the aspect ratio was increased. At low aspect ratios (R0 and RI), downwash dominated the wake, creating a highly three-dimensional shedding environment with maximum downwash at$L/W\approx 7$. Looping vortex structures were visualised using a phase eduction technique. The principal core of the loops generated the most noise perpendicular to the cylinder. For higher aspect ratios in RII and RIII, the main noise producing structures consisted of a series of inclined vortex filaments, where the angle of inclination varied between vortex cells.
Streak instability in turbulent channel flow: the seeding mechanism of large-scale motions
Authors: de Giovanetti Matteo , Sung Hyung Jin , Hwang Yongyun 
Published: October 2017

It has often been proposed that the formation of large-scale motion (or bulges) is a consequence of successive mergers and/or growth of near-wall hairpin vortices. In the present study, we report our direct observation that large-scale motion is generated by an instability of an ‘amplified’ streaky motion in the outer region (i.e. very-large-scale motion). We design a numerical experiment in turbulent channel flow up to $Re_{\unicode[STIX]{x1D70F}}\simeq 2000$ where a streamwise-uniform streaky motion is artificially driven by body forcing in the outer region computed from the previous linear theory (Hwang & Cossu, J. Fluid Mech., vol. 664, 2015, pp. 51–73). As the forcing amplitude is increased, it is found that an energetic streamwise vortical structure emerges at a streamwise wavelength of $\unicode[STIX]{x1D706}_{x}/h\simeq 1{-}5$ ($h$ is the half-height of the channel). The application of dynamic mode decomposition and the examination of turbulence statistics reveal that this structure is a consequence of the sinuous-mode instability of the streak, a subprocess of the self-sustaining mechanism of the large-scale outer structures. It is also found that the statistical features of the vortical structure are remarkably similar to those of the large-scale motion in the outer region. Finally, it is proposed that the largest streamwise length of the streak instability determines the streamwise length scale of very-large-scale motion.
Not all whites are farmers: privilege, the politics of representation, and the urban–rural divide in Zimbabwe
Authors: Pilossof Rory , Boersema Jacob 
Published: October 2017

AbstractWhiteness has always been visible and marked in Africa. This is what makes whiteness in Africa distinct from whiteness in the West. This article explores the question of how the visibility of whiteness matters for its politics by focusing on the case of Zimbabwe. Much of the work on whiteness in this country, concentrating solely on the white farming community, presents the white population as a homogeneous group. This article uses the urban–rural divide to challenge such a portrayal and to explore the relationship in Zimbabwe between the politics of representation and the politics of whiteness in the postcolonial era. Based on four years of ethnographic research, it investigates urban and rural whiteness together because they are interrelated. We make two specific observations: first, that urban privilege has remained invisible because white Zimbabweans and white privilege are imagined to be connected to the land and to being a farmer. Urban whites have perpetuated this stereotype, which helped mask their own privileged lives. Second, we demonstrate that the defence of white privilege happens through means other than simple denial. Our interview data shows that, despite urban whites’ acknowledgement and understanding of white privilege, they still defend and try to legitimize it. Finally, we conclude that raising awareness and demanding acknowledgement of white privilege might be a necessary but insufficient condition to end it.