bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automating human intuition for protein design
Authors: Nivón Lucas G. , Bjelic Sinisa , King Chris , Baker David 
Published: October 2013

ABSTRACTIn the design of new enzymes and binding proteins, human intuition is often used to modify computationally designed amino acid sequences prior to experimental characterization. The manual sequence changes involve both reversions of amino acid mutations back to the identity present in the parent scaffold and the introduction of residues making additional interactions with the binding partner or backing up first shell interactions. Automation of this manual sequence refinement process would allow more systematic evaluation and considerably reduce the amount of human designer effort involved. Here we introduce a benchmark for evaluating the ability of automated methods to recapitulate the sequence changes made to computer‐generated models by human designers, and use it to assess alternative computational methods. We find the best performance for a greedy one‐position‐at‐a‐time optimization protocol that utilizes metrics (such as shape complementarity) and local refinement methods too computationally expensive for global Monte Carlo (MC) sequence optimization. This protocol should be broadly useful for improving the stability and function of designed binding proteins. Proteins 2014; 82:858–866. © 2013 Wiley Periodicals, Inc.
Resistive switching behaviour of highly epitaxial CeO2 thin film for memory application
Authors: Zhang Jun , Zhao Hongbin , Wei Feng , Yang Mengmeng , Yang Zhimin , Chen Qiuyun , Chen Jun 
Published: October 2013

AbstractWe report on the remarkable potential of highly epitaxial and pure (001)‐oriented CeO2 thin films grown on conducting Nb‐doped SrTiO3 (NSTO) substrates by laser molecular beam epitaxy for nonvolatile memory application. Resistive switching (RS) devices with the structure of Au/epi‐CeO2/NSTO exhibit reversible and steady bipolar RS behaviour with large high/low resistance ratio and a narrow dispersion of the resistance values. Detailed analysis of the conduction mechanisms reveals that the trapping/detrapping processes and oxygen vacancies migration play important roles in the switching behaviour. In the light of XPS measurement results, the CeO2/NSTO interface with oxygen vacancies or defects is responsible for the RS effect. Furthermore, a model is proposed to explain this resistance switching behaviour. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Context and Implications Document for: Exposing the intricacies of pre‐service teacher education: Incorporating the insights of Freire and Bourdieu
Authors: Hooley Neil 
Published: October 2013

This guide accompanies the following article: Neil Hooley, Exposing the intricacies of pre‐service teacher education: Incorporating the insights of Freire and Bourdieu, Review of Education, 10.1002/rev3.3011
Less conservative stability criteria for linear systems with interval time‐varying delays
Authors: Sun Jian , Han Qing‐Long , Chen Jie , Liu Guo‐Ping 
Published: October 2013

SummaryThe problem of the stability of a linear system with an interval time‐varying delay is investigated. A new Lyapunov–Krasovskii functional that fully uses information about the lower bound of the time‐varying delay is constructed to derive new stability criteria. It is proved that the proposed Lyapunov–Krasovskii functional can lead to less conservative results than some existing ones. Based on the proposed Lyapunov–Krasovskii functional, two stability conditions are developed using two different methods to estimate Lyapunov–Krasovskii functional's derivative. Two numerical examples are given to illustrate that the two stability conditions are complementary and yield a larger maximum upper bound of the time‐varying delay than some existing results. Copyright © 2013 John Wiley & Sons, Ltd.
Learning from berberine: Treating chronic diseases through multiple targets
Authors: Yao Jing , Kong WeiJia , Jiang JianDong 
Published: October 2013

Abstract
Although advances have been made, chemotherapy for chronic, multifactorial diseases such as cancers, Alzheimer’s disease, cardiovascular diseases and diabetes is far from satisfactory. Agents with different mechanisms of action are required. The botanic compound berberine (BBR) has been used as an over-the-counter antibacterial for diarrhea in China for many decades. Recent clinical studies have shown that BBR may be therapeutic in various types of chronic diseases. This review addresses BBR’s molecular mechanisms of action and clinical efficacy and safety in patients with type 2 diabetes, hyperlipidemia, heart diseases, cancers and inflammation. One of the advantages of BBR is its multiple-target effects in each of these diseases. The therapeutic efficacy of BBR may reflect a synergistic regulation of these targets, resulting in a comprehensive effect against these various chronic disorders. The safety of BBR may be due to its harmonious distribution into those targets. Although the single-target concept is still the principle for drug discovery and research, this review emphasizes the concept of a multiple target strategy, which may be an important approach toward the successful treatment of multifactorial chronic diseases.
Evolution of Oxidative Values during Kinetic Studies on Olive Oil Oxidation in the Rancimat Test
Authors: Farhoosh Reza , Hoseini‐Yazdi Seyedeh‐Zohreh 
Published: October 2013

AbstractA comparative study was carried out in order to evaluate the kinetics of the formation of a number of primary and secondary oxidation products during oxidation of olive oil in the Rancimat test at 100–130 °C. There were good correlations between the Rancimat index (OSI) and stability indices (IP) measured in the Rancimat test with no significant differences in kinetic parameters calculated from them. Mean values of the temperature coefficient, Q10 number, activation energy (Ea), frequency factor (A), and free energy of activation (ΔG++) for olive oil oxidation were calculated to be −3.44 × 10−2°C−1, 2.21, 98.91 kJ/mol, 12.17 × 1012 h−1, and 128.25 kJ/mol, respectively. Each unit change in Ea was accompanied by an average 1.43 × 1012 change in A, indicating a higher contribution for factor A than for Ea to the olive oil stability. The Ea and A correlated well with the values of enthalpy and entropy, respectively. The values of OSI or IP could be described well by the ΔG++ values. Kinetic data indicated that olive oil stability is more affected by the indigenous antioxidants than by the fatty acid composition.
Enriched environment has limited capacity for the correction of hippocampal memory‐dependent schizoid behaviors in rats with early postnatal NMDAR dysfunction
Authors: Melik Enver , Babar Emine , Kocahan Sayad , Guven Mustafa , Akillioglu Kubra 
Published: October 2013

AbstractPre‐ and early postnatal stress can cause dysfunction of the N‐methyl‐d‐aspartate receptor (NMDAR) and thereby promote the development of hippocampus memory‐dependent schizoid abnormalities of navigation in space, time, and knowledge. An enriched environment improves mental abilities in humans and animals. Whether an enriched environment can prevent the development of schizoid symptoms induced by neonatal NMDAR dysfunction was the central question of our paper. The experimental animals were Wistar rats. Early postnatal NMDAR dysfunction was created by systemic treatment of rat pups with the NMDAR antagonist MK‐801 at PD10–20 days. During the development period (PD21–90 days), the rats were reared in cognitively and physically enriched cages. Adult age rats were tested on navigation based on pattern separation and episodic memory in the open field and on auto‐hetero‐associations based on episodic and semantic memory in a step‐through passive avoidance task. The results showed that postnatal NMDAR antagonism caused abnormal behaviors in both tests. An enriched environment prevented deficits in the development of navigation in space based on pattern separation and hetero‐associations based on semantic memory. However, an enriched environment was unable to rescue navigation in space and auto‐associations based on episodic memory. These data may contribute to the understanding that an enriched environment has a limited capacity for therapeutic interventions in protecting the development of schizoid syndromes in children and adolescents.
The latest Ursus spelaeus in Italy, a new contribution to the extinction chronology of the cave bear
Authors: Martini Ivan , Coltorti Mauro , Mazza Paul P.A. , Rustioni Marco , Sandrelli Fabio 
Published: October 2013

AbstractThe skeleton of a young prime adult cave bear, Ursus spelaeus, was found in Chiostraccio Cave (Siena, Tuscany, central Italy), only slightly buried under rock falls. The specimen was dated yielding a conventional age of 24,030 ± 100 14C yr BP (29,200–28,550 cal yr BP), which makes it the latest known representative of the species in Italy. The skeleton was accompanied by the remains of wolf (Canis lupus), wild boar (Sus scrofa), aurochs (Bos primigenius), red deer (Cervus elaphus), roe deer (Capreolus capreolus), bat (Vespertinus murinus), and crow (Corvus monedula). The site seems confirming that the latest Italian U. spelaeus populations shared the risk of intrusion. The association of the cave bear with other animals suggests that the assemblage is an attritional palimpsest of remains of different species not originally associated in life. Cave bears were probably more vegetarian than brown bears and possibly became extinct when plant productivity dropped at the onset of MIS 2. Central and southern Italy may have offered isolated and sheltered refugia for cave bears.
Public Reason and the Disempowerment of Aboriginal People in Canada
Authors: Tomm Matthew 
Published: October 2013

Abstract
Aboriginal perspectives are often not viewed as persuasive or reasonable in contemporary political and legal discourses, and Aboriginal people are compelled to articulate their claims in the normative vocabulary of the majority. Many see this as an injustice. Part I of this essay argues that some incarnations of the idea of public justifiability, a cornerstone of political theory, provide a normative justification for that injustice. Part II argues that the idea is at work in the Canadian courts, even as judges attempt to create space for Aboriginal views. The ambivalent stance of the courts is explored through a case study.
What Munn Missed
Authors: Wagner Robin 
Published: October 2013

American Librarian Ralph Munn's historic tour of Australian libraries in 1934 is well documented. Along with Ernest Pitt, Chief Librarian of the State Library of Victoria, he spent nearly ten weeks travelling from Sydney and back again, visiting libraries in all the state capitals and many regional towns throughout the country. Munn's trip was funded by the Carnegie Corporation of New York, which was then, through its Dominions fund, turning attention to philanthropic opportunities in the Antipodes. The resulting report, Australian Libraries: A Survey of Conditions and Suggestions for their Improvement (commonly referred to as the Munn–Pitt Report) is often credited with initiating the public library movement in Australia.
THE ‘MUSLIM QUESTION’ IN HITLER'S BALKANS
Authors: MOTADEL DAVID 
Published: October 2013

ABSTRACTThis article examines Germany's efforts to instrumentalize Islam in the Balkans during the Second World War. As German troops became more involved in the region from early 1943 onwards, German officials began to engage with the Muslim population, promoting Germany as the protector of Islam in south-eastern Europe. Focusing on Bosnia, Herzegovina, and the Sandžak of Novi Pazar, the article explores the relations between German authorities and religious leaders on the ground and enquires into the ways in which German propagandists sought to employ religious rhetoric, terminology, and iconography for political and military ends. Interweaving religious history with the history of military conflict, the article contributes more generally to our understanding of the politics of religion in the Second World War.
HERESY AND FORFEITURE IN MARIAN ENGLAND
Authors: CAVILL P. R. 
Published: October 2013

ABSTRACTThe work of the martyrologist John Foxe ensures that the burnings dominate modern accounts of the campaign waged again Protestantism in the reign of Mary I (1553–8). Drawing on other sources, this article examines forfeiture of property, a less noticed but more common penalty imposed upon Protestants. It describes the types of forfeiture that occurred and analyses their legal basis; it considers the impact of the penalty and highlights means of evasion. By examining forfeiture, the article extends and enhances the debate about the effectiveness of Marian religious policy and about the degree of support that the regime could command. Forfeiture, it is shown, could be a powerful form of coercion, but depended upon popular politics to be effective. Subsequent efforts in Elizabeth I's reign to obtain restitution substantiate the article's thesis that a deep-rooted belief in the rule of law constrained the penal religious policies of early modern England.
THE SUBJECTIVE DIMENSION OF NAZISM
Authors: FÖLLMER MORITZ 
Published: October 2013

ABSTRACTThe present historiographical review discusses the subjective dimension of Nazism, an ideology and regime that needed translation into self-definitions, gender roles, and bodily practices to implant itself in German society and mobilize it for racial war. These studies include biographies of some of the Third Reich's most important protagonists, which have important things to say about their self-understandings in conjunction with the circumstances they encountered and subsequently shaped; cultural histories of important twentieth-century figures such as film stars, housewives, or consumers, which add new insights to the ongoing debate about the Third Reich's modernity; studies that address participation in the Nazi Empire and the Holocaust through discourses and practices of comradeship, work in extermination camps, and female ‘help’ within theWehrmacht. In discussing these monographs, along the way incorporating further books and articles, the piece attempts to draw connections between specific topics and think about new possibilities for synthesis in an overcompartmentalized field. It aims less to define a ‘Nazi subject’ than to bring us closer to understanding how Hitler's movement and regime connected different, shifting subject positions through both cohesion and competition, creating a dynamic that kept producing new exclusions and violent acts.
Source attribution of human campylobacteriosis in Denmark
Authors: BOYSEN L. , ROSENQUIST H. , LARSSON J. T. , NIELSEN E. M. , SØRENSEN G. , NORDENTOFT S. , HALD T. 
Published: October 2013

SUMMARYThis study assesses the contribution of different sources of human campylobacteriosis in Denmark using two different source-attribution approaches. In total, 794 non-human isolates and 406 isolates from human cases (domestic, travel related, and cases with unknown travel history) were collected. Isolates were characterized by multilocus sequence typing,flaAtyping and susceptibility to antibiotics. Both models used indicate that the major burden of human campylobacteriosis in Denmark originates from the domestic broiler chicken reservoir. The second most important reservoir was found to be cattle. The Asymmetric Island model attributed 52% [95% credibility interval (CrI) 37–67] to Danish chicken, 17% (95% CrI 3–33) to imported chicken, and 17% (95% CrI 7–28) to cattle. Similarly, theCampylobactersource-attribution model apportioned 38% (95% CrI 28–47) to Danish chicken, 14% (95% CrI 10–18) to imported chicken, and 16% (95% CrI 7–25) to cattle. The addition offlaAtype as an extra discriminatory typing parameter did not change the attribution of cases markedly.
Linking sensory neurons to visually guided behavior: Relating MST activity to steering in a virtual environment
Authors: EGGER SETH W. , BRITTEN KENNETH H. 
Published: October 2013

AbstractMany complex behaviors rely on guidance from sensations. To perform these behaviors, the motor system must decode information relevant to the task from the sensory system. However, identifying the neurons responsible for encoding the appropriate sensory information remains a difficult problem for neurophysiologists. A key step toward identifying candidate systems is finding neurons or groups of neurons capable of representing the stimuli adequately to support behavior. A traditional approach involves quantitatively measuring the performance of single neurons and comparing this to the performance of the animal. One of the strongest pieces of evidence in support of a neuronal population being involved in a behavioral task comes from the signals being sufficient to support behavior. Numerous experiments using perceptual decision tasks show that visual cortical neurons in many areas have this property. However, most visually guided behaviors are not categorical but continuous and dynamic. In this article, we review the concept of sufficiency and the tools used to measure neural and behavioral performance. We show how concepts from information theory can be used to measure the ongoing performance of both neurons and animal behavior. Finally, we apply these tools to dorsal medial superior temporal (MSTd) neurons and demonstrate that these neurons can represent stimuli important to navigation to a distant goal. We find that MSTd neurons represent ongoing steering error in a virtual-reality steering task. Although most individual neurons were insufficient to support the behavior, some very nearly matched the animal’s estimation performance. These results are consistent with many results from perceptual experiments and in line with the predictions of Mountcastle’s “lower envelope principle.”
The Rediscovery of Samuel Lyde's Lost Nuṣayrī Kitāb al-Mashyakha (Manual for Shaykhs)
Authors: KRIEGER BELLA TENDLER 
Published: October 2013

AbstractTheK. al-Mashyakhais a manual for Nuṣayrī shaykhs. Its significance as a window into the otherwise secret world of Nuṣayrī ritual was augmented by the role it played in the formation of Nuṣayrī studies: in 1860, it served as the basis for the first monograph on the Nuṣayrī religion, Samuel Lyde's posthumously publishedAsian Mystery. However, for over 150 years, the K. al-Mashyakha has been missing. This article announces its rediscovery in two identical manuscripts and identifies two additional works based on this text, the well-known Nuṣayrī catechism, K. Taʿlīm diyānat al-nuṣayriyya, and the recently publishedK. al-Mashyakhaissued by the Lebanese press, Dār li-ajl al-maʿrifa. In solving the mystery of its disappearance and rediscovery in two copies, this article provides new insight into the nineteenth-century Nuṣayrī world from which theK. al-Mashyakhaemerged, as well as that of the European orientalists who pioneered this field.
Hafnium-Silicon Precipitate Structure Determination in a New Heat-Resistant Ferritic Alloy by Precession Electron Diffraction Techniques
Authors: Viladot Désirée , Portillo Joaquim , Gemí Mauro , Nicolopoulos Stavros , Llorca-Isern Núria 
Published: October 2013

AbstractThe structure determination of an HfSi4 precipitate has been carried out by a combination of two precession electron diffraction techniques: high precession angle, 2.2°, single pattern collection at eight different zone axes and low precession angle, 0.5°, serial collection of patterns obtained by increasing tilts of 1°. A three-dimensional reconstruction of the associated reciprocal space shows an orthorhombic unit cell with parameters a = 11.4 Å, b = 11.8 Å, c = 14.6 Å, and an extinction condition of (hkl) h + k odd. The merged intensities from the high angle precession patterns have been symmetry tested for possible space groups (SG) fulfilling this condition and a best symmetrization residual found at 18% for SG 65 Cmmm. Use of the SIR2011 direct methods program allowed solving the structure with a structure residual of 18%. The precipitate objects of this study were reproducibly found in a newly implemented alloy, designed according to molecular orbital theory.
Longitudinal Modeling of the Relationship Between Mean Plasma Glucose and HbA1c Following Antidiabetic Treatments
Authors: Møller JB , Overgaard RV , Kjellsson MC , Kristensen NR , Klim S , Ingwersen SH , Karlsson MO 
Published: October 2013

Late‐phase clinical trials within diabetes generally have a duration of 12–24 weeks, where 12 weeks may be too short to reach steady‐state glycated hemoglobin (HbA1c). The main determinant for HbA1c is blood glucose, which reaches steady state much sooner. In spite of this, few publications have used individual data to assess the time course of both glucose and HbA1c, for predicting HbA1c. In this paper, we present an approach for predicting HbA1c at end‐of‐trial (24–28 weeks) using glucose and HbA1c measurements up to 12 weeks. The approach was evaluated using data from 4 trials covering 12 treatment arms (oral antidiabetic drug, glucagon‐like peptide‐1, and insulin treatment) with measurements at 24–28 weeks to evaluate predictions vs. observations. HbA1c percentage was predicted for each arm at end‐of‐trial with a mean prediction error of 0.14% [0.01;0.24]. Furthermore, end points in terms of HbA1c reductions relative to comparator were accurately predicted. The proposed model provides a good basis to optimize late‐stage clinical development within diabetes.CPT: Pharmacometrics & Systems Pharmacology (2013) 2, e82; doi:10.1038/psp.2013.58; advance online publication 30 October 2013
Electrostatically driven micropump with peristaltically moving membrane
Authors: Kim Bonghwan 
Published: October 2013

An electrostatically driven valveless micropump with a peristaltically moving membrane for gas chromatography is presented. The one‐chamber micropump has a peristaltically moving membrane formed by polyimide with four electrodes used to separate the single chamber into four pump chambers. For a peristaltically moving membrane, several dielectrics were tested for their ability to endure high‐voltage breakdown, and the PI‐2545 polyimide was finally chosen to reduce the operating voltage. After testing a single‐sided micropump (SSM), a double‐sided micropump (DSM) was fabricated to enhance pump efficiency. Theoretically, the flow rate of the DSM is quadruple that of the SSM, and the electrodes in the membrane can recover from the motion of pulling down and pulling up with ease. To verify the peristaltic motion of the micropump, a transparent indium tin oxide (ITO) electrode was used. An ITO–ITO micropump was fabricated, and to measure flow rate, an ITO–Si micropump was fabricated as well. The micropump was fabricated on a glass substrate with ITO and on a silicon substrate with a polyimide membrane. A maximum flow rate of 27.19 µl/min was measured at 4 Hz and 100 V DC. The micropump was operated by four electrodes with a four‐phase sequencing actuation.
Topology of viral evolution
Authors: Chan Joseph Minhow , Carlsson Gunnar , Rabadan Raul 
Published: October 2013

SignificanceEvolution is mediated not only by random mutations over a number of generations (vertical evolution), but also through the mixture of genomic material between individuals of different lineages (horizontal evolution). The standard evolutionary representation, the phylogenetic tree, faithfully represents the former but not the latter scenario. Although many elaborations have been developed to address this issue, there is still no agreed-upon method of incorporating both vertical and horizontal evolution. Here, we present an alternative strategy based on algebraic topology to study evolution. This method extends beyond the limits of a tree to capture directly even complex horizontal exchanges between multiple parental strains, as well as uncover broader reticulate patterns, including the segregation of segments during reassortment.