bluuebunny/crossref_metadata_2025_split huggingface dataset:
Noise propagation with interlinked feed-forward pathways
Authors: Chepyala Surendhar Reddy , Chen Yi-Chen , Yan Ching-Cher Sanders , Lu Chun-Yi David , Wu Yi-Chun , Hsu Chao-Ping 
Published: March 2016

AbstractFunctionally similar pathways are often seen in biological systems, forming feed-forward controls. The robustness in network motifs such as feed-forward loops (FFLs) has been reported previously. In this work, we studied noise propagation in a development network that has multiple interlinked FFLs. A FFL has the potential of asymmetric noise-filtering (i.e., it works at either the “ON” or the “OFF” state in the target gene). With multiple, interlinked FFLs, we show that the propagated noises are largely filtered regardless of the states in the input genes. The noise-filtering property of an interlinked FFL can be largely derived from that of the individual FFLs and with interlinked FFLs, it is possible to filter noises in both “ON” and “OFF” states in the output. We demonstrated the noise filtering effect in the developmental regulatory network of Caenorhabditis elegans that controls the timing of distal tip cell (DTC) migration. The roles of positive feedback loops involving blmp-1 and the degradation regulation of DRE-1 also studied. Our analyses allow for better inference from network structures to noise-filtering properties and provide insights into the mechanisms behind the precise DTC migration controls in space and time.
Enzymatic properties, evidence for in vivo expression, and intracellular localization of shewasin D, the pepsin homolog from Shewanella denitrificans
Authors: Leal Ana Rita , Cruz Rui , Bur Daniel , Huesgen Pitter F. , Faro Rosário , Manadas Bruno , Wlodawer Alexander , Faro Carlos , Simões Isaura 
Published: March 2016

AbstractThe widespread presence of pepsin-like enzymes in eukaryotes together with their relevance in the control of multiple biological processes is reflected in the large number of studies published so far for this family of enzymes. By contrast, pepsin homologs from bacteria have only recently started to be characterized. The work with recombinant shewasin A from Shewanella amazonensis provided the first documentation of this activity in prokaryotes. Here we extend our studies to shewasin D, the pepsin homolog from Shewanella denitrificans, to gain further insight into this group of bacterial peptidases that likely represent ancestral versions of modern eukaryotic pepsin-like enzymes. We demonstrate that the enzymatic properties of recombinant shewasin D are strongly reminiscent of eukaryotic pepsin homologues. We determined the specificity preferences of both shewasin D and shewasin A using proteome-derived peptide libraries and observed remarkable similarities between both shewasins and eukaryotic pepsins, in particular with BACE-1, thereby confirming their phylogenetic proximity. Moreover, we provide first evidence of expression of active shewasin D in S. denitrificans cells, confirming its activity at acidic pH and inhibition by pepstatin. Finally, our results revealed an unprecedented localization for a family A1 member by demonstrating that native shewasin D accumulates preferentially in the cytoplasm.
Field-driven domain wall motion under a bias current in the creep and flow regimes in Pt/[CoSiB/Pt]N nanowires
Authors: Choi Y. H. , Yoshimura Y. , Kim K.-J. , Lee K. , Kim T. W. , Ono T. , You C.-Y. , Jung M. H. 
Published: March 2016

AbstractThe dynamics of magnetic domain wall (DW) in perpendicular magnetic anisotropy Pt/[CoSiB/Pt]N nanowires was studied by measuring the DW velocity under a magnetic field (H) and an electric current (J) in two extreme regimes of DW creep and flow. Two important findings are addressed. One is that the field-driven DW velocity increases with increasing N in the flow regime, whereas the trend is inverted in the creep regime. The other is that the sign of spin current-induced effective field is gradually reversed with increasing N in both DW creep and flow regimes. To reveal the underlying mechanism of new findings, we performed further experiment and micromagnetic simulation, from which we found that the observed phenomena can be explained by the combined effect of the DW anisotropy, Dzyaloshinskii-Moriya interaction, spin-Hall effect, and spin-transfer torques. Our results shed light on the mechanism of DW dynamics in novel amorphous PMA nanowires, so that this work may open a path to utilize the amorphous PMA in emerging DW-based spintronic devices.
High-affinity Anticalins with aggregation-blocking activity directed against the Alzheimer β-amyloid peptide
Authors: Rauth Sabine , Hinz Dominik , Börger Michael , Uhrig Markus , Mayhaus Manuel , Riemenschneider Matthias , Skerra Arne 
Published: March 2016

Amyloid beta (Aβ) peptides, in particular Aβ42 and Aβ40, exert neurotoxic effects and their overproduction leads to amyloid deposits in the brain, thus constituting an important biomolecular target for treatments of Alzheimer's disease (AD). We describe the engineering of cognate Anticalins as a novel type of neutralizing protein reagent based on the human lipocalin scaffold. Phage display selection from a genetic random library comprising variants of the human lipocalin 2 (Lcn2) with mutations targeted at 20 exposed amino acid positions in the four loops that form the natural binding site was performed using both recombinant and synthetic target peptides and resulted in three different Anticalins. Biochemical characterization of the purified proteins produced by periplasmic secretion in Escherichia coli revealed high folding stability in a monomeric state, with Tm values ranging from 53.4°C to 74.5°C, as well as high affinities for Aβ40, between 95 pM and 563 pM, as measured by real-time surface plasmon resonance analysis. The central linear VFFAED epitope within the Aβ sequence was mapped using a synthetic peptide array on membranes and was shared by all three Anticalins, despite up to 13 mutual amino acid differences in their binding sites. All Anticalins had the ability–with varying extent–to inhibit Aβ aggregation in vitro according to the thioflavin-T fluorescence assay and, furthermore, they abolished Aβ42-mediated toxicity in neuronal cell culture. Thus, these Anticalins provide not only useful protein reagents to study the molecular pathology of AD but they also show potential as alternative drug candidates compared with antibodies.
Influence of biological subject, shielding cage, and resonance frequency on radio wave propagation in a birdcage coil
Authors: Seo J.‐H. , Ryu Y. , Han S.‐D. , Song H. , Kim H.‐K. , Kim K.‐N. 
Published: March 2016

Radio wave propagation of three types of birdcage transmit/receive radio‐frequency (RF) coils (lowpass filter, highpass filter, and bandpass filter configurations) was analysed for mouse body magnetic resonance imaging at main magnetic fields of 1.5, 3.0, 4.7, 7.0, 9.4, and 11.7 T (Larmor frequencies of 63.87, 127.74, 200, 300, 400, and 500 MHz) in terms of magnetic (|B1|) field sensitivity and homogeneity. The observed radio wave propagation in the central axial |B1| field, as influenced by the biological subject, was calculated numerically in the finite‐difference time‐domain method and compared with assessment criteria using the mean value and standard deviation. The results for different Larmor frequencies RF shielding cage configurations, and biological subject loading versus unloading were compared and are discussed in detail.
Phosphorylation of OPTN by TBK1 enhances its binding to Ub chains and promotes selective autophagy of damaged mitochondria
Authors: Richter Benjamin , Sliter Danielle A. , Herhaus Lina , Stolz Alexandra , Wang Chunxin , Beli Petra , Zaffagnini Gabriele , Wild Philipp , Martens Sascha , Wagner Sebastian A. , Youle Richard J. , Dikic Ivan 
Published: March 2016

Significance
Selective autophagy of damaged mitochondria (mitophagy) requires protein kinases PINK1 and TBK1, ubiquitin ligase Parkin, and autophagy receptors such as OPTN, driving ubiquitin-labeled mitochondria into autophagosomes. Because all proteins have been genetically linked to either Parkinson’s disease (PINK1 and Parkin) or amyotrophic lateral sclerosis and frontotemporal lobar degeneration (TBK1 and OPTN), it is of great interest to understand their physiological functions. By utilizing quantitative proteomics we show that TBK1 phosphorylates four receptors on several autophagy-relevant sites. Constitutive interaction of TBK1 with OPTN and the ability of OPTN to bind to ubiquitin chains are essential for TBK1 recruitment and activation on mitochondria. TBK1-mediated phosphorylation of OPTN creates a signal amplification loop through combining recruitment and retention of OPTN/TBK1 on ubiquitinated mitochondria.
Knowledge management for logistics service providers: the role of learning culture
Authors: Cooper Andrew L. , Huscroft Joseph R , Overstreet Robert E. , Hazen Benjamin T 
Published: March 2016

Purpose– Knowledge management capabilities have proven to be key success factors for organizations within our increasingly information-based economy. Although knowledge management literature has a rich history, less is known about how an organization’s learning culture affects outcomes realized via knowledge management initiatives. Moreover, there is a dearth of understanding regarding how to successfully operationalize knowledge management activities in order to achieve performance in the dynamic logistics and supply chain management environment. Rooted in competence-based theory, the purpose of this paper is to examine the role that learning culture plays with regard to knowledge management capabilities, human capital, and organizational performance at logistics service providers.Design/methodology/approach– This study uses survey data from 448 managers and covariance based structural equation modeling to assess how knowledge management, learning culture, and human capital influence organizational performance.Findings– The results of this study indicate that knowledge management has a significant positive relationship with learning culture and human capital. There was also an indirect effect of knowledge management through learning culture on human capital and organizational performance. Interestingly, human capital did not have a significant relationship with organizational performance as hypothesized.Practical implications– The results support the vital role that leaders and managers have in creating a culture that is conducive to the success of knowledge management initiatives.Originality/value– This study goes beyond the simple direct relationship between knowledge management and personal and organizational outcomes that is usually examined by testing learning culture as an important mediator.
The effect of local business climate on employment
Authors: Fölster Stefan , Jansson Li , Nyrenström Gidehag Anton 
Published: March 2016

Purpose– The purpose of this paper is to analyse empirically whether policies to improve the local business climate affect employment in general, and among groups of immigrants that suffer from structural unemployment.Design/methodology/approach– The paper analyses the relation between Swedish entrepreneurs’ perception of the local business climate and total employment as well as employment among immigrants born outside of Europe, a group that tends to be particularly affected by structural unemployment. Instrumental variable and Arellano-Bond GMM estimation indicate that a better local business climate improves immigrants employment considerably more than total employment.Findings– The results suggest that improvements in institutions and policies that entrepreneurs perceive as shaping the business climate may have an important effect on employment, in particular employment of groups that tend to have high rates of structural unemployment. Given the limitations, the estimates appear robust over a variety of specifications.Research limitations/implications– The authors use a subjective measure of local business climate policies, but instrument this with an exogenous variable and lagged variables. The unit of observation are Swedish municipalities, which in contrast to other countries control many factors important for business.Practical implications– Employment policies often focus on labour market institutions. The results suggest that other policies and their local implementation may be equally important for employment. Unfortunately the study does not reveal much detail of which specific measures give the greatest effects. That remains to be done in future research.Social implications– The positive employment effects the authors find are particularly large for immigrants born outside of Europe. If the results are correct, then better local business climate could make an important contribution to social cohesion.Originality/value– While there are more studies that analyse the relation between entrepreneurship and employment, much fewer previous studies have tried to establish a link between business climate policies and employment. The authors do this with a novel approach.
The impact of higher quality government regulation of business and greater economic freedom on living standards
Authors: Cebula Richard , Rossi Fabrizio , Clark Jeff 
Published: March 2016

Purpose
– The purpose of this paper is to evaluate whether two specific forms of government policy influence entrepreneurship and hence the performance economy as a whole. Performance is measured in terms of living standards and growth therein. The policies are, as follows: higher quality government regulation of businesses and higher levels of economic freedom.

Design/methodology/approach
– The paper first provides a basic model focussing upon the regulation and economic freedom variables. The study then adds a dummy variable for G8 nations, a tax burden variable, and the long-term interest rate and provides six estimates. The empirical analysis involves pooled time-series/cross-section data for the OECD over the period 2003-2007.

Findings
– The findings indicate that for OECD nations, higher quality public regulation promotes entrepreneurial spirit and performance. Higher economic freedom does the same. The findings are that higher quality government regulation of business and higher levels of economic freedom lead to higher growth rates in the standard of living.

Originality/value
– The time period studied, i.e., just prior to the Great Recession, the context of the OECD, the adoption of pooled time-series/cross-section data, and the specific choice of variables in the analysis, along with the estimation of possibly unique or close to unique specifications involving the growth rate of living standards per se make this study different.
Rising damp in Portuguese cultural heritage – a flood risk map
Authors: Boinas Raquel , Guimarães Ana Sofia , Delgado João M.P.Q. 
Published: March 2016

Purpose
– The purpose of this paper is to present a critical review of a criterion of risk, created to assess the flood risk of the international heritage building. In order to evaluate this criterion, it was applied to a sample of Portuguese building heritage.

Design/methodology/approach
– This effort will start with the definition of the most important historical buildings in Portugal, its location and a full study about its constitution considering not only the materials they are made to but also the layers and the influence of the porosity/porometry for the drying process. Then it will also crucial the classification of the flood risk occurrence having in mind the previous information. A mapping will be made with the classification here developed.

Findings
– This work presents a critical review of the main information related with the Portuguese monuments classified as “National Monuments”. A new empirical model was proposed takes into account all of the factors defined as the most influent in flood risk determination. A risk map was created on the basis classification developed. It will be possible to observe that a significant amount of Portuguese monuments are classified as medium to high risk of flooding.

Originality/value
– This paper presents a new methodology to analyse the flood risk of international heritage building. The main benefit of the work is that it discusses the importance architectural heritage and justifies the need to safeguard it from extreme climatic phenomena such as floods.
Eosinophilic pustular folliculitis: A proposal of diagnostic and therapeutic algorithms
Authors: Nomura Takashi , Katoh Mayumi , Yamamoto Yosuke , Miyachi Yoshiki , Kabashima Kenji 
Published: March 2016

AbstractEosinophilic pustular folliculitis (EPF) is a sterile inflammatory dermatosis of unknown etiology. In addition to classic EPF, which affects otherwise healthy individuals, an immunocompromised state can cause immunosuppression‐associated EPF (IS‐EPF), which may be referred to dermatologists in inpatient services for assessments. Infancy‐associated EPF (I‐EPF) is the least characterized subtype, being observed mainly in non‐Japanese infants. Diagnosis of EPF is challenging because its lesions mimic those of other common diseases, such as acne and dermatomycosis. Furthermore, there is no consensus regarding the treatment for each subtype of EPF. Here, we created procedure algorithms that facilitate the diagnosis and selection of therapeutic options on the basis of published work available in the public domain. Our diagnostic algorithm comprised a simple flowchart to direct physicians toward proper diagnosis. Recommended regimens were summarized in an easy‐to‐comprehend therapeutic algorithm for each subtype of EPF. These algorithms would facilitate the diagnostic and therapeutic procedure of EPF.
Facultative grazing and bioturbation by macrodetritivores alter saltmarsh plant–plant interactions under stress
Authors: Howison Ruth A. , Olff Han , van Puijenbroek Marinka E. B. , Smit Christian 
Published: March 2016

Summary

The importance of positive plant–plant interactions is generally suggested to increase towards more stressful conditions, due to mutual stress amelioration between plants. Bioturbating macrodetritivores can also ameliorate stress through bioturbation, but can also become selective herbivores under food‐limited conditions, making the outcome of plant–plant interactions under stress in the presence of macrodetritivores unclear.

We studied how combining environmental stress (waterlogging) with the presence of the soil macrodetritivore Orchestia gammarellus affected the outcome of the interaction between two salt marsh plants: the tall, late successional Elytrigia atherica and the shorter, early successional Festuca rubra.

In a replacement design competition experiment under controlled conditions, we found that soil redox potential was negatively affected by waterlogging and positively affected by the presence of O. gammarellus. The survival and shoot biomass of E. atherica was not significantly affected by waterlogging or by the presence of bioturbators. The survival and shoot biomass of F. rubra was especially decreased when waterlogging was combined with the presence of O. gammarellus, as this macrodetritivore turned into a selective grazer on F. rubra under these conditions.

We found that E. atherica produced double shoot biomass and F. rubra produced much less shoot biomass in their mixed cultures than was expected from the monocultures of same waterlogging/Orchestia treatments. Hence, the presence of the bioturbator strongly promoted the competitive advantage of E. atherica over F. rubra due to the combination of stress amelioration for the first species and selective herbivory on the second species.

Synthesis. This study shows that the inclusion of bioturbating macrodetritivores complicates the standard prediction that plant–plant interactions become more positive towards more stressful conditions. A novel insight is that macrodetritivores can affect the structure and diversity of plant communities through multiple mechanisms. Under benign conditions bioturbating macrodetritivores ameliorated soil conditions, permitting co‐occurrence of competing plant species. At high environmental stress (waterlogging) macrodetritivores selectively graze higher quality plant species and emerging seedlings, thus promoting dominance of the lower quality species. Hence, the facultative feeding behaviour of macrodetritivores deserves further attention.
Revascularization with percutaneous coronary intervention does not affect androgen status in males with chronic stable angina pectoris
Authors: Gosai J. N. , Charalampidis P. , Nikolaidou T. , Parviz Y. , Morris P. D. , Channer K. S. , Jones T. H. , Grech E. D. 
Published: March 2016

SummaryThere is a clear association between low serum testosterone and coronary artery disease (CAD) in men. Hypotestosteronaemia is associated with accelerated atherosclerosis and a quarter of men with CAD are biochemically hypogonadal. Amongst those with CAD, hypotestosteronaemia is associated with increased mortality. Testosterone vasodilates coronary arteries, and exogenous testosterone reduces ischaemia. Whether hypotestosteronaemia is a cause or a consequence of CAD remains unanswered. The aim of this prospective observational study was to investigate whether coronary revascularization affected androgen status in men with stable angina pectoris. Twenty five men (mean age 62.7, SD 9.18) with angiographically significant CAD and symptomatic angina underwent full coronary revascularization by percutaneous coronary intervention. Androgen status and symptoms of angina, stress, depression and sexual function were assessed before, and at one and 6 months after the coronary revascularization. All patients underwent complete revascularization which was associated with a significant reduction in angina symptoms and ischaemia. No significant difference was seen in total testosterone (11.33 nmol/L baseline; 12.56, 1 month post; 13.04 at 6 months; p = 0.08). A significant and sustained rise in sex hormone‐binding globulin was seen (33.99 nm/L baseline; 36.11 nm/L 1 month post PCI; 37.94 nm/L at 6 months; p = 0.03) Overall, there was no significant alteration in any other marker of androgen status including free testosterone or bioavailable testosterone. There was no change in symptoms of anxiety, depression or sexual function. Coronary revascularization has no sustained effect on androgen status. This supports the hypothesis that hypotestosteronaemia is not a consequence of angina pectoris or myocardial ischaemia.
Challenges in nourishing the intrauterine growth‐restricted foetus – Lessons learned from studies in the intrauterine growth‐restricted foetal sheep
Authors: Hay William W. , Brown Laura D. , Rozance Paul J. , Wesolowski Stephanie R. , Limesand Sean W. 
Published: March 2016

AbstractPrevious attempts to improve growth and development of the intrauterine growth‐restricted (IUGR) foetus during pregnancy have not worked or caused harm. Our research identifies tissue‐specific mechanisms underlying foetal growth restriction and then tests strategies to improve growth and ameliorate many of the metabolic problems before the infant is born. The goal of our studies is to reduce the impact of foetal growth restriction at critical stages of development on the lifelong complications of IUGR offspring.ConclusionDefining specific mechanisms that cause growth restriction in the foetus might identify specific nutrients and hormones that could be given to the mother to improve foetal growth and reduce metabolic complications, using strategies first tested in our IUGR animal model.