bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploitation of Velocity Gradients by Sympatric Stream Salmonids: Basic Insights and Implications for Instream Flow Management
Authors: Naman Sean M. , Rosenfeld Jordan S. , Jordison Eva , Kuzyk Melanie , Eaton Brett C. 
Published: December 2019

Abstract
Hydraulic heterogeneity can strongly influence habitat selection by stream fishes. Velocity gradients created by channel roughness and flow obstructions may be particularly important for species that feed on drifting invertebrates, where maintaining focal points in low-velocity microhabitats adjacent to faster water allows fish to scan a larger water volume for prey while minimizing swimming costs. However, these velocity gradients are rarely integrated into habitat suitability criteria used for defining instream flow requirements, which are generally based on mean column velocity measurements at the focal point location. It is also unclear how velocity gradient exploitation differs among sympatric drift-feeding species. We measured the use of velocity gradients by two sympatric juvenile salmonids, Coho Salmon Oncorhynchus kisutch and steelhead O. mykiss, in a midorder cobble–boulder-dominated river. We compared focal point velocities of fish to adjacent velocities within their foraging area and compared the magnitude of velocity and kinetic energy gradients between species. We then explored how lateral velocity gradients may bias instream flow assessments by deriving two sets of velocity habitat suitability curves (HSCs): conventional HSCs using average water column velocities measured at focal point locations and spatially averaged HSCs incorporating adjacent velocities (four body lengths from focal points). These contrasting HSCs were then used as input into the physical habitat simulation model to predict the influence of flow on habitat availability. Both species often used focal velocities that were lower than adjacent points, but the magnitude of these velocity gradients was higher for steelhead, consistent with known differences in foraging behavior, habitat selection, and physiology. Incorporating adjacent velocities into HSCs resulted in a ~40% (steelhead) and ~10% (Coho Salmon) increase in flows predicted to optimize habitat availability. Thus, small-scale heterogeneity in velocity used by drift-feeding fish can lead to large biases in flow assessments.
Network traffic identification of several open source secure proxy protocols
Authors: Zhang Yidan , Chen Jiageng , Chen Kaiming , Xu Ruoyan , Teh Jesen , Zhang Shuai 
Published: December 2019

SummarySecure proxy technique has a wide range of applications especially in the area of VPN to protect the private communication from being surveilled. However, the adversaries may also take advantage of the VPN services for other purposes. Thus, knowing the characteristics of the corresponding security protocols will benefit the administration to narrow down the targets. Also, given the various VPN services on the market, we also want to know whether there exists some security flaws from the cryptographic protocol's point of view, so that can be used to improve analyzing the protocol. In this paper, we first target several widely used open source secure proxy protocols and provide their weaknesses through the static analysis. Then we apply the deep learning technique to train all the related network traffic, and our results showed that all the secure proxy traffics can be successfully distinguished with high accuracy.
Perivascular Neuropilin‐1 expression is an independent marker of improved survival in renal cell carcinoma
Authors: Morin Eric , Lindskog Cecilia , Johansson Martin , Egevad Lars , Sandström Per , Harmenberg Ulrika , Claesson‐Welsh Lena , Sjöberg Elin 
Published: December 2019

AbstractRenal cell carcinoma (RCC) treatment has improved in the last decade with the introduction of drugs targeting tumor angiogenesis. However, the 5‐year survival of metastatic disease is still only 10–15%. Here, we explored the prognostic significance of compartment‐specific expression of Neuropilin 1 (NRP1), a co‐receptor for vascular endothelial growth factor (VEGF). NRP1 expression was analyzed in RCC tumor vessels, in perivascular tumor cells, and generally in the tumor cell compartment. Moreover, complex formation between NRP1 and the main VEGF receptor, VEGFR2, was determined. Two RCC tissue microarrays were used; a discovery cohort consisting of 64 patients and a validation cohort of 314 patients. VEGFR2/NRP1 complex formation in cis (on the same cell) and trans (between cells) configurations was determined by in situ proximity ligation assay (PLA), and NRP1 protein expression in three compartments (endothelial cells, perivascular tumor cells, and general tumor cell expression) was determined by immunofluorescent staining. Expression of NRP1 in perivascular tumor cells was explored as a marker for RCC survival in the two RCC cohorts. Results were further validated using a publicly available gene expression dataset of clear cell RCC (ccRCC). We found that VEGFR2/NRP1 trans complexes were detected in 75% of the patient samples. The presence of trans VEGFR2/NRP1 complexes or perivascular NRP1 expression was associated with a reduced tumor vessel density and size. When exploring NRP1 as a biomarker for RCC prognosis, perivascular NRP1 and general tumor cell NRP1 protein expression correlated with improved survival in the two independent cohorts, and significant results were obtained also at the mRNA level using the publicly available ccRCC gene expression dataset. Only perivascular NRP1 expression remained significant in multivariable analysis. Our work shows that perivascular NRP1 expression is an independent marker of improved survival in RCC patients, and reduces tumor vascularization by forming complexes in trans with VEGFR2 in the tumor endothelium. © 2019 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
Association of autophagy status with amount of Fusobacterium nucleatum in colorectal cancer
Authors: Haruki Koichiro , Kosumi Keisuke , Hamada Tsuyoshi , Twombly Tyler S , Väyrynen Juha P , Kim Sun A , Masugi Yohei , Qian Zhi Rong , Mima Kosuke , Baba Yoshifumi , da Silva Annacarolina , Borowsky Jennifer , Arima Kota , Fujiyoshi Kenji , Lau Mai Chan , Li Peilong , Guo Chunguang , Chen Yang , Song Mingyang , Nowak Jonathan A , Nishihara Reiko , Yanaga Katsuhiko , Zhang Xuehong , Wu Kana , Bullman Susan , Garrett Wendy S , Huttenhower Curtis , Meyerhardt Jeffrey A , Giannakis Marios , Chan Andrew T , Fuchs Charles S , Ogino Shuji 
Published: December 2019

AbstractFusobacterium nucleatum (F. nucleatum), which has been associated with colorectal carcinogenesis, can impair anti‐tumour immunity, and actively invade colon epithelial cells. Considering the critical role of autophagy in host defence against microorganisms, we hypothesised that autophagic activity of tumour cells might influence the amount of F. nucleatum in colorectal cancer tissue. Using 724 rectal and colon cancer cases within the Nurses' Health Study and the Health Professionals Follow‐up Study, we evaluated autophagic activity of tumour cells by immunohistochemical analyses of BECN1 (beclin 1), MAP1LC3 (LC3), and SQSTM1 (p62) expression. We measured the amount of F. nucleatum DNA in tumour tissue by quantitative polymerase chain reaction (PCR). We conducted multivariable ordinal logistic regression analyses to examine the association of tumour BECN1, MAP1LC3, and SQSTM1 expression with the amount of F. nucleatum, adjusting for potential confounders, including microsatellite instability status; CpG island methylator phenotype; long‐interspersed nucleotide element‐1 methylation; and KRAS, BRAF, and PIK3CA mutations. Compared with BECN1‐low cases, BECN1‐intermediate and BECN1‐high cases were associated with lower amounts of F. nucleatum with odds ratios (for a unit increase in three ordinal categories of the amount of F. nucleatum) of 0.54 (95% confidence interval, 0.29–0.99) and 0.31 (95% confidence interval, 0.16–0.60), respectively (Ptrend < 0.001 across ordinal BECN1 categories). Tumour MAP1LC3 and SQSTM1 levels were not significantly associated with the amount of F. nucleatum (Ptrend > 0.06). Tumour BECN1, MAP1LC3, and SQSTM1 levels were not significantly associated with patient survival (Ptrend > 0.10). In conclusion, tumour BECN1 expression is inversely associated with the amount of F. nucleatum in colorectal cancer tissue, suggesting a possible role of autophagy in the elimination of invasive microorganisms. © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
How does knowledge of atmospheric gravity waves guide their parameterizations?
Authors: Plougonven Riwal , de la Cámara Alvaro , Hertzog Albert , Lott François 
Published: December 2019

AbstractThis note discusses the relation between our knowledge of gravity waves and the parameterization of their effects in global models. Improving these parameterizations represents a major motivation for current research on atmospheric gravity waves. Indeed, as a major portion of the gravity wave spectrum is on the subgrid scale, parameterizations are used to represent their impacts on large‐scale flow. Gravity wave parameterizations generally share a common framework, with assumptions on their propagation (columnar only) and their sources (tropospheric only). These assumptions are highly justified to leading order, and parameterizations have been successful in allowing models to reproduce a number of middle‐atmospheric features. Once this framework is set up, specifying the sources constitutes a poorly constrained step. In practice, sources are tuned to a large extent in order to improve the modelled atmospheric circulation, a process that includes compensating for model biases. Consequently, significant efforts have been made to better quantify the sources of gravity waves, combining observations, modelling and theory, stimulating ground‐breaking progress in our knowledge and understanding of atmospheric gravity waves. As emphasized in this note, however, the transfer to parameterizations is not straightforward: knowledge of the characteristics of lower‐stratospheric gravity waves does not directly translate into input parameters for parameterizations. The example of intermittency is used to illustrate the impact of a (minor) shift in the parameterization framework, leading to a redistribution of the resulting forcing in the middle atmosphere. Recent studies have highlighted a number of phenomena which fall outside of the classical framework of parameterizations, notably lateral propagation and secondary generation. This growing body of evidence calls for further investigations to determine which of these phenomena could have systematic and robust implications for the larger‐scale flow. To retain appropriate simplicity of the parameterizations, efforts to identify acceptable simplifications should also be undertaken in parallel, in a framework of a model hierarchy.
Stochastic robust finite‐time boundedness for semi‐Markov jump uncertain neutral‐type neural networks with mixed time‐varying delays via a generalized reciprocally convex combination inequality
Authors: Zhang Haiyang , Qiu Zhipeng , Liu Xinzhi , Xiong Lianglin 
Published: December 2019

SummaryThis article investigates the stochastic robust finite‐time boundedness problem for semi‐Markov jump uncertain (SMJU) neutral‐type neural networks with distributed and additive time‐varying delays (TDs). To derive less conservative stability criteria, a generalized reciprocally convex combination inequality (RCCI) is first proposed, which includes the existing RCCIs as its special cases. By taking full advantage of the characteristics of various TDs and SMJU parameters, a novel suitable Lyapunov‐Krasovskii functional is provided. Then, with the virtue of the new RCCI and other analysis approaches, some new criteria guaranteeing the underlying systems are stochastically robustly finite‐time bounded or stable and are derived in the form of linear matrix inequalities. Finally, three numerical examples are given to show the validity of the approaches presented in this article.
Self‐Assembled Collagen Microparticles by Aerosol as a Versatile Platform for Injectable Anisotropic Materials
Authors: Lama Milena , Fernandes Francisco M. , Marcellan Alba , Peltzer Juliette , Trouillas Marina , Banzet Sébastien , Grosbot Marion , Sanchez Clément , Giraud‐Guille Marie‐Madeleine , Lataillade Jean‐Jacques , Coulomb Bernard , Boissière Cédric , Nassif Nadine 
Published: December 2019

AbstractExtracellular matrices (ECM) rich in type I collagen exhibit characteristic anisotropic ultrastructures. Nevertheless, working in vitro with this biomacromolecule remains challenging. When processed, denaturation of the collagen molecule is easily induced in vitro avoiding proper fibril self‐assembly and further hierarchical order. Here, an innovative approach enables the production of highly concentrated injectable collagen microparticles, based on collagen molecules self‐assembly, thanks to the use of spray‐drying process. The versatility of the process is shown by performing encapsulation of secretion products of gingival mesenchymal stem cells (gMSCs), which are chosen as a bioactive therapeutic product for their potential efficiency in stimulating the regeneration of a damaged ECM. The injection of collagen microparticles in a cell culture medium results in a locally organized fibrillar matrix. The efficiency of this approach for making easily handleable collagen microparticles for encapsulation and injection opens perspectives in active tissue regeneration and 3D bioprinted scaffolds.
Effects of Ligand Concentration on the Thermal Properties, Structure, and Digestibility of Maize Starch Inclusion Complexes with Ascorbyl Palmitate
Authors: Zhou Dingpeng , Liu Shaowei , Liu Xue , Tang Xiaozhi 
Published: December 2019

AbstractThe alkaline method is used to form the complex between starch and ascorbyl palmitate (AP) in this study. Normal maize starch (NMS) and high amylose maize starch (HAMS) are screened to investigate the effects of AP concentrations (0%, 2.5%, 5.0%, 10.0%, 20.0%) on the properties of complexes at 60 °C. HAMS can bind more AP than NMS because of more amylose content. Comparing the endothermic peaks in DSC analysis, 5% and 10% AP levels are sufficient to interact with NMS and HAMS, respectively. The disappeared or weakened AP characteristic absorption peaks in FTIR spectra prove the formation of V‐amylose structure. The XRD analyses reveal that the inclusion complexes are formed with AP with six glucose units per turn due to the steric hindrance of AP, and the self‐aggregation of AP in the complexes is also detected. The self‐aggregation of AP do not affect the indigested ordered helical chain segments of starch in in vitro digestion. The 5% and 10% AP levels are enough to decrease the rate and extent of starch digestion in NMS and HAMS complexes, respectively. The formation of starch‐AP inclusion complexes also appear to enhance the stability of AP against light, heat, and oxidation.
Preparation and Properties of Compatible Starch‐PCL Composites: Effects of the NCO Functionality in Compatibilizer
Authors: Weng Fangqing , Zhang Peirui , Guo Duyu , Koranteng Ernest , Wu Zhengshun , Wu Qiangxian 
Published: December 2019

AbstractAs is well known, poor interfacial interactions between hydrophilic corn starch (CS) and hydrophobic thermoplastic matrices have been an obstacle in application of the quality biomass material like CS. The addition of compatibilizers is an effective method to improve the interface interaction. In this work, a special interficial structure using polyurethane crosslinked layer as compatible interface is designed and compatibilizers with different NCO functionality are also applied. The purpose of this work is to investigate the effects of compatibilizers with different NCO functionality (f,f= 0, 1, 2, 3) on the compatibility of corn starch‐polycaprolactone (CS‐PCL) composites. Subsequently, various CS‐PCL composites are prepared using compatiblizers with different NCO functionality (f= 0, 1, 2, 3) via melting process. The structural analysis, mechanical properties, and water absorption capability as well as the thermal stability of the composites reveal that the properties of the composites are only enhanced significantly when the NCO functionality is no less than 2. In short, whenf≥ 2, a crosslinked layer could be formed at the interface of the composite to afford a compatible CS‐PCL composite.
Observables and amplitudes for spinning particles and black holes
Authors: Maybee Ben , O’Connell Donal , Vines Justin 
Published: December 2019

AbstractWe develop a general formalism for computing classical observables for relativistic scattering of spinning particles, directly from on-shell amplitudes. We then apply this formalism to minimally coupled Einstein-gravity amplitudes for the scattering of massive spin 1/2 and spin 1 particles with a massive scalar, constructed using the double copy. In doing so we reproduce recent results at first post-Minkowskian order for the scattering of spinning black holes, through quadrupolar order in the spin-multipole expansion.
Scan–rescan and inter-vendor reproducibility of neurite orientation dispersion and density imaging metrics
Authors: Andica Christina , Kamagata Koji , Hayashi Takuya , Hagiwara Akifumi , Uchida Wataru , Saito Yuya , Kamiya Kouhei , Fujita Shohei , Akashi Toshiaki , Wada Akihiko , Abe Masahiro , Kusahara Hiroshi , Hori Masaaki , Aoki Shigeki 
Published: December 2019

Abstract
Purpose
The reproducibility of neurite orientation dispersion and density imaging (NODDI) metrics in the human brain has not been explored across different magnetic resonance (MR) scanners from different vendors. This study aimed to evaluate the scan–rescan and inter-vendor reproducibility of NODDI metrics in white and gray matter of healthy subjects using two 3-T MR scanners from two vendors.

Methods
Ten healthy subjects (7 males; mean age 30 ± 7 years, range 23–37 years) were included in the study. Whole-brain diffusion-weighted imaging was performed with b-values of 1000 and 2000 s/mm2 using two 3-T MR scanners from two different vendors. Automatic extraction of the region of interest was performed to obtain NODDI metrics for whole and localized areas of white and gray matter. The coefficient of variation (CoV) and intraclass correlation coefficient (ICC) were calculated to assess the scan–rescan and inter-vendor reproducibilities of NODDI metrics.

Results
The scan–rescan and inter-vendor reproducibility of NODDI metrics (intracellular volume fraction and orientation dispersion index) were comparable with those of diffusion tensor imaging (DTI) metrics. However, the inter-vendor reproducibilities of NODDI (CoV = 2.3–14%) were lower than the scan–rescan reproducibility (CoV: scanner A = 0.8–3.8%; scanner B = 0.8–2.6%). Compared with the finding of DTI metrics, the reproducibility of NODDI metrics was lower in white matter and higher in gray matter.

Conclusion
The lower inter-vendor reproducibility of NODDI in some brain regions indicates that data acquired from different MRI scanners should be carefully interpreted.
Regions of white matter abnormalities in the arcuate fasciculus in veterans with anger and aggression problems
Authors: David Szabolcs , Heesink Lieke , Geuze Elbert , Gladwin Thomas , van Honk Jack , Kleber Rolf , Leemans Alexander 
Published: December 2019

AbstractAggression after military deployment is a common occurrence in veterans. Neurobiological research has shown that aggression is associated with a dysfunction in a network connecting brain regions implicated in threat processing and emotion regulation. However, aggression may also be related to deficits in networks underlying communication and social cognition. The uncinate and arcuate fasciculi are integral to these networks, thus studying potential abnormalities in these white matter connections can further our understanding of anger and aggression problems in military veterans. Here, we use diffusion tensor imaging tractography to investigate white matter microstructural properties of the uncinate fasciculus and the arcuate fasciculus in veterans with and without anger and aggression problems. A control tract, the parahippocampal cingulum was also included in the analyses. More specifically, fractional anisotropy (FA) estimates are derived along the trajectory from all fiber pathways and compared between both groups. No between-group FA differences are observed for the uncinate fasciculus and the cingulum, however parts of the arcuate fasciculus show a significantly lower FA in the group of veterans with aggression and anger problems. Our data suggest that abnormalities in arcuate fasciculus white matter connectivity that are related to self-regulation may play an important role in the etiology of anger and aggression in military veterans.
Evolutionary dataset optimisation: learning algorithm quality through evolution
Authors: Wilde Henry , Knight Vincent , Gillard Jonathan 
Published: December 2019

AbstractIn this paper we propose a novel method for learning how algorithms perform. Classically, algorithms are compared on a finite number of existing (or newly simulated) benchmark datasets based on some fixed metrics. The algorithm(s) with the smallest value of this metric are chosen to be the ‘best performing’. We offer a new approach to flip this paradigm. We instead aim to gain a richer picture of the performance of an algorithm by generating artificial data through genetic evolution, the purpose of which is to create populations of datasets for which a particular algorithm performs well on a given metric. These datasets can be studied so as to learn what attributes lead to a particular progression of a given algorithm. Following a detailed description of the algorithm as well as a brief description of an open source implementation, a case study in clustering is presented. This case study demonstrates the performance and nuances of the method which we call Evolutionary Dataset Optimisation. In this study, a number of known properties about preferable datasets for the clustering algorithms known ask-means and DBSCAN are realised in the generated datasets.
Contemporary Artists’ Books and the Intimate Aesthetics of Illness
Authors: Bolaki Stella 
Published: December 2019

AbstractThis essay brings together critical perspectives from the discrete traditions of artists’ books and the medical humanities to examine artists’ books by three contemporary artists – Penny Alexander, Martha A. Hall and Amanda Watson-Will – that treat experiences of illness and wellbeing. Through its focus on a multimodal and multisensory art form that has allegiances with, but is not reduced to, narrative, the essay adds to recent calls to rethink key assumptions of illness narrative study and to challenge utilitarian approaches. In particular, it draws attention to the aesthetic and imaginative elements of illness communication by exploring how artists’ books represent lived experiences in a distinctively palpable way and offer an “intimate authority” that extends beyond narrative legitimacy or a form of struggle against the medical gaze. By interrogating narrative’s dominance in medical humanities research, the essay further expands awareness of illness experiences that resist conventional forms of representation (such as chronic illness), and of alternative reflective practices within healthcare education that encourage engagement with both mind and body.