bluuebunny/crossref_metadata_2025 huggingface dataset:
Population differentiation and historical demography of the threatened snowy plover Charadrius nivosus (Cassin, 1858)
Authors: D’Urban Jackson Josephine , Bruford Michael W. , Székely Tamás , DaCosta Jeffrey M. , Sorenson Michael D. , Russo Isa-Rita M. , Maher Kathryn H. , Cruz-López Medardo , Galindo-Espinosa Daniel , Palacios Eduardo , De Sucre-Medrano Atahualpa Eduardo , Cavitt John , Pruner Raya , Morales Alcides L. , Gonzalez Oscar , Burke Terry , Küpper Clemens
Published: February 2020

Delineating conservation units is a complex and often controversial process that is particularly challenging for highly vagile species. Here, we reassess population genetic structure and identify those populations of highest conservation value in the threatened snowy plover (Charadrius nivosus,Cassin, 1858), a partial migrant shorebird endemic to the Americas. We use four categories of genetic data—mitochondrial DNA (mtDNA), microsatellites, Z-linked and autosomal single nucleotide polymorphisms (SNPs)—to: (1) assess subspecies delineation and examine population structure (2) compare the sensitivity of the different types of genetic data to detect spatial genetic patterns, and (3) reconstruct demographic history of the populations analysed. Delineation of two traditionally recognised subspecies was broadly supported by all data. In addition, microsatellite and SNPs but not mtDNA supported the recognition of Caribbean snowy plovers (C. n. tenuirostris) and Floridian populations (easternC. n. nivosus) as distinct genetic lineage and deme, respectively. Low migration rates estimated from autosomal SNPs (m < 0.03) reflect a general paucity of exchange between genetic lineages. In contrast, we detected strong unidirectional migration (m = 0.26) from the western into the easternnivosusdeme. Within westernnivosus,we found no genetic differentiation between coastal Pacific and inland populations. The correlation between geographic and genetic distances was weak but significant for all genetic data sets. All demes showed signatures of bottlenecks occurring during the past 1000 years. We conclude that at least four snowy plover conservation units are warranted: in addition to subspeciesnivosusandoccidentalis,a third unit comprises the Caribbeantenuirostrislineage and a fourth unit the distinct easternnivosusdeme.
Unraveling Molecular Mechanisms of THAP1 Missense Mutations in DYT6 Dystonia
Authors: Cheng Fubo , Walter Michael , Wassouf Zinah , Hentrich Thomas , Casadei Nicolas , Schulze-Hentrich Julia , Barbuti Peter , Krueger Rejko , Riess Olaf , Grundmann-Hauser Kathrin , Ott Thomas
Published: February 2020

Mutations in THAP1 (THAP domain-containing apoptosis-associated protein 1) are responsible for DYT6 dystonia. Until now, more than eighty different mutations in THAP1 gene have been found in patients with primary dystonia, and two third of them are missense mutations. The potential pathogeneses of these missense mutations in human are largely elusive. In the present study, we generated stable transfected human neuronal cell lines expressing wild-type or mutated THAP1 proteins found in DYT6 patients. Transcriptional profiling using microarrays revealed a set of 28 common genes dysregulated in two mutated THAP1 (S21T and F81L) overexpression cell lines suggesting a common mechanism of these mutations. ChIP-seq showed that THAP1 can bind to the promoter of one of these genes, superoxide dismutase 2 (SOD2). Overexpression of THAP1 in SK-N-AS cells resulted in increased SOD2 protein expression, whereas fibroblasts from THAP1 patients have less SOD2 expression, which indicates that SOD2 is a direct target gene of THAP1. In addition, we show that some THAP1 mutations (C54Y and F81L) decrease the protein stability which might also be responsible for altered transcription regulation due to dosage insufficiency. Taking together, the current study showed different potential pathogenic mechanisms of THAP1 mutations which lead to the same consequence of DYT6 dystonia.
The effects of diagenesis on the petrophysical and geochemical attributes of the Asmari Formation, Marun oil field, southwest Iran
Authors: Jafari J. , Mahboubi A. , Moussavi-Harami R. , Al-Aasm I. S.
Published: February 2020

The distribution of good reservoir quality and its causes is the main challenges in carbonate reservoir characterization. This study investigates the effects of diagenetic processes on the reservoir quality of the carbonate successions of the Asmari Formation, in the Marun oil field, southwest Iran. The study applies an integrated approach including core petrography, petrophysical rock typing, stable carbon and oxygen isotopes as well as major and trace elements analyses. Petrographic studies and geochemical analyses express that the Asmari limestones have been affected mainly by compaction, dissolution, recrystallization, calcite and anhydrite cementation and dolomitization. Among those diagenetic overprints, dolomitization and dissolution played an important role to enhance the reservoir quality of the formation. Moreover, four types of dolomites were recognized and the rate of dolomitization increases toward the top of the Asmari carbonate successions. Possible models for dolomitization include mixing zone, brine reflux, seepage reflux and tidal pumping of seawater. Employing Flow Zone Index and Discrete Rock Type concepts led to classification of the Asmari reservoir into seven reservoir rock types. Integrating reservoir rock typing with petrographic studies and geochemical analyses also confirms that reservoir quality of the Asmari Fm. would have been mainly controlled by diagenetic processes. Moreover, stable isotopes, trace elements and facies analyses support the idea that carbonate intervals of the Asmari Formation were deposited in a warm, shallow-water environment under a saline condition.
Early mobilisation after transfemoral transcatheter aortic valve implantation: results of the MobiTAVI trial
Authors: Vendrik J. , Vlastra W. , van Mourik M. S. , Delewi R. , Beijk M. A. , Lemkes J. , Wykrzykowska J. J. , de Winter R. J. , Henriques J. S. , Piek J. J. , Vis M. M. , Koch K. T. , Baan J.
Published: February 2020

Background

Immobilisation of patients after transfemoral transcatheter aortic valve implantation (TF-TAVI) is the standard of care, mostly to prevent vascular complications. However, immobilisation may increase post-operative complications such as delirium and infections. In this trial, we determine whether it is feasible and safe to implement early ambulation after TF-TAVI.

Methods

We prospectively included TF-TAVI patients from 2016 to 2018. Patients were assessed for eligibility using our strict safety protocol and were allocated (based on the time at which the procedure ended) to the EARLY or REGULAR group.

Results

A total of 150 patients (49%) were deemed eligible for early mobilisation, of which 73 were allocated to the EARLY group and 77 to the REGULAR group. The overall population had a mean age of 80 years, 48% were male with a Society of Thoracic Surgeons Predicted Risk of Mortality (STS-PROM) score of 3.8 ± 1.8. Time to mobilisation was 4 h 49 min ± 31 min in the EARLY group versus 20 h 7 min ± 3 h 6 min in the REGULAR group (p < 0.0001). There were no differences regarding the primary endpoint. No major vascular complications occurred and a similar incidence of minor vascular complications was seen in both groups (4/73 [5.5%] vs 6/77 [7.8%], p = 0.570). The incidence of the combined secondary endpoint was lower in the EARLY group (p = 0.034), with a numerically lower incidence for all individual outcomes (delirium, infections, pain and unplanned urinary catheter use).

Conclusion

Early mobilisation (ambulation 4–6 h post-procedure) of TF-TAVI patients is feasible and safe. Early ambulation decreases the combined incidence of delirium, infections, pain and unplanned urinary catheter use, and its adoption into contemporary TAVI practice may therefore be beneficial.
Ammoniacal nitrogen removal by Eichhornia crassipes-based phytoremediation: process optimization using response surface methodology
Authors: Ting W. H. T. , Tan I. A. W. , Salleh S. F. , Abdul Wahab N.
Published: February 2020

Eutrophication is a serious environmental issue that needs urgent concern. There is necessity to treat wastewater with high ammoniacal nitrogen (AN) concentration to the permissible standard limit to protect the aquatic ecosystem. This study investigated the optimum condition for AN removal from wastewater using Eichhornia crassipes-based phytoremediation process. Face-centered central composite design (CCD) was employed as the experimental design, in which four operational variables including pH (4–10), retention time (2–14 days), macrophyte density (5–30 g/L) and salinity (0–5 g NaCl/L) were involved in the study, while five responses were investigated, namely AN removal efficiency (Y1), fresh biomass growth (Y2), COD (Y3), BOD (Y4) and TSS (Y5). AN removal was the main focus in this study. Through numerical optimization, the highest AN removal efficiency of 77.48% (initial AN concentration = 40 mg/L) was obtained at the following optimum condition: pH 8.51, retention time of 8.47 days, macrophyte density of 21.39 g/L and salinity of 0 g NaCl/L. The values predicted from the models agreed satisfactorily with the experimental values, which implied that response surface methodology was reliable and practical for experimental design developed using optimization of the phytoremediation process. The validation experiment using real semiconductor effluent further supported the high potential of the E. crassipes-based phytoremediation system to remove AN and other organic pollutants in this industrial effluent under optimal condition.
Prediction of Preheating Temperatures for S690QL High Strength Steel Using FEM-Simulation for High Power Laser Welding
Authors: Partes Knut , Schmidt Malte , Gorny Sven
Published: February 2020

This study investigates a method for predicting the effect of preheating temperatures on the resulting hardness for high power laser welding of high strength steel. An FEM model is introduced containing a hardness calculation based on an existing model. Moreover, the hardness values of experimental results have been measured in order to show the performance of the model. The hardness calculation requires the chemical composition and the t8/5-time at the point of measurement. It is claimed that a calibration of the melt pool width and depth at room temperature only is enough to get reasonable results from the FEM-model for higher preheating temperatures. From the experimental result of a single experiment the width of a weld seam and the depth was deducted. In this study experiments have been done at various preheating temperatures in order to show the correlation between the model and the experimental results at various temperatures. The hardness equation provides suitable results in the verification with the measurements. The prediction of preheating temperature can be done with the resulting t8/5-time of the FEM-model. This method can decrease the amount of time and costs within a production according to testing and analyzing a matrix of process parameters. Moreover it is concluded that this methodology might be used for single item production.
Transition Metal Aluminum Boride as a New Candidate for Ambient-Condition Electrochemical Ammonia Synthesis
Authors: Fu Yang , Richardson Peter , Li Kangkang , Yu Hai , Yu Bing , Donne Scott , Kisi Erich , Ma Tianyi
Published: February 2020

Achieving more meaningful N2 conversion by reducing the energy input and carbon footprint is now being investigated through a method of N2 fixation instead of the Haber–Bosch process. Unfortunately, the electrochemical N2 reduction reaction (NRR) method as a rising approach currently still shows low selectivity (Faradaic efficiency < 10%) and high-energy consumption [applied potential at least − 0.2 V versus the reversible hydrogen electrode (RHE)]. Here, the role of molybdenum aluminum boride single crystals, belonging to a family of ternary transition metal aluminum borides known as MAB phases, is reported for the electrochemical NRR for the first time, at a low applied potential (− 0.05 V versus RHE) under ambient conditions and in alkaline media. Due to the unique nano-laminated crystal structure of the MAB phase, these inexpensive materials have been found to exhibit excellent electrocatalytic performances (NH3 yield: 9.2 µg h−1 cm−2 mg
cat.
−1
, Faradaic efficiency: 30.1%) at the low overpotential, and to display a high chemical stability and sustained catalytic performance. In conjunction, further mechanism studies indicate B and Al as main-group metals show a highly selective affinity to N2 due to the strong interaction between the B 2p/Al 3p band and the N 2p orbitals, while Mo exhibits specific catalytic activity toward the subsequent reduction reaction. Overall, the MAB-phase catalyst under the synergy of the elements within ternary compound can suppress the hydrogen evolution reaction and achieve enhanced NRR performance. The significance of this work is to provide a promising candidate in the future synthesis of ammonia.
Two-Dimensional Materials in Large-Areas: Synthesis, Properties and Applications
Authors: Zavabeti Ali , Jannat Azmira , Zhong Li , Haidry Azhar Ali , Yao Zhengjun , Ou Jian Zhen
Published: February 2020

Large-area and high-quality two-dimensional crystals are the basis for the development of the next-generation electronic and optical devices. The synthesis of two-dimensional materials in wafer scales is the first critical step for future technology uptake by the industries; however, currently presented as a significant challenge. Substantial efforts have been devoted to producing atomically thin two-dimensional materials with large lateral dimensions, controllable and uniform thicknesses, large crystal domains and minimum defects. In this review, recent advances in synthetic routes to obtain high-quality two-dimensional crystals with lateral sizes exceeding a hundred micrometres are outlined. Applications of the achieved large-area two-dimensional crystals in electronics and optoelectronics are summarised, and advantages and disadvantages of each approach considering ease of the synthesis, defects, grain sizes and uniformity are discussed.
Preserving the Knowledge of the Past Through Virtual Visits: From 3D Laser Scanning to Virtual Reality Visualisation at the Istanbul Çatalca İnceğiz Caves
Authors: Büyüksalih Gürcan , Kan Tuna , Özkan Gözde Enç , Meriç Müge , Isın Lale , Kersten Thomas P.
Published: February 2020

Cultural landscapes are those that are shaped through the combined forces of cultural and natural activity, typically over a long period that may reach back to historic and prehistoric times. Amongst these, the documenting, modelling and visualisation of cave landscapes have always been particularly important for scientific communities such as speleology. In the current state of the art, terrestrial laser scanning provides a level of documentation of objects whose accuracy cannot be achieved by conventional methods. In addition to the highly accurate metric and geometric information, visual information brings incredible richness to the presentation of data. Virtual reality (VR) allows individuals to immerse themselves within virtual environments to explore monuments and other cultural heritage sites up close. More and more, VR systems are available at lower prices and are not only limited to VR labs. In this paper, we present research on the generation of a virtual 3D model of the İnceğiz caves, located at the Çatalca district of Istanbul, Turkey, and its integration within the Unity 3D game engine. This project, carried out as a collaboration between BİMTAŞ, a company of the Greater Municipality of Istanbul, Turkey and the Photogrammetry & Laser Scanning Lab of the HafenCity University Hamburg, Germany, aimed at developing an immersive and interactive VR visualisation of the cave for the HTC Vive Pro VR system. The entire workflow, from data acquisition to VR visualisation, is described here in detail with particular emphasis given to the 3D modelling of the cave and its integration within a VR environment.
Reception
Authors: Bridges Emma , Stead Henry
Published: February 2020

Chris Davies’ Blockbusters and the Ancient World is the latest addition to a growing body of scholarly literature on cinematic receptions of antiquity. The author takes as his focus the swathe of ancient world epics produced since the 9/11 terrorist attacks in 2001, ranging from movies set in the ancient Greek world (including the 2004 films Troy and Alexander, and, from 2007, 300) to the Roman occupation of Britain – as seen in King Arthur (2004), The Last Legion (2007), Centurion (2010), and The Eagle (2011) – as well as those which concentrate on aspects of Christianity (Agora, of 2009, set in Alexandria in the early fifth century ce, as contrasted with the 2004 biblical epic The Passion of the Christ). Structured around a series of case studies of these individual films, the book undoubtedly adds a set of valuable contributions to the scholarly literature on each piece; its real strength lies, however, in the way in which the author draws comparisons between these case studies while simultaneously situating the movies within their wider historical, political, and cultural contexts. Davies’ introduction alone – with a broad overview of the development of cinematic depictions of antiquity from the birth of cinema to contemporary productions, along with definitions of key terms – provides an excellent starting point for those new to thinking about ancient world films, and a comprehensive filmography of works referenced is a useful research tool. There is much here too, however, which will be of value to those seeking more in-depth discussion. Detailed analysis of the films themselves – with attention to staging, casting, and characterization – is accompanied by discussion of critical responses and evidence from published interviews with directors and producers. The author is careful to point out that artistic products often resist straightforward interpretation, and that multiple readings of each film are possible (for example, the critical reception of a movie may infer a different relationship to contemporary politics than the stated intentions of its creative team). He also explores the development and fluidity of genres, and the ways in which several of these films hybridize more than one genre (for example, traces of the western are strongly evident in the Roman Britain epics; and The Passion of the Christ carries striking elements of the horror genre). What results is a sensitive exploration of the films’ relationship to US politics, in the particular context of the ‘War on Terror’ and the US-led invasions of Iraq and Afghanistan, which examines ways in which the films ‘have inspired allegorical and metaphorical readings in which the past has been used to contextualise, warn or parallel the present’ (209).
‘Soft reinforcement’ of the round window for superior semi-circular canal dehiscence syndrome
Authors: Gona A , Phillips J S
Published: February 2020

Background

Individuals with superior semi-circular canal syndrome often describe vestibular symptoms elicited by loud sounds, as well as other pressure-induced symptoms. They also often report other symptoms, including autophony, hyperacusis, cognitive dysfunction, spatial disorientation, anxiety and migraine headaches. Symptoms occur due to the presence of a ‘third window’ created by the dehiscence of the superior semi-circular canal. This case report describes a minimally invasive technique to provide soft reinforcement of the round window.

Case report

Our patient underwent a permeatal procedure whereby the tympanic membrane was raised to allow inspection of the middle ear. The round window niche was identified and the round window membrane was reinforced with fat. The mucosa of the bony meatus leading to the round window was then disrupted before the application of a double layer of perichondrium to allow further reinforcement.

Conclusion

The case provides support for the use of ‘soft reinforcement’ as a simple and effective technique to treat the symptoms of superior canal dehiscence syndrome.
Walks of Experience: Site-Specific Performance Walks, Active Listening and Uncomfortable Witnessing
Authors: PINE EMILIE , CASSERLY MAEVE , LANE TOM
Published: February 2020

Digital-audio performance walks can be powerful performances, responding to troubling pasts, giving voice to testimony, and creating an affective geography that satisfies a participant's desire to connect with the city rather than just walk through it. Yet digital-audio performance walks also raise questions about performance and voyeurism, and the disconnection of private headphone experience, alongside issues of agency, detachment and appropriation. This article addresses key issues associated with digital-audio performance walks, using two case studies of performance walks (from Israel and Ireland), that aim to communicate politically charged and painful histories, which are at once ‘now’ and ‘then’, ‘here’ and ‘there’. The article considers some of the risks in digital-audio performance walks: dark tourism, privatization and empathic quietism. Finally, the article assesses what creative strategies are available to creators – and audiences – to make collaborative performance walks that galvanize spectators to become active witnesses.
Ship Type Recognition via a Coarse-to-Fine Cascaded Convolution Neural Network
Authors: Chen Xinqiang , Yang Yongsheng , Wang Shengzheng , Wu Huafeng , Tang Jinjun , Zhao Jiansen , Wang Zhihuan
Published: February 2020

Most previous research has handled the task of ship type recognition by exploring hand-craft ship features, which may fail to distinguish ships with similar visual appearances. This situation motivates us to propose a novel deep learning based ship type recognition framework which we have named coarse-to-fine cascaded convolution neural network (CFCCNN). First, the proposed CFCCNN framework formats the input training ship images and data, and provides trainable input data for the hidden layers of the CFCCNN. Second, the coarse and fine steps are run in a nesting manner to explore discriminative features for different ship types. More specifically, the coarse step is trained in a similar manner to the traditional convolution neural network, while the fine step introduces regularisation mechanisms to extract more intrinsic ship features, and fine tunes parameter settings to obtain better recognition performance. Finally, we evaluate the performance of the CFCCNN model for recognising the most common types of merchant ship (oil tanker, container, LNG tanker, chemical carrier, general cargo, bulk carrier, etc.). The experimental results show that the proposed framework obtains better recognition performance than the conventional methods of ship type recognition.
Challenges, strategies and research priorities in legume-based nitrogen management for organic small grain producers in the Northeastern US
Authors: Pickoff Margaret , Leahy Jessica , Mallory Ellen B.
Published: February 2020

High yields and crop quality in organic small grain production can only be achieved through successful management of nitrogen. Experienced farmers and advisors in the Northeastern U.S. were asked to discuss the most pressing challenges in organic nitrogen management for organic small grain systems, with a particular focus on legume green manures (LGMs). Eighteen semi-structured interviews with 12 farmers and eight advisors were conducted between December 2017 and March 2018. The farmers employed a range of materials and practices for fulfilling the nitrogen fertility needs of their crops, including LGMs, animal manures and organic fertilizers. Farmers and advisors identified cost, overdependence on external nitrogen sources, nitrogen source access, diversifying rotations, weed management and predicting nitrogen mineralization of organic residues as major challenges in nitrogen management. Results indicated that cost-effectiveness in nitrogen management is essential, but that farmers consider additional factors, such as weed pressure and long-term soil health effects, when choosing nitrogen sources or practices. Legume-based nitrogen fertility is promising for small grain systems in this region, but structural challenges, such as the lack of animal agriculture proximal to grain operations, and limited cash crop markets, impede the development of diverse rotations that feature long-term legume sods. Recommendations include additional field-based research, including on-farm, participatory LGM studies as one avenue. Programming and educational outreach should focus on bolstering farmers' understanding of nitrogen mineralization of incorporated LGM residues, as well as their ability to anticipate and respond to sources of variability in LGM systems.
Examining Local Time Variations in the Gains and Losses of Open Magnetic Flux During Substorms
Authors: Mooney M. K. , Forsyth C. , Rae I. J. , Chisham G. , Coxon J. C. , Marsh M. S. , Jackson D. R. , Bingham S. , Hubert B.
Published: February 2020

The open magnetic flux content of the magnetosphere varies during substorms as a result of dayside and nightside reconnection. The open flux can be calculated from the area of the polar cap, delineated by the open‐closed field line boundary (OCB). This study presents a superposed epoch analysis of the location of the OCB and the change in the magnetic flux content in individual nightside MLT sectors during substorm growth, expansion, and recovery phases. Far ultraviolet (FUV) observations from the IMAGE satellite are used to derive a proxy of the OCB location. In the hour prior to substorm onset, the total nightside flux content increases by up to 0.12 GWb on average, resulting in an equatorward expansion of the OCB. Following substorm onset, the OCB contracts toward the pole as the open magnetic flux content decreases by up to 0.14 GWb on average, but the rate of decrease of the total nightside open flux content differs by 5–66% between the three IMAGE far ultraviolet instruments. The OCB does not contract poleward uniformly in all nightside magnetic local time (MLT) sectors after substorm onset. Close to the substorm onset MLT sector, the OCB contracts immediately following substorm onset; however, the OCB in more dawnward and duskward MLT sectors continues to expand equatorward for up to 120 minutes after substorm onset. Despite the continued increase in flux in these sectors after substorm onset, the total nightside flux content decreases immediately at substorm onset, indicating that the nightside reconnection rate exceeds the dayside rate following substorm onset.
SKS Splitting Measurements in NE China: New Insights Into the Wudalianchi Intraplate Volcanism and Mantle Dynamics
Authors: Lu Mingwen , Lei Jianshe , Zhao Dapeng , Ai Yinshuang , Xu Xiwei , Zhang Guibin
Published: February 2020

To better understand the Wudalianchi intraplate volcanism and mantle dynamics in NE China, we collect abundant teleseismic waveform data during 2008 to 2018 recorded at 259 seismic stations around the Wudalianchi volcano. These stations include 148 WAVESArray portable stations, 66 NECESSArray portable stations and 45 Chinese provincial stations. Our newly deployed WAVESArray makes the station intervals of ~20–30 km around the Wudalianchi volcano. Using the minimum transverse‐energy grid‐search method, we make effective SKS splitting measurements at 192 stations. Our results show that the fast direction in the study region is mainly NW‐SE, but there are obvious contrasts within and between different tectonic units. To the east of the North‐South Gravity Lineament, around the Wudalianchi volcano, our SKS splitting measurements show a southeastward opening U‐shaped pattern in the fast direction and splitting time. Such a pattern of seismic anisotropy could be caused by horizontal and vertical flows in the big mantle wedge due to the deep subduction, long stagnancy, and deep dehydration of the Pacific slab in the mantle transition zone. The horizontal flow in the big mantle wedge could be obstructed by the thicker lithosphere under the Great Xing'an range and disturbed by hot and wet upwelling flow under the Wudalianchi volcano. Around the Nuominhe and Halaha volcanic groups, variations in the splitting parameters may also be associated with lithospheric deformation and delamination, though they are located at the edge of our study region. These results shed new light on the intraplate volcanism and mantle dynamics in NE China.
Machine Learning Predicts Reach‐Scale Channel Types From Coarse‐Scale Geospatial Data in a Large River Basin
Authors: Guillon Hervé , Byrne Colin F. , Lane Belize A. , Sandoval Solis Samuel , Pasternack Gregory B.
Published: February 2020

Hydrologic and geomorphic classifications have gained traction in response to the increasing need for basin‐wide water resources management. Regardless of the selected classification scheme, an open scientific challenge is how to extend information from limited field sites to classify tens of thousands to millions of channel reaches across a basin. To address this spatial scaling challenge, this study leverages machine learning to predict reach‐scale geomorphic channel types using publicly available geospatial data. A bottom‐up machine learning approach selects the most accurate and stable model among
20,000 combinations of 287 coarse geospatial predictors, preprocessing methods, and algorithms in a three‐tiered framework to (i) define a tractable problem and reduce predictor noise, (ii) assess model performance in statistical learning, and (iii) assess model performance in prediction. This study also addresses key issues related to the design, interpretation, and diagnosis of machine learning models in hydrologic sciences. In an application to the Sacramento River basin (California, USA), the developed framework selects a Random Forest model to predict 10 channel types previously determined from 290 field surveys over 108,943 two hundred‐meter reaches. Performance in statistical learning is reasonable with a 61% median cross‐validation accuracy, a sixfold increase over the 10% accuracy of the baseline random model, and the predictions coherently capture the large‐scale geomorphic organization of the landscape. Interestingly, in the study area, the persistent roughness of the topography partially controls channel types and the variation in the entropy‐based predictive performance is explained by imperfect training information and scale mismatch between labels and predictors.
Enhanced autocrine FGF19/FGFR4 signaling drives the progression of lung squamous cell carcinoma, which responds to mTOR inhibitor AZD2104
Authors: Li Fan , Li Ziming , Han Qing , Cheng Yirui , Ji Wenxiang , Yang Ying , Lu Shun , Xia Weiliang
Published: February 2020

Lung cancer occurrence and associated mortality ranks top in all countries. Despite the rapid development of targeted and immune therapies, many patients experience relapse within a few years. It is urgent to uncover the mechanisms that drive lung cancer progression and identify novel molecular targets. Our group has previously identified FGF19 as a prognostic marker and potential driver gene of lung squamous cell carcinomas (LSQ) in Chinese smoking patients. However, the underlying mechanism of how FGF19 promotes the progression of LSQ remains unclear. In this study, we characterized and confirmed that FGF19 serves as an oncogenic driver in LSQ development and progression, and reported that the amplification and high expression of FGF19 in LSQ was significantly associated with poor overall and progression-free survival. A higher serum level of FGF19 was found in lung cancer patients, which could also serve as a novel diagnostic index to screen lung cancer. Overproduction of FGF19 in LSQ cells markedly promoted cell growth, progression and metastasis, while downregulating FGF19 effectively inhibited LSQ progression in vitro and in vivo. Moreover, downregulating the receptor FGFR4 was also effective to suppress the growth and migration of LSQ cells. Since FGF19 could be induced by smoking or endoplasmic reticulum stress, to tackle the more malignant FGF19-overproducing LSQ, we reported for the first time that inhibiting mTOR pathway by using AZD2014 was effective and feasible. These findings have offered a new strategy by using anti-FGF19/FGFR4 therapy or mTOR-based therapy in FGF19-driven LSQ.
SIRT3-mediated inhibition of FOS through histone H3 deacetylation prevents cardiac fibrosis and inflammation
Authors: Palomer Xavier , Román-Azcona M. Silvia , Pizarro-Delgado Javier , Planavila Ana , Villarroya Francesc , Valenzuela-Alcaraz Brenda , Crispi Fátima , Sepúlveda-Martínez Álvaro , Miguel-Escalada Irene , Ferrer Jorge , Nistal J. Francisco , García Raquel , Davidson Mercy M. , Barroso Emma , Vázquez-Carrera Manuel
Published: February 2020

Sirtuin 3 (SIRT3) is a deacetylase that modulates proteins that control metabolism and protects against oxidative stress. Modulation of SIRT3 activity has been proposed as a promising therapeutic target for ameliorating metabolic diseases and associated cardiac disturbances. In this study, we investigated the role of SIRT3 in inflammation and fibrosis in the heart using male mice with constitutive and systemic deletion of SIRT3 and human cardiac AC16 cells. SIRT3 knockout mice showed cardiac fibrosis and inflammation that was characterized by augmented transcriptional activity of AP-1. Consistent with this, SIRT3 overexpression in human and neonatal rat cardiomyocytes partially prevented the inflammatory and profibrotic response induced by TNF-α. Notably, these effects were associated with a decrease in the mRNA and protein levels of FOS and the DNA-binding activity of AP-1. Finally, we demonstrated that SIRT3 inhibits FOS transcription through specific histone H3 lysine K27 deacetylation at its promoter. These findings highlight an important function of SIRT3 in mediating the often intricate profibrotic and proinflammatory responses of cardiac cells through the modulation of the FOS/AP-1 pathway. Since fibrosis and inflammation are crucial in the progression of cardiac hypertrophy, heart failure, and diabetic cardiomyopathy, our results point to SIRT3 as a potential target for treating these diseases.
Genome-wide association and multi-omic analyses reveal ACTN2 as a gene linked to heart failure
Authors: Arvanitis Marios , Tampakakis Emmanouil , Zhang Yanxiao , Wang Wei , Auton Adam ,   23andMe Research Team, Agee Michelle , Aslibekyan Stella , Bell Robert K. , Bryc Katarzyna , Clark Sarah K. , Elson Sarah L. , Fletez-Brant Kipper , Fontanillas Pierre , Furlotte Nicholas A. , Gandhi Pooja M. , Heilbron Karl , Hicks Barry , Hinds David A. , Huber Karen E. , Jewett Ethan M. , Jiang Yunxuan , Kleinman Aaron , Lin Keng-Han , Litterman Nadia K. , McCreight Jennifer C. , McIntyre Matthew H. , McManus Kimberly F. , Mountain Joanna L. , Mozaffari Sahar V. , Nandakumar Priyanka , Noblin Elizabeth S. , Northover Carrie A. M. , O’Connell Jared , Pitts Steven J. , Poznik G. David , Sathirapongsasuti J. Fah , Shastri Anjali J. , Shelton Janie F. , Shringarpure Suyash , Tian Chao , Tung Joyce Y. , Tunney Robert J. , Vacic Vladimir , Wang Xin , Zare Amir S. , Dutta Diptavo , Glavaris Stephanie , Keramati Ali , Chatterjee Nilanjan , Chi Neil C. , Ren Bing , Post Wendy S. , Battle Alexis
Published: February 2020

Heart failure is a major public health problem affecting over 23 million people worldwide. In this study, we present the results of a large scale meta-analysis of heart failure GWAS and replication in a comparable sized cohort to identify one known and two novel loci associated with heart failure. Heart failure sub-phenotyping shows that a new locus in chromosome 1 is associated with left ventricular adverse remodeling and clinical heart failure, in response to different initial cardiac muscle insults. Functional characterization and fine-mapping of that locus reveal a putative causal variant in a cardiac muscle specific regulatory region activated during cardiomyocyte differentiation that binds to the ACTN2 gene, a crucial structural protein inside the cardiac sarcolemma (Hi-C interaction p-value = 0.00002). Genome-editing in human embryonic stem cell-derived cardiomyocytes confirms the influence of the identified regulatory region in the expression of ACTN2. Our findings extend our understanding of biological mechanisms underlying heart failure.
Open access resource for cellular-resolution analyses of corticocortical connectivity in the marmoset monkey
Authors: Majka Piotr , Bai Shi , Bakola Sophia , Bednarek Sylwia , Chan Jonathan M. , Jermakow Natalia , Passarelli Lauretta , Reser David H. , Theodoni Panagiota , Worthy Katrina H. , Wang Xiao-Jing , Wójcik Daniel K. , Mitra Partha P. , Rosa Marcello G. P.
Published: February 2020

Understanding the principles of neuronal connectivity requires tools for efficient quantification and visualization of large datasets. The primate cortex is particularly challenging due to its complex mosaic of areas, which in many cases lack clear boundaries. Here, we introduce a resource that allows exploration of results of 143 retrograde tracer injections in the marmoset neocortex. Data obtained in different animals are registered to a common stereotaxic space using an algorithm guided by expert delineation of histological borders, allowing accurate assignment of connections to areas despite interindividual variability. The resource incorporates tools for analyses relative to cytoarchitectural areas, including statistical properties such as the fraction of labeled neurons and the percentage of supragranular neurons. It also provides purely spatial (parcellation-free) data, based on the stereotaxic coordinates of 2 million labeled neurons. This resource helps bridge the gap between high-density cellular connectivity studies in rodents and imaging-based analyses of human brains.
One-dimensional flat bands in twisted bilayer germanium selenide
Authors: Kennes D. M. , Xian L. , Claassen M. , Rubio A.
Published: February 2020

Experimental advances in the fabrication and characterization of few-layer materials stacked at a relative twist of small angle have recently shown the emergence of flat energy bands. As a consequence electron interactions become relevant, providing inroads into the physics of strongly correlated two-dimensional systems. Here, we demonstrate by combining large scale ab initio simulations with numerically exact strong correlation approaches that an effective one-dimensional system emerges upon stacking two twisted sheets of GeSe, in marked contrast to all moiré systems studied so far. This not only allows to study the necessarily collective nature of excitations in one dimension, but can also serve as a promising platform to scrutinize the crossover from two to one dimension in a controlled setup by varying the twist angle, which provides an intriguing benchmark with respect to theory. We thus establish twisted bilayer GeSe as an intriguing inroad into the strongly correlated physics of lowdimensional systems.
Rift Valley fever virus vaccination induces long-lived, antigen-specific human T cell responses
Authors: Harmon Jessica R. , Barbeau Dominique J. , Nichol Stuart T. , Spiropoulou Christina F. , McElroy Anita K.
Published: February 2020

Rift Valley fever virus (RVFV) is a zoonotic arbovirus of clinical significance in both livestock and humans. A formalin-inactivated virus preparation was initially developed for human use and tested in laboratory workers in the 1960s. Vaccination resulted in generation of neutralizing antibody titers in most recipients, but neutralization titers waned over time, necessitating frequent booster doses. In this study, T cell-based immune responses to the formalin-inactivated vaccine were examined in a cohort of seven individuals who received between 1 and 6 doses of the vaccine. RVFV-specific T cell responses were detectable up to 24 years post vaccination. Peripheral blood mononuclear cells from this cohort of individuals were used to map out the viral epitopes targeted by T cells in humans. These data provide tools for assessing human RVFV-specific T cell responses and are thus a valuable resource for future human RVFV vaccine efforts.
Author Correction: The Reprimo gene family member, reprimo-like (rprml), is required for blood development in embryonic zebrafish
Authors: Stanic Karen , Reig German , Figueroa Ricardo J. , Retamal Pedro A. , Wichmann Ignacio A. , Opazo Juan C. , Owen Gareth I. , Corvalán Alejandro H. , Concha Miguel L. , Amigo Julio D.
Published: February 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Kinetics of Photo-Oxidation of Oxazole and its Substituents by Singlet Oxygen
Authors: Zeinali Nassim , Oluwoye Ibukun , Altarawneh Mohammednoor , Dlugogorski Bogdan Z.
Published: February 2020

Oxazole has critical roles not only in heterocycle (bio)chemistry research, but also as the backbone of many active natural and medicinal species. These diverse and specialised functions can be attributed to the unique physicochemical properties of oxazole. This contribution investigates the reaction of oxazole and its derivatives with singlet oxygen, employing density functional theory DFT-B3LYP calculations. The absence of allylic hydrogen in oxazole eliminates the ene-mode addition of singlet oxygen to the aromatic ring. Therefore, the primary reaction pathway constitutes the [4 + 2]-cycloaddition of singlet oxygen to oxazole ring, favouring an energetically accessible corridor of 57 kJ/mol to produce imino-anhydride which is postulated to convert to triamide end-product in subsequent steps. The pseudo-first-order reaction rate for substituted oxazole (e.g., 4-methyl-2,5-diphenyloxazole, 1.14 × 106 M−1 s−1) appears slightly higher than that of unsubstituted oxazole (0.94 × 106 M−1 s−1) considering the same initial concentration of the species at 300 K, due to the electronic effect of the functional groups. The global reactivity descriptors have justified the relative influence of the functional groups along with their respective physiochemical properties.
Exploring the temporal dynamics of speech production with EEG and group ICA
Authors: Janssen Niels , Meij Maartje van der , López-Pérez Pedro Javier , Barber Horacio A.
Published: February 2020

Speech production is a complex skill whose neural implementation relies on a large number of different regions in the brain. How neural activity in these different regions varies as a function of time during the production of speech remains poorly understood. Previous MEG studies on this topic have concluded that activity proceeds from posterior to anterior regions of the brain in a sequential manner. Here we tested this claim using the EEG technique. Specifically, participants performed a picture naming task while their naming latencies and scalp potentials were recorded. We performed group temporal Independent Component Analysis (group tICA) to obtain temporally independent component timecourses and their corresponding topographic maps. We identified fifteen components whose estimated neural sources were located in various areas of the brain. The trial-by-trial component timecourses were predictive of the naming latency, implying their involvement in the task. Crucially, we computed the degree of concurrent activity of each component timecourse to test whether activity was sequential or parallel. Our results revealed that these fifteen distinct neural sources exhibit largely concurrent activity during speech production. These results suggest that speech production relies on neural activity that takes place in parallel networks of distributed neural sources.
Whole genome sequencing reveals extended natural transformation in Campylobacter impacting diagnostics and the pathogens adaptive potential
Authors: Golz Julia C. , Epping Lennard , Knüver Marie-Theres , Borowiak Maria , Hartkopf Felix , Deneke Carlus , Malorny Burkhard , Semmler Torsten , Stingl Kerstin
Published: February 2020

Campylobacter is the major bacterial agent of human gastroenteritis worldwide and represents a crucial global public health burden. Species differentiation of C. jejuni and C. coli and phylogenetic analysis is challenged by inter-species horizontal gene transfer. Routine real-time PCR on more than 4000 C. jejuni and C. coli field strains identified isolates with ambiguous PCR results for species differentiation, in particular, from the isolation source eggs. K-mer analysis of whole genome sequencing data indicated the presence of C. coli hybrid strains with huge amounts of C. jejuni introgression. Recombination events were distributed over the whole chromosome. MLST typing was impaired, since C. jejuni sequences were also found in six of the seven housekeeping genes. cgMLST suggested that the strains were phylogenetically unrelated. Intriguingly, the strains shared a stress response set of C. jejuni variant genes, with proposed roles in oxidative, osmotic and general stress defence, chromosome maintenance and repair, membrane transport, cell wall and capsular biosynthesis and chemotaxis. The results have practical impact on routine typing and on the understanding of the functional adaption to harsh environments, enabling successful spreading and persistence of Campylobacter.
Documentation of a new hypotrich species in the family Amphisiellidae, Lamtostyla gui n. sp. (Protista, Ciliophora) using a multidisciplinary approach
Authors: Liao Wanying , Gong Zhiwei , Ni Bing , Fan Xinpeng , Petroni Giulio
Published: February 2020

An integrated approach considering both morphologic and molecular data is now required to improve biodiversity estimations and provide more robust systematics interpretations in hypotrichs, a highly differentiated group of ciliates. In present study, we document a new hypotrich species, Lamtostyla gui n. sp., collected from Chongming wetland, Shanghai, China, based on investigations using living observation, protargol staining, scanning and transmission electron microscopy, and gene sequencing. The new species is mainly recognized by having a short amphisiellid median cirral row composed of four cirri, three frontoventral cirri, three dorsal kinetids, four to eight macronuclear nodules, and small colorless cortical granules distributed as rosettes around dorsal bristles. Transmission electron microscope observation finds the associated microtubules of cirri and pharyngeal discs of L. gui are distinct from those in other hypotrichs. Morphogenesis of this species indicates that parental adoral membranelles retained intact or partial renewed is a potential feature to separate Lamtostyla granulifera-group and Lamtostyla lamottei-group. Phylogenetic analysis based on small subunit ribosomal RNA (rRNA) gene shows that this molecular marker is not useful to resolve phylogenetic relationships of the genus Lamtostyla, as well as many other hypotrichous taxa. We additionally characterize the internal transcribed spacers (ITS) region and the almost complete large subunit rRNA, which will be essential for future studies aimed at solving phylogenetic problems of Lamtostyla, or even the family Amphisiellidae. As a final remark, the critical screening of GenBank using ITS genes of our organism allows us to recognize a large amount of hypotrichous sequences have been misclassified as fungi. This observation suggests that hypotrichs could be frequently found in fungi-rich environment and overlooked by fungal specialists.