bluuebunny/crossref_metadata_2025_split huggingface dataset:
High‐Resolution Modeling of Reservoir Release and Storage Dynamics at the Continental Scale
Authors: Shin Sanghoon , Pokhrel Yadu , Miguez‐Macho Gonzalo 
Published: December 2018

AbstractManmade reservoirs are important components of the terrestrial water balance. Thus, considering the hydro‐climatic effects of reservoirs is important in water cycle studies at a river basin to global scales; yet, reservoirs are represented poorly in large‐scale hydrological and climate models. Here we present a high‐resolution (5 km) continental‐scale reservoir storage dynamics and release scheme by enhancing existing schemes and adding critical novel parameterizations to improve reservoir storage and release simulations. The new scheme simulates river‐floodplain‐reservoir storages in an integrated manner considering their spatial and temporal variations. A new calibration scheme is also incorporated to better simulate reservoir dynamics considering cascade‐reservoir effects. Further, since no reservoir bathymetry data are available over large domains, we use a state‐of‐the‐art digital elevation model and reservoir extent data to derive reservoir bed elevation. The new scheme is integrated within the river‐floodplain routing scheme of a continental hydrological model LEAF‐Hydro‐Flood. Results from the simulation of ~1,900 reservoirs within the contiguous United States suggest that the model well captures the observed reservoir storage‐release dynamics. Comparison of our results with those from the existing schemes suggest a significant improvement; importantly, the new scheme reduces the excessive and frequent reservoir overfilling and underfilling. Comparison of results with satellite‐based surface water data shows that the model accurately reproduces the large‐scale patterns of reservoir‐floodplain inundation extents. It is expected that the results of this study will inform the incorporation of reservoirs in hyper‐resolution models to improve simulations of terrestrial water storage and flow and examine reservoir‐atmosphere interactions over large domains.
Three‐Dimensional Modeling of the Coevolution of Landscape and Soil Organic Carbon
Authors: Yan Qina , Le Phong V. V. , Woo Dong K. , Hou Tingyu , Filley Timothy , Kumar Praveen 
Published: December 2018

AbstractSoil organic carbon (SOC) is going through rapid reorganization due to anthropogenic influences. Understanding how biogeochemical transformation and erosion‐induced SOC redistribution influence SOC profiles and stocks is critical to our food security and adaptation to climate change. The important roles of erosion and deposition on SOC dynamics have drawn increasing attention in the past decades, but quantifying such dynamics is still challenging. Here we develop a process‐based quasi 3‐D model that couples surface runoff, soil moisture dynamics, biogeochemical transformation, and landscape evolution. We apply this model to a subcatchment in Iowa to understand how natural forcing and farming practices affect the SOC dynamics in the critical zone. The net soil thickness and SOC stock change rates are −0.336 (mm/yr) and −1.9 (g C/m2/year), respectively. Our model shows that in a fast transport landscape, SOC transport is the dominant control on SOC dynamics compared to biogeochemical transformation. The SOC profiles have “noses” below the surface at depositional sites, which are consistent with cores sampled at the same site. Generally, erosional sites are local net atmospheric carbon sinks and vice versa for depositional sites, but exceptions exist as seen in the simulation results. Furthermore, the mechanical soil mixing arising from tillage enhances SOC stock at erosional sites and reduces it at depositional ones. This study not only helps us understand the evolution of SOC stock and profiles in a watershed but can also serve as an instrument to develop practical means for protecting carbon loss due to human activities.
Compounding tropical and stratospheric forcing of the record low Antarctic sea-ice in 2016
Authors: Wang Guomin , Hendon Harry H. , Arblaster Julie M. , Lim Eun-Pa , Abhik S. , van Rensch Peter 
Published: December 2018

AbstractAfter exhibiting an upward trend since 1979, Antarctic sea ice extent (SIE) declined dramatically during austral spring 2016, reaching a record low by December 2016. Here we show that a combination of atmospheric and oceanic phenomena played primary roles for this decline. The anomalous atmospheric circulation was initially driven by record strength tropical convection over the Indian and western Pacific Oceans, which resulted in a wave-3 circulation pattern around Antarctica that acted to reduce SIE in the Indian Ocean, Ross and Bellingshausen Sea sectors. Subsequently, the polar stratospheric vortex weakened significantly, resulting in record weakening of the circumpolar surface westerlies that acted to decrease SIE in the Indian Ocean and Pacific Ocean sectors. These processes appear to reflect unusual internal atmosphere-ocean variability. However, the warming trend of the tropical Indian Ocean, which may partly stem from anthropogenic forcing, may have contributed to the severity of the 2016 SIE decline.
Selective single molecule sequencing and assembly of a human Y chromosome of African origin
Authors: Kuderna Lukas F. K. , Lizano Esther , Julià Eva , Gomez-Garrido Jessica , Serres-Armero Aitor , Kuhlwilm Martin , Alandes Regina Antoni , Alvarez-Estape Marina , Juan David , Simon Heath , Alioto Tyler , Gut Marta , Gut Ivo , Schierup Mikkel Heide , Fornas Oscar , Marques-Bonet Tomas 
Published: December 2018

AbstractMammalian Y chromosomes are often neglected from genomic analysis. Due to their inherent assembly difficulties, high repeat content, and large ampliconic regions, only a handful of species have their Y chromosome properly characterized. To date, just a single human reference quality Y chromosome, of European ancestry, is available due to a lack of accessible methodology. To facilitate the assembly of such complicated genomic territory, we developed a novel strategy to sequence native, unamplified flow sorted DNA on a MinION nanopore sequencing device. Our approach yields a highly continuous assembly of the first human Y chromosome of African origin. It constitutes a significant improvement over comparable previous methods, increasing continuity by more than 800%. Sequencing native DNA also allows to take advantage of the nanopore signal data to detect epigenetic modifications in situ. This approach is in theory generalizable to any species simplifying the assembly of extremely large and repetitive genomes.
Compound climate events transform electrical power shortfall risk in the Pacific Northwest
Authors: Turner S. W. D. , Voisin N. , Fazio J. , Hua D. , Jourabchi M. 
Published: December 2018

AbstractPower system reliability is sensitive to climate-driven variations in both energy demand and water availability, yet the combined effect of these impacts is rarely evaluated. Here we show that combined climate change impacts on loads and hydropower generation may have a transformative effect on the nature and seasonality of power shortfall risk in the U.S. Pacific Northwest. Under climate change, potential shortfall events occur more readily, but are significantly less severe in nature. A seasonal reversal in shortfall risk occurs: winter shortfalls are eradicated due to reduced building heating demands, while summer shortfalls multiply as increased peak loads for day-time cooling coincide with impaired hydropower generation. Many of these summer shortfalls go unregistered when climate change impacts on loads and hydropower dispatch are analyzed in isolation—highlighting an important role of compound events.
Quantum transport characteristics of heavily doped bismuth selenide nanoribbons
Authors: Tang Hao , Yan Xuejun , Xiong Yucheng , Dou Kunpeng , Zhao Yang , Jie Jiansheng , Wang Xiaomeng , Fu Qiang , Yang Juekuan , Lu Minghui , Xu Dongyan 
Published: December 2018

AbstractThis work experimentally investigated quantum transport characteristics of heavily doped bismuth selenide topological insulator nanoribbons to understand their physical origins. Transport properties of nanoribbons were measured via a suspended micro-device for eliminating the substrate effect. A series of quantum transport behaviors such as weak antilocalization, Shubnikov-de Haas oscillations, universal conductance fluctuation, and linear perpendicular-field magnetoresistance have been systematically studied to achieve a coherent understanding on their origins in topologically protected surface states, band bending, or bulk states. The parallel-field magnetoresistance, however, is found to be diverse, which can exhibit negative or positive values for the whole measurement range of the magnetic field strength or change from positive to negative values with the increase of the magnetic field strength. The tunable behavior of the parallel-field magnetoresistance is suggested to be the collective effects of the positive magnetoresistance from surface transport and the negative magnetoresistance possibly owing to the axial anomaly, resulting from long-range ionic impurity-scattering processes in bulk carriers.
Arithmetic of arithmetic Coxeter groups
Authors: Milea Suzana , Shelley Christopher D. , Weissman Martin H. 
Published: December 2018

Significance
Conway’s topograph provided a combinatorial-geometric perspective on integer binary quadratic forms—quadratic functions of two variables with integer coefficients. This perspective is practical for solving equations and easily bounds the minima of binary quadratic forms. It appears that Conway’s topograph is just the first in a series of applications of arithmetic Coxeter groups to arithmetic. Four other applications are described in this article, and dozens more may be possible.
Clocked atom delivery to a photonic crystal waveguide
Authors: Burgers A. P. , Peng L. S. , Muniz J. A. , McClung A. C. , Martin M. J. , Kimble H. J. 
Published: December 2018

Significance
Traditional atom–light coupling techniques have propelled the field of quantum optics and atomic physics. Now, by drawing on spectacular improvements in nanofabrication and nanophotonics, we advance a different platform for studying atom–light interactions. The data and simulations presented here are a first step in understanding how cold atoms are delivered to these nanophotonic structures.
Imperfect language learning vs. dynamic sound change
Authors: Reshef Yael , Gonen Einat 
Published: December 2018

Abstract
Modern Hebrew provides an idiosyncratic case for historical linguistic study: due to the discontinuity of its use as a spoken
language, differences between contemporary structures and classical ones do not necessarily reflect change processes, but may
instead result from imperfect language learning by the original L2 speakers of Modern Hebrew at the initial stages of speech
revival. This article offers a new research direction for delineating the boundaries between the two types of phenomena based on
the recent discovery of two collections of recordings of spontaneous Hebrew speech made in the 1960s. Focusing on one conspicuous
sound change in contemporary Modern Hebrew, namely the transition from [i] to [e] in the prefix of the verbal pattern
hif’il, we show that the variability in contemporary language between hif’il and
hef’il has two distinct sources: (i) an initial state of variability between [i] and [e] in forms derived
from weak root verbs (initial-[n] and middle-[w/y] roots, e.g. higi’a-hegi’a ‘arrived’) due to imperfect language
learning in the initial phases of the formation of Modern Hebrew; and (ii) a recent change from [i] to [e] in forms derived from
regular roots (e.g. hitxil-hetxil ‘started’). In this category, the 1960s recordings attest to a stable
realization of [i] amongst all age groups, with deviations from the rules of traditional Hebrew grammar occurring only marginally.
Based on this data, the measure of synchronic variation documented in the 1960s recordings is analyzed as a precursor of the sound
change that developed in the language at a later stage.
Nivel de competencia fonológica y edad de inicio de adquisición de español L2 en inmigrantes francófonos residentes en España
Authors: Planelles Almeida Margarita , de Saint Preux Anna Doquin 
Published: December 2018

ResumenEl presente estudio investiga la posibilidad de que exista relación entre la edad de inicio de adquisición de una L2 y el nivel de competencia fonológica alcanzado en inmigrantes francófonos residentes en España que aprenden español como L2. Los participantes fueron 20 aprendices francófonos de español con diferentes edades de inicio de adquisición y 6 nativos como grupo de control. Se evaluó el grado de acento extranjero en la pronunciación de los informantes a través de un panel de jueces nativos. Para el análisis de los resultados, los informantes fueron clasificados en dos grupos en función de su edad de inicio de adquisición. El análisis de los datos obtenidos muestra la existencia de una relación entre la edad de inicio de adquisición de la L2 y el nivel de competencia fonológica alcanzado. Sin embargo, el análisis de los resultados revela también la existencia de un aprendiz tardío que presentó un nivel de competencia fonológica similar al nativo, sugiriendo que es posible para los aprendices francófonos tardíos alcanzar un nivel de dominio de la pronunciación del español similar al nativo. Los resultados del estudio no son consistentes con la hipótesis de que las diferencias entre niños y adultos en la adquisición de la pronunciación de la L2 se deben a la superación de un periodo crítico (Abrahamsson, 2012;Asher y García, 1969;Granena y Long, 2012;Oyama, 1976).
Physical demands and power profile of different stage types within a cycling grand tour
Authors: Sanders Dajo , Heijboer Mathieu 
Published: December 2018

AbstractThis study aims to describe the intensity and load demands of different stage types within a cycling Grand Tour. Nine professional cyclists, whom are all part of the same World‐Tour professional cycling team, participated in this investigation. Competition data were collected during the 2016 Giro d'Italia. Stages within the Grand Tour were classified into four categories: flat stages (FLAT), semi‐mountainous stages (SMT), mountain stages (MT) and individual time trials (TT). Exercise intensity, measured with different heart rate and power output based variables, was highest in the TT compared to other stage types. During TT's the main proportion of time was spent at the high‐intensity zone, whilst the main proportion of time was spent at low intensity for the mass start stage types (FLAT, SMT, MT). Exercise load, quantified using Training Stress Score and Training Impulse, was highest in the mass start stage types with exercise load being highest in MT (329, 359 AU) followed by SMT (280, 311 AU) and FLAT (217, 298 AU). Substantial between‐stage type differences were observed in maximal mean power outputs over different durations. FLAT and SMT were characterised by higher short‐duration maximal power outputs (5–30 s for FLAT, 30 s–2 min for SMT) whilst TT and MT are characterised by high longer duration maximal power outputs (>10 min). The results of this study contribute to the growing body of evidence on the physical demands of stage types within a cycling Grand Tour.
Packing the Courts
Authors: Menounou Elli , Feldman Adam , Giallouri Thora , Peterson Jordan Carr 
Published: December 2018

AbstractWhat explains expansions to the federal judiciary? Whereas existing research focuses on unified government as an explanation, we argue ideological proximity between institutions involved in the expansion process more accurately predicts judicial expansions. We examine whether Congress chose to add seats to each federal district or circuit court annually from 1937 to 2012 and find expansions are more likely when (1) the ideological distance between chambers of Congress is smaller and (2) the ideological distance between Congress and individual district or circuit courts is greater. These findings suggest the administration of federal courts is influenced by the political concerns in another branch of government, raising important questions about judicial independence.
Generation of antibody-based therapeutics targeting the idiotype of B-cell malignancies
Authors: Weiss Emily , Sarnovsky Robert , Ho Mitchell , Arons Evgeny , Kreitman Robert , Angelus Evan , Antignani Antonella , FitzGerald David 
Published: December 2018

ABSTRACT

Background
A feature of many B-cell tumors is a surface-expressed immunoglobulin (sIg). The complementarity-determining regions (CDRs) of the sIg, termed the ‘idiotype’, are unique to each tumor. We report on a phage selection strategy to generate anti-idiotype therapeutics that reacts with sIg CDR3 sequences; the MEC1 B-cell tumor line was used as proof of concept.

Methods
To create a mimetic of the MEC1 idiotype, CDR3 sequences from heavy and light chains of the sIg were grafted into a single chain variable fragment (scFv) framework scaffold. Using the Tomlinson I phage library of human scFvs, we enriched for binders to MEC1 CDR3 sequences over unrelated CDR3 sequences.

Results
By ELISA we identified 10 binder phages. Of these, five were sequenced, found to be unique and characterized further. By flow cytometry each of the five phages bound to MEC1 cells, albeit with different patterns of reactivity. To establish specificity of binding and utility, the scFv sequences from two of these binders (phages 1 and 7) were converted into antibody-toxin fusion proteins (immunotoxins) and also cloned into a human IgG1 expression vector. Binders 1 and 7 immunotoxins exhibited specific killing of MEC1 cells with little toxicity for non-target B-cell lines. The full-length antibody recreated from the binder-1 scFv also exhibited specific binding.

Conclusion
Our results establish the utility of using engrafted CDR3 sequences for selecting phage that recognize the idiotype of B-cell tumors.
Surgical Management of Cosmetic Surgery Tourism-Related Complications: Current Trends and Cost Analysis Study of the Financial Impact on the UK National Health Service (NHS)
Authors: Thacoor Amitabh , van den Bosch Peter , Akhavani Mohammed Ali 
Published: December 2018

Abstract

Background
Cosmetic surgery tourism is thriving. Lower costs and all-inclusive cosmetic surgery holiday packages have led to more patients seeking cheaper aesthetic surgery abroad. However, limited postoperative care results in patients frequently presenting to UK National Health Service hospitals with postoperative complications requiring surgery.

Objectives
The authors sought to identify current trends and the financial impact of surgically managed complications from cosmetic surgery tourism.

Methods
A retrospective review of consecutive surgically managed patients attending a London Teaching Hospital between 2006 and 2018 with complications following cosmetic surgery abroad was performed. Patient demographics, procedure characteristics, and length of stay were determined and a comprehensive cost analysis was performed.

Results
Twenty-four patients presented with complications. Twenty-two were females aged a mean of 36 years (range, 25-58 years). Gluteal enhancement was the most common procedure (38%) and infection (92%) was the primary complication. Most procedures were undertaken in Turkey (29%) and performed in the last 5 years (63%). Twenty-one patients were inpatients and mean length of stay was 8 days (range, 1-49 days); abdominoplasty patients stayed the longest. The total cost to the hospital was $406,233, leading to an average cost per patient of $16,296 (range, $817-$41,778). Complications from abdominoplasty resulted in the highest cost per patient of $20,404.

Conclusions
Cosmetic surgery tourism is on the rise as patients travel for cheaper aesthetic surgery. There is urgent need to better address this issue to help reduce the growing financial strain on the National Health Service, safeguard patients, and optimize the use of valuable resources.
DeepCoil—a fast and accurate prediction of coiled-coil domains in protein sequences
Authors: Ludwiczak Jan , Winski Aleksander , Szczepaniak Krzysztof , Alva Vikram , Dunin-Horkawicz Stanislaw 
Published: December 2018

Abstract

Motivation
Coiled coils are protein structural domains that mediate a plethora of biological interactions, and thus their reliable annotation is crucial for studies of protein structure and function.

Results
Here, we report DeepCoil, a new neural network-based tool for the detection of coiled-coil domains in protein sequences. In our benchmarks, DeepCoil significantly outperformed current state-of-the-art tools, such as PCOILS and Marcoil, both in the prediction of canonical and non-canonical coiled coils. Furthermore, in a scan of the human genome with DeepCoil, we detected many coiled-coil domains that remained undetected by other methods. This higher sensitivity of DeepCoil should make it a method of choice for accurate genome-wide detection of coiled-coil domains.

Availability and implementation
DeepCoil is written in Python and utilizes the Keras machine learning library. A web server is freely available at https://toolkit.tuebingen.mpg.de/#/tools/deepcoil and a standalone version can be downloaded at https://github.com/labstructbioinf/DeepCoil.

Supplementary information
Supplementary data are available at Bioinformatics online.
AnnoFly: annotating Drosophila embryonic images based on an attention-enhanced RNN model
Authors: Yang Yang , Zhou Mingyu , Fang Qingwei , Shen Hong-Bin 
Published: December 2018

Abstract

Motivation
In the post-genomic era, image-based transcriptomics have received huge attention, because the visualization of gene expression distribution is able to reveal spatial and temporal expression pattern, which is significantly important for understanding biological mechanisms. The Berkeley Drosophila Genome Project has collected a large-scale spatial gene expression database for studying Drosophila embryogenesis. Given the expression images, how to annotate them for the study of Drosophila embryonic development is the next urgent task. In order to speed up the labor-intensive labeling work, automatic tools are highly desired. However, conventional image annotation tools are not applicable here, because the labeling is at the gene-level rather than the image-level, where each gene is represented by a bag of multiple related images, showing a multi-instance phenomenon, and the image quality varies by image orientations and experiment batches. Moreover, different local regions of an image correspond to different CV annotation terms, i.e. an image has multiple labels. Designing an accurate annotation tool in such a multi-instance multi-label scenario is a very challenging task.

Results
To address these challenges, we develop a new annotator for the fruit fly embryonic images, called AnnoFly. Driven by an attention-enhanced RNN model, it can weight images of different qualities, so as to focus on the most informative image patterns. We assess the new model on three standard datasets. The experimental results reveal that the attention-based model provides a transparent approach for identifying the important images for labeling, and it substantially enhances the accuracy compared with the existing annotation methods, including both single-instance and multi-instance learning methods.

Availability and implementation
http://www.csbio.sjtu.edu.cn/bioinf/annofly/

Supplementary information
Supplementary data are available at Bioinformatics online.