bluuebunny/crossref_metadata_2025_split huggingface dataset:
Remote sensing assessment of sediment variation in the Pearl River Estuary induced by Typhoon Vicente
Authors: Ye Haibin , Chen Chuqun , Tang Shilin , Tian Liqiao , Sun Zhaohua , Yang Chaoyu , Liu Fenfen 
Published: October 2017

A MODIS-based algorithm was developed to investigate the impact of Typhoon Vicente on the total suspended solid concentration in the Pearl River Estuary. This algorithm used two high resolution bands at 645 nm and 555 nm to map the concentrations. Regression between the remote sensing reflectance and in situ total suspended solid concentration showed good correlation (R2 = 0.91), indicating that the algorithm was valid for the high turbid waters in the Pearl River Estuary. MODIS-derived maps showed different total suspended solid concentration anomalies in different sub-regions of the estuary during the passage of Typhoon Vicente. In western inlets, the increase of total suspended solids (maximum values of 22.20 g m−3 before and 55.71 g m−3 after the typhoon) was possibly related to the larger rainfall discharge from the Pearl River. In Lingdingyang, the increase of total suspended solids (maximum values of 19.60 g m−3 before and 44.59 g m−3 after the typhoon) might be the result of typhoon-induced resuspension. In the southeastern portion of the Estuary, due to the typhoon-induced current, a significant decrease of total suspended solid area (decreased by 10 g m−3) was observed. Different changes were observed in different sub-regions under the influence of the typhoon, implying the complicated hydrological environment is an important feature in the Pearl River Estuary.
Lake Vänern: A historical outline
Authors: Drotz Marcus K. , Wängberg Sten-Åke , Jakobsson Eva , Gustavsson Eva , Nilsson Lars Göran 
Published: October 2017

Although Lake Vänern is the largest freshwater reservoir in Western Europe, it remains relatively unknown to the scientific community outside of Scandinavia. Therefore, we aim to give a brief outline of the lake and its geological history, in particular the landscape transformation, resource utilization, pollution history, and environmental development of the region. The landscape around Lake Vänern was shaped into its present form during the latest glaciations some 10,000 years ago. Large variation exists in its tributaries, with forest in the north and agricultural areas in the south. Human influence on the landscape was relatively small until the mid-18th century. Later, in the mid-19th century, the agriculture, forestry and shipping industries underwent large transformations as the towns around the lake grew and the economy changed. Development of fishing equipment, processes and changes in catching methods industrialized the fishing industry after mid-20th century. In the 1960s the lake was considered to be one of the most heavily mercury-polluted lakes in the world. After the passing of the first national environmental protection law in Sweden the lake turned into a success story: It has been declared to be healthy. However, old pollution still affects the fishing industry. With this new focus on the environment, the scientific community started to be interested in the lake. The lake has also played a very important role as the largest hydropower reservoir in Sweden. Here, too, the environmental question is in focus and the effects of the water regulation are still under debate. The result has been loss of biodiversity and an increased risk of an inflow of invasive species from international shipping. However, still many questions remain to be answered regarding the lake and effect of ongoing climate change on the sustainable development of the lake region.
Transport of harmful marine microalgae via ship's ballast water: Management and mitigation with special reference to the Arabian Gulf region
Authors: Hallegraeff Gustaaf M. 
Published: October 2017

The potential for transport of non-indigenous marine microalgae via ship's ballast water has been amply demonstrated, and nearly all known harmful algal bloom species have been documented in viable form from ship's ballast water. Ballast water uptake needs to be strongly discouraged during harmful algal bloom events. Efficacy of ballast water exchange in removing harmful microalgal cells is limited, since this nearly always leaves behind a viable inoculum. The precise location of ballast water exchange needs to be carefully chosen, and retention of dinoflagellate cysts and diatom spores in ballast tank sediments is of special concern. The only fully effective ballast water treatment for microalgae is the application of biocides, but heat treatment also offers considerable promise especially in subtropical and tropical waters. To manage harmful algal blooms, other key environmental drivers such as eutrophication and climate change also need to be addressed. Effective monitoring for harmful algal species and their toxins remains the critical tool to protect human health, fisheries, aquaculture and desalination industries. Challenges and opportunities for ballast water management in the Arabian Gulf region are discussed.
The fish community of Hamilton Harbour, Lake Ontario: Status, stressors, and remediation over 25 years
Authors: Boston C. M. , Randall R. G. , Hoyle J. A. , Mossman J. L. , Bowlby J. N. 
Published: October 2017

Hamilton Harbour is a large (21 km2) protected harbour located at the western end of Lake Ontario that was designated as an Area of Concern in 1985 by the International Joint Commission. As part of the designation, the fish community was deemed “impaired.” One of the long-term goals of the Hamilton Harbour Remedial Action Plan is to rehabilitate the fishery to a state, at least in part, to what it was prior to the degrading effects of industrial and municipal pollution, habitat loss, and invasive species. Since the Area of Concern designation, the nearshore fish community has been monitored regularly via a federal boat electrofishing program (1988–2013) and more recently, by a trap net program (2006–2012). During the study period, the harbour underwent significant physical and biological change which was related to both lake-wide (e.g. Dreissenids) and localized harbour events (e.g. habitat restoration). The fish community was assessed temporally using two indices of ecosystem health, the Great Lakes Index of Biotic Integrity and Proportion of Piscivore Biomass, and species-specific catch trends at unaltered sites or sites modified by habitat restoration. Early on, the fish community was dominated by tolerant species characteristic of degraded, eutrophic environments and piscivore abundance was low. The fish community responded positively to ecosystem actions during the first decade that improved water quality, increased physical habitat and reduced invasive species, but further progress was confounded by the interactions with other factors in the last decade that included new invasive species and a decline in water quality. Fish community assessments in the last decade, using both the indices found that the fish community was still impaired and dominated by non-native and pollution tolerant species. The Index of Biotic Integrity was a suitable indicator of ecosystem health strengthened by a consistent assessment with the Proportion of Piscivore Biomass index. A science based refinement of the existing Index in the future would benefit the ability to assess nearshore fish assemblages in the context of conservation goals.
Evaluation of the Remedial Action Plan goal for dissolved oxygen in Hamilton Harbour: A goal based on habitat requirements for Cisco
Authors: Bowlby J. N. , Hiriart-Baer V. P. , Blukacz-Richards E. A. , Yerubandi R. R. , Doka S. E. , Long T. L. , O'Connor K. M. 
Published: October 2017

The Hamilton Harbour Remedial Action Plan has adopted a dissolved oxygen goal for restoring habitat in the pelagic portion of Hamilton Harbour based on the ecological needs of Cisco (Coregonus artedii), a fish formerly abundant in Hamilton Harbour. The goal for dissolved oxygen is based on retaining an adequate volume of optimum Cisco habitat characterized as temperature &lt;20°C and dissolved oxygen &gt;6 mg l−1 during the June to September period. The goal also specifies minimum habitat requirements for when optimum conditions are not achieved, that being a smaller volume of refuge habitat with temperature &lt;20°C and dissolved oxygen &gt;3 mg l−1 for no more than 2 weeks per year. Weekly temperature and dissolved oxygen profiles during May to October, 1987 to 2012 in the center of Hamilton Harbour were assessed to evaluate optimum and refuge Cisco habitat relative to the Remedial Action Plan goal for dissolved oxygen. This goal was met only in 2009. However, this was fortuitous, based on a combination of cooler water temperatures in May and June and exchanges of cool oxygenated water from Lake Ontario. From 1987 to 2002 optimum habitat was estimated to be absent at least one week and up to seven weeks during June to September. Cisco could not have survived in Hamilton Harbour during six of these years when refuge habitat was absent for one or two weeks. Since 2003, Cisco habitat in Hamilton Harbour improved markedly, as some refuge habitat was always present. As well, the number of weeks with inadequate refuge habitat, and with no optimum habitat has declined. These improvements in Cisco habitat since 2003 were related to higher dissolved oxygen in the mid-depths of Hamilton Harbour.
Preliminary analysis of the intraseasonal air–sea interaction influenced by Xisha warm eddy
Authors: Li Jian , Zu Tingting , Zeng Lili , Li Ting , Chen Ju , Yao Jinglong 
Published: October 2017

A study of the Xisha eddy is a good supplement to comprehend the local oceanic and atmospheric currents. Our work aims at analyzing the intraseasonal Air–Sea interaction process during the occurring of the Xisha warm eddy. Using a Complex Empirical Orthogonal Function statistical technique, we found an eddy that propagated southwestward along the continental slope of the northwestern South China Sea, at a similar phase speed to that of Rossby waves, at 0.12 m s−1. Intraseasonal variability in spring is related to the ocean-to-atmosphere interaction, and involves the cloud-radiation effects on surface sea temperature, as well as its impact on lower-level convergence over the South China Sea. This process, induced by the warm eddy, results in abnormal surface sea temperature, downward shortwave/longwave radiation flux, surface latent heat flux, and wind changes. We used composite results and the Weather Research and Forecasting Model to explore how the observed surface sea temperature anomalies influence precipitation in the South China Sea. The results showed that the atmospheric transport of heat and moisture improved with respect to the surface sea temperature max and the air active events have caused lower atmosphere instability, along with the lower pressure and enhanced precipitation frequency in spring.
Characteristics of vertical exchange process in the Pearl River estuary
Authors: Hong Bo , Gong Wenping , Peng Shiqiu , Xie Qiang , Wang Dongxiao , Li Haobo , Xu Hongzhou 
Published: October 2017

Being an estuary with the occasional appearance of hypoxia, the Pearl River estuary was selected to investigate its vertical exchange process by a validated 3-D numerical model. The concept of vertical exchange time was used to quantify the vertical exchange process and was calculated by adding a conservative tracer to the hydrodynamic model. The results revealed vertical exchange time has significant seasonal variation modulated by seasonally changed external forcing, and has similar structure with spatial variation in salinity. During the wet season, remarkably long vertical exchange times (&gt;50 days) occurred at the lower estuary under 10 m depth, which was coincident with the frequently reported hypoxic zone. The entire Pearl River estuary was occupied by water mass with a vertical exchange time of &lt;5 days during the dry season, which indicated the estuary's health condition during this period. Further analyses revealed the seasonal trend of vertical exchange time was closely related with salinity stratification and river runoff in which the lowest vertical exchange times can be estimated by linear regressions in certain stages. Tide modulated these exchange times in different time scales. Spring tide better mixed the water column and thus facilitated the vertical exchange process compared with neap tide. As a result, minimum vertical exchange time during spring tide was about 10 days shorter than that during neap tide. Flood-ebb tide also modulated vertical exchange time in the Pearl River estuary. Vertical exchange time varies with the tide and reached minimum and maximum values during valley and high tides, respectively.
Status, threats and conservation challenges to key aquatic fauna (Crocodile and Dolphin) in National Chambal Sanctuary, India
Authors: Singh Hari , Rao R. J. 
Published: October 2017

The Chambal River in India supports a rich variety of fauna and flora including the endangered Ganges River Dolphin and Crocodile. Threats to the continued functioning of the Chambal River as a living system have reached a critical level due to the exponential expansion of human populations. Population status of Crocodiles and Dolphins in a 425 km stretch of the Chambal River was determined by surveys conducted every year during 2007 to 2010. The average number of Dolphins recorded during the surveys was 82.75 ± 09.1 yr−1 with an encounter rate of 0.19 km−1 (range 69–91), Gharial 916.25 ± 91.6 yr−1 with an encounter rate of 2.15 km−1 (range 870–996), and Mugger 235 ± 27.7 yr−1 with an encounter rate of 0.56 km−1 (range 194–301). Increasing demands for sand for development activities and water abstraction for irrigation and energy generation, coupled with mortality in fishing nets, are likely to affect these populations. Recommendations for management and research are made to ensure the effective conservation of these species in the Chambal River.
The 𝑠-multiplicity function of 2×2-determinantal rings
Authors: Miller Lance , Taylor William 
Published: October 2017

This article generalizes joint work of the first author and I. Swanson to the

s
s

-multiplicity recently introduced by the second author. For

k
k

a field and

X
=
[

x

i
,
j

]

X = [ x_{i,j}]

an

m
×
n

m \times n

-matrix of variables, we utilize Gröbner bases to give a closed form the length

λ
(
k
[
X
]

/

(

I
2

(
X
)
+

m

⌈
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q
⌉

+

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]

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)

\lambda ( k[X] / (I_2(X) + \mathfrak {m}^{ \lceil sq \rceil } + \mathfrak {m}^{[q]} ))

, where

s
∈

Z

[

p

−
1

]

s \in {\mathbf Z}[p^{-1}]

,

q
q

is a sufficiently large power of

p
p

, and

m

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is the homogeneous maximal ideal of

k
[
X
]

k[X]

. This shows this length is always eventually a polynomial function of

q
q

for all

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s

.
Evaluation of tools for long read RNA-seq splice-aware alignment
Authors: Križanović Krešimir , Echchiki Amina , Roux Julien , Šikić Mile 
Published: October 2017

Abstract

Motivation
High-throughput sequencing has transformed the study of gene expression levels through RNA-seq, a technique that is now routinely used by various fields, such as genetic research or diagnostics. The advent of third generation sequencing technologies providing significantly longer reads opens up new possibilities. However, the high error rates common to these technologies set new bioinformatics challenges for the gapped alignment of reads to their genomic origin. In this study, we have explored how currently available RNA-seq splice-aware alignment tools cope with increased read lengths and error rates. All tested tools were initially developed for short NGS reads, but some have claimed support for long Pacific Biosciences (PacBio) or even Oxford Nanopore Technologies (ONT) MinION reads.

Results
The tools were tested on synthetic and real datasets from two technologies (PacBio and ONT MinION). Alignment quality and resource usage were compared across different aligners. The effect of error correction of long reads was explored, both using self-correction and correction with an external short reads dataset. A tool was developed for evaluating RNA-seq alignment results. This tool can be used to compare the alignment of simulated reads to their genomic origin, or to compare the alignment of real reads to a set of annotated transcripts. Our tests show that while some RNA-seq aligners were unable to cope with long error-prone reads, others produced overall good results. We further show that alignment accuracy can be improved using error-corrected reads.

Availability and implementation
https://github.com/kkrizanovic/RNAseqEval, https://figshare.com/projects/RNAseq_benchmark/24391

Supplementary information
Supplementary data are available at Bioinformatics online.
PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy
Authors: Song Jiangning , Li Fuyi , Leier André , Marquez-Lago Tatiana T , Akutsu Tatsuya , Haffari Gholamreza , Chou Kuo-Chen , Webb Geoffrey I , Pike Robert N 
Published: October 2017

Abstract

Summary
Proteases are enzymes that specifically cleave the peptide backbone of their target proteins. As an important type of irreversible post-translational modification, protein cleavage underlies many key physiological processes. When dysregulated, proteases’ actions are associated with numerous diseases. Many proteases are highly specific, cleaving only those target substrates that present certain particular amino acid sequence patterns. Therefore, tools that successfully identify potential target substrates for proteases may also identify previously unknown, physiologically relevant cleavage sites, thus providing insights into biological processes and guiding hypothesis-driven experiments aimed at verifying protease–substrate interaction. In this work, we present PROSPERous, a tool for rapid in silico prediction of protease-specific cleavage sites in substrate sequences. Our tool is based on logistic regression models and uses different scoring functions and their pairwise combinations to subsequently predict potential cleavage sites. PROSPERous represents a state-of-the-art tool that enables fast, accurate and high-throughput prediction of substrate cleavage sites for 90 proteases.

Availability and implementation
http://prosperous.erc.monash.edu/

Supplementary information
Supplementary data are available at Bioinformatics online.
Protective effect of FGF-2 and low-molecular-weight heparin/protamine nanoparticles on radiation-induced healing-impaired wound repair in rats
Authors: Kinoda Jun , Ishihara Masayuki , Nakamura Shingo , Fujita Masanori , Fukuda Koichi , Sato Yoko , Yokoe Hidetaka 
Published: October 2017

Abstract
We examined the effectiveness of localized administration of fibroblast growth factor-2 containing low-molecular-weight heparin/protamine nanoparticles (FGF-2&LMWH/P NPs) on apoptosis in vivo and on healing of radiation-induced skin injury in a rat model. FGF-2 binds onto LMWH/P NPs, which can significantly enhance and stabilize FGF-2 as a local carrier. X-irradiation at a dose of 25 Gy was administered to the lower part of the back (using a lead sheet with two holes) 1 h before the administration of FGF-2&LMWH/P NPs. Cutaneous full-thickness defect wounds were then formed in X-irradiated areas to examine the time-course of wound healing, and the wound tissues were microscopically and histologically compared and examined. Wound healing was significantly delayed by X-irradiation, but FGF-2&LMWH/P NPs administration prior to irradiation led to a significantly shorter delay compared with FGF-2 alone, LMWH/P NPs alone, and controls. Furthermore, terminal deoxynucleotidyl transferase–mediated dUTP nick-end labeling (TUNEL) staining showed that the proportions of apoptotic dermal fibroblasts in X-irradiated skin were significantly lower in rats administered FGF-2&LMWH/P NPs than in controls. However, 8-hydroxy-2’-deoxyguanosine (8-OHdG) staining showed no differences. Thus, localized administration of FGF-2&LMWH/P NPs prior to irradiation may alleviate X-irradiation-induced healing-impaired wound repair in normal tissue.
Hearts and Minds
Authors: Joy George , Whiskey Eromona , Bolstridge Mark , Porras-Segovia Alejandro , McDonagh Theresa A. , Plymen Carla M. , Shergill Sukhi S. 
Published: October 2017

Abstract

Background
Schizophrenia has a 1% prevalence in the population; 30% of these patients are treatment refractory. Clozapine is the only drug licensed to treat treatment refractory psychosis, but concerns about potential adverse effects result in only a proportion of eligible patients being treated. Although a well-documented neutropenia risk is mitigated by routine blood testing, cardiac toxicity is a commonly cited reason to discontinue clozapine treatment. However, there is little data on the real-life cardiac outcomes in those receiving clozapine treatment.

Methods
Retrospective review of electrocardiogram, echocardiogram, and clinical outcomes in 39 inpatients with treatment-refractory schizophrenia, treated with clozapine and other antipsychotic medication, referred for cardiology opinion.

Results
Commonest reasons for referral were development of left ventricular (LV) impairment or sinus tachycardia with normal LV function. Patients were reviewed by a range of cardiologists, receiving varied interventions.
Median LV ejection fraction in the clozapine group was normal (52%). Serial echocardiograms demonstrated that clozapine-treated patients with LV impairment had no change in LV ejection fraction over a 4-month follow-up. Left ventricular ejection fraction did not differ between patients treated with clozapine and other antipsychotics. However, over an 11-year follow-up period, 48% of patients had discontinued clozapine treatment.

Conclusions
This naturalistic study demonstrates that clozapine is not associated with significant cardiac mortality or morbidity. There is a real need for multidisciplinary working between specialist cardiologists and psychiatrists caring for these complex patients to facilitate optimal long-term physical and mental health outcomes.