bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying the streamflow response to groundwater abstractions for irrigation or drinking water at catchment scale using SWAT and SWAT–MODFLOW
Authors: Liu Wei , Park Seonggyu , Bailey Ryan T. , Molina-Navarro Eugenio , Andersen Hans Estrup , Thodsen Hans , Nielsen Anders , Jeppesen Erik , Jensen Jacob Skødt , Jensen Jacob Birk , Trolle Dennis 
Published: September 2020

Abstract
Background
Groundwater abstraction can cause a decline in the water table, and thereby affects surface streamflow connected to the aquifer, which may impair the sustainability of both the water resource itself and the ecosystem that it supports. To quantify the streamflow response to groundwater abstractions for either irrigation or drinking water at catchment scale and compared the performance of the widely used semi-distributed hydrological model SWAT and an recently integrated surface–subsurface model SWAT–MODFLOW, we applied both SWAT and SWAT–MODFLOW to a groundwater-dominated catchment in Denmark and tested a range of groundwater abstraction scenarios.

Results
To accommodate the study area characteristics, the SWAT–MODFLOW model complex was further developed to enable the Drain package and an auto-irrigation routine to be used. A PEST (parameter estimation by sequential testing)-based approach which enables simultaneous calibration of SWAT and MODFLOW parameters was developed to calibrate SWAT–MODFLOW. Both models demonstrated generally good statistical performance for the temporal pattern of streamflow, with better R2 and NSE (Nash–Sutcliffe efficiency) for SWAT–MODFLOW but slightly better PBIAS (percent bias) for SWAT. Both models indicated that drinking water abstractions caused some degree of streamflow depletion, while abstractions for returned irrigation led to a slight total flow increase, but may influence the hydrology outside the catchment. However, the streamflow decrease caused by drinking water abstractions simulated by SWAT was unrealistically low, and the streamflow increase caused by irrigation abstractions was exaggerated compared with SWAT–MODFLOW.

Conclusion
We conclude that the SWAT–MODFLOW model produces much more realistic signals relative to the SWAT model when quantifying the streamflow response to groundwater abstractions for irrigation or drinking water; hence, it has great potential to be a useful tool in the management of water resources in groundwater-dominated catchments. With further development of SWAT–MODFLOW and the PEST-based approach developed for its calibration, this study would broaden the SWAT–MODFLOW application and benefit catchment managers.
A LINE-1 insertion situated in the promoter of IMPG2 is associated with autosomal recessive progressive retinal atrophy in Lhasa Apso dogs
Authors: Hitti-Malin Rebekkah J. , Burmeister Louise M. , Ricketts Sally L. , Lewis Thomas W. , Pettitt Louise , Boursnell Mike , Schofield Ellen C. , Sargan David , Mellersh Cathryn S. 
Published: September 2020

Abstract
Background
Canine progressive retinal atrophies are a group of hereditary retinal degenerations in dogs characterised by depletion of photoreceptor cells in the retina, which ultimately leads to blindness. PRA in the Lhasa Apso (LA) dog has not previously been clinically characterised or described in the literature, but owners in the UK are advised to have their dog examined through the British Veterinary Association/ Kennel Club/ International Sheep Dog Society (BVA/KC/ISDS) eye scheme annually, and similar schemes that are in operation in other countries. After the exclusion of 25 previously reported canine retinal mutations in LA PRA-affected dogs, we sought to identify the genetic cause of PRA in this breed.

Results
Analysis of whole-exome sequencing data of three PRA-affected LA and three LA without signs of PRA did not identify any exonic or splice site variants, suggesting the causal variant was non-exonic. We subsequently undertook a genome-wide association study (GWAS), which identified a 1.3 Mb disease-associated region on canine chromosome 33, followed by whole-genome sequencing analysis that revealed a long interspersed element-1 (LINE-1) insertion upstream of the IMPG2 gene. IMPG2 has previously been implicated in human retinal disease; however, until now no canine PRAs have been associated with this gene. The identification of this PRA-associated variant has enabled the development of a DNA test for this form of PRA in the breed, here termed PRA4 to distinguish it from other forms of PRA described in other breeds. This test has been used to determine the genotypes of over 900 LA dogs. A large cohort of genotyped dogs was used to estimate the allele frequency as between 0.07–0.1 in the UK LA population.

Conclusions
Through the use of GWAS and subsequent sequencing of a PRA case, we have identified a LINE-1 insertion in the retinal candidate gene IMPG2 that is associated with a form of PRA in the LA dog. Validation of this variant in 447 dogs of 123 breeds determined it was private to LA dogs. We envisage that, over time, the developed DNA test will offer breeders the opportunity to avoid producing dogs affected with this form of PRA.
An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton
Authors: Su Junji , Wang Caixiang , Ma Qi , Zhang Ai , Shi Chunhui , Liu Juanjuan , Zhang Xianliang , Yang Delong , Ma Xiongfeng 
Published: September 2020

Abstract
Background
Cotton (Gossypium spp.) fiber yield is one of the key target traits, and improved fiber yield has always been thought of as an important objective in the breeding programs and production. Although some studies had been reported for the understanding of genetic bases for cotton yield-related traits, the detected quantitative trait loci (QTL) for the traits is still very limited. To uncover the whole-genome QTL controlling three yield-related traits in upland cotton (Gossypium hirsutum L.), phenotypic traits were investigated under four planting environments and 9244 single-nucleotide polymorphism linkage disequilibrium block (SNPLDB) markers were developed in an association panel consisting of 315 accessions.

Results
A total of 53, 70 and 68 significant SNPLDB loci associated with boll number (BN), boll weight (BW) and lint percentage (LP), were respectively detected through a restricted two-stage multi-locus multi-allele genome-wide association study (RTM-GWAS) procedure in multiple environments. The haplotype/allele effects of the significant SNPLDB loci were estimated and the QTL-allele matrices were organized for offering the abbreviated genetic composition of the population. Among the significant SNPLDB loci, six of them were simultaneously identified in two or more single planting environments and were thought of as the stable SNPLDB loci. Additionally, a total of 115 genes were annotated in the nearby regions of the six stable SNPLDB loci, and 16 common potential candidate genes controlling target traits of them were predicted by two RNA-seq data. One of 16 genes (GH_D06G2161) was mainly expressed in the early ovule-development stages, and the stable SNPLDB locus (LDB_19_62926589) was mapped in its promoter region.

Conclusion
This study identified the QTL alleles and candidate genes that could provide important insights into the genetic basis of yield-related traits in upland cotton and might facilitate breeding cotton varieties with high yield.
The application of CRISPR/Cas9 in hairy roots to explore the functions of AhNFR1 and AhNFR5 genes during peanut nodulation
Authors: Shu Hongmei , Luo Ziliang , Peng Ze , Wang Jianping 
Published: September 2020

Abstract
Background
Peanut is an important legume crop growing worldwide. With the published allotetraploid genomes, further functional studies of the genes in peanut are very critical for crop improvement. CRISPR/Cas9 system is emerging as a robust tool for gene functional study and crop improvement, which haven’t been extensively utilized in peanut yet. Peanut plant forms root nodules to fix nitrogen through a symbiotic relationship with rhizobia. In model legumes, the response of plants to rhizobia is initiated by Nod factor receptors (NFRs). However, information about the function of NFRs in peanut is still limited. In this study, we applied the CRISPR/Cas9 tool in peanut hairy root transformation system to explore the function of NFR genes.

Results
We firstly identified four AhNFR1 genes and two AhNFR5 genes in cultivated peanut (Tifrunner). The gene expression analysis showed that the two AhNFR1 and two AhNFR5 genes had high expression levels in nodulating (Nod+) line E5 compared with non-nodulating (Nod-) line E4 during the process of nodule formation, suggesting their roles in peanut nodulation. To further explore their functions in peanut nodulation, we applied CRISPR technology to create knock-out mutants of AhNFR1 and AhNFR5 genes using hairy root transformation system. The sequencing of these genes in transgenic hairy roots showed that the selected AhNFR1 and AhNFR5 genes were successfully edited by the CRISPR system, demonstrating its efficacy for targeted mutation in allotetraploid peanut. The mutants with editing in the two AhNFR5 genes showed Nod- phenotype, whereas mutants with editing in the two selected AhNFR1 genes could still form nodules after rhizobia inoculation.

Conclusions
This study showed that CRISPR-Cas9 could be used in peanut hairy root transformation system for peanut functional genomic studies, specifically on the gene function in roots. By using CRISPR-Cas9 targeting peanut AhNFR genes in hairy root transformation system, we validated the function of AhNFR5 genes in nodule formation in peanut.
Maternal sciatic nerve administered bupivacaine induces hippocampal cell apoptosis in offspring
Authors: Mirkheshti Alireza , Shakeri Alireza , Memary Elham , Baniasadi Mansoureh , Zaringhalam Jalal , Tajbakhsh Ardeshir , Mirzaei Marzieh , Lak Elena 
Published: September 2020

Abstract
Background
Bupivacaine, an amid-type local anesthetic, is widely used for clinical patients especially in pregnant women. In addition to neurotoxicity effect of bupivacaine, it can cross the placenta, accumulates in this tissue and retained in fetal tissues. Nevertheless, whether bupivacaine can cause neurotoxicity in fetus remains unclear. Hence, this study was design to investigate the effects of maternal bupivacaine use on fetus hippocampal cell apoptosis and the possible related mechanism.

Methods
On day 15 of pregnancy, sciatic nerve of pregnant wistar rat (180–200 g) were exposed by lateral incision of the right thigh and 0.2 ml of bupivacaine was injected. After their delivery, we randomly selected one male offspring of every mother. On day 30 after of their birth, the rat’s hippocampi were isolated for molecular studies. Western blotting was used to examine the expression of cleaved caspase-3, caspase-8 and p-Akt in fetal hippocampus.

Results
Our results showed that maternal bupivacaine use caused a significant increment of cleaved caspase-3 and caspase-8 expression in fetal hippocampus compared with the sham group. In addition, maternally administered bupivacaine could significantly decrease hippocampal P.Akt/T.Akt ratio which was concurrent with an increment of cleaved caspase-3 and caspase-8 expression.

Conclusion
Our data suggest that maternal bupivacaine use increases fetal hippocampal cell apoptosis markers such as caspase 8 and cleaved caspase 3, at least in part, via inhibiting the Akt activation.
Effect of sedation with dexmedetomidine or propofol on gastrointestinal motility in lipopolysaccharide-induced endotoxemic mice
Authors: Chang Haiqing , Li Shuang , Li Yansong , Hu Hao , Cheng Bo , Miao Jiwen , Gao Hui , Ma Hongli , Gao Yanfeng , Wang Qiang 
Published: September 2020

Abstract
Background
Sepsis often accompanies gastrointestinal motility disorder that contributes to the development of sepsis in turn. Propofol and dexmedetomidine, as widely used sedatives in patients with sepsis, are likely to depress gastrointestinal peristalsis. We queried whether propofol or dexmedetomidine, at sedative doses, aggravated sepsis-induced ileus.

Methods
Sedative/Anesthetic Scores and vital signs of lipopolysaccharide (LPS)-induced endotoxemic mice were measured during sedation with propofol or dexmedetomidine. Endotoxemic mice were divided into 10% fat emulsion, propofol, saline, and dexmedetomidine group. The gastric emptying, small intestinal transit, tests of colonic motility, gastrointestinal transit and whole gut transit were evaluated at 15 mins and 24 h after intraperitoneal injection of sedatives/vehicles respectively.

Results
40 mg·kg− 1propofol and 80 μg·kg− 1 dexmedetomidine induced a similar depth of sedation with comparable vital signs except that dexmedetomidine strikingly decreased heart rate in endotoxemic mice. Dexmedetomidine markedly inhibited gastric emptying (P = 0.006), small intestinal transit (P = 0.006), colonic transit (P = 0.0006), gastrointestinal transit (P = 0.0001) and the whole gut transit (P = 0.034) compared with the vehicle, whereas propofol showed no depression on all parts of gastrointestinal motility 15 mins after administration. The inhibitive effects of dexmedetomidine in these tests vanished 24 h after the administration.

Conclusions
Deep sedation with dexmedetomidine, but not propofol, significantly inhibited gastrointestinal peristalsis in endotoxemic mice while the inhibitory effect disappeared 24 h after sedation. These data suggested that both propofol and dexmedetomidine could be applied in septic patients while dexmedetomidine should be used cautiously in patients with cardiac disease or ileus.
Suitability of administrative claims databases for bariatric surgery research – is the glass half-full or half-empty?
Authors: Li Xiaojuan , Lewis Kristina H. , Callaway Katherine , Wharam J. Frank , Toh Sengwee 
Published: September 2020

Abstract
Background
Claims databases are generally considered inadequate for obesity research due to suboptimal capture of body mass index (BMI) measurements. This might not be true for bariatric surgery because of reimbursement requirements and changes in coding systems. We assessed the availability and validity of claims-based weight-related diagnosis codes among bariatric surgery patients.

Methods
We identified three nested retrospective cohorts of adult bariatric surgery patients who underwent adjusted gastric banding, Roux-en-Y gastric bypass, or sleeve gastrectomy between January 1, 2011 and June 30, 2018 using different components of OptumLabs® Data Warehouse, which contains linked de-identified claims and electronic health records (EHRs). We measured the availability of claims-based weight-related diagnosis codes in the 6-month preoperative and 1-year postoperative periods in the main cohort identified in the claims data. We created two claims-based algorithms to classify the presence of severe obesity (a commonly used cohort selection criterion) and categorize BMI (a commonly used baseline confounder or postoperative outcome). We evaluated their performance by estimating sensitivity, specificity, positive predictive value, negative predictive value, and weighted kappa in two sub-cohorts using EHR-based BMI measurements as the reference.

Results
Among the 29,357 eligible patients identified using claims only, 28,828 (98.2%) had preoperative weight-related diagnosis codes, either granular indicating BMI ranges or nonspecific denoting obesity status. Among the 27,407 patients with granular preoperative codes, 12,346 (45.0%) had granular codes and 9355 (34.1%) had nonspecific codes in the 1-year postoperative period. Among the 3045 patients with both preoperative claims-based diagnosis codes and EHR-based BMI measurements, the severe obesity classification algorithm had a sensitivity 100%, specificity 71%, positive predictive value 100%, and negative predictive value 78%. The BMI categorization algorithm had good validity categorizing the last available preoperative or postoperative BMI measurements (weighted kappa [95% confidence interval]: preoperative 0.78, [0.76, 0.79]; postoperative 0.84, [0.80, 0.87]).

Conclusions
Claims-based weight-related diagnosis codes had excellent validity before and after bariatric surgical operation but suboptimal availability after operation. Claims databases can be used for bariatric surgery studies of non-weight-related effectiveness and safety outcomes that are well-captured.
The protocol of a clinical quality registry for dementia and mild cognitive impairment (MCI): the Australian dementia network (ADNeT) Registry
Authors: Lin Xiaoping , Wallis Kasey , Ward Stephanie A. , Brodaty Henry , Sachdev Perminder S. , Naismith Sharon L. , Krysinska Karolina , McNeil John , Rowe Christopher C. , Ahern Susannah 
Published: September 2020

Abstract
Background
Dementia was identified as a priority area for the development of a Clinical Quality Registry (CQR) in Australia in 2016. The Australian Dementia Network (ADNeT) Registry is being established as part of the ADNeT initiative, with the primary objective of collecting data to monitor and enhance the quality of care and patient outcomes for people diagnosed with either dementia or Mild Cognitive Impairment (MCI). A secondary aim is to facilitate the recruitment of participants into dementia research and trials. This paper describes the Registry protocol.

Methods
The ADNeT Registry is a prospective CQR of patients newly diagnosed with either dementia or MCI. Eligible patients will be identified initially from memory clinics and individual medical specialists (e.g., geriatricians, psychiatrists and neurologists) involved in the diagnosis of dementia. Participants will be recruited using either an opt-out approach or waiver of consent based on three key determinants (capacity, person responsible, and communication of diagnosis). Data will be collected from four sources: participating sites, registry participants, carers, and linkage with administrative datasets. It is anticipated that the Registry will recruit approximately 10,000 participants by the end of 2023. The ADNeT registry will be developed and implemented to comply with the national operating principles for CQRs and governed by the ADNeT Registry Steering Committee.

Discussion
The ADNeT Registry will provide important data on current clinical practice in the diagnosis, treatment and care of people with dementia and MCI in Australia as well as long-term outcomes among these people. These data will help to identify variations in clinical practice and patient outcomes and reasons underlying these variations, which in turn, will inform the development of interventions to improve care and outcomes for people with dementia and MCI.
Spatio-temporal impact of self-financed rotavirus vaccination on rotavirus and acute gastroenteritis hospitalisations in the Valencia region, Spain
Authors: López-Lacort Mónica , Orrico-Sánchez Alejandro , Martínez-Beneito Miguel Ángel , Muñoz-Quiles Cintia , Díez-Domingo Javier 
Published: September 2020

Abstract
Background
Several studies have shown a substantial impact of Rotavirus (RV) vaccination on the burden of RV and all-cause acute gastroenteritis (AGE). However, the results of most impact studies could be confused by a dynamic and complex space-time process. Therefore, there is a need to analyse the impact of RV vaccination on RV and AGE hospitalisations in a space-time framework to detect geographical-time patterns while avoiding the potential confusion caused by population inequalities in the impact estimations.

Methods
A retrospective population-based study using real-world data from the Valencia Region was performed among children aged less than 3 years old in the period 2005–2016. A Bayesian spatio-temporal model was constructed to analyse RV and AGE hospitalisations and to estimate the vaccination impact measured in averted hospitalisations.

Results
We found important spatio-temporal patterns in RV and AGE hospitalisations, RV vaccination coverage and in their associated adverted hospitalisations. Overall, ~ 1866 hospital admissions for RV were averted by RV vaccination during 2007–2016. Despite the low-medium vaccine coverage (~ 50%) in 2015–2016, relevant 36 and 20% reductions were estimated in RV and AGE hospitalisations respectively.

Conclusions
The introduction of the RV vaccines has substantially reduced the number of RV hospitalisations, averting ~ 1866 admissions during 2007–2016 which were space and time dependent. This study improves the methodologies commonly used to estimate the RV vaccine impact and their interpretation.
Histological diagnosis of immune checkpoint inhibitor induced acute renal injury in patients with metastatic melanoma: a retrospective case series report
Authors: Hultin Sebastian , Nahar Kazi , Menzies Alexander M. , Long Georgina V. , Fernando Suran L. , Atkinson Victoria , Cebon Jonathan , Wong Muh Geot 
Published: September 2020

Abstract
Background
Immune checkpoint inhibitors (ICI) have become the standard of care in many oncological conditions but are associated with a spectrum of renal immune-related adverse events (IrAEs). We aimed to describe the spectrum, histology, management and outcomes of renal IrAE in patients with metastatic melanoma undergoing ICI therapy.

Methods
We conducted a retrospective review of 23 patients with a diagnosis of metastatic melanoma treated with ICI between January 2017 and April 2019 who developed a renal IrAE. Baseline demographic data, biochemical and histopathological results, management and outcomes were analyzed.

Results
The majority of patients who developed renal irAE were male and received combination immunotherapy. The median time of onset from initiation of ICI therapy to renal IrAE was 4 months. 52% of the treated renal IrAE had histopathologically confirmed renal IrAE. The most common histological pattern of injury was acute tubulo-interstitial nephritis (92%). One patient developed anti-GBM disease with non-dialysis dependent stage 5 CKD. In tubulointerstitial injury, there was no association between peak creatinine, renal recovery and histologically reported inflammation or fibrosis. Patients with renal IrAE demonstrated persisting renal dysfunction at 3, 6 and 12 months with a mean baseline, 3 and 12 month creatinine of 90.0 μmol/L, 127.0 μmol/L and 107.5 μmol/L respectively.

Conclusion
Renal IrAE is most commonly attributable to steroid responsive acute tubulointerstitial nephritis. The outcome of rarer pathologies such as anti-GBM disease may be adversely affected by a delayed diagnosis. There is persisting renal dysfunction following an episode of renal IrAE that may have impact on future renal and overall survival outcomes.
IgM nephropathy complicated by cerebral venous sinus thrombosis: a case study
Authors: Downie Elizabeth , Diep Jason , Sungala Nagendraprasad , Wong Jeffrey 
Published: September 2020

Abstract
Background
IgM nephropathy is a rare disease with variable clinical presentations and is an unusual cause of nephrotic syndrome. Histopathological findings typically include mesangial hypercellularity with IgM and complement deposition, though the spectrum may range from normal glomeruli through to focal and segmental glomerulosclerosis. Thromboembolism is a well recognised complication of nephrotic syndrome, but cerebral venous sinus thrombosis is rarely described.

Case presentation
This is the case of a 23-year-old male presenting with the nephrotic syndrome, whose initial renal biopsy was consistent with minimal change disease. Complete remission was achieved with prednisone, however multiple relapses and steroid dependence prompted re-biopsy, the results of which were more consistent with IgM nephropathy. His last relapse was complicated by cerebral venous sinus thrombosis. He then received rituximab and a weaning course of prednisone to again enter remission.

Conclusions
This case highlights the need to consider IgM nephropathy in the differential diagnosis of nephrotic syndrome. Additionally, it emphasises the risk of thrombosis in patients with severe nephrosis.