bluuebunny/crossref_metadata_2025_split huggingface dataset:
Target enrichment sequencing of 307 germplasm accessions identified ancestry of ancient and modern hybrids and signatures of adaptation and selection in sugarcane (Saccharum spp.), a ‘sweet’ crop with ‘bitter’ genomes
Authors: Yang Xiping , Song Jian , Todd James , Peng Ze , Paudel Dev , Luo Ziliang , Ma Xiaokai , You Qian , Hanson Erik , Zhao Zifan , Zhao Yang , Zhang Jisen , Ming Ray , Wang Jianping 
Published: July 2018

SummarySugarcane (Saccharum spp.) is a highly energy‐efficient crop primarily for sugar and bio‐ethanol production. Sugarcane genetics and cultivar improvement have been extremely challenging largely due to its complex genomes with high polyploidy levels. In this study, we deeply sequenced the coding regions of 307 sugarcane germplasm accessions. Nearly five million sequence variations were catalogued. The average of 98× sequence depth enabled different allele dosages of sequence variation to be differentiated in this polyploid collection. With selected high‐quality genome‐wide SNPs, we performed population genomic studies and environmental association analysis. Results illustrated that the ancient sugarcane hybrids, S. barberi and S. sinense, and modern sugarcane hybrids are significantly different in terms of genomic compositions, hybridization processes and their potential ancestry contributors. Linkage disequilibrium (LD) analysis showed a large extent of LD in sugarcane, with 962.4 Kbp, 2739.2 Kbp and 3573.6 Kbp for S. spontaneum, S. officinarum and modern S. hybrids respectively. Candidate selective sweep regions and genes were identified during domestication and historical selection processes of sugarcane in addition to genes associated with environmental variables at the original locations of the collection. This research provided an extensive amount of genomic resources for sugarcane community and the in‐depth population genomic analyses shed light on the breeding and evolution history of sugarcane, a highly polyploid species.
Expanding the base editing scope in rice by using Cas9 variants
Authors: Hua Kai , Tao Xiaoping , Zhu Jian‐Kang 
Published: July 2018

SummaryBase editing is a novel genome editing strategy that enables irreversible base conversion at target loci without the need for double stranded break induction or homology‐directed repair. Here, we developed new adenine and cytosine base editors with engineered SpCas9 and SaCas9 variants that substantially expand the targetable sites in the rice genome. These new base editors can edit endogenous genes in the rice genome with various efficiencies. Moreover, we show that adenine and cytosine base editing can be simultaneously executed in rice. The new base editors described here will be useful in rice functional genomics research and will advance precision molecular breeding in crops.
Factors influencing confabulation in Japanese patients with Alzheimer's disease
Authors: Okamoto Toyoko , Yamamoto Yasuji , Sakai Kazuo , Matsuyama Kenichi , Hashimoto Takeshi , Hayashi Atsuko 
Published: July 2018

BackgroundConfabulations are often observed in patients with Alzheimer's disease (AD) and can increase family caregivers’ burdens. Previous studies have focused on the relationship between confabulation and cognitive ability. However, few studies have investigated the association between confabulation and familial factors. Here, we aimed to examine whether confabulation relates to familial factors, such as the level of family caregivers’ expressed emotion or the level of functioning of the family.MethodsTwenty‐seven outpatients with AD and their family caregivers participated in this study. We examined confabulations about episodic memory, semantic memory, and future planning using the Modified Confabulation Battery (MCB). We investigated correlations between scores on the MCB and scores on the Mini‐Mental State Examination (MMSE), Geriatric Depression Scale (GDS), Family Attitude Scale (FAS), and the Family Adaptability and Cohesion Evaluation Scale. Multiple regression analyses were performed using the total scores on the MCB and domain‐specific scores on the MCB as dependent variables, and the scores on the MMSE, GDS, and FAS as independent variables.ResultsMCB scores were positively related to FAS scores (P < 0.01) and negatively to GDS scores (P < 0.05), but not to MMSE scores. Regarding the three domains the MCB measured, confabulation about episodic memory and future planning showed a positive relationship with FAS scores.ConclusionsFamily attitude was the factor most related to confabulation in our study. Patients with AD may attempt to avoid confronting family caregivers’ high emotional expression through confabulation, or confabulation itself might result in high emotional expression among family caregivers. Psychoeducational or therapeutic approaches for family caregivers might reduce confabulation in patients with AD.
Effects of a 10‐week functional training programme on pain, mood state, depression, and sleep in healthy older adults
Authors: Laredo‐Aguilera José Alberto , Carmona‐Torres Juan Manuel , García‐Pinillos Felipe , Latorre‐Román Pedro Ángel 
Published: July 2018

BackgroundThe purpose of this study was to analyze the effects of a 10‐week functional training (FT) programme on pain, mood state, sleep, and depression in healthy older adults.MethodA group of 38 older adults (32 women, 6 men) voluntarily participated in this study. Participants were randomly assigned to either the experimental group (n = 20; age: 75.44 ± 5.31 years) or the control group (n = 18: age: 76.35 ± 6.45 years). Pain, depression, mood state, and sleep were tested before and after FT.ResultsAfter the treatment, the experimental group experienced significant improvements in geriatric depression (P < 0.001), vigour (P = 0.044), fatigue (P = 0.002), depression (P = 0.005), and hypersomnia (P = 0.014), whereas the control group experienced significant deterioration in geriatric depression (P = 0.003), pain (P < 0.001), vigour (P = 0.011), depression (P = 0.009), and hypersomnia (P = 0.018). In addition, the experimental group showed an iceberg profile of mood; the control group did not show this profile.ConclusionTen‐week FT improved mood state, depression, and sleep in healthy older adults. Therefore, FT exercises may be recommended for the prevention and treatment of insomnia, depression, and alterations in mood state.
Buffalo SCNT embryos exhibit abnormal gene expression of ERK/MAPK pathway and DNA methylation
Authors: Ashok Disha , Sood Tanushri Jerath , Sah Shrutika , Palta Prabhat , Mukesh Manishi , Chauhan Manmohan Singh , Manik Radhey Sham , Singla Suresh Kumar 
Published: July 2018

AbstractInhibition of ERK/MAPK pathway has been shown to decrease DNA methylation via down‐regulation of DNA methyltransferases (DNMTs) in several studies suggesting that this pathway plays an important role in regulation of DNA methylation. We examined the relative expression level of seven important genes related to ERK/MAPK pathway and DNMTs (DNMT1, DNMT3a and DNMT3b) by quantitative real‐time PCR in buffalo blastocysts produced by Hand‐made cloning and compared it with that in blastocyst‐stage embryos produced by in vitro fertilization (IVF). The expression level of six of seven genes related to ERK/MAPK pathway examined i.e., p21RAS, RAF1, AKT1, ERK2, PIK3R2 and c‐Myc was significantly higher (p < 0.05) in cloned than in IVF embryos. However, the expression level of FOS was lower (p < 0.005) in cloned than in IVF embryos. The relative expression level of DNMT3a and DNMT3b but not that of DNMT1 was significantly higher (p < 0.05) in cloned than in IVF embryos. These results indicate that the cloned embryos exhibit an abnormal expression of several important genes related to ERK/MAPK pathway and DNMTs. Although a direct link between ERK/MAPK pathway and DNMTs was not examined in the present study, it can be speculated that ERK/MAPK pathway may have a role in regulating the expression of DNMTs in embryos, as also observed in other tissues.
Effects of chlorogenic acid and caffeic acid on the quality of frozen‐thawed boar sperm
Authors: Namula Zhao , Hirata Maki , Wittayarat Manita , Tanihara Fuminori , Thi Nguyen Nhien , Hirano Takayuki , Nii Masahiro , Otoi Takeshige 
Published: July 2018

ContentsChlorogenic acid (CGA) and caffeic acid (CA) are potent antioxidants that are mostly found in coffee beans. This study aimed to investigate the effects of CGA and CA supplementation during semen freezing on the quality of frozen‐thawed boar spermatozoa. The antioxidants CGA and CA were added to a semen extender to achieve final concentrations of 50, 100, 200 and 400 µM. Supplementation of 100 µM CGA and CA yielded a significantly higher percentage of sperm viability (increased by 8%–10%) and plasma membrane integrity (increased by 4%–6%) than the control groups without the antioxidants at 0 and 3 hr after thawing (p < 0.05). At a concentration of 100 µM, CGA and CA also yielded beneficial effects on total and progressive sperm motility. Increases of CGA and CA concentrations to more than 200 µM did not enhance any sperm quality parameters. When the sperm penetrability and oocyte development by spermatozoa frozen with CGA and CA were evaluated, CGA and CA supplementations had no positive effects on the percentages of total fertilization, monospermic fertilization, cleavage and blastocyst formation. In conclusion, the supplementation of 100 µM CGA and CA during sperm freezing improved certain sperm parameters including motility, viability and plasma membrane integrity.
Children Are Exposed to Fecal Contamination via Multiple Interconnected Pathways: A Network Model for Exposure Assessment
Authors: Wang Yuke , Moe Christine L. , Teunis Peter F. M. 
Published: July 2018

AbstractIn recent decades, quantitative microbial risk assessment (QMRA) has been widely used to assess exposure to fecal microbes and associated health risks. In this study, a multipathway exposure assessment model was developed to evaluate exposure to fecal microbes for children under 5 in highly contaminated urban environments. Children had contact with various environmental compartments. The contamination levels of these compartments were estimated from fecal indicator counts in the environmental samples. Structured observations of child behavior (including activities, locations, and time) were used to model behavioral sequences as a dynamic network. The exposure model combines behavior sequences with environmental contamination, using additional exposure factors when needed, to estimate the number of fecal microbes transferred from environmental sources to human oral ingestion. As fecal exposure in a highly contaminated urban environment consists of contributions from multiple pathways, it is imperative to study their relative importance. The model helps us better understand the characteristics of the exposure pathways that may be driven by variation in contamination and by variable behavior, like hygiene and high‐risk activities. Importantly, the model also allows prediction of the quantitative effects of an intervention—the expected reduction in exposure due to infrastructural or behavioral changes—by means of scenario studies. Based on experience with this exposure model, we make specific recommendations for additional studies of child behavior and exposure factors in order to fill critical information gaps and improve the model structure and assumptions.
Informal one‐sided target zone model and the Swiss franc
Authors: Chen Yu‐Fu , Funke Michael , Moessner Richhild 
Published: July 2018

AbstractThis paper develops a new theoretical model with an asymmetric informal one‐sided exchange rate target zone, with an application to the Swiss franc following the removal of the minimum exchange rate of CHF 1.20 per euro in January 2015. We extend and generalize a standard target zone model by introducing perceived uncertainty about the lower edge of the band. We find that informal soft edge target zone bands lead to weaker honeymoon effects, wider target zone ranges, and higher exchange rate volatility than formal target zone bands. These results suggest that it would be beneficial for exchange rate policy intentions to be stated clearly in order to anchor exchange rate expectations and reduce exchange rate volatility. We also study how exchange rate dynamics can be characterized in models in which financial markets are aware of occasional changes in the policy regime. We show that expected changes in the central bank's exchange rate policy may lead to exchange rate oscillations, providing an additional source of exchange rate volatility, and to capture this it is important to take into account the possibility of regime changes in exchange rate policy.
Does More Consumption Promote Real GDP Growth?
Authors: Liao Shu‐Yi , Wang Lan‐Hsun , Huang Mao‐Lung 
Published: July 2018

AbstractThis paper employs Hansen's (1999) panel threshold regression model [Journal of Econometrics 39 (1999) 345–68] based on a time series dataset of 109 countries from 1960 to 2007 to investigate the threshold relationship between the change in real GDP per capita and the consumption size (consumption‐income ratio, APC). The results show that the consumption level should not exceed the 49.68% threshold of real GDP per capita for each country regardless of the income level. Also, the relationship between the change in real GDP per capita and the consumption size seems to have ‘Armey curve’ or ‘inverted‐U shape’ characteristic. In order to promote real GDP growth, our results suggest that the high‐income, low‐APC countries should encourage more consumption while the low‐income, high‐APC countries should encourage more saving.
Starch degradation, abscisic acid and vesicular trafficking are important elements in callose priming by indole‐3‐carboxylic acid in response to Plectosphaerella cucumerina infection
Authors: Gamir Jordi , Pastor Victoria , Sánchez‐Bel Paloma , Agut Blas , Mateu Diego , García‐Andrade Javier , Flors Víctor 
Published: July 2018

SummaryA fast callose accumulation has been shown to mediate defence priming in certain plant–pathogen interactions, but the events upstream of callose assembly following chemical priming are poorly understood, mainly because those steps comprise sugar transfer to the infection site. β‐Amino butyric acid (BABA)‐induced resistance in Arabidopsis against Plectosphaerella cucumerina is known to be mediated by callose priming. Indole‐3‐carboxylic acid (ICOOH, also known as I3CA) mediates BABA‐induced resistance in Arabidopsis against P. cucumerina. This indolic compound is found in a common fingerprint of primed metabolites following treatments with various priming stimuli. In the present study, we show that I3CA induces resistance in Arabidopsis against P. cucumerina and primes enhancement of callose accumulation. I3CA treatment increased abscisic acid (ABA) levels before infection with P. cucumerina. An intact ABA synthesis pathway is needed to activate a starch amylase (BAM1) to trigger augmented callose deposition against P. cucumerina during I3CA‐IR. To verify the relevance of the BAM1 amylase in I3CA‐IR, knockdown mutants and overexpressors of the BAM1 gene were tested. The mutant bam1 was impaired to express I3CA‐IR, but complemented 35S::BAM1‐YFP lines in the background of bam1 restored an intact I3CA‐IR and callose priming. Therefore, a more active starch metabolism is a committed step for I3CA‐IR, inducing callose priming in adult plants. Additionally, I3CA treatments induced expression of the ubiquitin ligase ATL31 and syntaxin SYP131, suggesting that vesicular trafficking is relevant for callose priming. As a final element in the callose priming, an intact Powdery Mildew resistant4 (PMR4) gene is also essential to fully express I3CA‐IR.
Retrospective evaluation of canine palpebral masses treated with debulking and cryotherapy: 46 cases
Authors: Zibura Ashley E. , Henriksen Michala de Linde , Rendahl Aaron , Lim Christine C. , Reilly Christopher 
Published: July 2018

AbstractPurposeTo evaluate the recurrence frequency and the time to recurrence of canine palpebral masses treated with debulking and cryotherapy.MethodsMedical records of dogs that underwent debulking and cryotherapy for palpebral masses from December 2010 to November 2015 at the University of Minnesota's Veterinary Medical Center were reviewed. A telephone survey with owners was used to determine recurrence and time to recurrence.ResultsForty‐six masses (31 dogs) were included in this retrospective study. Included palpebral masses were as follows: adenomas 17/46 (37%), epitheliomas 8/46 (17.4%), papillomas 6/46 (13%), inflammatory masses 6/46 (13%), mixed adenoma‐papillomas 6/46 (13%), mixed epithelioma‐papillomas 2/46 (4.4%), and a melanocytoma 1/46 (2.2%). Of the seven masses that were noted to recur (7/46, 15.2%), three were mixed adenoma‐papillomas (three of six adenoma‐papillomas, 50%), two were epitheliomas (two of eight epitheliomas, 25%), one was a papilloma (one of six papillomas, 16.7%), and one was a melanocytoma (one of one melanocytoma, 100%). Average recurrence time was 367.9 days [range: 30‐904 days]. A significant association between tumor type and tumor recurrence was found (P = .009). Adenomas were significantly less likely to recur (P = .017), and mixed adenoma‐papillomas were significantly more likely to recur (P = .001).ConclusionsDebulking and cryotherapy is an effective method of treatment for eyelid masses in dogs with a low study recurrence rate of 15.2% and average recurrence time of 367.9 days. Results also suggest that mixed adenoma‐papilloma masses have a significantly higher recurrence rate than other eyelid masses, whereas adenomas had no recurrence in our study population.
Modification of the metal endoprosthesis limb‐salvage procedure for excision of a large distal radial osteosarcoma in a dog: A case report
Authors: Wustefeld‐Janssens Brandan G. , Lafferty Mary , Séguin Bernard 
Published: July 2018

AbstractObjectiveTo report modification of the endoprosthesis surgical limb‐salvage technique to treat a locally extensive osteosarcoma in a dog and associated functional outcome.Study designClinical case report.AnimalsOne client‐owned dog.MethodsA 9‐year‐old dog was presented for treatment of a locally extensive distal radial osteosarcoma. A limb‐salvage surgery was performed with a second‐generation Veterinary Orthopedic Implants (VOI) endoprosthesis to reconstruct the radial segmental and carpal osseous defect. The endoprosthesis was stabilized with a 16‐mm‐wide locking VOI limb‐salvage plate. The level of the osteotomy of the radius/ulna was 3 cm proximal to the periosteal reaction seen on radiographs, and the distal osteotomy extended through the proximal metacarpal bones (II‐V), 3 cm from the distal extent of the soft tissue component of the tumor. A 3.5‐mm SOP (String of Pearls) plate was used as adjunct fixation.ResultsThe postoperative functional outcome was classified as acceptable. Ambulation was normal, with mild subjective lameness on the treated limb at examinations 20, 43, and 63 days after surgery. The dog was euthanized 92 days after surgery because of progressive metastatic disease.ConclusionThe modified endoprosthetic technique allowed complete excision of the carpal joint, which resulted in acceptable functional outcomes in the dog described here.Clinical significanceDistal ostectomies may include part of the manus during limb salvage surgery of locally extensive distal radial osteosarcoma and using an endoprosthesis implant to reconstruct the defect.
Primary appendicular hemangiosarcoma and telangiectatic osteosarcoma in 70 dogs: AVeterinarySociety ofSurgicalOncology retrospective study
Authors: Giuffrida Michelle A. , Kamstock Debra A. , Selmic Laura E. , Pass William , Szivek Anna , Mison Michael B. , Boston Sarah E. , Fox Leslie E. , Robat Cecilia , Grimes Janet A. , Maritato Karl C. , Bacon Nicholas J. 
Published: July 2018

AbstractObjectiveTo define and compare clinical characteristics of canine primary appendicular hemangiosarcoma (HSA) and telangiectatic osteosarcoma (tOSA), including signalment, presentation, response to treatment, and prognosis.Study designMulti‐institutional retrospective study.AnimalsSeventy dogs with primary appendicular HSA or tOSA.MethodsPatient data were obtained from institutions' medical records. Immunohistochemistry was applied to archived tissues to establish tumor type. Patient characteristics, treatment responses, and outcomes were described and compared by tumor type.ResultsForty‐one HSA and 29 tOSA were identified. Dogs with HSA were more likely than dogs with tOSA to be male and have hind limb tumors; 78% of HSA occurred in hind limbs, particularly the tibia. Dogs with tOSA weighed a median of 9.9 kg (95% CI 4.6‐15.3) more than dogs with HSA. Most dogs received antineoplastic treatment, predominantly amputation with or without adjuvant chemotherapy. Overall survival with local treatment and chemotherapy was 299 days (95% CI 123‐750) for HSA and 213 days (95% CI 77‐310) for tOSA. Younger age and more aggressive treatment were associated with longer survival in dogs with HSA but not tOSA. One‐year survival rates did not differ between dogs with HSA (28%) and those with tOSA (7%).ConclusionDistinct clinical features were identified between HSA and tOSA in this population. Both tumors were aggressive, with a high incidence of pulmonary metastases. However, local treatment combined with chemotherapy led to an average survival 7 months for tOSA and 10 months for HSA.Clinical significanceHSA should be considered as a differential in dogs with aggressive lytic bone lesions, particularly medium‐sized dogs with tibial lesions. HSA has a unique clinical presentation but similar therapeutic response and outcome to OSA. Amputation and chemotherapy appear to prolong survival in some dogs with HSA and tOSA.
In vitro characterization of neonatal, juvenile, and adult porcine islet oxygen demand, β‐cell function, and transcriptomes
Authors: Smith Kate E. , Purvis William G. , Davis Melissa A. , Min Catherine G. , Cooksey Amanda M. , Weber Craig S. , Jandova Jana , Price Nicholas D. , Molano Diana S. , Stanton James Brett , Kelly Amy C. , Steyn Leah V. , Lynch Ronald M. , Limesand Sean W. , Alexander Michael , Lakey Jonathan R. T. , Seeberger Karen , Korbutt Gregory S. , Mueller Kate R. , Hering Bernhard J. , McCarthy Fiona M. , Papas Klearchos K. 
Published: July 2018

AbstractBackgroundThere is currently a shortage of human donor pancreata which limits the broad application of islet transplantation as a treatment for type 1 diabetes. Porcine islets have demonstrated potential as an alternative source, but a study evaluating islets from different donor ages under unified protocols has yet to be conducted.MethodsNeonatal porcine islets (NPI; 1‐3 days), juvenile porcine islets (JPI; 18‐21 days), and adult porcine islets (API; 2+ years) were compared in vitro, including assessments of oxygen consumption rate, membrane integrity determined by FDA/PI staining, β‐cell proliferation, dynamic glucose‐stimulated insulin secretion, and RNA sequencing.ResultsOxygen consumption rate normalized to DNA was not significantly different between ages. Membrane integrity was age dependent, and API had the highest percentage of intact cells. API also had the highest glucose‐stimulated insulin secretion response during a dynamic insulin secretion assay and had 50‐fold higher total insulin content compared to NPI and JPI. NPI and JPI had similar glucose responsiveness, β‐cell percentage, and β‐cell proliferation rate. Transcriptome analysis was consistent with physiological assessments. API transcriptomes were enriched for cellular metabolic and insulin secretory pathways, while NPI exhibited higher expression of genes associated with proliferation.ConclusionsThe oxygen demand, membrane integrity, β‐cell function and proliferation, and transcriptomes of islets from API, JPI, and NPI provide a comprehensive physiological comparison for future studies. These assessments will inform the optimal application of each age of porcine islet to expand the availability of islet transplantation.