bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide evolutionary characterization and expression analysis of SIAMESE-RELATED family genes in maize
Authors: Zhang Zhengquan , Qu Jianzhou , Li Feifei , Li Silu , Xu Shutu , Zhang Renhe , Xue Jiquan , Guo Dongwei 
Published: July 2020

Abstracts
Background
The SIAMESE (SIM) locus is a cell-cycle kinase inhibitor (CKI) gene that has to date been identified only in plants; it encodes a protein that promotes transformation from mitosis to endoreplication. Members of the SIAMESE-RELATED (SMR) family have similar functions, and some are related to cell-cycle responses and abiotic stresses. However, the functions of SMRs are poorly understood in maize (Zea mays L.).

Results
In the present study, 12 putative SMRs were identified throughout the entire genome of maize, and these were clustered into six groups together with the SMRs from seven other plant species. Members of the ZmSMR family were divided into four groups according to their protein sequences. Various cis-acting elements in the upstream sequences of ZmSMRs responded to abiotic stresses. Expression analyses revealed that all ZmSMRs were upregulated at 5, 20, 25, and 35 days after pollination. In addition, we found that ZmSMR9/11/12 may have regulated the initiation of endoreplication in endosperm central cells. Additionally, ZmSMR2/10 may have been primarily responsible for the endoreplication regulation of outer endosperm or aleurone cells. The relatively high expression levels of almost all ZmSMRs in the ears and tassels also implied that these genes may function in seed development. The effects of treatments with ABA, heat, cold, salt, and drought on maize seedlings and expression of ZmSMR genes suggested that ZmSMRs were strongly associated with response to abiotic stresses.

Conclusion
The present study is the first to conduct a genome-wide analysis of members of the ZmSMR family by investigating their locations in chromosomes, identifying regulatory elements in their promoter regions, and examining motifs in their protein sequences. Expression analysis of different endosperm developmental periods, tissues, abiotic stresses, and hormonal treatments suggests that ZmSMR genes may function in endoreplication and regulate the development of reproductive organs. These results may provide valuable information for future studies of the functions of the SMR family in maize.
Screening and identification of BP100 peptide conjugates active against Xylella fastidiosa using a viability-qPCR method
Authors: Baró Aina , Badosa Esther , Montesinos Laura , Feliu Lidia , Planas Marta , Montesinos Emilio , Bonaterra Anna 
Published: July 2020

Abstract
Background
Xylella fastidiosa is one of the most harmful bacterial plant pathogens worldwide, causing a variety of diseases, with huge economic impact to agriculture and environment. Although it has been extensively studied, there are no therapeutic solutions to suppress disease development in infected plants. In this context, antimicrobial peptides represent promising alternatives to traditional compounds due to their activity against a wide range of plant pathogens, their low cytotoxicity, their mode of action that make resistance more difficult and their availability for being expressed in plants.

Results
Peptide conjugates derived from the lead peptide BP100 and fragments of cecropin, magainin or melittin were selected and tested against the plant pathogenic bacteria X. fastidiosa. In order to screen the activity of these antimicrobials, and due to the fastidious nature of the pathogen, a methodology consisting of a contact test coupled with the viability-quantitative PCR (v-qPCR) method was developed. The nucleic acid-binding dye PEMAX was used to selectively quantify viable cells by v-qPCR. In addition, the primer set XF16S-3 amplifying a 279 bp fragment was selected as the most suitable for v-qPCR. The performance of the method was assessed by comparing v-qPCR viable cells estimation with conventional qPCR and plate counting. When cells were treated with peptide conjugates derived from BP100, the observed differences between methods suggested that, in addition to cell death due to the lytic effect of the peptides, there was an induction of the viable but non-culturable state in cells. Notably, a contact test coupled to v-qPCR allowed fast and accurate screening of antimicrobial peptides, and led to the identification of new peptide conjugates active against X. fastidiosa.

Conclusions
Antimicrobial peptides active against X. fastidiosa have been identified using an optimized methodology that quantifies viable cells without a cultivation stage, avoiding underestimation or false negative detection of the pathogen due to the viable but non-culturable state, and overestimation of the viable population observed using qPCR. These findings provide new alternative compounds for being tested in planta for the control of X. fastidiosa, and a methodology that enables the fast screening of a large amount of antimicrobials against this plant pathogenic bacterium.
Responses of leaf morphology, NSCs contents and C:N:P stoichiometry of Cunninghamia lanceolata and Schima superba to shading
Authors: Liu Qingqing , Huang Zhijun , Wang Zhengning , Chen Yanfang , Wen Zhumei , Liu Bo , Tigabu Mulualem 
Published: July 2020

Abstract
Background
The non-structural carbohydrates (NSCs), carbon (C), nitrogen (N), and phosphorus (P) are important energy source or nutrients for all plant growth and metabolism. To persist in shaded understory, saplings have to maintain the dynamic balance of carbon and nutrients, such as leaf NSCs, C, N and P. To improve understanding of the nutrient utilization strategies between shade-tolerant and shade-intolerant species, we therefore compared the leaf NSCs, C, N, P in response to shade between seedlings of shade-tolerant Schima superba and shade-intolerant Cunninghamia lanceolate. Shading treatments were created with five levels (0, 40, 60, 85, 95% shading degree) to determine the effect of shade on leaf NSCs contents and C:N:P stoichiometry characteristics.

Results
Mean leaf area was significantly larger under 60% shading degree for C. lanceolata while maximum mean leaf area was observed under 85% shading degree for S. superba seedlings, whereas leaf mass per area decreased consistently with increasing shading degree in both species. In general, both species showed decreasing NSC, soluble sugar and starch contents with increasing shading degree. However shade-tolerant S. superba seedlings exhibited higher NSC, soluble sugar and starch content than shade-intolerant C. lanceolate. The soluble sugar/starch ratio of C. lanceolate decreased with increasing shading degree, whereas that of S. superb remained stable. Leaf C:N ratio decreased while N:P ratio increased with increasing shading degree; leaf C:P ratio was highest in 60% shading degree for C. lanceolata and in 40% shading degree for S. superba.

Conclusion
S. superba is better adapted to low light condition than C. lanceolata through enlarged leaf area and increased carbohydrate reserves that allow the plant to cope with low light stress. From mixed plantation viewpoint, it would be advisable to plant S. superba later once the canopy of C. lanceolata is well developed but allowing enough sunlight.
Nuclear proteome of virus-infected and healthy potato leaves
Authors: Rajamäki Minna-Liisa , Sikorskaite-Gudziuniene Sidona , Sarmah Nandita , Varjosalo Markku , Valkonen Jari P. T. 
Published: July 2020

Abstract
Background
Infection of plants by viruses interferes with expression and subcellular localization of plant proteins. Potyviruses comprise the largest and most economically damaging group of plant-infecting RNA viruses. In virus-infected cells, at least two potyviral proteins localize to nucleus but reasons remain partly unknown.

Results
In this study, we examined changes in the nuclear proteome of leaf cells from a diploid potato line (Solanum tuberosum L.) after infection with potato virus A (PVA; genus Potyvirus; Potyviridae) and compared the data with that acquired for healthy leaves. Gel-free liquid chromatography–coupled to tandem mass spectrometry was used to identify 807 nuclear proteins in the potato line v2–108; of these proteins, 370 were detected in at least two samples of healthy leaves. A total of 313 proteins were common in at least two samples of healthy and PVA-infected leaves; of these proteins, 8 showed differential accumulation. Sixteen proteins were detected exclusively in the samples from PVA-infected leaves, whereas other 16 proteins were unique to healthy leaves. The protein Dnajc14 was only detected in healthy leaves, whereas different ribosomal proteins, ribosome-biogenesis proteins, and RNA splicing–related proteins were over-represented in the nuclei of PVA-infected leaves. Two virus-encoded proteins were identified in the samples of PVA-infected leaves.

Conclusions
Our results show that PVA infection alters especially ribosomes and splicing-related proteins in the nucleus of potato leaves. The data increase our understanding of potyvirus infection and the role of nucleus in infection. To our knowledge, this is the first study of the nuclear proteome of potato leaves and one of the few studies of changes occurring in nuclear proteomes in response to plant virus infection.
Neonatal lupus with left bundle branch block and cardiomyopathy: a case report
Authors: Rumancik Brad , Haggstrom Anita N. , Ebenroth Eric S. 
Published: July 2020

Abstract
Background
Cardiac manifestations of neonatal lupus include an array of structural and conduction abnormalities due to placental transference of maternal anti-SSA/Ro and anti-SSB/La autoantibodies. Late-onset neonatal lupus cardiomyopathies, occurring outside the neonatal period, is an infrequently reported manifestation with unknown pathophysiology and poorly defined treatment regimens. Due to the rarity of this condition, additional studies and case reports are required to better understand and manage late-onset neonatal lupus cardiomyopathies.

Case presentation
A 4-week-old female, born to a mother with known anti-SSA/Ro and anti-SSB/La autoantibodies, presents with classic cutaneous manifestations for neonatal lupus and is found to have left bundle branch block, severely dilated cardiomyopathy with an ejection fraction of 25%, and a thin echogenic dyskinetic ventricular septum. Weekly second trimester and 30-week fetal echocardiograms showed no signs of structural or conduction abnormalities. There were no histologic signs of inflammation on cardiac tissue biopsy. After a complicated hospital course, she was successfully treated with biventricular pacemaker, intravenous immunoglobulin, and plasmapheresis.

Conclusions
We present a case of late-onset neonatal lupus with severe dilated cardiomyopathy, a dyskinetic ventricular septum, and left bundle branch block. To our knowledge, the dyskinetic ventricular septum has never been reported and left bundle branch block is rarely reported in NL. This case further validates the need for long term cardiac follow up for patients born with NL, even if lacking cardiac manifestations in the peripartum period. We characterize a unique presentation of a rare clinical entity, highlighting the diagnostic challenges, and describe a successful treatment course.
A stepped-wedge randomised-controlled trial assessing the implementation, impact and costs of a prospective feedback loop to promote appropriate care and treatment for older patients in acute hospitals at the end of life: study protocol
Authors: Lee Xing J. , Farrington Alison , Carter Hannah , Shield Carla , Graves Nicholas , McPhail Steven M. , Harvey Gillian , White Ben P. , Willmott Lindy , Cardona Magnolia , Hillman Ken , Callaway Leonie , Barnett Adrian G. 
Published: July 2020

Abstract
Background
Hospitalisation rates for the older population have been increasing with end-of-life care becoming a more medicalised and costly experience. There is evidence that some of these patients received non-beneficial treatment during their final hospitalisation with a third of the non-beneficial treatment duration spent in intensive care units. This study aims to increase appropriate care and treatment decisions and pathways for older patients at the end of life in Australia. This study will implement and evaluate a prospective feedback loop and tailored clinical response intervention at three hospitals in Queensland, Australia.

Methods
A stepped-wedge cluster randomised trial will be conducted with up to 21 clinical teams in three acute hospitals over 70 weeks. The study involves clinical teams providing care to patients aged 75 years or older, who are prospectively identified to be at risk of non-beneficial treatment using two validated tools for detecting death and deterioration risks. The intervention’s feedback loop will provide the teams with a summary of these patients’ risk profiles as a stimulus for a tailored clinical response in the intervention phase. The Consolidated Framework for Implementation Research will be used to inform the intervention’s implementation and process evaluation. The study will determine the impact of the intervention on patient outcomes related to appropriate care and treatment at the end of life in hospitals, as well as the associated healthcare resource use and costs. The primary outcome is the proportion of patients who are admitted to intensive care units. A process evaluation will be carried out to assess the implementation, mechanisms of impact, and contextual barriers and enablers of the intervention.

Discussion
This intervention is expected to have a positive impact on the care of older patients near the end of life, specifically to improve clinical decision-making about treatment pathways and what constitutes appropriate care for these patients. These will reduce the incidence of non-beneficial treatment, and improve the efficiency of hospital resources and quality of care. The process evaluation results will be useful to inform subsequent intervention implementation at other hospitals.

Trial registration
Australia New Zealand Clinical Trial Registry (ANZCTR), ACTRN12619000675123p (approved 6 May 2019),
Being active 1½ years after hip fracture: a qualitative interview study of aged adults’ experiences of meaningfulness
Authors: Rasmussen Birgit , Nielsen Claus Vinther , Uhrenfeldt Lisbeth 
Published: July 2020

Abstract
Background
Being active is vital and a source of well-being. However, 18 months after hip fracture (HF), progress seems to have come to a halt. Aged adults may feel vulnerable, experiencing ongoing dependency and limited possibilities for socializing. How they experience the meaningfulness of being active during these circumstances is unknown. The aim of this study was to explore experiences of the meaningfulness of being active for aged adults 18 months after HF.

Methods
A phenomenological-hermeneutic methodology based on the philosophies of Heidegger and Gadamer was applied. Data were collected using individual interviews conducted in participants’ homes. The study was part of a longitudinal study, and three former interviews helped build trusting relationships with participants and focus the semi-structured interview guide. An existential theory of well-being and suffering considering health to be a balancing of mobility and dwelling was applied.
Participants were nine aged adults 65 years or older with pre-fracture dependency included in the study 18 months earlier while still in hospital after HF. The interpretation was a process of analyzing data by moving between the parts and the whole as a means of gaining a deeper understanding and continuously testing pre-understandings. The analysis followed five steps: a) getting a sense of the whole b) delineating and condensing meaning units, c) interpreting meaning units, d) relating to study purpose, and e) developing themes and sub-themes.

Results
Two main themes emerged. The main-theme “Feeling the continuity of life “had four sub-themes: “Gratitude for present possibilities, ““Connected with earlier life-experience, ““Thoughtfully managing vulnerability, “and “Belonging with other people. “The main-theme “Feeling vulnerable “had two sub-themes: “Thwarted “and “Sad and regretting lost continuity in life.“.

Conclusions
Eighteen months after HF, aged adults seem to be struggling on their own to be active in meaningful ways. To maintain hope, relieve the strain in everyday life, and maintain a sense of safety and self-confidence, they may need help. However, to avoid suffering, there is a need to balance additional training and a struggle for progress with well-being experiences in terms of feeling gratitude, restoring a sense of normality, and feeling kinship with other people.
The value of CT, MRI, and PET-CT in detecting retropharyngeal lymph node metastasis of head and neck squamous cell carcinoma
Authors: Kim Jin Hwan , Choi Kyu Young , Lee Sang-Hyo , Lee Dong Jin , Park Bum Jung , Yoon Dae Young , Rho Young-Soo 
Published: July 2020

Abstract
Background
The diagnostic accuracies of the imaging studies should be clearly acknowledged in managing head and neck cancer patients; however, the accuracies of preoperative imaging studies in detecting retropharyngeal lymph node (RPLN) metastasis are still not clarified. This study was to evaluate diagnostic accuracies of computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography-computed tomography (PET-CT) in detecting RPLN metastasis of head and neck squamous cell carcinomas.

Methods
For 123 patients who had performed RPLN dissection during the surgery of their squamous cell carcinoma of the head and neck, preoperative CT, MRI, and/or PET-CT were reviewed for RPLN metastasis in a blinded fashion by one experienced radiologist. Sensitivity, specificity, positive predictive value, negative predictive value, and overall accuracy of each imaging modality were assessed, by comparing with the histopathologic findings of the resected RPLNs that served as the standard of reference.

Results
RPLNs were pathologically positive for metastasis in 43 of the 123 patients (35%). Sensitivity, specificity, positive predictive value, negative predictive value, and overall accuracy in detecting metastasis to RPLN were 65, 94, 85, 83, and 84% for CT; 74, 94, 87, 87 and 87% for MRI; 83, 93, 89, 89 and 89% for PET-CT, respectively. When all the three imaging modalities were considered together (n = 74), they offered sensitivity of 90%, specificity of 91%, positive predictive value of 87%, negative predictive value of 93%, and accuracy of 91%.

Conclusions
The preoperative imaging studies offered relatively high specificity rates, but rather low sensitivity rates. The three imaging modalities altogether increased diagnostic accuracies, which highlights the potential of the three studies when used altogether can minimize missed diagnoses of RPLN metastasis.
Impact of initial dialysis modality on the survival of patients with ESRD in eastern China: a propensity-matched study
Authors: Yao Xi , Lei Wenhua , Shi Nan , Lin Weiqiang , Du Xiaoying , Zhang Ping , Chen Jianghua 
Published: July 2020

Abstract
Background
There are conflicting research results about the survival differences between hemodialysis(HD) and peritoneal dialysis (PD). The present study estimated the survival and the relative mortality hazard for incident HD and PD patients with end stage renal disease (ESRD) in eastern China.

Methods
This study examined a cohort of patients with ESRD who initiated dialysis therapy in Zhejiang province between Jan of 2010 and Dec of 2014, followed up until the end of 2015. PD patients were matched in a 1:1 fashion with HD patients, and Kaplan–Meier analysis was used to explore the survival of them. The Cox proportional hazard regression model was applied to identify the factors that predict survival by treatment modality. Subgroup analyses were conducted by stratifying patients according to gender, age, causes of ESRD and comorbidities.

Results
Among a total of 22,379 enrolled patients (17,029 HD patients and 5350 PD patients), 5350 matched pairs were identified, and followed for a median of 29 months (3 ~ 72 months). Kaplan-Meier survival curve revealed that overall mortality rate was significantly higher in HD patients than in PD patients (log-rank test, P < 0.001), after adjusting by gender, age, primary causes of ESRD and comorbidities. HD was consistently associated with an increased risk for morality compared with PD in the matched cohort (adjusted hazard ratio (AHR): 1.140, 95%CI: 1.023 ~ 1.271). In subgroup analyses, male, younger patients, or nondiabetic patients aged less than 65 years after adjustment of covariates, initiating with PD was associated with a significantly lower mortality compared with HD. In the multivariate Cox proportional risks model, age, diabetic nephropathy (DN), other/unknown causes of ESRD, and patients with a history of cardiovascular disease or cancer showed statistical significance in explaining survival of incident ESRD patients.

Conclusions
ESRD patients who initiated dialysis with PD yielded superior survival rates compared to HD. Increased use of PD as initial dialysis modality in ESRD patients could be encouraged in Chinese population.
Detection of water-molecular-motion configuration in patients with lupus nephritis: a primary study using diffusion-weighted imaging
Authors: Shi Huilan , Wang Yanyan , Yan Tiekun , Jia Junya , Li Dong , Wei Li , Shang Wenya , Zheng Zhenfeng 
Published: July 2020

Abstract
Background
Lupus nephritis (LN) is one of most common types of secondary glomerulonephritis, which is characterized by longitudinal pathological changes. Microstructural lesions of LN will impact the motion of water molecules, which can be detected by diffusion-weighted imaging (DWI). There are few reported measurements of water diffusion in patients with LN, and the nature of water diffusion across the entire depth of the renal parenchyma remains largely unknown.

Methods
Twenty adult patients with LN and 11 healthy volunteers underwent DWI inspection. Renal biopsy samples were characterized based on the revised ISN/RPS 2003 classification. The apparent-diffusion coefficient (ADC) was calculated via fitting into a mono-exponential model. To compare the ADC level across the entire renal parenchyma between the two groups, repeated-measures analysis of variance (RM-ANOVA) was performed. ADC data derived from DWI pictures were transformed into tridimensional maps by MATLAB software.

Results
Compared with data from healthy volunteers, lower average ADC values with major undulatory magnitudes were found in patients with LN, especially in the cortical zone. Tridimensional maps of patients with LN displayed geographic terrain-like canyons and/or valleys that were different from the corresponding terrain-like flatlands and/or plateaus in healthy volunteers. A heterogeneity of ADC values was found in bilateral kidneys. Left kidneys predominated higher ADC values in patients with LN. The ADC values across the entire renal parenchyma exhibited statistically significant differences among the three identified pathological subclasses (P < 0.001).

Conclusions
Analysis of the motion of water molecules across the entire renal parenchyma may be helpful for better understanding the pathological conditions of LN, for which microstructural and functional heterogeneity may be detected and visualized via DWI.