bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction of the first high-density genetic linkage map and identification of seed yield-related QTLs and candidate genes in Elymus sibiricus, an important forage grass in Qinghai-Tibet Plateau
Authors: Zhang Zongyu , Xie Wengang , Zhang Junchao , Wang Na , Zhao Yongqiang , Wang Yanrong , Bai Shiqie 
Published: November 2019

Abstract
Background
Elymus sibiricus is an ecologically and economically important perennial, self-pollinated, and allotetraploid (StStHH) grass, widely used for forage production and animal husbandry in Western and Northern China. However, it has low seed yield mainly caused by seed shattering, which makes seed production difficult for this species. The goals of this study were to construct the high-density genetic linkage map, and to identify QTLs and candidate genes for seed-yield related traits.

Results
An F2 mapping population of 200 individuals was developed from a cross between single genotype from “Y1005” and “ZhN06”. Specific-locus amplified fragment sequencing (SLAF-seq) was applied to construct the first genetic linkage map. The final genetic map included 1971 markers on the 14 linkage groups (LGs) and was 1866.35 cM in total. The length of each linkage group varied from 87.67 cM (LG7) to 183.45 cM (LG1), with an average distance of 1.66 cM between adjacent markers. The marker sequences of E. sibiricus were compared to two grass genomes and showed 1556 (79%) markers mapped to wheat, 1380 (70%) to barley. Phenotypic data of eight seed-related traits (2016–2018) were used for QTL identification. A total of 29 QTLs were detected for eight seed-related traits on 14 linkage groups, of which 16 QTLs could be consistently detected for two or three years. A total of 6 QTLs were associated with seed shattering. Based on annotation with wheat and barley genome and transcriptome data of abscission zone in E. sibiricus, we identified 30 candidate genes for seed shattering, of which 15, 7, 6 and 2 genes were involved in plant hormone signal transcription, transcription factor, hydrolase activity and lignin biosynthetic pathway, respectively.

Conclusion
This study constructed the first high-density genetic linkage map and identified QTLs and candidate genes for seed-related traits in E. sibiricus. Results of this study will not only serve as genome-wide resources for gene/QTL fine mapping, but also provide a genetic framework for anchoring sequence scaffolds on chromosomes in future genome sequence assembly of E. sibiricus.
Stability of petal color polymorphism: the significance of anthocyanin accumulation in photosynthetic tissues
Authors: Del Valle José Carlos , Alcalde-Eon Cristina , Escribano-Bailón Mª. Teresa , Buide Mª. Luisa , Whittall Justen B. , Narbona Eduardo 
Published: November 2019

AbstractBackgroundAnthocyanins are the primary source of colour in flowers and also accumulate in vegetative tissues, where they have multiple protective roles traditionally attributed to early compounds of the metabolic pathway (flavonols, flavones, etc.). Petal-specific loss of anthocyanins in petals allows plants to escape from the negative pleiotropic effects of flavonoid and anthocyanins loss in vegetative organs, where they perform a plethora of essential functions. Herein, we investigate the degree of pleiotropy at the biochemical scale in a pink-white flower colour polymorphism in the shore campion,Silene littorea. We report the frequencies of pink and white individuals across 21 populations and underlying biochemical profiles of three flower colour variants: anthocyanins present in all tissues (pink petals), petal-specific loss of anthocyanins (white petals), and loss of anthocyanins in all tissues (white petals).ResultsIndividuals lacking anthocyanins only in petals represent a stable polymorphism in two populations at the northern edge of the species range (mean frequency 8–21%). Whereas, individuals lacking anthocyanins in the whole plant were found across the species range, yet always at very low frequencies (< 1%). Biochemically, the flavonoids detected were anthocyanins and flavones; in pigmented individuals, concentrations of flavones were 14–56× higher than anthocyanins across tissues with differences of > 100× detected in leaves. Loss of anthocyanin pigmentation, either in petals or in the whole plant, does not influence the ability of these phenotypes to synthesize flavones, and this pattern was congruent among all sampled populations.ConclusionsWe found that all colour variants showed similar flavone profiles, either in petals or in the whole plant, and only the flower colour variant with anthocyanins in photosynthetic tissues persists as a stable flower colour polymorphism. These findings suggest that anthocyanins in photosynthetic tissues, not flavonoid intermediates, are the targets of non-pollinator mediated selection.
Assessing causal treatment effect estimation when using large observational datasets
Authors: John E. R. , Abrams K. R. , Brightling C. E. , Sheehan N. A. 
Published: November 2019

AbstractBackgroundRecently, there has been a heightened interest in developing and evaluating different methods for analysing observational data. This has been driven by the increased availability of large data resources such as Electronic Health Record (EHR) data alongside known limitations and changing characteristics of randomised controlled trials (RCTs). A wide range of methods are available for analysing observational data. However, various, sometimes strict, and often unverifiable assumptions must be made in order for the resulting effect estimates to have a causal interpretation. In this paper we will compare some common approaches to estimating treatment effects from observational data in order to highlight the importance of considering, and justifying, the relevant assumptions prior to conducting an observational analysis.MethodsA simulation study was conducted based upon a small cohort of patients with chronic obstructive pulmonary disease. Two-stage least squares instrumental variables, propensity score, and linear regression models were compared under a range of different scenarios including different strengths of instrumental variable and unmeasured confounding. The effects of violating the assumptions of the instrumental variables analysis were also assessed. Sample sizes of up to 200,000 patients were considered.ResultsTwo-stage least squares instrumental variable methods can yield unbiased treatment effect estimates in the presence of unmeasured confounding provided the sample size is sufficiently large. Adjusting for measured covariates in the analysis reduces the variability in the two-stage least squares estimates. In the simulation study, propensity score methods produced very similar results to linear regression for all scenarios. A weak instrument or strong unmeasured confounding led to an increase in uncertainty in the two-stage least squares instrumental variable effect estimates. A violation of the instrumental variable assumptions led to bias in the two-stage least squares effect estimates. Indeed, these were sometimes even more biased than those from a naïve linear regression model.ConclusionsInstrumental variable methods can perform better than naïve regression and propensity scores. However, the assumptions need to be carefully considered and justified prior to conducting an analysis or performance may be worse than if the problem of unmeasured confounding had been ignored altogether.
Three cases of histologically proven hepatic epithelioid hemangioendothelioma evaluated using a second-generation microbubble contrast medium in ultrasonography: case reports
Authors: Arai Jun , Shimozuma Yuu , Otoyama Yumi , Sugiura Ikuya , Nakajima Yoko , Hayashi Eiichi , Kajiwara Atsushi , Omori Risa , Uozumi Shojiro , Miyashita Miyuki , Uchikoshi Manabu , Doi Hiroyoshi , Sakaki Masashi , Wang Tianpeng , Eguchi Junichi , Ito Takayoshi , Kurihara Toshikazu , Munechika Jiro , Gokan Takehiko , Saito Koji , Miura Sakiko , Tate Genshu , Takimoto Masafumi , Yoshida Hitoshi 
Published: November 2019

Abstract
Background
Hepatic epithelioid hemangioendothelioma (HEH) is rare; it is reported in < 1 person in 1,000,000 individuals. For accurate diagnosis, information regarding multiple graphic modalities in HEH is required. However, there is very little information concerning Sonazoid® contrast enhanced ultrasonography (CEUS) in HEH.

Case presentation
The present report describes the histologically proven three HEH cases evaluated using Sonazoid® CEUS. Case 1 was a 33-year-old female patient with no relevant past medical history, who experienced right upper quadrant pain. Conventional abdominal US revealed multiple low echoic liver nodules with vague borderlines. In CEUS, the vascularity of the nodules was similar to that seen in the neighboring normal liver. Later in the portal venous and late phases (PVLP) and post vascular phase, washout of Sonazoid® was detected in the nodules. Case 2 was a 93-year-old female patient with a previous medical history including operations for breast cancer and ovary cancer in her 50’s. Conventional abdominal US revealed multiple low echoic nodules, some of which contained cystic lesions. In the early vascular phase of CEUS, nodules excluding the central anechoic regions were enhanced from peripheral sites. Although the enhancement inside the nodules persisted in both the PVLP and post vascular phase, anechoic areas in the center of some nodules were not enhanced at all. Case 3 was a 39-year-old male patient presented with right upper-quadrant pain, without any relevant past medical history. Conventional abdominal US revealed multiple low echoic liver nodules. In the early vascular phase of CEUS, nodules were gradually enhanced from the peripheral sites as ringed enhancement. Sonazoid®was washed out from the nodules in the PVLP and post vascular phase.

Conclusions
The most important feature was peripheral enhancement in the early vascular phase. In case 2, the enhancement of the parenchyma of liver nodules persisted even in the PVLP; indicating the lower degree of malignant potential than others. Actually, the tumors did not extend without any treatment in case 2. Since case 2 is the first case report of HEH with cystic lesions, in patients with liver nodules including cystic lesions, HEH is a potential diagnosis.
Increased risk of aspirin-induced gastric mucosal erosion in elderly Chinese men harboring SLCO1B1*1b/*1b while using aspirin and an ACEI or ARB concomitantly
Authors: Duan Lei , Bai Yongyi , Li Man , Li Huiying , Li Yanping , Liu Hongbin 
Published: November 2019

Abstract
Background
It is well established that long-term use of aspirin can cause gastric mucosal injury. ACEIs and ARBs are inversely related to gastric ulcer development. This study aimed to evaluate the relationship between SLCO1B1 polymorphisms, which can affect ACEI and ARB transport, and gastric mucosal erosion in elderly male Chinese patients with cardiovascular disease who use aspirin.

Methods
Patients taking aspirin and an ACEI or ARB concomitantly who had undergone endoscopic screening for gastric erosion were analyzed for SLCO1B1 polymorphisms by a TaqMan assay.

Results
The frequency of the SLCO1B1*1b/*1b diplotype (42% vs. 24%; p = 0.002) was significantly higher in the gastric mucosal erosion group than in the control group. After adjustment for significant factors, SLCO1B1*1b/*1b (OR, 2.64; 95% CI, 1.59–4.17; p < 0.05) was found to be associated with gastric mucosal erosion in aspirin users.

Conclusions
The presence of the SLCO1B1*1b/*1b diplotype may be a risk factor for aspirin-induced gastric mucosal erosion in elderly Chinese men taking aspirin and an ACEI or ARB concomitantly.
Characterization of glomerular extracellular matrix in IgA nephropathy by proteomic analysis of laser-captured microdissected glomeruli
Authors: Paunas Flavia Teodora Ioana , Finne Kenneth , Leh Sabine , Osman Tarig Al-Hadi , Marti Hans-Peter , Berven Frode , Vikse Bjørn Egil 
Published: November 2019

Abstract
Background
IgA nephropathy (IgAN) involves mesangial matrix expansion, but the proteomic composition of this matrix is unknown. The present study aimed to characterize changes in extracellular matrix in IgAN.

Methods
In the present study we used mass spectrometry-based proteomics in order to quantitatively compare protein abundance between glomeruli of patients with IgAN (n = 25) and controls with normal biopsy findings (n = 15).

Results
Using a previously published paper by Lennon et al. and cross-referencing with the Matrisome database we identified 179 extracellular matrix proteins. In the comparison between IgAN and controls, IgAN glomeruli showed significantly higher abundance of extracellular matrix structural proteins (e.g periostin, vitronectin, and extracellular matrix protein 1) and extracellular matrix associated proteins (e.g. azurocidin, myeloperoxidase, neutrophil elastase, matrix metalloproteinase-9 and matrix metalloproteinase 2). Periostin (fold change 3.3) and azurocidin (3.0) had the strongest fold change between IgAN and controls; periostin was also higher in IgAN patients who progressed to ESRD as compared to patients who did not.

Conclusion
IgAN is associated with widespread changes of the glomerular extracellular matrix proteome. Proteins important in glomerular sclerosis or inflammation seem to be most strongly increased and periostin might be an important marker of glomerular damage in IgAN.
A qualitative exploration of potential determinants of accelerated summer weight gain among school-age children: perspectives from parents
Authors: Tanskey Lindsay A. , Goldberg Jeanne P. , Chui Kenneth , Must Aviva , Wright Catherine M. , Sacheck Jennifer M. 
Published: November 2019

Abstract
Background
There is growing evidence that school children in the United States gain weight more rapidly during the summer than the school year, but few studies have explored the causes of this phenomenon. The goal of this study was to qualitatively explore potential determinants of accelerated summer weight gain by interviewing parents of school-age children.

Methods
Key informant interviews were conducted with parents of third and fourth grade students enrolled in a school-based physical activity intervention in three peri-urban communities in Eastern Massachusetts. A structured interview guide was developed to assess school year and summertime differences in child diet, physical activity, daily routine, and family rules. Interviews were recorded and transcribed verbatim. Transcripts were coded and major themes were identified using thematic analysis.

Results
Summer activities varied substantially by family. Many parents characterized summer as a time with less structure and more relaxed rules, particularly around bedtime and screen use. Parents perceived their child to be more physically active in the summer and reported few barriers to summertime physical activity. Parents reported increases in both positive (increased consumption of fruits and vegetables) and negative (increased consumption of “sweets” and “junk foods”) dietary behaviors. They highlighted several stressors unique to summer, such as the high cost of camps and the need to coordinate childcare and manage children’s time.

Conclusions
Parents perceived their children to be more physically active in the summer and consume more fruits and vegetables than during the school year. However, they also perceived children to consume more energy-dense, nutrient poor foods, engage in more screen time, and have later bedtimes during the summer. These behaviors are important targets for summertime obesity prevention interventions. Large-scale quantitative studies are needed to determine whether these parent perceptions reflect meaningful risk factors for accelerated summer weight gain.
A review of autobiographical memory studies on patients with schizophrenia spectrum disorders
Authors: Zhang Yujia , Kuhn Sara K. , Jobson Laura , Haque Shamsul 
Published: November 2019

Abstract
Background
Patients suffering from schizophrenia spectrum disorders demonstrate various cognitive deficiencies, the most pertinent one being impairment in autobiographical memory. This paper reviews quantitative research investigating deficits in the content, and characteristics, of autobiographical memories in individuals with schizophrenia. It also examines if the method used to activate autobiographical memories influenced the results and which theoretical accounts were proposed to explain the defective recall of autobiographical memories in patients with schizophrenia.

Methods
PsycINFO, Web of Science, and PubMed databases were searched for articles published between January 1998 and December 2018. Fifty-seven studies met the inclusion criteria. All studies implemented the generative retrieval strategy by inducing memories through cue words or pictures, the life-stage method, or open-ended retrieval method. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) Statement guidelines were followed for this review.

Results
Most studies reported that patients with schizophrenia retrieve less specific autobiographical memories when compared to a healthy control group, while only three studies indicated that both groups performed similarly on memory specificity. Patients with schizophrenia also exhibited earlier reminiscence bumps than those for healthy controls. The relationship between comorbid depression and autobiographical memory specificity appeared to be independent because patients’ memory specificity improved through intervention, but their level of depression remained unchanged. The U-shaped retrieval pattern for memory specificity was not consistent. Both the connection between the history of attempted suicide and autobiographical memory specificity, and the relationship between psychotic symptoms and autobiographical memory specificity, remain inconclusive. Patients’ memory specificity and coherence improved through cognitive training.

Conclusions
The overgeneral recall of autobiographical memory by patients with schizophrenia could be attributed to working memory, the disturbing concept of self, and the cuing method implemented. The earlier reminiscence bump for patients with schizophrenia may be explained by the premature closure of the identity formation process due to the emergence of psychotic symptoms during early adulthood. Protocol developed for this review was registered in PROSPERO (registration no: CRD42017062643).
Diagnoses from lung specimen collected through flexible bronchoscopy from patients in a tertiary hospital in Dar es Salaam Tanzania: a retrospective cross-sectional study
Authors: Ndilanha Deus A. , Shayo Grace A. , Hassan Ramadhan , Byomuganyizi Moses , Lema Leonard E. K. 
Published: November 2019

Abstract
Background
Flexible bronchoscopy enables visualization of the respiratory airway mucosa from the oropharynx to third generation branching of the tracheobronchial tree. Bronchoscopic diagnoses vary from one locality to the other in accordance to the locality specific risk factors for lung diseases. This study aimed at describing diagnoses of all specimen of patients who underwent flexible bronchoscopy at Muhimbili National Hospital from January 2013 to November 2017.

Methods
A retrospective hospital-based cross sectional study was conducted among 451 patients. Data was collected from archives and included both demographic and clinical variables. Descriptive statistics were used to summarize the study findings.

Results
There was a 3 fold increase in the number of patients who underwent flexible bronchoscopy from 57 cases in 2013 to 180 cases in 2017. About 39% (174/451) of patients underwent lung biopsies while 64.5% (291/451) underwent bronchioalveolar lavage, bronchial washings or brush cytology, alone or in combination with biopsy. Generally, 64.4% (112/174) of all lung biopsies were malignant. Adenocarcinoma was the most common diagnosis seen in 33.9% (59/174). Of 76 cytological samples which were sent for bacterial culture and sensitivity, 11/76 (11.8%) were culture positive. A total of 6 (10.7%) out of 56 samples which were sent for GeneXpert MTB/RIF tested positive for M.tuberculosis.

Conclusion
Adenocarcinoma was the most common diagnosis. Bacterial and mycobacterial infections were among the most reported findings in cytological samples. Suspicious tuberculosis lesions during bronchoscopy made it possible to diagnose tuberculosis which was hard to diagnose before patients were sent for bronchoscopy.
The effect of a single consecutive volume aspiration on concentrated bone marrow from the proximal humerus for clinical application
Authors: Muench Lukas N. , Kia Cameron , Otto Alexander , Mehl Julian , Baldino Joshua B. , Cote Mark P. , McCarthy Mary Beth , Beitzel Knut , Mazzocca Augustus D. 
Published: November 2019

Abstract
Background
Low aspiration volumes have been recommended to allow for higher concentrations of progenitor cells during bone marrow harvesting. However, these guidelines then require multiple aspiration attempts in order to maximize cellular yield. The purpose of this study was to investigate the effect of a single, high-volume aspiration with four consecutive aliquots on the number of nucleated cells (NCs) and colony-forming units (CFUs) in concentrated bone marrow aspirate (cBMA) taken from the proximal humerus.

Methods
cBMA was taken from the proximal humerus of patients undergoing arthroscopic rotator cuff surgery. Four 12-mL double syringes were used consecutively from a single trocar to obtain four 10 cc aliquots. Each then underwent centrifugation to create a fractionated layer rich in nucleated cells. Following cellular separation, NCs were counted and CFUs were evaluated after incubation of 7–10 days. Cellular comparisons between each aliquot were performed along with their interaction with patient age and sex.

Results
Twenty-nine patients (55.9 ± 4.6 years) were included in this study. The number of NCs and CFUs showed significant differences between the four aliquots of aspirate, with the first 10 cc aliquot providing the highest amount (p < 0.001, respectively). No significant differences were found between the sum of the three sequential aliquots compared to the initial 10 cc sample. There were no significant differences between male and female patients (p > 0.05). Increasing age resulted in no significant decrease in the number of NCs and CFUs across the four consecutive aliquots (p > 0.05).

Conclusion
In conclusion, while the initial aliquot provided the greatest number of nucleated cells and cultured CFUs, the addition of each sequential volume aspirate yielded similar amounts in total. This demonstrates the potential effectiveness of obtaining of higher volume aspirates from the proximal humerus during rotator cuff repair.