bluuebunny/crossref_metadata_2025_split huggingface dataset:
Galbase: a comprehensive repository for integrating chicken multi-omics data
Authors: Fu Weiwei , Wang Rui , Xu Naiyi , Wang Jinxin , Li Ran , Asadollahpour Nanaei Hojjat , Nie Qinghua , Zhao Xin , Han Jianlin , Yang Ning , Jiang Yu 
Published: May 2022

Abstract
Background
Multi-omics data can provide a stereoscopic view to explore potential causal variations and genes, as well as underlying genetic mechanisms of complex traits. However, for many non-mammalian species, including chickens, these resources are poorly integrated and reused, greatly limiting genetic research and breeding processes of the species.

Results
Here, we constructed Galbase, an easily accessible repository that integrates public chicken multi-omics data from 928 re-sequenced genomes, 429 transcriptomes, 379 epigenomes, 15,275 QTL entries, and 7,526 associations. A total of 21.67 million SNPs, 2.71 million InDels, and 488,583 cis-regulatory elements were included. Galbase allows users to retrieve genomic variations in geographical maps, gene expression profiling in heatmaps, and epigenomic signals in peak patterns. It also provides modules for batch annotation of genes, regions, and loci based on multi-layered omics data. Additionally, a series of convenient tools, including the UCSC Genome Browser, WashU Epigenome Browser, BLAT, BLAST, and LiftOver, were also integrated to facilitate search, visualization, and analysis of sequence features.

Conclusion
Galbase grants new opportunities to research communities to undertake in-depth functional genomic studies on chicken. All features of Galbase make it a useful resource to identify genetic variations responsible for chicken complex traits. Galbase is publicly available at http://animal.nwsuaf.edu.cn/ChickenVar.
Chrysanthemum × grandiflora leaf and root transcript profiling in response to salinity stress
Authors: Liu He , Liu Yu , Xu Ning , Sun Ying , Li Qiang , Yue Liran , Zhou Yunwei , He Miao 
Published: May 2022

AbstractAs high soil salinity threatens the growth and development of plants, understanding the mechanism of plants’ salt tolerance is critical. The Chrysanthemum × grandiflora is a newly developed species with a strong salt resistance that possesses multiple genes controlling its quantitative salt resistance. Because of this multigene control, we chose to investigate the plant stress genes overall responses at the transcriptome level. C. grandiflora were treated with a 200 mM NaCl solution for 12 h to study its effect on the roots and leaves via Illumina RNA sequencing. PAL, CYP73A, and 4CL in the phenylpropanoid biosynthesis pathway were upregulated in roots and leaves. In the salicylic acid signal transduction pathway, TGA7 was upregulated in the roots and leaves, while in the jasmonic acid signal transduction pathway, TIFY9 was upregulated in the roots and leaves. In the ion transporter gene, we identified HKT1 that showed identical expression patterns in the roots and leaves. The impact of NaCl imposition for 12 h was largely due to osmotic effect of salinity on C. grandiflora, and most likely the transcript abundance changes in this study were due to the osmotic effect. In order to verify the accuracy of the Illumina sequencing data, we selected 16 DEGs for transcription polymerase chain reaction (qRT-PCR) analysis. qRT-PCR and transcriptome sequencing analysis revealed that the transcriptome sequencing results were reliable.
COVID-19 in Kidney Transplant Recipients: A Multicenter Experience from the First Two Waves of Pandemic
Authors: Demir Erol , Ucar Zuhal Atan , Dheir Hamad , Danis Ramazan , Yelken Berna , Uyar Murathan , Parmaksiz Ergun , Artan Ayse Serra , Sinangil Ayse , Merhametsiz Ozgur , Yadigar Serap , Dirim Ahmet Burak , Akin Baris , Garayeva Nurana , Safak Seda , Turkmen Aydin 
Published: May 2022

Abstract
Background
Kidney transplant recipients have an increased risk of complications from COVID-19. However, data on the risk of allograft damage or death in kidney transplant recipients recovering from COVID-19 is limited. In addition, the first and second waves of the pandemic occurred at different times all over the world. In Turkey, the Health Minister confirmed the first case in March 2020; after that, the first wave occurred between March and August 2020; afterward, the second wave began in September 2020. This study aims to demonstrate the clinical presentations of kidney transplant recipients in the first two waves of the pandemic in Turkey and explore the impact of COVID-19 on clinical outcomes after the initial episode.

Methods
Patients with COVID-19 from seven centers were included in this retrospective cohort study. Initially, four hundred and eighty-eight kidney transplant recipients diagnosed with COVID-19 between 1 March 2020 to 28 February 2021 were enrolled. The endpoints were the occurrence of all-cause mortality, acute kidney injury, cytokine storm, and acute respiratory distress syndrome. In addition, longer-term outcomes such as mortality, need for dialysis, and allograft function of the surviving patients was analyzed.

Results
Four hundred seventy-five patients were followed up for a median of 132 days after COVID-19. Forty-seven patients (9.9%) died after a median length of hospitalization of 15 days. Although the mortality rate (10.1% vs. 9.8%) and intensive care unit admission (14.5% vs. 14.5%) were similar in the first two waves, hospitalization (68.8% vs. 29.7%; p < 0.001), acute kidney injury (44.2% vs. 31.8%; p = 0.009), acute respiratory distress syndrome (18.8% vs. 16%; p = 0.456), and cytokine storm rate (15.9% vs. 10.1%; p = 0.072) were higher in first wave compared to the second wave. These 47 patients died within the first month of COVID-19. Six (1.4%) of the surviving patients lost allografts during treatment. There was no difference in the median serum creatinine clearance of the surviving patients at baseline (52 mL/min [IQR, 47–66]), first- (56 mL/min [IQR, 51–68]), third- (51 mL/min [IQR,48–67]) and sixth-months (52 mL/min [IQR, 48–81]). Development of cytokine storm and posttransplant diabetes mellitus were independent predictors for mortality.

Conclusions
Mortality remains a problem in COVID-19. All the deaths occur in the first month of COVID-19. Also, acute kidney injury is common in hospitalized patients, and some of the patients suffer from graft loss after the initial episode.
Dent-2 disease with a Bartter-like phenotype caused by the Asp631Glu mutation in the OCRL gene
Authors: Drosataki Eleni , Maragkou Sevasti , Dermitzaki Kleio , Stavrakaki Ioanna , Lygerou Dimitra , Latsoudis Helen , Pleros Christos , Petrakis Ioannis , Zaganas Ioannis , Stylianou Kostas 
Published: May 2022

Abstract
Background
Dent disease is an X-linked disorder characterized by low molecular weight proteinuria (LMWP), hypercalciuria, nephrolithiasis and chronic kidney disease (CKD). It is caused by mutations in the chloride voltage-gated channel 5 (CLCN5) gene (Dent disease-1), or in the OCRL gene (Dent disease-2). It is associated with chronic metabolic acidosis; however metabolic alkalosis has rarely been reported.

Case presentation
We present a family with Dent-2 disease and a Bartter-like phenotype. The main clinical problems observed in the proband included a) primary phosphaturia leading to osteomalacia and stunted growth; b) elevated serum calcitriol levels, leading to hypercalcemia, hypercalciuria, nephrolithiasis and nephrocalcinosis; c) severe salt wasting causing hypotension, hyperaldosteronism, hypokalemia and metabolic alkalosis; d) partial nephrogenic diabetes insipidus attributed to hypercalcemia, hypokalemia and nephrocalcinosis; e) albuminuria, LMWP.
Phosphorous repletion resulted in abrupt cessation of hypercalciuria and significant improvement of hypophosphatemia, physical stamina and bone histology. Years later, he presented progressive CKD with nephrotic range proteinuria attributed to focal segmental glomerulosclerosis (FSGS). Targeted genetic analysis for several phosphaturic diseases was unsuccessful. Whole Exome Sequencing (WES) revealed a c.1893C > A variant (Asp631Glu) in the OCRL gene which was co-segregated with the disease in male family members.

Conclusions
We present the clinical characteristics of the Asp631Glu mutation in the OCRL gene, presenting as Dent-2 disease with Bartter-like features. Phosphorous repletion resulted in significant improvement of all clinical features except for progressive CKD. Angiotensin blockade improved proteinuria and stabilized kidney function for several years.

Graphical abstract
Cardiovascular risk factors and breast cancer incidence in a large middle-aged cohort study
Authors: Zeng Xiaoqi , Jiang Shanshan , Ruan Simin , Zhu Lijun , Lian Huining , Liu Minfeng , Guo Zhaoze , Guo Jingyun , Ye Changsheng , Cheng Yunjiu , Dong Jianyu 
Published: May 2022

Abstract
Background
Several studies have demonstrated that cardiovascular risk factors play a role in the etiology of breast cancer. However, the combined effect of cardiovascular risk factors on the risk of breast cancer is still uncertain.

Methods
Data from the Atherosclerosis Risk in Communities (ARIC) study, a prospective cohort of middle-aged women, were used to investigate the association of individual and combined cardiovascular risk factors with breast cancer. Cox proportional hazards models were applied to calculate the hazard ratio (HR) and 95% confidence intervals (CI).

Results
A total of 7501 women were included. During a mean follow-up of 19.7 years, 576 women were diagnosed with breast cancer. White women and premenopausal status were independently associated with increased risk of breast cancer. Of the individual cardiovascular risk factors, only obesity was independently associated with an increased risk of breast cancer (HR 1.29, 95% CI 1.04–1.61). Compared with women without cardiovascular risk factors, women having three or greater, but not those with fewer than three cardiovascular risk factors, had a significantly higher risk of developing breast cancer (HR 1.27, 95% CI 1.06–1.53). Subgroup analyses indicated that women with three or greater cardiovascular risk factors had higher risk of breast cancer among postmenopausal Black women, but not among premenopausal Black and White women.

Conclusions
Combinations of cardiovascular risk factors are associated with increased risk of breast cancer in middle-aged women, especially in postmenopausal Black women. Joint interventions to modify cardiovascular risk factors could be used to prevent breast cancer in these higher-risk individuals.
Long-term follow-up of retinal morphology and physiology after 2000 mg sildenafil overdose as a means of attempted suicide: a case report
Authors: Miura Gen , Baba Takayuki , Hashimoto Ryusuke , Yamamoto Shuichi 
Published: May 2022

Abstract
Background
Few case reports have described sildenafil overdose, particularly ingestion of > 1000 mg, and overdose-induced changes in visual function remain unclear. We report retinal morphology, retinal sensitivity, and findings of electrophysiological evaluation over long-term follow-up in a case of sildenafil overdose (2000 mg).

Case presentation
Our patient developed visual abnormalities in the paracentral visual field accompanied by photophobia, decreased contrast sensitivity, and difficulty distinguishing colors in both eyes, 8 hours after the sildenafil overdose. These symptoms did not improve throughout the course, and although abnormalities of retinal morphology and sensitivity, as well as the electroretinogram findings showed slight improvement, the patient did not recover completely at 6-month follow-up.

Conclusions
We observed that high-dose sildenafil ingestion leads to retinal toxicity; the ocular abnormalities may persist for at least 6 months. Optical coherence tomography, Humphrey perimetry, microperimetry, and multifocal electroretinography are useful to quantitatively monitor temporal changes.
Effects of optic nerve head-related parameters on retinal vessel calibers measurement results on fundus photographs
Authors: Iwase Aiko , Tsutsumi Tae , Kawasaki Ryo , Suehiro Jun , Sekine Akihiko , Araie Makoto 
Published: May 2022

Abstract
Background
Although relationship between the retinal vessel caliber (RVC) and glaucoma is well known, there has been a paucity of information on the effects of glaucoma-related optic nerve head (ONH) structural factors on the RVC. Information on this relationship should be useful in studying possible roles of ocular circulation in the development and progression of glaucoma.

Method
Subjects were from Kumejima Study participants aged 40 years and older in Kumejima, Japan. Normal subjects and eyes were defined according to standardized systemic and ocular examinations. The central retinal artery and vein equivalents (CRAE and CRVE) were determined on fundus photographs by correcting the magnification using the refractive error, corneal curvature, and axial length (AL) of an individual eye and paraxial ray tracing; the ONH structural parameters were determined by planimetry.

Results
In a total of 558 right eyes (558 normal subjects), aged 49.0 ± 7.1 (standard deviation) years with gradable photographs and planimetric results, CRAE averaged 136.1 ± 12.3 μm and CRVE 216.9 ± 17.4 μm. After adjustment for the effects of confounding factors in multivariate analysis, the AL (P < 0.001), rim area (P = 0.019), disc area (P = 0.042), and smoking (P = 0.035–0.043) correlated positively, and the mean blood pressure (P < 0.001) negatively with CRAE; the AL (P < 0.001), rim area (P = 0.001), disc area (P = 0.005), smoking (P < 0.001), and male sex (P = 0.013) correlated positively, and the β-peripapillary atrophy (β-PPA) area (P = 0.044), vertical Cup/Disc ratio (v-C/D) (P = 0.035), and age (P < 0.001) negatively with CRVE.

Conclusion
The current study showed significant effects of rim area, v-C/D or β-PPA area determined on the photographs on the RVC measurement results. Further, it showed a necessity to incorporate the glaucoma-related ONH structural parameters as co-variables to correctly estimate the effects of various factors on the RVC.
For there is nothing either good or bad: a study of the mediating effect of interpretation bias on the association between mindfulness and reduced post-traumatic stress vulnerability
Authors: Deen Hannah , Notebaert Lies , Van Bockstaele Bram , Clarke Patrick J. F. , Todd Jemma 
Published: May 2022

Abstract
Background
Despite increasing interest in the association between mindfulness and reduced trauma vulnerability, and the use of mindfulness in the latest interventions for Post-Traumatic Stress Disorder (PTSD), few studies have examined the mechanisms through which mindfulness may influence post-trauma psychopathology. The present study aimed to determine whether negative interpretation bias, the tendency to interpret ambiguous information as negative or threatening rather than positive or safe, mediates the association between higher levels of trait mindfulness and lower levels of PTSD symptoms. Negative interpretation bias was examined due to prior evidence indicating it is associated with being less mindful and post trauma psychopathology.

Methods
The study examined 133 undergraduate students who reported exposure to one or more potentially traumatic events in their lifetime. Participants completed self-report measures of trait mindfulness (Five Facet Mindfulness Questionnaire – Short Form; FFMQ-SF) and PTSD symptoms (Post-Traumatic Stress Disorder Checklist – Civilian version; PCL-C) as well an interpretation bias task that assessed the degree to which participants interpreted a range of everyday hypothetical scenarios to be threatening to their physical and/or psychological wellbeing.

Results
Results of a mediation analysis indicated a significant negative direct effect of trait mindfulness on PTSD symptomatology (p < .001). There was no evidence that negative interpretation bias mediated this relationship [BCa CI [-0.04, 0.03)], nor was it associated with trait mindfulness (p = .90) and PTSD symptomatology (p = .37).

Conclusions
The results of the current study provide further evidence of the link between trait mindfulness and reduced post-trauma psychopathology while providing no support for the role of negative interpretation bias in this relationship.
The positive effects of parents’ education level on children’s mental health in Indonesia: a result of longitudinal survey
Authors: Fakhrunnisak Dian , Patria Bhina 
Published: May 2022

Abstract
Background
Mental health problems are associated with decreasing the quality of various aspects of life. Cases of mental health problems (e.g., depressive symptoms) have increased continuously. Researchers predicted depression to be the first cause of world burden diseases in 2030. One of the determinant factors of mental health is parents’ education levels, but there have been contradictory research findings. The current research investigates the effect parental education attainment has on children’s mental health.

Methods
We used public data from two waves of the Indonesia Family Life Survey (IFLS) conducted in 2007 and 2014. There were 767 participants aged 15-19 years old (M = 16.80, SD = 1.37) in 2007. All participants were re-interviewed in 2014. We examined the highest level of the parents’ formal education in 2007 and the children’s mental health in 2014 to find the longitudinal effects. We used depressive symptoms and happiness as representative variables of mental health. The structural equation model (SEM) was used to examine the hypothesis, and we prioritized predictive testing over the models’ goodness of fit. We have built 12 models of combinations of children’s and parents’ sexes and different independent variables.

Results
The hypothesis testing showed the longitudinal effects that fathers’ education in 2007 has on daughters’ depressive symptoms in 2014 (β = −.203, p < 0.01), while there were longitudinal effects from mothers’ education in 2007 on their daughters’ depressive symptoms (β = −.163, p < 0.01) and sons’ depressive symptoms (β = .096, p ≤ 0.05) in 2014. Testing the happiness models showed that fathers’ education in 2007 influenced the happiness of all of participants (β = .167, p < 0.01), including both sons (β = .206, p < 0.01) and daughters (β = 149, p < 0.01). On the contrary, no significant correlation was found between mothers’ education and children’s happiness across all three categories of participants.

Conclusions
The general results of this study showed that parents’ education levels were associated with their children’s mental health, but there are different associations found through the different combinations of children’s and parents’ sexes.
Application of the induced membrane technique of tibia using extracorporeal vs. intracorporeal formation of a cement spacer: a retrospective study
Authors: Luo Junhao , Bo Fanyu , Wang Jian , Wu Yongwei , Ma Yunhong , Yin Qudong , Liu Yu 
Published: May 2022

AbstractBackgroundThere were two ways of preparing the cement spacer: intracorporeal and extracorporeal formation. This study aimed to investigate the outcomes of extracorporeal vs. intracorporeal formation of a spacer using the induced membrane technique (IMT) for repairing bone defects of the tibia.MethodsSixty-eight patients with tibial defects treated with IMT were analyzed retrospectively. According to the mode of bone cement preparation, patients were divided into intracorporeal and extracorporeal groups (36 vs. 32 respectively). All patients were followed up for 12–48 months (average 18.7 months). The time interval between the first and second stages, the time required to remove the spacer, injury of the IM or bone ends, bone healing and infection control, as well as the functional recovery (Johner—Wruhs scoring), were compared.ResultsThere was no significant difference in the preoperative data between the two groups (P > 0.05). There was no significant difference in the time interval (12.64 ± 4.41vs. 13.22 ± 4.96 weeks), infection control (26/28 vs. 20/23), bone healing time (7.47 ± 2.13vs. 7.50 ± 2.14 mos), delayed union (2/36 vs. 2/32), nonunion (2/36 vs. 1/32), an excellent or good rate of limb functional recovery (30/36 vs. 26/32) between the intracorporeal and extracorporeal groups (P > 0.05). However, the time required to remove (3.97 ± 2.34 min) was longer and the injury of IM or bone ends (28/36) was greater in the intracorporeal group than those in the extracorporeal group (0.56 ± 0.38 min and 1/32, respectively), showing a significant difference (P < 0.05).ConclusionBoth approaches were shown to have similar effects on bone defect repair and infection control. However, intracorporeal formation had advantages in terms of additional stability, while extracorporeal formation had advantages in terms of removal. Therefore, the specific method should be selected according to specific clinical needs. We recommended the extracorporeal or the modified extracorporeal formation in most cases.
Non-operative treatment or volar locking plate fixation for dorsally displaced distal radius fractures in patients over 70 years – a three year follow-up of a randomized controlled trial
Authors: Südow Hanna , Severin Sara , Wilcke Maria , Saving Jenny , Sköldenberg Olof , Navarro Cecilia Mellstrand 
Published: May 2022

Abstract
Background
Surgical treatment of displaced distal radius fractures (DRF) in older patients has increased, despite lacking evidence of its superiority over non-operative treatment. How treatment choice affects these patients after the initial 12-month period remains unknown. This study presents a clinical and radiographic follow up at an average of 3 years after treatment in the context of a randomized clinical trial comparing outcomes in patients aged ≥70 years, with a dorsally displaced distal radius fracture treated either surgically with volar locking plate or non-operatively.

Methods
Between 2009 and 2017, 140 patients aged ≥70 years with dorsally displaced DRF were randomized to surgery with volar locking plate (VLP) or non-operative treatment. At an average of 3 years after inclusion the participants were invited to an additional follow-up. The primary outcome was Patient Rated Wrist Evaluation (PRWE). Secondary outcomes included additional Patient Reported Outcome Measures (PROM), grip strength, range of motion, complications and radiological results.

Results
Sixty six patients were available for a 3 year follow-up, 33 in the non-operatively treated group and 33 in the VLP-group. The mean age at injury was 77 years. At 3 years the median PRWE was better (0 points) in the VLP-group than in the non-operative treatment group (9 points) p-value: 0.027. No statistically significant difference was found in Disabilities of the Arm, Hand, and Shoulder (DASH), EuroQol 5 Dimensions (EQ-5D) or grip strength. Total arc of range of motion was larger in the operatively treated group. No significant difference in osteoarthritis was found. Both groups had regained grip strength. The complication rate was similar. Outcomes improved from the 1 year to the 3 year follow-up.

Conclusions
Surgery with volar locking plate gave less long-term disability compared to non-operative treatment for severely displaced distal radius fractures in patients aged ≥70 years. Our findings were statistically significant but in the lower range of clinical importance.

Trial registration
The study was registered at : NCT02154620 03/06/2014 and NCT01268397 30/12/2010. Ethical approval was obtained from Ethical Committee in Stockholm, Sweden (2009/37–31/3, 2013/105–31/2, 2014/1041–32, 2017/611–32).