bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying biomarkers of axonal degeneration in early glaucoma to find the disc at risk
Authors: Bartlett R. L. , Frost B. E. , Mortlock K. E. , Fergusson J. R. , White N. , Morgan J. E. , North R. V. , Albon J. 
Published: June 2022

AbstractTo evaluate regional axonal-related parameters as a function of disease stage in primary open angle glaucoma (POAG) and visual field (VF) sensitivity. Spectral domain optical coherence tomography was used to acquire 20° scans of POAG (n = 117) or healthy control (n = 52) human optic nerve heads (ONHs). Region specific and mean nerve fibre layer (NFL) thicknesses, border NFL and peripapillary NFL, minimum rim width (MRW)/ area (MRA) and prelamina thickness; and volume were compared across POAG disease stages and with visual field sensitivity. Differences identified between early glaucoma (EG), preperimetric glaucoma (PG) and control (C) ONHs included thinner PG prelamina regions than in controls (p < 0.05). Mean border NFL was thinner in EG (p < 0.001) and PG (p = 0.049) compared to control eyes; and EG mean, and inferior and ST, border NFL was thinner than in PG (p < 0.01). Mean, superior and inferior PG peripapillary NFL were thinner than in controls (p < 0.05), and EG ST peripapillary NFL was thinner than in PG (p = 0.023). MRW differences included: PG SN and inferior less than in controls (p < 0.05); thinner EG mean regional, inferior, nasal, and ST MRW versus PG MRW (p < 0.05). Regional border NFL, peripapillary NFL, MRW, MRA, prelamina thickness (except centre, p = 0.127) and prelamina volume (p < 0.05) were significantly associated with VF mean deviation (MD). Novel axon-derived indices hold potential as biomarkers to detect early glaucoma and identify ONHs at risk.
Linked-read sequencing for detecting short tandem repeat expansions
Authors: Chiu Readman , Rajan-Babu Indhu-Shree , Birol Inanc , Friedman Jan M. 
Published: June 2022

AbstractDetection of short tandem repeat (STR) expansions with standard short-read sequencing is challenging due to the difficulty in mapping multicopy repeat sequences. In this study, we explored how the long-range sequence information of barcode linked-read sequencing (BLRS) can be leveraged to improve repeat-read detection. We also devised a novel algorithm using BLRS barcodes for distance estimation and evaluated its application for STR genotyping. Both approaches were designed for genotyping large expansions (> 1 kb) that cannot be sized accurately by existing methods. Using simulated and experimental data of genomes with STR expansions from multiple BLRS platforms, we validated the utility of barcode and phasing information in attaining better STR genotypes compared to standard short-read sequencing. Although the coverage bias of extremely GC-rich STRs is an important limitation of BLRS, BLRS is an effective strategy for genotyping many other STR loci.
Clinical exome sequencing for inherited retinal degenerations at a tertiary care center
Authors: Ganapathi Mythily , Thomas-Wilson Amanda , Buchovecky Christie , Dharmadhikari Avinash , Barua Subit , Lee Winston , Ruan Merry Z. C. , Soucy Megan , Ragi Sara , Tanaka Joy , Clark Lorraine N. , Naini Ali B. , Liao Jun , Mansukhani Mahesh , Tsang Stephen , Jobanputra Vaidehi 
Published: June 2022

AbstractInherited retinal degenerations are clinically and genetically heterogeneous diseases characterized by progressive deterioration of vision. This study aimed at assessing the diagnostic yield of exome sequencing (ES) for an unselected cohort of individuals with hereditary retinal disorders. It is a retrospective study of 357 unrelated affected individuals, diagnosed with retinal disorders who underwent clinical ES. Variants from ES were filtered, prioritized, and classified using the ACMG recommendations. Clinical diagnosis of the individuals included rod-cone dystrophy (60%), macular dystrophy (20%), cone-rod dystrophy (9%), cone dystrophy (4%) and other phenotypes (7%). Majority of the cases (74%) were singletons and 6% were trios. A confirmed molecular diagnosis was obtained in 24% of cases. In 6% of cases, two pathogenic variants were identified with phase unknown, bringing the potential molecular diagnostic rate to ~ 30%. Including the variants of uncertain significance (VUS), potentially significant findings were reported in 57% of cases. Among cases with a confirmed molecular diagnosis, variants inEYS, ABCA4, USH2A, KIZ, CERKL, DHDDS, PROM1, NR2E3, CNGB1, ABCC6, PRPH2, RHO, PRPF31, PRPF8, SNRNP200, RP1, CHM, RPGRwere identified in more than one affected individual. Our results support the utility of clinical ES in the diagnosis of genetically heterogeneous retinal disorders.
Relationship between renal and liver function with diabetic retinopathy in patients with type 2 diabetes mellitus: a study based on cross-sectional data
Authors: Yao Xi , Pei Xiaoting , Fan Shuoning , Yang Xueke , Yang Yingrui , Li Zhijie 
Published: June 2022

AbstractThis study aims to explore the relationship between abnormal renal- and liver-function and diabetic retinopathy (DR) in patients with type 2 diabetes mellitus (T2DM). A total of 994 T2DM patients who received inpatient treatment in the Endocrinology Department of Henan Province People’s Hospital were included in the study. Logistic regression was performed to identify the relationship between abnormal renal and liver function with DR. Receiver operator characteristic analysis was performed to explore the efficacy of risk factors in predicting DR. Higher urine albumin [OR(95%CI) = 3.344(1.921–5.822), P < 0.001] and urine albumin/creatinine ratio [OR (95%CI) = 2.901(1.911–5.822), P < 0.001] were closely related to the occurrence of DR. People with low TP had a 1.624-times higher risk (95%CI: 1.008–2.617) of developing DR than those with normal total protein (P = 0.046). The more risk factors that are present, the greater the risk of DR. For every one-point incremental increase in the risk-factor score, the risk of DR increased by 31.0% (P < 0.001). The area under receiver operating curve of risk-factor score was 0.839 (0.812, 0.866), with a sensitivity of 81.9% and a specificity of 74.8%. The risk of developing DR increased with an increased risk-factor score. These findings are potentially valuable for DR screening and early diagnosis in patients with T2DM.
First ovum-in-ovo pathological titanosaurid egg throws light on the reproductive biology of sauropod dinosaurs
Authors: Dhiman Harsha , Verma Vishal , Prasad Guntupalli V. R. 
Published: June 2022

AbstractPathologic eggs have been documented in the amniote eggs of birds, turtles, and dinosaurs. These eggs occur either in the form of one egg within another egg, a condition known as ovum-in-ovo or multi-shelled eggs showing additional pathological eggshell layer/s besides the primary shell layer. Though multi-shelled eggs and eggshells were previously recorded only in reptiles and ovum-in-ovo eggs in birds, now it has been shown that multi-shelled egg pathology occurs in birds as well. However, no ovum-in-ovo egg has been reported in dinosaurs or for that matter in other reptiles. Here we describe an ovum-in-ovo pathological egg from a titanosaurid dinosaur nest from the Upper Cretaceous Lameta Formation of western Central India which makes it the first report of this pathology in dinosaurs. Birds possess a specialized uterus while other amniotes have a generalized uterus. However, alligators and crocodiles retain a specialized uterus like birds along with a reptilian mode of egg-laying. The discovery of ovum-in-ovo egg from a titanosaurid dinosaur nest suggests that their oviduct morphology was similar to that of birds opening up the possibility for sequential laying of eggs in this group of sauropod dinosaurs. This new find underscores that the ovum-in-ovo pathology is not unique to birds and sauropods share a reproductive behavior very similar to that of other archosaurs.
Rewritable acidochromic papers based on oxazolidine for anticounterfeiting and photosensing of polarity and pH of aqueous media
Authors: Razavi Bahareh , Roghani-Mamaqani Hossein , Salami-Kalajahi Mehdi 
Published: June 2022

AbstractOxazolidine is a new category of stimuli-chromic organic compounds with unique characteristics in response to polarity, pH changes, water, light, and metal ions that were well-known as solvatochromism, acidochromism, hydrochromism, photochromism, and ionochromism, respectively. Therefore, oxazolidine derivatives have been developed for their potential applications in chemosensors, anticounterfeiting, and rewritable hydrochromic papers. In this study, various oxazolidine derivatives containing hydroxyl and naphthalene substituted groups were synthesized by using two different indolenine compounds. The synthesized oxazolidine derivatives were used for investigation of solvatochromism in different solvents, and also acidochromism in various pHs by using UV–Vis and fluorescence spectroscopies. In addition, the oxazolidine derivatives were coated on cellulosic papers using a layer-by-layer strategy to develop rewritable acidochromic papers for printing of security tags on cellulosic papers by using acidic and alkaline solutions as water-based inks. Therefore, the developed rewritable acidochromic papers could be used as security papers.
Complete chloroplast genome of Lilium ledebourii (Baker) Boiss and its comparative analysis: lights into selective pressure and adaptive evolution
Authors: Sheikh-Assadi Morteza , Naderi Roohangiz , Kafi Mohsen , Fatahi Reza , Salami Seyed Alireza , Shariati Vahid 
Published: June 2022

AbstractLilium ledebourii (Baker) Boiss is a rare species, which exhibits valuable traits. However, before its genetic diversity and evolutionary were uncovered, its wild resources were jeopardized. Moreover, some ambiguities in phylogenetic relationships of this genus remain unresolved. Therefore, obtaining the whole chloroplast sequences of L. ledebourii and its comparative analysis along with other Lilium species is crucial and pivotal to understanding the evolution of this genus as well as the genetic populations. A multi-scale genome-level analysis, especially selection pressure, was conducted. Detailed third‑generation sequencing and analysis revealed a whole chloroplast genome of 151,884 bp, with an ordinary quadripartite and protected structure comprising 37.0% GC. Overall, 113 different genes were recognized in the chloroplast genome, consisting of 30 distinct tRNA genes, four distinct ribosomal RNAs genes, and 79 unique protein-encoding genes. Here, 3234 SSRs and 2053 complex repeats were identified, and a comprehensive analysis was performed for IR expansion and contraction, and codon usage bias. Moreover, genome-wide sliding window analysis revealed the variability of rpl32-trnL-ccsA, petD-rpoA, ycf1, psbI-trnS-trnG, rps15-ycf1, trnR, trnT-trnL, and trnP-psaJ-rpl33 were higher among the 48 Lilium cp genomes, displaying higher variability of nucleotide in SC regions. Following 1128 pairwise comparisons, ndhB, psbJ, psbZ, and ycf2 exhibit zero synonymous substitution, revealing divergence or genetic restriction. Furthermore, out of 78 protein-coding genes, we found that accD and rpl36 under positive selection: however, at the entire-chloroplast protein scale, the Lilium species have gone through a purifying selection. Also, a new phylogenetic tree for Lilium was rebuilt, and we believe that the Lilium classification is clearer than before. The genetic resources provided here will aid future studies in species identification, population genetics, and Lilium conservation.
Epidemiological investigation of swine Japanese encephalitis virus based on RT-RAA detection method
Authors: Nie Mincai , Zhou Yuancheng , Li Fengqin , Deng Huidan , Zhao Mengxi , Huang Yao , Jiang Chaoyuan , Sun Xiangang , Xu Zhiwen , Zhu Ling 
Published: June 2022

AbstractJEV is one of the zoonotic pathogens that cause serious diseases in humans. JEV infection can cause abortion, mummified foetus and stillbirth in sows, orchitis and semen quality decline in boars, causing huge economic losses to pig industry. In order to investigate the epidemiology of JEV in pigs in Sichuan province, a rapid and efficient fluorescent Reverse transcription recombinase-aided amplification (RT-RAA) detection method was established. Aborted fetuses and testicular swollen boar samples were detected by RT-RAA in pigs in the mountain areas around Sichuan Basin, and the detection rate of JEV was 6.49%. The positive samples were identified as JEV GI strain and GIIIstrain by sequencing analysis. We analyzed the whole gene sequence of a positive sample for the GI virus. The Envelope Protein (E protein) phylogenetic tree analysis was far related to the Chinese vaccine strain SA14-14-2, and was most closely related to the JEV GI strains SH17M-07 and SD0810 isolated from China. The results showed that we established an efficient, accurate and sensitive method for clinical detection of JEV, and JEV GI strains were prevalent in Sichuan area. It provides reference for the prevention and control of JEV in Sichuan.
Enterococcus faecium and Pediococcus acidilactici deteriorate Enterobacteriaceae-induced depression and colitis in mice
Authors: Jang Hyo-Min , Kim Jeon-Kyung , Joo Min-Kyung , Shin Yoon-Jung , Lee Kyung-Eon , Lee Chang Kyun , Kim Hyo-Jong , Kim Dong-Hyun 
Published: June 2022

AbstractGut dysbiosis is closely associated with the outbreak of inflammatory bowel disease (IBD) and psychiatric disorder. The Enterobacteriaceae population was higher in the feces of patients with inflammatory bowel disease (IBD-F) than in those of healthy control volunteers (HC-F). The Enterococcaceae and Lactobacillaceae populations were higher in the feces of IBD patients with depression (IBD/D+-F) vs. the feces of IBD patients without depression (IBD/D−-F). Therefore, we examined the effects of Klebsiella oxytoca, Escherichia coli, Cronobacter sakazakii, Enterococcus faecium, and Pediococcus acidolactici overpopulated in IBD/D+-F and their byproducts LPS and exopolysaccharide (EPS) on the occurrence of depression and colitis in mice. Oral gavages of Klebsiella oxytoca, Escherichia coli, and Cronobacter sakazakii belonging to Enterobacteriaceae, singly or together, caused dose-dependently colitis and depression-like behaviors in germ-free and specific-pathogen-free mice. Although Enterococcus faecium and Pediococcus acidolactici did not significantly cause colitis and depression-like behaviors, they significantly deteriorated Klebsiella oxytoca- or Escherichia coli-induced colitis, neuroinflammation, and anxiety/depression-like behaviors and increased blood LPS, corticosterone, and IL-6 levels. The EPSs from Enterococcus faecium and Pediococcus acidolactici also worsened Klebsiella oxytoca LPS-induced colitis, neuroinflammation, and depression-like behaviors in mice and increased the translocation of fluorescein isothiocyanate-conjugated LPS into the hippocampus. However, Bifidobacterium longum, which was lower in IBD/D+-F vs. IBD/D−-F, or its EPS suppressed them. In conclusion, Enterococcus faecium and Pediococcus acidolactici, known as a probiotic strain, and their EPSs may be a risk factor for the outbreak of depression and IBD.
The differences of the acromiohumeral interval between supine and upright radiographs of the shoulder
Authors: Sanguanjit Prakasit , Apivatgaroon Adinun , Boonsun Phanuwat , Srimongkolpitak Surasak , Chernchujit Bancha 
Published: June 2022

AbstractThe acromiohumeral interval (AHI) is a measurement used to determine the superior migration of the humeral head in rotator cuff (RC) tear patients. The purpose of this study was to compare the AHI of; supine, upright shoulder radiographs, and magnetic resonance imaging (MRI) of the shoulder. The 86 shoulders were divided into 3 groups that included; (1) non-full thickness tear (50%), (2) full thickness (FT) tear ≤3 cm (33.7%), and (3) FT tear > 3 cm (16.3%). The mean difference of AHI noted was significantly lower in the supine radiographs and MRIs than with the upright (1.34–1.37 mm, 1.62–1.87 mm, respectively). Upright AHI ≤ 7.0 mm had 27.9% sensitivity and 100% specificity in diagnosing FT tears with 64% accuracy (p < 0.001). The supine AHI ≤ 6.5 mm had 32.6% sensitivity, 100.0% specificity, and 66.3% accuracy (p < 0.01). The results revealed the AHI in supine radiographs were significantly lower than upright shoulder radiographs. For AHI ≤ 7 mm in upright shoulder radiographs, this remains as an appropriate diagnostic test for ruling in shoulders with full thickness rotator cuff tears. This value was not relevant for use as the cut point in the supine radiographs and MRIs.
Original karst tiankeng with underground virgin forest as an inaccessible refugia originated from a degraded surface flora in Yunnan, China
Authors: Shui Wei , Chen Yiping , Jian Xiaomei , Jiang Cong , Wang Qianfeng , Zeng Yue , Zhu Sufeng , Guo Pingping , Li Hui 
Published: June 2022

AbstractKarst tiankengs are rare natural habitats, having a local microclimate different from surrounding regions. A contrast study on plant communities at the inside and outside of the primitive tiankeng was carried out by performing the qualitative analysis of species compositions of arborous and shrub layers. We found that plant communities in the primitive tiankeng belong to the subtropical moist evergreen broad-leaf forest, whereas those outside the tiankeng belong to subtropical semi-moist needle-broadleaved mixed forest. Trapped habitat of primitive karst tiankeng protects the plant communities significantly different from those in external karst ecosystems, so karst tiankeng has the great value in the plant species protection. Although the trapped habitat decreases plant species abundance inside tiankeng to some extent, highly diverse shrub species are present in the inside-tiankeng plant communities, and the primitive karst tiankeng plays an important role in the plant diversity protection. The primitive karst tiankeng is an important refugia for plant not only as a plant species protection library, but a plant diversity protection library. When implementing measures for the reduction of damages to biodiversity due to global climate changes and human activities, more attention should be paid to the primitive karst tiankeng as a small ecological refugia and biodiversity protection library.
Platelets from patients with visceral obesity promote colon cancer growth
Authors: Cariello Marica , Piccinin Elena , Pasculli Emanuela , Arconzo Maria , Zerlotin Roberta , D’Amore Simona , Mastropasqua Francesca , Peres Claudia , Graziano Giusi , Villani Gaetano , Pesole Graziano , Moschetta Antonio 
Published: June 2022

AbstractSeveral studies highlighted the importance of platelets in the tumor microenvironment due to their ability to interact with other cell types such as leukocytes, endothelial, stromal and cancer cells. Platelets can influence tumor development and metastasis formation through several processes consisting of the secretion of growth factors and cytokines and/or via direct interaction with cancer cells and endothelium. Patients with visceral obesity (VO) are susceptible to pro-thrombotic and pro-inflammatory states and to development of cancer, especially colon cancer. These findings provide us with the impetus to analyze the role of platelets isolated from VO patients in tumor growth and progression with the aim to explore a possible link between platelet activation, obesity and colon cancer. Here, using xenograft colon cancer models, we prove that platelets from patients with visceral obesity are able to strongly promote colon cancer growth. Then, sequencing platelet miRNome, we identify miR-19a as the highest expressed miRNA in obese subjects and prove that miR-19a is induced in colon cancer. Last, administration of miR-19a per se in the xenograft colon cancer model is able to promote colon cancer growth. We thus elect platelets with their specific miRNA abundance as important factors in the tumor promoting microenvironment of patients with visceral obesity.
Host gut resistome in Gulf War chronic multisymptom illness correlates with persistent inflammation
Authors: Bose Dipro , Chatterjee Somdatta , Older Ethan , Seth Ratanesh , Janulewicz Patricia , Saha Punnag , Mondal Ayan , Carlson Jeffrey M. , Decho Alan W. , Sullivan Kimberly , Klimas Nancy , Lasley Stephen , Li Jie , Chatterjee Saurabh 
Published: June 2022

AbstractChronic multisymptom illness (CMI) affects a subsection of elderly and war Veterans and is associated with systemic inflammation. Here, using a mouse model of CMI and a group of Gulf War (GW) Veterans’ with CMI we show the presence of an altered host resistome. Results show that antibiotic resistance genes (ARGs) are significantly altered in the CMI group in both mice and GW Veterans when compared to control. Fecal samples from GW Veterans with persistent CMI show a significant increase of resistance to a wide class of antibiotics and exhibited an array of mobile genetic elements (MGEs) distinct from normal healthy controls. The altered resistome and gene signature is correlated with mouse serum IL-6 levels. Altered resistome in mice also is correlated strongly with intestinal inflammation, decreased synaptic plasticity, reversible with fecal microbiota transplant (FMT). The results reported might help in understanding the risks to treating hospital acquired infections in this population.
Somatic point mutations are enriched in non-coding RNAs with possible regulatory function in breast cancer
Authors: Rezaie Narges , Bayati Masroor , Hamidi Mehrab , Tahaei Maedeh Sadat , Khorasani Sadegh , Lovell Nigel H. , Breen James , Rabiee Hamid R. , Alinejad-Rokny Hamid 
Published: June 2022

AbstractNon-coding RNAs (ncRNAs) form a large portion of the mammalian genome. However, their biological functions are poorly characterized in cancers. In this study, using a newly developed tool, SomaGene, we analyze de novo somatic point mutations from the International Cancer Genome Consortium (ICGC) whole-genome sequencing data of 1,855 breast cancer samples. We identify 1030 candidates of ncRNAs that are significantly and explicitly mutated in breast cancer samples. By integrating data from the ENCODE regulatory features and FANTOM5 expression atlas, we show that the candidate ncRNAs significantly enrich active chromatin histone marks (1.9 times), CTCF binding sites (2.45 times), DNase accessibility (1.76 times), HMM predicted enhancers (2.26 times) and eQTL polymorphisms (1.77 times). Importantly, we show that the 1030 ncRNAs contain a much higher level (3.64 times) of breast cancer-associated genome-wide association (GWAS) single nucleotide polymorphisms (SNPs) than genome-wide expectation. Such enrichment has not been seen with GWAS SNPs from other cancers. Using breast cell line related Hi-C data, we then show that 82% of our candidate ncRNAs (1.9 times) significantly interact with the promoter of protein-coding genes, including previously known cancer-associated genes, suggesting the critical role of candidate ncRNA genes in the activation of essential regulators of development and differentiation in breast cancer. We provide an extensive web-based resource (https://www.ihealthe.unsw.edu.au/research) to communicate our results with the research community. Our list of breast cancer-specific ncRNA genes has the potential to provide a better understanding of the underlying genetic causes of breast cancer. Lastly, the tool developed in this study can be used to analyze somatic mutations in all cancers.