bluuebunny/crossref_metadata_2025_split huggingface dataset:
Culture-proven disseminated Mycobacterium Bovis infection (BCG-Osis) following intravesical BCG immunotherapy in a patient with bladder carcinoma-in-situ: ‘Case report’
Authors: Ghonaimy Ahmed , Qadeer Tariq , Lohani Sudhir , Schofield John , Madaan Sanjeev 
Published: February 2022

AbstractWe are reporting a case of culture-proven disseminated Mycobacterium Bovis infection (BCG-Osis), involving lung, bone-marrow and urinary tract, after intravesical Bacillus Calmette–Guérin (BCG) immunotherapy for bladder carcinoma-in-situ. A 71-year-gentleman presented with fever shortly after intravesical BCG instillation. He was initially treated for presumed Urinary Tract Infection, but negative urine culture and persistent fever prompted us to consider alternative diagnoses. Empirical treatment for BCG-Osis was commenced after initial negative workup including blood culture, echocardiography, computed tomography (CT) Chest, and Kidney-Ureter-Bladder (KUB). However, he remained febrile and leukopenic, so bone-marrow examination was performed along with repeating CT Chest, which revealed non-caseating granulomas and small nonspecific pulmonary nodules, respectively, supporting our provisional diagnosis. Interestingly, Mycobacterium Bovis was finally isolated from one of his urine specimens, confirming our diagnosis.
Predictions of the accuracy of genomic prediction: connecting R2, selection index theory, and Fisher information
Authors: Bijma Piter , Dekkers Jack C. M. 
Published: February 2022

Abstract
Background
Deterministic predictions of the accuracy of genomic estimated breeding values (GEBV) when combining information sources have been developed based on selection index theory (SIT) and on Fisher information (FI). These two approaches have resulted in slightly different results when considering the combination of pedigree and genomic information. Here, we clarify this apparent contradiction, both for the combination of pedigree and genomic information and for the combination of subpopulations into a joint reference population.

Results
First, we show that existing expressions for the squared accuracy of GEBV can be understood as a proportion of the variance explained. Next, we show that the apparent discrepancy that has been observed between accuracies based on SIT vs. FI originated from two sources. First, the FI referred to the genetic component that is captured by the marker genotypes, rather than the full genetic component. Second, the common SIT-based derivations did not account for the increase in the accuracy of GEBV due to a reduction of the residual variance when combining information sources. The SIT and FI approaches are equivalent when these sources are accounted for.

Conclusions
The squared accuracy of GEBV can be understood as a proportion of the variance explained. The SIT and FI approaches for combining information for GEBV are equivalent and provide identical accuracies when the underlying assumptions are equivalent.
MonaGO: a novel gene ontology enrichment analysis visualisation system
Authors: Xin Ziyin , Cai Yujun , Dang Louis T. , Burke Hannah M. S. , Revote Jerico , Charitakis Natalie , Bienroth Denis , Nim Hieu T. , Li Yuan-Fang , Ramialison Mirana 
Published: February 2022

Abstract
Background
Gene ontology (GO) enrichment analysis is frequently undertaken during exploration of various -omics data sets. Despite the wide array of tools available to biologists to perform this analysis, meaningful visualisation of the overrepresented GO in a manner which is easy to interpret is still lacking.

Results
Monash Gene Ontology (MonaGO) is a novel web-based visualisation system that provides an intuitive, interactive and responsive interface for performing GO enrichment analysis and visualising the results. MonaGO supports gene lists as well as GO terms as inputs. Visualisation results can be exported as high-resolution images or restored in new sessions, allowing reproducibility of the analysis. An extensive comparison between MonaGO and 11 state-of-the-art GO enrichment visualisation tools based on 9 features revealed that MonaGO is a unique platform that simultaneously allows interactive visualisation within one single output page, directly accessible through a web browser with customisable display options.

Conclusion
MonaGO combines dynamic clustering and interactive visualisation as well as customisation options to assist biologists in obtaining meaningful representation of overrepresented GO terms, producing simplified outputs in an unbiased manner. MonaGO will facilitate the interpretation of GO analysis and will assist the biologists into the representation of the results.
Reevaluating scorpion ecomorphs using a naïve approach
Authors: Coelho Pedro , Kaliontzopoulou Antigoni , Sousa Pedro , Stockmann Mark , van der Meijden Arie 
Published: February 2022

AbstractBackgroundEcomorphs create the opportunity to investigate ecological adaptation because they encompass organisms that evolved characteristic morphologies under similar ecological demands. For over 50 years, scorpions have been empirically assigned to ecomorphs based on the characteristic morphologies that rock, sand, vegetation, underground, and surface dwellers assume. This study aims to independently test the existence of scorpion ecomorphs by quantifying the association between their morphology and ecology across 61 species, representing 14 families of the Scorpiones order.ResultsWithout a priori categorization of species into ecomorphs, we identified four groups based on microhabitat descriptors, which reflect how scorpion ecospace is clustered. Moreover, these microhabitat groups, i.e., ecotypes, have significantly divergent morphologies; therefore, they represent ecomorphs. These ecomorphs largely correspond with the ones previously described in the literature. Therefore, we retained the names Lithophilous, Psammophilous, and Pelophilous, and proposed the name Phytophilous for vegetation dwellers. Finally, we sought to map the morphology-ecology association in scorpions and found that the morphological regions most tightly associated with ecology are at the extremities. Moreover, the major trend in ecomorphological covariation is that longer walking legs and relatively slender pedipalps (pincers) are associated with sandy microhabitats, while the inverse morphological proportions are associated with rocky microhabitats.ConclusionsScorpion ecomorphs are validated in a naïve approach, from ecological descriptors and whole body anatomy. This places them on a more solid quantitative footing for future studies of ecological adaptation in scorpions. Our results verify most of the previously defined ecomorphotypes and could be used as a current practice to understand the adaptive significance of ecological morphology.
Can DNA help trace the local trade of pangolins? Conservation genetics of white-bellied pangolins from the Dahomey Gap (West Africa)
Authors: Zanvo Stanislas , Djagoun Chabi A. M. S. , Azihou Akomian F. , Djossa Bruno , Afiademanyo Komlan , Olayemi Ayodeji , Agbangla Clément , Sinsin Brice , Gaubert Philippe 
Published: February 2022

AbstractBackgroundAfrican pangolins are currently experiencing unprecedented levels of harvesting, feeding both local demands and the illegal international trade. So far, the lack of knowledge on the population genetics of African pangolins has hampered any attempts at assessing their demographic status and tracing their trade at the local scale. We conducted a pioneer study on the genetic tracing of the African pangolin trade in the Dahomey Gap (DG). We sequenced and genotyped 189 white-bellied pangolins from 18 forests and 12 wildlife markets using one mitochondrial fragment and 20 microsatellite loci.ResultsTree-based assignment procedure showed that the pangolin trade is endemic to the DG region, as it was strictly fed by the the Dahomey Gap lineage (DGL). DGL populations were characterized by low levels of genetic diversity, an overall absence of equilibrium, important inbreeding levels, and lack of geographic structure. We identified a 92–98% decline in DGL effective population size 200–500 ya—concomitant with major political transformations along the ‘Slave Coast’—leading to contemporaneous estimates being inferior to minimum viable population size (< 500). Genetic tracing suggested that wildlife markets from the DG sourced pangolins through the entire DGL range. Our loci provided the necessary power to distinguish among all the genotyped pangolins, tracing the dispatch of a same individual on the markets and within local communities. We developed an approach combining rarefaction analysis of private allele frequencies with cross-validation of observed data that traced five traded pangolins to their forest origin, c. 200–300 km away from the markets.ConclusionsAlthough the genetic toolkit that we designed from traditional markers can prove helpful to trace the illegal trade in pangolins, our tracing ability was limited by the lack of population structure within the DGL. Given the deleterious combination of genetic, demographic, and trade-related factors affecting DGL populations, the conservation status of white-bellied pangolins in the DG should be urgently re-evaluated.
Differential responses of the rhizosphere microbiome structure and soil metabolites in tea (Camellia sinensis) upon application of cow manure
Authors: Sun Litao , Wang Yu , Ma Dexin , Wang Linlin , Zhang Xiaomei , Ding Yiqian , Fan Kai , Xu Ze , Yuan Changbo , Jia Houzhen , Ren Yonglin , Ding Zhaotang 
Published: February 2022

Abstract
Background
The rhizosphere is the narrow zone of soil immediately surrounding the root, and it is a critical hotspot of microbial activity, strongly influencing the physiology and development of plants. For analyzing the relationship between the microbiome and metabolome in the rhizosphere of tea (Camellia sinensis) plants, the bacterial composition and its correlation to soil metabolites were investigated under three different fertilization treatments (unfertilized, urea, cow manure) in different growing seasons (spring, early and late summer).

Results
The bacterial phyla Proteobacteria, Bacteroidetes, Acidobacteria and Actinobacteria dominated the rhizosphere of tea plants regardless of the sampling time. These indicated that the compositional shift was associated with different fertilizer/manure treatments as well as the sampling time. However, the relative abundance of these enriched bacteria varied under the three different fertilizer regimes. Most of the enriched metabolic pathways stimulated by different fertilizer application were all related to sugars, amino acids fatty acids and alkaloids metabolism. Organic acids and fatty acids were potential metabolites mediating the plant-bacteria interaction in the rhizosphere. Bacteria in the genera Proteiniphilum, Fermentimonas and Pseudomonas in spring, Saccharimonadales and Gaiellales in early summer, Acidobacteriales and Gaiellales in late summer regulated relative contents of organic and fatty acids.

Conclusion
This study documents the profound changes to the rhizosphere microbiome and bacterially derived metabolites under different fertilizer regimes and provides a conceptual framework towards improving the performance of tea plantations.
Whole-genome resequencing of Coffea arabica L. (Rubiaceae) genotypes identify SNP and unravels distinct groups showing a strong geographical pattern
Authors: Mekbib Yeshitila , Tesfaye Kassahun , Dong Xiang , Saina Josphat K. , Hu Guang-Wan , Wang Qing-Feng 
Published: February 2022

Abstract
Background
Coffea arabica L. is an economically important agricultural crop and the most popular beverage worldwide. As a perennial crop with recalcitrant seed, conservation of the genetic resources of coffee can be achieved through the complementary approach of in-situ and ex-situ field genebank. In Ethiopia, a large collection of C. arabica L. germplasm is preserved in field gene banks. Here, we report the whole-genome resequencing of 90 accessions from Choche germplasm bank representing garden and forest-based coffee production systems using Illumina sequencing technology.

Results
The genome sequencing generated 6.41 billion paired-end reads, with a mean of 71.19 million reads per sample. More than 93% of the clean reads were mapped onto the C. arabica L. reference genome. A total of 11.08 million variants were identified, among which 9.74 million (87.9%) were SNPs (Single nucleotide polymorphisms) and 1.34 million (12.1%) were InDels. In all accessions, genomic variants were unevenly distributed across the coffee genome. The phylogenetic analysis using the SNP markers displayed distinct groups.

Conclusions
Resequencing of the coffee accessions has allowed identification of genetic markers, such as SNPs and InDels. The SNPs discovered in this study might contribute to the variation in important pathways of genes for important agronomic traits such as caffeine content, yield, disease, and pest in coffee. Moreover, the genome resequencing data and the genetic markers identified from 90 accessions provide insight into the genetic variation of the coffee germplasm and facilitate a broad range of genetic studies.
Stroke-related health problems and associated actions identified with the post-stroke checklist among nursing home residents
Authors: Kjörk Emma K. , Gustavsson Martha , El-Manzalawy Nohad , Sunnerhagen Katharina S. 
Published: February 2022

Abstract
Background
Little is known about the needs of permanent nursing home residents after a stroke; comprehensive descriptions of needs are rare. The Post-Stroke Checklist facilitates the identification of health problems. The study aimed to use the Post-Stroke Checklist to identify the extent of health problems, and how they were addressed, in nursing home residents that experienced strokes in Sweden. We also investigated the feasibility of the Checklist in a nursing home context.

Methods
This is a cross-sectional explorative study. Twenty nursing homes in two regions of Sweden participated. We included residents that had experienced a stroke within approximately 3 years and the responsible staff members were approached. Questionnaires were completed during face-to-face meetings with staff members (n = 45) knowledgeable about the residents. Data collection included the Post-Stroke Checklist, Barthel Index, modified Rankin Scale, resident and staff characteristics, and a satisfaction-questionnaire completed by staff.

Results
At the included nursing homes 1061 residents, 22% (n = 239) had a history of stroke, and 6% (n = 65) had experienced strokes during the last 3.5 years. Forty-nine residents were included (41% men, median age, 86 years, range 59–97). Among the health problems identified with the Checklist, activities of daily living (82%) were most common, and spasticity (41%) and pain (29%) were least common. Residents had extensive care needs, with a median of six health problems per resident. The total number of health problems addressed by previous actions i.e., referrals, as suggested in the Checklist, was 124, when recalled by staff. The median Barthel index score was 35. Lack of follow-up after stroke (e.g., by using a checklist) was reported in 17/20 nursing homes. The staff were satisfied with the Post-Stroke Checklist.

Conclusions
We found that more than 1/5 of residents had experienced a stroke; thus, the Post-Stroke Checklist was a useful tool in nursing homes. Half of the residents had more than six health problems, identified with the Post-Stroke Checklist. Extensive needs, combined with a lack of follow-up, indicated a risk of insufficient care. These findings suggested that nursing home routines could be improved with the Post-Stroke Checklist.
Trial registration The project is registered in Research web, project number: 256021.
Sick sinus syndrome as the initial manifestation of neuromyelitis optica spectrum disorder: a case report
Authors: Hamaguchi Mai , Fujita Hiroaki , Suzuki Tomonari , Suzuki Keisuke 
Published: February 2022

Abstract
Background
Sick sinus syndrome (SSS) is known to occur due to lesions in the medulla oblongata. Although medullary lesions have occurred in patients with neuromyelitis optica spectrum disorder (NMOSD), there are few reports of SSS associated with NMOSD. We report a patient with NMOSD who developed refractory nausea, vomiting and SSS as the initial manifestation.

Case presentation
A 77-year-old female developed refractory nausea and frequent episodes of syncope. The patient was diagnosed with SSS because sinus pauses lasting five to six seconds were observed, and pacemaker implantation was performed. Two months later, she was referred to our hospital because of limb weakness and sensory impairment that progressed over a month. The patient was confirmed to have muscle weakness; manual muscle testing revealed grade 4 in the upper extremities and grade 3 in the lower extremities. Tendon reflexes were diminished, while no pathological reflexes were present. Thermal and pain sensations were impaired in the upper and lower extremities, and vibration sensation was impaired in both lower extremities. Bladder and rectal disturbances were also noted. Optic neuritis was not detected. T2-weighted magnetic resonance imaging (MRI) showed high-intensity lesions in the dorsal part of the medulla oblongata and C3–6 cervical cord. Her serum was positive for antibodies against aquaporin 4, and a diagnosis of NMOSD was made. She was treated with two courses of an intravenous methylprednisolone pulse and one course of plasma exchange. Then, she was transferred to another hospital for rehabilitation.

Conclusions
Because SSS is a life-threatening complication, clinicians should be aware of the possibility that medullary lesions in NMOSD can cause SSS as the initial manifestation.
Relationship between serum lipid levels and the immune microenvironment in breast cancer patients: a retrospective study
Authors: Goto Wataru , Kashiwagi Shinichiro , Kamei Yuri , Watanabe Chika , Aomatsu Naoki , Ikeda Katsumi , Ogawa Yoshinari , Hirakawa Kosei , Ohira Masaichi 
Published: February 2022

Abstract
Background
Therapeutic agents for dyslipidaemia, in particular statins, have been recently reported to suppress growth and metastasis of breast cancer. However, the predictive value of lipid control in breast cancer patients has not been discussed sufficiently. In addition, though immunometabolism is a relatively novel approach for tumour immunotherapy, the relationship between lipid metabolism and immune status has not been well documented. We therefore investigated the effects of lipid metabolism on antitumour immune response and cancer prognosis.

Methods
Except for patients with ductal carcinoma in situ, 938 patients treated with curative surgery were examined. The correlation between treatment for dyslipidaemia or serum lipid levels and clinicopathological features, including the prognosis, was evaluated retrospectively. Also, we stratified these results by intrinsic subtype of breast cancer, menopause, and type of therapeutic agents for dyslipidaemia. Moreover, neutrophil- to-lymphocyte ratio (NLR) and tumour-infiltrating lymphocytes (TILs) were used as indicators of systemic and local immune status, respectively.

Results
Of 194 patients treated for dyslipidaemia, recurrence-free survival (RFS) and overall survival (OS) did not differ significantly between users of drugs for dyslipidaemia and non-users (p = 0.775 and p = 0.304, log-rank, respectively). Among postmenopausal, hormone receptor (HR)-positive/human epidermal growth factor receptor 2 (HER2)-negative breast cancer patients treated for dyslipidaemia, the good serum lipid control group had significantly better RFS (p = 0.014, log-rank), lower postoperative NLR (p = 0.012), and higher TILs in resected tissues (p = 0.024) than the poor control group. Multivariate analysis showed that postoperative serum lipid levels were a risk factor for recurrence (hazard ratio = 4.722, 95% confidence interval 1.006–22.161, p = 0.049).

Conclusions
Good control of serum lipid metabolism may improve the tumour immune microenvironment and prognosis in postmenopausal HR-positive/HER2-negative breast cancer patients.
Ebstein anomaly associated with retinal venular dilatation, migraine, and visual snow syndrome: a case report
Authors: de Jong P. T. V. M. , Thee E. F. , Straver B. 
Published: February 2022

Abstract
Background
To present a case with Ebstein anomaly, a rare congenital heart disorder, with ophthalmological and neurophthalmological signs and symptoms. To date, retinal venous dilatation and visual snow syndrome have not been previously been published in this anomaly.

Case presentation
A 10-year-old white girl was diagnosed with Ebstein anomaly. From age 12, she regularly suffered from migraines with auras and photophobia. At age 16 she started to see short-term bouts of white snow, that after a year were present all day. At age 20, she was found to have a decreased retinal arteriovenous ratio.

Conclusions
Retinal arterial tortuosity and venular dilatation are common in congenital heart disease but have not been described in Ebstein anomaly, nor has the visual snow syndrome.
Effects of advance exposure to an animated surgery-related picture book on preoperative anxiety and anesthesia induction in preschool children: a randomized controlled trial
Authors: Yang Yanyan , Zhang Mazhong , Sun Ying , Peng Zhezhe , Zheng Xiaosu , Zheng Jijian 
Published: February 2022

Abstract
Background
Our aim was to investigate whether early surgical preparation by reading an animated picture book about procedure-related events could reduce the preoperative anxiety in preschoolers.

Methods
131 patients, aged 3–6 years and underwent elective minor surgery were randomized either to a control or a picture book group. Both groups received general information about surgery and anesthesia in pre-anesthesia clinic. Patients in study group also received a surgery-depicting picture book for them to read at home a week earlier before surgery. Child anxiety was evaluated with the modified Yale Preoperative Anxiety Scale Short Form in six observing time points before anesthesia induction, and the compliance of anesthesia induction was assessed with the Induction Compliance Checklist (ICC).

Results
There were significantly lower anxiety scores in picture book group than in control group at the time of ready for intravenous cannulation in operating room [51.9 (23.6) vs. 67.2 (22.0); mean difference 15.3; 95% confidence interval (CI) 6.4–24.1; P = 0.001] and at the time of pre-anesthesia visit [27.8 (7.6) vs. 33.2 (13.6); mean difference 5.3; 95%CI 0.93–9.8; P = 0.018]. No significant differences of anxiety levels were found between two groups at other observed time points: in the anesthesia outpatient clinic, in the holding area, at separation from parent to operating room (OR), and on entrance to OR (P = 0.584, 0.335, 0.228, 0.137, respectively). The percentage of children with poor induction compliance (i.e., ICC ≥ 6) was higher in control group compared with that in picture book group [38% vs.21%; odds ratio(95%CI): 0.78(0.61–0.99); P = 0.041].

Conclusions
Home-reading an animated picture book to get familiar with the perioperative events earlier prior to surgery could effectively reduce the preoperative anxiety level and increase the compliance during the induction of anesthesia in preschool children.

Trial registration
ChiCTR2000033583, 06/06/2020 www.chictr.org.cn.