bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unraveling transcriptomics of sorghum grain carotenoids: a step forward for biofortification
Authors: Cruet-Burgos Clara , Rhodes Davina H. 
Published: May 2023

Abstract
Background
Sorghum (Sorghum bicolor [L.] Moench) is a promising target for pro-vitamin A biofortification as it is a global staple crop, particularly in regions where vitamin A deficiency is prevalent. As with most cereal grains, carotenoid concentrations are low in sorghum, and breeding could be a feasible strategy to increase pro-vitamin A carotenoids to biologically relevant concentrations. However, there are knowledge gaps in the biosynthesis and regulation of sorghum grain carotenoids, which can limit breeding effectiveness. The aim of this research was to gain an understanding of the transcriptional regulation of a priori candidate genes in carotenoid precursor, biosynthesis, and degradation pathways.

Results
We used RNA sequencing of grain to compare the transcriptional profile of four sorghum accessions with contrasting carotenoid profiles through grain development. Most a priori candidate genes involved in the precursor MEP, carotenoid biosynthesis, and carotenoid degradation pathways were found to be differentially expressed between sorghum grain developmental stages. There was also differential expression of some of the a priori candidate genes between high and low carotenoid content groups at each developmental time point. Among these, we propose geranyl geranyl pyrophosphate synthase (GGPPS), phytoene synthase (PSY), and phytoene desaturase (PDS) as promising targets for pro-vitamin A carotenoid biofortification efforts in sorghum grain.

Conclusions
A deeper understanding of the controls underlying biosynthesis and degradation of sorghum grain carotenoids is needed to advance biofortification efforts. This study provides the first insights into the regulation of sorghum grain carotenoid biosynthesis and degradation, suggesting potential gene targets to prioritize for molecular breeding.
The transcriptome of Icerya aegyptiaca (Hemiptera: Monophlebidae) and comparison with neococcoids reveal genetic clues of evolution in the scale insects
Authors: Tang Xue-Fei , Huang Yu-Hao , Sun Yi-Fei , Zhang Pei-Fang , Huo Li-Zhi , Li Hao-Sen , Pang Hong 
Published: May 2023

AbstractBackgroundScale insects are worldwide sap-sucking parasites, which can be distinguished into neococcoids and non-neococcoids. Neococcoids are monophyletic with a peculiar reproductive system, paternal genome elimination (PGE). Different with neococcoids, Iceryini, a tribe in non-neococcoids including several damaging pests, has abdominal spiracles, compound eyes in males, relatively abundant wax, unique hermaphrodite system, and specific symbionts. However, the current studies on the gene resources and genomic mechanism of scale insects are mainly limited in the neococcoids, and lacked of comparison in an evolution frame.ResultWe sequenced and de novo assembled a transcriptome ofIcerya aegyptiaca(Douglas), a worldwide pest of Iceryini, and used it as representative of non-neococcoids to compare with the genomes or transcriptomes of other six species from different families of neococcoids. We found that the genes under positive selection or negative selection intensification (simplified as “selected genes” below) inI. aegyptiacaincluded those related to neurogenesis and development, especially eye development. Some genes related to fatty acid biosynthesis were unique in its transcriptome with relatively high expression and not detected in neococcoids. These results may indicate a potential link to the unique structures and abundant wax ofI. aegyptiacacompared with neococcoids. Meanwhile, genes related to DNA repair, mitosis, spindle, cytokinesis and oogenesis, were included in the selected genes inI. aegyptiaca, which is possibly associated with cell division and germ cell formation of the hermaphrodite system. Chromatin-related process were enriched from selected genes in neococcoids, along with some mitosis-related genes also detected, which may be related to their unique PGE system. Moreover, in neococcoid species, male-biased genes tend to undergo negative selection relaxation under the PGE system. We also found that the candidate horizontally transferred genes (HTGs) in the scale insects mainly derived from bacteria and fungi.bioDandbioB, the two biotin-synthesizing HTGs were exclusively found in the scale insects and neococcoids, respectively, which possibly show potential demand changes in the symbiotic relationships.ConclusionOur study reports the firstI. aegyptiacatranscriptome and provides preliminary insights for the genetic change of structures, reproductive systems and symbiont relationships at an evolutionary aspect. This will provide a basis for further research and control of scale insects.
Characterization of the physico-chemical properties of the natural habitat and in vitro culture effects on the biochemistry, proliferation and morphology of Lemna minuta
Authors: Maissour Abdellah , Bouqadida Mohammed , Oualili Hanane , El Omari Redouane , Belfaiza Malika , Makroum Kacem 
Published: May 2023

AbstractIn this study, the ecological conditions of the natural habitat of Lemna minuta Kunth in Morocco were investigated, and the impact of five synthetic growth media (Murashige-Skoog (MS), Schenk-Hildebrand (SH), Hoagland medium (HM), 10X Algal Assay Procedure (AAP), and Swedish Standard Institute medium (SIS)) on the morphophysiological and biochemical parameters was analysed. The morphophysiological parameters included root length, frond surface area, and fresh weight, while the biochemical parameters included photosynthetic pigments, carbohydrates, and protein content. The study was conducted in vitro in two phases: an uncontrolled aeration system (Phase I) and a controlled aeration system (Phase II).The results showed that the pH, conductivity, salinity, and ammonium levels in the natural habitat were within the optimal range for duckweed growth. The measured orthophosphate concentrations were higher compared to previous observations, while the recorded chemical oxygen demand values were low. The study also revealed a significant effect of the culture medium composition on the morphophysiological and biochemical parameters of the duckweed. The fresh weight biomass, relative growth rate in fronds, relative growth rate in surface area, root length, protein content, carbohydrates, chlorophyll (a), chlorophyll (b), total chlorophyll, carotenoids, and the chlorophyll (a/b) ratio were all affected by the culture medium.The most accurate regression models described the growth index GI(F) based on time and in vitro culture conditions in both phases. In Phase I, the best models for MS, SIS, AAP, and SH media were linear, weighted quadratic, cubic, and weighted cubic, respectively. In Phase II, the best models for all growth media were linear. The time coefficients (in days) for Phase II were 0.321, 0.547, 1.232, 1.470, and 0.306 for AAP, HM, MS, SH, and SIS, respectively.Comparing the morphophysiological and biochemical parameters of fronds from different media and analysing the regression model results showed that the SH and MS media were the best among the tested media for the in vitro culture of L. minuta in controlled aeration conditions. However, further research is needed to develop new synthetic media that best promote the growth and maintenance of this duckweed in long-term culture.
RETRACTED ARTICLE: Functional modular networks identify the pivotal genes associated with morphine addiction and potential drug therapies
Authors: Jiang Yage , Wei Donglei , Xie Yubo 
Published: May 2023

Abstract
Background
Chronic morphine usage induces lasting molecular and microcellular adaptations in distinct brain areas, resulting in addiction-related behavioural abnormalities, drug-seeking, and relapse. Nonetheless, the mechanisms of action of the genes responsible for morphine addiction have not been exhaustively studied.

Methods
We obtained morphine addiction-related datasets from the Gene Expression Omnibus (GEO) database and screened for Differentially Expressed Genes (DEGs). Weighted Gene Co-expression Network Analysis (WGCNA) functional modularity constructs were analyzed for genes associated with clinical traits. Venn diagrams were filtered for intersecting common DEGs (CDEGs). Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis for functional annotation. Protein–protein interaction network (PPI) and CytoHubba were used to screen for hub genes. Potential treatments for morphine addiction were figured out with the help of an online database.

Results
Sixty-five common differential genes linked to morphine addiction were identified, and functional enrichment analysis showed that they were primarily involved in ion channel activity, protein transport, the oxytocin signalling pathway, neuroactive ligand-receptor interactions, and other signalling pathways. Based on the PPI network, ten hub genes (CHN2, OLIG2, UGT8A, CACNB2, TIMP3, FKBP5, ZBTB16, TSC22D3, ISL1, and SLC2A1) were checked. In the data set GSE7762, all of the Area Under Curve (AUC) values for the hub gene Receiver Operating Characteristic (ROC) curves were greater than 0.8. We also used the DGIdb database to look for eight small-molecule drugs that might be useful for treating morphine addiction.

Conclusions
The hub genes are crucial genes associated with morphine addiction in the mouse striatum. The oxytocin signalling pathway may play a vital role in developing morphine addiction.
Reporting quality of randomized controlled trials evaluating non-vitamin K oral anticoagulants in atrial fibrillation: a systematic review
Authors: Yang YueGuang , Han YuBo , Zou GuoLiang , Sui YanBo , Jin Juan , Liu Li 
Published: May 2023

Abstract
Background
Randomized controlled trials (RCTs) are subject to bias if they lack methodological quality. Furthermore, optimal and transparent reporting of RCT findings aids their critical appraisal and interpretation. This study aimed to comprehensively evaluate the report quality of RCTs of non-vitamin K oral anticoagulants (NOACs) for the treatment of atrial fibrillation (AF) and to analyze the factors influencing the quality.

Methods
By searching PubMed, Embase, Web of Science, and Cochrane Library databases RCTs published from inception to 2022 evaluating the efficacy of NOACs on AF were collected. By using the 2010 Consolidated Standards for Reporting Tests (CONSORT) statement, the overall quality of each report was assessed.

Results
Sixty-two RCTs were retrieved in this study. The median of overall quality score in 2010 was 14 (range: 8.5–20). The extent of compliance with the Consolidated Standards of Reporting Trials reporting guideline differed substantially across items: 9 items were reported adequately (more than 90%), and 3 were reported adequately in less than 10% of trials. Multivariate linear regression analysis showed that the higher reporting scores were associated with higher journal impact factor (P = 0.01), international collaboration (P < 0.01), and Sources of trial funding (P = 0.02).

Conclusions
Although a large number of randomized controlled trials of NOACs for the treatment of AF were published after the CONSORT statement in 2010, the overall quality is still not satisfactory, thus weakening their potential utility and may mislead clinical decisions. This survey provides the first hint for researchers conducting trials of NOACs for AF to improve the quality of reports and to actively apply the CONSORT statement.
Upper gastrointestinal endoscopic findings in functional constipation and irritable bowel syndrome diagnosed using the Rome IV criteria: a cross-sectional survey during a medical check-up in Japan
Authors: Otani Koji , Watanabe Toshio , Takahashi Kanae , Nadatani Yuji , Ominami Masaki , Fukunaga Shusei , Hosomi Shuhei , Kamata Noriko , Tanaka Fumio , Nagami Yasuaki , Taira Koichi , Kimura Tatsuo , Fukumoto Shinya , Fujiwara Yasuhiro 
Published: May 2023

Abstract
Background
The Rome IV criteria have been established as an international standard for diagnosing disorders of gut–brain interaction. In this study, we aimed to examine the upper gastrointestinal (GI) endoscopic findings and symptoms of subjects with functional constipation (FC) and irritable bowel syndrome (IBS) of individuals undergoing a medical check-up.

Methods
A total of 13,729 subjects underwent a medical check-up at Osaka City University-affiliated clinic, MedCity21, between April 2018 and March 2019. Among the 5,840 subjects who underwent screening upper GI endoscopy and completed a questionnaire based on the Rome IV criteria, 5,402 subjects were consecutively enrolled after excluding subjects with a large amount of gastric residue (n = 6), those who had previously undergone partial or total gastrectomy (n = 40), or those with daily use of low-dose aspirin (n = 82), nonsteroidal anti-inflammatory drugs (n = 63), or acid secretion inhibitors (n = 308).

Results
Robust Poisson regression analyses adjusted for age, sex, Helicobacter pylori infection status, alcohol intake, and smoking habits showed a significant association between FC and corpus erosion (adjusted prevalence ratio [aPR], 2.93; 95% confidence interval [CI], 1.51–5.67; p < 0.01) and red streaks (aPR, 3.83; 95% CI, 2.53–5.79; p < 0.01), whereas IBS was significantly associated with erosive gastritis (aPR, 8.46; 95% CI, 4.89–14.67; p < 0.01) and duodenitis (aPR, 7.28; 95% CI, 3.64–14.59; p < 0.01). Red streaks tended to be associated with IBS (aPR, 1.96; 95% CI, 1.00–3.83; p = 0.05). Subjects with IBS were the most to complain of both upper and lower GI symptoms and psychological symptoms, followed by those with FC and controls. IBS subjects with erosive gastritis or duodenitis had significantly more complaints of stomachache and feeling stressed than those without erosive gastritis or duodenitis (54.5% vs. 18.8%; p = 0.03 and 66.7% vs. 25.0%; p = 0.01).

Conclusions
Subjects with FC and IBS had a variety of upper GI and psychological symptoms. In the upper GI endoscopic findings, corpus erosion and red streaks were associated with FC, and erosive gastritis, duodenitis, and possibly red streaks were associated with IBS.
Unmet needs in uncomplicated urinary tract infection in the United States and Germany: a physician survey
Authors: O’Brien Megan , Marijam Alen , Mitrani-Gold Fanny S. , Terry Laura , Taylor-Stokes Gavin , Joshi Ashish V. 
Published: May 2023

Abstract
Background
Uncomplicated urinary tract infections (uUTIs/acute cystitis) are among the most common infections in women worldwide. There are differences in uUTI treatment guidelines between countries and understanding the needs of physicians in diverse healthcare systems is important for developing new treatments. We performed a survey of physicians in the United States (US) and Germany to understand their perceptions of, and management approaches to uUTI.

Methods
This was a cross-sectional online survey of physicians in the US and Germany who were actively treating patients with uUTI (≥ 10 patients/month). Physicians were recruited via a specialist panel and the survey was piloted with 2 physicians (1 US, 1 Germany) prior to study commencement. Data were analyzed with descriptive statistics.

Results
A total of 300 physicians were surveyed (n = 200 US, n = 100 Germany). Across countries and specialties, physicians estimated 16–43% of patients did not receive complete relief from initial therapy and 33–37% had recurrent infections. Urine culture and susceptibility testing was more common in the US and among urologists. The most commonly selected first-line therapy was trimethoprim-sulfamethoxazole in the US (76%) and fosfomycin in Germany (61%). Ciprofloxacin was the most selected following multiple treatment failures (51% US, 45% Germany). Overall, 35% of US and 45% of German physicians agreed with the statement “I feel there is a good selection of treatment options” and ≥ 50% felt that current treatments provided good symptom relief. More than 90% of physicians included symptom relief amongst their top 3 treatment goals. The overall impact of symptoms on patients’ lives was rated “a great deal” by 51% of US and 38% of German physicians, increasing with each treatment failure. Most physicians (> 80%) agreed that antimicrobial resistance (AMR) is serious, but fewer (56% US, 46% Germany) had a high level of confidence in their knowledge of AMR.

Conclusions
Treatment goals for uUTI were similar in the US and Germany, although with nuances to disease management approaches. Physicians recognized that treatment failures have a significant impact on patients’ lives and that AMR is a serious problem, though many did not have confidence in their own knowledge of AMR.
Cyclic neutropenia and concomitant IgA nephropathy: a case report
Authors: Kapogiannis C. , Zaggogianni T. , Stergiou N. , Kakleas K. , Kapogiannis A. , Gakiopoulou H. , Kanaka-Gantenbein C. 
Published: May 2023

Abstract
Background
IgA nephropathy (IgAN) is universally recognized as one of the most common primary glomerular diseases in all ages. Cyclic neutropenia (CN) is a rare haematologic disorder that is associated with mutations of the ELANE gene. The co-occurrence of IgAN and CN is extremely rare. This is the first case report of a patient with IgAN and genetically confirmed CN.

Case presentation
We report a case of a 10-year-old boy who presented with recurrent viral upper respiratory tract infections accompanied by several episodes of febrile neutropenia, haematuria, proteinuria and acute kidney injury. Upon first admission, his physical examination was unremarkable. His kidney function was impaired, whereas his urine microscopy showed evidence of macroscopic haematuria and proteinuria. Further workup showed elevated IgA. The renal histology was consistent with mesangial and endocapillary hypercellularity with mild crescentic lesions, while immunofluorescence microscopy showed IgA-positive staining, which was characteristic of IgAN. Moreover, genetic testing confirmed the clinical diagnosis of CN, therefore Granulocyte colony-stimulating factor (G-CSF) was initiated to stabilize the neutrophil count. Regarding proteinuria control, the patient was initially treated with an Angiotensin-converting-enzyme inhibitor for approximately 28 months. However, due to progressive proteinuria (> 1 g/24 h), Corticosteroids (CS) were added for a period of 6 months according to the revised 2021 KDIGO guidelines with favorable outcome.

Conclusions
Patients with CN are more susceptible to recurrent viral infections, which can trigger IgAN attacks. In our case CS induced remarkable proteinuria remission. The use of G-CSF contributed to the resolution of severe neutropenic episodes, viral infections and concomitant AKI episodes, contributing to better prognosis of IgAN. Further studies are mandatory to determine whether there is a genetical predisposition for IgAN in children with CN.
Sub-symptom threshold aerobic exercise for patients with persisting post-concussion symptoms and exercise intolerance after mild traumatic brain injury – a study protocol with a nested feasibility study for a randomized controlled trial
Authors: Valaas Lars-Johan V. , Soberg Helene L. , Rasmussen Mari S. , Steenstrup Sophie E. , Andelic Nada , Kleffelgård Ingerid 
Published: May 2023

Abstract
Background
Persistent post-concussion symptoms (PPCS) affect between 34 and 46% after a mild traumatic brain injury (mTBI). Many also experience exercise intolerance. Sub-symptom threshold aerobic exercise, SSTAE (exercise at an intensity level that does not increase symptoms) is proposed as a treatment to both reduce the symptom burden and increase the exercise tolerance after the injury. It is unclear if this also applies in a more chronic phase after mTBI.

Main purpose
The main purpose of this study is to evaluate whether SSTAE in addition to ordinary rehabilitation will lead to clinically meaningful improvement of symptom burden, normalize exercise tolerance, increase physical activity, improve health-related quality of life, and reduce patient-specific activity limitations compared to a control group that only receives ordinary rehabilitation.

Design
Randomized, controlled, single-blind parallel-group study with three measurement times; T0 at baseline, T1 after the intervention and T2 six months after T1.

Methods
Patients between the ages of 18 and 60 with exercise intolerance and persistent PPCS (> 3 months) will be recruited to the study and randomized to two groups. All patients will receive follow-up at the outpatient TBI clinic. The intervention group will in addition receive SSTAE for 12 weeks with exercise diaries and a retest every 3 weeks for optimal dosage and progression. The Rivermead post-concussion symptoms questionnaire will be the main outcome measure. The secondary outcome measure will be a test of exercise tolerance—the Buffalo Concussion Treadmill Test. Other outcome measures include the patient-specific functional scale that measures patient-specific activity limitations, as well as outcome measures for diagnosis-specific health-related quality of life, anxiety and depression, specific symptoms such as dizziness, headache and fatigue, and physical activity.

Discussion
This study will add knowledge about the effect of SSTAE and whether it should be implemented in rehabilitation for the adult population with persistent PPCS after mTBI. The nested feasibility trial showed that the SSTAE intervention was safe and that the study procedures and delivery of the intervention overall were feasible. However, minor amendments to the study protocol were made prior to the commencement of the RCT.

Trial registration
Clinical Trials.gov, NCT05086419. Registered on September 5th, 2021.