bluuebunny/crossref_metadata_2025_split huggingface dataset:
De novo transcriptome analysis of white teak (Gmelina arborea Roxb) wood reveals critical genes involved in xylem development and secondary metabolism
Authors: Yaya Lancheros Mary Luz , Rai Krishan Mohan , Balasubramanian Vimal Kumar , Dampanaboina Lavanya , Mendu Venugopal , Terán Wilson 
Published: July 2021

Abstract
Background
Gmelina arborea Roxb is a fast-growing tree species of commercial importance for tropical countries due to multiple industrial uses of its wood. Wood is primarily composed of thick secondary cell walls of xylem cells which imparts the strength to the wood. Identification of the genes involved in the secondary cell wall biosynthesis as well as their cognate regulators is crucial to understand how the production of wood occurs and serves as a starting point for developing breeding strategies to produce varieties with improved wood quality, better paper pulping or new potential uses such as biofuel production.
In order to gain knowledge on the molecular mechanisms and gene regulation related with wood development in white teak, a de novo sequencing and transcriptome assembly approach was used employing secondary cell wall synthesizing cells from young white teak trees.

Results
For generation of transcriptome, RNA-seq reads were assembled into 110,992 transcripts and 49,364 genes were functionally annotated using plant databases; 5071 GO terms and 25,460 SSR markers were identified within xylem transcripts and 10,256 unigenes were assigned to KEGG database in 130 pathways. Among transcription factor families, C2H2, C3H, bLHLH and MYB were the most represented in xylem. Differential gene expression analysis using leaves as a reference was carried out and a total of 20,954 differentially expressed genes were identified including monolignol biosynthetic pathway genes. The differential expression of selected genes (4CL, COMT, CCoAOMT, CCR and NST1) was validated using qPCR.

Conclusions
We report the very first de novo transcriptome of xylem-related genes in this tropical timber species of commercial importance and constitutes a valuable extension of the publicly available transcriptomic resource aimed at fostering both basic and breeding studies.
Modelling segmental duplications in the human genome
Authors: Abdullaev Eldar T. , Umarova Iren R. , Arndt Peter F. 
Published: July 2021

AbstractBackgroundSegmental duplications (SDs) are long DNA sequences that are repeated in a genome and have high sequence identity. In contrast to repetitive elements they are often unique and only sometimes have multiple copies in a genome. There are several well-studied mechanisms responsible for segmental duplications: non-allelic homologous recombination, non-homologous end joining and replication slippage. Such duplications play an important role in evolution, however, we do not have a full understanding of the dynamic properties of the duplication process.ResultsWe study segmental duplications through a graph representation where nodes represent genomic regions and edges represent duplications between them. The resulting network (the SD network) is quite complex and has distinct features which allow us to make inference on the evolution of segmantal duplications. We come up with the network growth model that explains features of the SD network thus giving us insights on dynamics of segmental duplications in the human genome. Based on our analysis of genomes of other species the network growth model seems to be applicable for multiple mammalian genomes.ConclusionsOur analysis suggests that duplication rates of genomic loci grow linearly with the number of copies of a duplicated region. Several scenarios explaining such a preferential duplication rates were suggested.
Female-specific genomic regions and molecular sex identification of the clearhead icefish (Protosalanx hyalocranius)
Authors: Xing Teng-Fei , Li Yu-Long , Liu Jin-Xian 
Published: July 2021

AbstractBackgroundThe clearhead icefish,Protosalanx hyalocranius, is an economically important fishery species in China. Since 1980s,P. hyalocraniuswas widely introduced into lakes and reservoirs of northern China for aquaculture. However, the lack of a rapid and cost-effective sex identification method based on sex specific genetic markers has hindered study on sex determination mechanisms and breeding applications.ResultsFemale-specific genomic regions were discovered by comparing whole genome re-sequencing data of both males and females. Two female-specific genomic regions larger than 50 bp were identified, and one (598 bp) contained a putative FOXI gene, which was paralogous to another FOXI gene with sex-associated SNPs. The two FOXI sequences displayed significant length difference with nine deletions of total length of 230 bp. This deletion-type structural variation could be easily and efficiently detected by traditional PCR and agarose gel electrophoresis with one 569 bp band for males and two bands (569 and 339 bp) for females, which were validated in 50 females and 40 males with known phenotypic sexes.ConclusionsThe results provided structural genomic evidence for the ZZ/ZW sex determination system inP. hyalocraniusdiscovered in our previous study with association analysis of SNPs. Moreover, the female-specific markers and rapid and cost-effective PCR-based genetic sex identification method should have applications in further studies of sex determination mechanism for this species.
Natural variation in wild tomato trichomes; selecting metabolites that contribute to insect resistance using a random forest approach
Authors: Kortbeek Ruy W. J. , Galland Marc D. , Muras Aleksandra , van der Kloet Frans M. , André Bart , Heilijgers Maurice , van Hijum Sacha A. F. T. , Haring Michel A. , Schuurink Robert C. , Bleeker Petra M. 
Published: July 2021

AbstractBackgroundPlant-produced specialised metabolites are a powerful part of a plant’s first line of defence against herbivorous insects, bacteria and fungi. Wild ancestors of present-day cultivated tomato produce a plethora of acylsugars in their type-I/IV trichomes and volatiles in their type-VI trichomes that have a potential role in plant resistance against insects. However, metabolic profiles are often complex mixtures making identification of the functionally interesting metabolites challenging. Here, we aimed to identify specialised metabolites from a wide range of wild tomato genotypes that could explain resistance to vector insects whitefly (Bemisia tabaci) and Western flower thrips (Frankliniella occidentalis). We evaluated plant resistance,determined trichome density and obtained metabolite profiles of the glandular trichomes by LC-MS (acylsugars) and GC-MS (volatiles). Using a customised Random Forest learning algorithm, we determined the contribution of specific specialised metabolites to the resistance phenotypes observed.ResultsThe selected wild tomato accessions showed different levels of resistance to both whiteflies and thrips. Accessions resistant to one insect can be susceptible to another. Glandular trichome density is not necessarily a good predictor for plant resistance although the density of type-I/IV trichomes, related to the production of acylsugars, appears to correlate with whitefly resistance. For type VI-trichomes, however, it seems resistance is determined by the specific content of the glands. There is a strong qualitative and quantitative variation in the metabolite profiles between different accessions, even when they are from the same species. Out of 76 acylsugars found, the random forest algorithm linked two acylsugars (S3:15 and S3:21) to whitefly resistance, but none to thrips resistance. Out of 86 volatiles detected, the sesquiterpene α-humulene was linked to whitefly susceptible accessions instead. The algorithm did not link any specific metabolite to resistance against thrips, but monoterpenes α-phellandrene, α-terpinene and β-phellandrene/D-limonene were significantly associated with susceptible tomato accessions.ConclusionsWhiteflies and thrips are distinctly targeted by certain specialised metabolites found in wild tomatoes. The machine learning approach presented helped to identify features with efficacy toward the insect species studied. These acylsugar metabolites can be targets for breeding efforts towards the selection of insect-resistant cultivars.
Reprogramming of the wheat transcriptome in response to infection with Claviceps purpurea, the causal agent of ergot
Authors: Tente Eleni , Ereful Nelzo , Rodriguez Anyela Camargo , Grant Paul , O’Sullivan Donal M. , Boyd Lesley A. , Gordon Anna 
Published: July 2021

AbstractBackgroundErgot, caused by the fungal pathogenClaviceps purpurea, infects the female flowers of a range of cereal crops, including wheat. To understand the interaction betweenC. purpureaand hexaploid wheat we undertook an extensive examination of the reprogramming of the wheat transcriptome in response toC. purpureainfection through floral tissues (i.e. the stigma, transmitting and base ovule tissues of the ovary) and over time.ResultsC. purpureahyphae were observed to have grown into and down the stigma at 24 h (H) after inoculation. By 48H hyphae had grown through the transmitting tissue into the base, while by 72H hyphae had surrounded the ovule. By 5 days (D) the ovule had been replaced by fungal tissue. Differential gene expression was first observed at 1H in the stigma tissue. Many of the wheat genes differentially transcribed in response toC. purpureainfection were associated with plant hormones and included the ethylene (ET), auxin, cytokinin, gibberellic acid (GA), salicylic acid and jasmonic acid (JA) biosynthetic and signaling pathways. Hormone-associated genes were first detected in the stigma and base tissues at 24H, but not in the transmitting tissue. Genes associated with GA and JA pathways were seen in the stigma at 24H, while JA and ET-associated genes were identified in the base at 24H. In addition, several defence-related genes were differential expressed in response toC. purpureainfection, including antifungal proteins, endocytosis/exocytosis-related proteins, NBS-LRR class proteins, genes involved in programmed cell death, receptor protein kinases and transcription factors. Of particular interest was the identification of differential expression of wheat genes in the base tissue well before the appearance of fungal hyphae, suggesting that a mobile signal, either pathogen or plant-derived, is delivered to the base prior to colonisation.ConclusionsMultiple host hormone biosynthesis and signalling pathways were significantly perturbed from an early stage in the wheat –C. purpureainteraction. Differential gene expression at the base of the ovary, ahead of arrival of the pathogen, indicated the potential presence of a long-distance signal modifying host gene expression.
Mucormycosis causing massive lower gastrointestinal bleeding: a case report
Authors: Chiang Ting-Hsuan , Lee Yi-Wei , Tan Jui-Hsiang , Kao Chih-Chin , Chang Chun-Chao , Fang Kuan-Chieh 
Published: July 2021

Abstract
Background
Lower gastrointestinal bleeding (LGIB) is very common in the hospital setting. Most bleedings stop spontaneously, but rare infectious causes of LGIB may lead to rapid and serious complications if left untreated and are sometimes very difficult to diagnose preoperatively.

Case presentation
We described a young man with poorly controlled Type I diabetes mellitus and chronic alcohol abuse who presented with acute altered mental status. During his hospitalization for treatment of diabetic ketoacidosis, acute renal failure, and sepsis, he suddenly developed massive hematochezia of 1500 mL. Colonoscopy was performed and a deep ulcer covered with mucus with peripheral elevation was noted at the transverse colon. Biopsy of the ulcer later revealed nonpigmented, wide (5–20 µm in diameter), thin-walled, ribbon-like hyphae with few septations and right-angle branching suggestive of mucormycosis demonstrated by Periodic acid–Schiff stain. He received 2 months of antifungal treatment. Follow up colonoscopy post-treatment was normal with no ulcer visualized.

Conclusions
Early diagnosis and treatment of gastrointestinal (GI) mucormycosis infection is critical but can be challenging, especially in the setting of massive hematochezia. Therefore, clinical awareness for immunocompromised patients and prompt antifungal prophylaxis in cases with high suspicion of infection are essential.
Systematic geriatric assessment for older patients with frailty in the emergency department: a randomised controlled trial
Authors: Alakare Janne , Kemp Kirsi , Strandberg Timo , Castrén Maaret , Jakovljević Dimitrije , Tolonen Jukka , Harjola Veli-Pekka 
Published: July 2021

Abstract
Background
Comprehensive geriatric assessment provided in hospital wards in frail patients admitted to hospital has been shown to reduce mortality and increase the likelihood of living at home later. Systematic geriatric assessment provided in emergency departments (ED) may be effective for reducing days in hospital and unnecessary hospital admissions, but this has not yet been proven in randomised trials.

Methods
We conducted a single-centre, randomised controlled trial with a parallel-group, superiority design in an academic hospital ED.
ED patients aged ≥ 75 years who were frail, or at risk of frailty, as defined by the Clinical Frailty Scale, were included in the trial. Patients were recruited during the period between December 11, 2018 and June 7, 2019, and followed up for 365 days.
For the intervention group, systematic geriatric assessment was added to their standard care in the ED, whereas the control group received standard care only.
The primary outcome was cumulative hospital stay during 365-day follow-up. The secondary outcomes included: admission rate from the index visit, total hospital admissions, ED-readmissions, proportion of patients living at home at 365 days, 365-day mortality, and fall-related ED-visits.

Results
A total of 432 patients, 63 % female, with median age of 85 years, formed the analytic sample of 213 patients in the intervention group and 219 patients in the control group.
Cumulative hospital stay during one-year follow-up as rate per 100 person-years for the intervention and control groups were: 3470 and 3149 days, respectively, with rate ratio of 1.10 (95 % confidence interval, 0.55–2.19, P = .78). Admission rates to hospital wards from the index ED visit for the intervention and control groups were: 62 and 70 %, respectively (P = .10). No significant differences were observed between the groups for any outcomes.

Conclusion
Systematic geriatric assessment for older adults with frailty in the ED did not reduce hospital stay during one-year follow-up. No statistically significant difference was observed for any secondary outcomes. More coordinated, continuous interventions should be tested for potential benefits in long-term outcomes.

Trial registration
The trial was registered in the ClinicalTrials.gov (registration number and date NCT03751319 23/11/2018).
Regional citrate anticoagulation “non-shock” protocol with pre-calculated flow settings for patients with at least 6 L/hour liver citrate clearance
Authors: Yessayan Lenar , Sohaney Ryann , Puri Vidhit , Wagner Benjamin , Riddle Amy , Dickinson Sharon , Napolitano Lena , Heung Michael , Humes David , Szamosfalvi Balazs 
Published: July 2021

Abstract
Background
Regional citrate anticoagulation (RCA) for the prevention of clotting of the extracorporeal blood circuit during continuous kidney replacement therapy (CKRT) has been employed in limited fashion because of the complexity and complications associated with certain protocols. Hypertonic citrate infusion to achieve circuit anticoagulation results in variable systemic citrate- and sodium load and increases the risk of citrate accumulation and hypernatremia. The practice of “single starting calcium infusion rate for all patients” puts patients at risk for clinically significant hypocalcemia if filter effluent calcium losses exceed replacement. A fixed citrate to blood flow ratio, personalized effluent and pre-calculated calcium infusion dosing based on tables derived through kinetic analysis enable providers to use continuous veno-venous hemo-diafiltration (CVVHDF)-RCA in patients with liver citrate clearance of at least 6 L/h.

Methods
This was a single-center prospective observational study conducted in intensive care unit patients triaged to be treated with the novel pre-calculated CVVHDF-RCA “Non-shock” protocol. RCA efficacy outcomes were time to first hemofilter loss and circuit ionized calcium (iCa) levels. Safety outcomes were surrogate of citrate accumulation (TCa/iCa ratio) and the incidence of acid-base and electrolyte complications.

Results
Of 53 patients included in the study, 31 (59%) had acute kidney injury and 12 (22.6%) had the diagnosis of cirrhosis at the start of CVVHDF-RCA. The median first hemofilter life censored for causes other than clotting exceeded 70 h. The cumulative incidence of hypernatremia (Na > 148 mM), metabolic alkalosis (HCO3- > 30 mM), hypocalcemia (iCa < 0.9 mM) and hypercalcemia (iCa > 1.5 mM) were 1/47 (1%), 0/50 (0%), 1/53 (2%), 1/53 (2%) respectively and were not clinically significant. The median (25th–75th percentile) of the highest TCa/iCa ratio for every 24-h interval on CKRT was 1.99 (1.91–2.13).

Conclusions
The fixed citrate to blood flow ratio, as opposed to a titration approach, achieves adequate circuit iCa (< 0.4 mm/L) for any hematocrit level and plasma flow. The personalized dosing approach for calcium supplementation based on pre-calculated effluent calcium losses as opposed to the practice of “one starting dose for all” reduces the risk of clinically significant hypocalcemia. The fixed flow settings achieve clinically desirable steady state systemic electrolyte levels.
Improvements in clinical signs of Parkinson’s disease using photobiomodulation: a prospective proof-of-concept study
Authors: Liebert Ann , Bicknell Brian , Laakso E-Liisa , Heller Gillian , Jalilitabaei Parastoo , Tilley Sharon , Mitrofanis John , Kiat Hosen 
Published: July 2021

Abstract
Background
Parkinson’s disease (PD) is a progressive neurodegenerative disease with no cure and few treatment options. Its incidence is increasing due to aging populations, longer disease duration and potentially as a COVID-19 sequela. Photobiomodulation (PBM) has been successfully used in animal models to reduce the signs of PD and to protect dopaminergic neurons.

Objective
To assess the effectiveness of PBM to mitigate clinical signs of PD in a prospective proof-of-concept study, using a combination of transcranial and remote treatment, in order to inform on best practice for a larger randomized placebo-controlled trial (RCT).

Methods
Twelve participants with idiopathic PD were recruited. Six were randomly chosen to begin 12 weeks of transcranial, intranasal, neck and abdominal PBM. The remaining 6 were waitlisted for 14 weeks before commencing the same treatment. After the 12-week treatment period, all participants were supplied with PBM devices to continue home treatment. Participants were assessed for mobility, fine motor skills, balance and cognition before treatment began, after 4 weeks of treatment, after 12 weeks of treatment and the end of the home treatment period. A Wilcoxon Signed Ranks test was used to assess treatment effectiveness at a significance level of 5%.

Results
Measures of mobility, cognition, dynamic balance and fine motor skill were significantly improved (p < 0.05) with PBM treatment for 12 weeks and up to one year. Many individual improvements were above the minimal clinically important difference, the threshold judged to be meaningful for participants. Individual improvements varied but many continued for up to one year with sustained home treatment. There was a demonstrable Hawthorne Effect that was below the treatment effect. No side effects of the treatment were observed.

Conclusions
PBM was shown to be a safe and potentially effective treatment for a range of clinical signs and symptoms of PD. Improvements were maintained for as long as treatment continued, for up to one year in a neurodegenerative disease where decline is typically expected. Home treatment of PD by the person themselves or with the help of a carer might be an effective therapy option. The results of this study indicate that a large RCT is warranted.

Trial registration
Australian New Zealand Clinical Trials Registry, registration number: ACTRN12618000038291p, registered on 12/01/2018.
The significance of the oxidative stress markers in the one-year prognosis of patients with acute ischemic stroke: a case-control study
Authors: Shaafi Sheida , Hadisi Fina , Mahmoudinezhad Mahsa , Razmi Hamidreza , Nejadghaderi Seyed Aria , Khalili Mohammad 
Published: July 2021

AbstractBackgroundStroke is a major cause of mortality and morbidity. Also, free radicals and oxidative stress are deleterious factor in the stroke progression. We aimed to evaluate the association between oxidative stress markers and odds of having risk factor for stroke or developing stroke.MethodsThe present case-control study was conducted on 556 participants in Imam-Reza hospital, Tabriz, Iran. Subjects were divided into three group, including individuals with acute ischemic stroke, those who were at risk of stroke, and healthy controls. All enrolled participants except for controls underwent neurological examinations and brain magnetic resonance imaging (MRI). Stroke-related disability and stroke severity were evaluated by modified Rankin Scale (mRS) and National Institutes of Health Stroke Scale (NIHSS), respectively. Serum malondialdehyde (MDA) level and total antioxidant capacity (TAC) were measured within 48 h of the initiation of stroke. One-way ANOVA and Chi-square tests were used for comparing characteristics between groups. Multivariable logistic regression was implemented for odds of stroke based on MDA and TAC quartiles. Also, Spearman’s correlation was utilized.ResultsSerum MDA, systolic and diastolic blood pressure, cholesterol, and triglyceride were significantly higher in the stroke group than controls. High levels of MDA were associated with increased development of stroke (P-value < 0.001), however TAC and MDA were not associated with having risk factors for stroke (P-value = 1.00 and 0.27, respectively). Also, TAC level was negatively associated with baseline (ρ = − 0.28;P-value = 0.04) and follow-up (ρ = − 0.31;P-value = 0.03) NIHSS scores. Moreover, MDA was correlated with mRS score at follow-up (ρ = − 0.26;P-value = 0.04).ConclusionsThe balance between antioxidants and oxidants markers might reveal a new approach in this context. Further studies are warranted to identify the source of oxidative stress as well as cessation of the production of oxygen radicals in stroke.