bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome analysis of five ovarian stages reveals gonad maturation in female Macrobrachium nipponense
Authors: Zhang Yuning , Jiang Sufei , Qiao Hui , Xiong Yiwei , Fu Hongtuo , Zhang Wenyi , Gong Yongsheng , Jin Shubo , Wu Yan 
Published: July 2021

Abstract
Background
Macrobrachium nipponense is an economically important species of freshwater shrimp in China. Unlike other marine shrimps, the ovaries in adult female M. nipponense can mature rapidly and periodically during the reproductive period, but the resulting high stocking densities and environmental deterioration can negatively impact the harvest yield and economic benefits. To better understand ovary development in female M. nipponense, we performed systematic transcriptome sequencing of five different stages of ovarian maturation.

Results
We obtained 255,966 Gb of high quality transcriptome data from 15 samples. Of the 105,082 unigenes that were selected, 30,878 were successfully annotated. From these unigenes, we identified 17 differentially expressed genes and identified three distinct gene expression patterns related to different biological processes. We found that cathepins, legumains, and cystatin were enriched in the lysosome pathway, and they are related to vitellogenin hydrolysis. Additionally, we found that myosin heavy chain 67 participated in oocyte excretion.

Conclusions
We provide the first detailed transcriptome data relating to the ovarian maturation cycle in M. nipponense. Our results provide important reference information about the genomics, molecular biology, physiology, and population genetics of M. nipponense and other crustaceans. It is conducive to further solve the problem of M. nipponense rapid ovarian maturation from the aspects of energy supply and cell division.
Genome-wide identification, expression analysis, and functional study of the GRAS transcription factor family and its response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench]
Authors: Fan Yu , Yan Jun , Lai Dili , Yang Hao , Xue Guoxing , He Ailing , Guo Tianrong , Chen Long , Cheng Xiao-bin , Xiang Da-bing , Ruan Jingjun , Cheng Jianping 
Published: July 2021

Abstract
Background
GRAS, an important family of transcription factors, have played pivotal roles in regulating numerous intriguing biological processes in plant development and abiotic stress responses. Since the sequencing of the sorghum genome, a plethora of genetic studies were mainly focused on the genomic information. The indepth identification or genome-wide analysis of GRAS family genes, especially in Sorghum bicolor, have rarely been studied.

Results
A total of 81 SbGRAS genes were identified based on the S. bicolor genome. They were named SbGRAS01 to SbGRAS81 and grouped into 13 subfamilies (LISCL, DLT, OS19, SCL4/7, PAT1, SHR, SCL3, HAM-1, SCR, DELLA, HAM-2, LAS and OS4). SbGRAS genes are not evenly distributed on the chromosomes. According to the results of the gene and motif composition, SbGRAS members located in the same group contained analogous intron/exon and motif organizations. We found that the contribution of tandem repeats to the increase in sorghum GRAS members was slightly greater than that of fragment repeats. By quantitative (q) RT-PCR, the expression of 13 SbGRAS members in different plant tissues and in plants exposed to six abiotic stresses at the seedling stage were quantified. We further investigated the relationship between DELLA genes, GAs and grain development in S. bicolor. The paclobutrazol treatment significantly increased grain weight, and affected the expression levels of all DELLA subfamily genes. SbGRAS03 is the most sensitive to paclobutrazol treatment, but also has a high response to abiotic stresses.

Conclusions
Collectively, SbGRAs play an important role in plant development and response to abiotic stress. This systematic analysis lays the foundation for further study of the functional characteristics of GRAS genes of S. bicolor.
Diversity and prevalence of ANTAR RNAs across actinobacteria
Authors: Mehta Dolly , Ramesh Arati 
Published: July 2021

Abstract
Background
Computational approaches are often used to predict regulatory RNAs in bacteria, but their success is limited to RNAs that are highly conserved across phyla, in sequence and structure. The ANTAR regulatory system consists of a family of RNAs (the ANTAR-target RNAs) that selectively recruit ANTAR proteins. This protein-RNA complex together regulates genes at the level of translation or transcriptional elongation. Despite the widespread distribution of ANTAR proteins in bacteria, their target RNAs haven’t been identified in certain bacterial phyla such as actinobacteria.

Results
Here, by using a computational search model that is tuned to actinobacterial genomes, we comprehensively identify ANTAR-target RNAs in actinobacteria. These RNA motifs lie in select transcripts, often overlapping with the ribosome binding site or start codon, to regulate translation. Transcripts harboring ANTAR-target RNAs majorly encode proteins involved in the transport and metabolism of cellular metabolites like sugars, amino acids and ions; or encode transcription factors that in turn regulate diverse genes.

Conclusion
In this report, we substantially diversify and expand the family of ANTAR RNAs across bacteria. These findings now provide a starting point to investigate the actinobacterial processes that are regulated by ANTAR.
Integration of transcriptomic data identifies key hallmark genes in hypertrophic cardiomyopathy
Authors: Xu Jing , Liu Xiangdong , Dai Qiming 
Published: July 2021

Abstract
Background
Hypertrophic cardiomyopathy (HCM) represents one of the most common inherited heart diseases. To identify key molecules involved in the development of HCM, gene expression patterns of the heart tissue samples in HCM patients from multiple microarray and RNA-seq platforms were investigated.

Methods
The significant genes were obtained through the intersection of two gene sets, corresponding to the identified differentially expressed genes (DEGs) within the microarray data and within the RNA-Seq data. Those genes were further ranked using minimum-Redundancy Maximum-Relevance feature selection algorithm. Moreover, the genes were assessed by three different machine learning methods for classification, including support vector machines, random forest and k-Nearest Neighbor.

Results
Outstanding results were achieved by taking exclusively the top eight genes of the ranking into consideration. Since the eight genes were identified as candidate HCM hallmark genes, the interactions between them and known HCM disease genes were explored through the protein–protein interaction (PPI) network. Most candidate HCM hallmark genes were found to have direct or indirect interactions with known HCM diseases genes in the PPI network, particularly the hub genes JAK2 and GADD45A.

Conclusions
This study highlights the transcriptomic data integration, in combination with machine learning methods, in providing insight into the key hallmark genes in the genetic etiology of HCM.
Cost effectiveness of therapist delivered cognitive behavioural therapy and web-based self-management in irritable bowel syndrome: the ACTIB randomised trial
Authors: McCrone Paul , Everitt Hazel , Landau Sabine , Little Paul , Bishop Felicity L. , O’Reilly Gilly , Sibelli Alice , Holland Rachel , Hughes Stephanie , Windgassen Sula , Goldsmith Kim , Coleman Nicholas , Logan Robert , Chalder Trudie , Moss-Morris Rona 
Published: July 2021

Abstract
Background
Telephone therapist delivered CBT (TCBT) and web-based CBT (WCBT) have been shown to be significantly more clinically effective than treatment as usual (TAU) at reducing IBS symptom severity and impact at 12 months in adults with refractory IBS. In this paper we assess the cost-effectiveness of the interventions.

Methods
Participants were recruited from 74 general practices and three gastroenterology centres in England. Interventions costs were calculated, and other service use and lost employment measured and costed for one-year post randomisation. Quality-adjusted life years (QALYs) were combined with costs to determine cost-effectiveness of TCBT and WCBT compared to TAU.

Results
TCBT cost £956 more than TAU (95% CI, £601–£1435) and generated 0.0429 more QALYs. WCBT cost £224 more than TAU (95% CI, − £11 to £448) and produced 0.029 more QALYs. Compared to TAU, TCBT had an incremental cost per QALY of £22,284 while the figure for WCBT was £7724. After multiple imputation these ratios increased to £27,436 and £17,388 respectively. Including lost employment and informal care, TCBT had costs that were on average £866 lower than TAU (95% CI, − £1133 to £2957), and WCBT had costs that were £1028 lower than TAU (95% CI, − £448 to £2580).

Conclusions
TCBT and WCBT resulted in more QALYs and higher costs than TAU. Complete case analysis suggests both therapies are cost-effective from a healthcare perspective. Imputation for missing data reduces cost-effectiveness but WCTB remained cost-effective. If the reduced societal costs are included both interventions are likely to be more cost-effective.
Trial registration ISRCTN44427879 (registered 18.11.13).
Ticking on Pandora’s box: a prospective case-control study into ‘other’ tick-borne diseases
Authors: Hoornstra D. , Harms M. G. , Gauw S. A. , Wagemakers A. , Azagi T. , Kremer K. , Sprong H. , van den Wijngaard C. C. , Hovius J. W. 
Published: July 2021

Abstract
Background
Tick-borne pathogens other than Borrelia burgdorferi sensu lato – the causative agent of Lyme borreliosis – are common in Ixodes ricinus ticks. How often these pathogens cause human disease is unknown. In addition, diagnostic tools to identify such diseases are lacking or reserved to research laboratories. To elucidate their prevalence and disease burden, the study ‘Ticking on Pandora’s Box’ has been initiated, a collaborative effort between Amsterdam University Medical Center and the National Institute for Public Health and the Environment.

Methods
The study investigates how often the tick-borne pathogens Anaplasma phagocytophilum, Babesia species, Borrelia miyamotoi, Neoehrlichia mikurensis, spotted fever group Rickettsia species and/or tick-borne encephalitis virus cause an acute febrile illness after tick-bite. We aim to determine the impact and severity of these tick-borne diseases in the Netherlands by measuring their prevalence and describing their clinical picture and course of disease.
The study is designed as a prospective case-control study. We aim to include 150 cases – individuals clinically suspected of a tick-borne disease – and 3 matched healthy control groups of 200 persons each. The controls consist respectively of a group of individuals with either a tick-bite without complaints, the general population and of healthy blood donors. During a one-year follow-up we will acquire blood, urine and skin biopsy samples and ticks at baseline, 4 and 12 weeks. Additionally, participants answer modified versions of validated questionnaires to assess self-reported symptoms, among which the SF-36, on a 3 monthly basis.

Discussion
This article describes the background and design of the study protocol of ‘Ticking on Pandora’s Box’. With our study we hope to provide insight into the prevalence, clinical presentation and disease burden of the tick-borne diseases anaplasmosis, babesiosis, B. miyamotoi disease, neoehrlichiosis, rickettsiosis and tick-borne encephalitis and to assist in test development as well as provide recommendations for national guidelines.

Trial registration
NL9258 (retrospectively registered at Netherlands Trial Register, trialregister.nl in in February 2021).
Utility of interferon gamma/tumor necrosis factor alpha FluoroSpot assay in differentiation between active tuberculosis and latent tuberculosis infection: a pilot study
Authors: Zhang Lifan , Wan Shijun , Zhou Ziyue , Zhang Yueqiu , Liu Xiaoqing 
Published: July 2021

Abstract
Background
The differential diagnosis of active tuberculosis (ATB) and latent tuberculosis infection (LTBI) remains challenging in clinical practice. We aimed to evaluate the diagnostic accuracy of the IFN-γ/TNF-α FluoroSpot assay for differentiating ATB from LTBI.

Methods
We conducted a pilot study of case-control design, using the FluoroSpot assay to simultaneously detect IFN-γ and TNF-α secretion at the single-cell level. The frequencies of antigen-specific single TNF-α-, total TNF-α-, single IFN-γ-, total IFN-γ- and dual IFN-γ/TNF-α-secreting T cells were detected. The optimal cutoffs value of frequencies for differentiating ATB from LTBI were determined according to receiver operating characteristic curve analysis. The sensitivity, specificity, predictive values (PV) and likelihood ratios (LR) of the FluoroSpot assay were calculated.

Results
Thirty patients diagnosed microbiologically with ATB, 36 healthcare workers with LTBI and 36 healthy controls were enrolled. After stimulated by ESAT-6 or CFP-10 peptides, the median frequencies of single TNF-α-, total TNF-α-, single IFN-γ-, total IFN-γ- and dual IFN-γ/TNF-α-secreting T cells in ATB patients were all significantly higher than those in LTBI and HC groups (P < 0.01). The frequencies of total IFN-γ-secreting T cells detected by FluoroSpot assay correlated significantly with those of T-SPOT.TB (r = 0.910 for ESAT-6, P < 0.001, r = 0.845 for CFP-10, P < 0.001). After stimulated by ESAT-6 peptides, with total TNF-α-secreting T cells frequencies at a cut off value of 21 iSFCs/250,000 PBMCs, the sensitivity, specificity, PLR, NLR, PPV, NPV of IFN-γ/TNF-α FluoroSpot assay in differentiating ATB from LTBI were 96.7% (95%CI, 82.8–99.9%), 94.3% (95%CI, 80.8–99.3%), 16.92 (95%CI, 4.40–65.08), 0.04 (95%CI, 0.01–0.24), 93.6% (95%CI,78.6–99.2%) and 97.1% (95%CI, 84.7–99.9%), respectively. With the frequencies of total TNF-α- and total IFN-γ-secreting T cells stimulated by ESAT-6 peptides combined, the specificity was increased to 97.1%, and the positive likelihood ratio to 31.5. The combination with CFP-10 might not improve the diagnostic accuracy of the ESAT-6 for differentiating ATB from LTBI.

Conclusions
IFN-γ/TNF-α FluoroSpot assay might have potential to help differentiate ATB from LTBI, but the findings need to be further verified by cross-sectional or prospective cohort studies.
Complement activation and blockade in massive post-partum haemorrhage, thrombotic microangiopathy and acute kidney injury: a case report
Authors: Guzzo G. , Kissling S. , Pantaleo G. , Pascual M. , Sadallah S. , Teta D. 
Published: July 2021

Abstract
Background
Thrombotic microangiopathy (TMA)-mediated acute kidney injury (AKI) following massive haemorrhage is a rare but severe complication of the post-partum period. It is associated with a poor renal prognosis and a high risk of end-stage kidney disease. Complement activation may occur in this picture. However, whether complement activation, and thus complement blockade, may be critically relevant in this setting is unknown.

Case presentation
A 50 year-old woman presented with massive delayed post-partum haemorrhage (PPH). Despite bleeding control and normalization of coagulation parameters, she rapidly developed AKI stage 3 associated with dysmorphic microhematuria and proteinuria up to 2 g/day with the need of renal replacement therapy. Blood tests showed signs of TMA associated with markedly increased sC5b-9 and factor Bb plasma levels, respectively markers of terminal and alternative complement pathway over-activation. This clinical picture prompted us to initiate anti-C5 therapy. sC5b-9 normalized within 12 h after the first dose of eculizumab, factor Bb and C3 after seven days, platelet count after nine days and haptoglobin after 3 weeks. The clinical picture improved rapidly with blood pressure control within 48 h. Diuresis resumed after three days, kidney function rapidly improved and haemodialysis could be discontinued after the sixth and last dose. Serum creatinine returned to normal two years after presentation.

Conclusions
We suggest that massive PPH induced major activation of complement pathways, which ultimately lead to TMA-induced AKI. Various causes, such as oocyte-donation, the potential retention of placental material and the use of tranexamic acid may have contributed to complement activation due to PPH. The prompt administration of anti-C5 therapy may have rapidly restored kidney microcirculation patency, thus reversing signs of TMA and AKI. We propose that complement activation may represent a major pathophysiological player of this complication and may provide a novel therapeutic avenue to improve renal prognosis in TMA-induced AKI following massive PPH.
Recurrent membranous nephropathy with a possible alteration in the etiology: a case report
Authors: Matsumoto Ayumi , Matsui Isao , Mano Keiji , Mizuno Hitoshi , Katsuma Yusuke , Yasuda Seiichi , Shimada Karin , Inoue Kazunori , Oki Takashi , Hanai Tadashi , Kojima Keiko , Kaneko Tetsuya , Isaka Yoshitaka 
Published: July 2021

Abstract
Background
Phospholipase A2 receptor 1 (PLA2R1) and thrombospondin type-1 domain-containing 7A (THSD7A) are the two major pathogenic antigens for membranous nephropathy (MN). It has been reported that THSD7A-associated MN has a higher prevalence of comorbid malignancy than PLA2R1-associated MN. Here we present a case of MN whose etiology might change from idiopathic to malignancy-associated MN during the patient’s clinical course.

Case presentation
A 68-year-old man with nephrotic syndrome was diagnosed with MN by renal biopsy. Immunohistochemistry showed that the kidney specimen was negative for THSD7A. The first course of corticosteroid therapy achieved partial remission; however, nephrotic syndrome recurred 1 year later. Two years later, his abdominal echography revealed a urinary bladder tumor, but he did not wish to undergo additional diagnostic examinations. Because his proteinuria increased consecutively, corticosteroid therapy was resumed, but it failed to achieve remission. Another kidney biopsy was performed and revealed MN with positive staining for THSD7A. PLA2R1 staining levels were negative for both first and second biopsies. Because his bladder tumor had gradually enlarged, he agreed to undergo bladder tumor resection. Pathological examination indicated that the tumor was THDS7A-positive bladder cancer. Subsequently, his proteinuria decreased and remained in remission.

Conclusions
This case suggests that the etiology of MN might be altered during the therapeutic course. Intensive screening for malignancy may be preferable in patients with unexpected recurrence of proteinuria and/or change in therapy response.
LINC01287 facilitates proliferation, migration, invasion and EMT of colon cancer cells via miR-4500/MAP3K13 pathway
Authors: Fu Dazhi , Ren Yongjun , Wang Chunxiao , Yu Lei , Yu Rui 
Published: July 2021

Abstract
Background
Accumulated studies indicate that aberrant expression of long noncoding RNAs (lncRNAs) is associated with tumorigenesis and progression of colon cancer. In the present study, long intergenic non-protein coding RNA 1287 (LINC01287) was identified to up-regulate in colon cancer by transcriptome RNA-sequencing, but the exact function remained unclear.

Methods
Transcriptome RNA-sequencing was conducted to identify dysregulated lncRNAs. Expression of LINC01287 was evaluated by real-time quantitative PCR. The downstream targets of LINC01287 and miR-4500 were verified by luciferase reporter assay, pull down assay and western blot. The potential functions of LINC01287 were evaluated by cell viability assay, colony formation assay, soft agar assay, flow cytometry, transwell migration and invasion assay, and tumor xenograft growth in colon cancer cells.

Results
Our results indicated that LINC01287 was up-regulated in colon cancer patients. High LINC01287 expression was associated with advanced TNM stage, lymph node metastasis, distant metastasis and shorter overall survival. Knockdown of LINC01287 inhibited cell growth, colony formation in plates and soft agar, transwell cell migration and invasion, and epithelial-mesenchymal transition (EMT) of colon cancer cells, while LINC01287 overexpression had contrary effects. In addition, LINC01287 mediated MAP3K13 expression by sponging miR-4500, thus promoted NF-κB p65 phosphorylation. Restored MAP3K13 expression or miR-4500 knockdown partially abrogated the effects of silencing LINC01287 in colon cancer cells.

Conclusion
Our findings demonstrated that the LINC01287/miR-4500/MAP3K13 axis promoted progression of colon cancer. Therefore, LINC01287 might be a potential therapeutic target and prognostic marker for colon cancer patients.
Fundus flavimaculatus-like in myotonic dystrophy: a case report
Authors: Kirkegaard-Biosca Eric , Berges-Marti Mònica , Azarfane Brahim , Cilveti Esther , Distefano Laura , García-Arumí Jose 
Published: July 2021

Abstract
Background
Myotonic dystrophy is an inherited disease characterized by progressive muscle weakness and myotonia. It is a multisystemic disorder that affects different parts of the body, including the eye. Dysfunction of ocular muscles, ptosis and cataract are the most common ophthalmologic manifestations, but it can also present with pigmentary changes in the retina. This report presents and discusses an unusual case of a pigmented pattern dystrophy simulating a fundus flavimaculatus in a patient with myotonic dystrophy.

Case presentation
We present a case of a woman with a history of myotonic dystrophy and complaints of progressive vision loss who presented bilateral retinal pigmentary changes in posterior pole and midperiphery. The characteristics and distribution of pigmented deposits, as well as ancillary tests, showed a retinal phenotype compatible with a multifocal pattern dystrophy or a fundus flavimaculatus.

Conclusions
There are a few publications about retinal disorders in patients with myotonic dystrophy. When macular area is affected it tends to adopt a patterned-shape defined as butterfly dystrophy or reticular dystrophy. To our knowledge, this is the first report of a patient with myotonic dystrophy and multifocal pattern dystrophy or fundus flavimaculatus.
Prevalence of depression and associated factors among patients with type 2 diabetes mellitus in eastern Sudan
Authors: Omar Saeed M. , Musa Imad R. , Idrees Maysoon B. , Adam Ishag 
Published: July 2021

Abstract
Background
Diabetes mellitus (DM) represents a global health threat and burden. It is associated with medical and psychological complications, especially depression. Depression among patients with DM may affect the general prognosis. Hence, we conducted a cross-sectional study in Gadarif, eastern Sudan to evaluate the prevalence of depression and its associated factors among patients with type 2 DM (T2DM).

Methods
We performed a cross-sectional study. Data on anthropometric parameters, demographic characteristics and blood glucose levels were collected via questionnaire. Depression was assessed using the Patient Health Questionnaire (PHQ-9).

Results
Three hundred and fifty patients with T2DM were enrolled in the study and 205 (58.6%) were women. The median (interquartile range) age and duration of diabetes were 56.0 (14.0) years and 8 (8) years, respectively. The prevalence of depression in patients with T2DM was 35.6%. Logistic regression analysis showed significant associations between depression and rural residence (adjusted odds ratio [AOR] = 2.11, 95% confidence interval [CI] = 1.20–3.72), non-employee (AOR = 2.32, 95% CI = 1.34–4.00), co-morbidity (AOR = 2.35, 95% CI = 1.43–3.86) and obesity AOR = 2.19, 95% CI = 1.48–4.18).

Conclusion
The prevalence of depression is high among Sudanese patients with T2DM. Rural residence, unemployment, co-morbidity and obesity are significant risk factors for developing depression among patients with T2DM.