bluuebunny/crossref_metadata_2025_split huggingface dataset:
Weighted Gene Co-Expression Network Coupled with a Critical-Time-Point Analysis during Pathogenesis for Predicting the Molecular Mechanism Underlying Blast Resistance in Rice
Authors: Tian Dagang , Chen Zaijie , Lin Yan , Chen Ziqiang , Bui Khuynh The , Wang Zonghua , Wang Feng 
Published: December 2020

Abstract
Background
Rice blast, caused by the ascomycete fungus M. oryzae, is one of the most important diseases of rice. Although many blast resistance (R) genes have been identified and deployed in rice varieties, the molecular mechanisms responsible for the R gene-mediated defense responses are yet not fully understood.

Results
In this study, we used comparative transcriptomic analysis to explore the molecular mechanism involved in Piz-t-mediated resistance in a transgenic line containing Piz-t (NPB-Piz-t) compared to Nipponbare (NPB). Clustering and principal component analysis (PCA) revealed that the time-point at 24-h post inoculation (hpi) was the most important factor distinguishing the four time-points, which consisted of four genes of mitogen-activated protein kinases (MAPKs) signaling pathway, one gene related to WRKY DNA-binding domain containing protein, five pathogenesis-related protein (OsPR1s) genes, and three genes of R proteins involving in the most significant protein-protein interaction (PPI) pathway. Using weighted gene co-expression network analysis (WGCNA) to investigate RNA-seq data across 0, 24, 48, and 72 hpi, nine modules with similar patterns expression pattern (SEP) and three modules with differential expression pattern (DEP) between NPB-Piz-t and NPB across 0, 24, 48, and 72 hpi with KJ201 (referred to as Piz-t-KJ201 and NPB-KJ201) were identified. Among these the most representative SEP green-yellow module is associated with photosynthesis, and DEP pink module comprised of two specific expressed nucleotide-binding domain and leucine-rich repeat (NLR) genes of LOC_Os06g17900 and LOC_Os06g17920 of Pi2/9 homologous, three NLR genes of LOC_Os11g11810, LOC_Os11g11770, and LOC_Os11g11920 which are putatively associated with important agronomic traits, and a B3 DNA binding domain containing protein related genes (LOC_Os10g39190). Knockout of LOC_Os10g39190 via CRISPR-Cas9 resulted in plant death at the seedling stage.

Conclusions
The research suggested that Piz-t and multiple NLR network might play important roles in the regulation of the resistance response in the Piz-t-KJ201 interaction system. The identified genes provide an NLR repository to study the rice-M. oryzae interaction system and facilitate the breeding of blast-resistant cultivars in the future.
The impact of adding solifenacin to tamsulosin therapy for treatment of storage lower urinary tract symptoms owing to benign prostatic hyperplasia
Authors: Elbadry Mohamed , Ali Ahmed Issam , Saleh Eman , Kamal Amal , Gabr Ahmed H. 
Published: December 2020

Abstract
Background
Benign prostatic hyperplasia (BPH) is a common problem in aging males which has a potential impact on patients’ health-related quality of life. In the present prospective study, we evaluated the effect of adding solifenacin to tamsulosin, compared to tamsulosin alone on overactive bladder symptoms scores (OABSS) and patients’ quality of life (QoL) in patients with filling lower urinary tract symptoms due to BPH.

Methods
Patients included in our study were randomly assigned into 2 groups: group 1 included patients with BPH who received tamsulosin alone and group 2 included patients with BPH who received a combination of tamsulosin and sofinacin. Treatment period was 12 weeks in both groups. Quality of life and overactive bladder symptoms score questionnaires were obtained and compared in both groups before and after treatment.

Results
No significant differences were found between both groups before treatment. At the end of treatment period, The QoL score for Group 1 patients was significantly greater than the other group (mean rank was 138.98 in tamsulosin group versus 62.02 in the combination group, P-value < 0.01). Similarly, OABSS for tamsulosin only group was significantly higher than combined treatment patients (mean rank was 145.03 in tamsulin group versus 55.98 in the combination group, P-value < 0.01).

Conclusion
Adding solifenacin to tamsulosin was associated with an improvement of QoL and OABSS in patients with irritative urinary symptoms due to BPH when compared with tamsulosin monotherapy.
NYU-EDA in modelling the effect of COVID-19 on patient volumes in a Finnish emergency department
Authors: Tuominen Jalmari , Hällberg Ville , Oksala Niku , Palomäki Ari , Lukkarinen Timo , Roine Antti 
Published: December 2020

AbstractBackgroundEmergency departments (EDs) worldwide have been in the epicentre of the novel coronavirus disease (COVID-19). However, the impact of the pandemic and national emergency measures on the number of non-COVID-19 presentations and the assessed acuity of those presentations remain uncertain.MethodsWe acquired a retrospective cohort containing all ED visits in a Finnish secondary care hospital during years 2018, 2019 and 2020. We compared the number of presentations in 2020 during the national state of emergency, i.e. from March 16 to June 11, with numbers from 2018 and 2019. Presentations were stratified using localized New York University Emergency Department Algorithm (NYU-EDA) to evaluate changes in presentations with different acuity levels.ResultsA total of 27,526 presentations were observed. Compared to previous two years, total daily presentations were reduced by 23% (from 113 to 87,p < .001). In NYU-EDA classes, Non-Emergent visits were reduced the most by 42% (from 18 to 10,p < .001). Emergent presentations were reduced by 19 to 28% depending on the subgroup (p < .001). Number of injuries were reduced by 25% (from 27 to 20, p < .001). The NYU-EDA distribution changed statistically significantly with 4% point reduction in Non-Emergent visits (from 16 to 12%,p < .001) and 0.9% point increase in Alcohol-related visits (from 1.6 to 2.5%, p < .001).ConclusionsWe observed a significant reduction in total ED visits in the course of national state of emergency. Presentations were reduced in most of the NYU-EDA groups irrespective of the assessed acuity. A compensatory increase in presentations was not observed in the course of the 3 month lockdown. This implies either reduction in overall morbidity caused by decreased societal activity or widespread unwillingness to seek required medical advice.
Immunoglobulin G4-associated autoimmune hepatitis with peripheral blood eosinophilia: a case report
Authors: Chang Arunchai , Charoenlap Cheep , Akarapatima Keerati , Rattanasupar Attapon , Prachayakul Varayu 
Published: December 2020

Abstract
Background
Immunoglobulin G4 (IgG4) associated autoimmune hepatitis (AIH) has been recognized as a type of autoimmune disease that responds to corticosteroid. The diagnosis is based on elevation of the serum IgG4 level, abundance of IgG4 enhanced plasma cell infiltration in the portal region of the liver, and satisfaction of the criteria for “definite AIH” under the revised International Autoimmune Hepatitis Group (IAIHG) scoring system. However, the clinical course of the disease is unclear.

Case presentation
A 65-year-old man with jaundice and peripheral blood eosinophilia.
His IAIHG and simplified score was compatible with definite AIH and his IgG4 level was elevated. Magnetic resonance imaging did not reveal abnormalities in the hepatobiliary system or pancreas. A liver biopsy revealed interface hepatitis with IgG4 positive plasma cell infiltration in the portal region, without evidence of bile duct injury. He responded to 4-week period of induction prednisolone therapy and had no recurring symptoms under maintenance therapy of 5 mg prednisolone during the 3-year follow up.

Conclusions
This was a rare case that demonstrated an association between IgG4 associated AIH and the presence of peripheral blood eosinophilia.
Plasma levels and tissue expression of soluble TGFβrIII receptor in women with early-stage breast cancer and in healthy women: a prospective observational study
Authors: Grgurevic Lovorka , Novak Ruder , Trkulja Vladimir , Hrkac Stela , Salai Grgur , Bilandzic Josko , Hamzic Lejla Ferhatovic , Milas Ivan , Vucemilo Tiha , Balja Melita Peric , Bilic Karmen 
Published: December 2020

Abstract
Background
Mammary carcinogenesis is partly regulated by the transforming growth factor beta (TGFβ) signaling pathway. Its function in cancer progression and metastasis is highly dependent on disease stage, and it is likely modulated by the ratio of membrane-bound vs. soluble TGFβrIII (sTGFβrIII). In this prospective observational study, we assessed tissue expression and plasma levels of sTGFβrIII in healthy women, women with benign breast lesions and in early-stage breast cancer patients.

Methods
In a preliminary study, plasma sTGFβrIII levels were determined in 13 healthy women (age 19–40 years) at different phases of the ovarian cycle, and in 15 patients (age 35–75 years) at different times of the day. The main study assessed plasma concentrations of sTGFβrIII in: (i) 158 healthy women in whom breast lesions were excluded; (ii) 65 women with benign breast lesions; (iii) 147 women with newly diagnosed breast cancer classified as American Joint Committee on Cancer (AJCC) stages 0 to IIB. Completers provided blood samples before surgery and at 10–30 and 160–180 days after surgery. Plasma sTGFβrIII concentrations were determined using an indirect ELISA kit. Part of the removed tissues underwent immunohistochemical (IHC) staining and analysis of tissue TGFβrIII expression.

Results
There appeared no relevant variations in plasma sTGFßrIII levels at different times of the day or different ovarian cycle phases. Before surgery, breast cancer patients had somewhat higher sTGFβrIII than healthy women, or those with benign breast lesions (by 14.5 and 26 ng/mL, respectively), with a tendency of larger differences at higher age. This correlated with lower expression of TGFβrIII in breast cancer vs. healthy tissue samples. At 160–180 days after surgery, plasma sTGFβrIII levels in breast cancer patients declined by 23–26 ng/mL.

Conclusions
Plasma sTGFβrIII levels do not seem to relevantly vary during the day or the ovarian cycle. The coinciding higher plasma levels in newly diagnosed cancer patients than in healthy subjects and lower TGFβrIII expression in the malignant than in healthy breast tissue suggest ectodomain shedding as a source of circulating sTGFβrIII. Decline in plasma levels after tumor removal supports such a view.
Exogenous interleukin-33 promotes hepatocellular carcinoma growth by remodelling the tumour microenvironment
Authors: Wang Wenxiu , Wu Jun , Ji Mei , Wu Changping 
Published: December 2020

Abstract
Background
Interleukin-33 (IL-33) is an effective inducer of pro-inflammatory cytokines regulating innate and adaptive immunity. Inflammation could be a double-edged sword, promoting or inhibiting tumour growth. To date, the roles and mechanisms of IL-33 in tumours remain controversial. Here, we examined the effect of exogenous IL-33 on the biological characteristics of hepatocellular carcinoma (HCC) and the possible mechanism of action.

Methods
In this study, IL-33 expression in the tissues of 69 HCC patients was detected and its relationship with prognosis was evaluated. After establishing a mouse HCC model and IL-33 treatment operation, the infiltration of splenic myeloid-derived suppressor (MDSCs), dendritic (DCs), regulatory T, and natural killer (NK) cells was detected by flow cytometry analysis, and the vascular density of the tumour tissues was detected by immunohistochemistry to reveal the mechanism of IL-33 in HCC proliferation. Finally, the Cancer Genome Atlas database was used to analyse Gene Ontology terms the and Kyoto Encyclopaedia of Genes and Genomes pathway. Moreover, the chi-square test, two-tailed unpaired Student’s t-test, and multiple t-tests were performed using SPSS version 23.0 and GraphPad Prism 8.0 software.

Results
The IL-33 expression level was negatively correlated with the overall survival of HCC patients, suggesting its potential clinical significance in the prognosis of HCC. We found that systemic IL-33 administration significantly promoted the tumour size in vivo. Furthermore, the IL-33-treated mice presented decreased frequencies of tumouricidal NK and CD69+ CD8+ T cells. After IL-33 treatment, the incidence of monocytic MDSCs and conventional DCs increased, while that of granulocytic MDSCs decreased. Moreover, IL-33 promoted the formation of intracellular neovascularization. Therefore, IL-33 accelerated HCC progression by increasing the accumulation of immunosuppressive cells and neovascularization formation. Finally, we found that the transcription of IL-33 was closely related to the PI3K-Akt and MAPK pathways in Gene Set Enrichment Analysis plots, which were involved in the tumourigenesis and pathogenesis of HCC.

Conclusions
Taken together, IL-33 may be a key tumour promoter of HCC proliferation and tumourigenicity, an important mediator, and a potential therapeutic target for regulating HCC progression.
The posterior cortical axis as an alternative reference for femoral component placement in total knee arthroplasty
Authors: Nam Ji-Hoon , Koh Yong-Gon , Kang Kiwon , Park Joon-Hee , Kang Kyoung-Tak 
Published: December 2020

AbstractBackgroundAlthough several reference axes have been established for determining femoral rotational alignment during total knee arthroplasty (TKA), the most accurate axis is undetermined. This study determines the relationship between the posterior cortical axis (PCA) and the trochlear anterior line (TAL) of the femur in relation to the epicondylar axis.MethodsA total of 341 patients who underwent TKA for osteoarthritis were enrolled. Patients who had undergone previous bony surgery or replacement that might have changed the femoral geometry were excluded. Finally, 336 patients (200 females and 136 males) were included in the study. The angles between the transepicondylar axis (TEA) and TAL and TEA and the femoral PCA (FPCA) were evaluated. We also assessed whether there was any significant differences in variance and gender in these two angles. Student’sttests were used to determine the significance of coronal alignment and any gender-based differences. The variances between the TAL/TEA and FPCA/TEA angles were compared usingFtests.ResultsThe FPCA was externally rotated by 2.6° ± 3.6°, and the trochlear anterior line was internally rotated by 5.2° ± 5.5°, relative to the TEA. Gender-based differences were observed in the comparisons between anatomical references and TEA.ConclusionsThe FPCA is a more conservative landmark than the TAL for intraoperative or postoperative approximation of the TEA. When conventional reference axes, such as the posterior condylar axis and the anteroposterior axis, are inaccurate, surgeons can refer to this alternative reference. These findings demonstrate that the FPCA may be useful for determining the rotational alignment of the femoral component before and during TKA.
Characteristics and genetic testing outcomes of patients with clinically suspected paraganglioma/pheochromocytoma (PGL/PCC) syndrome in Singapore
Authors: Ting Kay Reen , Ong Pei Yi , Wei Samuel Ow Guan , Parameswaran Rajeev , Khoo Chin Meng , Deepak Doddabele Srinivasa , Lee Soo-Chin 
Published: December 2020

Abstract
Background
Hereditary paraganglioma (PGL) and pheochromocytoma (PCC) syndromes are rare conditions, with limited data on spectrum of causative gene variants of these syndromes in Asian patients.

Methods
We describe the clinical characteristics and genetic testing outcomes of patients with suspected hereditary PGL/PCC who were referred to a tertiary cancer genetics clinic in Singapore.

Results
Among 2196 patients with suspected hereditary cancer syndrome evaluated at the cancer genetics clinic from 2000 to 2019, 13/2196 (0.6%) patients fulfilled clinical suspicion for hereditary PGL/PCC syndrome. After genetic counselling, 10 patients underwent multi-gene next generation sequencing and deletion/duplication analysis, including SDHAF2, SDHA, SDHB, SDHC, SDHD, VHL, NF1, RET, MAX, and TMEM127. Seven of 10 patients (70%) were identified to carry pathogenic variants, including 3 unrelated Chinese patients with head and neck PGL who carried the same SDHD: c.3G > C (p.Met1Ile) variant that was previously reported to be a possible founder variant in Chinese, and 3 patients with urogenital PGL and 1 patient with retroperitoneal PGL who carried different SDHB variants. Variant carriers were younger, more likely to present with multiple tumours, or have family history of paraganglioma or pheochromocytoma, than non- variant carriers.

Conclusion
Hereditary PGL/PCC accounts for only 0.6% of patients seen in an adult cancer genetics clinic in Asia. SDHD and SDHB genes remain the most important causative genes of hereditary PGL/PCC in Asia even when patients are tested with multi-gene NGS panel.
Human stem cell-based models for studying autism spectrum disorder-related neuronal dysfunction
Authors: Cheffer Arquimedes , Flitsch Lea Jessica , Krutenko Tamara , Röderer Pascal , Sokhranyaeva Liubov , Iefremova Vira , Hajo Mohamad , Peitz Michael , Schwarz Martin Karl , Brüstle Oliver 
Published: December 2020

AbstractThe controlled differentiation of pluripotent stem cells (PSCs) into neurons and glia offers a unique opportunity to study early stages of human central nervous system development under controlled conditions in vitro. With the advent of cell reprogramming and the possibility to generate induced pluripotent stem cells (iPSCs) from any individual in a scalable manner, these studies can be extended to a disease- and patient-specific level. Autism spectrum disorder (ASD) is considered a neurodevelopmental disorder, with substantial evidence pointing to early alterations in neurogenesis and network formation as key pathogenic drivers. For that reason, ASD represents an ideal candidate for stem cell-based disease modeling. Here, we provide a concise review on recent advances in the field of human iPSC-based modeling of syndromic and non-syndromic forms of ASD, with a particular focus on studies addressing neuronal dysfunction and altered connectivity. We further discuss recent efforts to translate stem cell-based disease modeling to 3D via brain organoid and cell transplantation approaches, which enable the investigation of disease mechanisms in a tissue-like context. Finally, we describe advanced tools facilitating the assessment of altered neuronal function, comment on the relevance of iPSC-based models for the assessment of pharmaceutical therapies and outline potential future routes in stem cell-based ASD research.
Simplified modelling and backstepping control of the long arm agricultural rover
Authors: Wongvanich Napasool , Boksuwan Sungwan , Chesof Abdulhafiz 
Published: December 2020

AbstractThis paper presents the development of the simplified modelling and control of a long arm system for an agricultural rover, which also extends the modelling methodology from the previous work. The methodology initially assumes a flexible model and, through the use of the integral-based parameter identification method, the identified parameters are then correlated to an energy function to allow a construction of the friction induced nonlinear vibration model. To also capture the effect of the time delay, a delay model was also considered in the form of a second order delay differential equation. Both families of models were applied to identify and characterise a specialised long arm system. The nonlinear model was found to give significant improvement over the standard linear model in data fitting, which was further enhanced by the addition of the time delay consideration. A backstepping controller was also designed for both model families. Results show that the delay model expends less control efforts than the lesser non-delay model.
Quasi-6-day wave effects in ionospheric E and F region during the recent solar maximum 2014–2015
Authors: Liu Yi , Tang Qiong , Chen Guanyi , Wang Zhuangkai , Zhou Chen 
Published: December 2020

AbstractWe show the statistical characteristics of quasi-6-day wave (Q6DW) absolute amplitude in foE and foF2 during 2014–2015 by using six ionosondes at different latitudes. The results show that foE perturbations maximized at mid-latitudes during equinoxes, and the maximum amplitude of Q6DW in foF2 occurred near the northern crest of equatorial ionospheric anomaly (EIA). In addition, the absolute amplitude of Q6DW in foF2 increased with increasing solar activity. Our observations suggest that the dissipative Q6DW-like oscillations in the lower thermosphere may cause variations in the thermospheric neutral density via mixing effect and further result in foE disturbances in Q6DW events. Furthermore, the E region wind dynamo could also be modulated by the 6-day wave, thus leading to the disturbances in vertical plasma velocity via E × B drifts and F region electron density. Our observational investigation provides evidence of thermosphere–ionosphere coupling in the mid- and low-latitude region.
Prevalence and factors associated with postpartum use of long-acting reversible contraception in Bukombe District, Geita Region, Tanzania: a community- based study
Authors: Kiondo Kiondo Solomon , Maro Eusebious , Kiwango Sophia , Alloyce Julius Pius , Shayo Benjamin C. , Mahande Michael Johnson 
Published: December 2020

Abstract
Background
Globally, approximately half of all pregnancies occur before 24 months after child birth. In Sub Saharan Africa the unmet need for family planning is highest among postpartum women. There is a dearth of information regarding factors associated with postpartum use of long acting reversible contraception (LARC) in Tanzania particularly in the Lake zone. This study aimed to determine the prevalence and factors associated with postpartum use of LARC (< 24 months) in Bukombe District, Geita Region in the Lake zone, in 2018.

Methodology
Community based analytical cross-sectional study was conducted between May and June 2018 among women with less than 24 months since delivery. Multistage sampling technique was used to recruit participants. Face to face interviews with 768 postpartum women was conducted using standardized questionnaire. Data were analyzed using Stata Version 13.0. Multivariable logistic regression model was used to determine factors associated with postpartum use of LARC.

Results
Prevalence of postpartum use of LARC was 10.4%. Urban residence (AOR = 2.94, 95% CI: 1.07–8.06), having formal employment (AOR = 4.81, 95% CI: 1.85–12.57) and receiving family planning counseling (AOR = 4.39, 95% CI: 1.89–10.20) were significantly associated with postpartum LARC use.

Conclusion
The postpartum use of LARC was low in the studied population with implants being the most commonly used method. Urban residency, formal employment and receiving family planning counseling were associated with postpartum LARC use. Improving prenatal and quality of family planning counseling is warranted to increase postpartum LARC utilization in Bukombe.