bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance and Host Association of Spotted Lanternfly (Lycorma Delicatula) among Common Woody Ornamentals
Authors: Uyi Osariyekemwen , A. Keller Joseph , Hoover Kelli 
Published: April 2021

Abstract
Despite the broad host range of Lycorma delicatula, the performance of this invasive pest on non-Ailanthus host plant species is difficult to document realistically without using field conditions given this pest’s requirements for vast amounts of phloem. In spring 2020, we examined the performance of L. delicatula with and without access to Ailanthus altissima by tracking development, survival, host tree association and oviposition in large enclosures planted with one each of Juglans nigra, Salix babylonica and Acer saccharinum along with either one A. altissima or one Betula nigra. We reared nymphs with and without access to A. altissima, released them into the corresponding large enclosures as third instars, and monitored them from early July 2020 through November 2020. Insect survival was higher and development faster with access to A. altissima. Third and fourth instar nymphs were most frequently observed on A. altissima when it was present, while adults were equally associated with A. saccharinum and A. altissima. In the absence of A. altissima, nymphs were most frequently found on S. babylonica, while adults were most often on A. saccharinum. Females with access to A. altissima deposited nearly 7-fold more egg masses than those without access to A. altissima. In another experiment, the offspring of parents that had been reared without access to A. altissima showed similar survival and development time from egg to adult as offspring from parents that never had access to A. altissima. These findings suggest that managers need to be aware that even in the absence of A. altissima in the landscape, several hardwood host trees can be utilized by L. delicatula to develop and reproduce.
Involvement of FLOWERING LOCUS T in microgravity response of Arabidopsis thaliana plants under long- and short-day conditions
Authors: Wang Lihua , Xie Junyan , Wu Yuanyuan , Mou Chenghong , Jiao Yuwei , Dou Yanhui , Zheng Huiqiong 
Published: April 2021

Abstract
Microgravity have an impact on growth and development of higher plants in space at both vegetative stage and reproductive stage. A great deal of information has been available on the vegetative stage in space, but relatively little is known about the influence of microgravity on plants at the reproductive stage. In this study, we constructed a transgenic Arabidopsis thaliana plants expressing flowering control gene, FLOWERING LOCUS T (FT), together with green fluorescent protein gene(GFP) under control of a heat shock-inducible promoter (HSP17.4), by which we induced FT expression inflight through remote controlling heating shock treatment. Inflight photography data showed that induction of FT expression in plants in space could counteract the impact of microgravity and promote flowering. Whole-genome microarray analysis of gene expression changes in leaves of wild-type and these transgenic plants grown under different photoperiod conditions in space indicated that the function of the photoperiod-related microgravity response genes are mainly involved in protein synthesis and post-translation protein modulation, notably protein phosphorylation. In addition, changes of circadian component gene expression in response to microgravity under different photoperiod indicated that role of circadian oscillator could act as integrators of microgravity response and photoperiodic signals in Arabidopsis plant grown in space.
Surgical Treatment for Colorectal Cancer Partially Restores Gut Microbiome and Metabolome Traits
Authors: Shiroma Hirotsugu , Shiba Satoshi , Erawijantari Pande Putu , Takamaru Hiroyuki , Yamada Masayoshi , Sakamoto Taku , Kanemitsu Yukihide , Mizutani Sayaka , Soga Tomoyoshi , Saito Yutaka , Shibata Tatsuhiro , Fukuda Shinji , Yachida Shinichi , Yamada Takuji 
Published: April 2021

Abstract
Background: Postoperative colorectal cancer (CRC) patients are at increased risk of developing metachronous CRC. Despite accumulating evidence indicating that the gut microbiota and metabolites can promote CRC carcinogenesis, the influence of surgery for CRC on the gut microbiota and metabolites remains partially understood. We hypothesized that if surgery does not eliminate the bacteria and metabolites promoting CRC carcinogenesis, these bacteria and metabolites might be associated with the development of metachronous CRC. To test this hypothesis, we collected 170 fecal samples from 85 CRC patients in pre- and approximately one year postsurgery status, and performed shotgun metagenomics sequencing and capillary electrophoresis time-of-flight mass spectrometry-based metabolomics analyses and compared pre- and postsurgery status.Results: CRC-associated bacteria such as Parvimonas micra and Fusobacterium nucleatum were significantly (P < 0.005) decreased after surgery. On the other hand, cholate, carcinogenesis-associated deoxycholate, its biotransformed genes (bai operon) from cholate to deoxycholate, and the contributing bacterium (Clostridium scindens) were significantly (P < 0.005) increased. Additionally, these alterations were only observed in postleft surgery. Cholate and glycocholate were significantly (P < 0.005) increased in postright surgery. We also developed a method for potential CRC risk assessment based on the gut microbiota and metabolomic compositions using a random forest machine learning algorithm and then applied it to postoperative patients. The estimated CRC risk based on the random forest algorithm was partially restored postsurgery. Conclusions: Our results indicate that the high potential CRC risk in CRC postoperative patients is associated with metabolites derived from the gut microbiota, which targets interventions to reduce the CRC risk.
A Case of Colonic Micropapillary Carcinoma With a High Frequency of Apoptosis
Authors: Arai Kazumori , Iwasaki Tomohiro , Ishimatsu Hisato , Tsuchiya Chinatsu , Kubota Aki , Sonoda Akihiro , Ohata Ko 
Published: April 2021

Abstract
Purpose: Colorectal micropapillary carcinoma (MPC) exhibits aggressive biological characteristics, with empty spaces and reversed polarity, similar to the poorly differentiated clusters (PDCs) formed from detached cancer cells. Epithelial–mesenchymal transition, which is involved in the cancer cell acquisition of apoptosis resistance, is closely linked with histological findings of MPC, PDCs, and tumor buds (TBs), with MPC and TBs considered as apoptosis-resistant features. However, we encountered a case of colonic MPC with frequent apoptosis.Methods: We examined the case using immunohistochemistry and compared it with two cases of conventional colonic cancer with high PDC and TB presence.Results: In many of the tumor glands (TGs) of the MPC, empty spaces and tumor cell detachment toward the gland interior were observed. Moreover, TG ruptures were scattered, with PDCs adjacent to them. Apoptosis occurred mainly at the TG and PDC peripheries in the middle and deep tumor layers, and transforming growth factor beta 1 (TGF-β1) positivity was evident in those tumor cells. Cells positive for apoptosis-related M30 were distributed mainly in the deep layer with a significant PDC and TB presence. However, apoptosis and M30 positivity were low in the TBs. In the control cases, apoptosis hardly occurred. Furthermore, M30 positivity in the TGs was scattered and barely evident in the PDCs. Aberrant β-catenin positivity was found. In MPC, non-tumorous bud components, especially those in the deep layer, had poor abilities to promptly acquire apoptosis resistance. Conclusion: Apoptosis has the potential to reciprocally produce MPC, PDCs, and TBs, with TGF-β1 involvement.
Can the BMI-Based Dose Regimen be Used to Reduce Injection Activity and to Obtain a Constant Image Quality in Oncological Patients by 18F-FDG Total-Body PET/CT Imaging?
Authors: Xiao Jie , Yu Haojun , Sui Xiuli , Hu Yan , Yanyan Cao , Liu Guobing , Zhang Yiqiu , Hu Pengcheng , Wang Ying , Li Chenwei , Xu Baixuan , Shi Hongcheng 
Published: April 2021

Abstract
Purpose PET image quality is influenced by the patient size according to the current guideline. The purpose was to propose an optimized dose regimen to yield a constant image quality independent of patient size to meet the clinical needs.Methods A first patient cohort of 78 consecutives for oncological patients (59.7±13.7 years) who underwent a total-body PET/CT scan were retrospectively enrolled to develop the regimen. The patients were equally distributed in four BMI groups according to WHO criteria. The liver SNR (Signal noise ratio, SNRL) was obtained through manually drawing ROIs and normalized (SNRnorm) by the injected activity and acquisition time. And fits of SNRnorm against different patient-dependent parameters were performed to determine the best correlating parameter and fit method. A qualitative assessment on image quality was performed using a 5-point Likert scale to determine the acceptable threshold of SNRL. And thus, an optimized regimen was proposed and validated by a second patient cohort with prospectively enrolled 38 oncological patients. Results The linear fit showed SNRnorm was the strongest correlation (R2 = 0.69) with the BMI than other patient-dependent parameters. The qualitative assessment revealed a SNRL of 14.0 as a threshold to achieve a sufficient image quality. The optimized dose regimen was determined as a quadratic relation with BMI: Injected activity = 39.2 MBq/(-0.03*BMI+1.49)2. In the validation study, the SNRL no longer decreased with the increase of BMI. There was no significant difference of the image quality, the SNRL, between different BMI groups (p > 0.05). In addition, the injected activity was reduced by 75.6±2.9 %, 72.1±4.0 %, 67.1±4.4 % and 64.8±3.5 % compared to the first cohort for the four BMI groups, respectively.Conclusion The study recommended a quadratic relation between the 18F-FDG injected activity and the patient’s BMI and propose a regimen for total-body PET imaging. In the regimen, the image quality can maintain in a constant level independent of patient size and meet the clinical requirement even with a reduced injected activity.
First Record of Migonemyia Vaniae (Galati, Fonseca &amp; Marassá, 2007) (Diptera, Psychodidae, Phlebotominae) in the State of Rio De Janeiro.
Authors: Balthazar Thamiris , Santana Antônio de , Costa Luiz , Mallet Jacenir , Vilela Maurício 
Published: April 2021

Abstract
Entomological surveillance studies in areas that have not yet been evaluated become important for the survey of local fauna, where new taxons or species records can be observed. In an investigation carried out at the Jequitibá headquarters of the Três Picos State Park, the presence of the species Migonemyia vaniae was observed, until then described and recorded only in the state of São Paulo, thus, we report the first encounter of the species in the state of Rio de Janeiro. Two male specimens of Mg vaniae with CDC light traps (HP model) were captured. Specimens of Mg vaniae and Migonemyia migonei were submitted to the clarification process and mounted between slide and coverslip in Berlese and identified under microscope following the Galati classification. Morphometric analyses of the ejaculatory pump and edeagais ducts and photographs of the structures were performed in order to compare the differences between species and record the first report of the species Mg vaniae in the state of Rio de Janeiro.
Analysis of the Pan-Asian Subgroup of patients in the NALA Trial: A Randomized Phase III NALA Trial Comparing Neratinib + Capecitabine (N+C) vs Lapatinib + Capecitabine (L+C) in Patients with HER2+ Metastatic Breast Cancer (mBC) Previously Treated with Two or more HER2-Directed Regimens
Authors: Dai Ming-Shen , Feng Yin Hsun , Chen Shang Wen , Masuda Norikazu , Yau Chung Cheung Thomas , Chen Shou Tung , Lu Yen Shen , Yap Yoon Sim , Ang Peter Cher Siang , Chu Sung Chao , Kwong Ava , Lee Keun Seok , Ow Samuel , Kim Sung Bae , Lin Johnson , Chung Hyun Cheol , Ngan Roger , Kok Victor C. , Rau Kun Ming , Sangai Takafumi , Ng Ting Ying , Tseng Ling Ming , Bryce Richard , Keyvanjah Kiana , Bebchuk Judith , Chen Mei Chieh , Hou Ming-Feng 
Published: April 2021

Abstract
Purpose: Neratinib, an irreversible pan-HER tyrosine kinase inhibitor, has demonstrated systemic efficacy and intracranial activity in various stages of HER2+ breast cancer. NALA was a phase III randomized trial that assessed the efficacy and safety of neratinib + capecitabine (N+C) against lapatinib + capecitabine (L+C) in HER2+ metastatic breast cancer (mBC) patients who had received ≥2 HER2-directed regimens. Descriptive analysis results of the Asian subgroup in the NALA study are reported herein.Methods: 621 centrally-assessed HER2+ mBC patients were enrolled, 202 of whom were Asian. Those with stable, asymptomatic brain metastases (BM) were eligible for study entry. Patients were randomized 1:1 to N (240mg qd) + C (750mg/m2 bid, day 1-14) with loperamide prophylaxis, or to L (1250mg qd) + C (1000mg/m2 bid, day 1-14) in 21-day cycles. Co-primary endpoints were centrally-assessed progression free survival (PFS) and overall survival (OS). Secondary endpoints included time to intervention for central nervous system (CNS) disease, objective response rate, duration of response (DoR), clinical benefit rate, and safety.Results: 104 and 98 Asian patients were randomly assigned to receive N+C or L+C, respectively. Median PFS of N+C and L+C was 7.0 and 5.4 months (P=0.0014), respectively. Overall cumulative incidence of intervention for CNS disease was lower with N+C (27.9 versus 33.8%; P=0.039). Both median OS (23.8 versus 18.7 months; P=0.185) and DoR (11.1 versus 4.2 months; P<0.0001) were extended with N+C, compared to L+C. Diarrhea was the most frequent treatment-emergent adverse event (TEAE) in both arms (78.8 versus 51.0%). The incidence of grade 3/4 TEAEs and TEAEs leading to treatment discontinuation was comparable between the two arms.Conclusion: Consistent with the efficacy profile observed in the overall study population, Asian patients with HER2+ mBC, who had received ≥2 HER2-directed regimens, may also benefit from N+C. No new safety signals were noted. Clinical Trial Registration: NCT01808573
Mathematical Model With Phosphate Activation Effect Validates Batch (R)-phenylacetylcarbinol Biotransformation Process Utilizing Candida Tropicalis Pyruvate Decarboxylase in Phosphate Buffer&nbsp;
Authors: Khemacheewakul Julaluk , Taesuwan Siraphat , Nunta Rojarej , Techapun Charin , Phimolsiripol Yuthana , Rachtanapun Pornchai , Jantanasakulwong Kittisak , Porninta Kritsadaporn , Sommanee Sumeth , Mahakuntha Chatchadaporn , Chaiyaso Thanongsak , Seesuriyachan Phisit , Reungsang Alissara , Trinh Ngoc Thao Ngan , Wangtueai Sutee , Sommano Sarana Rose , Leksawasdi Noppol 
Published: April 2021

Abstract
The new (R) - phenylacetylcarbinol (PAC) batch biotransformation kinetics for partially purified Candida tropicalis TISTR 5350 pyruvate decarboxylase (PDC) were characterized and validated with a comprehensive mathematical model in 250 mL scale with 250 mM phosphate buffer / pH 7.0. PDC could convert initial 100 / 120 mM benzaldehyde / pyruvate substrates to the statistical significantly highest (p £ 0.05) maximum PAC concentration (95.8 ± 0.1 mM) and production rate (0.639 ± 0.001 mM min-1). A parameter search strategy aimed at minimizing overall residual sum of square (RSST) based on a system of six ordinary differential equations was applied to PAC biotransformation profiles with initial benzaldehyde / pyruvate concentration of 100/120 and 30/36 mM. Ten important biotransformation kinetic parameters were then elucidated including the zeroth order activation rate constant due to phosphate buffer species (ka) of (9.38 ± < 0.01) × 10-6 % relative PDC activity min-1 mM-1. The validation of this model to independent biotransformation kinetics with initial benzaldehyde / pyruvate concentration of 50 / 60 mM resulted in relatively good fitting with RSST, mean sum of square error (MSE), and coefficient of determination (R2) values of 662, 17.4, and 0.9863, respectively.Novelty: The existing (R) - phenylacetylcarbinol (PAC) biotransformation model in literatures did not include activation effect of buffering species into the enzyme deactivating rate equation, thereby background deactivation and buffering activation effects could not be discerned. A new mathematical model which incorporated activation effect, using 250 mM phosphate buffer as an example, was able to predict and validate PAC batch biotransformation systems reasonably well and could pave the way for model applications in more complex processes.
Intra-articular Injection of SHP2&nbsp;Inhibitor SHP099&nbsp;Promotes the Repair of Rabbit Full-thickness Cartilage Defect
Authors: Sun Ziying , Xu Xingquan , Lv Zhongyang , Li Jiawei , Sun Heng , Sun Kuoyang , Tan Guihua , Yan Wenqiang , Yang Yannick Xiaofan , Wu Rui , Xu Jia , Guo Hu , Jiang Qing , Shi Dongquan 
Published: April 2021

Abstract
Background Cartilage repair has been a challenge in the field of orthopedics for decades, highlighting the great significance of investigating potential therapeutic drugs. In this study, we explored the effect of SHP2 inhibitor, SHP099, as a small molecule drug on cartilage repair.Methods Human synovial mesenchymal stem cells (SMSCs) were isolated and their three-way differentiation potential was examined. After treated with chondrogenic medium, the chondrogenic effect of SHP099 on SMSCs was examined by Western blot, qPCR, and immunofluorescence (IF). To explore chondrogenic effects of SHP099 in vivo, full-thickness cartilage defects with microfracture were constructed in the right femoral trochlear of New Zealand White rabbits. Intra-articular injection of SHP099 or normal saline were performed twice a week for 6 weeks. Cartilage repair were evaluated by hematoxylin and eosin (H&E) staining, Safranin O/Fast Green staining. Immunohistochemistry (IHC) for collagen II (COL2) was also conducted to verify the abandance of cartilage extracellular matrix after SHP099 treatment. The mechanism involving yes associated protein (YAP) and WNT signaling was investigated in vitro.Result The SMSCs isolated from human synovium represented optimal multi-differentiation potential. SHP099 increased chondrogenic markers (SOX9, COL2) expression and decreased hypertrophic markers (COL10, RUNX2) in SMSCs. The inhibition of YAP and WNT signaling was also observed. Moreover, compared with the normal saline group at 6 weeks, intra-articular injection of SHP099 resulted in better defect filling which formed more hyaline cartilage-like tissue with more glycosaminoglycan (GAG) and COL2.Conclusion SHP099 promotes the repair of rabbit full-thickness cartilage defect, representing a potential therapeutic drug for cartilage repair.
Detecting global influence of transcription factor interactions on gene expression in lymphoblastoid cells using neural network models
Authors: Patel Neel , Bush William S. 
Published: April 2021

Abstract
Background Transcription factor(TF) interactions are known to regulate target gene(TG) expression in eukaryotes via TF regulatory modules(TRMs). Such interactions can be formed due to co-localizing TFs binding proximally to each other in the DNA sequence or over long distances between distally binding TFs via chromatin looping. While the former type of interaction has been characterized extensively, long distance TF interactions are still largely understudied. Furthermore, most prior approaches have focused on characterizing physical TF interactions without accounting for their effects on TG expression regulation. Understanding TRM based TG expression regulation could aid in understanding diseases caused by disruptions to these mechanisms. In this paper, we present a novel neural network based TRM detection approach that consists of using multi-omics TF based regulatory mechanism information to generate features for building non-linear multilayer perceptron TG expression prediction models in the GM12878 immortalized lymphoblastoid cells.Results We estimated main effects of 149 individual TFs and interaction effects of 48 distinct combinations of TFs forming TRMs based on their influence on TG expression. We identified several well-known and discovered multiple previously uncharacterized TF interactions within our detected set of TRMs. We further characterized the pairwise TRMs using long distance chromatin looping and motif co-occurrence data. We found that nearly all the TFs constituting TRMs detected by our approach interacted via chromatin looping, and that these TFs further interacted with promoters to influence TG expression through one of four possible regulatory configurations. Conclusion Here, we have provided a framework for detecting TRMs using neural network models containing multi-omics TF based regulatory features. We have also described these TRMs based on their regulatory potential along with presenting evidence for the possibility of TF interactions forming the TRMs occurring via chromatin looping.
Identifying potential novel insights for COVID-19 pathogenesis and therapeutics using an integrated bioinformatics analysis of host transcriptome
Authors: El-aarag Salem , Mahmoud Amal , ElHefnawi Mahmoud 
Published: April 2021

Abstract
The molecular mechanisms underlying the pathogenesis of COVID-19 has not been fully discovered. This study aims to decipher potentially hidden parts of the pathogenesis of COVID-19, potential novel drug targets, and to identify potential drug candidates. Two gene expression profiles (GSE147507-GSE153970) were analyzed and overlapping differentially expressed genes (DEGs) were selected for which top enriched transcription factors and kinases were identified and pathway analysis was performed. Protein-protein interaction (PPI) of DEGs was constructed, hub genes were identified and module analysis was also performed. DGIdb database was used to identify drugs for the potential targets (hub genes and the most enriched transcription factors and kinases for DEGs). A drug-potential target network was constructed and drugs are ranked according to the degree. L1000FDW web-based utility was used to identify drugs that can reverse transcriptional profiles of COVID-19. We identified drugs currently in clinical trials and novel potential 8 drugs. Besides the well-known pathogenic pathways, It was found that axon guidance is a potential pathogenic pathway. Sema7A, which may exacerbate hypercytokinemia, is considered a potential novel drug target. Another potential novel pathway is related to TINF2 overexpression which may induce potential telomere dysfunction and hence DNA damage that may exacerbate lung fibrosis.