bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Study of Trajectory Tracking Control for Automated Vehicles via Model Predictive Control and Robust H-infinity State Feedback Control
Authors: Yang Kai , Tang Xiaolin , Qin Yechen , Huang Yanjun , Wang Hong , Pu Huayan 
Published: August 2021

AbstractA comparative study of model predictive control (MPC) schemes and robust$$H_{\infty }$$H∞state feedback control (RSC) method for trajectory tracking is proposed in this paper. The main objective of this paper is to compare MPC and RSC controllers’ performance in tracking predefined trajectory under different scenarios. MPC controller is designed based on the simple longitudinal-yaw-lateral motions of a single-track vehicle with a linear tire, which is an approximation of the more realistic model of a vehicle with double-track motion with a non-linear tire mode. RSC is designed on the basis of the same method as adopted for the MPC controller to achieve a fair comparison. Then, three test cases are built in CarSim-Simulink joint platform. Specifically, the verification test is used to test the tracking accuracy of MPC and RSC controller under well road conditions. Besides, the double lane change test with low road adhesion is designed to find the maximum velocity that both controllers can carry out while guaranteeing stability. Furthermore, an extreme curve test is built where the road adhesion changes suddenly, in order to test the performance of both controllers under extreme conditions. Finally, the advantages and disadvantages of MPC and RSC under different scenarios are also discussed.
Regional cerebral blood flow as predictor of response to occipital nerve block in cluster headache
Authors: Medina Sonia , Bakar Norazah Abu , O’Daly Owen , Miller Sarah , Makovac Elena , Renton Tara , Williams Steve C. R. , Matharu Manjit , Howard Matthew A. 
Published: August 2021

AbstractBackgroundCluster headache is an excruciating disorder with no cure. Greater occipital nerve blockades can transiently suppress attacks in approximately 50% of patients, however, its mechanism of action remains uncertain, and there are no reliable predictors of treatment response. To address this, we investigated the effect of occipital nerve blockade on regional cerebral blood flow (rCBF), an index of brain activity, and differences between treatment responders and non-responders. Finally, we compared baseline perfusion maps from patients to a matched group of healthy controls.Methods21 male, treatment-naive patients were recruited while in a cluster headache bout. During a pain-free phase between headaches, patients underwent pseudo-continuous arterial spin labelled MRI assessments to provide quantitative indices of rCBF. MRIs were performed prior to and 7-to-21 days following treatment. Patients also recorded the frequency of their headache attacks in a daily paper diary. Neuropsychological assessment including anxiety, depression and quality of life measures was performed in a first, scanning free session for each patient.ResultsFollowing treatment, patients demonstrated relative rCBF reductions in posterior temporal gyrus, cerebellum and caudate, and rCBF increases in occipital cortex. Responders demonstrated relative rCBF increases, compared to non-responders, in medial prefrontal cortex and lateral occipital cortex at baseline, but relative reductions in cingulate and middle temporal cortices. rCBF was increased in patients compared to healthy controls in cerebellum and hippocampus, but reduced in orbitofrontal cortex, insula and middle temporal gyrus.ConclusionsWe provide new mechanistic insights regarding the aetiology of cluster headache, the mechanisms of action of occipital nerve blockades and potential predictors of treatment response. Future investigation should determine whether observed effects are reproducible and extend to other headache disorders.
Global Survey of Alternative Splicing in Rice by Direct RNA Sequencing During Reproductive Development: Landscape and Genetic Regulation
Authors: Li Haoxuan , Li Aixuan , Shen Wei , Ye Nenghui , Wang Guanqun , Zhang Jianhua 
Published: August 2021

AbstractAlternative splicing is a widespread phenomenon, which generates multiple isoforms of the gene product. Reproductive development is the key process for crop production. Although numerous forms of alternative splicing have been identified in model plants, large-scale study of alternative splicing dynamics during reproductive development in rice has not been conducted. Here, we investigated alternative splicing of reproductive development of young panicles (YP), unfertilized florets (UF) and fertilized florets (F) in rice using direct RNA sequencing, small RNA sequencing, and degradome sequencing. We identified a total of 35,317 alternative splicing (AS) events, among which 67.2% splicing events were identified as novel alternative splicing events. Intron retention (IR) was the most abundant alternative splicing subtype. Splicing factors that differentially expressed and alternatively spliced could result in global alternative splicing. Global analysis of miRNAs-targets prediction revealed that alternative spliced transcripts affected miRNAs’ targets during development. Degradome sequencing detected only 6.8% of the differentially alternative splicing transcripts, suggesting a productive transcripts generation during development. In addition, alternative splicing isoforms of Co-like, a transcription factor, interacted with Casein kinase 1-like protein HD1 (CKI) examined in luciferase assay, which could modulate normal male-floral organs development and flowering time. These results reveal that alternative splicing is intensely associated with developmental stages, and a high complexity of gene regulation.
Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation
Authors: Schäffer Alejandro A. , McVeigh Richard , Robbertse Barbara , Schoch Conrad L. , Johnston Anjanette , Underwood Beverly A. , Karsch-Mizrachi Ilene , Nawrocki Eric P. 
Published: August 2021

AbstractBackgroundThe DNA sequences encoding ribosomal RNA genes (rRNAs) are commonly used as markers to identify species, including in metagenomics samples that may combine many organismal communities. The 16S small subunit ribosomal RNA (SSU rRNA) gene is typically used to identify bacterial and archaeal species. The nuclear 18S SSU rRNA gene, and 28S large subunit (LSU) rRNA gene have been used as DNA barcodes and for phylogenetic studies in different eukaryote taxonomic groups. Because of their popularity, the National Center for Biotechnology Information (NCBI) receives a disproportionate number of rRNA sequence submissions and BLAST queries. These sequences vary in quality, length, origin (nuclear, mitochondria, plastid), and organism source and can represent any region of the ribosomal cistron.ResultsTo improve the timely verification of quality, origin and loci boundaries, we developed Ribovore, a software package for sequence analysis of rRNA sequences. The and programs are used to validate incoming sequences of bacterial and archaeal SSU rRNA. The program is used to create high-quality datasets of rRNAs from different taxonomic groups. Key algorithmic steps include comparing candidate sequences against rRNA sequence profile hidden Markov models (HMMs) and covariance models of rRNA sequence and secondary-structure conservation, as well as other tests. Nine freely available rRNA databases created and maintained with Ribovore are used for checking incoming GenBank submissions and used by the browser interface at NCBI. Since 2018, Ribovore has been used to analyze more than 50 million prokaryotic SSU rRNA sequences submitted to GenBank, and to select at least 10,435 fungal rRNA RefSeq records from type material of 8350 taxa.ConclusionRibovore combines single-sequence and profile-based methods to improve GenBank processing and analysis of rRNA sequences. It is a standalone, portable, and extensible software package for the alignment, classification and validation of rRNA sequences. Researchers planning on submitting SSU rRNA sequences to GenBank are encouraged to download and use Ribovore to analyze their sequences prior to submission to determine which sequences are likely to be automatically accepted into GenBank.
The baculum affects paternity success of first but not second males in house mouse sperm competition
Authors: Winkler Lennart , Lindholm Anna K. , Ramm Steven A. , Sutter Andreas 
Published: August 2021

AbstractThe vast variation observed in genital morphology is a longstanding puzzle in evolutionary biology. Studies showing that the morphology of the mammalian baculum (penis bone) can covary with a male’s paternity success indicate a potential impact of baculum morphology on male fitness, likely through influencing sperm competition outcomes. We therefore measured the size (measurements of length and width) and shape (geometric morphometric measurements) of the bacula of male house mice used in previously published sperm competition experiments, in which two males mated successively with the same female in staged matings. This enabled us to correlate baculum morphology with sperm competition success, incorporating potential explanatory variables related to copulatory plugs, male mating behavior and a selfish genetic element that influences sperm motility. We found that a wider baculum shaft increased a male’s paternity share when mating first, but not when mating second with a multiply-mating female. Geometric morphometric shape measurements were not clearly associated with fertilization success for either male. We found limited evidence that the effect of baculum morphology on male fertilization success was altered by experimental removal of the copulatory plug. Furthermore, neither genetic differences in sperm motility, nor covariation with male mating behavior mediated the effect of baculum morphology on male fertilization success. Taken together with previous findings, the mating-order effects we found here suggest that baculum-mediated stimulation by the first male might be particularly important for fertilization.
Mapping of quantitative trait loci underlying a magic trait in ongoing ecological speciation
Authors: Takahashi Tetsumi , Nagano Atsushi J. , Sota Teiji 
Published: August 2021

Abstract
Background
Telmatochromis temporalis is a cichlid fish endemic to Lake Tanganyika. The normal and dwarf morphs of this fish are a clear example of ongoing ecological speciation, and body size plays an important role in this speciation event as a magic trait. However, the genetic basis underlying this trait has not been studied.

Results
Based on double-digested restriction-site associated DNA (ddRAD) sequencing of a hybrid cross between the morphs that includes F0 male, F0 female, and 206 F2 individuals, we obtained a linkage map consisting of 708 ddRAD markers in 22 linkage groups, which corresponded to the previously reported Oreochromis niloticus chromosomes, and identified one significant and five suggestive quantitative trait loci (QTL) for body size. From the body-size distribution pattern, the significant and three of the five suggestive QTL are possibly associated with genes responsible for the difference in body size between the morphs.

Conclusions
The QTL analysis presented here suggests that multiple genes, rather than a single gene, control morph-specific body size. The present results provide further insights about the genes underlying the morph specific body size and evolution of the magic trait during ecological speciation.
Comparative ribosome profiling reveals distinct translational landscapes of salt-sensitive and -tolerant rice
Authors: Yang Xiaoyu , Song Bo , Cui Jie , Wang Lina , Wang Shuoshuo , Luo Linlin , Gao Lei , Mo Beixin , Yu Yu , Liu Lin 
Published: August 2021

Abstract
Background
Soil salinization represents a serious threat to global rice production. Although significant research has been conducted to understand salt stress at the genomic, transcriptomic and proteomic levels, few studies have focused on the translatomic responses to this stress. Recent studies have suggested that transcriptional and translational responses to salt stress can often operate independently.

Results
We sequenced RNA and ribosome-protected fragments (RPFs) from the salt-sensitive rice (O. sativa L.) cultivar ‘Nipponbare’ (NB) and the salt-tolerant cultivar ‘Sea Rice 86’ (SR86) under normal and salt stress conditions. A large discordance between salt-induced transcriptomic and translatomic alterations was found in both cultivars, with more translationally regulated genes being observed in SR86 in comparison to NB. A biased ribosome occupancy, wherein RPF depth gradually increased from the 5′ ends to the 3′ ends of coding regions, was revealed in NB and SR86. This pattern was strengthened by salt stress, particularly in SR86. On the contrary, the strength of ribosome stalling was accelerated in salt-stressed NB but decreased in SR86.

Conclusions
This study revealed that translational reprogramming represents an important layer of salt stress responses in rice, and the salt-tolerant cultivar SR86 adopts a more flexible translationally adaptive strategy to cope with salt stress compared to the salt susceptible cultivar NB. The differences in translational dynamics between NB and SR86 may derive from their differing levels of ribosome stalling under salt stress.
Disturbed microbial ecology in Alzheimer’s disease: evidence from the gut microbiota and fecal metabolome
Authors: Xi Jianxiong , Ding Ding , Zhu Huiwei , Wang Ruru , Su Feng , Wu Wanqing , Xiao Zhenxu , Liang Xiaoniu , Zhao Qianhua , Hong Zhen , Fu Hua , Xiao Qianyi 
Published: August 2021

Abstract
Background
Gut microbiota (GMB) alteration has been reported to influence the Alzheimer’s disease (AD) pathogenesis through immune, endocrine, and metabolic pathways. This study aims to investigate metabolic output of the dysbiosis of GMB in AD pathogenesis. In this study, the fecal microbiota and metabolome from 21 AD participants and 44 cognitively normal control participants were measured. Untargeted GMB taxa was analyzed through 16S ribosomal RNA gene profiling based on next-generation sequencing and fecal metabolites were quantified by using ultrahigh performance liquid chromatography-mass spectrometry (UPLC-MS).

Results
Our analysis revealed that AD was characterized by 15 altered gut bacterial genera, of which 46.7% (7/15 general) was significantly associated with a series of metabolite markers. The predicted metabolic profile of altered gut microbial composition included steroid hormone biosynthesis, N-Acyl amino acid metabolism and piperidine metabolism. Moreover, a combination of 2 gut bacterial genera (Faecalibacterium and Pseudomonas) and 4 metabolites (N-Docosahexaenoyl GABA, 19-Oxoandrost-4-ene-3,17-dione, Trigofoenoside F and 22-Angeloylbarringtogenol C) was able to discriminate AD from NC with AUC of 0.955 in these 65 subjects.

Conclusions
These findings demonstrate that gut microbial alterations and related metabolic output changes may be associated with pathogenesis of AD, and suggest that fecal markers might be used as a non-invasive examination to assist screening and diagnosis of AD.
OrchidBase 4.0: a database for orchid genomics and molecular biology
Authors: Hsiao Yu-Yun , Fu Chih-Hsiung , Ho Sau-Yee , Li Chung-I , Chen You-Yi , Wu Wan-Lin , Wang Jeen-Shing , Zhang Di-Yang , Hu Wen-Qi , Yu Xia , Sun Wei-Hong , Zhou Zhuang , Liu Ke-Wei , Huang Laiqiang , Lan Si-Ren , Chen Hong-Hwa , Wu Wei-Sheng , Liu Zhong-Jian , Tsai Wen-Chieh 
Published: August 2021

AbstractBackgroundThe Orchid family is the largest families of the monocotyledons and an economically important ornamental plant worldwide. Given the pivotal role of this plant to humans, botanical researchers and breeding communities should have access to valuable genomic and transcriptomic information of this plant. Previously, we established OrchidBase, which contains expressed sequence tags (ESTs) from different tissues and developmental stages ofPhalaenopsisas well as biotic and abiotic stress-treatedPhalaenopsis. The database includes floral transcriptomic sequences from 10 orchid species across all the five subfamilies of Orchidaceae.DescriptionRecently, the whole-genome sequences ofApostasia shenzhenica,Dendrobium catenatum, andPhalaenopsis equestriswere de novo assembled and analyzed. These datasets were used to develop OrchidBase 4.0, including genomic and transcriptomic data for these three orchid species. OrchidBase 4.0 offers information for gene annotation, gene expression with fragments per kilobase of transcript per millions mapped reads (FPKM), KEGG pathways and BLAST search. In addition, assembled genome sequences and location of genes and miRNAs could be visualized by the genome browser. The online resources in OrchidBase 4.0 can be accessed by browsing or using BLAST. Users can also download the assembled scaffold sequences and the predicted gene and protein sequences of these three orchid species.ConclusionsOrchidBase 4.0 is the first database that contain the whole-genome sequences and annotations of multiple orchid species. OrchidBase 4.0 is available athttp://orchidbase.itps.ncku.edu.tw/
Association between cytochrome P450 2C19 polymorphism and clinical outcomes in clopidogrel-treated Uygur population with acute coronary syndrome: a retrospective study
Authors: Yu Luhai , Wang Tingting , Bai Huidong , Zhu Weijiang , Li Yanju , Wu Jianhua , Liu Wenli , Sun Li , Yu Aiping , Li Hongjian 
Published: August 2021

AbstractBackgroundAcute coronary syndrome (ACS) has become a vital disease with high mortality in the Uygur populations. Clopidogrel plays an important role in reducing the risk of recurrent cardiovascular events after ACS; however, it is a prodrug that requires biotransformation by cytochromeP450(CYP450).ObjectivesTo determine the effect of genetic polymorphisms inCYP2C19*2,*3,and*17, and along with clinical, demographic factors, on variation in response to clinical outcomes in Uygur patients.MethodsA total of 351 patients with ACS were treated with clopidogrel and aspirin for at least 12 months; we recorded major adverse cardiovascular events (MACE) or bleeding within 1 year. Multivariable logistic regression analyses were carried out to identify factors associated with MACE or bleeding.ResultsWe analyze risk factors include age, BMI (body mass index), smoking, alcohol intake, NSTEMI (non-ST-segment elevation myocardial infarction), hypertension, dyslipidemia, concomitant medication,CYP2C19*2carriers,CYP2C19*17carriers and metabolizer phenotype.CYP2C19*2carriers had an odds of having MACE of 2.51 (95% CI: 1.534–4.09) compared with noncarriers (P < .001). However, no factors were significantly associated with bleeding (P > 0.05).ConclusionTheCYP2C19*2gene polymorphism contributes to the risk of MACE in dual clopidogrel—treated Uygur population with ACS with or without PCI (percutaneous coronary intervention). These data may provide valuable insights into the genetic polymorphisms affecting clopidogrel metabolism among minority groups in China.
A case report of COVID-19 in a patient with non-Hodgkin’s lymphoma
Authors: Eilami Owrang , Lopes Max Igor Banks Ferreira , Gryschek Ronaldo Cesar Borges , Taghipour Kaveh 
Published: August 2021

Abstract
Background
The current literature is scarce as to the outcomes of COVID-19 infection in non-Hodgkin's lymphoma patients and whether immunosuppressive or chemotherapeutic agents can cause worsening of the patients’ condition during COVID-19 infection.

Case presentation
Our case is a 59-year-old gentleman who presented to the Emergency Department of the Cancer Institute of Hospital das Clínicas da Universidade de São Paulo, São Paulo, Brazil on 10th May 2020 with a worsening dyspnea and chest pain which had started 3 days prior to presentation to the Emergency Department. He had a past history of non-Hodgkin's lymphoma for which he was receiving chemotherapy. Subsequent PCR testing demonstrated that our patient was SARS-CoV-2 positive.

Conclusion
In this report, we show a patient with non-Hodgkin lymphoma in the middle of chemotherapy, presented a mild clinical course of COVID-19 infection.
Non-fermentative gram-negative bloodstream infection in northern Italy: a multicenter cohort study
Authors: Pascale Renato , Corcione Silvia , Bussini Linda , Pancaldi Livia , Giacobbe Daniele Roberto , Ambretti Simone , Lupia Tommaso , Costa Cristina , Marchese Anna , De Rosa Francesco Giuseppe , Bassetti Matteo , Viscoli Claudio , Bartoletti Michele , Giannella Maddalena , Viale Pierluigi 
Published: August 2021

Abstract
Background
The management of non-fermentative gram-negative bloodstream infection (NFGN-BSI) offers numerous challenges. In this study the aim is to analyse a large cohort of patients with NFGN-BSI recruited in the northern Italy to describe epidemiology, etiological and susceptibility pattern, therapeutic management and outcome.

Methods
Multicentre retrospective cohort study of patients hospitalised at three large teaching hospitals in northern Italy in a fourth year period.

Results
355 BSI episodes were analyzed, due to P. aeruginosa (72.7%), A. baumannii (16.6%), and Stenotrophomonas maltophilia (10.7%). Overall, 21.4% of isolates were defined as DTR, highest rate among A. baumannii (64.4%). All-cause 30-day mortality rate was 17.5%. Rates of XDR or DTR A. baumannii isolation were significantly higher in non-surviving patients. Independent risk factors for 30-day mortality were: age (HR 1.03, 95%CI 1.00–1.04, p = 0.003), septic shock (HR 2.84, 95%CI 1.67–4.82, p < 0.001) and BSI due to Acinetobacter baumannii (HR 2.23, 95%CI 1.27–3.94, p = 0.005).

Conclusion
The overall prevalence of DTR was high in the NFGN BSI cohort analyzied, mainly among Acinetobacter baumannii episodes (64.4%). Acinetobacter baumannii is showed to be an independent predictor of mortality. These evidences marked the urgent need of new therapeutic options against this pathogen.
Trial registration number: 79/2017/O/OssN. Approved: March14th, 2017.
The accumulation of plasma acylcarnitines are associated with poor immune recovery in HIV-infected individuals
Authors: Qian Shi , Chen Xi , Wu Tong , Sun Yu , Li Xiaolin , Fu Yajing , Zhang Zining , Xu Junjie , Han Xiaoxu , Ding Haibo , Jiang Yongjun 
Published: August 2021

Abstract
Background
Antiretroviral therapy (ART) can reduce opportunistic infections and mortality rates among individuals infected with human immunodeficiency virus (HIV); however, some HIV-infected individuals exhibit poor immune recovery after ART. Hence, we explored the association between metabolome profiles and immune recovery in HIV-infected individuals following ART.

Methods
An untargeted metabolomics approach was used to analyze plasma samples from 18 HIV-negative individuals and 20 HIV-infected individuals, including 10 immunological non-responders (INR, CD4+ T cell rise < 100 cells/μl) and 10 immunological responders (IR, CD4+ T cell rise > 300 cells/μl) after 2 years of ART. These individuals were followed for the next 6 years and viral loads and CD4+ T cell count were measured regularly. Orthogonal projection on latent structures discriminant analysis (OPLS-DA), ANOVA, correlation, receiver operating characteristic (ROC), and survival analyses were used for selection of discriminant metabolites.

Results
Eighteen lipid metabolites were identified which could distinguish among control, INR, and IR groups. Among them, myristoylcarnitine (MC), palmitoylcarnitine (PC), stearoylcarnitine (SC), and oleoylcarnitine (OC) were significantly elevated in INR plasma samples compared with those from the IR and control groups and were negatively associated with CD4+ T cell count. Additionally, ROC analysis using a combination of MC, PC, SC, and OC had high sensitivity and specificity for differentiating INR from IR (AUC = 0.94). Finally, survival analysis for the combination of MC, PC, SC, and OC demonstrated that it could predict CD4+ T cell count in patients undergoing long-term ART.

Conclusions
High levels of lipid metabolites, MC, PC, SC, and OC are associated with poor immune recovery in patients receiving ART and these data provide potential new insights into immune recovery mechanisms.