bluuebunny/crossref_metadata_2025 huggingface dataset:
Changes in ocular pulse amplitude and choroidal thickness in childhood obesity patients with and without insulin resistance
Authors: Aydemir Gözde Aksoy , Aydemir Emre , Asik Abdulvahit , Bolu Semih
Published: August 2021

Purpose:

To compare choroidal thickness (CT) and ocular pulse amplitude (OPA) in childhood obesity with insulin resistance (IR) and without IR.

Methods:

Seventy-three childhood obesity and 62 healthy children, who were both age-matched and gender-matched, comprised the study population in this prospective study. Obesity was determined as having a body mass index (BMI) – standard deviation (SD) score that was > 2 SD. Intraocular pressure (IOP) and OPA were measured using a dynamic contour tonometer. The CT measurements were performed using enhanced depth imaging optical coherence tomography at three locations, comprising at the fovea, at a position 500 µm nasal, and also at a position 500 µm temporal to the fovea.

Results:

Mean BMI value was 28.72 ± 4.85 in the patients with childhood obesity and 21.47 ± 1.14 in the control group. The mean IOP and OPA values were determined 15.90 ± 2.30 and 14.10 ± 2.16 mm Hg, 1.50 ± 0.28 and 1.74 ± 0.32 mm Hg in the patients with childhood obesity and the control group, respectively ( p < 0.001, p < 0.001). The mean subfoveal CT value was 350.50 ± 81.51 μm in the eyes with childhood obesity and 390.02 ± 71.50 μm in those of the control group ( p = 0.003). When the patient groups with and without IR were compared, no significant difference was found between CT, OPA and IOP values ( p > 0.005).

Conclusions:

Our results showed that both OPA and CT values were significantly decreased in childhood obesity patients. We suggest further studies to verify longitudinal changes in OPA and CT, as also the evaluation of these parameters in other populations.
Ocrelizumab treatment for relapsing-remitting multiple sclerosis after a suboptimal response to previous disease-modifying therapy: A nonrandomized controlled trial
Authors: Weinstock-Guttman Bianca , Bermel Robert , Cutter Gary , Freedman Mark S , Leist Thomas P , Ma Xiaoye , Kile Deidre , Musch Bruno , Reder Anthony T , Wolinsky Jerry S
Published: August 2021

Background:

Many patients with multiple sclerosis (MS) experience suboptimal disease control despite the use of disease-modifying therapy (DMT).

Objective:

To assess the efficacy and safety of ocrelizumab (OCR) in patients with relapsing-remitting MS (RRMS) and suboptimal response to prior DMTs.

Methods:

Patients with RRMS and suboptimal responses (one clinically reported relapse and/or lesion activity) after ⩾ 6 months on another DMT were enrolled. OCR 600 mg was given intravenously every 24 weeks. The primary outcome was no evidence of disease activity (NEDA), defined as the absence of protocol-defined relapse, confirmed disability progression (CDP), T1 Gd-enhancing lesions, and new/enlarging T2 lesions.

Results:

The intention-to-treat (ITT) population included 608 patients; NEDA was analyzed in a modified ITT (mITT) population ( n = 576 (94.7%)). Over 96 weeks, 48.1% of mITT patients achieved NEDA, and most were free from protocol-defined relapse (89.6%), CDP (89.6%), and T1 Gd-enhancing lesions (95.5%); 59.5% had no new/enlarging T2 lesions. Safety observations were consistent with findings in the pivotal trials.

Conclusion:

Consistent efficacy of OCR on clinical and magnetic resonance imaging (MRI) disease activity measures and progression was shown in patients with RRMS and a suboptimal response to prior DMTs; no new safety signals were observed.
The socialization of hallucinations: Cultural priors, social interactions, and contextual factors in the use of psychedelics
Authors: Dupuis David
Published: August 2021

The effects of so-called “psychedelic” or “hallucinogenic” substances are known for their strong conditionality on context. While the so-called culturalist approach to the study of hallucinations has won the favor of anthropologists, the vectors by which the features of visual and auditory imagery are structured by social context have been so far little explored. Using ethnographic data collected in a shamanic center of the Peruvian Amazon and an anthropological approach dialoguing with phenomenology and recent models of social cognition of Bayesian inspiration, I aim to shed light on the nature of these dynamics through an approach I call the “socialization of hallucinations.” Distinguishing two levels of socialization of hallucinations, I argue that cultural background and social interactions organize the relationship not only to the hallucinogenic experience, but also to its very phenomenological content. I account for the underpinnings of the socialization of hallucinations proposing such candidate factors as the education of attention, the categorization of perceptions, and the shaping of emotions and expectations. Considering psychedelic experiences in the light of their noetic properties and cognitive penetrability debates, I show that they are powerful vectors of cultural transmission. I question the ethical stakes of this claim, at a time when the use of psychedelics is becoming increasingly popular in the global North. I finally emphasize the importance of better understanding the extrapharmacological factors of the psychedelic experience and its subjective implications, and sketch out the basis for an interdisciplinary methodology in order to do so.
Numerical and analytical investigation on the moment and deformation capacity of interior slab-column connections without shear reinforcement
Authors: Tang Ming , Yi Wei-Jian , Chen Hui , Wu Yue-Fan
Published: August 2021

In this study, nonlinear finite element analyses of reinforced concrete interior slab-column connections were performed to investigate their punching shear behavior under gravity and lateral loads without shear reinforcement. A numerical model based on the concrete damaged plasticity (CDP) model in ABAQUS was developed with suitable constitutive models for concrete and reinforcements using eight-node brick elements with reduced integration and three-dimensional truss elements, respectively. The model was calibrated in comparison with the test results of an interior slab-column connection without shear reinforcement. Moreover, the validity of the calibrated model was verified using other test results. Then, a parametric study was conducted to examine the influence of different design variables on the unbalanced moment and deformation capacity of slab-column connections. Finally, based on the existing experimental data and finite element analysis results obtained in this work, formulas for calculating the ultimate unbalanced moment and drift ratio were proposed using the nonlinear fitting method. The proposed formulas were compared with the existing methods provided by other national codes and researchers, verifying the rationality of the proposed formulas.
Predicting the dynamic response of a structure using an artificial neural network
Authors: Birky Donovan , Ladd Joshua , Guardiola Ivan , Young Andrew
Published: August 2021

Machine learning and artificial intelligence has been applied to other facets of structural mechanics and structural dynamics, mainly for structural optimization and structural reliability analysis, but have seen little use in surrogate modeling for structural time series prediction. The current research will focus on how data reduction tools (such as mathematical morphology) can be applied to dynamic structural data and can be used in conjunction with clustering methodologies as well as artificial neural networks (ANNs) to create a useful and highly computationally efficient dynamic model that can be used to make predictions on the acceleration response of a structural system. The current study utilizes training data developed from finite element modeling of a simple system that demonstrates a nonlinear behavior of interest (a change in the dynamic response with a change in loading magnitude), but the methodologies developed could be applied to other modeling or analysis schemes, test data, or in-situ measurements of a structure of interest. The results of the study show how mathematical morphology tools can reduce the dimensionality of time series data while still preserving important characteristics like natural frequency, and the use of ANNs shows promise as a surrogate model for dynamic response prediction.
Prediction of yarn unevenness based on BMNN
Authors: Jiang Hao , Song Jiuxiang , Zhang Baowei , Zhao Suna , Wang Yonghua
Published: August 2021

With the continuous development of deep learning, due to the complexity of the deep neural network structure and the limitation of training time, some scholars have proposed broad learning, the Broad Learning System (BLS). However, BLS currently only verifies that it has excellent effects on some of the network training data sets, and it does not necessarily have excellent effects on some actual data sets. In response to this, this paper uses the effect of BLS in predicting the unevenness of yarn quality in the yarn data set, and proposes a BLS-based multi-layer neural network (MNN) for the problems, which is called Broad Multilayer Neural Network (BMNN).
Dynamic input loads evaluation of a recreational vehicle frame using multibody dynamics hybrid modeling validated with experimental and full analytical modeling data
Authors: Blanchette Carl , Boisvert Maxime , Joubert Nicolas , Rancourt Denis , Desrochers Alain
Published: August 2021

Knowledge of frame loads at the limits of the intended driving conditions is important during the design process of a vehicle structure. Yet, retrieving these loads is not trivial as the load path between the road and the frame mounting point is complex. Fortunately, recent studies have shown that multibody dynamic (MBD) simulations could be a powerful tool to estimate these loads. Two main categories of MBD simulations exist. Firstly, full analytical simulations, which have received great attention in the literature, are run in a virtual environment using a tire model and a virtual road. Secondly, hybrid simulations, also named semi analytical, uses experimental data from Wheel Force Transducers and Inertial Measurement Units to replace the road and tire models. It is still unclear how trustworthy semi analytical simulations are for frame load evaluation. Both methods were tested for three loads cases. It was found that semi analytical simulations were slightly better in predicting vehicle dynamic and frame loads than the full analytical simulations for frequencies under the MF-Tyre model valid frequency range (8 Hz) with accuracy levels over 90%. For faster dynamic maneuvers, the prediction accuracy was lower, in the 50%–80% range, with semi analytical simulations showing better results.
Isolated giant true intercostal artery aneurysm with arteriovenous fistula: A case report
Authors: Honma Kenichi , Yamaoka Terutoshi , Matsuda Daisuke
Published: August 2021

Objectives

Intercostal artery aneurysm (IAA) is a very rare condition. Interestingly, only one study reported a case of intercostal aneurysm caused by an arteriovenous fistula (AVF). Here, we report the case of a patient with non-ruptured isolated giant true IAA caused by an AVF (size, 28 × 41 mm).

Methods

Treatment options for IAA include open surgery and endovascular treatment (EVT). We chose EVT, as it is minimally invasive. The right 11th intercostal artery and aneurysm diverged from the aorta. Two outflow arteries, one inflow artery, and an AVF from the aneurysm were confirmed, and coil embolization was performed. The artery of Adamkiewicz did not communicate with the right 11th intercostal artery. We performed angiography and confirmed occlusion of IAA with endoleak.

Results

There were no clinical findings indicative of spinal cord infarction after treatment. The patient did not develop complications and was discharged the day after treatment. Endoleak was not observed on computed tomography angiography findings at 1 month after treatment.

Conclusions

In our patient, an AVF might have caused IAA. Endovascular treatment for non-ruptured isolated giant IAA is a safe and minimally-invasive treatment. We found that performing EVT is beneficial when the size of the IAA exceeds 30 mm.
Multiple endocrine neoplasia 1: a broad overview
Authors: Thompson Rachel , Landry Christine S.
Published: August 2021

This review article discusses the diagnoses and treatment of patients with multiple endocrine neoplasia type 1 (MEN 1). The most common tumors associated with MEN 1 are located in the pancreas, pituitary, and parathyroid glands. Less common tumors include neuroendocrine tumors of the lung and thymus, adrenal tumors, and cutaneous lesions. This article describes the diagnosis, clinical manifestations, treatment, and surveillance of tumors associated with patients who are diagnosed with MEN 1.
Dual inhibition of IL-17A and IL-17F in psoriatic disease
Authors: Iznardo Helena , Puig Lluís
Published: August 2021

Psoriasis and psoriatic arthritis are chronic immune-mediated disorders with involvement of interleukin (IL)-17 cytokines in their pathogenesis. IL-17A has been considered to be the most biologically active, but IL-17F is also over-expressed in skin and synovial tissues of patients with these diseases. Many therapeutic advances have been made in the past years, but some needs remain unmet. Dual inhibitor and bispecific antibodies simultaneously targeting IL-17A and IL-17F could provide better disease control. Herein we review current evidence on bimekizumab and sonelokimab. The antigen-binding site of bimekizumab neutralizes both IL-17A and IL-17F; phase I, II, and III studies have demonstrated its efficacy and safety in psoriasis and psoriatic arthritis. Sonelokimab is a trivalent nanobody targeting IL-17A and IL-17F; phase I and II studies with this molecule have yielded promising results in psoriasis.
Who Gets Time Off? Prioritizing Planned, Family Responsibility Leave Requests
Authors: Bérubé Nicole
Published: August 2021

This role play focuses on team decision making and is designed for undergraduate and graduate human resource management (HRM) and organizational behavior (OB) courses. It can also support management seminars. Working within Employee Teams, Department Teams, or Manager Teams, students decide which three of five employees will obtain family responsibility leave. For HRM courses, the exercise focuses on interpreting and applying family responsibility leave, which illustrates day-to-day personnel planning. For OB courses, the debriefing centers on comparing decision-making models and discussing how beliefs and attitudes influence decision making; it also supports exchanges about the influence of conflict, domination, and groupthink on team decision making. For both OB and HRM courses, the exercise helps students compare individual and team decisions, discuss the effects of team composition on decision making, and analyze the fairness of their decisions. Instructors can conduct the activity in class or online.
Randomised controlled trial of a prognostic assessment and management pathway to reduce the length of hospital stay in normotensive patients with acute pulmonary embolism
Authors: Jiménez David , Rodríguez Carmen , León Francisco , Jara-Palomares Luis , López-Reyes Raquel , Ruiz-Artacho Pedro , Elías Teresa , Otero Remedios , García-Ortega Alberto , Rivas-Guerrero Agustina , Abelaira Jaime , Jiménez Sonia , Muriel Alfonso , Morillo Raquel , Barrios Deisy , Le Mao Raphael , Yusen Roger D. , Bikdeli Behnood , Monreal Manuel , Lobo José Luis
Published: August 2021

Background

The length of hospital stay (LOS) for acute pulmonary embolism (PE) varies considerably. Whether the upfront use of a PE prognostic assessment and management pathway is effective in reducing the LOS remains unknown.

Methods

We conducted a randomised controlled trial of adults hospitalised for acute PE: patients were assigned either to a prognostic assessment and management pathway involving risk stratification followed by predefined criteria for mobilisation and discharge (intervention group) or to usual care (control group). The primary end-point was LOS. The secondary end-points were the cost of prognostic tests and of hospitalisation, and 30-day clinical outcomes.

Results

Of 500 patients who underwent randomisation, 498 were included in the modified intention-to-treat analysis. The median LOS was 4.0 days (interquartile range (IQR) 3.7–4.2 days) in the intervention group and 6.1 days (IQR 5.7–6.5 days) in the control group (p<0.001). The mean total cost of prognostic tests was EUR 174.76 in the intervention group, compared with EUR 233.12 in the control group (mean difference EUR −58.37, 95% CI EUR −84.34­ to −32.40). The mean total hospitalisation cost per patient was EUR 2085.66 in the intervention group, compared with EUR 3232.97 in the control group (mean difference EUR −1147.31, 95% CI EUR −1414.97­ to −879.65). No significant differences were observed in 30-day readmission (4.0%versus4.8%), all-cause mortality (2.4%versus2.0%) or PE-related mortality (0.8%versus1.2%) rates.

Conclusions

The use of a prognostic assessment and management pathway was effective in reducing the LOS for acute PE.
Lrig1expression identifies airway basal cells with high proliferative capacity and restricts lung squamous cell carcinoma growth
Authors: Succony Laura , Gómez-López Sandra , Pennycuick Adam , Alhendi Ahmed S.N. , Davies Derek , Clarke Sarah E. , Gowers Kate H.C. , Wright Nicholas A. , Jensen Kim B. , Janes Sam M.
Published: August 2021

Background

Lung squamous cell carcinoma (LUSC) accounts for a significant proportion of cancer deaths worldwide, and is preceded by the appearance of progressively disorganised pre-invasive lesions in the airway epithelium. Yet the biological mechanisms underlying progression of pre-invasive lesions into invasive LUSC are not fully understood.LRIG1(leucine-rich repeats and immunoglobulin-like domains 1) is downregulated in pre-invasive airway lesions and invasive LUSC tumours and this correlates with decreased lung cancer patient survival.

Methods and results

Using anLrig1knock-in reporter mouse and human airway epithelial cells collected at bronchoscopy, we show that during homeostasis LRIG1 is heterogeneously expressed in the airway epithelium. In basal airway epithelial cells, the suspected cell of origin of LUSC, LRIG1 identifies a subpopulation of progenitor cells with higherin vitroproliferative and self-renewal potential in both the mouse and human. Using the N-nitroso-tris-chloroethylurea (NTCU)-induced murine model of LUSC, we find thatLrig1loss-of-function leads to abnormally high cell proliferation during the earliest stages of pre-invasive disease and to the formation of significantly larger invasive tumours, suggesting accelerated disease progression.

Conclusion

Together, our findings identify LRIG1 as a marker of basal airway progenitor cells with high proliferative potential and as a regulator of pre-invasive lung cancer progression. This work highlights the clinical relevance of LRIG1 and the potential of the NTCU-induced LUSC model for functional assessment of candidate tumour suppressors and oncogenes.
The AWESCORE, a patient-reported outcome measure: development, feasibility, reliability, validity and responsiveness for adults with cystic fibrosis
Authors: Button Brenda M. , Wilson Lisa M. , Burge Angela T. , Kimmel Lara , Finlayson Felicity , Williams Elyssa , Talbot Anthony , Tierney Audrey , King Susannah , Holland Anne E. , Keating Dominic , Kotsimbos Tom , Wilson John W.
Published: August 2021

Background

Quality of life has improved dramatically over the past two decades in people with cystic fibrosis (CF). Quantification has been enabled by patient-reported outcome measures (PROMs); however, many are lengthy and can be challenging to use in routine clinical practice. We propose a short-form PROM that correlates well with established quality-of-life measures.

Methods

We evaluated the utility of a 10-item score (AWESCORE) by measuring reliability, validity and responsiveness in adults with CF. The questions were developed by thematic analysis of survey questions to patients in a single adult CF centre. Each question was scored using a numerical rating scale 0 to 10. Total scores ranged from 0 to 100. Test–retest reliability was assessed over 24 h. To determine validity, comparisons were sought between stable subjects and those in pulmonary exacerbation, and between AWESCORE and Cystic Fibrosis Questionnaire – Revised (CFQ-R). Responsiveness to pulmonary exacerbation in individual subjects was evaluated.

Results

Five domains, each with two questions, were identified for respiratory, physical, nutritional, psychological and general health. A total of 246 consecutive adults attending the outpatient clinic completed the AWESCORE. Scores were higher during clinical stability compared to pulmonary exacerbation (mean±sd):73±11versus48±11 (p<0.001). Each domain scored worse during an acute exacerbation (p<0.001). No differences in reliability were observed in scores on retesting using Bland–Altman comparison. The CFQ-R scores (mean±sd: 813±125) and AWESCORE (81±13) were moderately correlated (Pearson's r=0.649; p=0.002).

Conclusions

The AWESCORE is valid, reliable and responsive to altered health status in CF.
Prothrombotic state in patients with stable COPD: an observational study
Authors: Kyriakopoulos Christos , Chronis Christos , Papapetrou Evaggelia , Tatsioni Athina , Gartzonika Konstantina , Tsaousi Christina , Gogali Athena , Katsanos Christos , Vaggeli Aikaterini , Tselepi Charikleia , Daskalopoulos Georgios , Konstantopoulos Stavros , Kostikas Konstantinos , Konstantinidis Athanasios
Published: August 2021

Background

COPD patients have an increased risk of cardiovascular disease and venous thromboembolism.

Methods

This study aimed to investigate whether patients with stable COPD have a prothrombotic state compared to COPD-free smokers. We conducted an observational study comparing levels of: D-dimers, INR, aPTT, coagulation factors; fibrinogen, FII, FV, FVII, FVIII, FIX, FX and coagulation inhibitors; protein S, proteins C and antithrombin between stable COPD patients and control subjects.

Results

A total of 103 COPD patients and 42 controls with similar age, sex, current smoking status, comorbidity burden and cardiovascular risk met the inclusion criteria. Compared to controls, COPD patients had higher levels of D-dimers (median (interquartile range): 360 (230–600) ng·mL−1versus240 (180–400) ng·mL−1, p=0.001), fibrinogen (mean±sd: 399±82 mg·dL−1versus346±65 mg·dL−1, p<0.001), FII (122±22%versus109±19%, p=0.004), FV (131±25%versus121±19%, p=0.015), FVIII (143±32%versus122±20%, p<0.001) and FX (111 (94–134)%versus98 (88–107)%, p=0.002), and lower levels of protein S (95 (85–105)%versus116 (98–121)%, p<0.001) and antithrombin (94.4±11.5%versus102.3±13.2%, p=0.001). In the COPD group, patients with more severe airflow limitation and frequent exacerbations had significantly higher levels of FII, FV and FX, whereas patients with higher COPD assessment test score had significantly higher levels of FX and lower levels of protein S.

Conclusion

Patients with stable COPD exhibited increased levels of key coagulation factors and decreased levels of coagulation inhibitors, namely protein S and antithrombin, compared to COPD-free smokers. Among COPD patients, increased levels of FII, FV and FX and decreased levels of protein S were found in patients with more severe disease.
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

A 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

Background

Cluster 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.

Methods

21 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.

Results

Following 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.

Conclusions

We 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

Alternative 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

Background

The 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.

Results

To 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.

Conclusion

Ribovore 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

The 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

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

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

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

Background

The 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.

Description

Recently, 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.

Conclusions

OrchidBase 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

Background

Acute 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).

Objectives

To 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.

Methods

A 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.

Results

We 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).

Conclusion

TheCYP2C19*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

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

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

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.