bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative phylogenetic analysis and transcriptomic profiling of Dengue (DENV-3 genotype I) outbreak in 2021 in Bangladesh
Authors: Sarkar Md. Murshed Hasan , Rahman M. Shaminur , Islam M. Rafiul , Rahman Arafat , Islam Md. Shariful , Banu Tanjina Akhtar , Akter Shahina , Goswami Barna , Jahan Iffat , Habib Md. Ahashan , Uddin Mohammad Mohi , Mia Md. Zakaria , Miah Md. Ibrahim , Shaikh Aftab Ali , Khan Md. Salim
Published: June 2023

Background

The next-generation sequencing (NGS) technology facilitates in-depth study of host-pathogen metatranscriptome. We, therefore, implicated phylodynamic and transcriptomic approaches through NGS technology to know/understand the dengue virus (DENV) origin and host response with dengue fever.

Methods

In this study, blood serum RNA was extracted from 21 dengue patients and 3 healthy individuals. Total transcriptomic data were analyzed for phylogenetic, phylodynamic, differential express gene (DEG), and gene ontology (GO) using respective bioinformatics tools.

Results

The viral genome sequence revealed dengue viral genome size ranges 10647 to 10707 nucleotide. Phylogenetic and phylodynamic analysis showed that the 2021 epidemic isolates were DENV-3 genotype-I and maintained as a new clade in compared to 2019 epidemic. Transcriptome analysis showed a total of 2686 genes were DEG in dengue patients compared to control with a q-value < 0.05. DESeq2 plot counts function of the top 24 genes with the smallest q-values of differential gene expression of RNA-seq data showed that 11 genes were upregulated, whereas 13 genes were downregulated. GO analysis showed a significant upregulation (p = < 0.001) in a process of multicellular organismal, nervous system, sensory perception of chemical stimulus, and G protein-coupled receptor signaling pathways in the dengue patients. However, there were a significant downregulation (p = < 0.001) of intracellular component, cellular anatomical entity, and protein-containing complex in dengue patients. Most importantly, there was a significant increase of a class of immunoregulatory proteins in dengue patients in compared to the controls, with increased GO of immune system process. In addition, upregulation of toll receptor (TLR) signaling pathways were found in dengue patients. These TLR pathways were particularly involved for the activation of innate system coupled with adaptive immune system that probably involved the rapid elimination of dengue virus infected cells. These differentially expressed genes could be further investigated for target based prophylactic interventions for dengue.

Conclusion

This is a first report describing DENV complete genomic features and differentially expressed genes in patients in Bangladesh. These genes may have diagnostic and therapeutic values for dengue infection. Continual genomic surveillance is required to further investigate the shift in dominant genotypes in relation to viral pathogenesis.
Cross-reactive immune responses to monkeypox virus induced by MVA vaccination in mice
Authors: Gao Feixia , He Cheng , Liu Min , Yuan Ping , Tian Shihua , Zheng Mei , Zhang Linya , Zhou Xu , Xu Fangjingwei , Luo Jian , Li Xiuling
Published: June 2023

Mpox (monkeypox) infection cases increased recently in non-Mpox outbreak areas, potentially causing an international threat. The desire to defend against a potential outbreak has led to renewed efforts to develop Mpox vaccines. In this report, mice were immunized with various doses of modified vaccinia virus Ankara (MVA) to evaluate the cross-reactive immune response of MVA immunization against protective antigens of the current monkeypox virus. We demonstrated that MVA induced specific antibodies against protective antigens (A29, A35, B6, M1, H3, and I1), mediating the neutralization abilities against the MVA and the monkeypox virus (MPXV). Moreover, recombinant protective antigens of the MPXV elicited cross-binding and cross-neutralizing activities for MVA. Hence, the MVA induced cross-reactive immune responses, which may guide future efforts to develop vaccines against the recent MPXV. Notably, compared to the other protective antigens, the predominant A29 and M1 antigens mediated higher cross-neutralizing immune responses against the MVA, which could serve as antigen targets for novel orthologous orthopoxvirus vaccine.
A review of social media platform policies that address cannabis promotion, marketing and sales
Authors: Berg Carla J. , LoParco Cassidy R. , Cui Yuxian , Pannell Alexandria , Kong Grace , Griffith Lynniah , Romm Katelyn F. , Yang Y. Tony , Wang Yan , Cavazos-Rehg Patricia A.
Published: June 2023

Background

Cannabis marketing exposure via social media may impact use in youth and young adults. Most states with recreational cannabis lack policies regarding social media-based marketing. Thus, we examined such policies among prominent platforms, particularly those popular among youth and young adults.

Methods

In September-October 2022, 3 research team members extracted policies applying to the general community, advertising, and any specific content regarding drug-related content for 11 social media sites: Discord, Facebook, Instagram, Pinterest, Reddit, Snapchat, TikTok, Tumblr, Twitch, Twitter, and YouTube. Using inductive thematic analysis, they then dual-coded restrictions on cannabis-related content (e.g., paid advertising, unpaid promotion, sales). Descriptive analyses were conducted.

Results

Ten (all except TikTok) referenced cannabis/marijuana, 7 (all except Discord, Instagram, TikTok, and YouTube) distinguished different cannabis-derived products, and 5 (Reddit, Snapchat, TikTok, Tumblr, Twitter) noted jurisdictional differences in cannabis regulations/legality. All prohibited sales, 9 (all except Snapchat and Tumblr) prohibited paid advertising, and 4 (Discord, Reddit, Snapchat, TikTok) prohibited unpaid promotion (e.g., user-generated content). All restricted underage access to cannabis-related content. However, policies varied and were ambiguous regarding how “promotion” was defined, whether/how jurisdictional differences in legality were addressed, how businesses may interact on social media, barriers implemented to inhibit the facilitation of sales, and enforcement protocols.

Conclusions

Social media policies regarding cannabis marketing are ambiguous and may facilitate cannabis marketing, promotion, sales, and underage exposure, thus compounding concerns regarding insufficient governmental regulations. Greater specificity in social media cannabis-related policies and enforcement is needed.
Impact of planning organ at risk volume margins and matching method on late gastrointestinal toxicity in moderately hypofractionated IMRT for locally advanced pancreatic ductal adenocarcinoma
Authors: Ogawa Ayaka , Yoshimura Michio , Nakamura Mitsuhiro , Adachi Takanori , Iwai Takahiro , Ashida Ryo , Mizowaki Takashi
Published: June 2023

Background

This study examined the differences in late gastrointestinal (GI) toxicities in moderately hypofractionated intensity-modulated radiation therapy (IMRT) for locally advanced pancreatic ductal adenocarcinoma (LA-PDAC) by changing the planning organs at risk volume (PRV) margin and the target matching method and assessed the causes of adverse events.

Methods

We examined 37 patients with LA-PDAC who underwent moderately hypofractionated IMRT between 2016 and 2020 at our institution; 23 patients were treated with wide PRV margins and soft tissue matching (Protocol A) and 14 with narrow PRV margins and fiducial marker matching (Protocol B). The GI toxicities, local control (LC) rate, and overall survival (OS) were assessed for each protocol. The initially planned and daily doses to the gross tumor volume (GTV), stomach, and duodenum, reproduced from cone-beam computed tomography, were evaluated.

Results

The late GI toxicity rate of grades 3–4 was higher in Protocol B (42.9%) than in Protocol A (4.3%). Although the 2-year LC rates were significantly higher in Protocol B (90.0%) than in Protocol A (33.3%), no significant difference was observed in OS rates. In the initial plan, no deviations were found for the stomach and duodenum from the dose constraints in either protocol. In contrast, daily dose evaluation for the stomach to duodenal bulb revealed that the frequency of deviation of V3 Gy per session was 44.8% in Protocol B, which was significantly higher than the 24.3% in Protocol A.

Conclusions

Reducing PRV margins with fiducial marker matching increased GI toxicities in exchange for improved LC. Daily dose analysis indicated the trade-off between the GTV dose coverage and the irradiated doses to the GI. This study showed that even with strict matching methods, the PRV margin could not be reduced safely because of GI inter-fractional error, which is expected to be resolved with online adaptive radiotherapy.
A classification algorithm based on dynamic ensemble selection to predict mutational patterns of the envelope protein in HIV-infected patients
Authors: Fili Mohammad , Hu Guiping , Han Changze , Kort Alexa , Trettin John , Haim Hillel
Published: June 2023

Background

Therapeutics against the envelope (Env) proteins of human immunodeficiency virus type 1 (HIV-1) effectively reduce viral loads in patients. However, due to mutations, new therapy-resistant Env variants frequently emerge. The sites of mutations on Env that appear in each patient are considered random and unpredictable. Here we developed an algorithm to estimate for each patient the mutational state of each position based on the mutational state of adjacent positions on the three-dimensional structure of the protein.

Methods

We developed a dynamic ensemble selection algorithm designated k-best classifiers. It identifies the best classifiers within the neighborhood of a new observation and applies them to predict the variability state of each observation. To evaluate the algorithm, we applied amino acid sequences of Envs from 300 HIV-1-infected individuals (at least six sequences per patient). For each patient, amino acid variability values at all Env positions were mapped onto the three-dimensional structure of the protein. Then, the variability state of each position was estimated by the variability at adjacent positions of the protein.

Results

The proposed algorithm showed higher performance than the base learner and a panel of classification algorithms. The mutational state of positions in the high-mannose patch and CD4-binding site of Env, which are targeted by multiple therapeutics, was predicted well. Importantly, the algorithm outperformed other classification techniques for predicting the variability state at multi-position footprints of therapeutics on Env.

Conclusions

The proposed algorithm applies a dynamic classifier-scoring approach that increases its performance relative to other classification methods. Better understanding of the spatiotemporal patterns of variability across Env may lead to new treatment strategies that are tailored to the unique mutational patterns of each patient. More generally, we propose the algorithm as a new high-performance dynamic ensemble selection technique.
Panax notoginseng alleviates oxidative stress through miRNA regulations based on systems biology approach
Authors: Tang Yun , Chen Yi-Gang , Huang Hsi-Yuan , Li Shang-Fu , Zuo Hua-Li , Chen Ji-Hang , Li Li-Ping , Mao Run-Bo , Lin Yang-Chi-Dung , Huang Hsien-Da
Published: June 2023

Background

Herbal medicine Sanqi (SQ), the dried root or stem of Panax notoginseng (PNS), has been reported to have anti-diabetic and anti-obesity effects and is usually administered as a decoction for Chinese medicine. Alternative to utilizing PNS pure compound for treatment, we are motivated to propose an unconventional scheme to investigate the functions of PNS mixture. However, studies providing a detailed overview of the transcriptomics-based signaling network in response to PNS are seldom available.

Methods

To explore the reasoning of PNS in treating metabolic disorders such as insulin resistance, we implemented a systems biology-based approach with RNA sequencing (RNA-seq) and miRNA sequencing data to elucidate key pathways, genes and miRNAs involved.

Results

Functional enrichment analysis revealed PNS up-regulating oxidative stress-related pathways and down-regulating insulin and fatty acid metabolism. Superoxide dismutase 1 (SOD1), peroxiredoxin 1 (PRDX1), heme oxygenase-1 (Hmox1) and glutamate cysteine ligase (GCLc) mRNA and protein levels, as well as related miRNA levels, were measured in PNS treated rat pancreatic β cells (INS-1). PNS treatment up-regulated Hmox1, SOD1 and GCLc expression while down-regulating miR-24-3p and miR-139-5p to suppress oxidative stress. Furthermore, we verified the novel interactions between miR-139-5p and miR-24-3p with GCLc and SOD1.

Conclusion

This work has demonstrated the mechanism of how PNS regulates cellular molecules in metabolic disorders. Therefore, combining omics data with a systems biology strategy could be a practical means to explore the potential function and molecular mechanisms of Chinese herbal medicine in the treatment of metabolic disorders.
SCARB1 downregulation in adrenal insufficiency with Allgrove syndrome
Authors: Bitetto Giacomo , Lopez Gianluca , Ronchi Dario , Pittaro Alessandra , Melzi Valentina , Peverelli Erika , Cribiù Fulvia Milena , Comi Giacomo P. , Mantovani Giovanna , Di Fonzo Alessio
Published: June 2023

Background

Allgrove disease is a rare genetic syndrome characterized by adrenal insufficiency, alacrimia, achalasia and complex neurological involvement. Allgrove disease is due to recessive mutations in the AAAS gene, which encodes for the nucleoporin Aladin, implicated in the nucleocytoplasmic transport. The adrenal insufficiency has been suggested to rely on adrenal gland-ACTH resistance. However, the link between the molecular pathology affecting the nucleoporin Aladin and the glucocorticoid deficiency is still unknown.

Results

By analyzing postmortem patient’s adrenal gland, we identified a downregulation of Aladin transcript and protein. We found a downregulation of Scavenger receptor class B-1 (SCARB1), a key component of the steroidogenic pathway, and SCARB1 regulatory miRNAs (mir125a, mir455) in patient’s tissues. With the hypothesis of an impairment in the nucleocytoplasmic transport of the SCARB1 transcription enhancer cyclic AMP-dependent protein kinase (PKA), we detected a reduction of nuclear Phospho-PKA and a cytoplasmic mislocalization in patient’s samples.

Conclusions

These results shed a light on the possible mechanisms linking ACTH resistance, SCARB1 impairment, and defective nucleocytoplasmic transport.
Extracorporeal hemoadsorption in critically ill COVID-19 patients on VV ECMO: the CytoSorb therapy in COVID-19 (CTC) registry
Authors: Hayanga J. W. Awori , Song Tae , Durham Lucian , Garrison Lawrence , Smith Deane , Molnar Zsolt , Scheier Joerg , Deliargyris Efthymios N. , Moazami Nader
Published: June 2023

Objectives

The CytoSorb therapy in COVID-19 (CTC) registry evaluated the clinical performance and treatment parameters of extracorporeal hemoadsorption integrated with veno-venous extracorporeal membrane oxygenation (VV ECMO) in critically ill COVID-19 patients with acute respiratory distress syndrome (ARDS) and respiratory failure under US FDA Emergency Use Authorization.

Design

Multicenter, observational, registry (NCT04391920).

Setting

Intensive care units (ICUs) in five major US academic centers between April 2020 and January 2022.

Patients

A total of 100 critically ill adults with COVID-19-related ARDS requiring VV ECMO support, who were treated with extracorporeal hemoadsorption.

Interventions

None.

Measurements and main results

Baseline demographics, clinical characteristics, laboratory values and outcomes were recorded following individual ethics committee approval at each center. Detailed data on organ support utilization parameters and hemoadsorption treatments were also collected. Biomarker data were collected according to the standard practice at each participating site, and available values were compared before and after hemoadsorption. The primary outcome of mortality was evaluated using a time-to-event analysis. A total of 100 patients (63% male; age 44 ± 11 years) were included. Survival rates were 86% at 30 days and 74% at 90 days. Median time from ICU admission to the initiation of hemoadsorption was 87 h and was used to define two post hoc groups: ≤ 87 h (group-early start, GE) and > 87 h (group-late start, GL). After the start of hemoadsorption, patients in the GE versus GL had significantly shorter median duration of mechanical ventilation (7 [2–26] vs. 17 [7–37] days, p = 0.02), ECMO support (13 [8–24] vs. 29 [14–38] days, p = 0.021) and ICU stay (17 [10–40] vs 36 [19–55] days, p = 0.002). Survival at 90 days in GE was 82% compared to 66% in GL (p = 0.14). No device-related adverse events were reported.

Conclusions

In critically ill patients with severe COVID-19-related ARDS treated with the combination of VV-ECMO and hemoadsorption, 90-day survival was 74% and earlier intervention was associated with shorter need for organ support and ICU stay. These results lend support to the concept of “enhanced lung rest” with the combined use of VV-ECMO plus hemoadsorption in patients with ARDS.
The effect of background noise and its removal on the analysis of single-cell expression data
Authors: Janssen Philipp , Kliesmete Zane , Vieth Beate , Adiconis Xian , Simmons Sean , Marshall Jamie , McCabe Cristin , Heyn Holger , Levin Joshua Z. , Enard Wolfgang , Hellmann Ines
Published: June 2023

Background

In droplet-based single-cell and single-nucleus RNA-seq experiments, not all reads associated with one cell barcode originate from the encapsulated cell. Such background noise is attributed to spillage from cell-free ambient RNA or barcode swapping events.

Results

Here, we characterize this background noise exemplified by three scRNA-seq and two snRNA-seq replicates of mouse kidneys. For each experiment, cells from two mouse subspecies are pooled, allowing to identify cross-genotype contaminating molecules and thus profile background noise. Background noise is highly variable across replicates and cells, making up on average 3–35% of the total counts (UMIs) per cell and we find that noise levels are directly proportional to the specificity and detectability of marker genes. In search of the source of background noise, we find multiple lines of evidence that the majority of background molecules originates from ambient RNA. Finally, we use our genotype-based estimates to evaluate the performance of three methods (CellBender, DecontX, SoupX) that are designed to quantify and remove background noise. We find that CellBender provides the most precise estimates of background noise levels and also yields the highest improvement for marker gene detection. By contrast, clustering and classification of cells are fairly robust towards background noise and only small improvements can be achieved by background removal that may come at the cost of distortions in fine structure.

Conclusions

Our findings help to better understand the extent, sources and impact of background noise in single-cell experiments and provide guidance on how to deal with it.
PYloroplasty versus No Intervention in GAstric REmnant REconstruction after Oesophagectomy: study protocol for the PYNI-GAREREO phase III randomized controlled trial
Authors: Okada Naoya , Kinoshita Yoshihiro , Nishihara Shoji , Kurotaki Takuma , Sato Aya , Kimura Kotaro , Kushiya Hiroki , Umemoto Kazufumi , Furukawa Shotaro , Yamabuki Takumi , Takada Minoru , Kato Kentaro , Ambo Yoshiyasu , Nakamura Fumitaka
Published: June 2023

Background

After esophagectomy for esophageal and esophagogastric cancer, more than half of patients have lost > 10% of their body weight at 12 months. In most cases, the gastric remnant is used for reconstruction after esophagectomy. One of the most serious nutritional complications of this technique is delayed gastric emptying caused by gastric remnant mobilization and denervation of the vagus nerve. The aim of the PYloroplasty versus No Intervention in GAstric REmnant REconstruction after Oesophagectomy (PYNI-GAREREO) trial is to analyze the clinical outcome of modified Horsley pyloroplasty (mH-P) as a method of preventing delayed gastric emptying.

Methods

The PYNI-GAREREO trial is designed as an open randomized, single-center superiority trial. Patients will be randomly allocated to undergo gastric remnant reconstruction with mH-P (intervention group) or no intervention (control group) in parallel groups. All patients with esophageal cancer or esophagogastric cancer planning to undergo curative minimally invasive esophagectomy will be considered for inclusion. A total of 140 patients will be included in the study and randomized between the groups in a 1:1 ratio. The primary outcome is the body weight change at 6 months postoperatively, and the secondary outcomes are the nutritional status, postoperative complications, functional outcome, and quality of life until 1 year postoperatively.

Discussion

We hypothesize that mH-P after minimally invasive esophagectomy more effectively maintains patients’ nutritional status than no pyloroplasty.

Trial registration

UMIN Clinical Trials Registry UMIN000045104. Registered on 25 August 2021. https://center6.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000051346.
Susceptibility‐guided sequential strategy versus empirical therapy for Helicobacter pylori infection: study protocol for a randomised controlled trial
Authors: Lu Kemei , Lang Cuicui , Zou Xuefei , Zang Lina , Sang WeiWei , Feng Qian , Mu Ying , Liu Lifeng , Xu Chunhong , Zhao Jingrun
Published: June 2023

Background

New treatment strategies are required against infections caused by Helicobacter pylori, which grows increasingly resistant to antibiotics. Polymerase chain reaction-based methods for antibiotic susceptibility testing are available for detecting H. pylori-specific mutations that confer resistance to clarithromycin and levofloxacin. Several meta-analyses have compared eradication rates for susceptibility-guided versus empirical therapy for H. pylori treatment; however, all have significant limitations and high heterogeneity, and the results are contradictory. The main objective of this trial is to assess whether a sequential strategy based on molecular susceptibility testing-guided therapy for H. pylori has a better eradication rate than empirical therapy.

Methods

This trial is designed as a prospective, randomised, open-label, active-controlled and single-centre study. Men and women who are H. pylori-positive, naïve to treatment, and aged 18–65 years will be recruited. A total of 500 participants will be randomised to receive either empirical therapy or a susceptibility-guided sequential strategy. Bismuth quadruple therapy will be the empirical first-line therapy, and in case of failure, high-dose dual (proton-pump inhibitor + amoxicillin) treatment will be the rescue therapy. For the susceptibility-guided sequential strategy, regimen selection will be based on H. pylori susceptibility to clarithromycin (first-line) and levofloxacin (rescue). A first-line treatment of clarithromycin triple therapy will be selected for clarithromycin-sensitive strains. For clarithromycin resistance, a high-dose dual therapy will be selected. During the rescue treatment, a levofloxacin quadruple regimen will be selected for levofloxacin-sensitive strains, and a furazolidone quadruple regimen will be selected for others. The primary outcome is the first-line eradication rate in both groups, and the overall (including first and rescue therapies) H. pylori eradication rate in both groups is one of the secondary outcomes. The eradication rates of H. pylori will be analysed by intention-to-treat analysis, modified intention-to-treat analysis, and per-protocol analysis.

Discussion

This randomised controlled trial will provide objective and valid evidence about the value of polymerase chain reaction-based molecular methods for antibiotic susceptibility testing in guiding H. pylori eradication.

Trial registration

Clinicaltrials.gov NCT05549115. Released on 18 September 2022. First posted on 22 September 2022. Enrolment of the first participant on 20 September 2022. The study is retrospectively registered.
Bizarre parosteal osteochondromatous proliferation: an educational review
Authors: Gitto Salvatore , Serpi Francesca , Messina Carmelo , Albano Domenico , Di Bernardo Andrea , Armiraglio Elisabetta , Cannavò Luca , Mazzoli Simone , Luzzati Alessandro , Parafioriti Antonina , Sconfienza Luca Maria
Published: June 2023

Bizarre parosteal osteochondromatous proliferation (BPOP) is a surface-based bone lesion belonging to the group of benign chondrogenic tumors. The aim of this review is to familiarize the readers with imaging features and differential diagnosis of BPOP, also addressing pathological presentation and treatment options. The peak of incidence of BPOP is in the third and fourth decades of life, although it can occur at any age. Hands are the most common location of BPOP (55%), followed by feet (15%) and long bones (25%). On imaging, BPOP appears as a well-marginated mass of heterotopic mineralization arising from the periosteal aspect of the bone. Typical features of BPOP are contiguity with the underlying bone and lack of cortico-medullary continuity, although cortical interruption and medullary involvement have been rarely reported. Histologically, BPOP is a benign bone surface lesion characterized by osteocartilaginous proliferation with disorganized admixture of cartilage with bizarre features, bone and spindle cells. Differential diagnosis includes both benign—such as florid reactive periostitis, osteochondroma, subungual exostosis, periosteal chondroma and myositis ossificans—and malignant lesions—such as periosteal chondrosarcoma and surface-based osteosarcoma. Treatment consists of surgical resection. Local recurrences are common and treated with re-excision.

Critical relevance statement Bizarre parosteal osteochondromatous proliferation is a benign mineralized mass arising from the periosteal aspect of bone cortex. Multi-modality imaging characteristics, pathology features and differential diagnosis are here highlighted to familiarize the readers with this entity and offer optimal patient care.
Low let-7d microRNA levels in chick embryos enhance innate immunity against Mycoplasma gallisepticum by suppressing the mitogen-activated protein kinase pathway
Authors: Wang Yingjie , Sun Huanling , Zhao Wenqing , Wang Tengfei , Zou Mengyun , Han Yun , Sun Yingfei , Peng Xiuli
Published: June 2023

Chick embryos are a valuable model for studying immunity and vaccines. Therefore, it is crucial to investigate the molecular mechanism of the Mycoplasma gallisepticum (MG)-induced immune response in chick embryos for the prevention and control of MG. In this study, we screened for downregulated let-7d microRNA in MG-infected chicken embryonic lungs to explore its involvement in the innate immune mechanism against MG. Here, we demonstrated that low levels of let-7d are a protective mechanism for chicken embryo primary type II pneumocytes (CP-II) in the presence of MG. Specifically, we found that depressed levels of let-7 in CP-II cells reduced the adhesion capacity of MG. This suppressive effect was achieved through the activated mitogen-activated protein kinase phosphatase 1 (MKP1) target gene and the inactivated mitogen-activated protein kinase (MAPK) pathway. Furthermore, MG-induced hyperinflammation and cell death were both alleviated by downregulation of let-7d. In conclusion, chick embryos protect themselves against MG infection through the innate immune molecule let-7d, which may result from its function as an inhibitor of the MAPK pathway to effectively mitigate MG adhesion, the inflammatory response and cell apoptosis. This study may provide new insight into the development of vaccines against MG.
A mixed-field sources localization algorithm based on high-order cumulant matrix reconstruction for general symmetric array
Authors: Lin Wei , Jin Qiang , Ba Bin , Wang Yinsheng , Zhang Jin
Published: June 2023

Sparse arrays are able to generate more lags to extend the array aperture, which is a distinct advantage in mixed-field localization. To exploit these lags, existing algorithms in the known literature can be mainly divided into two types: the subspace-based algorithm and the sparsity-based algorithm. However, the former algorithm cannot fully utilize the time delay information provided by sparse array, and the second algorithm has basis mismatch problem. In this paper, an interpolation processing method based on atomic norm is proposed to solve the sparse array localization problem. The high-order cumulant matrix is reconstructed by the interpolation method to generate an augmented cumulant matrix without holes, which can make full use of all the lags. Then, the atomic norm minimization method is used to recover the sparse matrix after interpolation in a gridless way. The matrix after recovery enables gridless direction-of-arrival (DOA) estimation. After the interpolation reconstruction, more lags can be exploited, the degrees of freedom are further increased. The proposed algorithm can not only make full use of the array receiving information but also avoid the base mismatch problem, and the accuracy of DOA estimation is improved. Numerical simulations verify the superiority of the proposed algorithm compared with the existing algorithms.
Inequalities for interval-valued Riemann diamond-alpha integrals
Authors: Bohner Martin , Nguyen Linh , Schneider Baruch , Truong Tri
Published: June 2023

We propose the concept of Riemann diamond-alpha integrals for time scales interval-valued functions. We first give the definition and some properties of the interval Riemann diamond-alpha integral that are naturally investigated as an extension of interval Riemann nabla and delta integrals. With the help of the interval Riemann diamond-alpha integral, we present interval variants of Jensen inequalities for convex and concave interval-valued functions on an arbitrary time scale. Moreover, diamond-alpha Hölder’s and Minkowski’s interval inequalities are proved. Also, several numerical examples are provided in order to illustrate our main results.
Sexual violence and associated factors among women of reproductive age in Rwanda: a 2020 nationwide cross-sectional survey
Authors: Nuwabaine Lilian , Kawuki Joseph , Amwiine Earnest , Asiimwe John Baptist , Sserwanja Quraish , Gatasi Ghislaine , Donkor Elorm , Atwijukiire Humphrey
Published: June 2023

Background

Sexual violence against women is a global public health issue with both short- and long-term effects on the physical and mental health of women. This study aimed to determine the prevalence of sexual violence and its associated factors among women of reproductive age in Rwanda.

Methods

We used secondary data from the 2020 Rwanda Demographic and Health Survey of 1,700 participants, who were selected using multistage stratified sampling. Multivariable logistic regression was conducted to explore factors associated with sexual violence using SPSS (version 25).

Results

Of the 1,700 women of reproductive age, 12.4% (95%CI: 11.0–14.1) had experienced sexual violence. Justified beating (AOR = 1.34, 95%CI: 1.16–1.65), not having health insurance (AOR = 1.46, 95%CI: 1.26–2.40), not being involved in healthcare decision-making (AOR = 1.64, 95%CI: 1.99–2.70), having a husband/partner with primary (AOR = 1.70, 95%CI: 5.47–6.21) or no education (AOR = 1.84, 95%CI: 1.21–3.37), as well as having a husband/partner who sometimes (AOR = 3.37, 95%CI: 1.56–7.30) or often (AOR = 12.87, 95%CI: 5.64–29.38) gets drunk were positively associated with sexual violence. However, women from male-headed households (AOR = 0.52, 95%CI: 0.29–0.92) were less likely to experience sexual violence.

Conclusions

There is a need to demystify negative culturally-rooted beliefs favouring sexual violence, such as justified beating, as well as increase efforts to promote women’s empowerment and healthcare access. Moreover, engaging men in anti-sexual violence strategies is paramount to addressing male-related issues that expose women to sexual violence.
Comparison of tramadol and lornoxicam for the prevention of postoperative catheter-related bladder discomfort: a randomized controlled trial
Authors: Liao Xin , Xie Min , Li Shuying , Yu Xiaolan
Published: June 2023

Background

Catheter-related bladder discomfort (CRBD is a painful complication of intraoperative urinary catheterization after anaesthesia. We conducted this study to compare the effect of tramadol and lornoxicam for the prevention of postoperative CRBD.

Methods

One-hundred twenty patients (aged 18–60 years, ASA physical status 1–2, undergoing elective uterine surgery requiring intraoperative urinary catheterization were randomly divided into three groups with 40 patients in each group. Group T received 1.5 mg/kg tramadol, group L received 8-mg lornoxicam, and group C received normal saline. The study drugs were administered intravenously at the end of the surgery. The incidence and severity of CRBD were reported at 0, 1, 2, and 6 h after arrival at the postanaesthesia care unit (PACU).

Results

The incidence of CRBD was significantly lower in groups T and L than in group C at 1, 2, and 6 h after surgery. The incidence of moderate to severe CRBD was also significantly lower in groups T and L than in group C at 0, 1, and 2 h after surgery. The severity of CRBD reported as mild, moderate, and severe was reduced in groups T and L compared with group C at most times after surgery. Group T had a higher incidence of nausea than group C, and there were no differences in dizziness, drowsiness, or vomit among the three groups.

Conclusions

Tramadol and lornoxicam administered intravenously at the end of the surgery were both effective in preventing the incidence and severity of CRBD after uterine surgery. However, tramadol increased the incidence of nausea compared with saline, but there was no difference between tramadol and lornoxicam.

Trial registration

ChiCTR2100052003. Registered on 12/10/2021.
Higher synchronization stability with piano experience: relationship with finger and presentation modality
Authors: Ito Kanami , Watanabe Tatsunori , Horinouchi Takayuki , Matsumoto Takuya , Yunoki Keisuke , Ishida Haruki , Kirimoto Hikari
Published: June 2023

Background

Synchronous finger tapping to external sensory stimuli is more stable for audiovisual combined stimuli than sole auditory or visual stimuli. In addition, piano players are superior in synchronous tapping and manipulating the ring and little fingers as compared to inexperienced individuals. However, it is currently unknown whether the ability to synchronize to external sensory stimuli with the ring finger is at the level of the index finger in piano players. The aim of this study was to compare the effect of piano experience on synchronization stability between the index and ring fingers using auditory, visual, and audiovisual combined stimuli.

Methods

Thirteen piano players and thirteen novices participated in this study. They were instructed to tap with their index or ring finger synchronously to auditory, visual, and audiovisual combined stimuli. The stimuli were presented from an electronic metronome at 1 Hz, and the tapping was performed 30 times in each condition. We analyzed standard deviation of intervals between the stimulus onset and the tap onset as synchronization stability.

Results

Synchronization stability for visual stimuli was lower during ring than index finger tapping in novices; however, this decline was absent in piano players. Also, piano players showed the higher synchronization stability for audiovisual combined stimuli than sole visual and auditory stimuli when tapping with the index finger. On the other hand, in novices, synchronization stability was higher for audiovisual combined stimuli than only visual stimuli.

Conclusions

These findings suggest that improvements of both sensorimotor processing and finger motor control by piano practice would contribute to superior synchronization stability.
Beam filtration for object-tailored X-ray CT of multi-material cultural heritage objects
Authors: Kiss Maximilian B. , Bossema Francien G. , van Laar Paul J. C. , Meijer Suzan , Lucka Felix , van Leeuwen Tristan , Batenburg K. Joost
Published: June 2023

Computed tomography (CT) is a powerful non-invasive tool to analyze cultural heritage objects by allowing museum professionals to obtain 3D information about the objects’ interior. These insights can help with the conservation or restoration of the objects, as well as provide contextual information on the objects’ history or making process. Cultural heritage objects exist in a wide variety and have characteristics which present challenges for CT scanning: multi-scale internal features, a diversity of sizes and shapes, and multi-material objects. Because X-ray absorption is related to the density, thickness of the material, and atomic composition, the challenges are greater when the object consists of multiple different materials with varying densities. This is especially true for cases with extreme density contrasts such as that between metals and textiles. An untailored acquisition of CT scans of multi-material objects can lead to reduced image quality and heavy visual errors called image artifacts, which can influence the perception or representation of information. A tailored acquisition can reduce these artifacts and lead to a higher information gain. In this work, we firstly discuss how the X-ray beam properties and the beam-object interaction influence CT image formation and how to use filters to manipulate the emitted X-ray beam to improve image quality for multi-material objects. We showcase that this can be achieved with limited resources in a low-cost DIY fashion with thin sheets of metal as filters, 3D-printed filter frames and a filter holder. Secondly, we give a qualitative analysis of the influence of the CT acquisition parameters illustrated with two case study objects from the textile collection of the Rijksmuseum, Amsterdam, The Netherlands. With this we provide insights and intuitions on tailoring the CT scan to the cultural heritage objects. Thirdly, we extract a general concept of steps for museum professionals to design an object-tailored CT scan for individual cases.
A comparative study of machine learning and deep learning methods for energy balance prediction in a hybrid building-renewable energy system
Authors: Mirjalili Mohammad Amin , Aslani Alireza , Zahedi Rahim , Soleimani Mohammad
Published: June 2023

Globally, the construction industry is experiencing an increase in energy demand, which has significant environmental and economic repercussions. To address these issues, it is now possible for buildings, vehicles, and renewable energy sources to collaborate and function as an advanced, integrated, and environmentally favorable system that meets the high energy demands of contemporary buildings. To attain maximum efficiency, however, it is necessary to create reliable energy demand forecasting models. In this research, by introducing the energy model of a neighbourhood with buildings with solar panels and electric vehicles, the final balance of energy production and consumption for each building and the whole neighbourhood as a micro grid is predicted. DesignBuilder is used to model neighbourhood buildings, and K-Nearest neighbor (KNN), Regression Support Vector (SVR), Adaptive Boosting (AdaBoost), and Deep neural networks (DNN) algorithms in machine learning are used to predict the final energy balance. a comparative analysis of the performance of the KNN, SVR, AdaBoost, and DNN algorithms was conducted to determine which algorithm is the most effective in predicting energy balance. Finally, the Root Mean Square Error (RMSE) has been used to validate the prediction models. The results show that the KNN, SVR, AdaBoost, and DNN algorithms had RMSE values of 0.56, 0.92, 0.95, and 0.53, respectively. Among these algorithms, the DNN and KNN algorithms had more accurate results than the other used algorithms and as a result of this research, An accurate forecast of neighbourhood energy balance was made. This study takes a novel approach by developing a model that takes into account an integrated system of houses, solar cells, and electric consumption for each building in a neighborhood, which can help to optimize energy consumption and reduce environmental impact.
Bridging the simulation-to-real gap for AI-based needle and target detection in robot-assisted ultrasound-guided interventions
Authors: Arapi Visar , Hardt-Stremayr Alexander , Weiss Stephan , Steinbrener Jan
Published: June 2023

Background

Artificial intelligence (AI)-powered, robot-assisted, and ultrasound (US)-guided interventional radiology has the potential to increase the efficacy and cost-efficiency of interventional procedures while improving postsurgical outcomes and reducing the burden for medical personnel.

Methods

To overcome the lack of available clinical data needed to train state-of-the-art AI models, we propose a novel approach for generating synthetic ultrasound data from real, clinical preoperative three-dimensional (3D) data of different imaging modalities. With the synthetic data, we trained a deep learning-based detection algorithm for the localization of needle tip and target anatomy in US images. We validated our models on real, in vitro US data.

Results

The resulting models generalize well to unseen synthetic data and experimental in vitro data making the proposed approach a promising method to create AI-based models for applications of needle and target detection in minimally invasive US-guided procedures. Moreover, we show that by one-time calibration of the US and robot coordinate frames, our tracking algorithm can be used to accurately fine-position the robot in reach of the target based on 2D US images alone.

Conclusions

The proposed data generation approach is sufficient to bridge the simulation-to-real gap and has the potential to overcome data paucity challenges in interventional radiology. The proposed AI-based detection algorithm shows very promising results in terms of accuracy and frame rate.

Relevance statement

This approach can facilitate the development of next-generation AI algorithms for patient anatomy detection and needle tracking in US and their application to robotics.

Key points

• AI-based methods show promise for needle and target detection in US-guided interventions.

• Publicly available, annotated datasets for training AI models are limited.

• Synthetic, clinical-like US data can be generated from magnetic resonance or computed tomography data.

• Models trained with synthetic US data generalize well to real in vitro US data.

• Target detection with an AI model can be used for fine positioning of the robot.

Graphical Abstract
Investigation of accessory transverse foramen in dry cervical vertebrae: incidence, variations, types, locations, and diagnostic implications
Authors: Ogut Eren , Guzelad Ozge , Yıldırım Fatos Belgin
Published: June 2023

Background

This research aimed to determine the incidence, variations, types, and potential locations of the accessory transverse foramen (ATF) in dry cervical vertebrae. A total of 250 Turkish dry cervical vertebrae were examined, with 500 transverse foramina investigated. The cervical vertebrae were categorized into five groups (C3–C7), and each cervical vertebra was assessed bilaterally to determine the location, incidence, and side of the ATF.

Results

ATF was observed in 21 vertebrae (8.4%) and was distributed posteriorly (76.2%), posterolaterally (19.04%), and posteromedially (4.8%) in relation to the location of the TF. The incidence of ATF was 4.8% in C3, 28.6% in C4, 9.5% in C5, 23.8% in C6, and 33.3% in C7. Furthermore, a statistically significant difference was observed in the unilateral or bilateral occurrence of the ATF (F = 3.079; p = 0.047, p < 0.05).

Conclusions

In this study, we have presented an investigative approach and discussed the potential implications of identifying the ATF in dry cervical vertebrae. The presence of ATF can be crucial in the diagnosis of variations in the vertebral artery (VA) and underlying disorders, potentially aiding in the determination of the cause of death or ancestry. Additionally, the posterior location of the ATF and its asymmetric distribution should be taken into account when evaluating dry cervical vertebrae, which may offer valuable information for the identification of variations.
Effect of the entomopathogenic fungus, Beauveria bassiana inhibiting whitefly transmission of squash leaf curl virus infecting squash
Authors: Abd El-Wahab Abeer Salah El-Deen , Nada Maha S. , El-Shazly Manal A. , Galal Azza , Amin Hala A.
Published: June 2023

Background

Squash leaf curl virus (SLCV) is efficiently transmitted and spread by the whitefly, Bemisia tabaci (Gennadius), which is the only vector that transmits begomoviruses naturally causing huge crop losses through feeding damage. The widespread use of chemical insecticides to control the whitefly B. tabaci has become extremely hazardous to the environment. Alternative methods such as biological control have been advocated. Entomopathogenic fungi (EPF) have been found as promising whitefly bio-pesticides.

Results

Naturally infected squash plants that showed symptoms of squash leaf curl disease were collected from Giza Governorate, Egypt. SLCV was detected using a PCR assay using coat protein-specific primers and generated an amplicon of 419 bp. Multiple sequence alignment showed that the SLCV-Giza isolate has a significant identity of 99.2% with the SLCV-Mx:BCS: La Paz isolate from Mexico and 99% with the SLQV.Q2521 isolate from Egypt. Phylogenetic analysis showed that SLCV-Giza is closely related to the SLCV-Mx:BCS: La Paz isolate from Mexico. The whitefly transmission test revealed that the virus transmitted to an extent of 13.3% and reached 100% of transmission using 15–20 viruliferous whiteflies; while the efficiency of syringe injection was (60%). B. tabaci newly emerge adults were able to acquire and transmit SLCV after an Acquisition Access Period (AAP) of 15 and 30 min by low rates of 13.3 and 22.2%, respectively. The transmission rate was increased gradually to reach the maximum of 100% after 24, 48, and 72 h (AAP). B. tabaci was able to inoculate SLCV after an Inoculation Access Period (IAP) of 15 and 30 min with rates of 46.7 and 62.2%. The whitefly was allowed to acquire SLCV from a squash plant (virus source) treated previously with EPF (Beauveria bassiana) and allowed to transmit the virus to the test plants. The transmission effectiveness of viruliferous whitefly was lower (33.4%) than that of non-treated whitefly (100%). The transmission efficiency was decreased on the second day by 6.8% and by the third day by 2.2% of treatment with the EPF. The results were validated by PCR assay for SLCV from tested squash plants and the PCR did not reveal specific amplification.

Conclusions

The use of EPF (B. bassiana) for B. tabaci control had a direct impact on SLCV accumulation and transmission.