bluuebunny/crossref_metadata_2025 huggingface dataset:
A tensor-based bi-random walks model for protein function prediction
Authors: Hu Sai , Zhang Zhihong , Xiong Huijun , Jiang Meiping , Luo Yingchun , Yan Wei , Zhao Bihai
Published: May 2022

Background

The accurate characterization of protein functions is critical to understanding life at the molecular level and has a huge impact on biomedicine and pharmaceuticals. Computationally predicting protein function has been studied in the past decades. Plagued by noise and errors in protein–protein interaction (PPI) networks, researchers have undertaken to focus on the fusion of multi-omics data in recent years. A data model that appropriately integrates network topologies with biological data and preserves their intrinsic characteristics is still a bottleneck and an aspirational goal for protein function prediction.

Results

In this paper, we propose the RWRT (Random Walks with Restart on Tensor) method to accomplish protein function prediction by applying bi-random walks on the tensor. RWRT firstly constructs a functional similarity tensor by combining protein interaction networks with multi-omics data derived from domain annotation and protein complex information. After this, RWRT extends the bi-random walks algorithm from a two-dimensional matrix to the tensor for scoring functional similarity between proteins. Finally, RWRT filters out possible pretenders based on the concept of cohesiveness coefficient and annotates target proteins with functions of the remaining functional partners. Experimental results indicate that RWRT performs significantly better than the state-of-the-art methods and improves the area under the receiver-operating curve (AUROC) by no less than 18%.

Conclusions

The functional similarity tensor offers us an alternative, in that it is a collection of networks sharing the same nodes; however, the edges belong to different categories or represent interactions of different nature. We demonstrate that the tensor-based random walk model can not only discover more partners with similar functions but also free from the constraints of errors in protein interaction networks effectively. We believe that the performance of function prediction depends greatly on whether we can extract and exploit proper functional similarity information on protein correlations.
A random priming amplification method for whole genome sequencing of SARS-CoV-2 virus
Authors: Chrzastek Klaudia , Tennakoon Chandana , Bialy Dagmara , Freimanis Graham , Flannery John , Shelton Holly
Published: May 2022

Background

Non-targeted whole genome sequencing is a powerful tool to comprehensively identify constituents of microbial communities in a sample. There is no need to direct the analysis to any identification before sequencing which can decrease the introduction of bias and false negatives results. It also allows the assessment of genetic aberrations in the genome (e.g., single nucleotide variants, deletions, insertions and copy number variants) including in noncoding protein regions.

Methods

The performance of four different random priming amplification methods to recover RNA viral genetic material of SARS-CoV-2 were compared in this study. In method 1 (H-P) the reverse transcriptase (RT) step was performed with random hexamers whereas in methods 2–4 RT incorporating an octamer primer with a known tag. In methods 1 and 2 (K-P) sequencing was applied on material derived from the RT-PCR step, whereas in methods 3 (SISPA) and 4 (S-P) an additional amplification was incorporated before sequencing.

Results

The SISPA method was the most effective and efficient method for non-targeted/random priming whole genome sequencing of SARS-CoV-2 that we tested. The SISPA method described in this study allowed for whole genome assembly of SARS-CoV-2 and influenza A(H1N1)pdm09 in mixed samples. We determined the limit of detection and characterization of SARS-CoV-2 virus which was 103 pfu/ml (Ct, 22.4) for whole genome assembly and 101 pfu/ml (Ct, 30) for metagenomics detection.

Conclusions

The SISPA method is predominantly useful for obtaining genome sequences from RNA viruses or investigating complex clinical samples as no prior sequence information is needed. It might be applied to monitor genomic virus changes, virus evolution and can be used for fast metagenomics detection or to assess the general picture of different pathogens within the sample.
Quantifying shifts in natural selection on codon usage between protein regions: a population genetics approach
Authors: Cope Alexander L. , Gilchrist Michael A.
Published: May 2022

Background

Codon usage bias (CUB), the non-uniform usage of synonymous codons, occurs across all domains of life. Adaptive CUB is hypothesized to result from various selective pressures, including selection for efficient ribosome elongation, accurate translation, mRNA secondary structure, and/or protein folding. Given the critical link between protein folding and protein function, numerous studies have analyzed the relationship between codon usage and protein structure. The results from these studies have often been contradictory, likely reflecting the differing methods used for measuring codon usage and the failure to appropriately control for confounding factors, such as differences in amino acid usage between protein structures and changes in the frequency of different structures with gene expression.

Results

Here we take an explicit population genetics approach to quantify codon-specific shifts in natural selection related to protein structure in S. cerevisiae and E. coli. Unlike other metrics of codon usage, our approach explicitly separates the effects of natural selection, scaled by gene expression, and mutation bias while naturally accounting for a region’s amino acid usage. Bayesian model comparisons suggest selection on codon usage varies only slightly between helix, sheet, and coil secondary structures and, similarly, between structured and intrinsically-disordered regions. Similarly, in contrast to prevous findings, we find selection on codon usage only varies slightly at the termini of helices in E. coli. Using simulated data, we show this previous work indicating “non-optimal” codons are enriched at the beginning of helices in S. cerevisiae was due to failure to control for various confounding factors (e.g. amino acid biases, gene expression, etc.), and rather than selection to modulate cotranslational folding.

Conclusions

Our results reveal a weak relationship between codon usage and protein structure, indicating that differences in selection on codon usage between structures are slight. In addition to the magnitude of differences in selection between protein structures being slight, the observed shifts appear to be idiosyncratic and largely codon-specific rather than systematic reversals in the nature of selection. Overall, our work demonstrates the statistical power and benefits of studying selective shifts on codon usage or other genomic features from an explicitly evolutionary approach. Limitations of this approach and future potential research avenues are discussed.
A novel compound heterozygous SPG7 variant is associated with progressive spastic ataxia and persecutory delusions found in Chinese patients: two case reports
Authors: Wang Shan , Wang Yaye , Wu Yue , Zhang Jinru , Zhang Weilin , Li Chang , Song Xueqin
Published: May 2022

Background

Hereditary spastic paraplegia 7 (SPG7) is one of the subtypes of autosomal-recessive hereditary spastic paraplegia, which is a clinically heterogeneous neurodegenerative disorder. SPG7 often displays a complicated phenotype, including optic atrophy, ophthalmoparesis, and impaired emotional communication. In the Chinese population, sporadic cases of SPG7 variant-associated spastic ataxia are rarely reported.

Case presentation

We carefully analysed the clinical features, imaging and genetic tests of two sporadic patients with SPG7, both from the Hebei region of China. One patient presented with progressive bilateral lower limb weakness, spastic-ataxia and no cognitive impairment. Brain MRI revealed mild cerebellar atrophy. Genetic analysis revealed c.1150_1151insCTAC (p.G384Afs*13) frameshift variant and exon1-3 heterozygous deletion. The other patient presented with progressive bilateral lower limb weakness, ataxia, dysarthria and a mild psychosis associated with persecutory delusions, which drew almost no attention, in addition to mild cognitive impairments characterized by a decrease in verbal memory and executive function. Genetic analysis identified two heterozygous variants in the SPG7 gene: c.1150_1151insCTAC (p.G384Afs*13) and c.1496delC (p.Q500Sfs*13).

Conclusions

The c.1496delC (p.Q500Sfs*13) variant in exon 11 has not been reported before. The c.1150_1151insCTAC variant is speculated to be a hotspot variant in the Chinese population. Patients with SPG7 may have cognitive impairments and psychosis, displaying specific characteristics, which should be of concern.
Multinomial network meta-analysis using response rates: relapsed/refractory multiple myeloma treatment rankings differ depending on the choice of outcome
Authors: van Beurden-Tan Chrissy H. Y. , Sonneveld Pieter , Groot Carin A. Uyl-de
Published: May 2022

Background

Due to the fast growing relapsed/refractory multiple myeloma (RRMM) treatment landscape, a comparison of all the available treatments was warranted. For clinical practice it is important to consider both immediate effects such as response quality and prolonged benefits such as progression-free survival (PFS) in a meta-analysis. The objective of this study was to assess the impact of the choice of outcome on the treatment rankings in RRMM.

Methods

A multinomial logistic network meta-analysis was conducted to estimate the ranking of sixteen treatments based on both complete and objective response rates (CRR and ORR). Seventeen phase III randomized controlled trials from a previously performed systematic literature review were included. Treatment ranking was based on the surface under the cumulative ranking curve (SUCRA). Sensitivity analysis was conducted.

Results

The ranking of treatments differed when comparing PFS hazard ratios rankings with rankings based on CRR. Pomalidomide, bortezomib and dexamethasone ranked highest, while a substantial lower ranking was observed for the triplet elotuzumab, lenalidomide, dexamethasone. The ranking of treatments did not differ when comparing PFS hazard ratios and ORR. The scenario analyses showed that the results were robust. In all scenarios the top three was dominated by the same triplets. The treatment with the highest probability of having the best PFS and ORR was the triplet daratumumab, lenalidomide plus dexamethasone in the base case.

Conclusion

This analysis shows that depending on the chosen outcome treatment rankings in RRMM may differ. When conducting NMAs, the response rate, a clinically recognized outcome, should therefore be more frequently considered.
Colorectal cancer concurrent gene signature based on coherent patterns between genomic and transcriptional alterations
Authors: Shen Ming-Hung , Huang Chi-Jung , Ho Thien-Fiew , Liu Chih-Yi , Shih Ying-Yih , Huang Ching-Shui , Huang Chi-Cheng
Published: May 2022

Background

The aim of the study was to enhance colorectal cancer prognostication by integrating single nucleotide polymorphism (SNP) and gene expression (GE) microarrays for genomic and transcriptional alteration detection; genes with concurrent gains and losses were used to develop a prognostic signature.

Methods

The discovery dataset comprised 32 Taiwanese colorectal cancer patients, of which 31 were assayed for GE and copy number variations (CNVs) with Illumina Human HT-12 BeadChip v4.0 and Omni 25 BeadChip v1.1. Concurrent gains and losses were declared if coherent manners were observed between GE and SNP arrays. Concurrent genes were also identified in The Cancer Genome Atlas Project (TCGA) as the secondary discovery dataset (n = 345).

Results

The “universal” concurrent genes, which were the combination of z-transformed correlation coefficients, contained 4022 genes. Candidate genes were evaluated within each of the 10 public domain microarray datasets, and 1655 (2000 probe sets) were prognostic in at least one study. Consensus across all datasets was used to build a risk predictive model, while distinct relapse-free/overall survival patterns between defined risk groups were observed among four out of five training datasets. The predictive accuracy of recurrence, metastasis, or death was between 61 and 86% (cross-validation area under the receiver operating characteristic (ROC) curve: 0.548-0.833) from five independent validation studies.

Conclusion

The colorectal cancer concurrent gene signature is prognostic in terms of recurrence, metastasis, or mortality among 1746 patients. Genes with coherent patterns between genomic and transcriptional contexts are more likely to provide prognostication for colorectal cancer.
Unmet health needs and barriers to health care among people experiencing homelessness in San Francisco’s Mission District: a qualitative study
Authors: Thorndike Anna L. , Yetman Hailey E. , Thorndike Anne N. , Jeffrys Mason , Rowe Michael
Published: May 2022

Background

People experiencing homelessness have unique health needs and barriers to medical and behavioral health care (mental health, substance use disorder, and overall well-being) compared to housed people. It remains unclear why many people experiencing homelessness do not access care when community-based homeless health care resources are available at low or no cost. This qualitative study examined perspectives of people experiencing homelessness and staff members at community-based homeless health and service organizations in San Francisco’s Mission District on unmet medical and behavioral health needs and barriers to accessing care.

Methods

We conducted 34 interviews between September and November 2020: 23 with people experiencing homelessness and 11 with staff at community-based homeless health and service organizations in the Mission District. Qualitative interviews were transcribed, coded, and analyzed using the Framework Method on NVivo Qualitative Data Analysis Software.

Results

Both staff and homeless participants reported unmet and common health needs of mental illness, physical injury and disability, food and nutrition insecurity, and substance use disorder. Barriers to care included negative prior health care experiences, competing priorities, and provider turnover. Recommendations for improving services included building more trust with people experiencing homelessness by training clinic staff to treat patients with respect and patience and expanding clinical outreach and health education programs.

Conclusions

People experiencing homelessness face many different health needs and barriers to care, some of which community-based organizations have the ability to address. These findings can help inform future strategies for homeless health care programs to identify and target the specific unmet health needs and barriers to care of people experiencing homelessness in their communities.
Knockdown of PAR2 alleviates cancer-induced bone pain by inhibiting the activation of astrocytes and the ERK pathway
Authors: Tang Yiting , Chen Yupeng , Yang Mingzhu , Zheng Qiuhui , Li Yaoyuan , Bao Yanju
Published: May 2022

Objective

Cancer-induced bone pain (CIBP) is a kind of pain with complex pathophysiology. Proteinase-activated receptor 2 (PAR-2) is involved in CIBP. This study explored the effects of PAR-2 on CIBP rats.

Methods

CIBP rat model was established by injecting Walker 256 rat breast cancer cells into the left tibia of female Sprague-Dawley rats and verified by tibial morphology observation, HE staining, and mechanical hyperalgesia assay. CIBP rats were injected with PAR-2 inhibitor, ERK activator, and CREB inhibitor through the spinal cord sheath on the 13th day after operation. CIBP behaviors were measured by mechanical hyperalgesia assay. On the 14th day after operation, L4-5 spinal cord tissues were obtained. PAR-2 expression, co-expression of PAR-2 and astrocyte marker GFAP, GFAP mRNA and protein levels and the ERK pathway-related protein levels were detected by Western blot, immunofluorescence double staining, RT-qPCR, and Western blot.

Results

CIBP rats had obvious mechanical hyperalgesia and thermal hyperalgesia from the 7th day after modeling; mechanical hyperalgesia threshold and thermal threshold were decreased; PAR-2 was increased in spinal cord tissues and was co-expressed with GFAP. PAR-2 silencing alleviated rat CIBP by inhibiting astrocyte activation. p-ERK/t-ERK and p-CREB/t-CREB levels in CIBP spinal cord were elevated, the ERK/CREB pathway was activated, while the ERK/CREB pathway was inhibited by PAR-2 silencing. The alleviating effect of PAR-2 inhibitor on hyperalgesia behaviors in CIBP rats were weakened by ERK activator, while were partially restored by CREB inhibitor.

Conclusions

PAR-2 knockdown inhibited the ERK/CREB pathway activation and astrocyte activation, thus alleviating CIBP in rats.
Use of massage therapy by mid-aged and older Australian women
Authors: Ladanyi Suzy , Adams Jon , Sibbritt David
Published: May 2022

Background

Massage is a widely acceptable and popular form of complementary medicine (CM) among Australian women. While there is some research that reports on massage use in younger women, there is minimal research exploring massage use in the treatment of chronic illness in older women. This study provides an estimate of the prevalence of massage use, as well as identifying the characteristics significantly associated with consultation with a massage therapist, for mid-age and older Australian women.

Methods

A cross-sectional sub-study was conducted on a sample of women drawn from the45 and Up Study; a large cohort study of adults aged 45 years and over.Data from 1795 women were included in the analyses and massage use was compared against measures of demographics, health status and health care utilisation.

Results

A total of 174 (7.7%) women consulted with a massage therapist in the previous 12 months. Women were more likely to consult a massage therapist if they have tertiary level education (O.R. = 1.67; 95% C.I.: 1.04, 2.65;p = 0.031), private health insurance (O.R. = 6.37; 95% C.I.: 4.41, 9.19;p < 0.001) and/or osteoarthritis (O.R. = 1.72; 95% C.I.: 1.19, 2.48;p = 0.004). They were also more likely to consult a massage therapist if they have a poorer health-related quality of life (HRQoL) (O.R. = 1.14; 95% C.I.: 1.04, 1.27;p = 0.007).

Conclusion

Older, tertiary-level educated Australian women with private health insurance were more likely to use massage therapy, as were women with osteoarthritis specifically. Women with lower HRQoL were found to be more likely to use massage therapy in the treatment of their chronic illness. This research provides insight into the determinants of massage use among ageing women and is useful for governments in consideration of accessibility to holistic healthcare when developing public policy for healthcare in Australia.
Pycnogenol a promising remedy for diabetic keratopathy in experimentally induced corneal alkali burns in diabetic rats
Authors: Hamed Mohamed A. , Farag Amany , Zahran Ibrahim S. , Hafez Ahmed , Rizk Mohamed Abdo , Abass Marwa
Published: May 2022

Aim

This study aimed to investigate the efficiency of topically applied pycnogenol (PYC) in healing the standardized alkaline corneal ulcer in diabetic and normal rats.

Materials and methods

The corneal alkali-burn injury (CA-I) model was unilaterally developed in Wistar rats by filter paper saturated with 0.01 M of NaOH and touching the eyes for 45 s. Rats were divided into four groups: Normal control (NC), normal PYC (NPYC), diabetic control (DC), and diabetic PYC (DPYC). Both NPYC and DPYC groups were daily treated with PY eye drops three times, whereas NC and DC ones were treated with ordinary saline for six successive days.

Results

The wound healing of corneal epithelial was improved in the NPYC group compared to the NC group. Meanwhile, it was significantly improved (P < 0.05) in the DPYC group than in the DC group. Histological examination revealed that corneal re-epithelialization was more accomplished in the DPYC group than in the DC group. In addition, the inflammatory cells were augmented in the DC group more than those in the DPYC one.

Conclusion

The findings obtained revealed the efficiency of PYC for enhancing the corneal re-epithelialization and reducing the inflammatory reaction post alkali burn in rats, and thus it could be beneficially valuable as a treatment for the diabetic keratopathy.
Hemoglobin A1C as a prognostic factor and the pre-diabetic paradox in patients admitted to a tertiary care medical center intensive cardiac care unit
Authors: Lupu Lior , Taha Louay , Farkash Rivka , Bayya Feras , Karmi Mohammad , Steinmetz Yoed , Shaheen Fauzi Fadi , Perel Nimrod , Hamayel Kamal , Levi Nir , Maller Tommer , Karameh Hani , Lichewitz Gavriel , Gavish Dov , Algur Nurit , Glikson Michael , Asher Elad
Published: May 2022

Background

Hemoglobin A1C (HbA1c) is a form of glycated hemoglobin used to estimate glycemic control in diabetic patients. Data regarding the prognostic significance of HbA1c levels in contemporary intensive cardiac care unit (ICCU) patients is limited.

Methods

All patients admitted to the ICCU at a tertiary care medical center between January 1, 2020, and June 30, 2021, with documented admission HbA1c levels were included in the study. Patients were divided into 3 groups according to their HbA1c levels: < 5.7 g% [no diabetes mellitus (DM)], 5.7–6.4 g% (pre-DM), ≥ 6.5 g% (DM).

Results

A total of 1412 patients were included. Of them, 974 (69%) were male with a mean age of 67(± 15.7) years old. HbA1c level < 5.7 g% was found in 550 (39%) patients, 5.7–6.4 g% in 458 (32.4%) patients and ≥ 6.5 g% in 404 (28.6%) patients. Among patients who did not know they had DM, 81 (9.3%) patients had high HbA1c levels (≥ 6.5 g%) on admission. The crude mortality rate at follow-up (up to 1.5 years) was almost twice as high among patients with pre-DM and DM than in patients with no DM (10.6% vs. 5.4%, respectively, p = 0.01). Interestingly, although not statistically significant, the trend was that pre-DM patients had the strongest association with mortality rate [HR 1.83, (95% CI 0.936–3.588); p = 0.077].

Conclusions

Although an HbA1c level of ≥ 5.7 g% (pre-DM & DM) is associated with a worse prognosis in patients admitted to ICCU, pre-DM patients, paradoxically, have the highest risk for short and long-term mortality rates.
Attitudes, practices, and determinants of community care-seeking behaviours for fever/malaria episodes in the context of the implementation of multiple first-line therapies for uncomplicated malaria in the health district of Kaya, Burkina Faso
Authors: Kaboré Jean Moise Tanga , Siribié Mohamadou , Hien Denise , Soulama Issiaka , Barry Nouhoun , Nombré Yacouba , Dianda Frederic , Baguiya Adama , Tiono Alfred Bewendtaoré , Burri Christian , Tchouatieu André-Marie , Sirima Sodiomon Bienvenu
Published: May 2022

Background

Malaria case management relies on World Health Organization (WHO)-recommended artemisinin-based combination therapy (ACT), and a continuous understanding of local community knowledge, attitudes, and practices may be a great support for the success of malaria disease control efforts. In this context, this study aimed to identify potential facilitators or barriers at the community level to inform a health district-wide implementation of multiple first-line therapies (MFT) as a new strategy for uncomplicated malaria case management.

Methods

A community-based cross-sectional study using a mixed-method design was carried out from November 2018 to February 2019, in the health district (HD) of Kaya in Burkina Faso. Quantitative data were collected using a standardized questionnaire from 1394 individuals who had fever/malaria episodes four weeks prior to the survey. In addition, 23 focus group discussions (FGDs) were conducted targeting various segments of the community. Logistic regression models were used to assess the predictors of community care-seeking behaviours.

Results

Overall, 98% (1366/1394) of study participants sought advice or treatment, and 66.5% did so within 24 h of fever onset. 76.4% of participants preferred to seek treatment from health centres as the first recourse to care, 5.8% were treated at home with remaining drug stock, and 2.3% preferred traditional healers. Artemether-lumefantrine (AL) was by far the most used anti-malarial drug (98.2%); reported adherence to the 3-day treatment regimen was 84.3%. Multivariate analysis identified less than 5 km distance travelled for care (AOR = 2.7; 95% CI 2.1–3.7) and education/schooling (AOR = 1.8; 95% CI 1.3–2.5) as determinants of prompt care-seeking for fever. Geographical proximity (AOR = 1.5, 95% CI 1.2–2.1), having a child under five (AOR = 4.6, 95% CI 3.2–6.7), being pregnant (AOR = 6.5, 95% CI 1.9–22.5), and living in an urban area (AOR = 2.8, 95% CI 1.8–4.2) were significant predictors for visiting health centres. The FGDs showed that participants had good knowledge about malaria symptoms, prevention tools, and effective treatment. Behaviour change regarding malaria treatment and free medication for children under five were the main reasons for participants to seek care at health centres.

Conclusions

The study showed appropriate knowledge about malaria and positive community care-seeking behaviour at health centres for fever/malaria episodes. This could potentially facilitate the implementation of a MFT pilot programme in the district.

ClinicalTrials.gov Identifier: NCT04265573.
Podocyte specific deletion of PKM2 ameliorates LPS-induced podocyte injury through beta-catenin
Authors: Alquraishi Mohammed , Chahed Samah , Alani Dina , Puckett Dexter L. , Dowker Presley D. , Hubbard Katelin , Zhao Yi , Kim Ji Yeon , Nodit Laurentia , Fatima Huma , Donohoe Dallas , Voy Brynn , Chowanadisai Winyoo , Bettaieb Ahmed
Published: May 2022

Background

Acute kidney injury (AKI) is associated with a severe decline in kidney function caused by abnormalities within the podocytes' glomerular matrix. Recently, AKI has been linked to alterations in glycolysis and the activity of glycolytic enzymes, including pyruvate kinase M2 (PKM2). However, the contribution of this enzyme to AKI remains largely unexplored.

Methods

Cre-loxP technology was used to examine the effects of PKM2 specific deletion in podocytes on the activation status of key signaling pathways involved in the pathophysiology of AKI by lipopolysaccharides (LPS). In addition, we used lentiviral shRNA to generate murine podocytes deficient in PKM2 and investigated the molecular mechanisms mediating PKM2 actions in vitro.

Results

Specific PKM2 deletion in podocytes ameliorated LPS-induced protein excretion and alleviated LPS-induced alterations in blood urea nitrogen and serum albumin levels. In addition, PKM2 deletion in podocytes alleviated LPS-induced structural and morphological alterations to the tubules and to the brush borders. At the molecular level, PKM2 deficiency in podocytes suppressed LPS-induced inflammation and apoptosis. In vitro, PKM2 knockdown in murine podocytes diminished LPS-induced apoptosis. These effects were concomitant with a reduction in LPS-induced activation of β-catenin and the loss of Wilms’ Tumor 1 (WT1) and nephrin. Notably, the overexpression of a constitutively active mutant of β-catenin abolished the protective effect of PKM2 knockdown. Conversely, PKM2 knockdown cells reconstituted with the phosphotyrosine binding–deficient PKM2 mutant (K433E) recapitulated the effect of PKM2 depletion on LPS-induced apoptosis, β-catenin activation, and reduction in WT1 expression.

Conclusions

Taken together, our data demonstrates that PKM2 plays a key role in podocyte injury and suggests that targetting PKM2 in podocytes could serve as a promising therapeutic strategy for AKI.

Trial registration

Not applicable.
Foxtail mosaic virus-induced gene silencing (VIGS) in switchgrass (Panicum virgatum L.)
Authors: Tiedge Kira , Destremps Janessa , Solano-Sanchez Janet , Arce-Rodriguez Magda Lisette , Zerbe Philipp
Published: May 2022

Background

Although the genome for the allotetraploid bioenergy crop switchgrass (Panicum virgatum) has been established, limitations in mutant resources have hampered in planta gene function studies toward crop optimization. Virus-induced gene silencing (VIGS) is a versatile technique for transient genetic studies. Here we report the implementation of foxtail mosaic virus (FoMV)-mediated gene silencing in switchgrass in above- and below-ground tissues and at different developmental stages.

Results

The study demonstrated that leaf rub-inoculation is a suitable method for systemic gene silencing in switchgrass. For all three visual marker genes, Magnesium chelatase subunit D (ChlD) and I (ChlI) as well as phytoene desaturase (PDS), phenotypic changes were observed in leaves, albeit at different intensities. Gene silencing efficiency was verified by RT-PCR for all tested genes. Notably, systemic gene silencing was also observed in roots, although silencing efficiency was stronger in leaves (~ 63–94%) as compared to roots (~ 48–78%). Plants at a later developmental stage were moderately less amenable to VIGS than younger plants, but also less perturbed by the viral infection.

Conclusions

Using FoMV-mediated VIGS could be achieved in switchgrass leaves and roots, providing an alternative approach for studying gene functions and physiological traits in this important bioenergy crop.
Adrenal carcinoma: a case report
Authors: Abeynayake D. R. , V Sopan , Perera K. J. C. , Paramanantham A. , Munasinghe T. M. J.
Published: May 2022

Background

Adrenocortical carcinoma is a rare malignancy (0.5–2 cases/million/year) with a poor prognosis. Hypercortisolism, virilization, and compressive features are among the common presentations of adrenocortical carcinoma. Hematuria is one of the rare initial presentations of adrenocortical carcinoma reported in the literature. We report a case of adrenal carcinoma presenting with microscopic hematuria.

Case presentation

A 67-year-old Sri Lankan patient with diabetes, hypertension, and ischemic heart disease presented with an acute coronary event. During the routine evaluation, microscopic hematuria was detected without proteinuria or active sediments. She denied any painful micturition, previous similar episodes, or abdominal pain. Further evaluation revealed a hypokalemia with biochemical evidence of hypercortisolism and high testosterone levels with suppressed adrenocorticotropic hormone levels. On imaging, there was evidence of a right suprarenal mass 7 cm × 3 cm × 6 cm in size that was hypoechoic and lobulated and suggestive of a lipid-poor tumor. She underwent adrenalectomy. By the time of surgery 3 weeks later, significant weight gain with features of Cushing syndrome, including hirsutism, skin atrophy, easy bruising without virilization, and proximal myopathy, were noted. Histology identified a right-sided adrenal tumor with capsular and vascular invasion. Hypercortisolism and hematuria disappeared after surgery. The patient was referred for further oncological management.

Conclusion

This case illustrates a rare presentation of adrenal carcinoma. Awareness of this presentation may facilitate early evaluation and management.
Chemical reaction network knowledge graphs: the OntoRXN ontology
Authors: Garay-Ruiz Diego , Bo Carles
Published: May 2022

The organization and management of large amounts of data has become a major point in almost all areas of human knowledge. In this context, semantic approaches propose a structure for the target data, defining ontologies that state the types of entities on a certain field and how these entities are interrelated. In this work, we introduce OntoRXN, a novel ontology describing the reaction networks constructed from computational chemistry calculations. Under our paradigm, these networks are handled as undirected graphs, without assuming any traversal direction. From there, we propose a core class structure including reaction steps, network stages, chemical species, and the lower-level entities for the individual computational calculations. These individual calculations are founded on the OntoCompChem ontology and on the ioChem-BD database, where information is parsed and stored in CML format. OntoRXN is introduced through several examples in which knowledge graphs based on the ontology are generated for different chemical systems available on ioChem-BD. Finally, the resulting knowledge graphs are explored through SPARQL queries, illustrating the power of the semantic approach to standardize the analysis of intricate datasets and to simplify the development of complex workflows.

Graphical Abstract
Revision of the genus Protadelomys, a middle Eocene theridomyoid rodent: evolutionary and biochronological implications
Authors: Vianey-Liaud Monique , Hautier Lionel
Published: May 2022

The generic status of the species referred to Protadelomys has long been problematic. Most Protadelomys species are now considered paraphyletic, except for the type species P. cartieri and for P. lugdunensis. Here, we revised these two species from their type locality, Egerkingen (Swiss Jura) for P. cartieri and Lissieu (Rhône, France) for P. lugdunensis. For the latter species, we also consider the locality of Laprade (Tarn-et-Garonne, Quercy, France). Additionally, we revised the material attributed to Protadelomys species that is now considered paraphyletic: ?P. alsaticus from Bouxwiller (Bas-Rhin, France) and Cuzal (Lot, Quercy, France), ?P. maximini from St-Maximin (Gard, France), and ?P. nievesae from Casa Ramon (Huesca, Spain). Our detailed morphological analysis enables us to better characterize the extent of the morphological and size variability in all Protadelomys and ?Protadelomys species. We show that both P. cartieri and P. lugdunensis co-existed in Egerkingen, Lissieu, and Laprade. We also erected a new genus and species, Homœtreposciurus egerkingensis, and reported the presence of Eoelfomys from Egerkingen. Eoelfomys is here described as a new genus and species from Laprade. Size and morphological comparisons enabled us to detect large intraspecific variation in the material of ?P. alsaticus from Bouxwiller, as well as in the type population of ?P. maximini. The co-occurrence of the two Protadelomys species, at least in two localities, in addition to the revision of the features characterizing the three species of ?Protadelomys, led us to question the existence of a single evolutionary lineage (chronospecies), as previously recognized from ?P. maximini to P. lugdunensis.
The role of diffusion-weighted MR imaging in discrimination between benign and malignant axillary lymph nodes in breast cancer patients
Authors: Zahran Amany Mohammed Hussein , Maarouf Rania Aly , Hussein Ahmed , Sheha Aliaa Sayed
Published: May 2022

Background

Noninvasive preoperative evaluation of axillary lymph nodes proved to have a significant role not only on the protocol of treatment of breast cancer but also impact the whole life of the patient. Complications of lymph node biopsy or axillary clearance increase the need for noninvasive reliable diagnostic tool. We aimed in the current study to evaluate the role of diffusion-weighted magnetic resonance imaging (DW-MRI) and apparent diffusion coefficient (ADC) in discrimination between benign and malignant axillary lymph nodes. We included 44 suspicious lymph nodes from 29 patients. Qualitative DW-MRI was analyzed into restricted or not; ADC maps and cut-off value were calculated, and they were correlated with histopathological results, which were the gold standard tool of the current study.

Results

The cut-off value of ADC-differentiated between malignant and benign lymph nodes was 0.89 × 10−3 mm2/s. The statistical indices including the sensitivity, specificity, PPV, NPV and accuracy were 89.66%, 86.67%, 93.9, 81.2% and 87.8%, respectively, with P value < 0.001, while DW-MRI results were classified into restricted or not restricted with qualitative statistical indices of 96.6%, 80%, 90.3%, 92.3% and 90.9% for sensitivity, specificity, PPV, NPV and accuracy, respectively, with P value < 0.001.

Conclusion

DW-MRI and ADC both have significant role in discrimination between benign and malignant axillary lymph nodes increasing the accuracy of MRI examination in breast cancer patients.
In vivo dosimetry in pelvic brachytherapy
Authors: Houlihan Orla Anne , Workman Geraldine , Hounsell Alan R , Prise Kevin M , Jain Suneil
Published: May 2022

Brachytherapy is an effective treatment in the curative management of prostate and gynaecological cancers. With advances in technology, brachytherapy has increased in complexity in recent years. Human error, equipment malfunction, patient organ motion and radioactive source displacement can result in substantial deviation of delivered dose from planned dose. To limit adverse clinical outcomes, adequate steps to improve the robustness of pathway processes, ensure the implementation of appropriate treatment margins and confirm the delivered dose must be considered. In vivo dosimetry is one such method of dose validation which, if implemented appropriately within clinical practice, is an attractive technique for reducing dosimetric uncertainties and identifying potential errors. This review aims to describe the dosimetric uncertainties and potential errors associated with brachytherapy, the potential for in vivo dosimetry in adaptive brachytherapy as a key method of dose validation, and the clinical considerations and future directions of in vivo dosimetry.

Advances in knowledge

This paper describes the potential role for in vivo dosimetry in the reduction of uncertainties in pelvic brachytherapy, the pertinent factors for consideration in clinical practice, and the future potential for in vivo dosimetry in the personalisation of brachytherapy.
Statistical monitoring of discrete and nonparametric statistics with exact run length properties
Authors: Περδίκης Θεόδωρος
Published: May 2022

Η παρούσα διατριβή επικεντρώνεται στο σχεδιασμό μονομεταβλητών διαγραμμάτων ελέγχου με σκοπό την ανίχνευση αλλαγών στο υπό μελέτη χαρακτηριστικό σε μια παραγωγική διαδικασία. Συγκεκριμένα, προτείνονται νέες και βελτιωμένες μέθοδοι σχετικά με τον αξιόπιστο και βέλτιστο σχεδιασμό των διαγραμμάτων. Αρχικά, παρουσιάζεται μια σύντομη ανασκόπηση της βιβλιογραφίας αναφορικά με μονομεταβλητά (παραμετρικά και μη παραμετρικά) διαγράμματα ελέγχου. Στη συνέχεια παρουσιάζονται δύο νέα μη παραμετρικά διαγράμματα ελέγχου βασισμένα στο προσημικο ελεγχο (Sign test) με σκοπό την ανίχνευση αλλαγών στη διάμεσο και διακύμανση του υπό μελέτη χαρακτηριστικού. Επιπλέον, προτείνονται δυο νέα διαγράμματα βασισμένα στον έλεγχο του Wilcoxon ( Wilcoxon Signed rank test). Για κάθε διάγραμμα παρουσιάζεται μια λεπτομερείς στατιστική ανάλυση αναφορικά με την απόδοση και το σχεδιασμό κάθε διαγράμματος. Τελος, δίνονται γενικά συμπεράσματα και προτάσεις για μελλοντική έρευνα.
Assessment of factors affecting the mental condition of patients with chronic myeloid leukemia treated with tyrosine kinase inhibitors
Authors: Gibek Katarzyna , Sacha Tomasz
Published: May 2022

Cel pracy

Celem pracy było dokonanie ogólnej oceny zdrowia psychicznego, w tym: objawów somatyzacji, depresyjności, lęku i zaburzeń funkcjonowania u chorych na przewlekłą białaczkę szpikową (PBSz), leczonych inhibitorami kinaz tyrozynowych (IKT) oraz ocena wpływu czynników jak długość trwania choroby, skutki uboczne terapii, wiek i płeć na występowanie powyższych zaburzeń. Kolejnym celem była identyfikacja pacjentów zagrożonych rozwojem zaburzeń psychicznych.

Metoda

Badaniem zostało 91 chorych. Do oceny zdrowia psychicznego zastosowano ankietę własną, Kwestionariusz Davida Goldberga GHQ-28 oraz czterowymiarowy Kwestionariusz 4DSQ, mierzący cztery wymiary sfery psychicznej.

Wyniki

Wykazano średni poziom kondycji psychicznej badanej grupy, zidentyfikowano 29 osób z zaburzeniami sfery psychicznej. Kobiety oraz osoby mieszkające samotnie uzyskały gorsze wyniki w niemal wszystkich wymiarach kwestionariuszy. Wiek, liczba skutków ubocznych oraz płeć okazały się istotnie wpływać na zaburzenia stanu psychicznego. Wysoką korelację zanotowano pomiędzy liczbą skutków ubocznych a objawami somatyzacji. Przeciętne korelacje wystąpiły pomiędzy wiekiem a występowaniem zaburzeń psychicznych i wszystkimi wymiarami Kwestionariusza GHQ-28.

Wnioski

Praca wskazuje, że należy podejmować próby zmniejszania skutków ubocznych, pracę z psychologiem nad akceptacją choroby, psychoedukację, terapie behawioralne, ewentualnie nawiązywać kontakty z psychiatrą w celu rozważenia włączenia farmakoterapii jako sposoby, których wdrożenie w proces leczenia może poprawy jakość życia chorych.
Intervención arquitectónica y diseño urbano en contextos históricos
Authors: Añón Abajas Rosa Mª , Ramos Carranza Amadeo , Torres Pérez María Elena
Published: May 2022

Dentro de las actividades de cooperación que los departamentos de nuestra universidad deben establecer, se encuentra la realización de eventos que den a conocer los trabajos de investigación que desarrollan sus profesores. Ello redunda en el fortalecimiento de relaciones entre instituciones académicas. En esta línea se ha realizado un primer encuentro con la Facultad de Arquitectura de la Universidad Autónoma de Yucatán, Mérida, México (FA-UADY) mediante el formato de Seminario Internacional. El objetivo principal de este seminario era dar a conocer la actividad investigadora de los profesores del departamento de Proyectos Arquitectónicos de la Universidad de Sevilla en otras universidades extranjeras. De la misma manera, conocer los proyectos y el contexto cultural de México de condiciones altamente diferentes. Un segundo objetivo era reivindicar el proyecto y la obra de arquitectura como investigación, parte esencial del proceso formativo de nuestros estudiantes. Para estos objetivos, se propone publicar los resúmenes de las ponencias del Seminario, acompañadas de referencias bibliográficas que permitan al lector profundizar en el tema que desee. El nombre del Seminario resulta clarificador de estas intenciones, Seminario Internacional de Investigación en Arquitectura y Cooperación Universitaria (SIACU), deseando que esta iniciativa tenga continuidad con otras universidades. Las ponencias se han agrupado en tres líneas temáticas que abordan desde diferentes puntos de vistas y situaciones culturales una amplia casuística de intervenciones arquitectónicas en contextos históricos en edificios y en espacios públicos. El término "contexto histórico" no se ciñe exclusivamente a los centros fundacionales de las grandes ciudades, dando apertura a otras valoraciones que afectan también a otras arquitecturas, menores o anónimas, al paisaje y al territorio, o a las periferias consolidadas donde nuevas arquitecturas plantearon nuevas situaciones. En todas ellas se manifiesta la importancia de la arquitectura como medio de transformación y adaptación de lo existente, desde una actitud comprometida y contemporánea.
El único e inigualable tepezcuintle: Un pilar de las interacciones en las selvas de México
Authors: Martínez Ceceñas Yuriana
Published: May 2022

Desde tiempos prehispánicos, el tepezcuintle ha sido un mamífero muy apreciado por diversas culturas. Para los chinantecos, pueblo originario de México que habita en el noreste del estado de Oaxaca y Veracruz, este roedor es la madre del sol y la luna, lo que explica su coloración y mejillas abultadas. En la actualidad, el tepezcuintle es un animal poco conocido a pesar de su gran importancia ecológica y cultural.
Amigos por conveniencia
Authors: Monroy-Gamboa Alina Gabriela
Published: May 2022

Las relaciones interespecíficas (con especies diferentes a las del individuo) si suceden en la vida silvestre. Estas relaciones pueden darse de varias maneras, inclusive ayudándose mutuamente.
Standalone, CMOS-based Faraday rotation in a silicon photonic waveguide
Authors: D’Mello Yannick , Bernal Santiago , Helmy Adam , Berikaa Essam , Carpentier Olivier , Alamgir Imtiaz , Alam Md Samiul , El-Fiky Eslam , Plant David V.
Published: May 2022

Nonreciprocity is a fundamental requirement of signal isolation in optical communication systems. However, on chip isolator designs require either post-processing steps or external magnetic biasing, which are impractical for commercial applications. This raises the need for standalone devices which support nonreciprocal functionality using standardized fabrication techniques. Here, we report the first design of an electromagnetic coil surrounding a waveguide which exclusively employed the complementary metal-oxide-semiconductor (CMOS) process flow. The coil supported an electric current up to 14 mA. In simulations, it generated an alternating magnetic flux density up to 1.16 mT inside a strip waveguide and thereby induced a rotation of 50.71 picodegrees for the fundamental transverse-magnetic mode at a wavelength of 1352 nm. Our analysis further revealed methods to increase the rotation by orders of magnitude. It demonstrated the scope of manufacturing processes and serves as a building block for the development of a commercially viable, on-chip optical isolator.
Terahertz spatio-temporal deep learning computed tomography
Authors: Hung Yi-Chun , Chao Ta-Hsuan , Yu Pojen , Yang Shang-Hua
Published: May 2022

Terahertz computed tomography (THz CT) has drawn significant attention because of its unique capability to bring multi-dimensional object information from invisible to visible. However, current physics-model-based THz CT modalities present low data use efficiency on time-resolved THz signals and low model fusion extensibility, limiting their application fields’ practical use. In this paper, we propose a supervised THz deep learning computed tomography (THz DL-CT) framework based on time-domain information. THz DL-CT restores superior THz tomographic images of 3D objects by extracting features from spatio-temporal THz signals without any prior material information. Compared with conventional and machine learning based methods, THz DL-CT delivers at least 50.2%, and 52.6% superior in root mean square error (RMSE) and structural similarity index (SSIM), respectively. Additionally, we have experimentally demonstrated that the pretrained THz DL-CT model can generalize to reconstruct multi-material systems with no prerequisite information. THz CT through the DL data fusion approach provides a new pathway for non-invasive functional imaging in object investigation.
Nonconstant positive steady states and pattern formation of a diffusive epidemic model
Authors: Gao Xiaoyan
Published: May 2022

It is our purpose in this paper to make a detailed description for the structure of the set of the nonconstant steady states for the two-dimensional epidemic S-I model with diffusion incorporating demographic and epidemiological processes with zero-flux boundary conditions. We first study the conditions of diffusion-driven instability occurrence, which induces spatial inhomogeneous patterns. The results will extend to the derivative of prey's functional response with prey is positive. Moreover, we establish the local and global structure of nonconstant positive steady state solutions. A priori estimates for steady state solutions will play a key role in the proof. Our results indicate that the diffusion has a great influence on the spread of the epidemic and extend well the finding of spatiotemporal dynamics in the epidemic model.
Solvability of thirty-six three-dimensional systems of difference equations of hyperbolic-cotangent type
Authors: Stevic Stevo
Published: May 2022

We present thirty-six classes of three-dimensional systems of difference equations of the hyperbolic-cotangent type which are solvable in closed form.