bluuebunny/crossref_metadata_2025 huggingface dataset:
Integration of probabilistic functional networks without an external Gold Standard
Authors: James Katherine , Alsobhe Aoesha , Cockell Simon J , Wipat Anil , Pocock Matthew
Published: July 2022

Background

Probabilistic functional integrated networks (PFINs) are designed to aid our understanding of cellular biology and can be used to generate testable hypotheses about protein function. PFINs are generally created by scoring the quality of interaction datasets against a Gold Standard dataset, usually chosen from a separate high-quality data source, prior to their integration. Use of an external Gold Standard has several drawbacks, including data redundancy, data loss and the need for identifier mapping, which can complicate the network build and impact on PFIN performance. Additionally, there typically are no Gold Standard data for non-model organisms.

Results

We describe the development of an integration technique, ssNet, that scores and integrates both high-throughput and low-throughout data from a single source database in a consistent manner without the need for an external Gold Standard dataset. Using data from Saccharomyces cerevisiae we show that ssNet is easier and faster, overcoming the challenges of data redundancy, Gold Standard bias and ID mapping. In addition ssNet results in less loss of data and produces a more complete network.

Conclusions

The ssNet method allows PFINs to be built successfully from a single database, while producing comparable network performance to networks scored using an external Gold Standard source and with reduced data loss.
Genome-wide identification and analysis of ACP gene family in Sorghum bicolor (L.) Moench
Authors: Ge Hanqiu , Xu Jingjing , Hua Mingzhu , An Wenwen , Wu Junping , Wang Baohua , Li Ping , Fang Hui
Published: July 2022

Background

Acyl carrier proteins (ACP) constitute a very conserved carrier protein family. Previous studies have found that ACP not only takes part in the fatty acid synthesis process of almost all organisms, but also participates in the regulation of plant growth, development, and metabolism, and makes plants adaptable to stresses. However, this gene family has not been systematically studied in sorghum.

Results

Nine ACP family members were identified in the sorghum genome, which were located on chromosomes 1, 2, 5, 7, 8 and 9, respectively. Evolutionary analysis among different species divided the ACP family into four subfamilies, showing that the SbACPs were more closely related to maize. The prediction results of subcellular localization showed that SbACPs were mainly distributed in chloroplasts and mitochondria, while fluorescence localization showed that SbACPs were mainly localized in chloroplasts in tobacco leaf. The analysis of gene structure revealed a relatively simple genetic structure, that there were 1–3 introns in the sorghum ACP family, and the gene structure within the same subfamily had high similarity. The amplification method of SbACPs was mainly large fragment replication, and SbACPs were more closely related to ACPs in maize and rice. In addition, three-dimensional structure analysis showed that all ACP genes in sorghum contained four α helices, and the second helix structure was more conserved, implying a key role in function. Cis-acting element analysis indicated that the SbACPs might be involved in light response, plant growth and development regulation, biotic and abiotic stress response, plant hormone regulation, and other physiological processes. What’s more, qRT-PCR analysis uncovered that some of SbACPs might be involved in the adaptive regulation of drought and salt stresses, indicating the close relationship between fatty acids and the resistance to abiotic stresses in sorghum.

Conclusions

In summary, these results showed a comprehensive overview of the SbACPs and provided a theoretical basis for further studies on the biological functions of SbACPs in sorghum growth, development and abiotic stress responses.
What happens after the kidney biopsy? The findings nephrologists should know
Authors: Montes Daniel , Beamish Claire , Waheed Sana , Osman Fauzia , Maursetter Laura
Published: July 2022

Background

Percutaneous kidney biopsies are important tools for the diagnosis of kidney diseases. Nephrologists must be familiar with the expected complications of the procedure to provide an adequate informed consent. Here, we present a quality improvement analysis that reviews the complication rate of percutaneous kidney biopsies performed over a 2-year period by nephrologists at a single center, and that tabulates the nature and timing of these events.

Methods

From a single center cohort, pre- and post-biopsy anthropomorphic and clinical measurements were collected. Post-biopsy complications were tracked and sorted into either major or minor complications. Statistical tests were used to analyze complication incidence across the pre- and post-biopsy measurements obtained.

Results

Of the 154 nephrologist-performed percutaneous native kidney biopsies, 2 biopsies (1.3%) were found to result in a major complication. Both major complications were detected within 4 hours of the biopsy. Analysis of the pre-biopsy and post-biopsy measurements found that the proportion of complications was higher in patients with hematuria prior to biopsy. It was also found that patients with complications were statistically younger and had fewer comorbidities. Under univariable analysis, older age was associated with a lower incidence rate ratio for complications. However, no pre-or-post biopsy measurement or characteristic had a statistically significant change in incidence rate ratio under multivariable analysis.

Conclusions

Percutaneous kidney biopsies were found to be low risk when performed by nephrologists in this single center cohort. Consistent with past literature, life threatening major complications rarely occurred and were reliably identified within 4 hours of biopsy, suggesting that centers can consider reduced observation times without compromising patient safety. Minor complications, such as pain, were more likely to occur in younger, healthier patients, and in those with hematuria prior to biopsy. This extensive tabulation of all biopsy adverse events is the first of its kind and will be beneficial for nephrologists to inform discussions with patients about expectations and risk-benefit of this procedure.
Effects of insomnia and levels of depression and anxiety symptoms on quality of life in people with epilepsy
Authors: Zhong Rui , Li Zhuan , Chen Qingling , Zhang Hanyu , Zhang Xinyue , Lin Weihong
Published: July 2022

Objectives

The association between insomnia and quality of life (QOL) in epilepsy is poorly understood and may involve interactive variables. We aimed to investigate whether and how insomnia, levels of depression and anxiety symptoms interact to influence QOL in people with epilepsy (PWE).

Methods

A consecutive cohort of 179 PWE was enrolled. We collected data on insomnia, levels of depression and anxiety symptoms, and QOL. The Insomnia Severity Index (ISI), Depression Inventory for Epilepsy (NDDI-E), Generalized Anxiety Disorder-7 (GAD-7), and QOL in Epilepsy Inventory (QOLIE-31) were used. The direct, indirect, and total effects of insomnia on QOL were estimated based on a moderated mediation model.

Results

Depression symptom levels mediated the association between insomnia and QOL (B = 0.09 SE = 0.03, p = 0.01). Depression symptom levels accounted for 34.7% of the total effect of insomnia on QOL. The mediating effect of depression symptom levels was positively moderated by anxiety symptom levels (B = 0.09, SE = 0.03, p = 0.01).

Conclusion

The effect of insomnia on QOL can be partially explained by the mediation of depression symptom levels. Additionally, improving anxiety symptoms may attenuate the indirect effect of insomnia on QOL through depression symptom levels.
Evaluation of open reduction of distal humerus fractures in children after implementation of an enhanced recovery after surgery program
Authors: Lu Jialing , Xue Mingfeng , Fu Peng , Qian Damei , Chen Xingguang , Yao Danhua , Zhang Yanli
Published: July 2022

Objective

This study assessed whether an enhanced recovery after surgery (ERAS) protocol could be beneficial for children with distal humerus fractures.

Methods

Children with distal humerus fractures (n = 85) were randomly assigned to the ERAS and control groups and subjected to different perioperative managements. This was followed by the evaluation of their intraoperative characteristics (operation time and bleeding), postoperative characteristics (food intake conditions, pain scores, and discharge time), and postoperative functions.

Results

The operation time, intraoperative bleeding, and postoperative hematological indices did not differ significantly between the two groups. Preoperative thirst and hunger were considerably less and the initial food intake duration following surgery was markedly shorter in the ERAS group than in the control group, whereas no difference between the groups was observed in the incidences of postoperative nausea and vomiting. A markedly reduced highest postoperative pain score and reduced mean pain score and demand for additional analgesic interventions were observed in the ERAS group compared with those in the control group, although the differences were not statistically significant. No noticeable between-group differences were observed in the incidences of postoperative incision problems, aspirational pneumonia, and gastroesophageal reflux. The total length of hospital stay was not significantly different between the two groups. However, the length of postoperative hospital stay was remarkably shorter and the elbow joint function at 2 months after surgery was significantly improved in the ERAS group compared with those in the control group.

Conclusion

The ERAS protocol can ameliorate preoperative discomfort and postoperative pain, shorten the postoperative hospital stay, and accelerate postoperative functional recovery without increasing the risks of postoperative nausea, vomiting, and poor incision healing and is, therefore, worthy of clinical application.
Oral health status and practices of 6- to 7-year-old children in Amman, Jordan: a cross-sectional study
Authors: Aljafari Ahmad , ElKarmi Rawan , Nasser Osama , Atef Ala’a , Hosey Marie Therese
Published: July 2022

Background

Dental caries affects the majority of children in Jordan, with some evidence of its prevalence steadily increasing. Previous studies have shown that families struggle to establish good oral health practices. The aim of this study was to evaluate the current oral health status and practices of 6- to7-year-old children in Amman, Jordan.r

Methods

A cross-sectional cohort study. The sample consisted of 6- to 7-year-old children attending six randomly selected schools in Amman, Jordan. Measures collected were: I) Caries experience (d3mft/D3MFT), II) Oral hygiene, measured using the Simplified Oral Hygiene Index, III) Dietary, toothbrushing, and dental attendance practices, measured using diaries and parental questionnaires, IV) Participants’ basic characteristics: age, education and employment. Data were analysed using SPSS20.

Results

In total, 942 children were recruited. Four hundred and fifty-seven were boys, 485 were girls. Their average age was 6.5 years. Eighty-nine percent had decay in their primary teeth. Mean d3mft was 5.1(1 (range = 0–12, SD = 2.9). Only 8% of carious teeth were restored. Mean DMFT score was 0.3 (range = 0–4, SD = 0.8). Mean debris score was 1.07 (range = 0–3, SD = 0.37). Children indicated that they brush their teeth 1.6 times a day (range = 0–3, SD = 0.6). The majority (81%) were unsupervised. Sixty-seven percent of parents did not know the appropriate fluoride toothpaste concentration. Children were having 1.5 sugary snacks in-between their meals (Range = 1–6, SD = 1.1). They scored a mean of 2.5 (Range = 0–5.87, SD = 1.7) in sweetened drinks intake (recommended ≤ 1) and 2.8 (Range = 0–18.57, SD = 1.5) in non-core food intake (recommended ≤ 2) on a dietary questionnaire. Most parents (84%) indicated that their child attends the dentist only when in pain, and 18% indicated that their child is extremely afraid of dentists. Only 32% and 18% were familiar with fluoride varnish and fissure sealants, respectively. Regression analysis revealed that debris score and dental attendance were reliable predictors of caries experience.

Conclusions

Six- to seven-year-old children in Amman, Jordan have a high caries experience. Most show signs of poor oral hygiene, excessive intake of cariogenic foods, and symptomatic dental attendance. Their parents lack knowledge on fluoride varnish and fissure sealants. There is a need for oral health promotion tailored to this cohort's need.
RGS1 and related genes as potential targets for immunotherapy in cervical cancer: computational biology and experimental validation
Authors: Zhang Siyang , Wang Han , Liu Jiao , Tao Tao , Zeng Zhi , Wang Min
Published: July 2022

Background

Effective treatment is needed for advanced, inoperable, or chemotherapy-resistant cervical cancer patients. Immunotherapy has become a new treatment modality for cervical cancer patients, and there is an urgent need to identify additional targets for cervical cancer immunotherapy.

Methods

In this study the core gene, RGS1, which affects immune status and the FIGO stage of cervical cancer patients was identified by WGCNA analysis and differential analysis using TCGA database. 10 related genes interacting with RGS1 were identified using PPI network, and the functional and immune correlations were analyzed. Based on the expression of RGS1 and related genes, the consensus clustering method was used to divide CESC patients into two groups (group 1, high expression of RGS1; group 2, low expression of RGS1). Then, the functional enrichment analysis was used to search for the functional differences in differentially expressed genes (DEGs) between group 1 and group 2. Immune infiltration analysis was performed using ESTIMATE, CIBERSORT, and ssGSEA, and the differences in expression of immune checkpoint inhibitors (ICIs) targets were assessed between the two groups. We investigated the effect of RGS1 on the clinical relevance of CESC patients, and experimentally verified the differences in RGS1 expression between cervical cancer patient tissues and normal cervical tissues, the role of RGS1 in cell function, and the effect on tumor growth in tumor-bearing mice.

Results

We found that RGS1 was associated with CD4, GNAI3, RGS2, GNAO1, GNAI2, RGS20, GNAZ, GNAI1, HLA-DRA and HLA-DRB1, especially CD4 and RGS2. Functional enrichment of DEGs was associated with T cell activation. Compared with group 2, group 1 had stronger immune infiltration and higher ICI target expression. RGS1 had higher expression in cervical cancer tissues than normal tissues, especially in HPV-E6 positive cancer tissues. In cervical cancer cell lines, knockdown of RGS1 can inhibited cell proliferation, migration, invasion, and tumor growth in nude mice and promoted apoptosis.

Conclusions

RGS1, as an oncogenic gene of cervical cancer, affects the immune microenvironment of patients with cervical cancer and may be a target of immunotherapy.
LncRNA RP3-525N10.2-NFKB1-PROS1 triplet-mediated low PROS1 expression is an onco-immunological biomarker in low-grade gliomas: a pan-cancer analysis with experimental verification
Authors: Zhou Yujie , Xiao Dongdong , Jiang Xiaobing
Published: July 2022

Background

Glioma is the most common cancer in the central nervous system, and low grade gliomas are notorious for many types of tumors and heterogeneity. PROS1 not only plays an important role in the blood coagulation system, and recent studies have found that it was correlated with the development of tumors, especially related to tumor immune infiltration. However, the study of underlying role and mechanism of PROS1 in gliomas, especially in low-grade gliomas, is almost absent.

Methods

We integrated the information of patients with LGG in The Cancer Genome Atlas (TCGA) cohort and Chinese Glioma Genome Atlas (CGGA) cohort. Then, we systematically demonstrated the differences and prognostic prognosis value of PROS1 based on multi-omics analyses. In addition, Cell counting kit-8 (CCK-8) assay, colony formation assay, 5-Ethynyl-2’-deoxyuridine (EdU) incorporation assay, and Transwell assays were performed to evaluate cell proliferation and invasion. qRT-PCR and immunohistochemistry were used to evaluate the expression of PROS1 in LGG.

Results

Various bioinformatics approaches revealed that PROS1 was a valuable prognostic marker and may influence tumour development via distinct mechanisms, including expression of DNA methyltransferase, RNA modification, and DNA mismatch repair system genes, copy number variation, single nucleotide variation frequency, genomic heterogeneity, cancer stemness, DNA methylation, and alternative PROS1 splicing. Our analyses indicated that the long non-coding RNA RP3-525N10.2 may “decoy” or “guide” the transcription factor NFKB1 and prevent its association with PROS1, thereby reducing PROS1 expression and improving poor LGG prognosis. PROS1 expression was also closely associated with tumour infiltration by immune cells, especially tumour-associated macrophages, as well as the expression of various immune checkpoint inhibitors, immunomodulators, and immune cell markers.

Conclusion

long non-coding RNA RP3-525N10.2-NFKB1-PROS1 triplet-mediated PROS1 expression could serve as a biomarker for cancer diagnosis, prognosis, therapy selection, and follow-up in LGG patients.
Co-expression of TNF receptors 1 and 2 on melanomas facilitates soluble TNF-induced resistance to MAPK pathway inhibitors
Authors: Sander Cindy A. , Rush Elizabeth A. , Shi Jian , Arantes Lidia M. R. B. , Tesi Raymond J. , Ross Mark A. , Calderon Michael J. , Watkins Simon C. , Kirkwood John M. , Ferris Robert L. , Butterfield Lisa H. , Vujanovic Lazar
Published: July 2022

Background

The effectiveness of MAPK pathway inhibitors (MAPKi) used to treat patients with BRAF-mutant melanoma is limited by a range of resistance mechanisms, including soluble TNF (solTNF)-mediated NF-kB signaling. solTNF preferentially signals through type-1 TNF receptor (TNFR1), however, it can also bind to TNFR2, a receptor that is primarily expressed on leukocytes. Here, we investigate the TNFR2 expression pattern on human BRAFV600E+ melanomas and its role in solTNF-driven resistance reprogramming to MAPKi.

Methods

Flow cytometry was used to test TNFR1, TNFR2 and CD271 expression on, as well as NF-kB phosphorylation in human BRAF-mutant melanoma. The ability of melanoma cell lines to acquire MAPKi resistance in response to recombinant or macrophage-derived TNF was evaluated using the MTT cytotoxicity assay. Gene editing was implemented to knock out or knock in TNF receptors in melanoma cell lines. Knockout and knock-in cell line variants were employed to assess the intrinsic roles of these receptors in TNF-induced resistance to MAPKi. Multicolor immunofluorescence microscopy was utilized to test TNFR2 expression by melanoma in patients receiving MAPKi therapy.

Results

TNFR1 and TNFR2 are co-expressed at various levels on 4/7 BRAFV600E+ melanoma cell lines evaluated in this study. In vitro treatments with solTNF induce MAPKi resistance solely in TNFR2-expressing BRAFV600E+ melanoma cell lines. TNFR1 and TNFR2 knockout and knock-in studies indicate that solTNF-mediated MAPKi resistance in BRAFV600E+ melanomas is predicated on TNFR1 and TNFR2 co-expression, where TNFR1 is the central mediator of NF-kB signaling, while TNFR2 plays an auxiliary role. solTNF-mediated effects are transient and can be abrogated with biologics. Evaluation of patient specimens indicates that TNFR2 is expressed on 50% of primary BRAFV600E+ melanoma cells and that MAPKi therapy may lead to the enrichment of TNFR2-expressing tumor cells.

Conclusions

Our data suggest that TNFR2 is essential to solTNF-induced MAPKi resistance and a possible biomarker to identify melanoma patients that can benefit from solTNF-targeting therapies.
Dose-escalated radiotherapy to 82 Gy for prostate cancer following insertion of a peri-rectal hydrogel spacer: 3-year outcomes from a phase II trial
Authors: See Andrew W. , Bowden Patrick , Wells Geoffrey , Appu Sree , Lawrentschuk Nathan , Liodakis Peter , Pandeli Chloe , Aarons Yolanda , Smyth Lloyd M. L. , McKenzie Dean P.
Published: July 2022

Background

Dose-escalation to above 80 Gy during external beam radiotherapy for localised prostate cancer leads to improved oncological outcomes but also substantially increased rectal toxicity. The aim of this study was to demonstrate the safety and efficacy of escalating the dose to 82 Gy following insertion of a peri-rectal hydrogel spacer (HS) prior to radiotherapy.

Methods

This was a single arm, open-label, prospective study of men with localised prostate cancer who were prescribed a course of intensity modulated radiotherapy escalated to 82 Gy in 2 Gy fractions following insertion of the SpaceOAR™ HS (Boston Scientific, Marlborough, MA). Patients were prescribed a standard course of 78 Gy in 2 Gy fractions where rectal dose constraints could not be met for the 82 Gy plan. The co-primary endpoints were the rate of grade 3 gastrointestinal (GI) and genitourinary (GU) adverse events (CTCAE, v4), and patient-reported quality of life (QoL) (EORTC QLQ-C30 and PR25 modules), up to 37.5 months post-treatment.

Results

Seventy patients received treatment on the study, with 64 (91.4%) receiving an 82 Gy treatment course. The median follow-up time post-treatment was 37.4 months. The rate of radiotherapy-related grade 3 GI and GU adverse events was 0% and 2.9%, respectively. There were 2 (2.9%) grade 3 adverse events related to insertion of the HS. Only small and transient declines in QoL were observed; there was no clinically or statistically significant decline in QoL beyond 13.5 months and up to 37.5 months post-treatment, compared to baseline. No late RTOG-defined grade ≥ 2 GI toxicity was observed, with no GI toxicity observed in any patient at 37.5 months post-treatment. Nine (12.9%) patients met criteria for biochemical failure within the follow-up period.

Conclusions

Dose-escalation to 82 Gy, facilitated by use of a hydrogel spacer, is safe and feasible, with minimal toxicity up to 37.5 months post-treatment when compared to rates of rectal toxicity in previous dose-escalation trials up to 80 Gy. Trials with longer follow-up of oncological and functional outcomes are required to robustly demonstrate a sustained widening of the therapeutic window.

Trial registration Australian New Zealand Clinical Trials Registry, ACTRN12621000056897, 22/01/2021. Retrospectively registered.
YKL-40 changes are not detected in post-mortem brain of patients with Alzheimer’s disease and frontotemporal lobar degeneration
Authors: Hok-A-Hin Yanaika S. , Hoozemans Jeroen J. M. , Hu William T. , Wouters Dorine , Howell Jennifer C. , Rábano Alberto , van der Flier Wiesje M. , Pijnenburg Yolande A. L. , Teunissen Charlotte E. , del Campo Marta
Published: July 2022

Background

YKL-40 (Chitinase 3-like I) is increased in CSF of Alzheimer’s disease (AD) and frontotemporal lobar degeneration (FTLD) patients and is therefore considered a potential neuroinflammatory biomarker. Whether changed YKL-40 levels in the CSF reflect dysregulation of YKL-40 in the brain is not completely understood yet. We aimed to extensively analyze YKL-40 levels in the brain of AD and different FTLD pathological subtypes. The direct relationship between YKL-40 levels in post-mortem brain and ante-mortem CSF was examined in a small set of paired brain-CSF samples.

Method

YKL-40 was analyzed in post-mortem temporal and frontal cortex of non-demented controls and patients with AD and FTLD (including FTLD-Tau and FTLD-TDP) pathology by immunohistochemistry (temporal cortex: 51 controls and 56 AD and frontal cortex: 7 controls and 24 FTLD patients), western blot (frontal cortex: 14 controls, 5 AD and 67 FTLD patients), or ELISA (temporal cortex: 11 controls and 7 AD and frontal cortex: 14 controls, 5 AD and 67 FTLD patients). YKL-40 levels were also measured in paired post-mortem brain and ante-mortem CSF samples from dementia patients (n = 9, time-interval collection: 1.4 years) by ELISA.

Results

We observed that YKL-40 post-mortem brain levels were similar between AD, FTLD, and controls as shown by immunohistochemistry, western blot, and ELISA. Interestingly, strong YKL-40 immunoreactivity was observed in AD cases with cerebral amyloid angiopathy (CAA; n = 6). In paired CSF-brain samples, YKL-40 concentration was 8-times higher in CSF compared to brain.

Conclusion

Our data suggest that CSF YKL-40 changes may not reflect YKL-40 changes within AD and FTLD pathological brain areas. The YKL-40 reactivity associated with classical CAA hallmarks indicates a possible relationship between YKL-40, neuroinflammation, and vascular pathology.
Microsurgical repair of severed thoracic spinal cord and clinical outcome: technical case report
Authors: Kaliaperumal Chandrasekaran
Published: July 2022

Background

This report describes a case of successful repair of severed thoracic spine in a young man who presented with a penetrating stab injury to spine resulting in Brown-Séquard syndrome. Surgical technique and post-operative management is discussed.

Case presentation

A 34-year-old fit and well healthy man was admitted with a history of stab injury to the thoracic spine at thoracic T2/3 level with ASIA impairment score (AIS) score D with an incomplete spinal cord affecting his left lower limb with complete paralysis and right lower limb paresis with impaired sensation below T6 level to L5. Neuroimaging confirmed a penetrating knife injury traversing the T2/3 level causing hemi-section of the spinal cord confirmed intraoperatively. He underwent an urgent exploratory surgery of his spine and a T2/3 laminectomy was performed to aid removal of the knife. The dura was noted to be contused and severed spinal cord was noted to be severed with associated cord oedema. A microsurgical repair of the severed cord was performed with duroplasty followed by intense neuro-rehabilitation. On a 3 month follow up his AIS score is E with lower limb power is 5/5 bilaterally and he is able to mobilise independently up to 8–10 steps without any supportive aid and with crutches he is independently functional and mobile.

Conclusion

This is the first documented case of microsurgical repair of severed thoracic spinal cord secondary to traumatic knife injury. In the management of such scenario, apart from the removal of foreign body, repair of the cord with duroplasty should be carefully considered. The role of spinal neuroplasticity in healing following timely repair of the spinal cord along with intense rehabilitation remains the key. This had resulted in a good clinical and functional outcome with in a 18-month follow up.
Molecular characterization and genetic divergence of seven Culex mosquito (Diptera: Culicidae) species using Mt COI gene from Odisha State, India
Authors: Panda Deepika , Barik Tapan Kumar
Published: July 2022

Background

Culexmosquitoes are involved in the transmission of arboviral diseases worldwide. Bio-ecology and identification of mosquitoes are of paramount importance to develop species-specific vector control strategies. Genetic-based species-specific approaches that reduce the burden of vector-borne diseases are made possible by molecular techniques.

Results

In the present study, the mitochondrial COI gene ofCulexmosquitoes was used for molecular identification in addition to morpho-taxonomy. Our findings suggested the presence of importantCulexmosquito vectors viz,Culex vishnui,Culex tritaeniorhynchus, Culex bitaeniorhynchus, Culex quinquefasciatus, Culex gelidus, Culex fuscocephala, andCulex fuscanusin the southern part of Odisha state, India.We examined the phylogeny and genetic diversity of the above seven differentCulexpopulations from different geographical locations. An average intra-specific K2P distance of the COI gene was found to be 0.9%. Further, to measure the diversity of theCulexpopulation among different geographical strains, haplotype diversity and nucleotide diversity were compared.Culex fuscanusshowed high polymorphisms and mutations with high nucleotide diversity (0.013) and theCulex quinquefasciatusshowed the lowest variation inP(i), 0.0013 in the intra-population polymorphism analysis of COI sequences. Similarly, the Haplotype diversity (Hd) found inCulex gelidusandCulex fuscocephalawith the value of 0.972 andCulex quinquefasciatus(0.583) showed the lowest value of haplotype diversity. A haplotype network was constructed to establish the genealogical relationship between haplotypes. The phylogenetic tree was constructed that produces distinctive conspecific clusters in differentCulexspecies. Population genetic study has illustrated the occurrence of genetic differentiation within the population.

Conclusions

The findings of this study contribute to greater evidence that DNA barcode sequences can be used to monitor mosquito species diversity. This study also adds valuable information about the systematics and molecular biology of seven public health important mosquito species acting as a significant vector for Japanese encephalitis in various Asian continents. This information is further used for the effective implementation of region-specific vector control strategies.
Occurrence, distribution, and management of tomato yellow leaf curl virus in China
Authors: Li Fangfang , Qiao Rui , Yang Xiuling , Gong Pan , Zhou Xueping
Published: July 2022

Tomato yellow leaf curl virus (TYLCV), belonging to the genus Begomovirus in the family Geminiviridae, is the most damaging virus for global tomato production. This virus has become one of the most studied plant viral pathogens because of its huge economic importance. Since it was firstly identified in Shanghai, China, in 2006, it has been spread to most parts of the country. The widespread occurrence, rapid spread to new regions, and enormous damage to tomato production, makes it an important agricultural pathogen in China. TYLCV has been characterized extensively at the molecular level. This review is focused on the occurrence and distribution of all TYLCV isolates in China, providing valuable information for further epidemiological studies. In addition, management strategies for TYLCV are also proposed, with the ultimate goal to prevent and control the further occurrence of this viral disease.
The role of Fast spin-echo T2-weighted and diffusion-weighted imaging for spine bone marrow changes evaluation in postmenopausal women with osteoporosis
Authors: Hammood Salman Mohammed Abed , Ali Talib Milad , Al-Baghdadi Firas Abdullah , Dehghani Sadegh
Published: July 2022

Background

To prospectively investigate the role of Fast spin-echo T2-weighted (FSE T2-w) and diffusion-weighted imaging (DWI) in magnetic resonance imaging (MRI) for detecting spine bone marrow changes in postmenopausal women with osteoporosis (OP). A total of 101 postmenopausal women, mean age of 60.97 ± 7.41 (range 52–68) years old, who underwent dual-energy X-ray absorptiometry of the spine, were invited to this study and divided into three bone density (normal, osteopenic, and osteoporotic) groups based on T-score. After that MRI scan with both FSE T2-w and DWI of the vertebral body was done to calculate the signal-to-noise ratio (SNR) and apparent diffusion coefficient (ADC). Finally, MRI findings were compared in patients, between three groups and correlated with bone marrow density.

Results

The osteoporotic group showed significantly lower mean ADC values, compared to osteopenic and normal groups (0.58 ± 0.02 vs. 0.36 ± 0.05 vs. 0.24 ± 0.06 × 10–3 mm2/s, p < 0.001). According to these results, a significant positive correlation was found between T-scores and ADC values (r = 0.652, p < 0.001). The mean SNR in FSE T2-w images for normal, osteopenic, and osteoporotic groups was calculated 5.61 ± 0.32, 5.48 ± 0.55, and 6.63 ± 0.67, respectively. No significant correlation was found between the mean SNR and T-score for all groups (r = − 0.304, p > 0.05).

Conclusions

DWI can be used as a noninvasive, quantitative, and valuable technique for OP evaluation. While, routine MRI needs more investigation to be demonstrated as a reliable diagnostic indicator for OP.
Translocation of Broca’s area in a case of low-grade glioma: reinforcing the importance of preoperative functional magnetic resonance imaging
Authors: Arora Suryansh , Vani Kavita
Published: July 2022

Background

Functional MRI has enabled us to map the anatomical location of functional areas of brain including language centers and thus provides useful insights in preoperative planning and assessment for neurosurgeons. In recent years, fMRI has also provided evidence for neuroplasticity which implies that brain pathways have an ability to reorganize in response to any injury.

Case presentation

We present a case of a 27-year-old male, postoperative case of left frontotemporal glioma (WHO grade II) with residual tumor in inferior frontal, temporal and insular lobe in whom functional magnetic resonance imaging was carried out to elicit language centers. fMRI revealed activation of Wernicke’s area in left cerebral hemisphere in the right-handed patient, while Broca’s area was activated in right cerebral hemisphere, thus eliciting the translocation of Broca’s area in response to low-grade glioma.

Conclusions

This case provided an example of the ability of brain to reorganize pathways in response to injury or insult. The routine use of preoperative fMRI in such cases will help in better planning and lead to an improved postoperative outcome.
Artificial Neural network-based prediction of SCF at the Intersection of CFST Y-joints
Authors: Xiao Lin , Wei Xing , Zhao Junming , Kang Zhirui
Published: July 2022

Stress concentration factors (SCFs) are used to quantify the hot-spots stress in tubular joints with circular hollow section for fatigue assessment, which are always obtained by finite element analysis or specimens testing. According to design specifications, complex formulas are recommended to calculate the SCFs at special locations of the intersection lines weld toe of tubular joints for individual load cases. To improve the fatigue performance of the joint, the concrete is filled in the chord to form a concrete-filled steel tube (CFST) joint. The capability of back-propagation neural network-based (BPNN) model in calculation of the SCFs in CFST Y-joints was investigated in this study. Three hundred FE numerical models were investigated to evaluate the effects of changes in different geometrical parameters on the SCFs of CFST Y-joint and the FEA results were used to train and test the neural networks. The nonlinear mapping relationships between the affecting variables and the SCFs distributions were established. Research results showed that SCFs prediction results of CFST Y-joints from BPNN models are close to the FE results, and properly trained and well calibrated BPNN can be reliable alternatives to complicated SCFs equations for predicting SCFs distribution at intersection line of CFST Y-joints.
Short-stay crisis units for mental health patients on crisis care pathways: systematic review and meta-analysis
Authors: Anderson Katie , Goldsmith Lucy P. , Lomani Jo , Ali Zena , Clarke Geraldine , Crowe Chloe , Jarman Heather , Johnson Sonia , McDaid David , Pariza Paris , Park A-La , Smith Jared A. , Stovold Elizabeth , Turner Kati , Gillard Steve
Published: July 2022

Background

Internationally, an increasing proportion of emergency department visits are mental health related. Concurrently, psychiatric wards are often occupied above capacity. Healthcare providers have introduced short-stay, hospital-based crisis units offering a therapeutic space for stabilisation, assessment and appropriate referral. Research lags behind roll-out, and a review of the evidence is urgently needed to inform policy and further introduction of similar units.

Aims

This systematic review aims to evaluate the effectiveness of short-stay, hospital-based mental health crisis units.

Method

We searched EMBASE, Medline, CINAHL and PsycINFO up to March 2021. All designs incorporating a control or comparison group were eligible for inclusion, and all effect estimates with a comparison group were extracted and combined meta-analytically where appropriate. We assessed study risk of bias with Risk of Bias in Non-Randomized Studies – of Interventions and Risk of Bias in Randomized Trials.

Results

Data from twelve studies across six countries (Australia, Belgium, Canada, The Netherlands, UK and USA) and 67 505 participants were included. Data indicated that units delivered benefits on many outcomes. Units could reduce psychiatric holds (42% after intervention compared with 49.8% before intervention; difference = 7.8%; P < 0.0001) and increase out-patient follow-up care (χ2 = 37.42, d.f. = 1; P < 0.001). Meta-analysis indicated a significant reduction in length of emergency department stay (by 164.24 min; 95% CI −261.24 to −67.23 min; P < 0.001) and number of in-patient admissions (odds ratio 0.55, 95% CI 0.43–0.68; P < 0.001).

Conclusions

Short-stay mental health crisis units are effective for reducing emergency department wait times and in-patient admissions. Further research should investigate the impact of units on patient experience, and clinical and social outcomes.
Visual phenomenology in schizophrenia and post-traumatic stress disorder: an exploratory study
Authors: Wearne Deborah , Ayalde Jeremiah , Curtis Guy , Gopisetty Aarethi , Banerjee Amit , Melvill-Smith Peter , Orr Kenneth , Rajanthiran Leon , Waters Flavie
Published: July 2022

Background

Visual experiences such as hallucinations are commonly reported by people with psychosis, psychological trauma and dissociative states, although questions remain about their similarities and differences. For diagnostic and therapeutic purposes, clinical research must better delineate and compare the characteristics of these experiences in post-traumatic stress disorder (PTSD) and in schizophrenia.

Aims

To compare visual phenomena and dissociation in participants with a primary psychotic illness and those with a trauma diagnosis.

Method

A quantitative group design study comparing visual phenomena in three participant groups who also have a history of hearing voices: schizophrenia and no trauma history (n = 19), PTSD with dissociation (n = 17) and comorbid schizophrenia and PTSD (n = 20). Validated clinical measures included the North-East Visual Hallucination Interview, PTSD Symptoms Scale Interview, Clinician Administered Dissociative States Scale, Psychotic Symptoms Rating Scales and Positive and Negative Syndrome Scale.

Results

There was a remarkable similarity in visual experiences, including rates of complex visual hallucinations, between the three diagnostic groups. There were no significant differences in the severity or components of distress surrounding the visual experiences. Dissociation predicted visual hallucination severity for the comorbid schizophrenia and PTSD group, but not for PTSD or schizophrenia alone.

Conclusions

Visual experiences in PTSD can include visual hallucinations that are indistinguishable from those experienced in schizophrenia. Multimodal hallucinations are frequently observed in both schizophrenia and PTSD. A model for visual hallucinations in PTSD is suggested, following two separate neurobiological pathways based on distinct responses to trauma.
Manifestations of Opioid Stigma in Patients With Advanced Cancer: Perspectives From Patients and Their Support Providers
Authors: Bulls Hailey W. , Hamm Megan , Wasilko Rachel , de Abril Cameron Flor , Belin Shane , Goodin Burel R. , Liebschutz Jane M. , Wozniak Antoinette , Sabik Lindsay M. , Merlin Jessica S. , Schenker Yael
Published: July 2022

PURPOSE:

Stigma surrounding prescription opioids, or opioid stigma, is increasingly recognized as a barrier to effective and guideline-concordant cancer pain management. Patients with advanced cancer report high rates of pain and prescription opioid exposure, yet little is known about how opioid stigma may manifest in this population.

METHODS:

We conducted in-depth qualitative interviews with 20 patients with advanced cancer and 11 support providers between March 2020, and May 2021. We took a rigorous inductive, qualitative descriptive approach to characterize how opioid stigma manifests in the lives of patients with advanced cancer.

RESULTS:

Patients and their support providers described three primary manifestations of opioid stigma: (1) direct experiences with opioid stigma and discrimination in health care settings (eg, negative, stigmatizing interactions in pharmacies or a pain clinic); (2) concerns about opioid stigma affecting patient care in the future, or anticipated stigma; and (3) opioid-restricting attitudes and behaviors that may reflect internalized stigma and fear of addiction (eg, feelings of guilt).

CONCLUSION:

This qualitative study advances our understanding of opioid stigma manifestations in patients with advanced cancer, as well as coping strategies that patients may use to alleviate their unease (eg, minimizing prescription opioid use, changing clinicians, and distancing from perceptions of addiction). In recognition of the costs of undermanaged cancer pain, it is important to consider innovative treatment strategies to address opioid stigma and improve pain management for patients with advanced cancer. Future research should examine opportunities to build an effective, multilevel opioid stigma intervention targeting patients, clinicians, and health care systems.
Prediction of Vitamin D Deficiency in Older Adults: The Role of Machine Learning Models
Authors: Sluyter John D , Raita Yoshihiko , Hasegawa Kohei , Reid Ian R , Scragg Robert , Camargo Carlos A
Published: July 2022

Context

Conventional prediction models for vitamin D deficiency have limited accuracy.

Background

Using cross-sectional data, we developed models based on machine learning (ML) and compared their performance with those based on a conventional approach.

Methods

Participants were 5106 community-resident adults (50-84 years; 58% male). In the randomly sampled training set (65%), we constructed 5 ML models: lasso regression, elastic net regression, random forest, gradient boosted decision tree, and dense neural network. The reference model was a logistic regression model. Outcomes were deseasonalized serum 25-hydroxyvitamin D (25(OH)D) <50 nmol/L (yes/no) and <25 nmol/L (yes/no). In the test set (the remaining 35%), we evaluated predictive performance of each model, including area under the receiver operating characteristic curve (AUC) and net benefit (decision curves).

Results

Overall, 1270 (25%) and 91 (2%) had 25(OH)D <50 and <25 nmol/L, respectively. Compared with the reference model, the ML models predicted 25(OH)D <50 nmol/L with similar accuracy. However, for prediction of 25(OH)D <25 nmol/L, all ML models had higher AUC point estimates than the reference model by up to 0.14. AUC was highest for elastic net regression (0.93; 95% CI 0.90-0.96), compared with 0.81 (95% CI 0.71-0.91) for the reference model. In the decision curve analysis, ML models mostly achieved a greater net benefit across a range of thresholds.

Conclusion

Compared with conventional models, ML models predicted 25(OH)D <50 nmol/L with similar accuracy but they predicted 25(OH)D <25 nmol/L with greater accuracy. The latter finding suggests a role for ML models in participant selection for vitamin D supplement trials.
Target-dependent suppression of siRNA production modulates the levels of endogenous siRNAs in the Caenorhabditis elegans germline
Authors: Gajic Zoran , Kaur Diljeet , Ni Julie , Zhu Zhaorong , Zhebrun Anna , Gajic Maria , Kim Matthew , Hong Julia , Priyadarshini Monika , Frøkjær-Jensen Christian , Gu Sam
Published: July 2022

Despite the prominent role of endo-siRNAs in transposon silencing, their expression is not limited to these ‘nonself’ DNA elements. Transcripts of protein-coding genes (‘self’ DNA) in some cases also produce endo-siRNAs in yeast, plants and animals. How cells distinguish these two populations of siRNAs to prevent unwanted silencing of active genes in animals is not well understood. To address this question, we inserted various self-gene or gfp fragments into an LTR retrotransposon that produces abundant siRNAs and examined the propensity of these gene fragments to produce ectopic siRNAs in the Caenorhabditis elegans germline. We found that fragments of germline genes are generally protected from production of ectopic siRNAs. This phenomenon, which we termed ‘target-directed suppression of siRNA production’ (or siRNA suppression), is dependent on the germline expression of target mRNA and requires germline P-granule components. We found that siRNA suppression can also occur in naturally produced endo-siRNAs. We suggest that siRNA suppression plays an important role in regulating siRNA expression and preventing self-genes from aberrant epigenetic silencing.

This article has an associated ‘The people behind the papers’ interview.
The potential of a nomogram combined PI-RADS v2.1 and contrast-enhanced ultrasound (CEUS) to reduce unnecessary biopsies in prostate cancer diagnostics
Authors: Liu Yunyun , Wang Shuai , Xiang Li-Hua , Xu Guang , Dong Lin , Sun Yikang , Ye Beibei , Zhang Yifeng , Xu Huixiong
Published: July 2022

Objectives:

To develop a nomogram prediction model based on Prostate Imaging Reporting and Data System v.2.1 (PI-RADS v2.1) and contrast-enhanced ultrasound (CEUS) for predicting prostate cancer (PCa) and clinically significant prostate cancer (csPCa) in males with prostate-specific antigen (PSA) 4–10 ng ml−1 to avoid unnecessary biopsy.

Methods:

A total of 490 patients who underwent prostate biopsy for PSA 4–10 ng ml−1 were enrolled and randomly divided into a pilot cohort (70%) and a validation cohort (30%). Univariate and multivariate logistic regression models were constructed to select potential predictors of PCa and csPCa, and a nomogram was created. The area under receiver operating characteristic (ROC) curve (AUC) was calculated, and compared using DeLong’s test. The diagnostic performance and unnecessary biopsy rate of the nomogram prediction model were also assessed. Hosmer-Lemeshow goodness-of-fit test was employed to test for model fitness.

Results:

The multivariate analysis revealed that features independently associated with PCa and csPCa were age, PI-RADS score and CEUS manifestations. Incorporating these factors, the nomogram achieved good discrimination performance of AUC 0.843 for PCa, 0.876 for csPCa in the pilot cohort, and 0.818 for PCa, 0.857 for csPCa in the validation cohort, respectively, and had well-fitted calibration curves. And the diagnostic performance of the nomogram was comparable to the model including all the parameters (p > 0.05). Besides, the nomogram prediction model yielded meaningful reduction in unnecessary biopsy rate (from 74.8 to 21.1% in PCa, and from 83.7 to 5.4% in csPCa).

Conclusions:

The nomogram prediction model based on age, PI-RADS v2.1 and CEUS achieved an optimal prediction of PCa and csPCa. Using this model, the PCa risk for an individual patient can be estimated, which can lead to a rational biopsy choice.

Advances in knowledge:

This study gives an account of improving pre-biopsy risk stratification in males with “gray zone” PSA level through PI-RADS v2.1 and CEUS.