bluuebunny/crossref_metadata_2025 huggingface dataset:
Colposcopic accuracy in diagnosing squamous intraepithelial lesions: a systematic review and meta-analysis of the International Federation of Cervical Pathology and Colposcopy 2011 terminology
Authors: Qin Dongxu , Bai Anying , Xue Peng , Seery Samuel , Wang Jiaxu , Mendez Maria Jose Gonzalez , Li Qing , Jiang Yu , Qiao Youlin
Published: February 2023

Background

Colposcopy is an important tool in diagnosing cervical cancer, and the International Federation of Cervical Pathology and Colposcopy (IFCPC) issued the latest version of the guidelines in 2011. This study aims to systematically assess the accuracy of colposcopy in predicting low-grade squamous intraepithelial lesions or worse (LSIL+) / high-grade squamous intraepithelial lesions or worse (HSIL+) under the 2011 IFCPC terminology.

Methods

We performed a systematic review and meta-analysis, following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We searched for studies about the performance of colposcopy in diagnosing cervical intraepithelial neoplasia under the new IFCPC colposcopy terminology from PubMed, Embase, Web of Science and the Cochrane database. Data were independently extracted by two authors and an overall diagnostic performance index was calculated under two colposcopic thresholds.

Results

Totally, fifteen articles with 22,764 participants in compliance with the criteria were included in meta-analysis. When colposcopy was used to detect LSIL+, the combined sensitivity and specificity were 0.92 (95% CI 0.88–0.95) and 0.51 (0.43–0.59), respectively. When colposcopy was used to detect HSIL+, the combined sensitivity and specificity were 0.68 (0.58–0.76) and 0.93 (0.88–0.96), respectively.

Conclusion

In accordance with the 2011 IFCPC terminology, the accuracy of colposcopy has improved in terms of both sensitivity and specificity. Colposcopy is now more sensitive with LSIL+ taken as the cut-off value and is more specific to HSIL+. These findings suggest we are avoiding under- or overdiagnosis both of which impact on patients’ well-being.
Comparison of simultaneous vs sequential pars plana vitrectomy and cataract surgery
Authors: Awidi Abdelhalim A. , Mathews Priya M. , Shekhawat Nakul , Woreta Fasika A. , Srikumaran Divya , Daoud Yassine J.
Published: February 2023

Background

To compare the clinical outcomes of patients undergoing sequential pars plana vitrectomy (PPV) followed by cataract extraction surgery (CE) [PPV/CE], simultaneous PPV and CE (PPV + CE), and sequential CE followed by PPV [CE/PPV].

Methods

A retrospective observational cohort study of 427 eyes of 404 patients who underwent either sequential or simultaneous PPV and CE surgery between March 2016 and May 2021. Pre-operative and post-operative assessments (up to 2 years of follow-up visits) of uncorrected visual acuity (UCVA), corrected distance visual acuity (CDVA), spherical equivalent (SEQ), and refractive prediction error (RPE) was done. Main outcome measures were both visual (UCVA, CDVA) and refractive (RPE, SEQ).

Results

There was a statistically significant difference in CDVA of the PPV/CE, PPV + CE, CE/PPV groups (logMAR 0.34 ± 0.40, 0.65 ± 0.61, and 0.55 ± 0.60, respectively) at one month postoperatively (POM1) (P < 0.001), and at the POM12 visits (logMAR 0.25 ± 0.34, 0.53 ± 0.68, and 0.44 ± 0.48; P = 0.04). In the subgroup analysis of patients with a diagnosis of either epiretinal membrane or vitreous opacities, there was no statistically significant difference in SEQ (P = 0.09) and RPE (P = 0.13) at the combined 1 month and 3 month visits.

Conclusion

Simultaneous PPV and cataract surgery demonstrated similar improvements in visual acuity and refractive outcomes, as well as comparable intraoperative and postoperative complication profiles to sequential surgery.
Validity and reliability of the Chinese version of the Health Literacy Scale Short-Form in the Chinese population
Authors: Sun Xiaonan , Lv Ke , Wang Fei , Ge Pu , Niu Yuyao , Yu Wenli , Sun Xinying , Ming Wai-Kit , He Miao , Wu Yibo
Published: February 2023

Background

Health literacy is closely related to health status. Measuring public health literacy levels helps to warn of health status and manage health problems through timely interventions. The items of relevant evaluation tools are complex and numerous in China, and there is no recognized health literacy brief scale for the whole population. To translate the 12-item short-form health literacy scale (HLS-SF12) and test the validity and reliability of the Chinese version of the HLS-SF12 in the Chinese population.

Methods

The HLS-SF12 was translated into Chinese using the procedures of translation, back translation, and cultural debugging. 10,951 residents were selected by quota sampling method to test the validity and reliability of the scale, and 33 people were selected to retest after 2 weeks. The reliability was tested by using internal consistency coefficient and test-retest reliability. The validity was tested by using confirmatory factor analysis, content validity, convergent validity and discriminant validity.

Results

The Cronbach’s Alpha coefficient for the total scale was 0.94, and the test-retest reliability was 0.89. The Cronbach’s Alpha coefficients for the three subscales of health care, disease prevention, and health promotion respectively were 0.86, 0.86, 0.87, and the test-retest reliability respectively were 0.91, 0.79, 0.63. The confirmatory factor analysis identified a three factors model and showed nice goodness of fit indices for Chinese HLS-SF12 (GFI = 0.96, CFI = 0.97, IFI = 0.97, TLI = 0.96, and RMSEA = 0.07).

Conclusion

The Chinese version of the HLS-SF12 has good reliability and validity, and can be used as a tool to evaluate the health literacy of Chinese people.
COVID-19 induced changes in physical activity patterns, screen time and sleep among Swedish adolescents - a cohort study
Authors: Helgadóttir Björg , Fröberg Andreas , Kjellenberg Karin , Ekblom Örjan , Nyberg Gisela
Published: February 2023

Background

The coronavirus disease 2019 (COVID-19) pandemic had a huge impact on daily life, even in countries such as Sweden where the restrictions were relatively mild. This paper assesses the effects of the COVID-19 pandemic restrictions on physical activity (PA) patterns, screen time, and sleep among Swedish adolescents. The exposures explored include gender, parental education, anthropometrics, and cardiovascular fitness (CVF).

Methods

Cohort data were collected from September 26th to December 6th, 2019, and from April 12th to June 9th, 2021. Participants were 13–14 years-old (7th graders) at baseline with 585 participating at both baseline and follow-up. At both baseline and follow-up PA and sedentary time were measured with accelerometers, and sleep and screen time with questionnaires. The exposure variables (gender, parental education, anthropometrics and CVF) were collected at baseline. Multilevel linear regression analyses were performed.

Results

Moderate-to-vigorous-physical activity (MVPA) remained unchanged while light physical activity (LiPA) decreased and sedentary time increased. Sleep duration decreased and screen time increased. Girls, adolescents with overweight/obesity (BMI and percent body fat), and those with lower CVF at baseline had less favourable changes in PA patterns, sleep and screen time.

Conclusions

Although no significant (α = 0.05) changes were seen in MVPA, both LiPA and sedentary time as well as sleep and screen time changed in unfavourable ways. More intense activities are often organised and seem to have withstood the pandemic, while less intense activities decreased. Some groups were more vulnerable and will need directed intervention in the post-pandemic period as well as when future pandemics hit.
Association between children living with obesity and Mental Health problems: a data analysis of the Welsh Health Survey, UK
Authors: Beynon Claire
Published: February 2023

Background

Obesity and mental health problems in children are both significant and growing public health issues. There is mixed evidence on the relationship between obesity and mental health in children. This study examines the association between obesity and mental health problems in a nationally representative sample of children using the Welsh Health Survey for Children (n = 11,279 aged 4–15 years).

Methods

The Chi-square test assessed the difference in the proportion of children reporting abnormal mental health scores (strengths and difficulties score ≥ 20) in children living with obesity (≥ 95 centile for age and sex). Then, a multivarible logistic regression was used to assess any association after accounting for confounding variables.

Results

There were 1,582 children living with obesity in the study (19.6%). The Chi-square test indicated a significant difference in the proportion of children with abnormal mental health scores in children living with obesity (p = 0.001). This study found a very small but significant positive association between mental health and childhood obesity after accounting for confounding variables, Odds Ratio 1.02 (95%CI: 1.01 to 1.02, p = 0.001). However, socio-economic status was more of a driver.

Conclusion

The findings of this study show a very small but significant association between childhood obesity and mental health problems. The multivariable logistic regression indicates that the focus must remain on reducing health inequalities as this is a more important driver of child health and well-being. However, as a precautionary measure it may be worth considering if children living with obesity who present for weight-management services may benefit from a review of their mental health status to identify if further support is needed, if capacity allows, and this can be done in a supportive way.
Promotion of the resistance of human oral epithelial cells to herpes simplex virus type I infection via N6-methyladenosine modification
Authors: Xu Junping , Qi Yuping , Ju Qi
Published: February 2023

Objective

This study aimed to explore the mechanism behind N6-methyladenosine (m6A) modification of the total ribonucleic acid (RNA) involved in the resistance to herpes simplex virus type I (HSV-1) infection in oral epithelial cells.

Method

The variation in m6A modification level on messenger RNA following HSV-1 infection was determined using the RNA dot blot method. The expression levels of alpha-ketoglutarate-dependent dioxygenase lab homolog 5 (ALKBH5) protein and fatty mass and obesity-associated genes (FTO) were determined using real-time fluorescence quantification polymerase chain reaction and the western blot technique, respectively. Next, after suppressing the expression of ALKBH5 or FTO via small interfering RNA, human immortalised oral epithelial cells (HIOECs) were infected with HSV-1, followed by measurement of the viral load or expression level of type I interferon (I-IFN) and interferon-stimulated genes (ISGs).

Results

The m6A modification level was significantly increased following HSV-1 infection of the HIOECs (P < 0.05), while the expression of ALKBH5 and FTO genes was reduced (P < 0.01). Moreover, the suppression of ALKBH5 or FTO increased the production of I-IFN and ISGs during the HSV-1 infection of the HIOECs (P < 0.01), and the viral load was significantly reduced (P < 0.01).

Conclusion

During oral HSV-1 infection, the m6A level was increased through the down-regulation of ALBHK5 and FTO expression, increasing I-IFN production and the promotion of HSV-1 clearing in HIOECs.
Dying, death and bereavement: developing a national survey of bereaved relatives
Authors: Ó Coimín Diarmuid , Rohde Daniela , Foley Conor , O’Carroll Tracy , Murphy Róisín
Published: February 2023

Background

Assessing and measuring the experience and quality of care provided is central to the improvement of care delivery of all healthcare systems. This paper reports on the development of a survey instrument to capture the experiences of care at end of life from the perspective of bereaved relatives in the Republic of Ireland.

Methods

A multi-method, multi-stakeholder, sequential approach was adopted for this study. Items for inclusion in the survey instrument bank were identified through (1) a feasibility study and scoping literature review, (2) expert panel programme board review, (3) focus groups and (4) gap analysis. The following steps were undertaken to prioritise the items for inclusion in the final survey instrument: (1) a Delphi study (2) technical expert panel review (3) cognitive interviews with bereaved relatives and an (4) expert panel programme board review.

Results

Following an iterative process with key stakeholders, a survey instrument was developed with sections focusing on the provision of care at home, in the last nursing home / residential care facility, hospice and hospital, as well as care experience in the last 2 days of life, the relative’s experiences of care and support, the circumstances of care surrounding death and demographic information. In total, a bank of 123 questions were prioritised to be included in the National End of Life Survey instrument.

Conclusion

The survey will provide a standardised national approach to capturing the experience of care of those who have died, from the perspective of bereaved relatives in the Republic of Ireland. This will allow health service providers, policy makers and regulators to gather important insights into the experiences of care at end of life and will help fulfil the requirement of healthcare services to ensure they are providing high-quality care.
Clinical analysis of 312 patients with stage IB1-IIA2 cervical squamous cell carcinoma and research on the influencing factors of postoperative recurrence
Authors: Zeng Jia , Zuo Jing , Li Ning , Yao HongWen , Zhang YuanYuan , Zhao YuXi , Wang TianTian , Xiu Lin , Li Jian , Yu Jing , Liang LeiLei , Wu LingYing
Published: February 2023

Objective

To investigate the influencing factors of the recurrence of IB1-IIA2 cervical squamous cell carcinoma after surgical treatment, and to explore the relationship between high-risk human papillomavirus (HR-HPV) infection and postoperative cervical squamous cell carcinoma recurrence.

Methods

Patients (n = 312) diagnosed with stage IB1-IIA2 cervical cancer and treated by radical hysterectomy and lymphadenectomy at this hospital were accrued between January 2014 and December 2016. The clinical data of these patients were analysed, and the association among clinicopathological factors, the association among clinicopathological factors, HPV infection and recurrences was investigated through Cox regression.

Results

The median follow-up time was 59.2 months (with a range of 14–77.9 months). The pre-operative HPV infection rate was 85.3% (266/312), and 74 patients had a high level of HPV-DNA (> 5 × 106 copy number / 104 cells). Twenty-nine patients had a postoperative persistent high level of HPV-DNA (9.3%). On multivariate analysis, deep 1/3 stromal invasion (hazard ratio [HR] 114.79, 95% confidence interval [CI] 2.821–4670.111, p = 0.012*) and postoperative persistence of high HPV-DNA levels within 12 months (HR 269.044, 95% CI 14.437–5013.754, p < 0.001*) and 24 months (HR 31.299, 95% CI 1.191–822.215, p = 0.039*) were associated with a higher local recurrence rate.

Conclusion

Continuous high HPV-DNA levels within 24 months of an operation and deep 1/3 interstitial infiltration were independent risk factors for local recurrences of cervical cancer.
Neuroimaging studies of acupuncture on Alzheimer’s disease: a systematic review
Authors: Yin Zihan , Wang Ziqi , Li Yaqin , Zhou Jun , Chen Zhenghong , Xia Manze , Zhang Xinyue , Wu Jiajing , Zhao Ling , Liang Fanrong
Published: February 2023

Background

Acupuncture effectively improves cognitive function in Alzheimer’s disease (AD). Many neuroimaging studies have found significant brain alterations after acupuncture treatment of AD, but the underlying central modulation mechanism is unclear.

Objective

This review aims to provide neuroimaging evidence to understand the central mechanisms of acupuncture in patients with AD.

Methods

Relevant neuroimaging studies about acupuncture for AD were retrieved from eight English and Chinese medicine databases (PubMed, Embase, Cochrane Library, Web of Science, SinoMed, CNKI, WF, VIP) and other resources from inception of databases until June 1, 2022, and their methodological quality was assessed using RoB 2.0 and ROBINS - I. Brain neuroimaging information was extracted to investigate the potential neural mechanism of acupuncture for AD. Descriptive statistics were used for data analysis.

Results

Thirteen neuroimaging studies involving 275 participants were included in this review, and the overall methodological quality of included studies was moderate. The approaches applied included task-state functional magnetic resonance imaging (ts-fMRI;n = 9 studies) and rest-state functional magnetic resonance imaging (rs-fMRI;n = 4 studies). All studies focused on the instant effect of acupuncture on the brains of AD participants, including the cingulate gyrus, middle frontal gyrus, and cerebellum, indicating that acupuncture may regulate the default mode, central executive, and frontoparietal networks.

Conclusion

This study provides evidence of the neural mechanisms underlying the effect of acupuncture on AD involving cognitive- and motor-associated networks. However, this evidence is still in the preliminary investigation stage. Large-scale, well-designed, multimodal neuroimaging trials are still required to provide comprehensive insight into the central mechanism underlying the effect of acupuncture on AD. (Systematic review registration at PROSPERO, No. CRD42022331527).
Process control: simply a matter of efficiency or of survival and costs? A single-centre quality improvement project in living donor renal transplant
Authors: Paoletti Filippo , Giorgio Vittori , Jaser Adel , Zanoni Natalia Romina , Ricciardi Walter , Citterio Franco , De Belvis Antonio Giulio
Published: February 2023

Background

Rising incidence and prevalence of end-stage renal disease is a worldwide concern for sustainability of healthcare systems and societies. Living donor renal transplant [LDRT] provides highest health achievements and cost containment than any alternative form of renal replacement therapy. Nonetheless, about 25% of potential LDRTs are missed for causes directly related with inadequate timing in donor assessment. Our quality improvement (QI) project implement process control tools and strategy aiming at reducing total evaluation time for donor candidates and minimizing dialysis exposure for intended recipients, which are the two main determinants of clinical outcomes and costs.

Methods

The study includes patients who underwent donor nephrectomy between January 1, 2017 and December 31, 2021. Six Sigma DMAIC approach was adopted to assess Base Case performance (Jan2017-Jun2019) and to design and implement our QI project. Study of current state analysis focused on distribution of time intervals within the assessment process, analysis of roles and impacts of involved healthcare providers and identification of targets of improvement. Improved Scenario (Jul2019-Dec2021) was assessed in terms of total lead time reduction, total pre-transplantation dialysis exposure and costs reduction, and increase in pre-emptive transplantations. The study was reported following SQUIRE 2.0 Guidelines for QI projects.

Results

Study population includes 63 patients, 37 in Base Case and 26 in Improved Scenario. Total lead time reduced from a median of 293 to 166 days and this in turn reduced pre-transplantation dialysis exposure and costs by 45%. Rate of potential pre-emptive donors’ loss changes from 44% to 27%.

Conclusions

Lean methodology is an effective tool to improve quality and efficiency of healthcare processes, in the interest of patients, healthcare professionals and payers.
Ultrasmall and highly biocompatible carbon dots derived from natural plant with amelioration against acute kidney injury
Authors: Wang Xiaoke , Wu Tong , Yang Yingxin , Zhou Long , Wang Shuxian , Liu Jiaxing , Zhao Yafang , Zhang Meiling , Zhao Yan , Qu Huihua , Kong Hui , Zhang Yue
Published: February 2023

Background

Acute kidney injury (AKI) refers to a tricky clinical disease, known by its high morbidity and mortality, with no real specific medicine for AKI. The carbonization product from Pollen Typhae (i.e., Pu-huang in China) has been extensively employed in clinic, and it is capable of relieving the renal damage and other diseases in China since acient times.

Results

Inspired by the carbonization process of Traditional Chinese Medicine (TCM), a novel species of carbon dots derived from Pollen Typhae (PT-CDs) was separated and then collected using a one-pot pyrolysis method. The as-prepared PT-CDs (4.85 ± 2.06 nm) with negative charge and abundant oxygenated groups exhibited high solubility, and they were stable in water. Moreover, the rhabdomyolysis (RM)-induced AKI rat model was used, and it was first demonstrated that PT-CDs had significant activity in improving the level of BUN and CRE, urine volume and kidney index, and histopathological morphology in RM-induced AKI rats. It is noteworthy that interventions of PT-CDs significantly reduced degree of inflammatory reaction and oxidative stress, which may be correlated with the basial potential mechanism of anti-AKI activities. Furthermore, cytotoxicity assay and biosafety evaluation exhibited high biocompatibility of PT-CDs.

Conclusion

This study offers a novel relieving strategy for AKI based on PT-CDs and suggests its potential to be a related candidate for clinical applications.

Graphical Abstract
High-dose proton beam therapy versus conventional fractionated radiation therapy for newly diagnosed glioblastoma: a propensity score matching analysis
Authors: Matsuda Masahide , Mizumoto Masashi , Kohzuki Hidehiro , Sugii Narushi , Sakurai Hideyuki , Ishikawa Eiichi
Published: February 2023

Background

High-dose proton beam therapy (PBT) uses excellent dose concentricity based on the unique characteristic termed the Bragg peak. PBT is a highly feasible treatment option that improves survival in select patients with newly diagnosed glioblastoma (GBM). However, selection bias remains an issue in prior studies that evaluated the efficacy of PBT. The aim of the present study was to compare the survival outcomes and toxicities of high-dose PBT and conventional radiation therapy (CRT) using propensity score-matched treatment cohorts.

Methods

The analysis included patients with newly diagnosed GBM treated with high-dose PBT of 96.6 Gy (RBE) or CRT of 60 Gy from 2010 to 2020. Propensity score generation and 1:1 matching of patients were performed based on the following covariates: age, sex, tumor location, extent of resection, chemotherapy, immunotherapy, and pre-radiation Karnofsky performance scale score.

Results

From a total of 235 patients, 26 were selected in each group by propensity score matching. The median overall survival (OS) of the PBT group was 28.3 months, while the median OS of the CRT group was 21.2 months. Although acute radiation-related toxicities were equivalent between the PBT and CRT groups, radiation necrosis as a late radiation-related toxicity was observed significantly more frequently in the PBT group.

Conclusions

High-dose PBT provided significant survival benefits for patients with newly diagnosed GBM compared to CRT as shown by propensity score matching analysis. Radiation necrosis remains an issue in high-dose PBT; thus, the establishment of an effective treatment strategy centered on bevacizumab would be essential.
Gut microbiota composition during hospitalization is associated with 60-day mortality after severe COVID-19
Authors: Trøseid Marius , Holter Jan Cato , Holm Kristian , Vestad Beate , Sazonova Taisiia , Granerud Beathe K. , Dyrhol-Riise Anne Ma , Holten Aleksander R. , Tonby Kristian , Kildal Anders Benjamin , Heggelund Lars , Tveita Anders , Bøe Simen , Müller Karl Erik , Jenum Synne , Hov Johannes R. , Ueland Thor ,   Norwegian SARS-CoV-2 study group
Published: February 2023

Background

Gut microbiota alterations have been reported in hospitalized COVID-19 patients, with reduced alpha diversity and altered microbiota composition related to respiratory failure. However, data regarding gut microbiota and mortality are scarce.

Methods

Rectal swabs for gut microbiota analyses were collected within 48 h after hospital admission (baseline; n = 123) and three-month post-admission (n = 50) in a subset of patients included in the Norwegian SARS-CoV2 cohort study. Samples were analysed by sequencing the 16S rRNA gene. Gut microbiota diversity and composition at baseline were assessed in relation to need for intensive care unit (ICU) admission during hospitalization. The primary objective was to investigate whether the ICU-related gut microbiota was associated with 60-day mortality.

Results

Gut microbiota diversity (Shannon index) at baseline was lower in COVID-19 patients requiring ICU admission during hospitalization than in those managed in general wards. A dysbiosis index representing a balance of enriched and reduced taxa in ICU compared with ward patients, including decreased abundance of butyrate-producing microbes and enrichment of a partly oral bacterial flora, was associated with need of ICU admission independent of antibiotic use, dexamethasone use, chronic pulmonary disease, PO2/FiO2 ratio, C-reactive protein, neutrophil counts or creatinine levels (adjusted p < 0.001). The ICU-related dysbiosis index at baseline correlated with systemic inflammation and was associated with 60-day mortality in univariate analyses (Hazard ratio 3.70 [2.00–8.6], p < 0.001), as well as after separate adjustment for covariates. At the three-month follow-up, the dysbiosis index remained elevated in ICU patients compared with ward patients (adjusted p = 0.007).

Conclusions

Although our data should be regarded as exploratory due to low number of clinical end points, they suggest that gut microbiota alterations during hospitalization could be related to poor prognosis after severe COVID-19. Larger studies of gut involvement during COVID-19 in relation to long-term clinical outcome are warranted.

Trial registrationNCT04381819. Retrospectively registered May 11, 2020.
Cheese-whey permeate improves the fitness of Escherichia coli cells during recombinant protein production
Authors: de Divitiis Marcella , Ami Diletta , Pessina Alex , Palmioli Alessandro , Sciandrone Barbara , Airoldi Cristina , Regonesi Maria Elena , Brambilla Luca , Lotti Marina , Natalello Antonino , Brocca Stefania , Mangiagalli Marco
Published: February 2023

Background

Escherichia coli cells are the most frequently used hosts in recombinant protein production processes and mainly require molecules such as IPTG or pure lactose as inducers of heterologous expression. A possible way to reduce the production costs is to replace traditional inducers with waste materials such as cheese whey permeate (CWP). CWP is a secondary by-product generated from the production of the valuable whey proteins, which are obtained from ultrafiltration of cheese whey, a main by-product of the dairy industry, which is rich in lactose.

Results

The effects of CWP collected from an Italian plant were compared with those of traditional inducers on the production of two model proteins (i.e., green fluorescent protein and the toxic Q55 variant of ataxin-3), in E. coli BL21 (DE3) cells. It was found that the high lactose content of CWP (165 g/L) and the antioxidant properties of its micronutrients (vitamins, cofactors and osmolytes) sustain production yields similar to those obtained with traditional inducers, accompanied by the improvement of cell fitness.

Conclusions

CWP has proven to be an effective and low-cost alternative inducer to produce recombinant proteins. Its use thus combines the advantage of exploiting a waste product with that of reducing the production costs of recombinant proteins.
Double-head transformer neural network for molecular property prediction
Authors: Song Yuanbing , Chen Jinghua , Wang Wenju , Chen Gang , Ma Zhichong
Published: February 2023

Existing molecular property prediction methods based on deep learning ignore the generalization ability of the nonlinear representation of molecular features and the reasonable assignment of weights of molecular features, making it difficult to further improve the accuracy of molecular property prediction. To solve the above problems, an end-to-end double-head transformer neural network (DHTNN) is proposed in this paper for high-precision molecular property prediction. For the data distribution characteristics of the molecular dataset, DHTNN specially designs a new activation function, beaf, which can greatly improve the generalization ability of the nonlinear representation of molecular features. A residual network is introduced in the molecular encoding part to solve the gradient explosion problem and ensure that the model can converge quickly. The transformer based on double-head attention is used to extract molecular intrinsic detail features, and the weights are reasonably assigned for predicting molecular properties with high accuracy. Our model, which was tested on the MoleculeNet [1] benchmark dataset, showed significant performance improvements over other state-of-the-art methods.
Thyroid hormone receptor knockout prevents the loss of Xenopus tail regeneration capacity at metamorphic climax
Authors: Wang Shouhong , Shibata Yuki , Fu Liezhen , Tanizaki Yuta , Luu Nga , Bao Lingyu , Peng Zhaoyi , Shi Yun-Bo
Published: February 2023

Background

Animal regeneration is the natural process of replacing or restoring damaged or missing cells, tissues, organs, and even entire body to full function. Studies in mammals have revealed that many organs lose regenerative ability soon after birth when thyroid hormone (T3) level is high. This suggests that T3 play an important role in organ regeneration. Intriguingly, plasma T3 level peaks during amphibian metamorphosis, which is very similar to postembryonic development in humans. In addition, many organs, such as heart and tail, also lose their regenerative ability during metamorphosis. These make frogs as a good model to address how the organs gradually lose their regenerative ability during development and what roles T3 may play in this. Early tail regeneration studies have been done mainly in the tetraploid Xenopus laevis (X. laevis), which is difficult for gene knockout studies. Here we use the highly related but diploid anuran X. tropicalis to investigate the role of T3 signaling in tail regeneration with gene knockout approaches.

Results

We discovered that X. tropicalis tadpoles could regenerate their tail from premetamorphic stages up to the climax stage 59 then lose regenerative capacity as tail resorption begins, just like what observed for X. laevis. To test the hypothesis that T3-induced metamorphic program inhibits tail regeneration, we used TR double knockout (TRDKO) tadpoles lacking both TRα and TRβ, the only two receptor genes in vertebrates, for tail regeneration studies. Our results showed that TRs were not necessary for tail regeneration at all stages. However, unlike wild type tadpoles, TRDKO tadpoles retained regenerative capacity at the climax stages 60/61, likely in part by increasing apoptosis at the early regenerative period and enhancing subsequent cell proliferation. In addition, TRDKO animals had higher levels of amputation-induced expression of many genes implicated to be important for tail regeneration, compared to the non-regenerative wild type tadpoles at stage 61. Finally, the high level of apoptosis in the remaining uncut portion of the tail as wild type tadpoles undergo tail resorption after stage 61 appeared to also contribute to the loss of regenerative ability.

Conclusions

Our findings for the first time revealed an evolutionary conservation in the loss of tail regeneration capacity at metamorphic climax between X. laevis and X. tropicalis. Our studies with molecular and genetic approaches demonstrated that TR-mediated, T3-induced gene regulation program is responsible not only for tail resorption but also for the loss of tail regeneration capacity. Further studies by using the model should uncover how T3 modulates the regenerative outcome and offer potential new avenues for regenerative medicines toward human patients.
Assessing food security among young farmers in Africa: evidence from Kenya, Nigeria, and Uganda
Authors: Adeyanju Dolapo , Mburu John , Gituro Wainaina , Chumo Chepchumba , Mignouna Djana , Ogunniyi Adebayo , Akomolafe John Kehinde , Ejima Joseph
Published: February 2023

Food insecurity remains a serious challenge for many households in Africa and the situation is even more prevalent among young people. However, there is a dearth of empirical evidence on youth food security status in Africa. We assessed the level and determinants of food security among young farmers in Africa. We adopted a multi-stage sampling technique to select 400, 429, and 606 young farmers in Kenya, Nigeria, and Uganda, respectively. Individual food consumption was assessed following a 7 days recall method. The Food Consumption Score, which combines dietary diversity and consumption frequency was used to assess food security status while the determinants of food security were identified using a logistic regression model. Results suggest low dietary diversity across the three countries. Also, the majority of the respondents had an unacceptable food consumption score, suggesting that despite being food producers, young farmers are still food insecure. The odds of being food secure was positively determined by access to extension services, participation in the ENABLE TAAT business incubation programme, and access to market information but, negatively by access to credit, number of employees, Covid-19 pandemic, and location. Additionally, the food security status of young female farmers was positively influenced by age, suggesting that younger youths are less food secure compared to older ones. These results suggest that more efforts should be directed towards improving the food security of young African farmers and that policy- and programme-level interventions should support access to extension services, market information, and land. Additionally, more investments should be directed towards developing need-based agribusiness incubation programmes with an effort to scale existing programmes beyond the regular one-time period.
Core-predominant gut fungus Kazachstania slooffiae promotes intestinal epithelial glycolysis via lysine desuccinylation in pigs
Authors: Hu Jun , Chen Jianwei , Hou Qiliang , Xu Xiaojian , Ren Jing , Ma Libao , Yan Xianghua
Published: February 2023

Background

Gut fungi are increasingly recognized as important contributors to host physiology, although most studies have focused on gut bacteria. Post-translational modifications (PTMs) of proteins play vital roles in cell metabolism. However, the contribution of gut fungi to host protein PTMs remains unclear. Mining gut fungi that mediate host protein PTMs and dissecting their mechanism are urgently needed.

Results

We studied the gut fungal communities of 56 weaned piglets and 56 finishing pigs from seven pig breeds using internal transcribed spacer (ITS) gene amplicon sequencing and metagenomics. The results showed that Kazachstania slooffiae was the most abundant gut fungal species in the seven breeds of weaned piglets. K. slooffiae decreased intestinal epithelial lysine succinylation levels, and these proteins were especially enriched in the glycolysis pathway. We demonstrated that K. slooffiae promoted intestinal epithelial glycolysis by decreasing lysine succinylation by activating sirtuin 5 (SIRT5). Furthermore, K. slooffiae-derived 5′-methylthioadenosine metabolite promoted the SIRT5 activity.

Conclusions

These findings provide a landscape of gut fungal communities of pigs and suggest that K. slooffiae plays a crucial role in intestinal glycolysis metabolism through lysine desuccinylation. Our data also suggest a potential protective strategy for pigs with an insufficient intestinal energy supply.
Modified atmosphere packaging with chitosan coating to prevent deterioration of fresh in-hull Badami’s pistachio fruit
Authors: Rezaiyan Attar Farnaz , Sedaghat Naser , Pasban Atena , Yeganehzad Samira , Hesarinejad Mohammad Ali
Published: February 2023

Background

Fresh in-hull pistachio fruits are very perishable and hence have a limited storage life, with marketers and customers wishing for a longer shelf life. The present research was performed to explore the combined effects of different packaging conditions (ambient atmospheric condition, and passive- and active-modified atmosphere packaging) as well as chitosan coating (0, 1, and 1.5%w/v) on postharvest quality of fresh in-hull pistachios stored at 5 °C and 85–90% relative humidity for 45 days. The efficacy of treatments in prolongation of pistachio fruit shelf life was evaluated by determining weight loss, kernel firmness, acid (AV) and peroxide values (PV), mold and yeast count, aflatoxin content, and hull color parameters (L*, a*, b*, C*, h°, and BI) at 0, 15, 30 and 45 days of storage. In addition, O2 and CO2 concentrations in MAP headspace were monitored.

Results

By applying high molecular weight chitosan coatings and MAP conditions, PV and AV values, microbial growth, aflatoxin B1 production, and weight loss values were inhibited, as well as kernel firmness reduction and hull color deterioration during storage were controlled. Active-MAP treatments in most cases performed better than passive-MAP treatments in this regard (P < 0.05). Combining chitosan coating with MAP demonstrated additive synergistic effects. At the end of storage, 1.5% chitosan-coated treatment under active-MAP maintained firmness (87% of the control treatment), hull lightness (76% of the control treatment), and microbial count (similar to the control treatment). It also maintained minimum weight loss (6.39%), acid (0.91 meq O2 kg−1 oil) and peroxide (0.49 goleic acid/100 goil) values compared to other treatments, proving that chitosan coating combined with MAP was more effective in preserving pistachio quality parameters. The equilibrium O2 and CO2 levels of passive-MAP treatments were maintained at higher values than those of active-MAP treatments which indicated that passive-MAP treatments had higher respiration rates than those of active-MAP treatments during storage.

Conclusions

The results revealed that applying the combination technique of MAP and chitosan coating effectively preserved the quality attributes and lengthened the shelf life of fresh in-hull pistachios. Therefore, it could potentially be commercialized as a new approach for future industry application.

Graphical Abstract
Examining the relationships between students’ perceptions of technology, pedagogy, and cognition: the case of immersive virtual reality mini games to foster computational thinking in higher education
Authors: Agbo Friday Joseph , Olaleye Sunday Adewale , Bower Matt , Oyelere Solomon Sunday
Published: February 2023

Researchers are increasingly exploring educational games in immersive virtual reality (IVR) environments to facilitate students’ learning experiences. Mainly, the effect of IVR on learning outcomes has been the focus. However, far too little attention has been paid to the influence of game elements and IVR features on learners’ perceived cognition. This study examined the relationship between game elements (challenge, goal clarity, and feedback) as pedagogical approach, features of IVR technology (immersion and interaction), and learners’ perceived cognition (reflective thinking and comprehension). An experiment was conducted with 49 undergraduate students who played an IVR game-based application (iThinkSmart) containing mini games developed to facilitate learners’ computational thinking competency. The study employed partial least squares structural equation modelling to investigate the effect of educational game elements and learning contents on learner’s cognition. Findings show that goal clarity is the main predictor of learners’ reflective thinking and comprehension in an educational game-based IVR application. It was also confirmed that immersion and interaction experience impact learner’s comprehension. Notably, adequate learning content in terms of the organisation and relevance of the content contained in an IVR game-based application significantly moderate learners’ reflective thinking and comprehension. The findings of this study have implications for educators and developers of IVR game-based intervention to facilitate learning in the higher education context. In particular, the implication of this study touches on the aspect of learners’ cognitive factors that aim to produce 21st-century problem-solving skills through critical thinking.
A novel and diverse group of Candidatus Patescibacteria from bathypelagic Lake Baikal revealed through long-read metagenomics
Authors: Haro-Moreno Jose M. , Cabello-Yeves Pedro J. , Garcillán-Barcia M. Pilar , Zakharenko Alexandra , Zemskaya Tamara I. , Rodriguez-Valera Francisco
Published: February 2023

Background

Lake Baikal, the world’s deepest freshwater lake, contains important numbers ofCandidatusPatescibacteria (formerly CPR) in its deepest reaches. However, previously obtained CPR metagenome-assembled genomes recruited very poorly indicating the potential of other groups being present. Here, we have applied for the first time a long-read (PacBio CCS) metagenomic approach to analyze in depth theCa.Patescibacteria living in the bathypelagic water column of Lake Baikal at 1600 m.

Results

The retrieval of nearly complete 16S rRNA genes before assembly has allowed us to detect the presence of a novel and a likely endemic group ofCa.Patescibacteria inhabiting bathypelagic Lake Baikal. This novel group seems to possess extremely high intra-clade diversity, precluding complete genomes' assembly. However, read binning and scaffolding indicate that these microbes are similar to otherCa.Patescibacteria (i.e. parasites or symbionts), although they seem to carry more anabolic pathways, likely reflecting the extremely oligotrophic habitat they inhabit. The novel bins have not been found anywhere, but one of the groups appears in small amounts in an oligotrophic and deep alpine Lake Thun. We propose this novel group be named Baikalibacteria.

Conclusion

The recovery of 16S rRNA genes via long-read metagenomics plus the use of long-read binning to uncover highly diverse “hidden” groups of prokaryotes are key strategies to move forward in ecogenomic microbiology. The novel group possesses enormous intraclade diversity akin to what happens withCa.Patescibacteria at the interclade level, which is remarkable in an environment that has changed little in the last 25 million years.
Protocol for a pilot randomised controlled trial to evaluate integrated support from pharmacist independent prescriber and third sector worker for people experiencing homelessness: the PHOENIx community pharmacy study
Authors: Paudyal Vibhu , Lowrie Richard , Mair Frances S. , Middleton Lee , Cheed Versha , Hislop Jennifer , Williamson Andrea , Barnes Nigel , Jolly Catherine , Saunders Karen , Allen Natalie , Jagpal Parbir , Provan George , Ross Steven , Hunter Carole , Tearne Sarah , McPherson Andrew , Heath Helena , Lombard Cian , Araf Adnan , Dixon Emily , Hatch Amy , Moir Jane , Akhtar Shabana
Published: February 2023

Background

People experiencing homelessness (PEH) have complex health and social care needs and most die in their early 40 s. PEH frequently use community pharmacies; however, evaluation of the delivery of structured, integrated, holistic health and social care intervention has not been previously undertaken in community pharmacies for PEH. PHOENIx (Pharmacy Homeless Outreach Engagement Non-medical Independent prescribing Rx) has been delivered and tested in Glasgow, Scotland, by NHS pharmacist independent prescribers and third sector homelessness support workers offering health and social care intervention in low threshold homeless drop-in venues, emergency accommodation and emergency departments, to PEH. Building on this work, this study aims to test recruitment, retention, intervention adherence and fidelity of community pharmacy-based PHOENIx intervention.

Methods

Randomised, multi-centre, open, parallel-group external pilot trial. A total of 100 PEH aged 18 years and over will be recruited from community pharmacies in Glasgow and Birmingham. PHOENIx intervention includes structured assessment in the community pharmacy of health, housing, benefits and activities, in addition to usual care, through weekly visits lasting up to six months. A primary outcome is whether to proceed to a definitive trial based on pre-specified progression criteria. Secondary outcomes include drug/alcohol treatment uptake and treatment retention; overdose rates; mortality and time to death; prison/criminal justice encounters; healthcare utilisation; housing tenure; patient-reported measures and intervention acceptability. Analysis will include descriptive statistics of recruitment and retention rates. Process evaluation will be conducted using Normalisation Process Theory. Health, social care and personal resource use data will be identified, measured and valued.

Discussion

If the findings of this pilot study suggest progression to a definitive trial, and if the definitive trial offers positive outcomes, it is intended that PHOENIx will be a publicly funded free-to-access service in community pharmacy for PEH. The study results will be shared with wider stakeholders and patients in addition to dissemination through medical journals and scientific conferences.

Trial registration

International Clinical Trial Registration ISRCTN88146807.

Approved protocol version 2.0 dated July 19, 2022.