bluuebunny/crossref_metadata_2025 huggingface dataset:
Diagnostic power of one-step and two-step RT-qPCR methods to SARS‑CoV‑2 detection
Authors: Malekshahi Asra , Khanizadeh Sayyad , Fallahi Shirzad , Talei Gholamreza , Birjandi Mehdi , Hajizadeh Faezeh
Published: May 2022

Background

Coronavirus-2019 (COVID-2019) is a novel coronavirus known as Acute Respiratory Syndrome (SARS-CoV-2). The premier standard test for SARS-CoV-2 diagnosis is a one-step RT-qPCR method, which requires specific probes and reagents. Therefore, detection on a large scale is expensive and cannot be very accurate.

Methods

A cost-effective technique based on SYBR green was evaluated in the current study. The specific primers for S and N genes were designed, then performed the cross-reactivity test with other coronavirus and respiratory viruses positive samples. Moreover, the analytical sensitivity test was carried out with 8 dilutions (1:10). Lastly, the SARS-CoV-2 clinical samples (n = 210) were tested by these two methods, and receiver operating characteristic (ROC) analysis was performed to investigate the incremental diagnostic value of each gene in the study methods.

Results

The two-step method detected up to 6th dilutions of the SARS-CoV-2 samples and did not show any amplification of the positive samples of other respiratory viruses. ROC analysis revealed a diagnostic ability of the two-step method for SARS-CoV-2 with an area under the ROC curve of ≥ 0.7 (P ˂ 0.05) and relatively high sensitivity and specificity. The combination of N and S genes increased the sensitivity up to 88%, specificity up to 86%, and area under the ROC curve up to 0.85 (95% confidence interval (95% CI) 0.72 to 0.93, P = 0.0461).

Conclusion

Our findings indicated that the two-step method has comparable sensitivity and specificity to the one-step method. Therefore, this method can be considered a potential diagnostic method for diagnosing and monitoring COVID-19 patients. It suggests that when the one-step RT-qPCR method is not available, the two-step RT-qPCR can be used to identify SARS-CoV-2.
Timing of adjuvant chemotherapy initiation and mortality among colon cancer patients at a safety-net health system
Authors: Lu Yan , Gehr Aaron W. , Meadows Rachel J. , Ghabach Bassam , Neerukonda Latha , Narra Kalyani , Ojha Rohit P.
Published: May 2022

Background

Prior studies reported survival benefits from early initiation of adjuvant chemotherapy for stage III colon cancer, but this evidence was derived from studies that may be sensitive to time-related biases. Therefore, we aimed to estimate the effect of initiating adjuvant chemotherapy ≤8 or ≤ 12 weeks on overall and disease-free survival among stage III colon cancer patients using a study design that helps address time-related biases.

Methods

We used institutional registry data from JPS Oncology and Infusion Center, a Comprehensive Community Cancer Program. Eligible patients were adults aged < 80 years, diagnosed with first primary stage III colon cancer between 2011 and 2017, and received surgical resection with curative intent. We emulated a target trial with sequential eligibility. We subsequently pooled the trials and estimated risk ratios (RRs) along with 95% confidence limits (CL) for all-cause mortality and recurrence or death at 5-years between initiators and non-initiators of adjuvant chemotherapy ≤8 or ≤ 12 weeks using pseudo-observations and a marginal structural model with stabilized inverse probability of treatment weights.

Results

Our study population comprised 222 (for assessing initiation ≤8 weeks) and 310 (for assessing initiation ≤12 weeks) observations, of whom the majority were racial/ethnic minorities (64–65%), or uninsured with or without enrollment in our hospital-based medical assistance program (68–71%). Initiation of adjuvant chemotherapy ≤8 weeks of surgical resection did not improve overall survival (RR for all-cause mortality = 1.04, 95% CL: 0.57, 1.92) or disease-free survival (RR for recurrence or death = 1.07, 95% CL: 0.61, 1.88). The results were similar for initiation of adjuvant chemotherapy ≤12 weeks of surgical resection.

Conclusions

Our results suggest that the overall and disease-free survival benefits of initiating adjuvant chemotherapy ≤8 or ≤ 12 weeks of surgical resection may be overestimated in prior studies, which may be attributable to time-related biases. Nevertheless, our estimates were imprecise and differences in population characteristics are an alternate explanation. Additional studies that address time-related biases are needed to clarify our findings.
Condom failure and pre-exposure prophylaxis use experience among female sex workers in Ethiopia: a qualitative study
Authors: Amogne Minilik Demissie , Sanders Eduard J. , Belihu Wudinesh Belete , Sundewall Jesper , Agardh Anette
Published: May 2022

Background

Female sex workers (FSW) remain a highly exposed group for HIV/STIs due to different factors including condom failure. In Ethiopia, pre-exposure prophylaxis (PrEP) has recently been introduced as an intervention strategy to prevent new HIV infections, but knowledge about FSWs’ experiences of condom failure and PrEP use remains scarce. Therefore, this study explores FSWs’ experiences concerning condom failure and their attitudes towards, and experiences of, PrEP uptake.

Method

A qualitative study using in-depth interviews was conducted among FSWs in Addis Ababa. A manifest and latent content analysis method was applied to identify categories and emerging themes.

Result

Seventeen FSWs (10 who started on PrEP, 1 who discontinued, and 6 who didn’t start) were interviewed. FSWs described the reasons behind condom failure, the mechanisms they used to minimize the harm, and their attitudes towards PrEP use. FSWs struggled with the continuous risk of condom failure due to factors related to clients’ and their own behavior. PrEP was mentioned as one the strategies FSWs used to minimize the harm resulting from condom failure, but PrEP use was compounded with doubts that deterred FSWs from uptake. FSWs’ misconceptions, their lack of confidence, and PrEP side effects were also mentioned as the main challenges to start taking PrEP and/or to maintain good adherence.

Conclusion

The demands and behavior of the clients and FSWs’ own actions and poor awareness were factors that increased the exposure of FSWs to condom failure. In addition, the challenges associated with PrEP uptake suggest the need for user-friendly strategies to counteract these barriers and facilitate PrEP uptake.
Prevalence, characteristics, and psychological outcomes of workplace cyberbullying during the COVID-19 pandemic in Japan: a cross-sectional online survey
Authors: Ikeda Tomohiko , Hori Daisuke , Sasaki Hiroaki , Komase Yu , Doki Shotaro , Takahashi Tsukasa , Oi Yuichi , Ikeda Yu , Arai Yo , Muroi Kei , Ishitsuka Mami , Matsuura Asako , Go Wyi , Matsuzaki Ichiyo , Sasahara Shinichiro
Published: May 2022

Background

The rapid introduction of teleworking due to the coronavirus disease 2019 pandemic has led to concerns about increases in cyberbullying (CB) worldwide. However, little is known about workplace CB in non-Western countries. The first objective was to clarify the prevalence and characteristics regarding workplace CB victimization in Japan. The second objective was to demonstrate the psychological outcomes of CB victimization in combination with traditional bullying (TB).

Methods

We conducted an anonymous, cross-sectional, Internet-based survey targeting regular employees in Japan (N = 1200) in January 2021. We investigated CB victimization using the Inventory of Cyberbullying Acts at Work and TB victimization by using the Short Negative Act Questionnaire. Possible explanatory factors for TB/CB victimization were sociodemographic variables, personality trait, chronic occupational stress, organizational climate, and gratitude at work. We also measured psychological distress, insomnia, and loneliness to assess adverse effects of workplace bullying. Two-step cluster analysis was used in determining the patterns combined with TB and CB victimization. Hierarchical binomial logistic regression analysis was used.

Results

In total, 8.0% of employees reported experiencing CB on a weekly basis. CB victimization was associated with younger age, managerial position, higher qualitative workload, and active information dissemination via the Internet, and frequency of teleworking. Three clusters based on TB and CB victimization patterns were identified: those who belong to the first cluster suffered neither from TB and CB (81.0%), the second cluster suffered only from TB (14.3%), and the third cluster suffered from both TB and CB (4.8%). The third cluster exhibited higher odds ratios (ORs) and 95% confidence intervals (CIs) for psychological distress (OR = 12.63, 95% CI = 4.20–38.03), insomnia (OR = 6.26, 95% CI = 2.80–14.01), and loneliness (OR = 3.24, 95% CI = 1.74–6.04) compared to the first cluster.

Conclusions

These findings firstly clarify the prevalence and correlated factors of CB victimization among employees in Japan. Further, we showed that psychological wellbeing can be impaired by the coexistence of TB and CB. Our research could be the first step to develop the effective countermeasures against workplace CB.
The effect of two multi-component behavior change interventions on cognitive functions
Authors: Bojsen-Møller Emil , Wang Rui , Nilsson Jonna , Heiland Emerald G. , Boraxbekk Carl-Johan , Kallings Lena V. , Ekblom Maria
Published: May 2022

Background

We previously reported the effects of two cluster-randomized 6-month multi-component workplace interventions, targeting reducing sedentary behavior or increasing physical activity among office workers, on movement behaviors and cardiorespiratory fitness. The primary aim of this study was to investigate the effects of these interventions on cognitive functions compared to a wait-list control group. The secondary aims were to examine if changes in cognition were related to change in cardiorespiratory fitness or movement behaviors and if age, sex, or cardiorespiratory fitness moderated these associations.

Methods

Both interventions encompassed multi-components acting on the individual, environmental, and organizational levels and aimed to change physical activity patterns to improve mental health and cognitive function. Out of 263 included participants, 139 (mean age 43 years, 76% females) completed a neuropsychological test battery and wore accelerometers at baseline and 6-month follow-up. The intervention effect (aim 1) on cognitive composite scores (i.e., Executive Functions, Episodic Memory, Processing Speed, and Global Cognition) was investigated. Additionally, associations between changes in movement behaviors and cardiorespiratory fitness, and changes in cognition were examined (aim 2). Moreover, age, sex, and cardiorespiratory fitness level were investigated as possible moderators of change associations (aim 3).

Results

Overall, cognitive performance improved from baseline to follow-up, but the change did not differ between the intervention groups and the control group. Changes in cardiorespiratory fitness or any movement behavior category did not predict changes in cognitive functions. The association between changes in time in bed and changes in both Executive Function and Global Cognition were moderated by age, such that a more positive relation was seen with increasing age. A less positive association was seen between changes in sedentary behavior and Processing Speed for men vs. women, whereas higher cardiorespiratory fitness was related to a more positive association between changes in moderate-intensity physical activity and Global Cognition.

Conclusion

The lack of an intervention effect on cognitive functions was expected since the intervention did not change movement behavior or fitness. Age, sex, and cardiorespiratory fitness level might moderate the relationships between movement behaviors and cognitive functions changes.

Trial registration

ISRCTN92968402. Registered 09/04/2018.
Cone-beam computed tomography analysis of primary root canals transportation and dentin loss after instrumentation with two-pediatric rotary files
Authors: Abd El fatah Yasmine Ahmed Mortada , Khattab Nagwa Mohamed Ali , Gomaa Yasser Fathi , Elheeny Ahmad Abdel Hamid
Published: May 2022

Background

This in vitro study aims to compare rotary files (Fanta and Zuanba) with manual K files according to the amount of dentin removed and canal transportation in primary mandibular second molars by CBCT images.

Methods

This experimental study was conducted on 60 extracted human second primary molars. That were divided into three groups according to root canal preparation group "I" instrumented with manual K-files, group "II" instrumented with rotary Fanta files, and group "III" instrumented with rotary Zuanba files. After root canal preparation, teeth were scanned before and after mechanical preparation with CBCT scanner. Then the amount of dentin removed was determined at three levels, including the coronal, middle and apical levels. Data were statically analysed using the Kruskal–Wallis test.

Result

No statistically significant difference in the amount of dentin removed were noted between the manual and the rotary groups at the coronal and apical RC levels (P = 0.420) and (P = 0.819) respectively but significant difference was noted at the middle third (P = 0.043). Regarding RC transportation, no significant difference was noted among the three groups with the exception of the apical RC level (P = 0.043).

Conclusion

Although no significant differences were noted between rotary and manual files, the rotary files showed better performance.
Development and assessment of PharmaCheck: an electronic screening tool for the prevention of twenty major adverse drug events
Authors: Skalafouris Christian , Reny Jean-Luc , Stirnemann Jérôme , Grosgurin Olivier , Eggimann François , Grauser Damien , Teixeira Daniel , Jermini Megane , Bruggmann Christel , Bonnabry Pascal , Guignard Bertrand
Published: May 2022

Background

Adverse drug events (ADEs) can be prevented by deploying clinical decision support systems (CDSS) that directly assist physicians, via computerized order entry systems, and clinical pharmacists performing medication reviews as part of medical rounds. However, physicians using CDSS are known to be exposed to the alert-fatigue phenomenon. Our study aimed to assess the performance of PharmaCheck—a CDSS to help clinical pharmacists detect high-risk situations with the potential to lead to ADEs—and its impact on clinical pharmacists’ activities.

Methods

Twenty clinical rules, divided into four risk classes, were set for the daily screening of high-risk situations in the electronic health records of patients admitted to our General Internal Medicine Department. Alerts to clinical pharmacists encouraged them to telephone prescribers and suggest any necessary treatment adjustments. PharmaCheck’s performance was assessed using the intervention’s positive predictive value (PPV), which characterizes the proportion of interventions for each alert triggered. PharmaCheck’s impact was assessed by considering clinical pharmacists as a filter for ruling out futile alerts and by comparing the final clinical PPV with a pharmacist (the proportion of interventions that led to a change in the medical regimen) to the final clinical PPV without a pharmacist.

Results

Over 132 days, 447 alerts were triggered for 383 patients, leading to 90 interventions (overall intervention PPV = 20.1%). By risk class, intervention PPVs made up 26.9% (n = 65/242) of abnormal laboratory value alerts, 3.1% (4/127) of alerts for contraindicated medications or medications to be used with caution, 28.2% (20/71) of drug–drug interaction alerts, and 14.3% (1/7) of inadequate mode of administration alerts. Clinical PPVs reached 71.0% (64/90) when pharmacists filtered alerts and 14% (64/242) if they were not doing it.

Conclusion

PharmaCheck enabled clinical pharmacists to improve their traditional processes and broaden their coverage by focusing on 20 high-risk situations. Alert management by pharmacists seemed to be a more effective way of preventing risky situations and alert-fatigue than a model addressing alerts to physicians exclusively. Some fine-tuning could enhance PharmaCheck's performance by considering the information quality of triggers, the variability of clinical settings, and the fact that some prescription processes are already highly secured.
The impact of IgG subclass deficiency on the risk of mortality in hospitalized patients with COPD
Authors: Lee Hyun , Kovacs Cara , Mattman Andre , Hollander Zsuzsanna , Chen Virginia , Ng Raymond , Leung Janice M. , Sin Don D.
Published: May 2022

Background

Immunoglobulin G (IgG) deficiency increases the risk of acute exacerbations and mortality in chronic obstructive pulmonary disease (COPD). However, the impact of IgG subclass deficiency on mortality in COPD is unknown. Here, we determined which IgG subclass, if any, is associated with increased risk of mortality in COPD.

Methods

We measured serum IgG subclass concentrations of 489 hospitalized patients with COPD who were enrolled in the Rapid Transition Program (clinicaltrials.gov identifier NCT02050022). To evaluate the impact of IgG subclass deficiency on 1-year mortality, Cox proportional hazards regression analyses were performed with adjustments for potential confounders.

Results

Deficiencies in IgG1, IgG2, IgG3, and IgG4 were present in 1.8%, 12.1%, 4.3%, and 11.2% of patients, respectively. One-year mortality was 56% in patients with IgG1 deficiency, 27% in IgG2 deficiency, 24% in IgG3 deficiency, and 31% in IgG4 deficiency. Cox proportional modeling showed that IgG1 and IgG4 deficiencies increased the 1-year mortality risk with an adjusted hazard ratio of 3.92 (95% confidence interval [CI] = 1.55–9.87) and 1.74 (95% CI = 1.02–2.98), respectively. Neither IgG2 nor IgG3 deficiency significantly increased 1-year mortality. Two or more IgG subclass deficiencies were observed in 5.3%. Patients with 2 or more IgG subclass deficiencies had a higher 1-year mortality than those without any deficiencies (46.2% vs. 19.7%, p < 0.001), with an adjusted hazard ratio of 2.22 (95% CI = 1.18–4.17).

Conclusions

IgG1 and IgG4 deficiency was observed in 1.8% and 11.2% of hospitalized patients with COPD, respectively, and these deficiencies were associated with a significantly increased risk of 1-year mortality.
Impaired lung function and mortality in Eastern Europe: results from multi-centre cohort study
Authors: Sarycheva Tatyana , Capkova Nadezda , Pająk Andrzej , Malyutina Sofia , Simonova Galina , Tamosiunas Abdonas , Bobák Martin , Pikhart Hynek
Published: May 2022

Background

The association between impaired lung function and mortality has been well documented in the general population of Western European countries. We assessed the risk of death associated with reduced spirometry indices among people from four Central and Eastern European countries.

Methods

This prospective population-based cohort includes men and women aged 45–69 years, residents in urban settlements in Czech Republic, Poland, Russia and Lithuania, randomly selected from population registers. The baseline survey in 2002–2005 included 36,106 persons of whom 24,993 met the inclusion criteria. Cox proportional hazards models were used to estimate the hazard ratios of mortality over 11–16 years of follow-up for mild, moderate, moderate-severe and very severe lung function impairment categories.

Results

After adjusting for covariates, mild (hazard ratio (HR): 1.25; 95% CI 1.15‒1.37) to severe (HR: 3.35; 95% CI 2.62‒4.27) reduction in FEV1 was associated with an increased risk of death according to degree of lung impairment, compared to people with normal lung function. The association was only slightly attenuated but remained significant after exclusion of smokers and participants with previous history of respiratory diseases. The HRs varied between countries but not statistically significant; the highest excess risk among persons with more severe impairment was seen in Poland (HR: 4.28, 95% CI 2.14‒8.56) and Lithuania (HR: 4.07, 95% CI 2.21‒7.50).

Conclusions

Reduced FEV1 is an independent predictor of all-cause mortality, with risk increasing with the degree of lung function impairment and some country-specific variation between the cohorts.
Metallothionein 2A (MT2A) controls cell proliferation and liver metastasis by controlling the MST1/LATS2/YAP1 signaling pathway in colorectal cancer
Authors: Liu Xi , Quan Jun , Shen Zhaolong , Zhang Zequn , Chen Zhijian , Li Liang , Li Xiaorong , Hu Gui , Deng Xiaofeng
Published: May 2022

Background

Colorectal cancer (CRC) is one of the three major cancers in the world and is the cancer with the most liver metastasis. The present study aimed to investigate the role of metallothionein 2A (MT2A) in the modulation of CRC cell proliferation and liver metastasis, as well as its molecular mechanisms.

Methods

The expression profile of metallothionein 2A (MT2A) in colorectal cancer retrieved from TCGA, GEO and Oncomine database. The biological effect of MT2A overexpression was investigated mainly involving cell proliferation and migration in CRC cells as well as growth and metastasis in CRC animal models. To explore the specific mechanism of MT2A metastasis in CRC, transcriptome sequencing was used to compare the overall expression difference between the control group and the MT2A overexpression group.

Results

Metallothionein 2A (MT2A) was downregulated in the tumor tissues of patients with CRC compared to adjacent normal tissues and was related to the tumor M stage of patients. MT2A overexpression inhibited CRC cell proliferation and migration in cells, as well as growth and metastasis in CRC animal models. While knockdown of MT2A had the opposite effect in cells. Western blotting confirmed that MT2A overexpression promoted the phosphorylation of MST1, LAST2 and YAP1, thereby inhibiting the Hippo signaling pathway. Additionally, specific inhibitors of MST1/2 inhibited MT2A overexpression-mediated phosphorylation and relieved the inhibition of the Hippo signaling pathway, thus promoting cell proliferation. Immunohistochemistry in subcutaneous grafts and liver metastases further confirmed this result.

Conclusions

Our results suggested that MT2A is involved in CRC growth and liver metastasis. Therefore, MT2A and MST1 may be potential therapeutic targets for patients with CRC, especially those with liver metastases.
The understanding, application and influence of complexity in national physical activity policy-making
Authors: Rigby Benjamin P. , Dodd-Reynolds Caroline J. , Oliver Emily J.
Published: May 2022

Background

Complexity theory and systems-thinking are increasingly popular in physical activity (PA) research and policy discourse. The impact of this perspective shift, across many sectors, may be underwhelming. We explore why, by focusing on how these concepts are understood and applied by PA policy-makers. This is of particular interest given the challenges of multisectoral interest and poorly defined stakeholder boundaries that are associated with PA promotion. In this study, we critique key elements of complexity theory and consider how it is understood and put into practice in PA policy-making.

Methods

We adopted a complex realist position. Ten semi-structured interviews were conducted with national-level policy-makers from United Kingdom government settings (five civil servants, three politicians, two policy advisors). An inductive thematic analysis was conducted, and managed with NVivo 10 software.

Results

Three overarching themes were constructed to reflect policy-makers’uncertaintyabout complexity and the application of such perspectives to this policy space, their sense that PA was anunexceptionable yet unclaimed policy issue, and their desire forinfluence and change. Participants discussed complexity in contrasting ways. Its meaning was context-dependent and dynamic, which generated uncertainty about applying the concept. Participants also perceived an increasingly diverse but ill-defined PA policy system that spans the domains of expertise and responsibility. Collaborative practices may contribute to a previously unobserved sense of detachment from the systems’ complexity. Nevertheless, participants suggested potentially effective ways to stimulate system change, which require passionate and enterprising leadership, and included varied evidence use, a focus on localised implementation and different ways to connect people.

Conclusions

This research highlighted the importance of extending complexity theory and systems-thinking. While emphasizing the prevalence of these ideas across the PA sector, there is uncertainty as to their meaning and implications. This may prevent their use in ways that enhance PA policies and programmes. Participants conceptualised PA as a tool, which was imposed on the system. While this may support participative decision-making and localised implementation, further research is needed to understand how local systems foster leadership, the practical application of complexity and systems-thinking, and how to support system-wide change in the development and implementation of PA policies.
Prehospital fluid therapy in patients with suspected infection: a survey of ambulance personnel’s practice
Authors: Jensen Marie Egebjerg , Jensen Arne Sylvester , Meilandt Carsten , Jørgensen Kristian Winther , Væggemose Ulla , Bach Allan , Kirkegaard Hans , Jessen Marie Kristine
Published: May 2022

Background

Fluid therapy in patients with suspected infection is controversial, and it is not known whether fluid treatment administered in the prehospital setting is beneficial. In the absence of evidence-based guidelines for prehospital fluid therapy for patients with suspected infection, Emergency Medical Services (EMS) personnel are challenged on when and how to initiate such therapy.

This study aimed to assess EMS personnel’s decision-making in prehospital fluid therapy, including triggers for initiating fluid and fluid volumes, as well as the need for education and evidence-based guidelines on prehospital fluid therapy in patients with suspected infection.

Methods

An online survey concerning fluid administration in prehospital patients with suspected infection was distributed to all EMS personnel in the Central Denmark Region, including ambulance clinicians and prehospital critical care anaesthesiologists (PCCA). The survey consisted of sections concerning academic knowledge, statements about fluid administration, triggers to evaluate patient needs for intravenous fluid, and clinical scenarios.

Results

In total, 468/807 (58%) ambulance clinicians and 106/151 (70%) PCCA responded to the survey. Of the respondents, 73% (n = 341) of the ambulance clinicians and 100% (n = 106) of the PCCA felt confident about administering fluids to prehospital patients with infections. However, both groups primarily based their fluid-related decisions on “clinical intuition”. Ambulance clinicians named the most frequently faced challenges in fluid therapy as “Unsure whether the patient needs fluid” and “Unsure about the volume of fluid the patient needs”. The five most frequently used triggers for evaluating fluid needs were blood pressure, history taking, skin turgor, capillary refill time, and shock index, the last of which only applied to ambulance clinicians. In the scenarios, the majority administered 500 ml to a normotensive woman with suspected sepsis and 1000 ml to a woman with suspected sepsis-related hypotension. Moreover, 97% (n = 250) of the ambulance clinicians strongly agreed or agreed that they were interested in more education about fluid therapy in patients with suspected infection.

Conclusion

The majority of ambulance clinicians and PCCA based their fluid administration on “clinical intuition”. They faced challenges deciding on fluid volumes and individual fluid needs. Thus, they were eager to learn more and requested research and evidence-based guidelines.
Trinity of G-tetrads and origin of translation
Authors: Kankia Besik
Published: May 2022

Background

The RNA world hypothesis cannot address most of the questions of the origin of life without violating the continuity principle (small Darwinian steps without foresight and miracles). Moreover, the RNA world is an isolated system incapable of accommodating the genetic code and evolving into extant biochemistry. All these problems are rooted in the central assumption of the hypothesis: de novo appearance of the ribozymes, production of which represents a multistep reaction requiring the complementarity principle. Thus, even the basis of the RNA world is at odds with the continuity principle—it uses foresight (multistep reaction) and a miracle (complementarity principle). Can a three-dimensional (3D) architecture, capable of molecular recognition and catalysis, be formed in a single-step reaction without the complementarity or any other preexisting rules?

Hypothesis

At first glance, the above question sounds rhetoric since the complementarity principle is the essential feature of the RNA world; it turns an RNA polymer into a genetic material. Without it, the RNA world becomes as shapeless and unconvincing as other hypotheses based on the non-hereditary molecules (i.e., protein world). However, it was suggested recently that the quadruplexes could initiate life and take necessary evolutionary steps before the arrival of the complementarity rules. The hypothesis relies on the unique properties of guanines (Gs) to self-assemble into G-tetrads and efficiently polymerize without any external help or preexisting rules. Interestingly, polyG folds into an unusually stable and well-structured monomolecular architecture that uses the quadruplex domain (QD) assembly. The QD has a strictly defined zigzag-like building pattern to accommodate only three G-tetrads. Since both QD architecture and codon length are based on triplets, the inevitable question arises: are they related? Or could QD play the role of the early adapter and determine the codon length? The current paper is an attempt to answer this question.

Conclusion

While without translation apparatus most of the steps of the extant translation are physically impossible, the QD-mediated translation is sterically feasible and can be explained by physicochemical properties of the QD and the amino acids without violating the continuity principle. Astonishingly, the quadruplex world hypothesis can address all the shortcomings of the RNA world, including its most significant challenge—step-by-step evolution from the polymerization of the first polynucleotide to the extant biochemistry.
Genetic modifications of critical regulators provide new insights into regulation modes of raw-starch-digesting enzyme expression in Penicillium
Authors: Zhao Shengfang , Xiang Boyu , Yang Le , Chen Jie , Zhu Cui , Chen Yu , Cui Jun , Hu Shengbiao , Hu Yibo
Published: May 2022

Background

Starch is a very abundant and renewable carbohydrate and an important feedstock for industrial applications. However, most starch-based products are not cost-efficient due to the high energy input needed in traditional enzymatic starch conversion processes. Raw-starch-digesting enzymes (RSDEs) from filamentous fungi have great commercial value in starch processing. However, the regulatory mechanisms associated with their production in filamentous fungi remain unknown.

Results

In this study, we reported the novel finding that cellulolytic fungus Penicillium oxalicum 114-2 has broad RSDE activity. Four regulators, including the amylase transcription activator AmyR, the catabolite repression repressor CreA, the group III G protein α subunit PGA3, and the nonhistone chromosomal protein HepA, have been found to play a crucial regulatory role in RSDE expression. Enzymatic assays revealed that RSDE production significantly increased after the overexpression of AmyR and HepA, the deletion of CreA and the dominant activation of PGA3. RT-qPCR analysis demonstrated that there is a mutual regulation mode between the four regulators, and then formed a cascade regulation mechanism that is involved in RSDE expression. Comparative transcriptomic analysis between the wild-type strain and genetically engineered strains revealed differentially expressed genes that may mediate the RSDE expression.

Conclusions

The four different types of regulators were systematically investigated and found to form a regulatory network controlling RSDE gene expression. Our results provide a new insight into the regulatory mechanism of fungal amylolytic enzyme expression and offer a theoretical basis to rationally improve the RSDE yield in the future.
Alternative splicing diversifies the skeletal muscle transcriptome during prolonged spaceflight
Authors: Henrich Mason , Ha Pin , Wang Yuanyuan , Ting Kang , Stodieck Louis , Soo Chia , Adams John S. , Chun Rene
Published: May 2022

Background

As the interest in manned spaceflight increases, so does the requirement to understand the transcriptomic mechanisms that underlay the detrimental physiological adaptations of skeletal muscle to microgravity. While microgravity-induced differential gene expression (DGE) has been extensively investigated, the contribution of differential alternative splicing (DAS) to the plasticity and functional status of the skeletal muscle transcriptome has not been studied in an animal model. Therefore, by evaluating both DGE and DAS across spaceflight, we set out to provide the first comprehensive characterization of the transcriptomic landscape of skeletal muscle during exposure to microgravity.

Methods

RNA-sequencing, immunohistochemistry, and morphological analyses were conducted utilizing total RNA and tissue sections isolated from the gastrocnemius and quadriceps muscles of 30-week-old female BALB/c mice exposed to microgravity or ground control conditions for 9 weeks.

Results

In response to microgravity, the skeletal muscle transcriptome was remodeled via both DGE and DAS. Importantly, while DGE showed variable gene network enrichment, DAS was enriched in structural and functional gene networks of skeletal muscle, resulting in the expression of alternatively spliced transcript isoforms that have been associated with the physiological changes to skeletal muscle in microgravity, including muscle atrophy and altered fiber type function. Finally, RNA-binding proteins, which are required for regulation of pre-mRNA splicing, were themselves differentially spliced but not differentially expressed, an upstream event that is speculated to account for the downstream splicing changes identified in target skeletal muscle genes.

Conclusions

Our work serves as the first investigation of coordinate changes in DGE and DAS in large limb muscles across spaceflight. It opens up a new opportunity to understand (i) the molecular mechanisms by which splice variants of skeletal muscle genes regulate the physiological adaptations of skeletal muscle to microgravity and (ii) how small molecule splicing regulator therapies might thwart muscle atrophy and alterations to fiber type function during prolonged spaceflight.
A minimal bile salt excretory pump promoter allows bile acid-driven physiological regulation of transgene expression from a gene therapy vector
Authors: Martínez-García Javier , Molina Manuela , Odriozola Leticia , Molina Angie , González-Aseguinolaza Gloria , Weber Nicholas D. , Smerdou Cristian
Published: May 2022

Background

Bile acid (BA) homeostasis is mainly regulated by bile salt excretory pump (BSEP), a hepatocyte transporter that transfers BAs to the bile. BSEP expression is regulated by BA levels through activation of farnesoid X receptor transcription factor, which binds to the inverted repeat (IR-1) element in the BSEP promoter. Gene therapy of cholestatic diseases could benefit from using vectors carrying endogenous promoters physiologically regulated by BAs, however their large size limits this approach, especially when using adeno-associated viral vector (AAV) vectors.

Results

We evaluated the functionality and BA-mediated regulation of minimal versions of human and mouse BSEP promoters containing IR-1 using AAV vectors expressing luciferase. Unexpectedly, a minimal mouse BSEP promoter (imPr) showed higher BA-mediated expression and inducibility than a minimal human promoter (ihPr) or than full-length BSEP promoters in human hepatic cells. In addition, in mice receiving an AAV8 vector carrying imPr promoter-driven luciferase expression was efficiently regulated by administration of a BA-enriched diet. Interestingly, this vector also expressed significantly higher luciferase levels in Abcb4−/− mice, which have high levels of BAs, compared to wild type mice, or to mice receiving a vector containing the luciferase gene downstream of the constitutive alpha-1 antitrypsin promoter. In contrast, the AAV vector containing ihPr showed very low luciferase expression with no inducibility. Finally, we optimized imPr by adding three IR-1 repeats at its 5′ end. This new promoter provided higher levels of luciferase than imPr both in vitro and in vivo.

Conclusions

The imPr could represent a useful tool for gene therapy approaches in which physiological BA regulation is desired.
The multifaceted role of the SASP in atherosclerosis: from mechanisms to therapeutic opportunities
Authors: Sun Yu , Wang Xia , Liu Tianwei , Zhu Xiaoyan , Pan Xudong
Published: May 2022

Background

The global population of older individuals is growing, and ageing is a key risk factor for atherosclerotic cardiovascular diseases. Abnormal accumulation of senescent cells can cause potentially deleterious effects on the organism with age. As a vital marker of cellular senescence, the senescence-associated secretory phenotype (SASP) is a novel mechanism to link cellular senescence with atherosclerosis.

Main body

In this review, we concretely describe the characteristics of the SASP and its regulation mechanisms. Importantly, we provide novel perspectives on how the SASP can promote atherosclerosis. The SASP from different types of senescent cells have vital roles in atherosclerosis progression. As a significant mediator of the harmful effects of senescent cells, it can play a pro-atherogenic role by producing inflammation and immune dysfunction. Furthermore, the SASP can deliver senescence signals to the surrounding vascular cells, gradually contributing to the development of atherosclerosis. Finally, we focus on a variety of novel therapeutic strategies aimed to reduce the burden of atherosclerosis in elderly individuals by targeting senescent cells and inhibiting the regulatory mechanisms of the SASP.

Conclusion

This review systematically summarizes the multiple roles of the SASP in atherosclerosis and can contribute to the exploration of new therapeutic opportunities.
Bone morphogenetic protein signaling regulation of AMPK and PI3K in lung cancer cells and C. elegans
Authors: Vora Mehul , Mondal Arindam , Jia Dongxuan , Gaddipati Pranya , Akel Moumen , Gilleran John , Roberge Jacques , Rongo Christopher , Langenfeld John
Published: May 2022

Background

Bone morphogenetic protein (BMP) is a phylogenetically conserved signaling pathway required for development that is aberrantly expressed in several age-related diseases including cancer, Alzheimer’s disease, obesity, and cardiovascular disease. Aberrant BMP signaling in mice leads to obesity, suggesting it may alter normal metabolism. The role of BMP signaling regulating cancer metabolism is not known.

Methods

To examine BMP regulation of metabolism, C. elegans harboring BMP gain-of-function (gof) and loss-of-function (lof) mutations were examined for changes in activity of catabolic and anabolic metabolism utilizing Western blot analysis and fluorescent reporters. AMP activated kinase (AMPK) gof and lof mutants were used to examine AMPK regulation of BMP signaling. H1299 (LKB1 wild-type), A549 (LKB1 lof), and A549-LKB1 (LKB1 restored) lung cancer cell lines were used to study BMP regulation of catabolic and anabolic metabolism. Studies were done using recombinant BMP ligands to activate BMP signaling, and BMP receptor specific inhibitors and siRNA to inhibit signaling.

Results

BMP signaling in both C. elegans and cancer cells is responsive to nutrient conditions. In both C. elegans and lung cancer cell lines BMP suppressed AMPK, the master regulator of catabolism, while activating PI3K, a regulator of anabolism. In lung cancer cells, inhibition of BMP signaling by siRNA or small molecules increased AMPK activity, and this increase was mediated by activation of LKB1. BMP2 ligand suppressed AMPK activation during starvation. BMP2 ligand decreased expression of TCA cycle intermediates and non-essential amino acids in H1299 cells. Furthermore, we show that BMP activation of PI3K is mediated through BMP type II receptor. We also observed feedback signaling, as AMPK suppressed BMP signaling, whereas PI3K increased BMP signaling.

Conclusion

These studies show that BMP signaling suppresses catabolic metabolism and stimulates anabolic metabolism. We identified feedback mechanisms where catabolic induced signaling mediated by AMPK negatively regulates BMP signaling, whereas anabolic signaling produces a positive feedback regulation of BMP signing through Akt. These mechanisms were conserved in both lung cancer cells and C. elegans. These studies suggest that aberrant BMP signaling causes dysregulation of metabolism that is a potential mechanism by which BMP promotes survival of cancer cells.
Gut microbiome mediates the protective effects of exercise after myocardial infarction
Authors: Zhou Qiulian , Deng Jiali , Pan Xue , Meng Danni , Zhu Yujiao , Bai Yuzheng , Shi Chao , Duan Yi , Wang Tianhui , Li Xinli , Sluijter Joost PG , Xiao Junjie
Published: May 2022

Background

Gut microbiota plays important roles in health maintenance and diseases. Physical exercise has been demonstrated to be able to modulate gut microbiota. However, the potential role of gut microbiome in exercise protection to myocardial infarction (MI) remains unclear.

Results

Here, we discovered exercise training ameliorated cardiac dysfunction and changed gut microbial richness and community structure post-MI. Moreover, gut microbiota pre-depletion abolished the protective effects of exercise training in MI mice. Furthermore, mice receiving microbiota transplants from exercised MI mice had better cardiac function compared to mice receiving microbiota transplants from non-exercised MI mice. Mechanistically, we analyzed metabolomics in fecal samples from exercised mice post-MI and identified 3-Hydroxyphenylacetic acid (3-HPA) and 4-Hydroxybenzoic acid (4-HBA), which could be applied individually to protect cardiac dysfunction post-MI and apoptosis through NRF2.

Conclusions

Together, our study provides new insights into the role of gut microbiome in exercise protection to MI, offers opportunities to modulate cardiovascular diseases by exercise, microbiome and gut microbiota-derived 3-HPA and 4-HBA.
Extracellular miR-6723-5p could serve as a biomarker of limbal epithelial stem/progenitor cell population
Authors: Ruiz M. , González S. , Bonnet C. , Deng S. X.
Published: May 2022

Background

Dysfunction or loss of limbal stem cells can result in limbal stem cell deficiency (LSCD), a disease that cause corneal opacity, pain, and loss of vision. Cultivated limbal epithelial transplantation (CLET) can be used to restore stem cell niche homeostasis and replenish the progenitor pool. Transplantation has been reported with high success rate, but there is an unmet need of prognostic markers that correlate with clinical outcomes. To date, the progenitor content in the graft is the only parameter that has been retrospectively linked to success.

Methods

In this study, we investigate extracellular micro RNAs (miRNAs) associated with stem/progenitor cells in cultivated limbal epithelial cells (cLECs). Using micro RNA sequencing and linear regression modelling, we identify a miRNA signature in cultures containing high proportion of stem/progenitor cells. We then develop a robust RNA extraction workflow from culture media to confirm a positive miRNA correlation with stem/progenitor cell proportion.

Results

miR-6723-5p is associated with cultures containing high proportion of stem/progenitor cells, and is detected in the basal layer of corneal epithelium.

Conclusions

These results indicate that miR-6723-5p could potentially serve as a stem/progenitor cell marker in cLECs.
Convergent evolution and multi-wave clonal invasion in H3 K27-altered diffuse midline gliomas treated with a PDGFR inhibitor
Authors: Arunachalam Sasi , Szlachta Karol , Brady Samuel W. , Ma Xiaotu , Ju Bensheng , Shaner Bridget , Mulder Heather L. , Easton John , Raphael Benjamin J. , Myers Matthew , Tinkle Christopher , Allen Sariah J. , Orr Brent A. , Wetmore Cynthia J. , Baker Suzanne J. , Zhang Jinghui
Published: May 2022

The majority of diffuse midline gliomas, H3 K27-altered (DMG-H3 K27-a), are infiltrating pediatric brain tumors that arise in the pons with no effective treatment. To understand how clonal evolution contributes to the tumor’s invasive spread, we performed exome sequencing and SNP array profiling on 49 multi-region autopsy samples from 11 patients with pontine DMG-H3 K27-a enrolled in a phase I clinical trial of PDGFR inhibitor crenolanib. For each patient, a phylogenetic tree was constructed by testing multiple possible clonal evolution models to select the one consistent with somatic mutations and copy number variations across all tumor regions. The tree was then used to deconvolute subclonal composition and prevalence at each tumor region to study convergent evolution and invasion patterns. Somatic variants in the PI3K pathway, a late event, are enriched in our cohort, affecting 70% of patients. Convergent evolution of PI3K at distinct phylogenetic branches was detected in 40% of the patients. 24 (~ 50%) of tumor regions were occupied by subclones of mixed lineages with varying molecular ages, indicating multiple waves of invasion across the pons and extrapontine. Subclones harboring a PDGFRA amplicon, including one that amplified a PDGRFAY849C mutant allele, were detected in four patients; their presence in extrapontine tumor and normal brain samples imply their involvement in extrapontine invasion. Our study expands the current knowledge on tumor invasion patterns in DMG-H3 K27-a, which may inform the design of future clinical trials.
The response of the hydrological cycle to temperature changes in recent and distant climatic history
Authors: Pratap Shailendra , Markonis Yannis
Published: May 2022

The relationship between the hydrological cycle and the temperature is rather complex and of great importance to human socioeconomic activities. The prevailing theory suggests that as temperature increases the hydrological cycle is intensified. Practically, this means more and heavier precipitation. However, the exact magnitude of hydrological cycle response and its spatio-temporal characteristics is still under investigation. Looking back in Earth’s hydroclimatic history, it is easy to find some periods where global temperature was substantially different than present. Here, we examine some of these periods to present the current knowledge about past hydrological cycle variability (specifically precipitation), and its relationship to temperature. The periods under investigation are the Mid-Miocene Climate Optimum, the Eemian Interglacial Stage, the Last Glacial Maximum, the Heinrich and Dansgaard–Oeschger Events, the Bølling–Allerød, the Younger Dryas, the 8.2 ka event, the Medieval Climate Anomaly, and the Little Ice Age. We report that the hypothesis that a warmer climate is a wetter climate could be an oversimplification, because the response of water cycle appears to be spatio-temporally heterogeneous.