bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of acupuncture for relieving preoperative anxiety in adolescents
Authors: Yu Ziru , Xian Jin , Sun Mi , Zhang Wenxiu , Li Linwei , Zhang Xin , Yu Huijuan
Published: December 2021

Background:

Preoperative anxiety is a frequent burden affecting adolescent patients before various surgical procedures. Acupuncture has shown promise for addressing symptoms of preoperative anxiety in adolescents. This study is designed to evaluate the effectiveness of acupuncture for preoperative anxiety in adolescents.

Methods:

We will search the relevant randomized controlled trials by the following databases: PubMed, the Cochrane Central Register of Controlled Trials, EMBASE, China National Knowledge Infrastructure, Wan Fang, VIP, China Biomedical Literature Database, and TCM Literature Analysis and Retrieval Database. The process of selecting studies, extracting data and evaluating methodological quality will be conducted by 2 researchers independently. We will use Cochrane risk of bias tool for randomized trials to assess the risk of bias of included studies. Statistical analyses will be performed using R (version3.6.3).

Ethics and dissemination:

No patient's privacy are involved in this study, ethical approval will not be required. Our research results are intended to be published through conference reports and peer-reviewed journals.

INPLASY registration number:

INPLASY2021110096
Buyang huanwu decoction combined with probiotics or prebiotics for functional recovery from stroke
Authors: Liang Runyu , Tang Qiang , Wang Linjing , Yue Peng , Zhu Luwen
Published: December 2021

Background:

Stroke is a global disease that compromises human health. Considering the side effects of Western medicine, alternative medicine, such as Chinese medicine, is widely used. Concurrently, the research and development on the microbiota-gut-brain axis in recent years have made intestinal microflora the new target of treatment. We aim to scientifically evaluate the advantages and clinical guidance of using Buyang-Huanwu (BYHW) decoction combined with probiotics in the intestinal microflora.

Methods:

The search will focus on published Randomized Controlled Trial (RCTs) that used BYHW decoction, probiotics, prebiotics, synbiotics, or similar microecological preparations to treat stroke. We will search for relevant studies in six databases: PubMed, Embase, Cochrane Library, Web of Science, China National Knowledge Infrastructure, Wanfang Data, and Chongqing VIP Information. The retrieval date will be limited to the period from inception to June 2021 and will not be restricted by language. The extracted data will be subjected to systematic review and meta-analysis to evaluate its clinical advantages and efficacy. Patient-centred and most responsive outcomes will be selected as major outcomes, including the Fugl-Meyer (FMA) and Barthel scales. Secondary outcomes will be clinically assessed factors, including inflammatory factors in serum, platelet aggregation, other laboratory parameters, and the number and distribution of flora in the gut. We will evaluate the bias of each included study using the latest version of the Cochrane Handbook and the RoB tool. The analysis of all data and the drawing of forest maps will be performed using STAT 15.1 SE software. Regardless of the I
2 values generated between the studies, we will perform a subgroup analysis. The grouping method will be based on all included research characteristics and factors that may cause heterogeneity, and may depend on differences in intervention methods, sources of subjects, and other relevant factors.

Results:

We plan to present the results of this systematic review in a peer-reviewed scientific journal, conferences, and popular press.

Conclusion:

The efficacy and safety of Buyang-Huanwu decoction combined with probiotics for the treatment of stroke will be evaluated, and the conclusion will be published to provide medical evidence for a better clinical decision of patients with stroke.
Bevacizumab combined with chemotherapy for ovarian cancer
Authors: Liao Ting , Li Li , Wang Liya
Published: December 2021

Background:

The impact of bevacizumab (an anti-vascular endothelial growth factor therapy) remains uncertain, which has been the focus of studies on the management of ovarian cancer (OC). We performed a protocol for systematic review and meta-analysis to assess the efficacy and safety of bevacizumab combined with chemotherapy in OC.

Methods:

The presentation of methods and results in this systematic review was performed according to the evaluation guidelines for health care interventions provided in the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocol. This study will use the Cochrane Library, Web of Science, PubMed, Embase, Allied and Complementary Medicine Database, China Biomedical Literature Database, China National Knowledge Infrastructure, China Science and Technology Journal Database, Wanfang Database, and Ongoing Clinical Trials Database. The risk of bias of included studies is estimated by taking into consideration the characteristics including random sequence generation, allocation concealment, blinding of patients, blinding of outcome assessment, completeness of outcome data, selective reporting, and other bias by Cochrane Collaboration's tool. All analyses were performed with Review Manager (RevMan) software, version 5.3.

Results:

The results of this systematic review and meta-analysis will be published in a peer-reviewed journal.

Conclusion:

Bevacizumab combined with chemotherapy may improve progression-free survival and overall survival in patients with OC.
Risk factors of postoperative stricture after endoscopic submucosal dissection for superficial esophageal neoplasms
Authors: Lin Nan , Lin Jie , Gong Jinrong
Published: December 2021

Background:

As larger-sized superficial esophageal neoplasms became candidates for endoscopic submucosal dissection (ESD), post-ESD esophageal stricture has inevitably developed into a significant complication during long-term follow-up.

Method:

The PubMed, Cochrane Central Register of Controlled Trials, MEDLINE, EMBASE, Web of Science, as well as China National Knowledge Infrastructure, the Wanfang Database, and the Chinese Biomedical Literature Database, were searched to identify all the appropriate studies published from January 2000 through October 2019. For risk factor assessment between postoperative stricture and control groups, pooled odds ratios (OR) and weighted mean differences (WMD) estimation was done. All meta-analytical procedures were conducted by using Stata version 15.1 software.

Results:

The results showed that 11 studies with 2248 patients (284 structure cases and 1964 controls) were eligible for this meta-analysis. Statistical results indicated 6 substantial risk factors: lesion characteristics involving the upper third of the esophagus (OR 1.51, [1.02–2.25]), macroscopic type of IIa/IIc (OR 2.76, [1.55–4.92]), tumor depth of invasion above m1 (OR 7.47, [3.31–16.86]), and m2 (OR 12.67, [4.00–40.10]), longitudinal length (WMD 13.75 mm, [7.76–19.74]), circumferential diameter (WMD 10.87 mm, [8.13–13.60]), and circumferential range >3/4 (OR 38.17, [9.94–146.52]). Each additional 10% of the circumferential range increased the risk of stricture by 149% (OR 9282.46, [978.14–88089.35]).

Conclusions:

Six risk factors were assessed to have a key role in the elevated risk levels of post-ESD esophageal stricture. The results can help doctors identify patients with increased risk and thus can guide management of the adequate period of surveillance after ESD and take available approaches of stricture prevention.
Clinical impact of COVID-19 on Turkish children with neurological and neuromuscular diseases
Authors: Okur Dicle Sener
Published: December 2021

This study aims to explore the effects of new type of coronavirus disease (COVID-19) in children with neurological and/or neuromuscular diseases

A retrospective study was conducted at State Hospital of Denizli. Pediatric patients diagnosed with COVID-19 who were hospitalized between March 18, 2020 and January 18, 2021 were included in the study. Children were divided into two groups: those with (group I) and without neurological and /or neuromuscular disorders (group II).

Male cases were more than female cases in group I. The difference between group I and group II was significant in terms of seizure (47.3%; 1.7%), dyspnea (36.8%, 6.2%) and number of days with fever (2.6 ± 1.9; 1.58 ± 1.42) (P < .01, P < .01, P = .02). Hypoxemia (7, 11; 36.8%, 4.5%) and abnormal auscultation findings (8, 44; 42.1%, 18.1%) were more common in children in group I, hypertension was more common in group II (0, 8; 0%, 3.3%). Lung involvement of COVID-19 was found to be more severe in group I (P = .04). The frequency of hospitalization in the intensive care unit (P < .01) and application of noninvasive mechanical ventilation (NIMV) (P < .01); the number of days followed-up in the intensive care (P < .01) and in the hospital (P = .02) of the patients in group I were higher than those in group II.

It is recognized that children with underlying neurological and/or neuromuscular diseases are severely affected by COVID-19.
Clinical features of patients with Legionnaires disease showing initial clinical improvement but radiological deterioration
Authors: Kim Jinyeong , Park Sunghee , Yang Eunmi , Kim Haein , Seo Hyeonji , Chung Hyemin , Jung Jiwon , Kim Min Jae , Chong Yong Pil , Lee Sang-Oh , Choi Sang-Ho , Kim Yang Soo , Kim Sung-Han
Published: December 2021

Patients with Legionnaires disease occasionally experience initial clinical improvement but radiological progression. However, data on this issue are so far limited. The aim of this study was to investigate changes in chest radiograph findings in patients with Legionnaires disease who showed initial clinical improvement and to identify risk factors and outcomes in these patients.

All patients diagnosed with Legionnaires disease at a tertiary hospital in South Korea between March 2011 and May 2020 were retrospectively enrolled. Legionnaires disease was defined as abnormal chest radiographs accompanied by a positive finding on at least one of the following tests: urinary antigen test, sputum Legionella polymerase chain reaction, and sputum Legionella culture. Clinical improvement was defined as defervescence and decreased C-reactive protein level. Clinical and radiological records were reviewed on treatment days 7 and 14 and at discharge. We describe the characteristics of patients with clinical improvement but radiological deterioration on treatment for Legionnaires disease and compared them with patients with initial clinical improvement and stable or resolving chest radiograph findings.

Of 140 patients with Legionnaires disease, 33 (24%) showed initial clinical deterioration, while the remaining 107 (76%) showed initial clinical improvement on day 7. The latter 107 patients were analyzed in this study; 22 (21%) showed radiological progression despite the clinical improvement. Risk factors for these patients were a high pneumonia severity index score and the use of mechanical ventilation. Mortality did not significantly differ between those with initial clinical improvement but radiological deterioration and those with both initial clinical and radiological improvement (28% vs 12%, P = .49).

About one-fifth of patients with Legionnaires disease, especially those who had a high pneumonia severity index score and underwent mechanical ventilation, showed radiological deterioration despite of clinical improvement 1 week after appropriate treatment, while outcomes were not significantly worse in these patients. Therefore, our findings support that close monitoring without modification of antibiotics use is warranted in those who have clinical improvement regardless of radiologic findings.
Effectiveness of microperimetry in evaluating anti-vascular endothelial growth factor therapy for diabetic macular edema patients with relatively good vision
Authors: Sugimoto Masahiko , Wakamatsu Yasuko , Miyata Ryohei , Kato Kumiko , Matsubara Hisashi , Kondo Mineo
Published: December 2021

No studies have evaluated the retinal sensitivity (RS) for diabetic macular edema (DME) patients with good vision. Therefore, this study aimed to determine the effectiveness of microperimetry in evaluating the effectiveness of anti-vascular endothelial growth factor (anti-VEGF) treatment for DME patients with relatively good vision.

Twenty-seven eyes of 27 patients (mean age, 61.3 ± 11.2 years) with DME and decimal best-corrected visual acuity (BCVA) ≥0.6 were studied. All patients received 3 consecutive monthly injections of intravitreal anti-VEGF agents. The BCVA, central subfield macular thickness (CMT), and RS were evaluated by microperimetry (MAIA) within the 10 degree of the foveal center. To determine significant differences between the values, we used paired t tests.

Patients were evaluated at baseline and 4 weeks after the third injection. The BCVA improved significantly from 0.18 ± 0.06 logarithm of the minimum angle of resolution (logMAR) units to 0.13 ± 0.13 logMAR units (P = .002; paired t test). The CMT decreased significantly from 464.3 ± 91.8 μm to 393.4 ± 129.0 μm (P = .005), and the RS also improved significantly from 21.8 ± 3.1 dB to 24.1 ± 2.8 dB at 4 weeks after treatment (P = .006). Among the patients with a decimal BCVA of 0.7 or better at baseline, there was no significant improvement in the BCVA (P = .28). However, the CMT decreased significantly from 479.5 ± 79.1 μm to 394.0 ± 99.8 μm at 4 weeks after treatment (P = .007). The RS also improved significantly from 22.0 ± 2.4 dB to 24.0 ± 3.1 dB at 4 weeks after treatment (P = .004).

Measuring RS by microperimetry is a good option for evaluating the effectiveness of anti-VEGF treatment for DME patients with a relatively good BCVA.
Association between homocysteine, C-reactive protein, lipid level, and sleep quality in perimenopausal and postmenopausal women
Authors: Zhang Hongyan , Wang Qianwen , Deng Miao , Chen Yijie , Liu Wenhua , Huang Jian , Zhang Zhifen
Published: December 2021

This study aimed to investigate the correlation between homocysteine (HCY), C-reactive protein (CRP), lipid levels, and sleep quality in perimenopausal and postmenopausal women.

We collected data from 217 patients (perimenopause and postmenopausal) who visited the gynecological endocrine outpatient department of our hospital between January 2017 and January 2019. The quality and patterns of sleep were measured using the Pittsburgh Sleep Quality Index, and relationships between HCY, CRP, lipid levels, and sleep quality were analyzed according to a Pittsburgh Sleep Quality Index ≥ 8.

There were significant differences in age, education level, and occupation among patients with different levels of sleep quality (P < .05). HCY, CRP, total cholesterol, triglyceride, and low-density lipoprotein levels were significantly higher in patients with poor sleep quality than in those with good sleep quality (P < .05). Age, education level, occupation, HCY, CRP, and lipid levels (total cholesterol, triglyceride, low-density lipoprotein, high-density lipoprotein) were all significant influencing factors for sleep quality in perimenopausal and postmenopausal women (all P < .05). After adjusting for age, education level, occupation, HCY, and CRP levels were all significant and independent risk factors for sleep quality in perimenopausal and postmenopausal women (all P < .05).

Levels of HCY, CRP, and lipids were significantly correlated with sleep quality in perimenopausal and postmenopausal women. HCY and CRP were identified as independent risk factors for sleep quality in perimenopausal and postmenopausal women, thus providing theoretical support for the clinical improvement of sleep quality.
Effect of Japanese Kampo medicine, eppikajutsuto, in patients with lymphatic malformation
Authors: Ogawa-Ochiai Keiko , Osuga Keigo , Nozaki Taiki , Tazuke Yuko , Sakai Seisho , Uehara Shuichiro , Hoshi Reina , Ishikawa Hideki , Yoshimura Kenichi , Okuyama Hiroomi
Published: December 2021

Lymphatic malformations (LMs) are congenital malformations of the lymphatic system that cause considerable cosmetic and functional complications. In this study, we present 8 children with LM who were treated with the Kampo medicine eppikajutsuto (EKJT).

Between 2001 and 2020, 8 children (male: 4, female: 4) with LMs who underwent magnetic resonance imaging (MRI) evaluation both before and after treatment or observation were selected for investigating the effect of EKJT. Two patients were observed without any treatment for 24 and 60 months. EKJT was evaluated based on percentage reduction, defined as the percentage of total lesions that decreased in size, confirmed by radiological examination after initiating treatment with EKJT or determined by observation alone. Volumetric analysis of LMs on MRI was performed using the Digital Imaging and Communications in Medicine viewer.

Six patients were treated with EKJT. The mean observational period was 13.2 months (range: 6–24 months). The mean reduction in LM volume on MRI was 73.0% in treated patients and –66.3% in observed patients. Two of the 6 lesions exhibited complete reduction, 2 exhibited marked (>90%) reduction, 1 exhibited moderate reduction, and 1 exhibited a small response. The treatment was well-tolerated, with no severe adverse events.

This preliminary study demonstrated the beneficial effects of EKJT. Prospective evaluations of this promising therapeutic modality are warranted based on the results of this study.
Acute autoimmune transverse myelitis following COVID-19 vaccination
Authors: Hirose Satoshi , Hara Makoto , Koda Kento , Natori Naotoshi , Yokota Yuki , Ninomiya Satoko , Nakajima Hideto
Published: December 2021

Rationale:

Transverse myelitis is an infectious or noninfectious inflammatory spinal cord syndrome. We report a rare case of transverse myelitis following vaccination against COVID-19.

Patient concerns:

A 70-year-old male presented with progressive sensorimotor dysfunction of the bilateral lower limbs 7 days after receiving the mRNA-1273 vaccine against COVID-19. Spinal magnetic resonance imaging revealed intramedullary lesions with gadolinium enhancement on the Th1/2 and Th5/6 vertebral levels. Cerebrospinal fluid (CSF) testing showed a mildly increased level of total protein and positive oligoclonal bands (OCB).

Diagnosis:

The patient was diagnosed with acute transverse myelitis.

Intervention:

The patient received 5 days of intravenous methylprednisolone pulse (1000 mg/day) followed by oral prednisolone (30 mg/day with gradual tapering).

Outcomes:

The patient fully recovered from muscle weakness of the lower limbs. He was discharged from our hospital and able to independently walk without unsteadiness.

Lesson:

This is a rare case of transverse myelitis following COVID-19 vaccination. Positive OCB in CSF in the present case highlights the possibility of autoimmune processes, including polyclonal activation of B lymphocytes, following vaccination.
Effect of acupuncture treatment on cognitive impairment after traumatic brain injury in adults
Authors: Li Na , Wang Ruihui , Ai Xia , Guo Xinrong , Liu Juan , Sun Lei , Zhang Rongchao
Published: December 2021

Background:

Acupuncture has been widely used to treat cognitive impairment after traumatic brain injury (TBI). But its efficiency has not been scientifically and methodically evaluated. The objective of this study is to evaluate the efficiency and safety of the acupuncture treatment for cognitive impairment after TBI in adults.

Methods:

This protocol of systematic review will be conducted in accordance with the Preferred Reporting Items for Systematic Review and Meta-analysis Protocols. We will conduct the literature searching in the following electronic databases: the Cochrane Library, MEDLINE, EMBASE, Web of Science, Springer, the Chinese Science Citation Database (CSCD), China National Knowledge Infrastructure (CNKI), the Chinese Biomedical Literature Database (CBM), Wanfang, and the Chinese Scientific Journal Database (VIP). The time limit for retrieving studies is from establishment to November 2021 for each database. All published randomized controlled trials related to this review will be included. Review Manager (V.5.3.5) will be implemented for the assessment of bias risk and data analyses. The selection of the studies, data abstraction, and validations will be performed independently by 2 researchers.

Results:

This review will assess the clinical efficacy and safety, as well as the acupoints characteristics of acupuncture on CI of TBI in adults.

Conclusion:

This review will summarize the current evidence of acupuncture on CI of TBI outcomes and provide guidance for clinicians and patients to select acupuncture for CI of TBI in adults.

Trail registration number:

This protocol of systematic review has been registered on INPLASY website (No. INPLASY2021110113).
Hypernatremia in the intensive care unit
Authors: Chand Raja , Chand Ranjeeta , Goldfarb David S.
Published: December 2021

Purpose of review

Hypernatremia is a relatively frequent electrolyte disorder seen in critically ill patients. As many as 27% of patients in intensive care units (ICUs) develop hypernatremia of variable severity during an ICU stay. Debate among specialists often ensues as to whether to correct hypernatremia or not. Some practitioners, particularly intensivists, believe that correction of hypernatremia with fluids may cause expansion of the extracellular fluid volume (ECFV) thereby worsening ventilation and impeding extubation. Other practitioners, including many nephrologists, do not expect correction of hypernatremia to lead to clinically apparent ECFV expansion, and fear other deleterious effects of hypernatremia. In this review we address the controversy regarding appropriate practice.

Recent findings

There are no randomized, clinical trials (RCTs) to guide the administration of electrolyte-free fluid administration in hypernatremic patients. However, there are associations, demonstrated in the literature, suggesting that hypernatremia of any severity will increase the mortality and length of stay in these patients. These associations generally support the practice of correction of hypernatremia. In addition, our knowledge of the distribution of total body water influences us towards correcting hypernatremia as an appropriate therapy. We do not expect that adequate RCTs addressing this question will be performed.

Allowing persistence of any degree of hypernatremia is associated with increased mortality, length of stay (LOS) and postdischarge mortality. We expect that proper use of electrolyte-free water intake will avoid adverse outcomes.
Meeting the Environmental and Staffing Demands of the COVID-19 Pandemic
Authors: Rouse Melissa , Christy LaDonna
Published: December 2021

In a large academic medical center in Houston, Texas, the COVID-19 pandemic prompted creativity to meet staffing demands and challenges. Through interprofessional collaboration, nursing professional development practitioners and the leadership team created new roles, planned and implemented new processes, provided training, and embraced a new care model. One hundred seventeen staff members were upskilled over a 4-week period to fulfill the new roles and to work in a team-based care model.
Two Cases of Fatal Inhalation of Easily Available “Recreational” Substances
Authors: Schwark Thorsten , Schaul Martine , Schneider Serge , Yegles Michel
Published: December 2021

We present 2 cases of fatal inhalation of easily available highly volatile substances that occurred in a recreational context. Case 1 concerns an 18-year-old man who was found dead with a 25-L plastic bag pulled over his head and a whipped cream steel siphon connected to the bag. The deceased was known to previously have inhaled nitrous oxide. Autopsy results were unremarkable, toxicological analysis using static headspace gas chromatography coupled to mass spectrometry analysis proved the presence of nitrous oxide in lung tissue and blood. Asphyxiation was ascertained as the cause of death. Case 2 describes the death of a 54-year-old man found dead on his bed wearing a rubber gas mask. A bottle with ethyl chloride-containing cold spray was found beside him. Autopsy did not reveal relevant pathological findings; a subsequent toxicological analysis proved the presence of ethyl chloride. Respiratory arrest because of ethyl chloride inhalation was established as the cause of death. The 2 cases presented here demonstrate the danger of easily available, volatile substances with a high potential for abuse. A careful investigation of the death scene, proper specimen collection during the autopsy, and extensive toxicological tests, including headspace gas chromatography coupled to mass spectrometry analysis, are necessary to prove inhalation of these substances.
Reduction of Waiting Times and Patients Leaving Without Being Seen in the Tertiary Pediatric Emergency Department
Authors: Adriani Luca , Dall'Oglio Immacolata , Brusco Carla , Gawronski Orsola , Piga Simone , Reale Antonino , Buonomo Ersilia , Cerone Gennaro , Palombi Leonardo , Raponi Massimiliano
Published: December 2021

Objectives

Analyze the effectiveness of an intervention to reduce waiting time and patients leaving without being seen in the pediatric emergency department.

Methods

A comparative observational study was carried out from November 2018 to April 2019.

Patients aged 3 months to 17 years were included. The new organizational model consisted of a dedicated outpatients' clinic for nonurgent codes and a fast track for traumatic and surgical emergency cases.

Results

The comparative group included 14,822, and the intervention group included 15,585 patients. The new organizational model significantly reduced the numbers of patients who left the ED without being seen from 12.9% to 5.9%.

Conclusions

This new organizational model in the pediatric emergency department could be successfully used to reduce overcrowding, waiting time, and the numbers of patients leaving without being seen. However, more needs to be done by the pediatric services in the community to reduce nonurgent accesses to the emergency department.
Unfolding and characterizing the barriers and facilitators of scaling-up evidence-based interventions from the stakeholders’ perspective: a concept mapping approach
Authors: Zhang Xiaoyan , Zhao Junqiang , Li XueJing , Yan Lijiao , Hao Yufang , Liu Jianping
Published: December 2021

Introduction and aims:

Much attention has been paid to scaling-up evidence-based interventions (EBIs) in previous implementation science studies. However, there is limited research on how stakeholders perceive factors of the scaling-up of EBIs. This study aimed to identify the barriers and facilitators of scaling-up the nurse-led evidence-based practice of post-stroke dysphagia identification and management (EBP-PSDIM) from the stakeholders’ perspective, and to assess their importance and feasibility.

Methods:

This study was conducted using concept mapping. Through purposive sampling, 18 stakeholders were recruited for brainstorming in which they responded to the focus prompt. Here, statements regarding perceived barriers and facilitators to EBI scaling-up were elicited and then sorted by similarity before being rated based on the importance and feasibility. Cluster analysis, multidimensional scaling, and descriptive statistics were utilized to analyze the data.

Results:

Ultimately, 61 statements perceived to influence the scaling-up were grouped into four primary clusters, that is, community-related factors, resource team-related factors, evidence-based practice program-related factors, and scaling-up strategy-related factors. The ‘perceived needs of the community’ was rated as the most important and feasible factor to address, whereas ‘costs/resource mobilization’ was rated as the least important and feasible one.

Conclusion:

From the stakeholders’ perspective, factors involved in the EBP-PSDIM program scaling-up were initially validated as being multidimensional and conceptually distinct;The importance and feasibility ratings of the barriers and facilitators could be used to help decision-makers to prioritize the most appropriate factors to be considered when developing implementation strategies.
Harmonizing labeling and analytical strategies to obtain protein turnover rates in intact adult animals
Authors: Hammond Dean E , Simpson Deborah M , Franco Catarina , Muelas Marina Wright , Waters John , Ludwig R W , Prescott Mark C , Hurst Jane L , Beynon Robert J , Lau Edward
Published: December 2021

Changes in the abundance of individual proteins in the proteome can be elicited by modulation of protein synthesis (the rate of input of newly synthesized proteins into the protein pool) or degradation (the rate of removal of protein molecules from the pool). A full understanding of proteome changes therefore requires a definition of the roles of these two processes in proteostasis, collectively known as protein turnover. Because protein turnover occurs even in the absence of overt changes in pool abundance, turnover measurements necessitate monitoring the flux of stable isotope labeled precursors through the protein pool such as labeled amino acids or metabolic precursors such as ammonium chloride or heavy water. In cells in culture, the ability to manipulate precursor pools by rapid medium changes is simple, but for more complex systems such as intact animals, the approach becomes more convoluted. Individual methods bring specific complications, and the suitability of different methods has not been comprehensively explored. In this study we compare the turnover rates of proteins across four mouse tissues, obtained from the same inbred mouse strain maintained under identical husbandry conditions, measured using either [13C6]lysine or [2H2]O as the labeling precursor. We show that for long-lived proteins, the two approaches yield essentially identical measures of the first order rate constant for degradation. For short-lived proteins, there is a need to compensate for the slower equilibration of lysine through the precursor pools. We evaluate different approaches to provide that compensation. We conclude that both labels are suitable, but careful determination of precursor enrichment kinetics in amino acid labeling is critical and has a considerable influence on the numerical values of the derived protein turnover rates.
Glycolytic flux-signaling controls mouse embryo mesoderm development
Authors: Miyazawa Hidenobu , Snaebjornsson Marteinn T. , Prior Nicole , Kafkia Eleni , Hammarén Henrik M. , Tsuchida-Straeten Nobuko , Patil Kiran R. , Beck Martin , Aulehla Alexander
Published: December 2021

How cellular metabolic state impacts cellular programs is a fundamental, unresolved question. Here we investigated how glycolytic flux impacts embryonic development, using presomitic mesoderm (PSM) patterning as the experimental model. First, we identified fructose 1,6-bisphosphate (FBP) as an in vivo sentinel metabolite that mirrors glycolytic flux within PSM cells of post-implantation mouse embryos. We found that medium-supplementation with FBP, but not with other glycolytic metabolites, such as fructose 6-phosphate and 3-phosphoglycerate, impaired mesoderm segmentation. To genetically manipulate glycolytic flux and FBP levels, we generated a mouse model enabling the conditional overexpression of dominant active, cytoplasmic Pfkfb3 (cytoPfkfb3). Overexpression of cytoPfkfb3 indeed led to increased glycolytic flux/FBP levels and caused an impairment of mesoderm segmentation, paralleled by the downregulation of Wnt-signaling, reminiscent of the effects seen upon FBP-supplementation. To probe for mechanisms underlying glycolytic flux-signaling, we performed subcellular proteome analysis and revealed that cytoPfkfb3 overexpression altered subcellular localization of certain proteins, including glycolytic enzymes, in PSM cells. Specifically, we revealed that FBP supplementation caused depletion of Pfkl and Aldoa from the nuclear-soluble fraction. Combined, we propose that FBP functions as a flux-signaling metabolite connecting glycolysis and PSM patterning, potentially through modulating subcellular protein localization.
Nucleocapsid 203 mutations enhance SARS-CoV-2 immune evasion
Authors: Lin Xiaoyuan , Xue Weiwei , Zhang Yueping , Fu Beibei , Trimpert Jakob , Xing Na , Kunec Dusan , Tang Wanyan , Xiao Yang , Meng Kaiwen , Shi Shuobo , Wu Haibo , Meng Geng , Zhu Zhenglin
Published: December 2021

Previous work indicated that the nucleocapsid 203 mutation increase the virulence and transmission of the SARS-CoV-2 Alpha variant. However, Delta later outcompeted Alpha and other lineages, promoting a new wave of infections. Delta also possesses a nucleocapsid 203 mutation, R203M. Large-scale epidemiological analyses suggest a synergistic effect of the 203 mutation and the spike L452R mutation, associated with Delta expansion. Viral competition experiments demonstrate the synergistic effect in fitness and infectivity. More importantly, we found that the combination of R203M and L452R brings in a 3.2-fold decrease in neutralizing titers to the neutralizing serum relative to L452R-only virus. R203M/L452R show an increased fitness after the initiation of global vaccination programmes, possibly associated with the enhanced immune evasion. Another rapidly emerging variant Omicron also bears the 203 mutation. Thus, we proposed that nucleocapsid mutations play an essential role for the rise and predominance of variants in concern.
Characterization of antibiotic resistance in clinical isolates of Klebsiella pneumoniae in Denmark
Authors: Fang Xin , Westh Henrik , Kemp Michael , Ellermann-Eriksen Svend , Palsson Bernhard O. , Johansen Helle Krogh , Monk Jonathan M.
Published: December 2021

Klebsiella pneumoniae (KP) is a major global health problem as it leads to hospital outbreaks all over the world and is becoming more difficult to treat due to its increasing antimicrobial resistance (AMR). Optimization and development of new treatments of KP requires understanding of its population structure and AMR properties. Therefore, in this study, we collected and sequenced 491 KP strains from four major Danish microbiology departments covering 51% of the Danish population. The isolates were whole genome sequenced (WGS), phenotypically characterized and compared with 2,124 KP strains from 13 different countries (PATRIC strains). We found that while genomic content varies significantly across the Danish strains, they also differ significantly from strains from other countries, due to the lack of certain AMR sequence types (e.g. ST258 and ST307) in Denmark. Genomic and experimental analysis suggest that Danish strains contain fewer virulence mechanisms and are more susceptible to antimicrobials compared to strains from other countries, likely due to the relatively low antibiotic usage in Denmark where 70% of hospital antibiotic usage is penicillins. We also identified potential novel AMR determinants to tigecycline through statistical analysis of genomic and phenotypic data. To conclude, we obtained a more comprehensive understanding of the KP strains in Denmark and provided valuable insights for future experiments and strategies to combat AMR in KP.
Multi-layered networks of SalmoNet2 enable strain comparisons of the Salmonella genus on a molecular level
Authors: Olbei Marton , Bohar Balazs , Fazekas David , Madgwick Matthew , Sudhakar Padhmanand , Hautefort Isabelle , Métris Aline , Baranyi Jozsef , Kingsley Robert A. , Korcsmaros Tamas
Published: December 2021

Serovars of the genus Salmonella primarily evolved as gastrointestinal pathogens in a wide range of hosts. Some serotypes later evolved further, adopting a more invasive lifestyle in a narrower host range associated with systemic infections. A system-level knowledge of these pathogens has the potential to identify the complex adaptations associated with the evolution of serovars with distinct pathogenicity, host range and risk to human health. This promises to aid the design of interventions and serve as a knowledge base in the Salmonella research community. Here we present SalmoNet2, a major update to SalmoNet, the first multi-layered interaction resource for Salmonella strains, containing protein-protein, transcriptional regulatory and enzyme enzyme interactions. The new version extends the number of Salmonella genomes from 11 to 20, including strains such as S. Typhimurium D23580, an epidemic multidrug-resistant strain leading to invasive non-typhoidal Salmonella Disease (iNTS), and a strain from Salmonella bongori, another species in the Salmonella genus. The database now uses strain specific metabolic models instead of a generalised model to highlight differences between strains. This has increased the coverage of high-quality protein-protein interactions, and enhances interoperability with other computational resources by adopting standardised formats. The resource website has been updated with tutorials to help researchers analyse their Salmonella data using molecular interaction networks from SalmoNet2. SalmoNet2 is accessible at http://salmonet.org/.

Importance

Multi-layered network databases collate information from multiple sources, and are powerful both as a knowledge base and platform for analysis. Here we present SalmoNet2, an integrated network resource of 20 Salmonella strains, containing protein-protein, transcriptional regulatory, and metabolic interactions. Key improvements to the update include expanding the number of strains, strain-specific metabolic networks, an increase in high quality protein-protein interactions, community standard computational formats to help interoperability, and online tutorials to help users analyse their data using SalmoNet2.
CameraEEG: Synchronized Recording of Video with Electroencephalogram data on an Android Application
Authors: Madhavan Srihari , Hazarika Doli , Gupta Cota Navin
Published: December 2021

We present a novel android application named CameraEEG that enables synchronized acquisition of Electroencephalogram(EEG) and camera data using a smartphone. Audio-visual events of interest experienced by the subject were also recorded using a button press on the CameraEEG app. Unlike lab-restricted experiments, which usually constrain the subject’s mobility, this wearable solution enables monitoring of the human brain during everyday life activities. The app was built using Android SDK version 28 and Smarting mobi SDK from mbraintrain. It works on all android devices having a minimum Android OS - Lollipop.

We successfully recorded thirty minutes of synchronized Video and EEG during eyes closed and walking tasks using the app. Event markers enabled by the subject using the app during walking tasks were also recorded. Timing tests showed that temporal synchronization of video and EEG data was good. We analysed the recorded data and were able to identify the task performed by the subject from the event markers. The power spectrum density of the two tasks showed different power spectrums with a peak in the alpha band for eyes closed task. We also provide android studio codes for download and detailed help documentation for the community to test the developed application.
The role of intraspinal sensory neurons in the control of quadrupedal locomotion
Authors: Gerstmann Katrin , Jurčić Nina , Kunz Severine , Wanaverbecq Nicolas , Zampieri Niccolò
Published: December 2021

From swimming to walking and flying, animals have evolved specific locomotor strategies to thrive in different habitats. All types of locomotion depend on integration of motor commands and sensory information to generate precise movements. Cerebrospinal fluid-contacting neurons (CSF-cN) constitute a vertebrate sensory system that monitors CSF composition and flow. In fish, CSF-cN modulate swimming activity in response to changes in pH and bending of the spinal cord, yet their role in higher vertebrates remains unknown. We used mouse genetics to study their function in quadrupedal locomotion and found that CSF-cN are directly integrated into spinal motor circuits by forming connections with motor neurons and premotor interneurons. Elimination of CSF-cN selectively perturbs the accuracy of foot placement required for skilled movements at the balance beam and horizontal ladder. These results identify an important role for mouse CSF-cN in adaptive motor control and indicate that this sensory system evolved a novel function from lower vertebrates to accommodate the biomechanical requirements of terrestrial locomotion.
Evaluation of Commercially Available Glucagon Receptor Antibodies and Glucagon Receptor Expression
Authors: Bomholt Anna Billeschou , Johansen Christian Dall , Kjeldsen Sasha A. S. , Galsgaard Katrine D. , Christensen Jens Bager , Winther-Sørensen Marie , Serizawa Reza , Hornum Mads , Porrini Esteban , Pedersen Jens , Ørskov Cathrine , Gluud Lise L. , Sørensen Charlotte Mehlin , Holst Jens J. , Albrechtsen Reidar , Albrechtsen Nicolai J. Wewer
Published: December 2021

Glucagon is a key regulator of numerous metabolic functions including glucose, protein and lipid metabolism, and glucagon-based therapies are explored for diabetes, fatty liver disease and obesity. Insight into tissue and cell specific expression of the glucagon receptor (GCGR) is important to understand the biology of glucagon as well as to differentiate between direct and indirect actions of glucagon. However, it has been challenging to accurately localize the GCGR in tissue due to low expression levels and lack of specific methodologies. Immunohistochemistry has frequently been used for GCGR localization, but G-protein-coupled receptors (GPCRs) targeting antibodies are notoriously unreliable. In this study, we systematically evaluated all commercially available GCGR antibodies. Initially, twelve GCGR antibodies were evaluated using HEK293 cells transfected with mouse or human GCGR cDNA. Of the twelve antibodies tested, eleven showed positive staining of GCGR protein from both species. Human liver tissue was investigated using the same GCGR antibodies. Five antibodies failed to stain human liver biopsies (despite explicit claims to the contrary from the vendors). Immunohistochemical (IHC) staining demonstrated positive staining of liver tissue from glucagon receptor knockout (Gcgr−/−) mice and their wild-type littermates (Gcgr+/+) with only one out of the twelve available GCGR antibodies. Three antibodies were selected for further evaluation by western blotting and bands corresponding to the predicted size of the GCGR (62 kDa) were identified using two of these. Finally, a single antibody (no. 11) was selected for specific GCGR localization studies in various tissues. In mouse tissue the most intense immunostainings were found in lever, kidney, ileum, heart, and pancreas. Western blotting, performed on liver tissue from Gcgr+/+ and Gcgr−/− mice, confirmed the specificity of antibody no. 11, detecting a band at high intensity in material from Gcgr+/+and no bands in liver tissue from Gcgr−/−mice. Staining of human kidney tissue, with antibody no. 11, showed GCGR localization to the distal tubules. Autoradiography was used as an antibody-independent approach to support the antibody-based findings, revealing specific binding in liver, pancreas, and kidney. As a final approach, RNA-sequencing and single-cell RNA (scRNA)-sequencing were implemented. RNA-sequencing confirmed GCGR presence within liver and kidney tissue. The GCGR was specifically found to be expressed in hepatocytes by scRNA-sequencing and potentially also in collecting and distal tubule cells in the kidney. Our results clearly indicate the liver and the kidneys as the primary targets of glucagon action.
Structural basis for antibody resistance to SARS-CoV-2 omicron variant
Authors: Cerutti Gabriele , Guo Yicheng , Liu Lihong , Zhang Zhening , Liu Liyuan , Luo Yang , Huang Yiming , Wang Harris H. , Ho David D. , Sheng Zizhang , Shapiro Lawrence
Published: December 2021

The recently reported B.1.1.529 Omicron variant of SARS-CoV-2 includes 34 mutations in the spike protein relative to the Wuhan strain that initiated the COVID-19 pandemic, including 15 mutations in the receptor binding domain (RBD). Functional studies have shown omicron to substantially escape the activity of many SARS-CoV-2-neutralizing antibodies. Here we report a 3.1 Å resolution cryo-electron microscopy (cryo-EM) structure of the Omicron spike protein ectodomain. The structure depicts a spike that is exclusively in the 1-RBD-up conformation with increased mobility and inter-protomer asymmetry. Many mutations cause steric clashes and/or altered interactions at antibody binding surfaces, whereas others mediate changes of the spike structure in local regions to interfere with antibody recognition. Overall, the structure of the omicron spike reveals how mutations alter its conformation and explains its extraordinary ability to evade neutralizing antibodies.

Highlights

SARS-CoV-2 omicron spike exclusively adopts 1-RBD-up conformation

Omicron substitutions alter conformation and mobility of RBD

A subset of omicron mutations change the local conformation of spike

The structure reveals the basis of antibody neutralization escape
Expanded FLP toolbox for spatiotemporal protein degradation and transcriptomic profiling in C. elegans
Authors: Fragoso-Luna Adrián , Romero-Bueno Raquel , Eibl Michael , Ayuso Cristina , Muñoz-Jiménez Celia , Benes Vladimir , Cases Ildefonso , Askjaer Peter
Published: December 2021

Control of gene expression in specific tissues and/or at certain stages of development allows the study and manipulation of gene function with high precision. Site-specific genome recombination by the Flippase (FLP) and Cre enzymes has proven particularly relevant. Joint efforts of many research groups have led to the creation of efficient FLP and Cre drivers to regulate gene expression in a variety of tissues in Caenorhabditis elegans. Here, we extend this toolkit by the addition of FLP lines that drive recombination specifically in distal tip cells, the somatic gonad, coelomocytes and the epithelial P lineage. In some cases, recombination-mediated gene knockouts do not completely deplete protein levels due to persistence of long-lived proteins. To overcome this, we developed a spatiotemporally regulated degradation system for GFP fusion proteins (GFPdeg) based on FLP-mediated recombination. Using two stable nuclear pore proteins, MEL-28/ELYS and NPP-2/NUP85 as examples, we report the benefit of combining tissue-specific gene knockout and protein degradation to achieve complete protein depletion. We also demonstrate that FLP-mediated recombination can be utilized to identify transcriptomes in a C. elegans tissue of interest. We have adapted RNA polymerase DamID (RAPID) for the FLP toolbox and by focusing on a well-characterized tissue, the hypodermis, we show that the vast majority of genes identified by RAPID are known to be expressed in this tissue. These tools allow combining FLP activity for simultaneous gene inactivation and transcriptomic profiling, thus enabling the inquiry of gene function in various complex biological processes.