bluuebunny/crossref_metadata_2025 huggingface dataset:
Racial differences in institutional trust and COVID-19 vaccine hesitancy and refusal
Authors: Bagasra Anisah B. , Doan Sara , Allen Christopher T.
Published: November 2021

Background

Previous research has indicated that demographic differences affect COVID-19 vaccination rates. Trust, in both the vaccine itself and institutional trust, is one possible factor. The present study examines racial differences in institutional trust and vaccine status among a nationally representative sample of adults in the United States.

Methods

Data for the current study was collected as part of Wave 8 Omnibus 2000 survey conducted by RAND ALP and consisted of 2080 participants. Responses were collected through the online RAND ALP survey in March 2021.

Results

Trust in the scientific community was the strongest predictor for already receiving at least one dose of the COVID-19 vaccine at the time of study. Asians had a significantly higher trust in the scientific community compared to all other groups. Results also showed a significant difference in level of trust of the government’s response to the COVID-19 pandemic with Indian/Alaskan Natives reporting lower trust compared to Whites, Blacks and Asians. Asians also had a significantly higher level of trust when compared to those who identified as racial Other. Those who identify as American Indian/Alaskan Natives had the lowest levels of institutional trust. Trust in the government’s response was not indicative of vaccination within the sample.

Conclusions

Strategies to increase trust of the scientific community can be employed to address vaccine hesitancy through community-based initiatives and building of partnerships between the scientific community and local community stakeholders.
COVID19 vaccine intentions in South Africa: health communication strategy to address vaccine hesitancy
Authors: Kollamparambil Umakrishnan , Oyenubi Adeola , Nwosu Chijioke
Published: November 2021

Background

Vaccine hesitancy is emerging as a significant challenge in many parts of the world in the fight against the COVID19 pandemic. The continued infection amongst the unvaccinated can lead to a heightened risk of further virus mutation, exposing even those vaccinated to new virus strains. Therefore, there are social benefits in minimising vaccine hesitancy. The objective of this study is to assess the level of COVID19 vaccine hesitancy in South Africa, identify the socio-economic patterns in vaccine hesitancy and highlight insights from the national survey that can inform the development of a COVID-19 vaccination acceptance communication campaign.

Methods

The study uses the nationally representative National Income Dynamics Study - Coronavirus Rapid Mobile Survey (NIDS-CRAM) survey. The analysis combines univariate and bivariate statistics, as well as multivariate regression models like binomial/ordinal and multinomial logit.

Results

The study finds that vaccine acceptance is lower than that of non-pharmaceutical intervention like face-mask use. Only 55% fully accept the vaccine, while a further 16% are moderately accepting of vaccines. Together, vaccine acceptance is estimated at 70.8%, and vaccine hesitancy against COVID19 is estimated at 29.2% amongst the adult South African population.

The study has identified the perceived risk of infection with the mediating role of efficacy as a key predictor of vaccine intention. Higher awareness of COVID19 related information and higher household income are correlated with lower vaccine hesitancy. The non-black African population group has significantly high vaccine hesitancy compared to black Africans.

Conclusions

There are other significant differences across socio-economic and demographic variables in vaccine hesitancy. From a communication perspective, it is imperative to continue risk messaging, hand in hand with clearer information on the efficacy of the vaccines.
The association of sensory phenotype and concomitant mood, sleep and functional impairment with the outcome of carpal tunnel surgery
Authors: Kennedy Donna L. , Ridout Deborah , Lysakova Ladislava , Vollert Jan , Alexander Caroline M. , Rice Andrew S. C.
Published: November 2021

Background

Up to 25% of people who have had carpal tunnel release surgery (CTR) fail to report improvement; however, evidence for prognostic indicators in this surgical cohort is limited. To identify candidate prognostic factors, this study investigated the association of quantitative sensory testing (QST) derived sensory phenotype and attendant impairment with patient-reported surgical outcome.

Methods

With ethical approval and informed consent, this prospective observational longitudinal study recruited patients from two London hospitals. Multimodal phenotyping measures including quantitative sensory testing (QST), pain parameters, insomnia, pain-related worry, mood and function, were evaluated prior to; and at 3- and 6-months post-surgery. Pain in median nerve distribution with electrophysiologically confirmed conduction delay and DN4 score ≥ 4 was defined as neuropathic. Primary outcome was patient-rated change at 6 months, dichotomised as poor outcome; “worse” or “no change” and good outcome; “slightly better”, “much better” or “completely cured”.

Results

Seventy-six patients participated. Prior to surgery, substantial heterogeneity in established categories of somatosensory function was observed with 21% of participants categorised as having a healthy sensory phenotype; 29% with thermal hyperalgesia; 32% mechanical hyperalgesia and 18% sensory loss. Seventy six percent of participants were classified as having neuropathic pain, 33% with high levels of pain related worry and 64% with clinical insomnia. Observed differences in pain, sleep impairment, psychological factors and function, between sensory phenotypic groups, was not significant. At 3- and 6-months post-surgery there was significant improvement in all phenotyping measures with a moderate to large effect size. Thermal and mechanical measures of somatosensation improved (p < 0.001), as did functional ability (p < 0.001). Symptom severity diminished (p < 0.001), as did pain-related worry (p < 0.001), anxiety (p = 0.02) and insomnia (p < 0.001). Patient-rated surgical outcome was good in 92% of the cohort, poor in 8%. Baseline sensory phenotype category was not associated with surgical outcome however pain-related worry, anxiety and functional interference were significantly associated with outcome (p ≤ 0.05).

Conclusion

In patients undergoing carpal tunnel surgery, pain-related worry, anxiety and pain functional interference are candidate prognostic outcome factors and require further elucidation.
Development, reliability and validity of infectious disease specialist Nurse’s Core competence scale
Authors: Wu Chao , Yan Jiaran , Wu Jing , Wu Ping , Cheng Feixia , Du Lina , Du Yanling , Lei Shang , Lang Hongjuan
Published: November 2021

Aim

This study aims to develop an instrument to measure infectious disease specialist nurses’ core competence and examining the scale’s validity and reliability.

Background

With the increase of infectious diseases, more and more attention has been paid to infectious disease nursing care. The core competence of the infectious disease specialist nurses is directly related to the quality of nursing work. In previous researches, infectious disease specialist nurses’ core competence was measured by the tools developed for general nurses instead of specialized tools, which made it difficult to clarify the core competence of nurses in infectious diseases department.

Methods

Preliminary items were developed through literature review, theoretical research, qualitative interview and Delphi method. The confirmed 47 items were applied in the two rounds of data collection. Evaluation data on 516 infectious disease specialist nurses’ core competence in the first round were utilized to preliminarily evaluate and explore the scale’s constrution, while evaluation data on 497 infectious disease specialist nurses’ core competence in the second round were utilized to do reliability analysis and validity analysis. In this study, factor analysis, Cronbach’s α, Pearson correlation coefficients were all adopted.

Results

The final scale is composed of 34 items and 5 factors, and adopted the 5-point scoring method. The factors are Professional Development Abilities, Infection Prevention and Control Abilities, Nursing Abilities for Infectious Diseases, Professionalism and Humanistic Accomplishment, and Responsiveness to Emergency Infectious Diseases. The explanatory variance of the five factors was 75.569%. The reliability and validity of the scale is well validated. The internal consistency, split-half reliability and test-retest reliability were 0.806, 0.966 and 0.831 respectively. The scale has good structural validity and content validity. The content validity was 0.869. Discrimination analysis showed that there were significant differences in the scores of core competence and its five dimensions among infectious disease specialist nurses of different ages, working years in infectious diseases, titles, educational background, marital status and wages (allP < 0.05).

Conclusions

The proposed scale takes on high reliability and validity, and is suitable for assessing the infectious disease specialist nurses’ core competence.

Relevance to clinical practice

This scale provides a reference for clinical assessment of infectious disease nursing.
Formation of nuclear condensates by the Mediator complex subunit Med15 in mammalian cells
Authors: Shi Yuanyuan , Chen Jian , Zeng Wei-Jie , Li Miao , Zhao Wenxue , Zhang Xing-Ding , Yao Jie
Published: November 2021

Background

The Mediator complex is an evolutionarily conserved multi-subunit protein complex that plays major roles in transcriptional activation and is essential for cell growth, proliferation, and differentiation. Recent studies revealed that some Mediator subunits formed nuclear condensates that may facilitate enhancer-promoter interactions and gene activation. The assembly, regulation, and functions of these nuclear condensates remain to be further understood.

Results

We found that Med15, a subunit in the tail module of the Mediator complex, formed nuclear condensates through a novel mechanism. Nuclear foci of Med15 were detected by both immunostaining of endogenous proteins and live cell imaging. Like Med1 foci and many other biomolecular condensates, Med15 foci were sensitive to 1, 6-Hexanediol and showed rapid recovery during fluorescence recovery after photobleaching. Interestingly, overexpressing DYRK3, a dual-specificity kinase that controls the phase transition of membraneless organelles, appeared to disrupt Med1 foci and Med15 foci. We identified two regions that are required to form Med15 nuclear condensates: the glutamine-rich intrinsically disordered region (IDR) and a short downstream hydrophobic motif. The optodroplet assay revealed that both the IDR and the C-terminal region of Med15 contributed to intracellular phase separation.

Conclusions

We identified that the Mediator complex subunit Med15 formed nuclear condensates and characterized their features in living cells. Our work suggests that Med15 plays a role in the assembly of transcription coactivator condensates in the nucleus and identifies Med15 regions that contribute to phase separation.
α1-Antitrypsin attenuates acute rejection of orthotopic murine lung allografts
Authors: Nakagiri Tomoyuki , Wrenger Sabine , Sivaraman Kokilavani , Ius Fabio , Goecke Tobias , Zardo Patrick , Grau Veronika , Welte Tobias , Haverich Axel , Knöfel Ann-Kathrin , Janciauskiene Sabina
Published: November 2021

Background

α1-Antitrypsin (AAT) is an acute phase glycoprotein, a multifunctional protein with proteinase inhibitory, anti-inflammatory and cytoprotective properties. Both preclinical and clinical experiences show that the therapy with plasma purified AAT is beneficial for a broad spectrum of inflammatory conditions. The potential effects of AAT therapy have recently been highlighted in lung transplantation (LuTx) as well.

Methods

We used a murine fully mismatched orthotopic single LuTx model (BALB/CJ as donors and C57BL/6 as recipients). Human AAT preparations (5 mg, n = 10) or vehicle (n = 5) were injected to the recipients subcutaneously prior to and intraperitoneally immediately after the LuTx. No immune suppressive drugs were administered. Three days after the transplantation, the mice were sacrificed, and biological samples were assessed.

Results

Histological analysis revealed significantly more severe acute rejection in the transplanted lungs of controls than in AAT treated mice (p < 0.05). The proportion of neutrophil granulocytes, B cells and the total T helper cell populations did not differ between two groups. There was no significant difference in serum CXCL1 (KC) levels. However, when compared to controls, human AAT was detectable in the serum of mice treated with AAT and these mice had a higher serum anti-elastase activity, and significantly lower proportion of Th1 and Th17 among all Th cells. Cleaved caspase-3-positive cells were scarce but significantly less abundant in allografts from recipients treated with AAT as compared to those treated with vehicle.

Conclusion

Therapy with AAT suppresses the acute rejection after LuTx in a mouse model. The beneficial effects seem to involve anti-protease and immunomodulatory activities of AAT.
A nanodrug system overexpressed circRNA_0001805 alleviates nonalcoholic fatty liver disease via miR-106a-5p/miR-320a and ABCA1/CPT1 axis
Authors: Li Jian , Qi Jing , Tang Yishu , Liu Huaizheng , Zhou Kefu , Dai Zheren , Yuan Lehong , Sun Chuanzheng
Published: November 2021

Our study aimed to explore the function of circRNA_0001805 in the pathogenesis of NAFLD and the underlying mechanism. A nanodrug system (GA-RM/GZ/PL) was constructed to overexpress circRNA_0001805 specifically in hepatocytes for the treatment of NAFLD. Fat droplet accumulation in cultured cells and mouse hepatic tissues was detected using Oil Red O or H&E staining. The relative expression of circRNAs, genes associated with lipogenesis was quantified by qRT-PCR. Interactions between circRNA_0001805 and miR-106a-5p/miR-320a, between miR-106a-5p/miR-320a and ABCA1/CPT1 were confirmed by dual-luciferase reporter assay. A novel metalorganic framework nanocarrier (GZ) was prepared from glycyrrhizic acid and zinc ions (Zn2+), and this nanocarrier was loaded with the circRNA_0001805 plasmid to construct a nanocore (GZ/PL). Then, this GZ/PL was coated with a galactose-modified RBC membrane (GA-RM) to generate GA-RM/GZ/PL. CircRNA_0001805 expression was downregulated in FFA-challenged primary hepatocytes, HFD-fed mice and NAFLD patients. Overexpressed circRNA_0001805 attenuated NAFLD development by suppressing lipid metabolism disorder and inflammation. CircRNA_0001805 targeted miR-106a-5p/miR-320a, which served as an upstream inhibitor of ABCA1/CPT1 and collaboratively regulated NAFLD progression. GA-RM/GZ/PL targeted hepatocytes, overexpressed circRNA_0001805, released glycyrrhizic acid to reduce the accumulation of lipids in the liver and played a synergistic role against NAFLD-induced lipid metabolism disorder.

Graphical Abstract
Content validation of observer-reported sickle cell pain diaries (SCPD-CS and SCPD-CN): results from interviews with caregivers
Authors: White Michelle K. , Foster April M. , Bailey Miranda , D’Alessio Denise , Rizio Avery , Stebbins Patricia , Pierre Danielle St. , Saucier Cory
Published: November 2021

Background

Patients with sickle cell disease (SCD) experience daily pain and acute episodes known as sickle cell pain crises (SCPCs). The Sickle Cell Pain Diary-Caregiver Report (SCPD-C) is an observer-reported diary for use by caregivers of children ages < 12 years with SCD. This study reports on the content validity of the SCPD-C.

Methods

The SCPD-C was developed based on a literature review, measurement expert input, and a patient advisory board including clinicians. Three rounds of interviews (including both concept elicitation and cognitive debriefing methodologies) were conducted with caregivers of children with SCD aged < 12 to evaluate the content validity of the SCPD-C.

Results

Across three rounds of interviews, caregivers confirmed concepts in the SCPD-C and described observed impacts that were important and were added. Overall, caregivers evaluated the SCPD-C as easy to understand, with some minor adaptations for clarity. Additionally, the diary was split into two versions based on the child’s age and school enrollment status (SCPD-CS for school-aged and SCPD-CN for non-school age children).

Conclusions

Caregivers provided valuable input that led to important additions and changes to the measures. The SCPD-CS and SCPD-CN are appropriate and fit-for-purpose observer-reported outcome measures of SCPC-related pain frequency and severity, and impacts on health-related quality of life.
Characteristics of intramedullary nail breakage in pertrochanteric femur fractures: a summary of 70 cases
Authors: Li Pengfei , Zhang Zhishan , Zhou Fang , Lv Yang , Guo Yan , Tian Yun
Published: November 2021

Objective

To reveal noteworthy characteristics of intramedullary (IM) nail breakage in pertrochanteric femur fractures.

Materials and methods

The data from 6 patients with IM nail breakage in our hospital between August 2008 and May 2018 were reviewed retrospectively. With an additional 64 cases reported in articles in the PubMed database prior to October 2019, a total of 70 cases were reviewed and analysed; epidemiological patient data and data on the initial trauma, fracture type, nail selected for the original surgery, time from surgery to breakage, mechanism and location of breakage, status of fracture healing, salvage treatment and prognosis were assessed.

Results

Seventy patients with pertrochanteric fractures, including 2 stable fractures and 68 unstable fractures, experienced IM nail breakage at a mean of 9.4 months after the initial surgery. Among them, 9 (12.9%) occurred within 3 months, 23 (32.9%) between 3 and 6 months and 38 (54.3%) after 6 months. The mean age was 72.3 years, and 16 (22.9%) patients were younger than 65 years old. When nail breakage occurred, 66 fractures (94.3%) exhibited delayed union/non-union. Self-dynamisation was found in 12 cases (17.1%). The salvage procedures included 4 partial/total implant removal procedures, 17 hemi/total hip arthroplasty procedures, 3 conservative treatment procedures, and 46 revised osteosyntheses, of which 7 cases (15.2%) sustained secondary implant failure. No significant differences were found between the failure rates of IM nails and extramedullary(EM) devices (odds ratio [OR], 3.429; 95% confidence interval [CI], 0.632–18.877; p = 0.330).

Conclusion

IM nail breakage is a rare complication lack of time regularity and mostly occurs in unstable pertrochanteric fractures in the presence of delayed union/non-union. Osteosynthesis revision can be conduct by a new IM nail or EM device but considerable secondary failure rate is noteworthy. Self-dynamisation may be a warning sign of nail breakage.
Arthroscopic triangular fibrocartilage complex reconstruction with free tendon graft for chronic distal radioulnar joint instability
Authors: Yeh Kuang-Ting , Shih Jui-Tien
Published: November 2021

Background

Tears in the triangular fibrocartilage complex (TFCC) often manifest as ulnar wrist pain and limited wrist function. In chronic cases, the treatment of large tears with irreparable TFCC degeneration combined with distal radioulnar joint (DRUJ) instability is difficult. In the current report, we describe the outcomes of a minimally invasive technique for TFCC reconstruction using the free palmaris longus (PL) tendon via arthroscopy.

Methods

We examined the cases of 67 adult patients [54 men and 13 women; age range, 19–34 years (mean age, 26.4 years)] treated for chronic and irreparable TFCC tears from 2001 to 2019. We used the arthroscopic TFCC reconstruction method with the free PL tendon for all chronic and irreparable TFCC injuries with DRUJ instability in our clinic. Thereafter, the patients underwent the rehabilitation program, which included wrist motion and occupational therapy. The mean time period from the event causing the tear to the operation was 22.6 months.

Results

The function results of these patients significantly improved, and the ulnar wrist pain significantly decreased at postoperative follow-up. Of the 67 patients, 38 rated their wrists as “excellent,” 26 as “good,” and 3 as “fair.” None of the patients developed wound infections or complications.

Conclusions

The results of this study suggest that arthroscopic TFCC reconstruction using the free PL tendon is an effective method for treating chronic and irreparable TFCC tears with DRUJ instability.
A systematic review of the effect of sleep interventions on presenteeism
Authors: Takano Yuta , Iwano Suguru , Aoki Shuntaro , Nakano Norihito , Sakano Yuji
Published: November 2021

Background

Sleep problems interfere with work performance. Decreased work productivity due to health problems is defined as presenteeism. Although empirical data on the improvement of presenteeism by sleep interventions have been published, a systematic review elucidating whether there is a difference in the improvement of presenteeism across various types of sleep interventions has not yet been published. This systematic review of studies aimed to clarify which sleep interventions are more likely to be effective in improving presenteeism.

Methods

The electronic databases PubMed, PsycINFO, and MEDLINE were used to perform a literature search (the start and end search dates were October 20, 2019, and March 11, 2020, respectively). A combination of terms such as “employee*,” “sleep,” “insomnia,” and “presenteeism” was used for the search. Both randomized and non-randomized control trials were included in this systematic review.

Results

Six types of sleep interventions were identified, including cognitive behavioral therapy for insomnia (CBT-I), sleep hygiene education, yoga, mindfulness, weight loss program, and changing the color temperature of fluorescent lights in the workplace. Only CBT-I improved both sleep problems and presenteeism compared with a control group. The results of this review also show that there is heterogeneity in the measurement of presenteeism.

Conclusions

The results of this systematic review suggested that CBT-I could be adapted for workers with sleep problems and presenteeism. We discussed whether CBT-I improved both sleep problems and presenteeism compared with other interventions. In addition, methods for measuring presenteeism in future research are proposed.
CXCL14 facilitates the growth and metastasis of ovarian carcinoma cells via activation of the Wnt/β-catenin signaling pathway
Authors: Gao Li-Na , Hao Man , Liu Xiao-Hui , Zhang Li , Dong Yan , Zhang Yu-Fang , He Xiao-Chun
Published: November 2021

Background

There is an urgent need to identify potential targets in anticancer therapy to improve the survival and prognosis of patients with ovarian cancer (OC). Herein, we investigated the functional significance of chemokine (C-X-C motif) ligand 14 (CXCL14) in OC cell growth and epithelial–mesenchymal transition (EMT).

Methods

qRT PCR and western blotting was used to detect CXCL14 mRNA level and protein expression, respectively. The functional mechanism of CXCL14 in OC was investigated by CCK-8, colony formation and transwell assays. The migration ability of OC cell was determined using wound healing. The protein expressions of CXCL14 and β-catenin in OC tissues were determined by immumohistochemical staining.

Results

We demonstrated that high levels of CXCL14 were associated with a worse prognosis in patients with OC. CXCL14 knockdown considerably restrained the growth, migration and invasion of OC cell in vitro. In contrast, ectopic CXCL14 overexpression yielded the opposite results. Investigations to determine the underlying molecular mechanisms revealed that the Wnt/β-catenin signaling pathway is involved in CXCL14-facilitated OC cell invasiveness.

Conclusion

These data collectively demonstrate that CXCL14 contributes to OC cell growth and metastatic potential by regulating the Wnt/β-catenin signaling pathway.
Background frequency can enhance the prognostication power of EEG patterns categories in comatose cardiac arrest survivors: a prospective, multicenter, observational cohort study
Authors: Kim Youn-Jung , Kim Min-Jee , Kim Yong Hwan , Youn Chun Song , Cho In Soo , Kim Su Jin , Wee Jung Hee , Park Yoo Seok , Oh Joo Suk , Lee Dong Hoon , Kim Won Young ,   the Korean Hypothermia Network Investigators, Kim Ji Hoon , Park Kyu Nam , Jeong Won Jung , Choi Seung Pill , Lee Mi Jin , Lee Jong-Seok , Kim Su Jin , Jang Tae Chang , Kim Inbyung , Kim Yong Hwan , Kim Won Young , Shin Jonghwan , Lee Ji Hwan , Moon Hyung Jun , Kim Giwoon , Choi Wook-jin , Oh Joo Suk , Han Chul , Lee Byung Kook , Jeong Taeoh , Lee Dong Hoon , Hong Min Jin , Cho Gyu Chong , Lee Young Hwan , Sohn Youdong , Cho In Soo , You Je Sung , Kim Changsun , Cha Kyoung-Chul , Cho Soo Hyung
Published: November 2021

Background

We assessed the prognostic accuracy of the standardized electroencephalography (EEG) patterns (“highly malignant,” “malignant,” and “benign”) according to the EEG timing (early vs. late) and investigated the EEG features to enhance the predictive power for poor neurologic outcome at 1 month after cardiac arrest.

Methods

This prospective, multicenter, observational, cohort study using data from Korean Hypothermia Network prospective registry included adult patients with out-of-hospital cardiac arrest (OHCA) treated with targeted temperature management (TTM) and underwent standard EEG within 7 days after cardiac arrest from 14 university-affiliated teaching hospitals in South Korea between October 2015 and December 2018. Early EEG was defined as EEG performed within 72 h after cardiac arrest. The primary outcome was poor neurological outcome (Cerebral Performance Category score 3–5) at 1 month.

Results

Among 489 comatose OHCA survivors with a median EEG time of 46.6 h, the “highly malignant” pattern (40.7%) was most prevalent, followed by the “benign” (33.9%) and “malignant” (25.4%) patterns. All patients with the highly malignant EEG pattern had poor neurologic outcomes, with 100% specificity in both groups but 59.3% and 56.1% sensitivity in the early and late EEG groups, respectively. However, for patients with “malignant” patterns, 84.8% sensitivity, 77.0% specificity, and 89.5% positive predictive value for poor neurologic outcome were observed. Only 3.5% (9/256) of patients with background EEG frequency of predominant delta waves or undetermined had good neurologic survival. The combination of “highly malignant” or “malignant” EEG pattern with background frequency of delta waves or undetermined increased specificity and positive predictive value, respectively, to up to 98.0% and 98.7%.

Conclusions

The “highly malignant” patterns predicted poor neurologic outcome with a high specificity regardless of EEG measurement time. The assessment of predominant background frequency in addition to EEG patterns can increase the prognostic value of OHCA survivors.

Trial registration KORHN-PRO, NCT02827422. Registered 11 September 2016—Retrospectively registered.
Promotech: a general tool for bacterial promoter recognition
Authors: Chevez-Guardado Ruben , Peña-Castillo Lourdes
Published: November 2021

Promoters are genomic regions where the transcription machinery binds to initiate the transcription of specific genes. Computational tools for identifying bacterial promoters have been around for decades. However, most of these tools were designed to recognize promoters in one or few bacterial species. Here, we present Promotech, a machine-learning-based method for promoter recognition in a wide range of bacterial species. We compare Promotech’s performance with the performance of five other promoter prediction methods. Promotech outperforms these other programs in terms of area under the precision-recall curve (AUPRC) or precision at the same level of recall. Promotech is available at https://github.com/BioinformaticsLabAtMUN/PromoTech.
Experimental induction of necrotic enteritis with or without predisposing factors using netB positive Clostridium perfringens strains
Authors: Mohiuddin Mudassar , Yuan Weikang , Song Zhongfeng , Liao Shenquan , Qi Nanshan , Li Juan , Lv Minna , Wu Caiyan , Lin Xuhui , Hu Junjing , Cai Haiming , Sun Mingfei
Published: November 2021

Background

Poultry necrotic enteritis (NE) is an economically important disease caused by C. perfringens. The disease causing ability of this bacterium is linked with the production of a wide variety of toxins. Among them, necrotic enteritis B-like (NetB) toxin is reported to be involved in the pathogenesis of NE; in addition there is some circumstantial evidence that tpeL toxin may enhance virulence, but this is yet to be definitely shown. The situation becomes more complicated in the presence of a number of predisposing factors like co-infection with coccidia, type of diet and use of high protein diet. These co-factors alter the intestinal environment, thereby favoring the production of more toxins, leading to a more severe disease. The objective of this study was to develop a successful animal model that would induce clinical signs and lesions of NE using C. perfringens type G strains obtained from field outbreaks. A separate trial was simultaneously considered to establish the role of dietary factor with coccidial co-infection in NE.

Results

The results have shown that use of net-B positive C. perfringens without predisposing factors induce moderate to severe NE (Av. Lesion score 1.79 ± 1.50). In a separate trial, addition of fish meal to a feed of C. perfringens challenged birds produced higher number of NE cases (Av. Lesion score 2.17 ± 1.28). However, use of less virulent E. necatrix strain along with fish meal in conjunction with net-B positive strain did not alter the severity of NE lesions in specific pathogen free chicken (Av. Lesion score 2.21 ± 1.13).

Conclusions

This study suggests that virulent C. perfringens type G strains can induce NE lesions in the absence of other predisposing factors. Birds in the clostridia challenged group showed moderate to severe NE lesions. Use of less virulent coccidia strain contributed to a lesser extent in increasing the severity of disease. Maize based diet along with fishmeal (1:1) increased the severity of lesions but statistically it was non-significant. The NE lesions in all experimental groups were found to be present more frequently in the duodenum. In this way, this study provided an effective model for in vivo production of NE in poultry birds.
Collecting quantitative experimental data from a non-WEIRD population: challenges and practical recommendations from a field experiment in rural Sierra Leone
Authors: Luetke Lanfer Hanna , Reifegerste Doreen , Kargbo Sorie Ibrahim
Published: November 2021

Objective

Standardized pretest–posttest experimental designs with quantitative surveys are frequently applied to evaluate the effectiveness of health programs. However, this method is strongly informed by research on samples from Western, Educated, Industralized, Rich, and Democratic (WEIRD) societies and may not produce meaningful results in a distinct cultural, educational and socioeconomic context.

Results

This paper reports several methodological challenges encountered along the research process of collecting quantitative survey data (i.e., during recruitment, obtaining informed consent, matching pretest–posttest data and data collection) for a mixed-methods field experiment on domestic handwashing in Sierra Leone. Ethical dilemmas of certain research practices are pointed out and potential solutions or alternatives are recommended for each challenge. Analysis of these challenges highlights the importance of reflecting on the aptness of research methodologies for non-WEIRD samples. While this is not to say that quantitative surveys are not suitable in a non-WEIRD context, their employment require considerable time for extensive pilot testing, involving local interviewers and participants in designing research projects and the modification of data collection strategies.
Epigenetic modelling of former, current and never smokers
Authors: Langdon Ryan J. , Yousefi Paul , Relton Caroline L. , Suderman Matthew J.
Published: November 2021

Background

DNA methylation (DNAm) performs excellently in the discrimination of current and former smokers from never smokers, where AUCs > 0.9 are regularly reported using a single CpG site (cg05575921;AHRR). However, there is a paucity of DNAm models which attempt to distinguish current, former and never smokers as individual classes. Derivation of a robust DNAm model that accurately distinguishes between current, former and never smokers would be particularly valuable to epidemiological research (as a more accurate smoking definition vs. self-report) and could potentially translate to clinical settings. Therefore, we appraise 4 DNAm models of ternary smoking status (that is, current, former and never smokers): methylation at cg05575921 (AHRR model), weighted scores from 13 CpGs created by Maas et al. (Maas model), weighted scores from a LASSO model of candidate smoking CpGs from the literature (candidate CpG LASSO model), and weighted scores from a LASSO model supplied with genome-wide 450K data (agnostic LASSO model). Discrimination is assessed by AUC, whilst classification accuracy is assessed by accuracy and kappa, derived from confusion matrices.

Results

We find that DNAm can classify ternary smoking status with reasonable accuracy, including when applied to external data. Ternary classification using only DNAm far exceeds the classification accuracy of simply assigning all classes as the most prevalent class (63.7% vs. 36.4%). Further, we develop a DNAm classifier which performs well in discriminating current from former smokers (agnostic LASSO model AUC in external validation data: 0.744). Finally, across our DNAm models, we show evidence of enrichment for biological pathways and human phenotype ontologies relevant to smoking, such as haemostasis, molybdenum cofactor synthesis, body fatness and social behaviours, providing evidence of the generalisability of our classifiers.

Conclusions

Our findings suggest that DNAm can classify ternary smoking status with close to 65% accuracy. Both the ternary smoking status classifiers and current versus former smoking status classifiers address the present lack of former smoker classification in epigenetic literature; essential if DNAm classifiers are to adequately relate to real-world populations. To improve performance further, additional focus on improving discrimination of current from former smokers is necessary.
Evaluating volatile organic compounds from Chinese traditional handmade paper by SPME-GC/MS
Authors: Ding Li , Yang Qin , Liu Jianhui , Lee Zheng
Published: November 2021

Once printed, books are always accompanied by the smells of volatile organic compounds (VOCs) which are continuously emitted not only by inks but also by papers themselves throughout their lives. Although the VOCs from papers may bring mild discomfort to readers, they are considered as very important factors that feature the degradation of papers and show potential applications in cultural relic appraisal. In this study, an analytical approach based on solid phase microextraction combined with gas chromatography-mass spectrometry (SPME-GC/MS) was proposed for the evaluation of volatile organic compounds (VOCs) emitted by Chinese traditional handmade papers. The VOCs evaluations and artificial aging processes were both applied to recent-made papers and naturally aged papers from a traditional Chinese calligraphy and painting scroll (collected by the National Museum of China). To be noticed, a large number of aliphatic acids, aldehydes, ketones, furan derivatives, benzene series and terpenoid substances indicated that the VOCs signals not only reveal the degradation of paper but also tentatively reflect the storage environment along hundreds of years ago. The semi-quantitative evaluation of markers indicated that the historical paper is under a serious degradation due to the high capacity it releases. Our results provided a path way to get the degradation information of ancient paintings as well as potential realistic applications such as the conservation of paper-based relics and the environmental protection in libraries and museums.
CRISPR/Cas9 mediated editing of the Quorn fungus Fusarium venenatum A3/5 by transient expression of Cas9 and sgRNAs targeting endogenous marker gene PKS12
Authors: Wilson Fiona M. , Harrison Richard J.
Published: November 2021

Background

Gene editing using CRISPR/Cas9 is a widely used tool for precise gene modification, modulating gene expression and introducing novel proteins, and its use has been reported in various filamentous fungi including the genus Fusarium. The aim of this study was to optimise gene editing efficiency using AMA1 replicator vectors for transient expression of CRISPR constituents in Fusarium venenatum (A3/5), used commercially in the production of mycoprotein (Quorn™).

Results

We present evidence of CRISPR/Cas9 mediated gene editing in Fusarium venenatum, by targeting the endogenous visible marker gene PKS12, which encodes a polyketide synthase responsible for the synthesis of the pigment aurofusarin. Constructs for expression of single guide RNAs (sgRNAs) were cloned into an AMA1 replicator vector incorporating a construct for constitutive expression of cas9 codon-optimised for Aspergillus niger or F. venenatum. Vectors were maintained under selection for transient expression of sgRNAs and cas9 in transformed protoplasts. 100% gene editing efficiency of protoplast-derived isolates was obtained using A. niger cas9 when sgRNA transcription was regulated by the F. venenatum 5SrRNA promoter. In comparison, expression of sgRNAs using a PgdpA-ribozyme construct was much less effective, generating mutant phenotypes in 0–40% of isolates. Viable isolates were not obtained from protoplasts transformed with an AMA1 vector expressing cas9 codon-optimised for F. venenatum.

Conclusions

Using an AMA1 replicator vector for transient expression of A. niger cas9 and sgRNAs transcribed from the native 5SrRNA promoter, we demonstrate efficient gene editing of an endogenous marker gene in F. venenatum, resulting in knockout of gene function and a visible mutant phenotype in 100% of isolates. This establishes a platform for further development of CRISPR/Cas technology in F. venenatum for use as a research tool, for understanding the controls of secondary metabolism and hyphal development and validating prototypes of strains produced using traditional methods for strain improvement.
Compromised maternal nutritional status in early pregnancy and its relation to the birth size in young rural Indian mothers
Authors: Gokhale Devaki , Rao Shobha
Published: November 2021

Background

Low birth weight is highly prevalent in rural India. As a chronic undernutrition problem, poor birth outcomes are closely related to various nutritional factors more prominently the poor maternal anthropometry at conception. The purpose of the study was to identify how compromised maternal nutritional status in early pregnancy affects the birth size of rural Indian mothers.

Methods

It was a prospective observational study on singleton pregnant women (n = 204) from 14 villages in Mulshi Taluka of Pune District, Maharashtra, India. Maternal weight (Wt), height (Ht), body fat percent (BF%), head circumference (HC), and sitting height (SHT) were measured at early pregnancy (< 13 weeks of gestation) and infants’ weight and length were measured within 24 h of birth. Groups means were tested using a ‘t’ test while the trend in means was tested using ANOVA.

Results

Mothers were young (21.46 ± 2.09 yrs), thin (46.46 ± 6.1 kg), short (153.39 ± 5.79 cm), and poorly nourished (19.74 ± 2.41 kg/m2). Mean birth weight was low (2655 ± 507 g) and prevalence of LBW and stunting at birth was highest among mothers in the lower tertile of each of the anthropometric indicators. In particular, stunting was significantly higher for mothers in lower tertile compared to higher tertile of Wt (44.6 Vs 64.6%) and was also true for HC (43.7 Vs 60.6%). Risk for LBW and stunting at birth was almost similar and was significant (p < 0.01) for mothers in the lower tertile of Wt, Ht, BMI, SHT, HC, and BF% as compared to those in the higher tertile of these measurements.

Conclusion

All the anthropometric indicators of current undernutrition at first trimester as well as that in utero reflected by smaller HC, impose risk for LBW and stunting at birth especially among young rural mothers.
An open-access and inexpensive 3D printed otoscope for low-resource settings and health crises
Authors: Capobussi Matteo , Moja Lorenzo
Published: November 2021

Limited access to key diagnostic tools is detrimental to priority health needs of populations. Ear pain, tenderness, itching, and different degree of hearing loss are common problems which require otoscopy as first diagnostic assessment. Where an otoscope is not available because of budget constraints, a self-fabricated low-cost otoscope might represent a feasible opportunity. In this paper, we share the design and construction process of an open-source, 3D printed, otoscope. The prototype was compared to a commercial solution, demonstrating similar overall quality between the instruments.
Does the cardiovascular drug levosimendan prevent iodinated contrast medium nephrotoxicity with glycerol aggravation in rats?
Authors: Durur-Subasi Irmak , Kose Duygu , Yayla Muhammed , Sirin Busra , Karaman Adem , Calik Ilknur , Alper Fatih
Published: November 2021

Background

We investigated whether levosimendan prevents contrast medium nephrotoxicity with glycerol aggravation in rats.

Methods

Forty-eight Wistar albino rats were assigned to eight groups (n = 6 × 8). No medication was administered to group I (controls); glycerol (intramuscular injection of 25% glycerol, 10 mL/kg) group II; intravenous iohexol 10 mL/kg to group III; glycerol and iohexol to group IV; iohexol and intraperitoneal levosimendan 0.25 mg/kg to group V; glycerol, iohexol, and levosimendan 0.25 mg/kg to group VI; iohexol and levosimendan 0.5 mg/kg to group VII; and glycerol, iohexol, and levosimendan 0.5 mg/kg to group VIII. One-day water withdrawal and glycerol injection prompted renal damage; iohexol encouraged nephrotoxicity; levosimendan was administered 30 min after glycerol injection and continued on days 2, 3, and 4. The experiment was completed on day 5. Serum blood urea nitrogen (BUN) and creatinine levels, superoxide dismutase (SOD) activity, glutathione (GSH), malondialdehyde (MDA) levels, tumour necrosis factor-α (TNF-α), nuclear factor kappa ß (NFK-ß), interleukin 6 (IL-6), and histopathological marks were assessed. One-way analysis of variance and Duncan’s multiple comparison tests were used.

Results

Levosimendan changed serum BUN (p = 0.012) and creatinine (p = 0.018), SOD (p = 0.026), GSH (p = 0.012), and MDA (p = 0.011). Levosimendan significantly downregulated TNF-α (p = 0.022), NFK-ß (p = 0.008), and IL-6 (p = 0.033). Histopathological marks of hyaline and haemorrhagic cast were improved in levosimendan-injected groups.

Conclusion

Levosimendan showed nephroprotective properties due to its vasodilator, oxidative distress decreasing and inflammatory cytokine preventing belongings.
Sex-related differences regarding cephalic vein lead access for CIEDs implantation
Authors: Taleski Jane , Stankovik Svetlana , Risteski Dejan , Janusevski Filip , Pocesta Bekim , Zimbakov Zan , Poposka Lidija
Published: November 2021

Background

Minimally invasive and safe central venous access is imperative for lead insertion of cardiac implantable electronic devices (CIEDs). The purpose of this trial was to explore and compare the usability of the cephalic vein (CV) between both sexes.

Methods and results

This single-center prospective study included 102 consecutive patients in a period of six months. Pre-procedural contrast-enhanced venographic images of the upper arm were performed in all included patients. Our attention was focused on comparing several morpho-anatomical CV characteristics such as venous diameter, presence of valves and angle of entrance of the CV into the subclavian vein (SV). Study results concerning the CV morpho-anatomical differences were more favorable regarding the female patient group, with significant differences in CV diameter (p-0.030). There was also a difference in favor of the female group regarding the favorable CV angle of entrance into the SV, found in the 61.7% versus 54.4% in the male patient group. The comparison of usability of the CV and CVC technique was explored by comparing the number of leads inserted through the CV in both sexes. Two leads were implanted in 11.7% in the female group versus 5.8% in the male group, and 0 leads through the CV in 38.2% of the female patients versus 50% of male group.

Conclusion

Female patients have more favorable cephalic vein morpho-anatomical futures and better usability for lead placement than male patients.
Hepatic adrenal rest tumor in a patient with multifactorial liver cirrhosis: a case report with CT and MRI findings and pathologic correlation
Authors: Boraschi Piero , Turini Francesca , Donati Francescamaria , Peruzzi Francesca , Bartolucci Annamaria , Roffi Niccolò , Colombatto Piero , Urbani Lucio
Published: November 2021

Background

Adrenal rest tumor is an ectopic collection of adrenocortical cells in an extra-adrenal site, more frequently located around the kidney, retroperitoneum, spermatic cord, para-testicular region and broad ligament, but very rarely occurring also in the liver. Hepatic adrenal rest tumor poses a diagnostic challenge in differentiating it from hepatocellular carcinoma, particularly in a cirrhotic liver.

Case presentation

An 83-years-old male was referred to our hospital by his family doctor for hepatological evaluation due to multifactorial liver cirrhosis. Ultrasound revealed a centimetric hypoechoic nodule in the VI hepatic segment in the context of a liver with signs of cirrhosis and steatosis. The patient first underwent MRI and then CT, which showed a fat containing focal liver lesion in the subcapsular location of the right lobe, strictly adjacent to the homolateral adrenal gland. The nodule was hypervascular in the arterial phase, washed out in the portal-venous and transitional phases, resulting hypointense in the hepato-biliary phase at MR imaging. In the suspicion of a hepatocellular carcinoma, the nodule was surgically removed, and the patient’s postoperative course was unremarkable. The final histopathological diagnosis was of adrenal rest tumor of the liver.

Conclusions

Hepatic adrenal rest tumor is an extremely rare hepatic tumor, often without any clinical manifestation, that can also occur in the cirrhotic liver as in our case. Although there are not specific imaging findings, the possible diagnosis of HART should be considered when we observe a well-defined lesion in the subcapsular location of the right lobe, with fat containing, hypervascularity after contrast medium injection and vascular supply from the right hepatic artery.