bluuebunny/crossref_metadata_2025 huggingface dataset:
Heritability Estimation Approaches Utilizing Genome‐Wide Data
Authors: Srivastava Amit K. , Williams Scott M. , Zhang Ge
Published: April 2023

Prior to the development of genome‐wide arrays and whole genome sequencing technologies, heritability estimation mainly relied on the study of related individuals. Over the past decade, various approaches have been developed to estimate SNP‐based narrow‐sense heritability () in unrelated individuals. These latter approaches use either individual‐level genetic variations or summary results from genome‐wide association studies (GWAS). Recently, several studies compared these approaches using extensive simulations and empirical datasets. However, sparse information on hands‐on training necessitates revisiting these approaches from the perspective of a stepwise guide for practical applications. Here, we provide an overview of the commonly used SNP‐heritability estimation approaches utilizing genome‐wide array, imputed or whole genome data from unrelated individuals, or summary results. We not only discuss these approaches based on their statistical concepts, utility, advantages, and limitations, but also provide step‐by‐step protocols to apply these approaches. For illustration purposes, we estimate of height and BMI utilizing individual‐level data from The Northern Finland Birth Cohort (NFBC) and summary results from the Genetic Investigation of ANthropometric Traits (GIANT;) consortium. We present this review as a template for the researchers who estimate and use heritability in their studies and as a reference for geneticists who develop or extend heritability estimation approaches. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.

Basic Protocol 1: GREML (GCTA)

Alternate Protocol 1: Stratified GREML

Basic Protocol 2: LDAK

Alternate Protocol 2: Stratified LDAK

Basic Protocol 3: Threshold GREML

Basic Protocol 4: LD score (LDSC) regression

Basic Protocol 5: SumHer
Establishment, Long‐Term Maintenance, and Characterization of Primary Liver Cells from Astyanax mexicanus
Authors: Rajendran Naresh , Deng Fengyan , Wang Yan , Kenzior Olga , Krishnan Jaya , Biswas Tathagata , Parmely Tari , Rohner Nicolas , Zhao Chongbei
Published: April 2023

The tetra fish species Astyanax mexicanus comprises two morphotypes: cavefish that live in caves and surface fish that inhabit rivers and lakes. Because cavefish have adapted to the nutrient‐poor conditions in their habitat whereas the surface fish populations can be used as a proxy for the ancestral condition, this species has become a powerful model system for understanding genetic variation underlying metabolic adaptation. The liver plays a critical role in glucose and fat metabolism in the body and hence is an important tissue for studying altered metabolism in health and disease. Cavefish morphs of A. mexicanus have been shown to develop fatty livers and exhibit massive differences in gene expression and chromatin architecture. Primary cell lines from various tissues have become invaluable tools for biochemical, toxicology, and cell biology experiments, as well as genetic and genomic analyses. To enhance the utility of the model system by enabling an expanded set of biochemical and in vitro experiments, we developed protocols for the isolation and maintenance of primary liver cells from A. mexicanus surface fish and cavefish. We also describe methods that can be used for primary cell characterization, including cloning, characterization of cell growth pattern, and lentivirus transduction. © 2023 Wiley Periodicals LLC.

Basic Protocol 1: Primary culture of liver cells

Support Protocol 1: Maintenance of A. mexicanus primary liver cells

Support Protocol 2: Banking of A. mexicanus primary liver cells

Support Protocol 3: Recovery of A. mexicanus primary liver cells

Support Protocol 4: Primary liver cell cloning

Support Protocol 5: Characterization of A. mexicanus primary liver cell growth pattern

Basic Protocol 2: Lentiviral transduction of A. mexicanus primary liver cells
Design, synthesis, and biological evaluation of thienopyrimidine derivatives as multifunctional agents against Alzheimer's disease
Authors: Eissa Kholoud I. , Kamel Mona M. , Mohamed Lamia W. , Doghish Ahmed S. , Alnajjar Radwan , Al‐Karmalawy Ahmed A. , Kassab Asmaa E.
Published: April 2023

A series of 12 S‐substituted tetrahydrobenzothienopyrimidines were designed and synthesized based on the donepezil scaffold. All the newly synthesized compounds were evaluated for their acetylcholinesterase (AChE) inhibitory activity and the most active compounds were tested for their butyrylcholinesterase (BuChE) inhibitory activity. Moreover, all the synthesized compounds were evaluated for their inhibitory effects against Aβ aggregation and antioxidant activity using the oxygen radical absorbance capacity method. Compounds 4b, 6b, and 8b displayed the most prominent AChE inhibitory action comparable to donepezil. Compound 6b showed the greatest AChE inhibitory action (IC50 = 0.07 ± 0.003 µM) and the most potent BuChE inhibitory action (IC50 = 0.059 ± 0.004 µM). Furthermore, the three compounds exhibited significant antioxidant activity. Compounds 6b and 8b exerted more inhibitory action on Aβ aggregation than donepezil. The cytotoxic activity of compounds 4b, 6b, and 8b against the WI‐38 cell line in comparison with donepezil was examined using 3‐(4,5‐dimethylthiazolyl‐2)‐2,5‐diphenyltetrazolium bromide assay. The results revealed that compounds 6b and 8b were less cytotixic than donepezil, while compound 4b showed nonsignificant cytotoxicity compared to donepezil. For more insights about the binding patterns of the most promising compounds (4b, 6b, and 8b) with the AChE at molecular levels; molecular docking and molecular dynamics simulations were performed. The density functional theory calculations and absorption, distribution, metabolism, excretion and toxicity properties were described as well. The results highlighted compound 6b, which incorporates a phenylpiperazine moiety coupled to a thienopyrimidone scaffold via two‐atom spacer, to be a promising multifunctional therapeutic agent for the treatment of Alzheimer's disease. It is a potent dual AChE and BuChE inhibitor. Furthermore, it had stronger Aβ aggregation inhibitory action than donepezil. Additionally, compound 6b exerted significant antioxidant activity.
Dermal fillers: History 101
Authors: Andrews Laura , Shope Chelsea , Snyder Alan , Schlesinger Todd
Published: April 2023

Introduction

Dermal fillers are an efficacious option for treating age‐related volume deficiency, as well as scars and wrinkles. Additionally, they are useful for facial sculpting and contouring, and to augment anatomical structures such as the lips.

Discussion

The start of the search for an ideal dermal filler can be traced back to the late 1800s. Characteristics of this ideal filler product include nontoxic, nonmigratory, noncarcinogenic, easily applied, noninfectious, painless, and long‐lasting. It would also have predictable and consistent results, feel natural, and require no patient downtime. Over the past century and a half, numerous products have been used or developed in an attempt to achieve a filler possessing these characteristics. However, only in the past few decades have safe, injectable filler products approved by the US Food and Drug Administration (FDA), been developed. Herein, we discuss the various injectable agents used in the past, as well as the most commonly used agents of present day.

Conclusion

Reflecting upon the history of dermal filler development serves as an important reminder to proceed with caution, as serious complications may occur with their use. Importantly, no single filler is ideal for all patients or indications, therefore optimal treatment requires awareness of the properties and characteristics of each available product, and discretionary use by providers.
Cementum is key to periodontal tissue regeneration: A review on apatite microstructures for creation of novel cementum‐based dental implants
Authors: Saito Mari M. , Onuma Kazuo , Yamakoshi Yasuo
Published: April 2023

The cementum is the outermost layer of hard tissue covering the dentin within the root portion of the teeth. It is the only hard tissue with a specialized structure and function that forms a part of both the teeth and periodontal tissue. As such, cementum is believed to be critical for periodontal tissue regeneration. In this review, we discuss the function and histological structure of the cementum to promote crystal engineering with a biochemical approach in cementum regenerative medicine. We review the microstructure of enamel and bone while discussing the mechanism underlying apatite crystal formation to infer the morphology of cementum apatite crystals and their complex structure with collagen fibers. Finally, the limitations of the current dental implant treatments in clinical practice are explored from the perspective of periodontal tissue regeneration. We anticipate the possibility of advancing periodontal tissue regenerative medicine via cementum regeneration using a combination of material science and biochemical methods.
Effect of intravenous iron replacement on recurrent heart failure hospitalizations and cardiovascular mortality in patients with heart failure and iron deficiency: A Bayesian meta‐analysis
Authors: Anker Stefan D. , Khan Muhammad Shahzeb , Butler Javed , von Haehling Stephan , Jankowska Ewa A. , Ponikowski Piotr , Friede Tim
Published: April 2023

Aims

Iron deficiency is common in patients with heart failure (HF) and reduced ejection fraction (HFrEF) and is associated with a poor prognosis. Whether intravenous iron replacement improves recurrent HF hospitalizations and cardiovascular mortality of these patients is uncertain although several trials were conducted. Moreover, none of the trials were powered to assess the effect of intravenous iron in clinically important subgroups. Therefore, we conducted a Bayesian analysis to derive precise estimates of the effect of intravenous iron replacement on recurrent HF hospitalizations and cardiovascular mortality in iron‐deficient HFrEF patients using consistent subgroup definitions across trials.

Methods and results

Individual participant data were used from the FAIR‐HF (n = 459), CONFIRM‐HF (n = 304) and AFFIRM‐AHF (n = 1108) trials. These data were re‐analysed following as closely as possible the approach taken in the analyses of IRONMAN (n = 1137), for which study level data were used. Definitions of outcomes and subgroups from the FAIR‐HF, CONFIRM‐HF and AFFIRM‐AHF were matched with those used in IRONMAN. The primary endpoint was recurrent HF hospitalizations and cardiovascular mortality. The analysis of recurrent events was based on rate ratios (RR) derived from the Lin‐Wei‐Yang‐Ying model, and the data were pooled using Bayesian random‐effects meta‐analysis. Compared with placebo, intravenous iron significantly reduced the rates of recurrent HF hospitalizations and cardiovascular mortality (RR 0.73, 95% credible interval [CI] 0.48–0.99; between‐trial heterogeneity tau = 0.16). The pooled treatment effects did not provide evidence for any differential effects for subgroups based on sex (ratio of rate ratios [RRR] 1.49 [95% CI 0.95–2.37], age <69.4 vs. ≥69.4 years) (RRR 0.68 [0.40–1.15]), ischaemic versus non‐ischaemic aetiology of HF (RRR 0.73 [0.42–1.33]), transferrin saturation <20% vs. ≥20% (RRR 0.75 [0.40–1.34]), estimated glomerular filtration rate ≤60 versus >60 ml/min/1.73 m2 (RRR 0.97 [0.56–1.68]), haemoglobin <11.8 versus ≥11.8 (RRR 0.95 [0.53–1.60]), ferritin <35 versus ≥35 μg/L (RRR 1.26 [0.72–2.48]) and New York Heart Association class II versus III/IV (RRR 0.91 [0.54–1.56]).

Conclusions

Treatment of iron‐deficient HFrEF patients with intravenous iron – namely with ferric carboxymaltose or ferric derisomaltose – results in significant reduction in recurrent HF hospitalizations and cardiovascular mortality. Results were nominally consistent across the subgroups studied, but for several of these subgroups uncertainty remains present.
Cross-Species Extrapolation of Biological Data to Guide the Environmental Safety Assessment of Pharmaceuticals—The State of the Art and Future Priorities
Authors: Margiotta-Casaluci Luigi , Owen Stewart F. , Winter Matthew J.
Published: April 2023

The extrapolation of biological data across species is a key aspect of biomedical research and drug development. In this context, comparative biology considerations are applied with the goal of understanding human disease and guiding the development of effective and safe medicines. However, the widespread occurrence of pharmaceuticals in the environment and the need to assess the risk posed to wildlife have prompted a renewed interest in the extrapolation of pharmacological and toxicological data across the entire tree of life. To address this challenge, a biological “read-across” approach, based on the use of mammalian data to inform toxicity predictions in wildlife species, has been proposed as an effective way to streamline the environmental safety assessment of pharmaceuticals. Yet, how effective has this approach been, and are we any closer to being able to accurately predict environmental risk based on known human risk? We discuss the main theoretical and experimental advancements achieved in the last 10 years of research in this field. We propose that a better understanding of the functional conservation of drug targets across species and of the quantitative relationship between target modulation and adverse effects should be considered as future research priorities. This pharmacodynamic focus should be complemented with the application of higher-throughput experimental and computational approaches to accelerate the prediction of internal exposure dynamics. The translation of comparative (eco)toxicology research into real-world applications, however, relies on the (limited) availability of experts with the skill set needed to navigate the complexity of the problem; hence, we also call for synergistic multistakeholder efforts to support and strengthen comparative toxicology research and education at a global level. Environ Toxicol Chem 2024;43:513–525. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Abstract

Enhancing chemical safety assessment with high-precision ecotoxicology predictions.
Clinical efficacy of ulinastatin in the treatment of unliquefied pyogenic liver abscess complicated by septic shock: A randomized controlled trial
Authors: Guo Mingfeng , Zhou Bing
Published: April 2023

Introduction

This study determined the therapeutic effect of ulinastatin (UTI) on unliquefied pyogenic liver abscesses complicated by septic shock (UPLA‐SS).

Methods

This was a randomized controlled trial involving patients with UPLA‐SS who underwent treatment at our hospital between March 2018 and March 2022. The patients were randomly divided into control (n = 51) and study groups (n = 48). Both groups received routine treatment, but the study group received UTI (200,000 units q8h for >3 days). Differences in liver function, inflammatory indices, and effectiveness between the two groups were recorded.

Results

Following treatment, the white blood cell count, and lactate, C‐reactive protein, procalcitonin, tumor necrosis factor‐α, and interleukin‐6 levels were significantly decreased in all patients compared to the admission values (p < .05). The study group had a faster decline with respect to the above indices compared to the control group (p < .05). The study group length of intensive care unit stay, fever duration, and vasoactive drug maintenance time were all significantly shorter than the control group (p < .05). The total bilirubin, alanine aminotransferase, and aspartate aminotransferase levels were significantly lower in the study and control groups after treatment compared to before treatment (p < .05); however, the study group had a faster recovery of liver function than the control group (p < .05). The overall mortality rate was 14.14% (14/99); 10.41% of the study group patients died and 17.65% of the control group patients died, but there was no statistically significant difference between the two groups (p > .05).

Conclusion

UTI combined with conventional treatment significantly controlled the infection symptoms, improved organ function, and shortened the treatment time in patients with UPLA‐SS.
Research integrity in randomized clinical trials: A scoping umbrella review
Authors: Núñez‐Núñez María , Maes‐Carballo Marta , Mignini Luciano E. , Chien Patrick F. W. , Khalaf Yacoub , Fawzy Mohamed , Zamora Javier , Khan Khalid S. , Bueno‐Cavanillas Aurora
Published: April 2023

Background

Randomized clinical trials (RCTs) are experiencing a crisis of confidence in their trustworthiness. Although a comprehensive literature search yielded several reviews on RCT integrity, an overarching overview is lacking.

Objectives

The authors undertook a scoping umbrella review of the research integrity literature concerning RCTs.

Search strategy and selection criteria

Following prospective registration (https://osf.io/3ursn), two reviewers independently searched PubMed, Scopus, The Cochrane Library, and Google Scholar, without language or time restrictions, until November 2021. The authors included systematic reviews covering any aspect of research integrity throughout the RCT lifecycle.

Data collection and analysis

The authors assessed methodological quality using a modified AMSTAR 2 (A Measurement Tool to Assess Systematic Reviews) tool and collated the main findings.

Main results

A total of 55 relevant reviews, summarizing 6001 studies (median per review, 63; range, 8–1106) from 1964 to 2021, had an overall critically low quality of 96% (53 reviews). Topics covered included general aspects (15%), design and approval (22%), conduct and monitoring (11%), reporting (38%), postpublication concerns (2%), and future research (13%). The most common integrity issues covered were ethics (18%) and transparency (18%).

Conclusions

Low‐quality reviews identified various integrity issues across the RCT lifecycle, emphasizing the importance of high ethical standards and professionalism while highlighting gaps in the integrity landscape. Multistakeholder consensus is needed to develop specific RCT integrity standards.
Neonatal condition at birth of twins conceived by medically assisted reproductive technology compared to those conceived spontaneously: A retrospective study
Authors: Abu Nofal Mais , Abd Elgani Suzan , Zafran Noah , Garmi Gali , Romano Shabtai , Salim Raed
Published: April 2023

Objective

To examine neonatal outcomes at birth among twins conceived spontaneously or by medically assisted reproduction (MAR).

Methods

A retrospective study was conducted at a single university teaching hospital on data collected between January 1995 and September 2019. Live twin deliveries at more than 24 weeks of pregnancy were included. The study group consisted of women who conceived by MAR and the controls were spontaneously conceived twins. The study group was further divided into two groups: in vitro fertilization (IVF) and ovulation induction (OI) groups. The primary outcomes were umbilical artery pH less than 7.1 and/or Apgar score less than 7 of any twin 5 min after birth.

Results

Overall, 2235 eligible twin gestations were included, corresponding to a total of 4470 live neonates; 1009 (45.1%) conceived by MAR (762 [75.5%] IVF and 247 [24.5%] OI) and 1226 (54.9%) conceived spontaneously. Incidence of the primary outcome was 5.3% and 5.1% in the study and control groups, respectively (P = 0.71). The primary outcome was comparable among the IVF (5%), OI (6.2%), and control (5.1%) groups. The results did not change even after adjusting for demographic and obstetric variables, including mode of delivery, which differed between the groups.

Conclusion

Neonatal condition of twin pregnancies at birth among MAR subgroups is similar to spontaneously conceived twins.
Causal effects of COVID‐19 on cancer risk: A Mendelian randomization study
Authors: Li Jia , Bai Haocheng , Qiao Hao , Du Chong , Yao Peizhuo , Zhang Yu , Cai Yifan , Jia Yiwei , Wei Xinyu , Li Chaofan , Liu Xuanyu , Wang Weiwei , Sun Shiyu , Feng Cong , Hu Yijian , Zhou Zhangjian , Zhang Shuqun , Zhang Yinbin
Published: April 2023

In contemporary literature, little attention has been paid to the association between coronavirus disease‐2019 (COVID‐19) and cancer risk. We performed the Mendelian randomization (MR) to investigate the causal associations between the three types of COVID‐19 exposures (critically ill COVID‐19, hospitalized COVID‐19, and respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection) and 33 different types of cancers of the European population. The results of the inverse‐variance‐weighted model indicated that genetic liabilities to critically ill COVID‐19 had suggestive causal associations with the increased risk for HER2‐positive breast cancer (odds ratio [OR] = 1.0924; p‐value = 0.0116), esophageal cancer (OR = 1.0004; p‐value = 0.0226), colorectal cancer (OR = 1.0010; p‐value = 0.0242), stomach cancer (OR = 1.2394; p‐value = 0.0331), and colon cancer (OR = 1.0006; p‐value = 0.0453). The genetic liabilities to hospitalized COVID‐19 had suggestive causal associations with the increased risk for HER2‐positive breast cancer (OR = 1.1096; p‐value = 0.0458), esophageal cancer (OR = 1.0005; p‐value = 0.0440) as well as stomach cancer (OR = 1.3043; p‐value = 0.0476). The genetic liabilities to SARS‐CoV‐2 infection had suggestive causal associations with the increased risk for stomach cancer (OR = 2.8563; p‐value = 0.0019) but with the decreasing risk for head and neck cancer (OR = 0.9986, p‐value = 0.0426). The causal associations of the above combinations were robust through the test of heterogeneity and pleiotropy. Together, our study indicated that COVID‐19 had causal effects on cancer risk.
SARS‐CoV‐2 vaccine antibody response and breakthrough infections in transplant recipients
Authors: Vanlerberghe Benedict , Vrij Casper , Bogaerts Kris , Vermeersch Pieter , Lagrou Katrien , Molenberghs Geert , Rega Filip , Ceulemans Laurens J. , van Raemdonck Dirk , Jochmans Ina , Monbaliu Diethard , Pirenne Jacques , Vanuytsel Tim , Gillard Pieter , Schoemans Hélène , Cleemput Johan Van , Kuypers Dirk , Vos Robin , Nevens Frederik , Verbeek Jef
Published: April 2023

Rates and modulators of SARS‐CoV‐2 vaccine nonresponse and breakthrough infections remain unclear in serially vaccinated transplant recipients. In a prospective, mono‐centric, observational study, 1878 adult solid organ and hematopoietic cell transplant recipients, with prior SARS‐CoV‐2 vaccination, were included between March 2021 and February 2022. SARS‐CoV‐2 anti‐spike IgG antibodies were measured at inclusion and details on SARS‐CoV‐2 vaccine doses and infection were collected. No life‐threatening adverse events were reported after a total of 4039 vaccine doses. In transplant recipients without prior SARS‐CoV‐2 infection (n = 1636), antibody response rates ranged widely, from 47% in lung transplant to 90% in liver transplant and 91% in hematopoietic cell transplant recipients after third vaccine dose. Antibody positivity rate and levels increased after each vaccine dose in all types of transplant recipients. In multivariable analysis, older age, chronic kidney disease and daily dose of mycophenolate and corticosteroids were negatively associated with antibody response rate. Overall rate of breakthrough infections was 25.2% and mainly (90.2%) occurred after third and fourth vaccine dose. Lung transplant recipients had the highest rates of severe breakthrough infection (10.5%) and death (2.5%). In multivariable analysis, older age, daily dose of mycophenolate and corticosteroids were associated with severe breakthrough infection. Transplant recipients with infection before first vaccine dose (n = 160) had higher antibody response rates and levels after each vaccine dose, and a significantly lower overall rate of breakthrough infections compared to those without prior infection. Antibody response after SARS‐CoV‐2 vaccination and rate of severe breakthrough infections vary largely between different transplant types and are modulated by specific risk factors. The observed heterogeneity supports a tailored approach against COVID‐19 in transplant recipients.
Identifying predictors of tooth loss using a rule‐based machine learning approach: A retrospective study at university‐setting clinics
Authors: Lee Chun‐Teh , Zhang Kai , Li Wen , Tang Kaichen , Ling Yaobin , Walji Muhammad F. , Jiang Xiaoqian
Published: April 2023

Background

This study aimed to identify predictors associated with tooth loss in a large periodontitis patient cohort in the university setting using the machine learning approach.

Methods

Information on periodontitis patients and 18 factors identified at the initial visit was extracted from electronic health records. A two‐step machine learning pipeline was proposed to develop the tooth loss prediction model. The primary outcome is tooth loss count. The prediction model was built on significant factors (single or combination) selected by the RuleFit algorithm, and these factors were further adopted by the count regression model. Model performance was evaluated by root‐mean‐squared error (RMSE). Associations between predictors and tooth loss were also assessed by a classical statistical approach to validate the performance of the machine learning model.

Results

In total, 7840 patients were included. The machine learning model predicting tooth loss count achieved RMSE of 2.71. Age, smoking, frequency of brushing, frequency of flossing, periodontal diagnosis, bleeding on probing percentage, number of missing teeth at baseline, and tooth mobility were associated with tooth loss in both machine learning and classical statistical models.

Conclusion

The two‐step machine learning pipeline is feasible to predict tooth loss in periodontitis patients. Compared to classical statistical methods, this rule‐based machine learning approach improves model explainability. However, the model's generalizability needs to be further validated by external datasets.
Warm root‐zone temperature ensures the mineral concentrations in cucumber plants under elevated [CO2] by improving the migration pathways of mineral elements from the soil to plants
Authors: Li Di , Li Xun , Dong Jinlong , Gruda Nazim S. , Duan Zengqiang
Published: April 2023

Background

The mineral nutrient concentrations in plants are usually decreased under elevated CO2 concentration ([CO2]), while warm root‐zone temperature (RZT) can improve plant growth and the absorption of mineral nutrients in plants.

Aims

The effects of RZT on the growth and mineral nutrient concentrations in cucumber (Cucumis sativus L.) plants were investigated under different [CO2] levels.

Methods

A soil‐cultured pot experiment was carried out on cucumber plants under two [CO2] levels (ambient and elevated) and two RZT levels (cold and warm) in four open‐top chambers.

Results

Although elevated [CO2] promoted root growth, it did not counteract the decrease in the concentration of nitrogen ([N]), potassium ([K]), calcium ([Ca]), and magnesium ([Mg]) in cucumber plants due to the decreased mass flow indicated by the decreased transpiration rate (Tr) under cold RZT. In comparison, warm RZT increased the [N], [K], [Ca], and [Mg] in cucumber plants under elevated [CO2], attributed to a higher Tr and better root growth. In addition, the concentration of phosphorus ([P]), iron ([Fe]), manganese ([Mn]), and zinc ([Zn]) in cucumber plants was maintained or increased under elevated [CO2] by the promoted root growth related to interception by warm RZT.

Conclusions

Under elevated [CO2], warm RZT could ensure the [N], [K], [Ca], and [Mg] in cucumber plants mainly by increasing the Tr and improving the root growth. Whereas warm RZT maintained or increased [P], [Fe], [Mn], and [Zn] primarily relied on the improved interception as indicated by the better root growth.
Proteomics‐based milk whey proteome profiling of Indian Jersey crossbreed cows followed by chromosomal mapping
Authors: Singh Manish Kumar , Kumar Arvind , Nimmanapalli Ramadevi , Pandey Anand Kumar
Published: April 2023

BACKGROUND

Milk contains a massive class of minor proteins that are known for their various biological and molecular functions. Many whey proteins transfer the host defense mechanism to the human body. In this assay, electrophoresis followed by a high‐resolution mass spectrometry‐based proteomic approach has been applied to identify the whey proteome of Indian Jersey crossbreed bovines.

RESULTS

Two search engines, MS Amanda and Sequest HT, have shown more than 29 minor proteins. Chromosomal mapping revealed that chromosomes 5 and 9 are expressing maximum proteins in the whey proteome. The principal component analysis, outlier plots, scree plots, score plots, and loading plots were generated to further assess the results.

CONCLUSION

The majorly expressed ones are glycosylation‐dependent cell adhesion molecule‐1, ubiquitin, desmoglein, annexin, glycoprotein, arginase, histones, peroxiredoxin, vimentin, desmin, catenin, peripherin, and 70 kDa heat shock protein. © 2023 Society of Chemical Industry.
Outcomes of Cranioplasty Reconstructions: Review of Cranioplasty Implants and Free Flap Coverage Variables that Affect Implant Exposure
Authors: Slijepcevic Allison A , Scott Brian , Lilly Gabriela L , Young Gavin , Taghizadeh Farshid , Li Ryan , Petrisor Daniel , Pipkorn Patrik , Rich Jason , Jackson Ryan , Wax Mark K , Puram Sidharth
Published: April 2023

Background

Complex scalp wounds with cranial/dural involvement are challenging to reconstruct. Successful reconstruction can be achieved with cranial implants/hardware and free flap coverage. Wounds can breakdown and require revision procedures. We addressed reconstructive outcomes of different implants requiring free flaps.

Objective

To determine the factors associated with implant exposure.

Design

Multi‐institutional retrospective review of 82 patients, 2000–2020, repaired with cranial implants and free flap coverage.

Results

Implant exposure occurred in 13/82 (16%) reconstructions. Flap atrophy or thinning leading to implant exposure occurred in 11/82 (13%) reconstructions, including partial flap atrophy OR 0.05 (95% CI 0.0–0.35) and total flap atrophy OR 0.34 (95% CI 0.02–19.66). Revision surgeries that occurred subsequent to flap reconstruction were also associated with implant exposure (OR 0.02 (95% CI 0.0–0.19)). Implant exposure was not associated with radiation therapy, patient health history, implant type, flap type, or postoperative complications.

Conclusions

Implant exposure is associated with free flap atrophy, leading to inadequate implant coverage and the need for revision surgeries. Completing reconstruction with adequate soft tissue bulk and coverage and avoiding revision surgery may decrease the risk for implant exposure over time.

Level of Evidence

4 Laryngoscope, 133:2954–2958, 2023
m7G‐related genes—NCBP2 and EIF4E3 determine immune contexture in head and neck squamous cell carcinoma by regulating CCL4/CCL5 expression
Authors: Xu Xuhui , Zhao Yue , Ying Yukang , Zhu Haoran , Luo Jun , Mou Tingchen , Zhang Zhenxing
Published: April 2023

Aberrant N7‐methylguanosine (m7G) levels closely correlate with tumor genesis and progression. NCBP2 and EIF4E3 are two important m7G‐related cap‐binding genes. This study aimed to identify the relationship between the EIF4E3/NCBP2 function and immunological characteristics of head and neck squamous cell carcinoma (HNSCC). Hierarchical clustering was employed in classifying HNSCC patients into two groups based on the expressions of NCBP2 and EIF4E3. The differentially expressed genes were identified between the two groups, and GO functional enrichment was subsequently performed. Weighted gene co‐expression network analysis was conducted to identify the hub genes related to EIF4E3/NCBP2 expression and immunity. The differential infiltration of immune cells and the response to immunotherapy were compared between the two groups. Single‐cell sequence and trajectory analyses were performed to predict cell differentiation and display the expression of EIF4E3/NCBP2 in each state. In addition, quantitative real‐time PCR, spatial transcriptome analysis, transwell assay, and western blotting were conducted to verify the biological function of EIF4E3/NCBP2. Here, group A showed a higher EIF4E3 expression and a lower NCBP2 expression, which had higher immune scores, proportion of most immune cells, immune activities, expression of immunomodulatory targets, and a better response to cancer immunotherapy. Besides, 56 hub molecules with notable immune regulation significance were identified. A risk model containing 17 hub genes and a prognostic nomogram was successfully established. Moreover, HNSCC tissues had a lower EIF4E3 expression and a higher NCBP2 expression than normal tissues. NCBP2 and EIF4E3 played a vital role in the differentiation of monocytes. Furthermore, the expression of CCL4/CCL5 can be regulated via EIF4E3 overexpression and NCBP2 knockdown. Collectively, NCBP2 and EIF4E3 can affect downstream gene expression, as well as immune contexture and response to immunotherapy, which could induce “cold‐to‐hot” tumor transformation in HNSCC patients.
Multilingualism for pluralising knowledge and decision making about people and nature relationships
Authors: Droz Laÿna , Brugnach Marcela , Pascual Unai
Published: April 2023

The need for a pluralistic approach to biodiversity conservation science and policy is increasingly being recognized. We argue that plural perspectives require multilingualism in the sources and processes.

Unless the linguistic bias and the related issues in terms of legitimacy and validity, resistance to inclusion, and knowledge coproduction are meaningfully addressed, biodiversity science and its positive effects for conservation policy and practices will necessarily be limited.

We propose a series of options to address the linguistic biases in biodiversity conservation science and policy, including extending and tightening collaboration with environmental humanities scholars from diverse traditions as well as researchers from diverse linguistic contexts.

We conclude by showing how multilingualism is especially relevant for cross‐scale and global biodiversity governance.

Read the free Plain Language Summary for this article on the Journal blog.
Disparities in care of pediatric, adolescent, and young adult patients with solid tumors: A systematic review
Authors: Roberts Bailey , Cooke‐Barber Jo , Ingram Martha‐Conley , Danko Melissa , Trudeau Maeve , Glick Richard D. , Short Scott S. , Robertson Daniel J. , Raval Mehul V. , Dasgupta Roshni , Rich Barrie S. ,   the American Academy of Pediatrics Section on Surgery Delivery of Surgical Care Committee
Published: April 2023

Background

Numerous studies have demonstrated a variety of social inequalities within pediatric and young adult patients with solid tumors. This systematic review examines and consolidates the existing literature regarding disparities in pediatric and young adult solid tumor oncology.

Procedure

A MeSH search was performed on the following databases: MEDLINE, PubMed, OvidSP Cochrane, Central, Embase, Cinhal, and Scopus. The systematic review was performed using Rayyan QCRI.

Results

Total 387 articles were found on the initial search, and 34 articles were included in final review. Twenty‐seven studies addressed racial and ethnic disparities; 23 addressed socioeconomic disparities. Patients with Hispanic ethnicity, Black race, and lower socioeconomic status were more likely to present at later stages, have differences in treatments and higher mortality rates.

Conclusion

This qualitative systematic review identified both racial and socioeconomic disparities in pediatric cancer patients across a variety of solid tumor types. Patients with Hispanic ethnicity, Black race, and lower socioeconomic status are associated with disparities in stage at presentation, treatment, and outcome. Characterization of existing disparities provides the evidence necessary to support changes at a systemic level.
Bioinformatic analysis of the SPs and NFTs proteomes unravel putative biomarker candidates for Alzheimer's disease
Authors: Ferreira Maria J. Cardoso , Soares Martins Tânia , Alves Steven R. , Rosa Ilka Martins , Vogelgsang Jonathan , Hansen Niels , Wiltfang Jens , da Cruz e Silva Odete A. B. , Vitorino Rui , Henriques Ana Gabriela
Published: April 2023

Aging is the main risk factor for the appearance of age‐related neurodegenerative diseases, including Alzheimer's disease (AD). AD is the most common form of dementia, characterized by the presence of senile plaques (SPs) and neurofibrillary tangles (NFTs), the main histopathological hallmarks in AD brains. The core of these deposits are predominantly amyloid fibrils in SPs and hyperphosphorylated Tau protein in NFTs, but other molecular components can be found associated with these pathological lesions. Herein, an extensive literature review was carried out to obtain the SPs and NFTs proteomes, followed by a bioinformatic analysis and further putative biomarker validation. For SPs, 857 proteins were recovered, and, for NFTs, 627 proteins of which 375 occur in both groups and represent the common proteome. Gene Ontology (GO) enrichment analysis permitted the identification of biological processes and the molecular functions most associated with these lesions. Analysis of the SPs and NFTs common proteins unraveled pathways and molecular targets linking both histopathological events. Further, validation of a putative phosphotarget arising from the in silico analysis was performed in serum‐derived extracellular vesicles from AD patients. This bioinformatic approach contributed to the identification of putative molecular targets, valuable for AD diagnostic or therapeutic intervention.
Development and validation of a simple prostate cancer risk prediction model based on age, family history, and polygenic risk
Authors: Dite Gillian S. , Spaeth Erika , Murphy Nicholas M. , Allman Richard
Published: April 2023

Background

Accurate prostate cancer risk assessment will enable identification of men who are at increased risk of the disease. Using the UK Biobank population‐based cohort, we developed and validated a simple model comprising age, family history, and a polygenic risk score (PRS) to predict 5‐year risk of prostate cancer.

Methods

Eligible participants were unaffected Caucasian men aged 40–69 years at their baseline assessment who had genotyping data available and had completed 6 or more weeks of follow‐up. Family history was the number of affected first‐degree relatives: 0, 1, or 2+. We used 264 single‐nucleotide polymorphisms (SNPs) of a previously developed 269‐SNP PRS and population standardized the PRS to have a mean of 1. Age was categorized into 10‐year groups: 40–49, 50–59, and 60–69. In a 70% training data set, we used Cox regression with age as the time axis to model family history, PRS, and age group. The model estimates were used with prostate cancer incidences to derive 5‐year risks of prostate cancer. Using 5 years of follow‐up in a 30% testing data set, the model was tested in terms of its association per quintile of risk, discrimination, and calibration.

Results

Of the 198 334 eligible participants, 8996 (4.5%) were diagnosed with incident prostate cancer during follow‐up and had a mean age of 67.9 (SD = 5.8) years at diagnosis. The best‐fitting model included the PRS, family history, 10‐year age group, interactions between age and PRS, and age and family history. In the 30% testing data set with follow‐up limited to 5 years, the hazard ratio per SD of 5‐year risk was 3.058 (95% confidence interval [CI], 2.720–3.438) and the Harrell's C‐index was 0.811 (95% CI, 0.800–0.821). Overall, there were 1088 observed and 1159.1 expected prostate cancers, a standardized incidence ratio of 0.939 (95% CI, 0.885–0.996).

Conclusions

Men at increased risk of prostate cancer could benefit from informed discussions around the risks and benefits of available options for screening for prostate cancer. Although the model was developed in Caucasian men, it can be used with ethnicity‐specific polygenic risk and incidence rates for other populations.
Vertical divergence profiles as detected by two wind‐profiler mesonets over East China: Implications for nowcasting convective storms
Authors: Guo Xiaoran , Guo Jianping , Zhang Da‐Lin , Yun Yuxing
Published: April 2023

Low‐level convergence is one of the most important dynamic variables in governing the convection initiation (CI) and development of storms. However, our ability to obtain high‐resolution horizontal divergence profiles remains limited due to the lack of high‐resolution vertical wind observations. In this study, horizontal divergence (and vertical motion) profiles are derived from horizontal winds measured by two radar wind‐profiler (RWP) mesonets in East China, and then used to examine their relationship with CI occurring within a mesonet and an intense squall line moving across another mesonet. Results show that the RWP mesonets together with automated surface observations could provide realistically the lower‐tropospheric profiles of horizontal divergence (and upward motion) associated with the CI in the presence of the urban heat island effects, and lake and sea breezes; and the evolution of the squall line respectively. High‐resolution surface observations resolve better divergence induced by localized CI than the RWP measurements, whereas the latter capture well significant convergence below 4‐km altitude that precedes the onset of squall precipitation. A statistical analysis of the RWP data during the summer months of 2018 indicates that the lower‐tropospheric convergence can be detected up to about 40 min in advance of the occurrence of heavy rainfall, and the correlation is higher when it is closer to the heavy rainfall time. Nearly 40% of heavy rainfall moments (at 6‐min intervals) are accompanied by strong convergence signals occurring mostly near the top of the boundary layer. This work indicates that the RWP and surface wind measurements should be integrated to aid in nowcasting the location and timing of CI and development of convective storms.
Scheme for Measuring Topological Transitions in a Continuous Variable System
Authors: Wang Bi‐Yao , Zhang Hao‐Long , Yang Shou‐Bang , Wu Fan , Yang Zhen‐Biao , Zheng Shi‐Biao
Published: April 2023

A scheme for measuring topological properties in a two‐photon‐driven Kerr‐nonlinear (KNR) resonator subjected to a single‐photon modulation is proposed. The topological properties are revealed through the observation of the Berry curvature and hence the first Chern number, as a nonadiabatic response of the physical observable to the change rate of the control parameter of the modulated drive. The parameter manifold, constructed from the system's Hamiltonian that determines its dynamics constrained in the state space spanned by the even and odd cat states as two basis states, is adjusted so that the degeneracy crossing the manifold indicates a topological transition. The scheme, with such continuous variable states in mesoscopic systems, provides a new perspective for exploration of the geometry and the related topology with complex systems.
Expected position and attitude adjustment control method of coal mine roadway support robot
Authors: Chen Hongyue , Chen Hongyan , Ma Ying , Xu Yajun , Zhang Desheng
Published: April 2023

This paper proposes an expected position‐attitude adjustment control method of coal mine roadway support robot (CMRSR) based on a real‐time position‐attitude detection system. Taking advantage of lateral adjustment mechanism and control method, the CMRSR has flexible maneuverability and high dynamic expected position‐attitude adjustment performance. It can guarantee stability and safety of the relative position‐attitude in time‐varying roadway environment in underground coal mines. First, the structural characteristics, hydraulic system characteristics, and kinematic characteristics of the CMRSR are considered, and the spatial mathematical relationship model on position‐attitude parameters and sensor data information, roadway environment dimensions, and CMRSR structural dimensions are established. In addition, the real‐time position‐attitude of the CMRSR with respect to the roadway is recognized by the position‐attitude detection system. Then, according to real‐time roadway environment and relative position‐attitude, the expected position‐attitude parameters are set, and the adjustment parameters and types of each lateral hydraulic cylinder are selected based on different deviated position‐attitude conditions. A position‐attitude adjustment controller is designed based on the sliding mode variable structure control algorithm to achieve precise position‐attitude adjustment of the CMRSR. In addition, the position‐attitude detection system is used to provide feedback control to maintain the relative position‐attitude of the CMRSR. Finally, the practical performance illustrates high effectiveness and feasibility of the proposed control method. The average error of distance can be controlled within ±30 mm, the average error of angle can be controlled within ±0.5°, and the adjustment time can be controlled within 20 s.
Human–river relationships depend on human–human relationships: River and watershed organizations in three western US states
Authors: Flint Courtney G. , Holdaway Bailey M. , Rogers Caitlyn S.
Published: April 2023

Human–nature relationship concepts are held collectively within society and guide environmentally oriented actions. This article explores the roles played by environmental organizations, particularly those focused on rivers and watersheds, in catalyzing interaction and action driven by human–river relationship goals. Interviews were conducted with representatives from 64 river and watershed organizations in Montana, Utah, and Wyoming in 2022. Organizational representatives were asked about mission focus areas, human–river relationships, the knowledge they draw upon to guide their efforts, and factors and obstacles that enable and constrain their progress and success. These qualitative data reveal a strong orientation toward steward and partner types of human–nature relationship concepts; however, there are discrepancies in conceptual interpretations. For river and watershed organizations in the US Intermountain West, human–river relationship goals depend strongly on human–human relationships in the form of diverse knowledge integration, collaboration, partnerships, trust, and communication in order to achieve their river‐related goals.